WO2010042742A2 - Chimeric therapeutics, compositions, and methods for using same - Google Patents

Chimeric therapeutics, compositions, and methods for using same Download PDF

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Publication number
WO2010042742A2
WO2010042742A2 PCT/US2009/060038 US2009060038W WO2010042742A2 WO 2010042742 A2 WO2010042742 A2 WO 2010042742A2 US 2009060038 W US2009060038 W US 2009060038W WO 2010042742 A2 WO2010042742 A2 WO 2010042742A2
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Prior art keywords
therapeutic
seq
modified
protein
nucleic acid
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PCT/US2009/060038
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French (fr)
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WO2010042742A3 (en
Inventor
Miguel De Los Rios
John Mendlein
Timothy L. Bullock
Kenneth J. Oh
Patrick T. Johnson
Jacek Ostrowski
Stephanie De Los Rios
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Chimeros Inc.
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Publication of WO2010042742A2 publication Critical patent/WO2010042742A2/en
Publication of WO2010042742A3 publication Critical patent/WO2010042742A3/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/69—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit
    • A61K47/6901—Conjugates being cells, cell fragments, viruses, ghosts, red blood cells or viral vectors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/69—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit
    • A61K47/6905—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a colloid or an emulsion
    • A61K47/6919—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a colloid or an emulsion the form being a ribbon or a tubule cochleate
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/69—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit
    • A61K47/6921—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N7/00—Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3513—Protein; Peptide
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/30—Special therapeutic applications
    • C12N2320/32—Special delivery means, e.g. tissue-specific
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
    • C12N2710/00011—Details
    • C12N2710/20011—Papillomaviridae
    • C12N2710/20023—Virus like particles [VLP]

Definitions

  • Effective therapeutics that include nucleic acids such as interfering RNA may require stability in order to reach target cells or targets before the therapeutic is degraded or excreted. For example, such therapeutics must get into the target cells, link up with a intracellular target, and exert a therapeutic effect. In order to be effective, such therapeutics should exert enough of an effect to improve the health of the person taking it. Further, therapeutics that include nucleic acid should be effective without causing significant toxic effects in for example, tissues. [0004] Many proposed therapeutic agents have not been successful because of a limited ability to reach the target tissue. Further, some agents can be taken up by cells, and therefore may not allow efficient drug accumulation at a target site in a patient.
  • protein and nucleic acid therapeutics are typically administered intravenously due to their instability at a high pH in e.g. the stomach after oral administration.
  • Viral core proteins such as wild type hepatitis C, human papilloma virus type 6 Ll and L2, and/or cowpea chlorotic mottle virus coat protein may form a capsid with a terminal tail and/or an inward facing surface.
  • wild type viral core proteins may be unsuitable for use in therapeutics in part because of uncertainty in binding properties with e.g. a nucleic acid that targets a specific gene of interest.
  • nucleic acid based therapeutics that are long lasting and provide effective treatment for diseases and disorders associated with gene targets.
  • a protein capable of forming a capsid includes a structural core portion chosen from the structural core portion of a HPV, SV40, CCMV, DGNNV, TBSV, Norwalk Virus, and HCV; and a modified portion capable of binding to a nucleic acid with a binding affinity that allows release of said nucleic acid when said protein bound to said polynucleotide is administered in vivo.
  • a modified portion may be a modified C-terminal tail portion and/or a modified N-terminal tail portion, for example, a modified tail portion comprises about 4 to about 30 lysines, or may include a lysine domain of about 4 to about 30 lysines, or about 5 to about 20 lysines in length.
  • a modified tail portion comprises a histidine tag of about 1 to about 10 histidines in length.
  • Modified tail portions may further comprise a linker segment. Also disclosed herein are nucleic acids encoding disclosed proteins.
  • a chimeric therapeutic comprising a modified viral core protein chosen from HPV, SV40, CCMV, DGNNV, TBSV, Norwalk Virus, and HCV, having a modified tail portion; and a nucleic acid bound to said modified viral core protein.
  • the nucleic acid bound to a modified viral core protein of a disclosed chimeric therapeutic may have a binding affinity of about 50 nM to about 500 nM, at 2OmM NaHCO 3 , and a pH of 9.5, or about 55 nM to about 400 nM, at 2OmM NaHCO 3 , and a pH of 9.5, and/or about 50 nM to about 500 nM, at 2OmM (CH 2 OH) 3 CNH 2 , and a pH of 7.7.
  • the nucleic acid of a disclosed chimeric therapeutic is substantially bound to the modified viral core protein by Coulombic interactions.
  • the disclosed chimeric therapeutics, compositions, and/or particles may be substantially free of nuclease and/or substantially free of endogenous nucleic acids.
  • a disclosed chimeric therapeutic and/or particle having a nucleic acid bound to a viral core protein may be substantially protected from serum degradation when administered in vivo, for example, a nucleic acid bound to a viral core protein may be substantially protected from serum degradation for at least two weeks when a disclosed therapeutic chimeric and/or particle and/or composition is exposed at 37 0 C to a composition comprising a 1:1 weight ratio of human serum to water.
  • Disclosed viral core proteins may include a modified structural core portion comprises a conjugation site allowing attachment of a chemical linker moiety and/or a modified structural core portion may comprise one or more stability modifications [0014]
  • Disclosed viral core proteins may include a modified tail portion that comprises about 10 to about 35 amino acids.
  • a modified tail portion comprises truncations, substitutions and/or additions of amino acids as compared to a wild type tail portion.
  • a modified tail portion may include about 4 to about 30 lysines, e.g., may include a lysine domain of about 5 to about 20 lysines, e.g. about 9 lysines.
  • a disclosed modified tail portion may comprise a histidine tag of about 1 to about 10 histidines, e.g. about 5 to about 6 histidines.
  • Disclosed modified tail portions may further comprise a linker segment comprising about 1 to about 20 amino acids.
  • the chimeric therapeutics disclosed herein may include a nucleic acid that is e.g., an inhibiting nucleic acid, and/or is chemically modified, e.g. has a thiophosphate linkage.
  • Contemplated nucleic acids that may e.g. form part of disclosed chimeric therapeutics, particles and/or compositions include double stranded RNA, antisense nucleic acid, hairpin RNA, and microRNA.
  • a contemplated nucleic acid may be about 25 to about 44 bases in length, or about 10 to about 30 bases in length, or about 19 to about 23 bases in length.
  • compositions that include disclosed particles and/or chimeric therapeutics and a pharmaceutically acceptable carrier.
  • a therapeutic composition that includes a particle formed from a plurality of disclosed chimeric therapeutics, wherein the particle further comprises a coating; and a pharmaceutically acceptable excipient.
  • a therapeutic composition comprises: a particle formed from at least: i) a first discrete number of modified viral core proteins; and ii) a second discrete number of nucleic acids each bound to one of said modified viral core protein.
  • the nucleic acids bound to said modified viral core proteins may be substantially nonimmunogenic.
  • disclosed particles may include optionally, a coating associated with said particle and/or a pharmaceutically acceptable excipient.
  • the first discrete number may be about, for example, 150 to about 600, for example, the first discrete number may be about 500, or about 343, or about 164, or about 313, or about 336, or about 510, or about 171.
  • the second discrete number may be about, for example, 2 to about 60, or about 8 to about 20, or about 14 to about 18.
  • a therapeutic particle in another embodiment, includes a plurality of viral core proteins each comprising a structural core portion and a modified tail portion, wherein the structural core portions form a capsid; and the modified tail portions are substantially disposed within said capsid; and a plurality of nucleic acids, bound to said modified tail portion, wherein the nucleic acids are resistant to degradation with a nuclease when said particle is placed in an aqueous solution.
  • a particle comprises about 180 to about 250 viral core proteins, or about 170 to about 190 viral core proteins.
  • the particle includes about 3 to about 50 nucleic acids, or about 6 to about 28 nucleic acids.
  • a chemical linker moiety in some embodiments, may be bound to the capsid, e.g., a chemical linker moiety may be formed by contacting said capsid with PE-maleimide.
  • a coating may be provided, in some embodiments, that is e.g., associated with a disclosed particle, and may include one or more lipids.
  • at least one lipid molecule may be covalently bound through lipid linker moiety to one of the viral core proteins that form e.g., the particle.
  • Disclosed coatings may include, cholesterol or one or more neutral lipids. Claims appended to this disclosure are incorporated by reference and form part of this disclosure.
  • FIGURE 1 is a schematic depicting phosphatidyl ethanolamine (PE) conjugation to an exemplary lipid linker moiety.
  • PE phosphatidyl ethanolamine
  • FIGURE 2 is a schematic depicting conjugating a maleimide-containing linker on a lipid, to a sulfhydryl-containing protein.
  • FIGURE 3 is a flow diagram depicting the construction of a therapeutic particle.
  • FIGURE 4 depicts results from a capsid stability assay.
  • FIGURE 5 is a quantitative representation of the results of a nuclease protection assay.
  • FIGURE 6 is a quantitative representation of the results of a serum stability assay.
  • FIGURE 7 is line graph depicting the binding curve for K9 mutants.
  • FIGURE 8 is a line graph depicting the binding curves for K7 and KI l mutants.
  • FIGURE 9 depicts a chromatogram obtained by a purification method.
  • FIGURE 10 depicts a particle size measurement.
  • the present disclosure is generally directed, at least in part, to chimeric therapeutics, e.g. a therapeutic that includes a nucleic acid, e.g. an inhibitory nucleic acid, bound to a modified protein, and particles and/or compositions that include such chimeric therapeutics.
  • chimeric therapeutics e.g. a therapeutic that includes a nucleic acid, e.g. an inhibitory nucleic acid, bound to a modified protein, and particles and/or compositions that include such chimeric therapeutics.
  • amphipathic lipid refers, in part, to any suitable material wherein the hydrophobic portion of the lipid material orients into a hydrophobic phase, while the hydrophilic portion orients toward the aqueous phase.
  • Hydrophilic characteristics derive from the presence of polar or charged groups such as carbohydrates, phosphate, carboxylic, sulfato, amino, sulfhydryl, nitro, hydroxyl, and other like groups. Hydrophobicity can be conferred by the inclusion of apolar groups that include, but are not limited to, long chain saturated and unsaturated aliphatic hydrocarbon groups and such groups substituted by one or more aromatic, cycloaliphatic or heterocyclic group(s).
  • amphipathic compounds include, but are not limited to, phospholipids, aminolipids and sphingolipids.
  • phospholipids include, but are not limited to, phosphatidylcholine such as egg phosphatidylcholine or hydrogenated soy phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, phosphatidic acid, pahnitoyloleoyl phosphatidylcholine, lysophosphatidylcholine, lysophosphatidylethanolamine, dipalmitoylphosphatidylcholine, dioleoylphosphatidylcholine, distearoylphosphatidylcholine, phosphatidyl glycerol, monosialoganlgolioside, spingomyelin, dimyristoylphosphatidylcholine, and dilinoleoy
  • amphipathic lipids Other compounds lacking in phosphorus, such as sphingolipid, glycosphingolipid families, diacylglycerols, and ⁇ -acyloxyacids, are also within the group designated as amphipathic lipids. Additionally, the amphipathic lipid described above can be mixed with other lipids including triglycerides and sterols.
  • anionic lipid refers to any lipid that is negatively charged at physiological pH. These lipids include, but are not limited to, phosphatidylglycerols, cardiolipins, diacylphosphatidylserines, diacylphosphatidic acids, N-dodecanoyl phosphatidylethanolamines, N-succinyl phosphatidylethanolamines, N- glutarylphosphatidylethanolamines, lysylphosphatidylglycerols, palmitoyloleyolphosphatidylglycerol (POPG), and other anionic modifying groups joined to neutral lipids.
  • phosphatidylglycerols cardiolipins
  • diacylphosphatidylserines diacylphosphatidic acids
  • N-dodecanoyl phosphatidylethanolamines N-succinyl phosphatidylethanolamines
  • cationic lipid refers to any of a number of lipid species that carry a net positive charge at a selected pH, such as physiological pH (e.g., pH of about 7.0).
  • cationic lipids include, but are not limited to, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), dioctadecyldimethylammonium (DODMA), distearyldimethylammonium (DSDMA), N-(l-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N-(l-(2,3-dioleoyloxy)propyl)- N,N,N-trimethylammonium chloride (DOTAP), 3-(N-(N',N'-dimethylaminoethane
  • DODAC N,
  • an "effective amount” or “therapeutically effective amount” of a therapeutic, composition or particle contemplated herein is an amount sufficient to produce a desired effect, e.g., inhibition of expression of a target in comparison to the normal expression level detected in the absence of administration.
  • the therapeutically effective amount will vary depending upon the subject and disease condition being treated, the rate of target transcript turnover, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like.
  • certain compositions of the present invention may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.
  • gene refers to a nucleic acid (e.g., DNA or RNA) sequence that comprises partial length or entire length coding sequences necessary for the production of a polypeptide or precursor polypeptide.
  • inhibitory nucleic acid refers to a single-stranded or double- stranded RNA, siRNA (small interfering RNA), shRNA (short hairpin RNA), or antisense RNA, or a portion thereof, or an analog or mimetic thereof, that when administered to a mammal results in a decrease (e.g., by 10%, 25%, 50%, 75%, 90%, 95%, or 100%) in the expression of a target.
  • an inhibitory nucleic acid comprises or corresponds to at least a portion of a target nucleic acid or gene, or an ortholog thereof, or comprises at least a portion of the complementary strand of a target nucleic acid or gene.
  • An inhibitory nucleic acid typically has substantial or complete identity or homology (e.g. 60%, 70%, 80%, 85%, 90%, 95%, 99% or
  • lipid refers to a group of organic compounds that include, but are not limited to, esters of fatty acids and are characterized by being insoluble in water, but soluble in many organic solvents. They are usually divided into at least three classes: (1) “simple lipids,” which include fats and oils as well as waxes; (2) “compound lipids,” which include phospholipids and glycolipids; and (3) “derived lipids” such as steroids.
  • modulation is art-recognized and refers to up regulation (i.e., activation or stimulation), down regulation (i.e., inhibition or suppression) of a response, or the two in combination or apart.
  • neutral lipid refers to any of a number of lipid species that exist either in an uncharged or neutral zwitterionic form at a selected pH. At physiological pH, such lipids include, for example, diacylphosphatidylcholine, diacylphosphatidylethanolamine, ceramide, sphingomyelin, cephalin, cholesterol, cerebrosides, and diacylglycerols.
  • nucleic acid refers to a polymer containing at least two deoxyribonucleotides or ribonucleotides in either single- or double- stranded form and includes DNA and RNA.
  • DNA may be in the form of, e.g., antisense molecules, plasmid DNA, pre- condensed DNA, a PCR product, vectors (Pl, PAC, BAC, YAC, artificial chromosomes), expression cassettes, chromosomal DNA, or derivatives and combinations of these groups.
  • RNA may be in the form of inhibitory RNA, mRNA, tRNA, rRNA, tRNA, vRNA, and combinations thereof.
  • Nucleic acids include nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, and which have similar binding properties as the reference nucleic acid.
  • nucleotides contain a deoxyribose (DNA) or ribose (RNA), a sugar, a nitrogenous base, and a phosphate group or analog thereof. Nucleotides are linked together through the phosphate groups.
  • Bases include purines and pyrimidines, which further include natural compounds adenine, thymine, guanine, cytosine, uracil, inosine, and natural analogs, and synthetic derivatives of purines and pyrimidines, which include, but are not limited to, modifications which place new reactive groups such as, but not limited to, amines, alcohols, thiols, carboxylates, and alkylhalides.
  • a "patient,” “subject” or “host” to be treated by a disclosed method may mean either a human or non-human animal.
  • composition or vehicle such as a liquid or solid filler, diluent, excipient, or solvent, involved in carrying or transporting any subject composition or component thereof from one organ, or portion of the body, to another organ, or portion of the body.
  • excipient must be "acceptable” in the sense of being compatible with the subject composition and its components and not injurious to the patient.
  • materials which may serve as pharmaceutically acceptable excipients include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydro
  • portion when used in reference to a protein refers to fragments of that protein.
  • Target refers to a nucleic acid or variants thereof required for expression of a polypeptide that is the site or potential site of therapeutic intervention by a therapeutic agent; or a non-peptide entity including a microorganism, virus, bacterium, or single cell parasite (wherein the entire genome of a virus may be regarded as a target); and/or a naturally occurring interfering RNA or microRNA or precursor thereof.
  • target may refer to the sequence of nucleotides corresponding to the portion of a gene's coding mRNA.
  • serum- stable in relation to nucleic acid-lipid particles means that the particle is not significantly degraded after exposure to a serum or nuclease assay that would significantly degrade free DNA or RNA.
  • Suitable assays include, for example, a standard serum assay, a DNase assay, or an RNase assay.
  • the chimeric therapeutics disclosed herein may be capable of forming a particle, which may be a particle, e.g. a nanoparticle, for example, a plurality of disclosed chimeric therapeutics may self- assemble in to a particle or capsid.
  • Such therapeutic chimerics may include a modified viral core protein with a nucleic acid associated with, e.g. bound to, the modified viral core protein.
  • the nucleic acid may be bound to the modified viral core protein by substantially Coulombic forces, or in another embodiment, by Coulombic forces and/or hydrogen bonding.
  • Nucleic acids associated with a disclosed viral core protein may be, e.g., substantially homologous to a target, e.g.
  • the nucleic acid when bound to the modified viral core protein, may be substantially non-immunogenic.
  • a nucleic acid bound to a modified viral core protein may be substantially less immunogenic as compared to an identical unbound nucleic acid.
  • a chimeric therapeutic in another embodiment, includes an e.g. modified viral core protein and a nucleic acid bound to the modified viral core protein (e.g., to a modified tail portion of the viral core protein) with a binding affinity that allows release of the nucleic acid when the chimeric therapeutic is administered in vivo.
  • the nucleic acid of a chimeric therapeutic, wherein bound to a disclosed modified viral core protein may be resistant in an aqueous solution to degradation with a nuclease, e.g. benzoase.
  • a nucleic acid bound to a disclosed modified viral core protein at 1.9 units/nmole, 100 unit/nmole, 500 units/nmole or 945 units/nmole and incubated for 1 hour at room temperature does not substantially degrade as compared to an identical, but unbound, nucleic acid.
  • a nucleic acid bound to a disclosed modified viral core protein is substantially protected from serum degradation in vivo or in vitro, for example, when a chimeric therapeutic is exposed at 37 0 C to a composition comprising a 1:1 weight ratio of human serum to water.
  • Disclosed chimeric therapeutics may be substantially free of nuclease and/or may be substantially free of endogenous nucleic acids.
  • a therapeutic multiplex that includes a plurality of capsids, such as disclosed herein, for example, wherein each capsid comprises a viral core protein having a structural core portion and a tail portion, and a nucleic acid bound to said tail portion.
  • a coating may substantially surround two or more of capsids, e.g. may surround about six capsids.
  • Any viral core protein that is capable, together with other viral core proteins, of self-assembling into a capsid is suitable for use in the disclosed therapeutics.
  • self-assembling core proteins include human and duck Hepatitis B Virus core protein, Hepatitis C Virus core protein (HCV), Human Papillomavirus (HPV), Simian Virus 40 (SV40), Cowpea Chlorotic Mottle Virus (CCMV), Dragon Grouper Nervous Necrosis Virus (DGNNV), Tomato Bushy Stunt Virus (TBSV), and Norwalk Virus. It may be appreciated that different strains of viral proteins may have slight variations in sequences, and that any strain can be utilized.
  • HPV Human Papillomavirus
  • Cowpea Chlorotic Mottle Virus (CCMV) (Uni-prot Accession # P03601): (SEQ
  • DGNNV Dragon Grouper Nervous Necrosis Virus
  • Norwalk Virus (Swiss-Prot Accession # Q83884): (SEQ ID NO: 6) MMMASKDATSSVDGASGAGQLVPEVNASDPLAMDPVAGSSTAVATAGQVNPIDPWIINNFVQAPQGEFTI SPNNTPGDVLFDLSLGPHLNPFLLHLSQMYNGWVGNMRVRIMLAGNAFTAGKI IVSCIPPGFGSHNLTIA QATLFPHVIADVRTLDPIEVPLEDVRNVLFHNNDRNQQTMRLVCMLYTPLRTGGGTGDSFVVAGRVMTCP SPDFNFLFLVPPTVEQKTRPFTLPNLPLSSLSNSRAPLPI SSMGI SPDNVQSVQFQNGRCTLDGRLVGTT PVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPD TFVPHLGS IQANGIGSGNYVGVLSWI SPPSHPSGSQVDLWKIPNYGS
  • HCV Hepatitis C Virus core protein consensus sequence (HCV) (from Kunkel et al., 2001): (SEQ ID NO: 7)
  • a modified viral core protein contemplated herein may include a structural core protein and a tail portion.
  • a modified viral core protein for use in the disclosed therapeutics may include a modified structural core portion and a tail portion, e.g., a carboxyl terminal tail portion and/or a N-terminal tail portion, or may include a structural core portion and a modified tail portion, or may include a modified structural core portion and a modified tail portion, e.g., a modified structural core portion and/or modified tail portion as compared to the wild-type viral core protein, such as discussed above.
  • the structural core portions of modified viral core proteins may form a capsid, and the tail portion of the modified viral core proteins may be substantially disposed within the capsid.
  • an inward facing surface of formed capsid may act as modification location.
  • a modified viral core protein e.g., a modified HPV core protein may include a modified structural core portion and a modified C-terminal tail portion.
  • modifications can include alterations, truncations and/or mutations, etc. to the structural core portion and/or the modified tail portion of the viral core protein.
  • modifications may enhance the structural and functional characteristics of the HPV C-protein and may provide more effective therapeutics, e.g., a modified viral core protein is bound to a nucleic acid, e.g., an inhibitory nucleic acid.
  • a modified e.g. C-terminal or N-terminal tail portion of a viral core protein e.g.
  • HPV may provide a therapeutic that is substantially free of endogenous nucleic acids and/or substantially free of nuclease.
  • modifications to viral core protein can be made or engineered according to any method known in the art, including without limitation genetic engineering, chemical modifications, etc.
  • Modification to the viral core protein may also optimize binding and release of a nucleic acid bound to a viral core protein.
  • the binding affinity of a nucleic acid bound to a disclosed modified viral core protein may be about 50 nM to about 500 nM, or about 55 nM to about 400 nM, at 2OmM NaHCO 3 , and a pH of 9.5, or may be about 50 nM to about 500 nM, or about 55 nM to about 400 nM, at 2OmM (CH 2 OH) 3 CNH 2 , and a pH of 7.7.
  • Disclosed viral core proteins can be expressed and purified using common molecular biology and biochemistry techniques.
  • recombinant expression vectors can be used which can be engineered to carry a viral core protein gene into a host cell to provide for expression of the viral core protein.
  • Such vectors for example, can be introduced into a host cell by transfection means including, but not limited to, heat shock, calcium phosphate, DEAE-dextran, electroporation or liposome-mediated transfer.
  • Recombinant expression vectors include, but are not limited to, Escherichia coli based expression vectors such as BL21 (DE3) pLysS, COS cell-based expression vectors such as CDM8 or pDC201, or CHO cell-based expression vectors such as pED vectors.
  • a C-protein gene coding region can be linked to one of any number of promoters in an expression vector that can be activated in the chosen cell line.
  • a cassette (capsid gene and promoter) is carried by a vector that contains a selectable marker such that cells receiving the vector can be identified.
  • promoters to express the capsid proteins within a cell line can be drawn from those that are functionally active within the host cell.
  • Such promoters can include, but are not limited to, a T7 promoter, a CMV promoter, a SV40 early promoter, a herpes TK promoter, and others known in recombinant DNA technology.
  • Inducible promoters can be used, and include promoters such as metallothionine promoter (MT), mouse mammary tumor virus promoter (MMTV), and others known to those skilled in the art.
  • Exemplary selectable markers and their attendant selection agents can be drawn, for example, from the group including, but not limited to, ampicillin, kanamycin, aminoglycoside phosphotransferase/G418, hygromycin-B phosphotransferase/hygromycin-B, and amplifiable selection markers such as dihydrofolate reductase/methotrexate and others known to skilled practitioners.
  • a variety of eukaryotic, prokaryotic, insect, plant and yeast expression vector systems e.g., vectors which contain the necessary elements for directing the replication, transcription, and translation of viral core protein coding sequences
  • vectors which contain the necessary elements for directing the replication, transcription, and translation of viral core protein coding sequences
  • microorganisms such as bacteria transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing the capsid protein coding sequences; yeast transformed with recombinant yeast expression vectors containing the capsid protein coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the capsid protein coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing the capsid protein coding sequences.
  • microorganisms such as bacteria transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing the capsid protein coding sequences; yeast transformed with recombinant yeast expression vectors containing the capsid protein
  • the C-terminal tail of HPV core protein can be engineered to, for example, provide appropriate properties for binding a nucleic acid to the modified viral core protein.
  • a therapeutic chimeric is provided that includes a viral core protein with a modified tail portion and a nucleic acid associated with, e.g., bound to the modified tail portion.
  • Wild type HPV is typically a non-enveloped, dsDNA virus that forms about a 60 nm diameter capsid.
  • the capsid is typically formed by 72 pentamers of the major virus coat protein, Ll, in association with the minor virus coat protein, L2.
  • the Ll protein is 531 amino acids of which the C-terminal 31 amino acids are disordered in the crystal structure of the capsid and typically project toward the interior of the capsid.
  • This C-terminal portion of the HPV viral core protein functions as a nucleic acid binding domain of the HPV virion.
  • SEQ ID NO: 8 HPV C-terminal tail amino acid sequence 501 to 531
  • This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a HPV structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
  • Wild type SV40 forms an about 45 nm diameter, non-enveloped virus that in some embodiments is highly similar to HPV.
  • the outer shell of the capsid is typically formed by pentamers of the major capsid protein VPl while proteins VP2 and VP3 form a bridge between the outer shell and the dsDNA viral genome.
  • the VPl protein is typically about 364 amino acids of which the first N-terminal 21 amino acids are disordered in the crystal structure.
  • SEQ ID NO: 9 SV40 N-terminal tail amino acid sequence 1 to 21 MKMAPTKRKGSCPGAAPKKPK
  • This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
  • the first 21 amino acid tail may be removed and replaced by polylysine domains as discussed below.
  • CCMV is a 28 nm diameter virus composed of 180 capsid protein subunits.
  • the capsid protein is typically about 190 amino acids of which the first N-terminal 26 amino acids are disordered in the crystal structure and may interact with the viral RNA. (G. Vriend, BJ. M. Verduin, M. A. Hemminga, /. MoI. Biol, 191, 453-460 (1986)). Removal of these residues followed by replacement with polylysine segments plus linker regions, may, in some embodiments, serve as alternative nucleic acid binding domains.
  • SEQ ID NO: 10 CCMV N-terminal tail amino acid sequence 1 to 26
  • This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
  • Wild type DGNNV is a 27 nm diameter non-enveloped virus composed of 180 capsid protein subunits.
  • the capsid protein is typically about 338 amino acids of which the first 25 N-terminal amino acids are known to bind to the RNA genome of the virus. It is possible, in some embodiments, to e.g. remove and/or alter the first 25 amino acids of the capsid protein and e.g., replace it with a modified tail portion to construct alternative nucleic acid binding domains.
  • SEQ ID NO: 11 CCMV N-terminal tail amino acid sequence 1 to 25 MVRKGEKKLAKPPTTKAANPQPRRR
  • This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
  • Wild type TBSV is a 34 nm diameter virus composed of 180 capsid protein subunits.
  • the capsid protein is typically about 388 amino acids of which the first 65 N- terminal amino acids are known to bind to the RNA genome of the virus.
  • up to 52 amino acids from the N-terminus of the capsid protein may be removed and/or altered and e.g., replaced with a modified tail portion to construct alternative nucleic acid binding domains.
  • SEQ ID NO: 12 TBSV N-terminal tail amino acid sequence 1 to 52 MAMVKRNNNTGMIPVSTKQLLALGAAAGATALQGFVKNNGMAIVEGAVDLTK
  • This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
  • Wild type Norwalk virus is a 38 nm virus composed of 180 capsid protein subunits.
  • the capsid protein is typically about 530 amino acids of which the first 27 N- terminal amino acids is presumed to hang inside the viral capsid and are either all or partially disordered in the crystal structure. Deletion of the first 20 amino acids of the capsid protein followed by insertion of a poly-lysine region with varying linkers, could provide an alternative nucleic-acid binding domain.
  • SEQ ID NO: 13 Norwalk virus N-terminal tail amino acid sequence 1 to 20
  • This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
  • Wild type HCV is an enveloped virus that is 60 nm in diameter.
  • P21 is cleaved from a P23 precursor by a signal peptidase in the endoplasmic reticulum.
  • the RNA binding domain of the sequence has been located to the first 75 N-terminal amino acids (Santolini, et al., J. Virol, 68, 3631-3641, (1994)).
  • SEQ ID NO: 14 HCV N-terminal tail amino acid sequence 1 to 20 MSTNPKPQRKTKRNTNRRPQ [0081]
  • This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
  • a modified tail portion e.g., a modified C-terminal tail portion and/or a modified N-terminal tail portion may include a modification that includes one or more poly-lysines.
  • the modified tail portion may include about 4 to about 30 lysines, or about 5 to about 20 lysines, e.g., about 7, 8, 9, or 10 lysines.
  • the modified tail portion may include one or more lysine domains.
  • each poly-lysine domain may comprise about one to about thirty lysine residues.
  • the poly-lysine domain may comprise about 5 lysine residues to about 20 lysine residues.
  • the poly-lysine domains can be separated by about 1 to about 20 amino acid residues. In some embodiments, where more than one polylysine domain is present the each poly-lysine domain can comprise about 4 lysine residues to about 20 lysine residues (or any specific amino acid length disposed with the range). In some embodiments, at least four or at least five consecutive lysine residues are included in a modified C-terminal and/or N-terminal tail portion.
  • Poly-lysines and poly-lysine domains and/or a polyhistidine tag can form part of a modified C-terminal tail and/or N-terminal tail separately or in combination.
  • a polyhistidine tag may, in some embodiments, facilitate purification of the proteins.
  • Exemplary modified C-terminal and/or N-terminal tail portions include those having e.g., 5 lysines (K5), 7 lysines (K7), 9 lysines (K9), 10 lysines (KIO), 11 lysines (KU), 13 lysines (K13), or 20 lysines (K20).
  • exemplary modified tail portions include those with a poly-lysine region with nine lysines alternating with a poly-alanine region with nine alanines (KA9), a poly-lysine region with nine lysines alternating with a poly- glycine region with nine glycines (KG9) and a poly-lysine region with nine lysines interrupted by a sequence of at least four amino acids between the fourth and fifth lysines (K4-5).
  • an about four amino acid stretch between the fourth and fifth lysines of the K4-5 tail may be amino acids Ser-Gln-Ser-Pro.
  • a modified tail portion may be represented by: KLAAA [ KKKKK ] 1 LE [ H ] 3 SEQ ID NO: 15 wherein i is an integer from 4 to 21, and j is an integer from 0 to 10.
  • modified tail portion may form part of a modified viral core protein.
  • exemplary modified viral core proteins provided herein include:
  • a modified tail portion may be formed from alternating lysines, for example, a modified tail portion can include the sequence represented by;
  • DKLAA [ AK ] P LE [ H ] D (SEQ ID NO: 23) wherein p is an integer from 5 to 12, and j is an integer from 0 to 10.
  • p may be 5, 6, 7, 8, 9, 10, 11, or 12; j may be 0, 1, 2, 3, 4, 5 or more.
  • mutations creating e.g., various poly-lysine domains of differing lengths can be engineered using any methods known in the art.
  • the core protein gene can be amplified via PCR and various numbers of lysine (or other) residues can be added.
  • a modified tail portion includes one or more arginines.
  • the modified tail portion may include about 4 to about 30 arginines, or about 5 to about 20 arginines, e.g. about 7, 8, 9, or 10 arginines.
  • the modified tail portion may include one or more arginine domains.
  • the poly-arginine domains can be separated by about 1 to about 20 amino acid residues.
  • each poly-arginine domain may comprise about one to about thirty arginine residues.
  • the each poly-arginine domain can comprise about 4 arginine residues to about 20 arginine residues (or any specific amino acid length disposed with the range).
  • a modified C-terminal tail and/or N-terminal tail includes at least four or at least five consecutive arginine residues.
  • a modified C-terminal tail and/or N-terminal tail may include both arginines and lysines, e.g., may include both arginine and lysine domains.
  • Poly-arginine domains and/or a poly histidine tag can be added to the C-terminal tails separately or in combination.
  • a poly histidine tag may, in some embodiments, facilitate purification of the proteins.
  • Exemplary modified tail portions may include for example, 5 arginines (R5), 7 arginines (R7), 9 arginines (R9), 11 arginines (RI l), 13 arginines (R13), or 20 arginines (R20).
  • modified tail portions may be represented by:
  • q may be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20; j may be 0, 1, 2, 3, 4, 5 or more.
  • modified viral core proteins that include such modified tail portions include:
  • a modified tail portion includes one or more truncation mutations.
  • the modified tail portion may include truncations of about 3 to about 50 amino acids, about 5 to about 40 amino acids, e.g. about 10, about 20, or about 30 amino acids or more.
  • Some modified tail portions may or may not include a histidine tag.
  • a linker segment may be optionally present between e.g. a modified core portion and a modified tail portion.
  • the linker segment is about 3 amino acids to about 15 amino acids in length (or any specific amino acid length disposed with the range) and can link e.g. a poly-lysine and/or a polyarginine domain to an amino acid corresponding to the end of a structural core portion of a corresponding viral core protein, for example, to provide flexibility to a modified tail portion.
  • an e.g., poly-lysine and/or poly arginine domain can be followed by a poly-histidine tag and/or followed by an Xhol restriction site.
  • the poly-histidine tag can include, in some embodiments, at least six histidine residues added to the C-terminal tail.
  • such linker segments may be represented by one of: [ SAG ] 3 (SEQ ID NO: 32)
  • r, s and t are, each independently, integers from 1 to 6 or more.
  • r, s and t are, each independently, integers from 1 to 6 or more.
  • DGNNV Linker 1 K9 HHHHHHELKKKKKKKGASGASANNRRRSNRTDAPVSKASTVTGFGRGTNDVHLSGMSRISQAVLPAGTGTDGYV VVDATIVPDLLPRLGHAARIFQRYAVETLEFEIQPMCPANTGGGYVAGFLPDPTDNDHTFDALQATRGAVVAKWWE SRTVRPQYTRTLLWTSSGKEQRLTSPGRLILLCVGNNTDVVNVSVLCRWSVRLSVPSLETPEETTAPIMTQGSLYN DSLSTNDFKS ILLGSTPLDIAPDGAVFQLDRPLS IDYSLGTGDVDRAVYWHLKKFAGNAGTPAGWFRWGIWDNFNK TFTDGVAYYSDEQPRQILLPVGTVCTRVDSEN TBSV Linker 1 K9 (SEQ ID NO: 39)
  • HCV Linker 1 K9 (SEQ ID NO: 41)
  • the modification of the tail portion may allow a nucleic acid to bind to the tail portion with a binding affinity that may allow release of the nucleic acid when the chimeric therapeutic (e.g. viral core protein bound to a nucleic acid) is administered e.g. in vivo.
  • a modified tail portion that includes lysine may bind a nucleic acid using substantially Coulombic forces only, such that the nucleic acid may, in some embodiments, be released when exposed to a ionic solution e.g. a salt solution.
  • the disclosed chimeric therapeutics e.g. that do not include a modified tail portion with a substantial number of arginines such as those arranged as in a wild type tail portion, may be substantially free of endogenous nucleic acids.
  • the structural core of a modified viral core protein may be modified to e.g., (a) strengthen and promote assembly of the viral core protein, e.g. HPV core protein monomers, into a capsid; (b) enhance and promote a coating of one or more capsids with a layer comprising a lipid , (c) facilitate the attachment of other moieties, e.g., chemical modifiers and/or targeting agents; and/or (d) facilitate the disassembly of the entire capsid in the bloodstream following administration.
  • the wild type HPV Ll protein is 531 amino acids of which the first 500 amino acids may form a structural core.
  • a structural core portion based on amino acid 1-500 of SEQ ID NO: 1, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid.
  • An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 42, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 42 and additionally, a modified or unmodified tail portion, e.g. a modified tail portion such as those described above.
  • ADLDQFPLGRKFLLQLGL (SEQ ID NO: 42) wherein the X, at a given location is selected from:
  • the wild type SV40 protein is 364 amino acids of which the carboxyl 343 amino acids may form a structural core.
  • a structural core portion based on amino acid 22-364 of SEQ ID NO: 2, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid.
  • An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 43, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 43 and additionally, a modified or unmodified tail portion, e.g.
  • the wild type CCMV protein is 190 amino acids of which the carboxyl 164 amino acids may form a structural core.
  • a structural core portion based on amino acid 27-190 of SEQ ID NO: 3, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid.
  • An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 44, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 44and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
  • the wild type DGNNV protein is 338 amino acids of which the carboxyl 313 amino acids may form a structural core.
  • a structural core portion based on amino acid 26-373 of SEQ ID NO: 4, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid.
  • An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 45.
  • cysteine residues may be mutated into a most apical solvent-exposed surface of the capsid protein.
  • a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 45 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
  • the wild type TBSV protein is 388 amino acids of which the carboxyl 336 amino acids form a structural core.
  • a structural core portion based on amino acid 53-388 of SEQ ID NO: 5, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid.
  • An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 46, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 46 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
  • the wild type Norwalk Virus protein is 530 amino acids of which the carboxyl 510 amino acids form a structural core.
  • a structural core portion based on amino acid 21-530 of SEQ ID NO: 6, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid.
  • An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 47, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 47 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
  • PDGFLTCVPNGASSGPQQLPiNGVFVFvswvsRFYQLKPVGTASSARGRLGLRR (SEQ ID NO: 47) wherein the X, at a given location is selected from:
  • HCV HCV
  • carboxyl 171 amino acids may form a structural core of HCV.
  • a structural core portion may be based on amino acid 21-191 of SEQ ID NO: 7, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid.
  • An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 48.
  • cysteine residues may be mutated into a most apical solvent-exposed surface of the capsid protein.
  • a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 48 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
  • the various viral capsids are typically approximate spherical macromolecular assemblies composed of monomers of core proteins.
  • the CCMV capsid is comprised of 180 capsid protein subunits.
  • the intermolecular interactions between dimers that stabilize the assembly can be formed by e.g., disulfide bonds, salt bridges, and hydrophobic interactions.
  • the structural core portion may include mutation of interacting amino acid side chains to either stabilize or destabilize the interactions and therefore, the capsid assembly.
  • the stabilizing and destabilizing mutations can be introduced singly and in combination to fine-tune capsid stability.
  • expressed viral core proteins in solution may form a dimer that is naturally stabilized by salt bridges, hydrophobic interactions, and covalent inter- and intramolecular disulfide bonds.
  • intra-molecular bonds may be engineered so that viral core protein stability can be tuned to a desired level.
  • inter-molecular disulfide bonds can be engineered so as to affect the stability of the capsid.
  • Specific salt bridges between dimers that help form the capsid can also be mutated to cysteines so that disulfide bonds form and stabilize the capsid structure.
  • various alterations or mutations may be made on the structural core (which may form the outer surface of the capsid) that may introduce blood protease recognition sequences, e.g., protease recognition sites at hinge and loop regions.
  • the protease may recognize and cleave this loop thereby promoting disassembly.
  • Exemplary blood protease recognition sequences include for example, thrombin (SEQ ID NO: 49) and factor Xa (SEQ ID NO: 50.) GPGAPGLVPRGS (SEQ ID NO: 49)
  • the structural core portion of the viral core protein may be modified to include a conjugation site that allows the attachment of a chemical linker, e.g. a lipid linker moiety.
  • a chemical linker e.g. a lipid linker moiety.
  • either of the amino acids cysteine or lysine may be placed in the structural core in such a way so that when formed in a capsid these modifications protrude away from the capsid surface toward the plasma membrane.
  • such modifications may permit the addition of one or more lipid linker moieties which can serve to promote or facilitate a lipid layer.
  • such a modification may permit the addition ⁇ e.g. the attachment of) one or more targeting agents, as described below.
  • Cysteine mutations can also be introduced at other locations in the viral protein.
  • the choice of lysine or cysteine at each position is dependent of the orientation and geometry of each amino acid as judged from the crystal structure of the viral capsid protein.
  • Exemplary modified structural portions, with a wild type terminal tail, are provided below: HPV attachment mutant S280C (SEQ ID NO: 51)
  • a chemical linker may bind another moiety to a particle formed from viral core proteins that include a modified structure core portion, e.g. that include one or more cysteine residues.
  • exemplary chemical linkers include moieties such as those formed by contacting a cysteine residue with a maleimide containing compound such as phosphoethanolamine-maleimide (PE-maleimide or PE- mal).
  • Phospholipids for example, may be directly linked through a chemical linker to a modified structural core portion e.g. to link a lipid molecule and/or a targeting agent.
  • cysteine residues may be engineered into the structural core portion region to provide a covalent linker to a modified viral core protein.
  • a S- protein may guide the coating of the lipid layer or lipid/cholesterol layer.
  • Contemplated S- proteins for attaching to a disclosed capsid or particle may be modified to have cysteines as well to complement the disulfide bridge formation between C-protein monomers.
  • a S-protein can be replaced by a peptide such as a transmembrane engineered peptide.
  • An exemplary transmembrane engineered peptide may have e.g., a flexible region that ends with a cysteine so as to form disulfide bridges with the cage, with the opposite end comprising primarily of hydrophobic residues.
  • a non-limiting example of such a S-protein transmembrane engineered peptide has the amino acid sequence: CARGARGARGARG I LGVF I LLYM (SEQ ID NO: 56) [0115]
  • compositions and Particles are Compositions and Particles
  • compositions that include particles formed from a plurality of chimeric therapeutics as described above. Such particles may include a coating, or alternatively, a set of particles may be associated with each other, and such set of particles may include a coating over the set. Therapeutic compositions may include a pharmaceutically acceptable excipient.
  • a therapeutic composition comprising a particle formed from at least: i) a first discrete number of modified viral core proteins; and ii) a second discrete number of nucleic acids each bound to one of said modified viral core proteins.
  • a particle may include different modified viral core proteins, e.g., those with different modified tail portions, or a particle may be, e.g., formed from all the same modified viral core proteins.
  • only a portion of modified viral core proteins are bound to a nucleic acid.
  • the formed particles may include a coating associated with a given particle or may include a coating associated with or surrounding several particles.
  • the first discrete number of modified viral core proteins is about the number necessary to form a capsid from a disclosed viral core protein, e.g. about 170 to about 200 modified viral core proteins, or about 180 modified viral core proteins, for e.g. a CCMV capsid.
  • the second discrete number of nucleic acids, wherein each nucleic acid is bound to one of the viral core proteins is about for example, 2 to about 60, about 8 to about 20, or about 14 to about 18, e.g. about 15, 16, or 17 nucleic acids.
  • a disclosed particle is formed from 180 modified viral core proteins, about 14 to about 18 of those modified viral core proteins are bound to a nucleic acid.
  • a given particle can include e.g. about 8 to about 20 of the same nucleic acid, or one or more nucleic acids may be substantially different, e.g. directed to a different area of a gene target or to a different gene target.
  • a therapeutic particle that includes a plurality of viral core proteins each comprising a structural core portion and a modified tail portion, wherein said structural core portions form a capsid; and said modified tail portions are substantially disposed within said capsid; and a plurality of nucleic acids, bound to a modified tail portion of one of the viral core proteins.
  • the number of nucleic acids bound to a modified tail portion is less than that number of viral core proteins present in the particle.
  • Disclosed particles may further, in some embodiments, comprise a partial or substantially complete coating disposed on the particle that includes one or more lipids.
  • at least one lipid molecule may covalently bound through a chemical linker moiety, e.g. a lipid linker moiety, to a viral core protein, e.g., to a structural core portion of a disclosed viral core protein.
  • the lipid may be attached via bond or chemical linker moiety, to an engineered location on the structural core portion of the viral core protein.
  • a therapeutic multiplex comprising two or more capsids, e.g., a plurality of capsids, for example, about 3 to about 12, e.g. 4, 5, or 6 capsids, each capsid comprising a disclosed modified viral core protein having, e.g., a modified structural core portion and a modified tail portion, and a nucleic acid bound to said tail portion, and a coating at least partially surrounding the two or more capsids.
  • Contemplated lipid linker moieties may include those formed from contacting e.g. a succinimidyl derivative such as succinimidyl-4-(p-maleimidophenyl)butyrate (SMPB) or m- maleimidobenzoyl-N-hydroxysuccinimide ester with a structural core portion of the viral core protein.
  • SMPB succinimidyl-4-(p-maleimidophenyl)butyrate
  • m- maleimidobenzoyl-N-hydroxysuccinimide ester with a structural core portion of the viral core protein.
  • a disclosed particle may have a layer or coating comprising one or more lipids, e.g., a neutral lipid, an anionic lipid, and/or a cationic lipid.
  • a neutral lipid and/or an amphipathic lipid for example, a phospholipid such as phophatidyl serine, may be covalently bonded to a lipid linker moiety.
  • Such covalently bound lipid molecules may guide the placement of a coating, e.g. that may include one more neutral lipids, and/or may include an anionic lipid that is surface neutral, such as POPG.
  • Exemplary phospholipids suitable for use include, but are not limited to, hydrogenated soy phosphatidylcholine (HSPC), egg phosphatidylcholine (EPC), phosphatidyl ethanolamine (PE), phosphatidyl glycerol (PG), phosphatidyl inositol (PI), monosialogangolioside, spingomyelin (SPM), distearoylphosphatidylcholine (DSPC), dimyristoylphosphatidylcholine (DMPC), or dimyristoylphosphatidylglycerol (DMPG).
  • HSPC hydrogenated soy phosphatidylcholine
  • EPC egg phosphatidylcholine
  • PE phosphatidyl ethanolamine
  • PG phosphatidyl glycerol
  • PI phosphatidyl inositol
  • SPM distearoylphosphatidylcholine
  • DMPC dimy
  • particles contemplated herein include one or more lipids including one, two, or more of lipids such as palmitoyloleoylphosphatidylglycerol (POPG), hydrogenated soy phosphatidylcholine (HSPC).
  • Contemplated lipids include PEG- phospholipids, including poly(ethylene glycol) -derivatized distearoylphosphatidylethanolamine (PEG-DSPE) and/or poly(ethylene glycol)-derivatized ceramides (PEG-CER).
  • particles that may include a coating comprising one or more lipids and cholesterol, for example, may include various amounts of cholesterol, HSPC or
  • a coating may comprise, for example, (a) about 20% cholesterol and about 80 % HSPC; (b) about 50% cholesterol and about 50 % HSPC; (c) about 20% cholesterol and about 20 % HSPC and about 60% POPG; (d) about 50% cholesterol and about 50% POPG; (e) 20% cholesterol and 80 % POPG; or (f) about 10 % Cholesterol and about 15% HSPC and about 65% POPG.
  • a coating may include about 20% Cholesterol, about 20 % HSPC and about 60% POPG.
  • a coating composition may have a mass value of the particle of about 10% to about 60%, about 10% to about 50%, about 15 to about 40%, about 20% to about 35% of the total protein (w/w), or any specific percentage with the recited ranges.
  • a lipid coating composition may coat a particle at a mass value of about 30% (w/w).
  • a coating may be modified to enhance e.g. the ability of the particles to enter target cells and/or to at least partially evade the immune system in vivo.
  • PEG polyethylene glycol
  • PTD protein transduction domains
  • suitable PTDs are the Human Immunodeficiency Virus (HIV) transactivator of transcription (Tat) peptide and/or poly-arginine (poly-Arg).
  • HAV Human Immunodeficiency Virus
  • a cholesterol-tagged PEG may be anchored into a lipid coating and/or cholesterol tagged PTDs may be anchored into a coating.
  • Suitable ratios of protein: lipid for the coating process may range, in an embodiment, from approximately 1:1 protein:lipid (w:w) to approximately 1:30 protein:lipid (w:w).
  • a disclosed particle that includes a lipid coating may be generally prepared by 1) first mixing a modified viral core protein with an nucleic acid of choice; 2) placing the core protein in a buffered solution, e.g., phosphate, citrate, tris, sodium buffer, causing particles to be formed that substantially encapsulate the nucleic acid; 3) adding sonicated phospholipids solution to the mixture which may bind with modified sites on the viral core protein; 4) adding cholesterol or lipid-tagged polyethylene glycol to the mixture; and 5) purifying the system by centrifugation or size exclusion chromatography.
  • a buffered solution e.g., phosphate, citrate, tris, sodium buffer
  • the viral core proteins may be maintained in any suitable chemical denaturant or denaturing agent known in the art (e.g., urea, guanidine hydrochloride (GuHCl), sodium dodecyl sulfate (SDS)) in a concentration of about IM to about 6M, about 1.5M to about 5M, about 1.75M to about 4.5M, or any integer disposed within said ranges.
  • the chemical denaturant may be urea, which may be present in e.g. a concentration of about 2M to about 6M, about 3M to about 5M, about 3.5M to about 4.5M, e.g.
  • the ionic strength of the solution can be raised to a final concentration of about 50 mM to about 600 mM using e.g. a salt, e.g. NaCl.
  • the final concentration can be about 100 mM to about 550 mM, about 150 mM to about 500 mM, about 200 to about 450 mM, about 250 mM to about 400 mM or about 300 mM to about 350 mM, or any integer disposed within said ranges.
  • the final ionic concentration of the solution may be directly related to the amount of chemical denaturant present in the solution.
  • temperature may facilitate self-assembly of the capsid.
  • a temperature of about 25° C to about 105° C, about 40 ° C to about 90 ° C or about 55° C to about 75° C (or any specific temperature within the recited ranges) may trigger self-assembly of the capsid.
  • reducing agents such as DTT or beta-mercaptoethanol may be used to facilitate self-assembly of a capsid.
  • Particles disclosed herein may be substantially non-replicating.
  • the viral core proteins may be designed so that once the particle starts to disintegrate, they are degraded quickly so as to limit any potential immune response. Disclosed particles do not substantially incorporate any attenuated wild type virus.
  • Various targeting agents can be incorporated into e.g. a coating layer of the disclosed particles, e.g. incorporated or bound to a lipid layer or lipid/cholesterol layer coat to direct the particle to a tissue or cell target.
  • a targeting agent may be bound directly, e.g. chemically linked, directly or through a chemical linker moiety, to a disclosed particle.
  • An exemplary targeting agent may be an antibody.
  • exposed sulfhydryl groups on the heavy chain of an antibody can be used to link the antibody to e.g. a free sulfate group on a coating comprising one or more lipids.
  • a lipid can be attached to antibodies through different chemical means, such as reacting an activated lipid such as PE-maleimide to activated free amines of an antibody with agents such as Traut' s Reagent.
  • a reduced antibody heavy chain-light chain complex above can also be attached directly to the naked particle.
  • the modified viral core protein may incorporate cysteine residues with reactive sulfhydryl groups as described above which then can be linked with the partially disassociated antibody chains.
  • Antibodies suitable for use as targeting agents include antibodies directed to cell surface antigens which cause the antibody-particle complex to be internalized, either directly or indirectly.
  • Specific non-limiting examples of suitable antibodies include antibodies to CD 19, CD20, CD22, CD33 and CD74.
  • CD33 and CD22 are over-expressed on lymphomas and binding to these antigens caused endocytosis and thereby internalization of the antibody- particle complex.
  • Methods for incorporating monoclonal antibodies to CD22 into the lipid coating can be found in U.S. Patent Publication No. 20070269370, which is incorporated herein by reference.
  • a coating of a particle, or the particle itself may be modified, to enhance e.g.
  • a large polymer ⁇ e.g. PEG), cholesterol-tagged or lipid-tagged polyethylene glycol (PEG) and/or protein transduction domains (PTD) may form part of a coating, and/or may be covalently linked through a bond or a chemical linker moiety to the coating and/or to specific site(s) (e.g. cysteine sites) on the modified structural core portion of the viral core protein.
  • PTDs are the Human Immunodeficiency Virus (HIV) transactivator of transcription (Tat) peptide and/or poly- arginine (poly-Arg).
  • the particles and/or coatings may be modified by attaching a PEG.
  • a PEG For example, one or more cholesterol-tagged PEGs may be anchored into a lipid coating or particle, and/or one or more cholesterol tagged PTD may be anchored into a coating or particle.
  • the particle and/or coating may be modified, e.g., covalently bonded through a chemical linker, to e.g. a carbohydrate and/or a sugar (e.g. branched sugar) moiety.
  • Antibody mimetics and/or peptide mimetics that include complementarity determining region (CDR) subunits may also be, in some embodiments, associated with or bound to (e.g. via linker) to a coating or particle disclosed herein.
  • CDR complementarity determining region
  • an targeting agent that binds FcRN, s-protein or other moiety can be bound or associated with either a coating, e.g. a lipid coating, or may be bound directly to a modified viral core.
  • a coating e.g. a lipid coating
  • targeting agents include those in US Patent Application 20070254831
  • the therapeutic chimerics, particles and compositions disclosed here include at least one nucleic acid substantially homologous to a particular target bound to, or associated with, a viral core protein.
  • an nucleic acid molecule when bound to a viral core protein, is "substantially non-immunogenic" i.e., does not elicit, induce, or invoke a substantial immune response, for example, a humoral and/or a cellular immune response in a mammalian subject, such as a human subject.
  • an inhibitory nucleic acid molecule that is not bound to the viral core protein, e.g.
  • Exemplary nucleic molecules that may form part of the e.g., disclosed therapeutics, particles and/or compositions disclosed herein include inhibitory nucleic acids.
  • Inhibitory nucleic acid molecules include an inhibitory double-stranded RNA, i.e., a "interfering RNA" or "iRNA" of about 10 to about 60, about 15 to about 50, about 15 to about 40, about 15 to about 30, or about 15 to about 20 nucleotides in length.
  • an inhibitory double stranded RNA is about 25 to about 45, about 27 to about 40, about 30 to about 40, about 33 to about 40, or about 36 to about 40 nucleotides in length. In other embodiments, an inhibitory double stranded RNA is about 15 to about 30, about 15 to about 25, about 19 to about 25, about 19 to about 23, or about 19 to about 21 nucleotides in length. In yet other embodiments, an inhibitory double stranded RNA is about 20 to about 24 or about 21 to about 22 or to about 23 nucleotides in length. An inhibitory double stranded RNA may be transcribed from a transcriptional cassette in a DNA plasmid.
  • Such inhibitory double stranded RNA reduces, inhibits or silences expression of a target gene by mediating the degradation of mRNAs, which are complementary to the sequence of an inhibitory RNA.
  • An inhibitory double stranded RNA can be formed by two complementary strands or by a single, self-complementary strand.
  • the relationship between a target mRNA and the sense strand of an inhibitory RNA is that of identity.
  • the sense strand of an inhibitory RNA is also called a passenger strand, if present.
  • the relationship between a target mRNA (a sense strand) and the antisense strand of an inhibitory RNA is that of complementarity.
  • the antisense strand of an inhibitory RNA is also called a guide strand.
  • Exemplary inhibitory double stranded RNA duplex may comprise 3' overhangs of about 1 to about 4 nucleotides, for example of about 2 to about 3 nucleotides, and 5' phosphate termini.
  • an inhibitory double stranded RNA duplex may have no overhangs on one or both ends (blunt ends).
  • Some exemplary inhibitory double stranded RNAs may lack a terminal phosphate.
  • inhibitory double stranded RNA molecules include, without limitation, a double- stranded polynucleotide molecule assembled from two separate oligonucleotides, wherein one strand is the sense strand and the other is the complementary antisense strand; a double-stranded polynucleotide molecule assembled from a single oligonucleotide, where the sense and antisense regions are linked by a nucleic acid-based or non-nucleic acid-based linker; a double- stranded polynucleotide molecule with a hairpin secondary structure having self- complementary sense and antisense regions; and a circular single-stranded polynucleotide molecule with two or more loop structures and a stem having self-complementary sense and antisense regions, where the circular polynucleotide may be processed in vivo or in vitro to generate an active inhibitory double- stranded RNA molecule.
  • an inhibitory double-stranded RNA to be delivered by the present invention must have a sufficient identity to a target nucleic acid in order to mediate target- specific RNA interference.
  • an inhibitory double-stranded RNA has an identity of at least about 85%, 90%, 95%, or 100% to the desired target nucleic acid.
  • the identity of a double-stranded RNA molecule to the target sequence may also be defined to include a 3' overhang, particularly an overhang having a length from 1-3 nucleotides, with a sequence identity of at least about 50%, about 70% , or about 85% or more to the target sequence.
  • the nucleotides from the 3' overhang and up to 2 nucleotides from the 5' and/or 3' terminus of the double strand may be modified without significant loss of activity.
  • Inhibitory nucleic acids may include one or more mismatch motifs or mismatch regions, which refer to a portion of an nucleic acid sequence that does not have 100% complementary to its target sequence.
  • a nucleic acid may have at least one, two, three, four, five, six, or more mismatch regions.
  • the mismatch regions may be contiguous or may be separated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more nucleotides.
  • the mismatch motifs or regions may comprise a single nucleotide or may comprise two, three, four, five, or more nucleotides.
  • Inhibitory double stranded RNA contemplated herein may be sufficiently identical or sufficiently complementary, e.g.
  • a contemplated inhibitory double stranded RNA may be identical or exactly complementary (excluding the RRMS containing subunit(s)) to a target RNA, e.g., the target RNA and the inhibitory double stranded RNA anneal, e.g., to form a hybrid made of Watson-Crick base pairs in the region of exact identity or complementarity.
  • a sufficiently identical or sufficiently complementary target RNA may include an internal region (e.g., of at least 10 nucleotides) that is exactly identical or complementary to a target.
  • an inhibitory double stranded RNA may specifically discriminate a single-nucleotide difference, for example, mediating RNA interference if exact identity or complementary is found in the region of the single-nucleotide difference (e.g., within 7 nucleotides of the single-nucleotide difference).
  • Suitable inhibitory double stranded RNA sequences that target a gene of interest may be identified using any means known in the art. Typically, methods such as gene walking or the methods described in Elbashir et al., Nature 411:494-498 (2001) and Elbashir et al., EMBO J 20: 6877-6888 (2001) are combined with rational design rules set forth in Reynolds et al., Nature Biotech. 22:326-330 (2004), each of which are incorporated herein by reference.
  • a sequence within about 50 to about 100 nucleotides 3' of the AUG start codon of a transcript from the target gene of interest is scanned for dinucleotide sequences (e.g., AA, CC, GG, or UU) (see, e.g., Elbashir, et al, EMBO J 20: 6877-6888 (2001)).
  • the nucleotides immediately 3' to the dinucleotide sequences are identified as potential inhibitory double stranded RNA target sequences.
  • the 19, 21, 23, 25, 27, 29, 31, 33, 35, 38, 40, 42, or more nucleotides immediately 3' to the dinucleotide sequences are identified as potential inhibitory double stranded RNA target sites.
  • the dinucleotide sequence may be, for example, an AA sequence and the 19 to about 40 nucleotides immediately 3' to the AA dinucleotide are identified as a potential inhibitory double stranded RNA target site.
  • inhibitory double stranded RNA target sites are spaced at different positions along the length of the target gene.
  • potential inhibitory double stranded RNA target sites may be analyzed to identify sites that do not contain regions of homology to other coding sequences.
  • a suitable inhibitory double stranded RNA target site of about 21 base pairs may not have more than 16-17 contiguous base pairs of homology to other coding sequences. If inhibitory double stranded RNA sequences are to be expressed from an RNA Pol III promoter, inhibitory double stranded RNA target sequences lacking more than 4 contiguous A's or T's may be selected.
  • inhibitory double stranded RNA sequences may be analyzed by a rational design algorithm to identify sequences that have one or more of the following features: (1) G/C content of about 25% to about 60% G/C; (2) at least 2 or 3 A/Us at positions 15-19 of the sense strand; (3) no internal repeats; (4) an A at position 19 of the sense strand; (5) an A at position 3 of the sense strand; (6) a U at position 10 of the sense strand; (7) an A at position 14 of the sense strand; (8) no G/C at position 19 of the sense strand; and (9) no G at position 13 of the sense strand.
  • Inhibitory double stranded RNA design tools that incorporate algorithms that assign suitable values of each of these features and are useful for selection of inhibitory double stranded RNA can be found at, e.g., http://boz094.ust.hk/RNAi/siRNA.
  • sequences with one or more of the foregoing characteristics may be selected for further analysis and testing as potential inhibitory double stranded RNA sequences.
  • Inhibitory double stranded RNA sequences complementary to target nucleic acid sites may also be designed. Techniques for selecting target sequences for inhibitory RNAs are provided by Tuschl, T.
  • initial search parameters can include G/C contents between 35% and 55% and siRNA lengths between 19 and 27 nucleotides.
  • the target sequence may be located in the coding region or in the 5' or 3' untranslated regions of the mRNA.
  • inhibitory double stranded RNA target sequences with one or more of the following criteria can often be eliminated as inhibitory double stranded RNA: (1) sequences comprising a stretch of 4 or more of the same base in a row; (2) sequences comprising homopolymers of Gs (i.e., to reduce possible non-specific effects due to structural characteristics of these polymers; (3) sequences comprising triple base motifs (e.g., GGG, CCC, AAA, or TTT); (4) sequences comprising stretches of 7 or more G/Cs in a row; and (5) sequence comprising direct repeats of 4 or more bases within the candidates resulting in internal fold-back structures.
  • sequences with one or more of the foregoing characteristics may still be selected for further analysis and testing as potential inhibitory double stranded RNA sequences.
  • the importance of various criteria can vary greatly. For instance, a C base at position 10 of the sense strand may make a minor contribution to duplex functionality. In contrast, the absence of a C at position 3 of the sense strand is may be very important.
  • GC content may be important for easement of the unwinding of an inhibitory double stranded RNA duplex.
  • Duplex unwinding has been shown to be crucial for inhibitory double stranded RNA functionality in vivo.
  • the internal structure is measured in terms of the melting temperature (Tm) of the single strand of inhibitory double stranded RNA, which is the temperature at which 50% of the molecules will become denatured.
  • RNA sequences are disclosed in Naito et al, Nucleic Acids Res 33: W589-591, 2005, Henschel et al, Nucleic Acids Res 32: Wl 13- 120, 2004, Naito et al, Nucleic Acids Res 32: W124-129, 2004 (for mammalian- specific interfering RNAs) and Naito et al, Nucleic Acids Res 34: W448-450, 2006 (for viral- specific interfering RNAs), each of which is incorporated herein by reference.
  • a person skilled in the art may use one or more algorithms to select an inhibitory RNA sequence. Further, a person skilled in the art will appreciate the use of multiple parameters and algorithms in selecting and optimizing an inhibitory RNA sequence.
  • Inhibitory double stranded RNA selected according to the aforementioned criteria or one of the aforementioned algorithms are also, for example, useful in the simultaneous screening and functional analysis of multiple genes and gene families using high throughput strategies, as well as in direct gene suppression or silencing.
  • Useful applications for inhibitory nucleic acid molecules include, but are not limited to, target validation, gene functional analysis, research and drug discovery, gene therapy and therapeutics. Methods for using inhibitory nucleic acid molecules including inhibitory double-stranded RNA molecules in these applications are well known to persons of skill in the art.
  • Inhibitory double stranded RNA molecules contemplated herein may be applicable across a broad range of species, including but not limited to all mammalian species, such as humans, dogs, horses, cats, cows, mice, hamsters, chimpanzees and gorillas, as well as other species and organisms such as bacteria, viruses, insects, plants and C. elegans.
  • nucleic acids applicable for use for silencing a broad range of genes, including but not limited to the roughly 45,000 genes of a human genome.
  • Potential inhibitory double stranded RNA target sequences may be further analyzed based on inhibitory double stranded RNA duplex asymmetry as described in, e.g., Khvorova et al., Cell, 115:209-216 (2003); and Schwarz et al., Cell, 115: 199-208 (2003).
  • Potential inhibitory double stranded RNA target sequences may be further analyzed based on secondary structure at the mRNA target site as described in, e.g., Luo et al., Biophys. Res. Commun., 318:303-310 (2004).
  • mRNA secondary structure may be modeled using the Mfold algorithm (available at http://www.bioinfo.rpi.edu/applications/mfold/rna/forml.cgi) to select inhibitory double stranded RNA sequences which favor accessibility at the mRNA target site where less secondary structure in the form of base-pairing and stem-loops is present.
  • Mfold algorithm available at http://www.bioinfo.rpi.edu/applications/mfold/rna/forml.cgi
  • the sequence may be analyzed for the presence of any immunostimulatory properties, e.g., using an in vitro cytokine assay or an in vivo animal model. Motifs in the sense and/or antisense strand of the inhibitory double stranded RNA sequence such as GU-rich motifs (e.g., 5'-GU-3', 5'- UGU-3', 5'-GUGU-3', 5'-UGUGU-3', etc.) may also provide an indication of whether the sequence may be immunostimulatory.
  • GU-rich motifs e.g., 5'-GU-3', 5'- UGU-3', 5'-GUGU-3', 5'-UGUGU-3', etc.
  • an inhibitory double stranded RNA molecule may, in certain embodiments, be modified to decrease its immunostimulatory properties.
  • the detectable immune response may comprise production of a cytokine or growth factor such as, e.g., TNF- ⁇ , IFN-CC, IFN- ⁇ , IFN- ⁇ , IL-6, IL- 12, or a combination thereof.
  • an inhibitory double stranded RNA identified as being immunostimulatory can be modified to decrease its immuno stimulatory properties by replacing at least one (but less than about 30%) of the nucleotides on the sense and/or antisense strand with modified nucleotides such as 2'0Me nucleotides (e.g., 2'OMe-guanosine, 2'0Me- uridine, 2'OMe-cytosine, and/or 2'OMe-adenosine), as described in further detail herein.
  • 2'0Me nucleotides e.g., 2'OMe-guanosine, 2'0Me- uridine, 2'OMe-cytosine, and/or 2'OMe-adenosine
  • Suitable in vitro assays for detecting an immune response include, but are not limited to, the double monoclonal antibody sandwich immunoassay technique of David et al. (U.S. Pat. No. 4,376,110); monoclonal-polyclonal antibody sandwich assays (Wide et al., in Kirkham and Hunter, eds., Radioimmunoassay Methods, E. and S. Livingstone, Edinburgh (1970)); the "Western blot" method of Gordon et al. (U.S. Pat. No. 4,452,901); immunoprecipitation of labeled ligand (Brown et al, J. Biol. Chem.
  • Inhibitory nucleic acid molecules may be provided in several forms including, e.g., as one or more isolated RNA duplexes, e.g. siRNA, longer double- stranded RNA (dsRNA) or RNA transcribed from a transcriptional cassette in a DNA plasmid. Inhibitory nucleic acid molecules, such as inhibitory double stranded RNAs may also be chemically synthesized. The inhibitory double stranded RNA sequences may have overhangs (e.g., 3' or 5' overhangs as described in Elbashir et al, Genes Dev. 15:188 (2001) or Nykanen et al, Cell 107:309 (2001), or may lack overhangs (i.e., to have blunt ends).
  • RNA duplexes e.g. siRNA, longer double- stranded RNA (dsRNA) or RNA transcribed from a transcriptional cassette in a DNA plasmid.
  • Exemplary RNA population may be used to provide long precursor RNAs, or long precursor RNAs that have substantial or complete identity to a selected target sequence may be used to make the inhibitory dsRNA.
  • the RNAs can be isolated from cells or tissue, synthesized, and/or cloned according to methods well known to those of skill in the art.
  • the RNA may be a mixed population (obtained from cells or tissue, transcribed from cDNA, subtracted, selected etc.), or may e.g. represent a single target sequence.
  • RNA may be naturally occurring, (e.g., isolated from tissue or cell samples), synthesized in vitro (e.g., using T7 or SP6 polymerase and PCR products or a cloned cDNA), or chemically synthesized.
  • RNA complement is transcribed in vitro and hybridized to form a dsRNA.
  • the RNA complements are also provided (e.g., to form dsRNA for digestion by E. coli RNAse III or Dicer), e.g., by transcribing cDNAs corresponding to the RNA population, or by using RNA polymerases.
  • the precursor RNAs are then hybridized to form double stranded RNAs for digestion.
  • one or more DNA plasmids encoding one or more inhibitory dsRNA templates are used to provide the inhibitory dsRNA.
  • Inhibitory dsRNA can, in some embodiments, be transcribed as sequences that automatically fold into duplexes with hairpin loops from DNA templates in plasmids having RNA polymerase III transcriptional units, for example, based on the naturally occurring transcription units for small nuclear RNA U6 or human RNase P RNA Hl (see, Brummelkamp, et al, Science 296:550 (2002); Donze, et al, Nucleic Acids Res. 30:e46 (2002); Paddison, et al, Genes Dev. 16:948 (2002); Yu, et al, PNAS USA 99:6047 (2002); Lee, et al., Nat. Biotech.
  • a transcriptional unit or cassette will contain an RNA transcript promoter sequence, such as an Hl-RNA or a U6 promoter, operably linked to a template for transcription of a desired inhibitory dsRNA sequence and a termination sequence, comprised of 2-3 uridine residues and a polythymidine (T5) sequence (polyadenylation signal) (Brummelkamp, Science, supra).
  • the selected promoter may e.g. provide for constitutive or inducible transcription.
  • compositions and methods for DNA-directed transcription of RNA interference molecules is described in detail in U.S. Pat. No. 6,573,099.
  • the transcriptional unit is incorporated into a plasmid or DNA vector from which the interfering RNA is transcribed.
  • Plasmids suitable for in vivo delivery of genetic material for therapeutic purposes are described in detail in U.S. Pat. Nos. 5,962,428 and 5,910,488, and such plasmids may provide for transient or stable delivery of a target cell. It will be apparent to those of skill in the art that plasmids originally designed to express desired gene sequences can be modified to contain a transcriptional unit cassette for transcription of inhibitory dsRNA.
  • a inhibitory nucleic acid molecules are chemically synthesized.
  • the single stranded molecules that comprise a modified inhibitory nucleic acid molecule may be synthesized using any of a variety of techniques known in the art, such as those described in Usman et al., J. Am. Chem. Soc. 109:7845 (1987); Scaringe et al., Nuc. Acids Res.
  • oligonucleotides makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end and phosphoramidites at the 3'-end.
  • small scale syntheses may be conducted on an Applied Biosystems synthesizer using a 0.2 ⁇ mol scale protocol with a 2.5 min. coupling step for 2'-O-methylated nucleotides.
  • syntheses at the 0.2 ⁇ mol scale may be performed on a 96- well plate synthesizer from Protogene (Palo Alto, Calif.).
  • RNA deprotection a larger or smaller scale of synthesis is also within the scope of the present invention.
  • Suitable reagents for oligonucleotide synthesis, methods for RNA deprotection, and methods for RNA purification are known to those of skill in the art.
  • an inhibitory dsRNA may be synthesized via a tandem synthesis technique, wherein both strands are synthesized as a single continuous oligonucleotide fragment or strand separated by a cleavable linker that is subsequently cleaved to provide separate fragments or strands that hybridize to form the inhibitory dsRNA duplex.
  • a linker can be a polynucleotide linker or a non-nucleotide linker.
  • a tandem synthesis of modified inhibitory dsRNA may be readily adapted to both multiwell/multiplate synthesis platforms as well as large scale synthesis platforms employing batch reactors, synthesis columns, and the like.
  • the modified inhibitory dsRNA can be assembled from two distinct oligonucleotides, wherein one oligonucleotide comprises the sense strand and the other comprises the antisense strand of the inhibitory dsRNA.
  • each strand can be synthesized separately and joined together by hybridization or ligation following synthesis and/or deprotection.
  • the modified inhibitory dsRNA can be synthesized as a single continuous oligonucleotide fragment, wherein the self-complementary sense and antisense regions hybridize to form an inhibitory dsRNA duplex having hairpin secondary structure.
  • Inhibitory dsRNAs described herein may comprise at least one modified nucleotide in the sense and/or antisense strand.
  • Exemplary contemplated modifications include the introduction of phosphorothioate linkages and 2'-substitutions on the ribose unit, e.g., 2'-deoxy, 2'-deoxy-2'-fluoro, 2'-O-methyl, 2'-O-methoxyethyl (2'-0-MOE), 2'-O-aminopropyl (2'-0-AP), 2'-O-dimethylaminoethyl (2'-0-DMAOE), 2'-O-dimethylaminopropyl (2'-0-DMAP), 2'-O- dimethylaminoethyloxyethyl (2'-0-DMAEOE), 2'-O-N-methylacetamido (2'-0-NMA) substitutions, 5-C-methyl, 2'-methoxyethyl, 4'-thio
  • Modified nucleotides having a Northern conformation such as those described in, e.g., Saenger, Principles of Nucleic Acid Structure, Springer- Verlag Ed. (1984), are also suitable for use in an inhibitory dsRNA of the present invention.
  • modified nucleotides include, without limitation, locked nucleic acid (LNA) nucleotides (e.g., 2'-O, 4'-C-methylene-(D-ribofuranosyl) nucleotides), 2'-methoxyethoxy (MOE) nucleotides, 2'-methyl-thio-ethyl nucleotides, 2'-deoxy- 2'-fluoro nucleotides, 2'-deoxy-2'-chloro nucleotides, and 2'-azido nucleotides.
  • LNA locked nucleic acid
  • MOE 2'-methoxyethoxy
  • MOE 2'-methyl-thio-ethyl nucleotides
  • 2'-deoxy- 2'-fluoro nucleotides 2'-deoxy-2'-chloro nucleotides
  • 2'-azido nucleotides include one or more G-clamp nucleotides.
  • a G-clamp nucleotide refers to a modified cytosine analog wherein the modifications confer the ability to hydrogen bond both Watson-Crick and Hoogsteen faces of a complementary guanine nucleotide within a duplex (see, e.g., Lin et al., J. Am. Chem. Soc. 120:8531-8532 (1998)).
  • nucleotides having a nucleotide base analog such as, for example, C-phenyl, C- naphthyl, other aromatic derivatives, inosine, azole carboxamides, and nitroazole derivatives such as 3-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole (see, e.g., Loakes, Nucl. Acids Res. 29:2437-2447 (2001)) can be incorporated into the inhibitory dsRNA.
  • a nucleotide base analog such as, for example, C-phenyl, C- naphthyl, other aromatic derivatives, inosine, azole carboxamides, and nitroazole derivatives such as 3-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole (see, e.g., Loakes, Nucl. Acids Res. 29:2437-2447 (2001))
  • a cholesterol moiety e.g., on the 3'-end of the sense strand
  • a T- modification e.g., a 2'-O-methyl or 2'-deoxy-2'-fluoro-modification
  • a phosphorothioate e.g., on the 3'-most one or two nucleotides of the sense and antisense strands
  • a cholesterol moiety e.g., on the 3'-end of the sense strand
  • a T- modification e.g., a 2'-O-methyl or 2'-deoxy-2'-fluoro-modification
  • a phosphorothioate e.g., on the 3'-most one or two nucleotides of the sense and antisense strands
  • 2'- substitutions may be made to the 5' nucleotide of a 5'-UA-3' dinucleotide, a 5'-UG-3' dinucleotide, a 5'-CA-3' dinucleotide, a 5'-UU-3' dinucleotide, or a 5'- CC-3' dinucleotide on the sense strand and, optionally, also on the antisense strand of the inhibitory dsRNA, or to all pyrimidine-base comprising nucleotides.
  • the 5'-most pyrimidines in substantially occurrences of the sequence motifs 5'-UA-3', 5'-CA-3', 5'-UU-3', and 5'-UG-3' may be 2'-modified nucleotides, or for example, substantially all pyrimidines in the sense strand are 2'-modified nucleotides, and 5'-most pyrimidines in substantially all occurrences of the sequence motifs 5'-UA-3' and 5'-CA-3', e.g.
  • all pyrimidines in the sense strand are 2'-modified nucleotides
  • the 5'-most pyrimidines in all occurrences of the sequence motifs 5'-UA-3', 5'-CA-3', 5'-UU-3', and 5'-UG-3' are 2'-modified nucleotides in the antisense strand.
  • the inhibitory dsRNA may include one or more chemical modifications such as terminal cap moieties, phosphate backbone modifications, and the like.
  • terminal cap moieties include, without limitation, inverted deoxy abasic residues, glyceryl modifications, 4',5'-methylene nucleotides, l-( ⁇ -D-erythrofuranosyl) nucleotides, 4'-thio nucleotides, carbocyclic nucleotides, 1,5-anhydrohexitol nucleotides, L- nucleotides, OC- nucleotides, modified base nucleotides, threo-pentofuranosyl nucleotides, acyclic 3',4'-seco nucleotides, acyclic 3,4-dihydroxybutyl nucleotides, acyclic 3,5-dihydroxypentyl nucleotides, 3'-3'-inverted nucleotide moieties,
  • Non-limiting examples of phosphate backbone modifications include phosphorothioate, phosphorodithioate, methylphosphonate, phosphotriester, morpholino, amidate, carbamate, carboxymethyl, acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal, thioformacetal, and alkylsilyl substitutions (see, e.g., Hunziker et al., Nucleic Acid Analogues: Synthesis and Properties, in Modern Synthetic Methods, VCH, 331-417 (1995); Mesmaeker et al., Novel Backbone Replacements for Oligonucleotides, in Carbohydrate Modifications in Antisense Research, ACS, 24-39 (1994)).
  • the sense and/or antisense strand may include, for example, a 3'-terminal overhang having about 1 to about 4 (e.g.,. 1, 2, 3, or 4) 2'-deoxy ribonucleotides and/or any combination of modified and unmodified nucleotides. Additional examples of modified nucleotides and types of chemical modifications that can be introduced into the modified inhibitory dsRNA are described, e.g., in UK Patent No. GB 2,397,818 B and U.S. Patent Publication Nos. 20040192626 and 20050282188.
  • Modified inhibitory dsRNA described herein may include one or more non- nucleotides in one or both strands of the inhibitory dsRNA.
  • non- nucleotide refers to any group or compound that can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their activity.
  • the group or compound is abasic in that it does not contain a commonly recognized nucleotide base such as adenosine, guanine, cytosine, uracil, or thymine and therefore lacks a base at the 1 '-position.
  • Chemical modification of the inhibitory dsRNA may include attaching a conjugate to the chemically-modified inhibitory dsRNA.
  • the conjugate may be attached at the 5' and/or 3'-end of the sense and/or antisense strand of the chemically-modified inhibitory dsRNA via a covalent attachment such as, e.g., a biodegradable linker.
  • the conjugate may also be attached to the chemically-modified inhibitory dsRNA, e.g., through a carbamate group or other linking group (see, e.g., U.S. Patent Publication Nos. 20050074771, 20050043219, and 20050158727).
  • the conjugate is a molecule that facilitates the delivery of the chemically- modified inhibitory dsRNA into a cell.
  • conjugate molecules suitable for attachment to a chemically-modified inhibitory dsRNA include, without limitation, steroids such as cholesterol, glycols such as polyethylene glycol (PEG), human serum albumin (HSA), fatty acids, carotenoids, terpenes, bile acids, folates (e.g., folic acid, folate analogs and derivatives thereof), sugars (e.g., galactose, galactosamine, N-acetyl galactosamine, glucose, mannose, fructose, fucose, etc.), phospholipids, peptides, ligands for cellular receptors capable of mediating cellular uptake, and combinations thereof (see, e.g., U.S.
  • Other examples include the lipophilic moiety, vitamin, polymer, peptide, protein, nucleic acid, small molecule, oligosaccharide, carbohydrate cluster, intercalator, minor groove binder, cleaving agent, and cross-linking agent conjugate molecules described in U.S. Patent Publication Nos. 20050119470 and 20050107325.
  • Yet other examples include the 2'-O-alkyl amine, 2'-O- alkoxyalkyl amine, polyamine, C5-cationic modified pyrimidine, cationic peptide, guanidinium group, amidininium group, cationic amino acid conjugate molecules described in U.S. Patent Publication No. 20050153337. Additional examples include the hydrophobic group, membrane active compound, cell penetrating compound, cell targeting signal, interaction modifier, and steric stabilizer conjugate molecules described in U.S. Patent Publication No. 20040167090. Further examples include the conjugate molecules described in U.S. Patent Publication No. 20050239739.
  • the type of conjugate used and the extent of conjugation to the chemically- modified inhibitory dsRNA molecule may be evaluated for improved pharmacokinetic profiles, bioavailability, and/or stability of the inhibitory dsRNA.
  • one skilled in the art can screen chemically-modified inhibitory dsRNA having various conjugates attached thereto to identify ones having improved properties using any of a variety of well-known in vitro cell culture or in vivo animal models.
  • inhibitory dsRNAs may enhance stabilization towards degradation in biological environments and may improve pharmacological properties, e.g. pharmacodynamic properties.
  • Other suitable modifications to a sugar, base, or backbone of an inhibitory dsRNA are described in PCT Publication No. WO 2004/064737.
  • an inhibitory dsRNA can include a non-naturally occurring base, such as the bases described in PCT Publication No. WO 2004/094345 and/or may include a non-naturally occurring sugar, such as a non-carbohydrate cyclic carrier molecule.
  • Exemplary features of non-naturally occurring sugars for use in inhibitory dsRNAs are described in PCT Publication No.
  • An inhibitory dsRNA may include, in some embodiments, an internucleotide linkage (e.g., the chiral phosphorothioate linkage) useful for increasing nuclease resistance.
  • an inhibitory dsRNA may include, for example, a ribose mimic for increased nuclease resistance.
  • An inhibitory dsRNA may include ligand-conjugated monomer subunits and monomers for oligonucleotide synthesis, and/or may be complexed with an amphipathic moiety.
  • the sense and antisense sequences of an inhibitory dsRNA may be palindromic, and/or may have non-canonical pairings, such as between the sense and antisense sequences of the iRNA duplex. Examples of these modifications are described in PCT Publication No. WO 2004/080406 and U.S. Patent Publication No. 2005/0107325. Enhanced Nuclease Resistance
  • An inhibitory dsRNA e.g., an inhibitory dsRNA that targets ApoB
  • increased resistance may include identifying cleavage sites and modifying such sites to inhibit cleavage.
  • the dinucleotides 5'-UA-3', 5'-UG-3 ⁇ 5'-CA-3 ⁇ 5'-UU-3', or 5'-CC-3' can serve as cleavage sites, as described in PCT Publication No. WO 2005/115481.
  • an inhibitory dsRNA e.g., the sense and/or antisense strands of the inhibitory dsRNA
  • the 2' hydroxyl group (OH) can be modified or replaced with a number of different "oxy" or "deoxy" substituents.
  • the integer n may be any integer, e.g. 0 to 10.
  • "Deoxy" modifications include hydrogen (i.e. deoxyribose sugars, which are of particular relevance to the overhang portions of partially dsRNA); halo (e.g., fluoro); amino (e.g.
  • Exemplary substitutents include 2'-methoxyethyl, 2'-OCH 3 , 2'-O-allyl, 2'-C-allyl, and 2'-fluoro.
  • 2' modifications may be used in combination with one or more phosphate linker modifications (e.g., phosphorothioate).
  • All the pyrimidines of an inhibitory dsRNA may carry a 2'-modification which may have enhanced resistance to endonucleases.
  • enhanced nuclease resistance may also be achieved by modifying the 5' nucleotide, resulting, for example, in at least one 5'-uridine-adenine-3' (5'-UA-3') dinucleotide wherein the uridine is a 2'-modified nucleotide; at least one 5'-uridine-guanine-3' (5'-UG-3') dinucleotide, wherein the 5'-uridine is a 2'-modified nucleotide; at least one 5'-cytidine-adenine-3' (5'-CA-3') dinucleotide, wherein the 5'-cytidine is a 2'-modified nucleotide; at least one 5'-uridine-uridine-3' (5'-UU-3') dinucleotide,
  • the inhibitory dsRNA may include, in some embodiments, at least 2, at least 3, at least 4 or at least 5 of such dinucleotides.
  • 5'-most pyrimidines in substantially all occurrences of the sequence motifs 5'-UA-3', 5'-CA-3', 5'-UU-3', and 5'-UG-3' may be 2'-modified.
  • an inhibitory dsRNA may be further modified by including a 3' cationic group, or by inverting the nucleoside at the 3'- terminus with a 3'-3' linkage.
  • the 3'-terminus may be blocked with an aminoalkyl group, e.g., a 3' C5-aminoalkyl dT, or other 3' conjugates such as naproxen or ibuprofen, small alkyl chains, aryl groups, or heterocyclic conjugates or modified sugars (D- ribose, deoxyribose, glucose etc.).
  • a 5' conjugate may be included, such as naproxen or ibuprofen, may inhibit exonucleolytic cleavage by sterically blocking the exonuclease from binding to the 5'-end of oligonucleotide.
  • an inhibitory dsRNA may have increased resistance to nucleases when a duplexed inhibitory dsRNA includes a single- stranded nucleotide overhang on at least one end.
  • the nucleotide overhang includes 1 to 4, e.g. about 2 to 3, unpaired nucleotides.
  • an unpaired nucleotide of the single- stranded overhang that is directly adjacent to the terminal nucleotide pair contains a purine base, and the terminal nucleotide pair is a G-C pair, or at least two of the last four complementary nucleotide pairs are G-C pairs.
  • a nucleotide overhang may have 1 or 2 unpaired nucleotides, and in an exemplary instance a nucleotide overhang is 5'-GC-3', for example on the 3'-end of the antisense strand.
  • the inhibitory dsRNA includes the motif 5'- CGC-3' on the 3'-end of the antisense strand, such that a 2-nt overhang 5'-GC-3' is formed.
  • an inhibitory dsRNA may include monomers which have been modified so as to inhibit degradation, e.g., by nucleases, e.g., endonucleases or exonucleases, found in the body of a subject. These monomers are referred to herein as NRMs, or Nuclease Resistance promoting Monomers or modifications.
  • inhibitory dsRNA will modulate other properties of the inhibitory dsRNA as well, e.g., the ability to interact with a protein, e.g., a transport protein, e.g., serum albumin, or a member of the RISC, or the ability of the first and second sequences to form a duplex with one another or to form a duplex with another sequence, e.g., a target molecule.
  • a protein e.g., a transport protein, e.g., serum albumin, or a member of the RISC
  • the ability of the first and second sequences to form a duplex with one another or to form a duplex with another sequence, e.g., a target molecule.
  • Modifications that may be useful for producing inhibitory dsRNA that invoke nuclease resistance may include one or more of the following chemical and/or stereochemical modifications of the sugar, base, and/or phosphate backbone:
  • chiral (Sp) thioates e.g., that include nucleotide dimers with a particular chiral form of a modified phosphate group containing a heteroatom at the nonbridging position, e.g., Sp or Rp, at the position X, where this is the position normally occupied by the oxygen.
  • the atom at X may be for example, selected from S, Se, Nr2, or Br3.
  • the linkage may be an enriched or chirally pure Sp linkage.
  • a 5'-end of an antisense sequence has a terminal —OH or phosphate group so that a NRM is not used at the 5'-end of an antisense sequence.
  • the group should be attached at a position on the base which minimizes interference with H bond formation and hybridization, e.g., away form the face which interacts with the complementary base on the other strand, e.g., at the 5' position of a pyrimidine or a 7-position of a purine.
  • nonphosphate linkages at the termini for example a NRM that includes non- phosphate linkages, e.g., a linkage of 4 atoms which confers greater resistance to cleavage than does a phosphate bond.
  • NRM non- phosphate linkages
  • a-nucleosides e.g. L nucleosides and dimeric nucleotides derived from L-nucleosides
  • 2'-5' phosphate, non-phosphate and modified phosphate linkages e.g., thiophosphates, phosphoramidates and boronophosphates
  • conjugate groups e.g., a targeting moiety or a conjugated ligand described herein conjugated with the monomer, e.g., through the sugar, base, or backbone;
  • abasic linkages e.g., an abasic monomer as described herein (e.g., a nucleobaseless monomer); an aromatic or heterocyclic or polyheterocyclic aromatic monomer as described herein; and
  • NRM's may include monomers, e.g. at the terminal position, e.g., the 5' position, in which one or more atoms of the phosphate group is derivatized with a protecting group, which protecting group or groups, may be removed as a result of the action of a component in the subject's body, e.g., a carboxyesterase or an enzyme present in the subject's body.
  • one or more different NRM modifications may be introduced into an inhibitory dsRNA or into a sequence of an inhibitory dsRNA.
  • An NRM modification can be used more than once in a sequence or in an inhibitory dsRNA.
  • NRMs interfere with hybridization the total number incorporated should be such that acceptable levels of inhibitory dsRNA duplex formation are maintained.
  • NRM modifications may be introduced into the terminal cleavage site or in the cleavage region of a sequence (a sense strand or sequence) which does not target a desired sequence or gene in the subject, which may reduce off-target silencing.
  • Nuclease resistant modifications may include those placed only at the terminus and others which may be placed at any position. Such modifications may inhibit hybridization, and in some embodiments, modifications are used only in terminal regions.
  • a NRM can be used anywhere in a sense sequence, provided that sufficient hybridization between the two sequences of the inhibitory dsRNA is maintained. In some instances it is desirable to put a NRM at the cleavage site or in the cleavage region of a sequence which does not target a subject sequence or gene, as it can minimize off-target silencing.
  • any nuclease-resistance promoting modifications will be distributed differently depending on whether the sequence will target a sequence in the subject (often referred to as an antisense sequence) or will not target a sequence in the subject (often referred to as a sense sequence). If a sequence is to target a sequence in the subject, modifications which interfere with or inhibit endonuclease cleavage should not be inserted in the region which is subject to RISC mediated cleavage, e.g., the cleavage site or the cleavage region (As described in Elbashir et al., 2001, Genes and Dev. 15: 188, hereby incorporated by reference). Such modifications may be introduced into the terminal regions, e.g., at the terminal position or within 2, 3, 4, or 5 positions of the terminus, of a sequence which targets or a sequence which does not target a sequence in the subject.
  • Inhibitory dsRNA may, in some embodiments, include a 5' phosphorylate or include a phosphoryl analog at the 5' prime terminus. Possible 5'-phosphate modifications of the antisense strand include those which are compatible with RISC mediated gene silencing.
  • Suitable modifications include: 5'-monophosphate ((HO) 2 (O)P-O-S'); 5'-diphosphate ((HO) 2 (O)P-O-P(HO)(O)-O-5'); 5'-triphosphate ((HO) 2 (O)P-O-(HO)(O)P-O-P(HO)(O)- 0-5'); 5'-guanosine cap (7-methylated or non-methylated) (7m-G-O-5'-(HO)(O)P-O- (H0)(0)P-0-P(H0)(0)-0-5'); 5'-adenosine cap (Appp), and any modified or unmodified nucleotide cap structure (N-O-5'-(HO)(O)P-O-(HO)(O)P-O-P(HO)(O)-O-5'); 5'- monothiophosphate (phosphorothioate; (HO) 2 (S)P- 0-5'); 5'-
  • a sense strand can be modified in order to inactivate the sense strand and prevent formation of an active RISC, thereby potentially reducing off-target effects, for example, by a modification which prevents 5'-phosphorylation of the sense strand, e.g., by modification with a 5'-O-methyl ribonucleotide (see Nykanen et al., (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309-321.) Other modifications which prevent phosphorylation can also be used, e.g., simply substituting the 5'-OH by H rather than O-Me. Alternatively, a large bulky group may be added to the 5'-phosphate turning it into a phosphodiester linkage.
  • a modification which prevents 5'-phosphorylation of the sense strand e.g., by modification with a 5'-O-methyl ribonucleotide (see Nykanen et al., (2001) ATP
  • inhibitory dsRNA such as phosphate group and/or sugar group modifications, replacement of the phosphate group and/or ribophosphate backbone, terminal modifications or base modifications, as well as preferred inhibitory dsRNA formula, can be found in U.S. Patent Publication No. 2007/0275914.
  • a candidate inhibitory dsRNA may be evaluated for its ability to downregulate target gene expression.
  • a candidate inhibitory dsRNA may be contacted with a cell that expresses the target gene either endogenously or because it has been transfected with a construct from which the gene can be expressed.
  • the level of target gene expression prior to and following contact with the candidate inhibitory dsRNA can be compared, e.g. on an mRNA or protein level. If it is determined that the amount of RNA or protein expressed from the target gene is lower following contact with the inhibitory dsRNA, then it can be concluded that the inhibitory dsRNA downregulates target gene expression.
  • the level of target RNA or protein in the cell can be determined by any method desired.
  • the level of target RNA can be determined by Northern blot analysis, reverse transcription coupled with polymerase chain reaction (RT-PCR), or RNAse protection assay.
  • the level of protein can be determined, for example, by Western blot analysis.
  • a functional assay can also be used in some embodiments, to evaluate a modified candidate inhibitory dsRNA.
  • a functional assay can be applied to determine if the modification alters the ability of the molecule to silence gene expression.
  • a cell e.g., a mammalian cell, such as a mouse or human cell
  • a plasmid expressing a fluorescent protein, e.g., GFP, and a candidate inhibitory dsRNA homologous to the transcript encoding the fluorescent protein (see, e.g., WO 00/44914).
  • a fluorescent protein e.g., GFP
  • a candidate inhibitory dsRNA homologous to the transcript encoding the fluorescent protein see, e.g., WO 00/44914.
  • a modified inhibitory dsRNA homologous to the GFP mRNA can be assayed for the ability to inhibit GFP expression by monitoring for a decrease in cell fluorescence, as compared to a control cell, in which the transfection did not include the candidate inhibitory dsRNA, e.g., controls with no inhibitory dsRNA added and/or controls with a non-modified inhibitory dsRNA added.
  • Efficacy of the candidate inhibitory dsRNA on gene expression can be assessed by comparing cell fluorescence in the presence of the modified and unmodified inhibitory dsRNA molecules.
  • a candidate inhibitory dsRNA may be evaluated with respect to stability, e.g., its susceptibility to cleavage by an endonuclease or exonuclease, such as when the inhibitory dsRNA is introduced into the body of a subject.
  • stability e.g., its susceptibility to cleavage by an endonuclease or exonuclease, such as when the inhibitory dsRNA is introduced into the body of a subject.
  • methods can be employed to e.g., identify sites that are susceptible to modification, particularly cleavage, e.g., cleavage by a component found in the body of a subject.
  • a further inhibitory dsRNA can be designed and/or synthesized wherein the potential cleavage site is made resistant to cleavage, e.g. by introduction of a 2'-modification on the site of cleavage, e.g. a 2'-O-mathyl group.
  • This further inhibitory dsRNA can be retested for stability, and this process may be iterated until an inhibitory dsRNA is found exhibiting the desired stability.
  • a candidate inhibitory dsRNA e.g., a modified inhibitory dsRNA, may be scanned for a selected property by e.g.
  • a candidate modified inhibitory dsRNA ⁇ e.g., a control molecule, usually the unmodified form) can be exposed to degradative conditions, e.g., exposed to a milieu, which includes a degradative agent, e.g., a nuclease.
  • a biological sample e.g., one that is similar to a milieu, which might be encountered, in therapeutic use, e.g., blood or a cellular fraction, e.g., a cell-free homogenate or disrupted cells.
  • the candidate and control could then be evaluated for resistance to degradation by any of a number of approaches.
  • the candidate and control may be labeled, e.g. prior to exposure, with, e.g., a radioactive or enzymatic label, or a fluorescent label, such as Cy3 or Cy5.
  • Control and modified inhibitory dsRNA can be incubated with the degradative agent, and optionally a control, e.g., an inactivated, e.g., heat inactivated, degradative agent.
  • a control e.g., an inactivated, e.g., heat inactivated, degradative agent.
  • a physical parameter, e.g., size, of the modified and control molecules are then determined. They can be determined by a physical method, e.g., by polyacrylamide gel electrophoresis or a sizing column, to assess whether the molecule has maintained its original length, or assessed functionally.
  • Northern blot analysis can be used to assay the length of an unlabeled modified molecule.
  • an inhibitory dsRNA identified as being capable of inhibiting target gene expression can be tested for functionality in vivo in an animal model (e.g., in a mammal, such as in mouse or rat).
  • the inhibitory dsRNA can be administered to an animal, and the inhibitory dsRNA evaluated with respect to its biodistribution, stability, and its ability to inhibit target gene expression.
  • an inhibitory dsRNA can be administered directly to the target tissue, such as by injection, or an inhibitory dsRNA can be administered to the animal model in the same manner that it would be administered to a human.
  • An inhibitory dsRNA can also be evaluated for its intracellular distribution. Such evaluation may include determining whether the inhibitory dsRNA was taken up into the cell and/or may include determining the stability (e.g., the half-life) of the inhibitory dsRNA.
  • an evaluation of an inhibitory dsRNA in vivo can be facilitated by use of an inhibitory dsRNA conjugated to a traceable marker (e.g., a fluorescent marker such as fluorescein; a radioactive label, such as 35 S, 32 P, 33 P, or 3 H; gold particles; or antigen particles for immunohistochemistry).
  • a traceable marker e.g., a fluorescent marker such as fluorescein; a radioactive label, such as 35 S, 32 P, 33 P, or 3 H; gold particles; or antigen particles for immunohistochemistry.
  • an inhibitory dsRNA useful for monitoring biodistribution can lack gene silencing activity in vivo.
  • the inhibitory dsRNA can target a gene not present in the animal (e.g., an inhibitory dsRNA injected into mouse can target luciferase), or an inhibitory dsRNA can have a non-sense sequence, which does not target any gene, e.g., any endogenous gene).
  • Localization/biodistribution of the inhibitory dsRNA can be monitored, e.g. by a traceable label attached to the inhibitory dsRNA, such as a traceable agent described above.
  • Inhibitory dsRNA may be evaluated with respect to its ability to modulate, e.g. down regulate a given target gene expression.
  • Levels of target gene expression in vivo can be measured, for example, by in situ hybridization, or by the isolation of RNA from tissue prior to and following exposure to the inhibitory dsRNA. Where the animal needs to be sacrificed in order to harvest the tissue, an untreated control animal will serve for comparison.
  • Target mRNA can be detected by any desired method, including but not limited to RT-PCR, Northern blot, branched-DNA assay, or RNAase protection assay. Alternatively, or additionally, target gene expression can be monitored by performing Western blot analysis on tissue extracts treated with the inhibitory dsRNA.
  • a candidate inhibitory dsRNA homologous to an endogenous mouse gene e.g., a maternally expressed gene, such as c-mos
  • an immature mouse oocyte can be injected into an immature mouse oocyte to assess the ability of the inhibitory dsRNA to inhibit gene expression in vivo (see, e.g., WO 01/36646).
  • a phenotype of the oocyte e.g., the ability to maintain arrest in metaphase II, can be monitored as an indicator that the inhibitory dsRNA is inhibiting expression. For example, cleavage of c-mos mRNA by the inhibitory dsRNA may cause the oocyte to exit metaphase arrest and initiate parthenogenetic development (Colledge et al.
  • a modified inhibitory dsRNA on target RNA levels may be verified by, for example, a Northern blot to assay for a decrease in the level of target mRNA, or by Western blot to assay for a decrease in the level of target protein, as compared to a negative control.
  • Such controls may include e.g. cells in which no inhibitory dsRNA is added and/or cells in which a non-modified inhibitory dsRNA is added.
  • Disclosed chimeric therapeutics, particles and/or compositions include a nucleic acid, for example a RNA, as described above.
  • a nucleic acid is targeted to specific gene target, such as apoB, for example, a provided nucleic acid is substantially homologous to a region of the apoB gene, for example, a mammalian (e.g. human or mouse) apoB gene.
  • chimeric therapeutics, particles and/or compositions include a nucleic acid targeted to one or more of: prothrombin, FIX, angiotensinogen, renin (see US20070270365), TFPI (see US7022672), CCR5, HCV (see US20070149470), SYK (see US 7173015), RANKL, IL-23 (see WO2004/094636), Complement C3 (see US20070178068), Factor H, IL-4Ralpha (see US 2005014333), RBP4, glucagon/glucagon receptor (see US2008/0113372), ghrelin (see US20080140056), GOAT, gastrin, PTPlB, leptin, PCSK-9, IGF-IR, cMet, DR4, DR5, VEGF-A, HGF, sclerostin, and/or myostatin.
  • prothrombin FIX
  • angiotensinogen see US20070
  • compositions, particles or therapeutics disclosed herein may localize in the liver or to the gut, e.g., the intestine, such as to the jejunum of the intestine after administration to a patient.
  • a disease or disorder characterized by e.g., a particular target expression, e.g. target misexpression, including, but not limited to those diseases and disorders associated with misexpression.
  • Such methods can further include administration (e.g., concurrently or consecutively) with conventional agents used to treat such diseases or disorders.
  • Various methodologies such as those described herein (gene walks, algorithm computation) can be utilized to select candidate nucleic acids targeting particular targets. For example, nucleic acids targeting specific targets may be identified using the methods set forth herein.
  • contemplated nucleic acids e.g. RNAs targeting specific gene targets include those recited in the following patents and patent applications, hereby incorporated by reference, and targeting the following genes: VEGF (see U.S. Patent 7,176,304), HIFl (see U.S. Patent Publication No. 20080188430), SARS (see U.S. Patent Publication No. 20070270360), HDAC (see U.S. Patent Publication No. 20070185049); Nogo and Nogo Receptor (see U.S. Patent Publication No. 20070185043), WHN (see U.S. Patent Publication No. 20070179104), PCSK9 (see U.S. Patent Publication No.
  • Patent Publication No. 200400924636 PIM-I (see U.S. Patent Publication No. 20040092463), TNFSF14 (see U.S. Patent Publication No. 20040096835), MAGE-Dl (see U.S. Patent Publication No. 20040110702), CDlD (see U.S. Patent Publication No. 20040110700), SEDL (see U.S. Patent Publication No. 20040110160), NRF (see U.S. Patent Publication No. 20040110156), BAF53 (see U.S. Patent Publication No. 20040110147), MALTl (see U.S. Patent Publication No. 20040110145), CDK9 (see U.S. Patent Publication No.
  • Contemplated nucleic acids include those targeting targets associated with viral infections, for example, those nucleic acids targeting the following viruses and recited in the following patent applications: Influenza Virus (see U.S. Patent Publication No. 20070197460), HCV (see U.S. Patent Publication No. 20080207542), RSV (see U.S. Patent Publication No. 20060287267), and HIV (see U.S. Patent Publication No. 20050191618), wherein each patent and patent application is incorporated by reference.
  • Disclosed chimeric therapeutics, compositions and/or particles may be administered to a patient by any conventional route. These include, but are not limited to, the systemic routes, e.g. subcutaneous, intradermal, intramuscular or intravenous route, and mucosal routes, e.g. oral, nasal, pulmonary or anogenital route.
  • an intratumoral route may be used in e.g. the treatment of solid tumors.
  • the choice of the route of administration will depend on the nature of the disease; for example, particles and/or compositions may be administered via a pulmonary route in the case of cystic fibrosis (e.g. wherein the particles are formulated in aerosol form) or e.g.
  • disclosed particles may be administered a composition that comprises a biocompatible aqueous solution.
  • Contemplated solutions may include water and/or saline, and may optionally contain pharmaceutical excipients known to those skilled in the art, for example, buffers, stabilizing molecules, preservatives, sugars, amino acids, proteins, carbohydrates and vitamins, and the like.
  • the administration of disclosed particles or compositions can be carried out at a single dose or at a dose repeated once or several times after a certain time interval.
  • the appropriate dosage varies according to various parameters, for example the therapeutically effective dosage is dictated by and directly dependent on the individual treated, the mode of administration, the unique characteristics of the nucleic acid and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals. Appropriate doses can be established by persons skilled in the art of pharmaceutical dosing such as physicians.
  • the particles can be included in a container, pack, or dispenser together with instructions for administration.
  • the particles and compositions disclosed herein may allow for sustained release of a nucleic acid, e.g. an inhibitory nucleic acid, to e.g. a specific body target site, e.g., the liver.
  • a nucleic acid e.g. an inhibitory nucleic acid
  • the disclosed compositions and/or particles may allow for release of a nucleic acid over about 1 day to about 7 days or more, e.g. about 1 day to about 3 days or more, or about 1 day to about 3 weeks or more.
  • long-term storage stability of disclosed particles may be increased and/or enhanced by for example, freezing and lyophilizing particles disclosed herein in the presence of one or more protective agents such as sucrose, mannitol, trehalose or the like.
  • the suspension may, for example, retain essentially all nucleic acid previously encapsulated and/or may retain substantially the same particle size. Rehydration may be accomplished by e.g., adding purified or sterile water or 0.9% sodium chloride injection or 5% dextrose solution followed by gentle swirling of the suspension.
  • HPV S280C His-tagged protein is cloned into the Ndel/Xhol restriction sites of vector pET21b (Novagen). This plasmid is transformed into E. coli BL21 (DE3) pLysS cells (Stratagene) for protein expression.
  • the amino acid sequence of the His-tagged HPV S280C protein is depicted below:
  • DNA fragment containing the HPV K5 construct is synthesized via PCR using the HPV K5 template and primers.
  • the HPV K5 template consists of the HPV nucleic acid sequence cloned into the Ndel/Xhol restriction sites of vector pET22b.
  • PCR primers are designed to introduce 5 lysine residues to the HPV tail portion.
  • Each PCR reaction is composed of 12.5 ⁇ l of 5X GC polymerase buffer (Finnzyme), 1.25 ⁇ l of a 1OmM dNTP mixture, 1.5 ⁇ l of 5 ⁇ M forward primer, 1.5 ⁇ l of 5 ⁇ M reverse primer, 0.6 ⁇ l of Stratagene mini-prepped template, 0.8 ⁇ l of2 unit/ ⁇ l Phusion Hot Start polymerase (Finnzyme), and 44.25 ⁇ l of water.
  • the PCR reaction consists of a one-time incubation at 98 0 C for 1 minute, followed by incubation at 98°C for 25 seconds, incubation at 70°C for 30 seconds, and incubation at 72°C for 1 minute and 10 seconds.
  • the PCR product and a pET22b vector are both digested with restriction enzymes Ndel and Xhol at 37 0 C for 2 hours.
  • the digested products are run on an agarose gel, the bands excised, and purified via gel extraction (Stratagene).
  • Ligation reaction is composed of 5 ⁇ l of digested and purified PCR product, 1 ⁇ l of digested and purified pET22b vector, 1 ⁇ l of T4 DNA ligase buffer (NEB), 1 ⁇ l of T4 DNA ligase (NEB), and 2 ⁇ l of water and is incubated at room temperature for 12 hours.
  • the ligation reaction is transformed into XLI Blue E. coli cells (Stratagene) and the resulting colonies are grown in IX LB broth and the plasmid purified via mini-prep (Stratagene).
  • the purified plasmid is sequenced (see below) and transformed into E. coli BL21 (DE3) pLysS cells (Stratagene) for protein expression. This strategy can be used for proteins containing from 0 to 30 lysine residues.
  • DNA fragment containing the SV40 K137C construct is synthesized via PCR using the SV40 K137C template .
  • Each PCR reaction consists of 5 ⁇ l of 1OX Pfu Turbo polymerase buffer (Stratagene), 1 ⁇ l of a 10 mM dNTP mixture, 1.5 ⁇ l of 5 ⁇ M forward primer, 1.5 ⁇ l of 5 ⁇ M reverse primer, 1 ⁇ l of Stratagene mini-prepped template, 1 ⁇ l of 2.5 unit/ ⁇ l Pfu Turbo polymerase (Stratagene), and 39 ⁇ l of water.
  • the PCR reaction consists of a one-time incubation at 98°C for 1 minute, followed by incubation at 98°C for 30 seconds, incubation at 64-72°C (depending on primer T m ) for 1 minute, and incubation at 72°C for 6 minutes. These last three steps are repeated 20 times.
  • the PCR product is digested with the restriction enzyme Dpnl at 37°C for 1.5 hours to rid the reaction of any un-mutated template.
  • the digested product is run on a 1% agarose gel, the bands excised, and purified via gel extraction (Stratagene).
  • the PCR product is then transformed into E. coli BL21 (DE3) PlysS cells (Stratagene) and the resulting colonies are grown in IX LB broth and the plasmid purified via mini-prep (Stratagene). The purified plasmid is then sequenced to confirm the change in nucleic acid sequence.
  • This strategy can be applied to single amino acid changes or the deletion or insertion of multiple amino acid residues such as the removal of a poly-histidine tag.
  • a pET-lla vector containing the full-length HPV-protein gene is transformed into E. coli DE3 cells and grown at 37 0 C in LB media, fortified with 2-4% glucose, trace elements and 200 ⁇ g/mL carbenicillin. Protein expression is induced by the addition of 2mM IPTG (isopropyl-beta-D-thiogalactopyranoside). Cells are harvested by pelleting after three hours of induction. SDS-PAGE is used to assess expression of C-protein.
  • HPV protein is purified from E. coli by resuspending in a solution of 50 mM Tris- HCl, pH 7.4, ImM EDTA, 5 mM DTT, ImM AEBSF, O.lmg/mL DNasel and 0.1 mg/mL RNase. Cells are then lysed by passage through a French pressure cell. The suspension is centrifuged at 2600OxG for one hour. The pellet is discarded and solid sucrose added to the supernatant to a final concentration of 0.15 M and centrifuged at 10000OxG for one hour.
  • the pellet is discarded and solid (NH 4 ) I SO 4 is then added to a final concentration of 40% saturation, stirred for one hour and then centrifuged for one hour at 2600OxG.
  • the pellet is resuspended in a solution of 100 mM Tris-HCI at pH 7.5, 100 mM NaCl, 50 rnM sucrose and 2 mM DTT (Buffer A) and loaded onto a Sepharose CL-4B (Phannacia Biotech, Piscataway, NJ) column (5 cm diameter X 95 cm) equilibrated with Buffer A. and the column eluted at 2mL/minute.
  • HPV viral capsids are separated from large aggregates and from soluble proteins of lower molecular weight.
  • the fractions are pooled according to chromatographic profile and SDS-PAGE analysis and the solution concentrated by ultrafiltration using Diaflo YM 100 ultrafiltration membrane (Amicon, Beverly, MA) to about 10 mg/mL.
  • Concentrated HPV protein is dialyzed against 50 mM Tris-HCI, pH 7.5 and 0.15 M sucrose. The solution is then adjusted to pH 9.5 with ION NaOH and urea added to a final concentration of 3.5 M.
  • the solution is then filtered using a Millex-HA 0.45 urn pore size filter unit (Millipore, Bedford, MA) and applied to a column (6.0 cm diameter X 60 cm) of Superdex 75 (Pharmacia Biotech, Piscataway, NJ) equilibrated with 100 mM sodium bicarbonate, pH 9.5, containing 2 mM DTT.
  • the column is eluted at 5 niL/minute.
  • the fractions containing dimeric protein as assessed by SDS-PAGE are pooled.
  • the pET vector containing the gene for HPV His-tagged protein is kept in BL21 (DE3) PlysS cells for expression.
  • the starter culture can be inoculated from a colony on an IX Luria Broth (IXLB) agar plate or from a 10% glycerol stock, stored at -80 0 C.
  • the IXLB is autoclaved in a 2 L flask and cooled. 100 mg of ampicillin (Amp) is added to the IXLB.
  • a started culture is inoculated and allowed to grow for up to 24 hours with shaking at 200 rpm at 37 0 C.
  • the bacterial pellets are transferred into two 50 mL conical tubes. Each tube is labeled with date/construct/prep number and frozen at -20 0 C. [0239] Two 50 ml tubes (approximately 20 mL each) of cell paste are thawed and the following steps are applied to each tube. 40 mL resuspension buffer (5 M urea, 50 mM NaHCO 3 (pH 9.5), 10 mM imidazole) is added into each tube. The cells are suspended by continuous pipetting and poured into a 400 mL beaker. More resuspension buffer is added until there is -100 mL total cell resuspension in the beaker.
  • resuspension buffer 5 M urea, 50 mM NaHCO 3 (pH 9.5), 10 mM imidazole
  • the beaker containing resuspended cells is placed in an ice bath and sonicated for 5 minutes using a Branson probe sonifier (pulse mode at approximately 40% duty cycling and power setting of 5).
  • the cell mixture should be sonicated in several intervals, and allowed to rest on ice in-between, if it appears that the sample is heating to higher than room temperature.
  • the cell lysate is diluted 2 fold to 200 mL total, and 200 ⁇ L of 100 mg/mL DNaseis added to the suspension. This suspension is stirred while on ice for 10 minutes. The sonication step is repeated for 5 more minutes while on ice.
  • the lysate is transferred to six 50 rnL plastic centrifuge tubes, and centrifuged at 32000 g for 45 minutes. Supernatant is discarded.
  • a 50 rnL Ni 2+ -NTA agarose (Qiagen) column is washed and equilibrated in the resuspension buffer.
  • a full 12 L cell growth is lysed for each run of the column.
  • the centrifuged lysate from 12 L worth of cells is combined and diluted to 500 mL with resuspension buffer.
  • the centrifuged cell lysate is loaded onto the column, and the protein solution is allowed to sink to the top of the nickel matrix. 50 mL of resuspension buffer is passed through the column.
  • An optional salt wash can be performed by washing the column with 250 mL of NaCl wash buffer (5 M urea, 50 mM NaHCO 3 (pH 9.5), 20 mM imidazole, 250 mM NaCl).
  • This salt wash reduces the A260/A280 ratio of the final purified protein by a value of 0.1 A.U..
  • the column is washed with 250 mL of wash buffer (5 M Urea, 50 mM NaHCO 3 (pH 9.5), 20 mM imidazole), and 200 mL of elution buffer (5 M Urea, 2 mM NaHCO 3 (pH 9.5), 250 mM imidazole) is through the column.
  • Fractions are collected at every 5 mL, which should yield 5 to 8 fractions that contain protein. [0241] The presence and/or concentration of protein is detected by measuring the absorbance of the fractions. SDS polyacrylamide gel electrophoresis (SDS PAGE) analysis is performed on the proteins to determine purity. Fractions containing protein are pooled, and transferred to dialysis tubing. Dialysis is performed in 4 L of storage buffer (5 M Urea, 2 mM NaHCO 3 (pH 9.5)) for at least 4 hours at 4 0 C. The protein can then be concentrated in an Amicon stirred cell concentrator (Millipore) to a final protein concentration of up to 75 mg/ml. A 12 L cell growth yields approximately 500 mg of pure protein. Pure dialyzed protein can be stored at -80 0 C for 6-8 months.
  • SDS PAGE SDS polyacrylamide gel electrophoresis
  • PE phosphatidyl ethanolamine
  • TAA triethylamine
  • the solution is maintained under an argon or nitrogen atmosphere.
  • the reaction can also be done in dry chloroform.
  • 50 mg of SMPB (Pierce) is added to the PE solution and mixed well to dissolve.
  • the solution is maintained under an argon or nitrogen atmosphere while the reaction proceeds for 2 hours at room temperature. Methanol is removed from the reaction solution by rotary evaporation and the solids are redissolved in chloroform (5 mL).
  • the water-soluble reaction by-products is extracted from the chloroform with an equal volume of 1% NaCl. Extraction is performed twice.
  • the MPB-PE derivative is purified by chromatography on a column of silicic acid (Martin FJ et al., Immuno specific targeting of liposomes to cells: A novel and efficient method for covalent attachment of Fab' fragments via disulfide bonds. Biochemistry, 1981; 20:4229-38). Chloroform is removed from the MBP-PE by rotary evaporation, and the derivative is stored at -20 0 C under a nitrogen atmosphere until use.
  • the solution is purged under a nitrogen or argon atmosphere for 20 minutes.
  • the maleimide-containing linker is dissolved in the same buffer as above, and purged under a nitrogen or argon atmosphere for 20 minutes, to obtain a 10-fold molar excess.
  • the instant example describes a general method for forming a therapeutic particle containing inhibitory dsRNA .
  • the protein is allowed to thaw to 25 0 C.
  • the inhibitory dsRNA-containing solution is added to the protein solution at a molar ratio of 9.58:1 or 9.42: 1 for non-modified or modified inhibitory dsRNA, respectively.
  • the solution is mixed for 1 hour at 25 0 C.
  • BME is added at a molar ratio of 3: 1 to the protein to protect cysteine functional groups.
  • This reaction is incubated for 1 hour at 25 0 C.
  • a 2:1 volume ratio of 10 mM NaCl solution is added to reaction mixture containing protein and inhibitory dsRNA.
  • the solution is kept in a water bath set to 25 0 C for 48 hours.
  • PE- MAL l,2-Dipalmitoyl-sn-Glycero-3-Phosphoethanolamine-N-[4-(p-maleimidophenyl)- butyramide] (Sodium Salt)
  • DMF dimethylformamide
  • lipid coating material cholesterol (Avanti Lipids, Alabaster, AL, USA), HSPC (L- ⁇ -Phosphatidylcholine, Hydrogenated (Soy), Avanti Lipids, Alabaster, AL, USA) and POPG (l-Palmitoyl-2-Oleoyl-sft-Glycero-3-[Phospho-rac-(l -glycerol)] (Sodium Salt), Avanti Lipids, Alabaster, AL, USA) in dry power forms are premixed in a 3:1:1 molar ratio, respectively, in a glass beaker. The mixture is predissolved and homogenized with 2.0 mL of chloroform.
  • the chloroform is allowed to evaporate (20 to 30 minutes on a hot plate set to 50 0 C).
  • 0.5X PBS pH 9.5 phosphate buffered saline with 5 mM NaHCO 3
  • This solution is sonicated for at least 3.0 min at 62 0 C.
  • the lipid coating material is added immediately after sonication to the solution containing functionalized protein and inhibitory dsRNA at a mass ratio of 5: 1 protein:lipid coating material. The material is allowed to cool to 25 0 C.
  • the chimeric protein for forming the capsid is purified via FPLC (fast performance liquid chromatography) (Amersham Pharmacia).
  • FPLC fast performance liquid chromatography
  • the large FPLC column (Pharmacia XK- 16 16mm x 700mm) is ran at 1.0 niL/min using 0.5X PBS pH 9.5 buffer as the mobile phase, and Sepharose CL-4B (Amersham Pharmacia) matrix as the stationary phase.
  • Fractions containing therapeutic particles are collected and combined (typically eluting at 70 mL based on the stationary phase and column configuration described above). Protein concentration is determined using the Agilent 2100 Bioanalyzer system. Samples are diluted 1:1 with 0.5X PBS pH 9.5 and ran on a Protein 80 chip in triplicates as described by manufacturer.
  • Example of Chromatogram obtained by the purification method described above is shown in Figure 9.
  • Example of particle size measurement as determined by the instrument is shown in Figure 10.
  • the instant example describes two general methods for quantifying the inhibitory dsRNA contained within the therapeutic particle.
  • the first method describes SDS Extraction of inhibitory dsRNA from a therapeutic particle.
  • a standard curve of inhibitory dsRNA is generated for concentrations of 175, 250, 350, 500, 700 nM; samples are prepared in triplicates.
  • 100 ⁇ L of the therapeutic particle is mixed with 5 ⁇ L of 10% SDS solution.
  • the solution is heated at 7O 0 C for 30 minutes and cooled to room temperature.
  • 30 ⁇ L of a 75% glycerol stock is added to the particle/SDS solution.
  • the lysed particles and the inhibitory dsRNA standards are run on a 15% urea-PAGE gel (Biorad 161-1135) at 230 V for 35 minutes in IX TBE buffer.
  • the gel is then stained with SYBR Green II (140 mL of water and 4 ⁇ L of stock SYBR Green II) on an orbiting platform for 30 minutes.
  • the stained gel is scanned on a Typhoon Trio using 488 nm excitation with a 526 nm SP filter and the PMT set at 350 V.
  • the Image Quant TL (V 7.0) software the densitometry of the bands is measured and the concentration of the inhibitory dsRNA is determined using a standard curve.
  • the second method describes extraction using phenol/chloroform.
  • a standard curve of inhibitory dsRNA is generated for concentrations of 175, 250, 350, 500, 700 nM; samples are prepared in triplicates.
  • 100 ⁇ L of therapeutic particles are mixed with 100 ⁇ L of phenol: chloroform (95:5) solution. These solutions are vortexed for 5 minutes and spun at 13,000 g for 60 seconds.
  • 50 ⁇ L of aqueous solution is mixed with 15 ⁇ L of a 75% glycerol stock.
  • the lysed particles and the inhibitory dsRNA standards are run on a 15% urea-PAGE gel (Biorad 161-1135) at 230 V for 35 minutes in IX TBE buffer.
  • the gel is stained with SYBR Green II (140 mL of water and 4 ⁇ L of stock SYBR Green II) on an orbiting platform for 30 minutes.
  • the stained gel is scanned on a Typhoon Trio using 488 nm excitation with a 526 nm SP filter and the PMT set at 350 V.
  • the Image Quant TL (V 7.0) software the densitometry of the bands is measured and the concentration of the inhibitory dsRNA is determined using a standard curve.
  • the instant example describes two general methods for analyzing the lipid contained as part of the therapeutic particles.
  • the first example is a NMR- Analysis (dry extraction). 30 mL of the therapeutic particle is dried under vacuum in a speedvac. The resulting material is scraped into a 10 mL glass beaker. 3 mL of water and 3 mL of chloroform are added to the solids. This solution is sonicated for 20 seconds and the mixture is incubated for 30 minutes at room temperature. The solution is centrifuged and the chloroform layer is isolated and filtered through a glass plug. The chloroform is removed under vacuum and the NMR spectrum is measured of the material. [0260] The second example is a NMR- Analysis (wet extraction). 30 mL of the therapeutic particles is mixed with 10 mL of chloroform.
  • One mole equivalent of purified coated particle is treated with 200 mole equivalents of PE-maleimide lipid (1,2-Dipalrnitoyl-sra-Glycero 3-Phosphoethanolamine-N-[4-(p- maleimidophenyl)-butyramide] (Sodium Salt)) (dissolved in DMF). Following 30 minutes of incubation, 1 mole equivalent of the particle is treated with 30 mole equivalents of the modified antibodies. The reaction is allowed to proceed overnight. Excess antibodies are removed via a packed column (16 x 200 mm) packed with Sepharose CL-4B matrix with the isocratic mobile phase (0.25X PBS pH7.4). This gives a typical yield of about 60 % and has about 20-30 antibodies per particle as determined by SDS-PAGE gels.
  • PE-maleimide lipid 1,2-Dipalrnitoyl-sra-Glycero 3-Phosphoethanolamine-N-[4-(p- maleimidophenyl)-butyr
  • Example 10 HPV K5 protein-RNA complex via electrophoresis of labeled inhibitory dsRNA and HPV K5 protein
  • Inhibitory dsRNA that is 3 '-labeled with Dy547 is purchased from Dharmacon (Lafayette,CO). Labeled and unlabelled inhibitory dsRNA solutions are diluted to 4 ⁇ M in 4 M Urea, 10 mM Hepes, pH 8.15. To label the protein, 3 ⁇ M of the HPV K5 protein is incubated with 30 ⁇ M maleimido-cy5 (Pierce) in 4 M Urea, 10 mM Hepes, pH 8.15 for 1 hour. Labeled and unlabeled protein solutions are diluted to 3 ⁇ M in 4M Urea.
  • Example 11 Transmission Electron Microscopy and Dynamic Light Scattering are utilized to assess and validate formation of the therapeutic particle.
  • TEM Transmission Electron microscopy
  • PTA phosphotungstic acid in water, pH adjusted to 7.0 with IN NaOH
  • ELISA is a useful tool in determining the ability of the particles to bind various bioactive agents.
  • Protein constructs (3 mg/ml) are mixed with 20OuM of RNA at a ratio of 6.25 protein dimers per RNA duplex and incubated for 15 minutes. This mixture is then diluted 1:1 with a buffer containing 30 mM Sodium, Hepes pH 7.5, and 60 mM NaCI in order to encapsulate RNA. Encapsulation is allowed to proceed overnight at room temperature. The samples are loaded on a 1.0 % agarose gel containing ethidium bromide, run for 40 minutes at 100 Volts, and visualized on a Molecular Dynamics Typhoon imager.
  • 96-well ELISA plates are coated overnight with either 50 ⁇ L of mCD22Ig protein or 2% BSA (w/v) in 0.1 M borate buffered saline at a concentration of 50 ug/ml. Plates are washed 3 times in Tris buffered saline (TBS). All wells are then blocked with 2% BSA in TBS for 1 hour, followed by 3 TBS rinses.
  • Anti-CD22 targeted particle constructs and non-targeted particle constructs (no antibody) containing 4% DiI embedded within the lipid coat are incubated in triplicates, at multiple concentrations, in buffer containing 2% BSA and 0.1% tween in TBS for 4 hours.
  • 96-well ELISA plates are coated overnight with either 50 ⁇ L of mCD22Ig protein or 2% BSA (w/v) in 0.1 M borate buffered saline at a concentration of 50 ⁇ g/ml. Plates are washed 3 times in Tris buffered saline (TBS). All wells are then blocked with 2% BSA in TBS for 1 hour, followed by 3 TBS rinses. Anti-CD22 targeted particle constructs and non-targeted particle constructs are incubated in triplicates, at multiple concentrations, in buffer containing 2% BSA and 0.1% tween in TBS for 4 hours.
  • Wells are then rinsed 3 times in TBS followed by incubation with antibodies against (1) rabbit-anti HBV core protein (AbCam), (2) mouse anti-HBV core protein (GenTex), or (3) no antibody in 2% BSA and 0.1% tween in TBS for 1 hour.
  • Wells are rinsed 3 times again in TBS followed by 1 hour incubation in (1) goat anti- rabbit conjugated to alkaline phosphatase, (2) goat anti-mouse Fc region conjugated to alkaline phosphatase, or (3) no antibodies in 2% BSA and 0.1% tween in TBS. All wells are rinsed 3 times in TBS, one time in PBS, and incubated in DDAO-phosphate (1:100,000) in PBS.
  • Anti-core protein antibodies are used to detect the presence of therapeutic particles.
  • Non-targeted particle binding data are normalized to the % of anti-CD22 targeted particle binding.
  • B Cell (BCLI and Ramos) and T cell lines (Jurkat and HH) are purchased from ATCC and grown at 37 0 C (5% CO2) in RPMI medium with 10% fetal bovine serum, supplements and antibiotics. Cells grown under these conditions consistently exhibit "normal" growth characteristics. All cell experiments are conducted while cells are exhibiting log-phase growth characteristics.
  • Cells are rinsed again 3 times in 5 mL sterile PBS, spun down and resuspended in 150 ⁇ l of PBS. To fix the cells, 150 ⁇ l of 2% paraformaldehyde is slowly added to the cells. Cells are allowed to fix for 10 minutes, and 100 ⁇ l of cell suspension is added to each well of a 96- well plate in triplicates. Plates are spun down using a clinical centrifuge. To detect fluorescence, a Typhoon Molecular Imager is used with Cy3 excitation/emission settings. Background fluorescence of "cells alone" is included for comparison.
  • Adherent BCLI cells are plated onto glass coverslips (Fisher Scientific) in sterile 24- well tissue culture plates 12 hours prior to experimentation. Cells are allowed to grow to semi- confluency (cell density estimated at 200,000 cells/well) in complete RPMI media (see Cell Growth above). Prior to experiments, cells are rinsed with once with media and 500 ⁇ l of media is added to each well. Following experimental incubations (see below) adherent cells are rinsed once in media, 3 times in PBS, resuspended in 150 ⁇ l PBS. To fix the cells, 150 ⁇ l of 2% paraformaldehyde is slowly added to the tubes.
  • a total of 200,000 suspension cells (Ramos, Jurkat, and HH Cells) are added to sterile 24-well tissue culture plates. Media volumes are adjusted (upwards) to 500 ⁇ l. Following experimental incubations (see below) suspension cells are sequentially pelleted and rinsed once in media and 3 times in PBS. Cells are then resuspended in 150 ⁇ l PBS. To fix the cells, 150 ⁇ l of 2% paraformaldehyde is slowly added to the tubes.
  • cells are incubated with fluorescent anti-CD22 targeted particles, non-targeted particles (both with 3% DiI embedded in the lipid coat), or an equal volume of "media only" at 37 0 C at multiple particle concentrations [300,000 cages/cell (-30 nM), 100,000 cages/cell ( ⁇ 10nM), 30,000 cages/cell (-3 nM), 10,000 cages/cell (-1 nM), 3000 cages/cell (-300 pM), and 1000 cages/cell (-100 pM)] in 500 ⁇ l media for 2 hours.
  • cells are coverslipped in 5 % n- propyl gallate in glycerol (w/v) and sealed under cover-slips using nail polish. Internalized fluorescent particles are quantified using standard fluorescence microscopy. Two-hundred cells are counted per coverslip and the percentage of cells with internalized particles is quantified.
  • Particle constructs are generated using standard procedures. Following antibody attachment to the particle, removal of free antibodies from the particles was not conducted. This results in the presence of free antibody (>10: 1) in targeted particle preparations. Fluorescent internalization experiments are conducted using BCLl cells and identical experimental conditions as stated above. Experimental incubations for this experiment included the comparison between identical concentrations of purified targeted particles and non-purified targeted particles. Particle concentrations for all experiments are determined by quantifying core protein concentration, so free antibody does not effect concentration calculations. Analysis of internalized particles in these experiments is identical to those mentioned above.
  • Capsids are formed in the presence of fluorescently-labeled RNA molecules.
  • the core protein is incubated with the RNA at a ratio of 10:1 protein:RNA and then 70 mM NaCl is added at a 1:1 ratio to the protein/RNA mixture to initiate capsid formation. Capsid formation can be confirmed by light scattering and/or size-exclusion chromatography.
  • the pre-formed capsids are incubated in 4M urea at a temperature of 55 0 C to force degradation of the capsids. Aliquots of the capsids are taken at various time points and analyzed on a 1% agarose gel. The gel analysis reveals the amount of RNA that is present as free molecules or inside the intact capsid and as such serves as a gauge of intact capsid present at the various time points. The amount of RNA in the intact capsid band can be quantified by densitometry and plotted over time.
  • Figure 4 depicts results from a capsid stability assay performed using a HBV(hepatitis B) core protein.
  • the purpose of this assay is to determine if the K9 core protein protects the encapsulated inhibitory dsRNA molecules from the benzonase nuclease.
  • a sample is prepared with no benzonase as a negative control. The mixture is incubated for 1 hour at room temperature. The samples are run on a 1.0% TAE-agarose gel containing ethidium bromide. The gel is imaged and the intensity of the RNA bands is determined.
  • Figure 5 depicts results from a benzonase protection assay performed using a HBV K9 protein. Free RNA band is degraded at about 20 units/nmol. RNA associated with the HBV K9 protein does not degrade at any nuclease concentrations tested, indicating that the RNA is effectively protected. This assay shows that RNA is significantly protected against nuclease activity by encapsulation with K9 core protein.
  • Example 15 Serum protection assay
  • RNA sample is mixed with human serum. The total volume of sample and serum is between 2-4 mL. Freeze several aliquots of sample and serum immediately for time zero time points, and place the remaining samples at 37 0 C. Multiple 50 ⁇ L aliquots are removed from samples at regular intervals, labeled and froze at - 8O 0 C. To process the samples, 10% SDS is added to achieve a final concentration of 0.7% SDS. The mixture is incubated at room temperature for 5 minutes. Samples are ran at 200 V for 30 minutes on a 1.0% TAE-agarose gel containing ethidium bromide. The lifetime of the RNAs is quantitated to determine the amount of protection.
  • Figure 6 depicts results from a serum protection assay using HBV K9 protein.
  • Figure 6 demonstrates that the control samples, using Hep B particles had degraded by the first time point (1 day) while the particle -protected (Hep B) RNA survived without appreciable degradation for the duration of the experiment, 4 days. These results indicate that the particle protects the RNA cargo from serum degradation. Additional experiments indicate that RNA stability is achieved at 14 days without the degradation of the RNA payload. Free RNA, in the presence and absence of empty particle, is completely degraded by 1 day.
  • f-RNA buffer 20 nM fluorescent duplex (Siglo cycB, RNA from Dharmacon) in 10 rnM Tris is referred to as f-RNA buffer.
  • HPV K5 protein stock is diluted to 6 ⁇ M in f-RNA buffer. The dilution is performed quickly and on ice, so that particle assembly is less apt to form. Successive dilutions of HPV K5 is made in f-RNA buffer. The RNA-protein dilutions are removed from ice and allowed to sit at room temperature for 5 minutes.
  • FIG. 7 indicates that fluorescent inhibitory dsRNA binds to a HBV (Hep B) K9 mutant protein with a K d of 115 nM. This is a tight affinity, which is characteristic of RNA-protein interactions. This tight binding affinity is well below the concentrations of RNA and protein used for assembly of particles. Therefore, these data suggests that during assembly the RNA binding sites of K9 protein are saturated with RNA. B.
  • HPV K5 protein stock is diluted to 40 ⁇ M in the same buffer.
  • RNA and protein solutions are mixed 1:1 and allowed to bind at room temperature for 5 minutes.
  • the final protein concentration in the binding reactions ranges three orders magnitude, from 20 ⁇ M to 20 nM.
  • a 1/5 volume of 6X RNA loading buffer xylene cyanol in 55% glycerol 20 mM Tris, pH 7.7 is added.
  • the samples are then loaded on a 1.0% TAE-agarose gel (13cmxl6cm), at 80 ⁇ L/lane. The gel is run for 180 V for 35 minutes and documented on a Molecular Dynamics Typhoon scanner.
  • the assay is performed using the HBV K7 and KI l mutant proteins.
  • Figure 8 indicates that fluorescent inhibitory dsRNA bound to HBV K7 with a K d of 370 nM and to Kl 1 with a K d of 69 nM. This is a tight affinity which is characteristic of RNA-protein interactions.
  • the increase affinity observed for KI l relative to K9 and K7 is attributable to the larger number of cationic residues at the C-terminal end of this protein.
  • C 166 cells stably expressing the enhanced green fluorescent protein (eGFP) are grown at 37 0 C, 5% CO2, in DMEM media with 10% fetal bovine serum and supplements.
  • Cell stocks are grown in T25, T75, or T125 flasks and transferred to 24-well plates for experimentation. Cells are also grown on glass coverslips in 24-well plates when microscopy is to be performed. Cells grown under these conditions consistently exhibit "normal" growth characteristics and doubling times.
  • C166 cells are grown on glass coverslips in 24-well plates. Cells are plated onto coverslips 24 hours prior to the addition of lipid particles containing inhibitory dsRNA. 100 ⁇ l of lipid particles containing 3 nM final concentration of red- fluorescent inhibitory dsRNA directed against Cyclophilin B (SEQ ID NO:58) are added to 1 mL of media and incubated at 37 0 C for 4 hours. Control cells are incubated in 100 ⁇ l of PBS (no lipid particles present). Cells are rinsed 3 times in cold PBS and fixed in 1% paraformaldehyde in PBS. Hoescht 33342 (1: 10,000) is added for the visualization of cell nuclei, and coverslips are mounted onto glass slides (cells facing down). Slides are visualized using standard fluorescence microscopy.
  • Microscope settings are held constant for both experimental and control slides. Lipid particles containing red fluorescent inhibitory dsRNA enter eGFP-expressing C 166 cells when incubated at 3 nM for 4 hours, thus staining these cells red.
  • C. Lipid Particles Containing Inhibitory dsRNA Directed Against eGFP Inhibit eGFP mRNA Expression In Vitro C166 cells are grown on glass coverslips in 24-well plates. Cells are plated onto coverslips 24 hours prior to the addition of lipid particles. 250 ⁇ l of lipid particles containing inhibitory dsRNA directed against eGFP (eGFP- 19) with the following sequences:
  • GCUGACCCUGAAGUUCAUC-dTdT (SEQ ID NO:59)
  • dTdT-CGACUGGGACUUCAAGUAG (SEQ ID NO:60) are added to 1 rnL of media and incubated at 37 0 C for 24 and 48 hours.
  • the final concentration of inhibitory dsRNA within the particle is 10 nM.
  • Control cells are incubated in 250 ⁇ l of PBS (no lipid particles present). Cells are rinsed 3 times in cold PBS and homogenized using buffer RLT (Qiagen) with 0.1% BME. Three wells are used for each experimental condition at each time point.
  • RNA is purified using the RNEasy kit (Qiagen) as recommended by the manufacturer, including an on-column DNAse digestion step. RNA is quantified on the Nanodrop (Thermofisher). 1 ⁇ g of total RNA is reverse transcribed using iScript reverse transcriptase (BioRad) as recommended by the manufacturer. Quantitative polymerase chain reactions (qPCR) are performed using cDNA, SybrGreen master mix (BioRad) as recommended by the manufacturer, and prequalified primer sets designed using Beacon Designer 6.0 (Premier Biosoft). eGFP gene inhibition is quantified using the ⁇ Ct method by comparing eGFP expression levels in each sample to the geometric mean of 3 housekeeping genes in the same sample. All samples are run in triplicates.
  • C166 cells are grown on glass coverslips in 24-well plates. Cells are plated onto coverslips 24 hours prior to the addition of lipid particles. lOO ⁇ l of lipid particles red- fluorescent inhibitory dsRNA directed against eGFP (F-eGFP 19 with the following sequence:
  • DY547-GCUGACCCUGAAGUUCAUC-dTdT (SEQ ID NO:61) dTdT-CGACUGGGACUUCAAGUAG (SEQ ID NO:60) are added to 1 niL of media and allowed to sit at 37 0 C for 18 hours. The final concentration of inhibitory dsRNA within the particle is 10 nM. Control cells are incubated in lOO ⁇ l of PBS (no lipid particles present). Cells are rinsed 3 times in cold PBS and fixed in 1% paraformaldehyde in PBS.
  • Hoescht 33342 (1:10,000) is added for the visualization of cell nuclei, and coverslips are mounted onto glass slides (cells facing down) in 5 % n-propyl gallate in glycerol. Slides are visualized using confocal microscopy. Microscope gain and PMT settings are held constant for both experimental and control conditions. Lipid particles containing red fluorescent inhibitory dsRNA directed against eGFP can enter cells and inhibit eGFP protein expression after an 18 hour incubation. eGFP (green) expression is reduced in cells incubated with lipid particles loaded with inhibitory dsRNA (red).
  • mice Female C57BL/6-Tg(ACTb-eGFP)10sb/J mice ( ⁇ 8 weeks old) are treated with 200 ⁇ l of lipid particles loaded with a total of -620 ng inhibitory dsRNA (eGFP 19 of SEQ ID NO:59 and SEQ ID NO:60) through tail injections. The mice are sacrificed 24 or 48 hours later. 20 animals are injected with lipid particles loaded with inhibitory dsRNA, and 20 animals are injected with 200 ⁇ l of PBS alone. 16 animals are sacrificed from each group at 24- 48 hours, and 4 animals from each group are sacrificed at 48 hours. RNA is harvested from the liver, kidney, heart, lung, spleen, and pancreas using RNA later storage solution (Ambion).
  • RNA is purified from -25 mg of tissue from each organ using the RNEasy total RNA purification kit and DNAse digestion is conducted on column. 1 ⁇ g of total RNA is reverse transcribed using the iScript reverse transcription kit. Equal amounts of cDNA are added to qPCR reactions. Levels of eGFP are normalized to the geometric mean of 3 housekeeping genes and percent inhibition is calculated using the ⁇ Ct method. All qPCR samples are run in triplicates.
  • a female C57BL/6-Tg(ACTb-eGFP)10sb/J mouse (-9 weeks old) is injected with 200 ⁇ L of lipid particles loaded with a total of -40 ng siGlo-conjugated inhibitory dsRNA (F- eGFP 19 of SEQ ID NO:61 and SEQ ID NO: 60).
  • the mouse is sacrificed 24 hours later.
  • a total of 1 animal received 200 ⁇ L lipid particles containing inhibitory dsRNA in PBS and 3 naive animals (female animals from the same litter) received no injection.
  • Liver tissue is harvested and immediately placed in 4% paraformaldehyde in PBS and stored at 4 0 C.
  • Liver extracts are diluted 1:10 in PBS and tested for eGFP fluorescence on a fluorescent spectrophotometer. To determine relative levels of eGFP fluorescence from individual liver extracts, 100 ⁇ L of 1 : 10 diluted extract is loaded into a 96 well plate and read on a Turner fluorescent plate reader. Each sample is read in duplicates. To determine inhibition, eGFP fluorescence is compared between livers treated with or without inhibitory dsRNA.
  • Example 18 To demonstrate in vitro knockdown of ApoB protein by ApoB2 loaded therapeutic particles, ApoAl protein expression is monitored for normalization of protein expression. In both cases, ApoB and ApoAl, protein expression is quantified via ELISA.
  • HepG2 cells grown in HepG2 media are plated overnight on coated 96-well plates. The volume of cells per well is 100 uL. A therapeutic particle stock containing 171 nM ApoB2 inhibitory dsRNA is prepared at a ratio of 4.5 inhibitory dsRNA's per particle.
  • Cells are approximately 60% confluent at the beginning of the experiment. Media is replaced with HEPG2 media containing 20% stock therapeutic particles. Cells are incubated with particles or control (HepG2 containing 20% of vehicle) at 37 0 C. After 48 hours, the media is replaced with HepG2 media and allowed to incubate 24, 48 or 72 hours. [0310] At the three time points for both particle-containing and control conditions, media from three wells are harvested for analysis of ApoB and ApoAl levels.
  • ApoB and ApoAl levels are detected by ELISA.
  • antibodies are immobilized on high binding polystyrene 96 well plates (Corning Costar cat#3590).
  • the capturing antibody is Apolipoprotein B antibody BlGl (cat# GTX27616), diluted 1 :2000 in 0. IM sodium bicarbonate pH 9.6.
  • PBS-BSA PBS + lOmg/ml BSA
  • Samples are prepared in HepG2 conditioned media diluted 1:10 in PBS-O.
  • IXBSA PBS + lmg/ml BSA).
  • a standard is generated by serial dilution of an ApoB standard (Alerchek).
  • the detection antibody is an ApoB-Horse Radish Peroxidase antibody conjugate (Genetex cat # GTX40047), diluted 1:1000 in PBS-BSA. Each well is measured in triplicates. Between capture antibody, block, sample, and detection antibody applications, wells are washed 3 times with 200 uL of PBST (PBS containing 0.1% TWEEN 20). HRP is detected with ULTRA-TMB reagent (Thermofisher).
  • an ApoAl ELISA kit is purchased from Alerchek (cat# Cardiocheck Apolipoprotein Al) and used according to manufacturer's directions. ApoAl and ApoB levels are determined. The ratio of ApoB to ApoAl (ApoB/ApoAl) is also determined.
  • Anti-CD22 Targeted Particles loaded with Doxorubicin are evaluated for their ability to Target and Kill CD-22 Expressing Cells
  • B cells (Ramos), and T cells (Jurkat) are added to sterile 96-well plates containing 500,000 cells/ml in early log growth phase. Multiple concentrations (lOpM, 10OpM, InM, 1OnM, and 10OnM) of both CD22-targeted particles and non-targeted particles loaded with doxorubicin are added to the cells along with complete media (see previously). Cells are assayed for viability using Trypan Blue exclusion at multiple time points (12hr, 24Hr, 36hr, 48hr, 60hr, and 72hr).
  • Cell viability is normalized to cell viability at the beginning of the experiments for each cell line and is expressed as a % of "normal”. Cell density is also calculated and plotted across each time point for each concentration. All experiments at individual concentrations are conducted in triplicates for each time point.
  • Example 20 [0315] Anti-CD22 Targeted Particles loaded with Doxorubicin are evaluated for their ability to Reduce Tumor Growth, in vivo.
  • mice Female athymic BALB/c nu/nu mice (Harlan Sprague-Dawley), 7-9 weeks of age are maintained on a normal diet ad libitum and under pathogen-free conditions. Raji or Ramos cells are harvested in logarithmic growth phase and 2.5-5.0 x 10 6 cells are injected subcutaneously into both sides of the abdomen of each mouse. Studies are initiated 3 weeks after implantation, when tumors are 100-300 mm . Experimental groups consist of untreated, doxorubicin alone, naked particles loaded with doxorubicin, and particles loaded with doxorubicin and coated with HB 22.7.
  • Tumor volume is calculated by the formula for hemiellipsoids (DeNardo GL, Kukis DL, Shen S, et al., Clin Cancer Res 1997;3:71-79).
  • Initial tumor volume is defined as the volume on the day prior to treatment.
  • Mean tumor volume is calculated for each group on each day of measurement; tumors that have completely regressed are considered to have a volume of zero.
  • Tumor responses are categorized as follows: C, cure (tumor disappeared and did not regrow by the end of the 84 day study); CR, complete regression (tumor disappeared for at least 7 days, but later regrew); PR, partial regression (tumor volume decreased by 50% or more for at least 7 days, then regrew).
  • HepG2 cells human hepatocellular carcinoma cell line- ATCC
  • DMEM fetal bovine serum
  • 2mM 1-glutamine penicillin/streptomycin
  • Cells are seeded in 96-well poly-lysine coated plates at -50,000 cells/well and allowed to settle overnight. The following day, when cells have reached >90% confluency, viral core protein particles as prepared as above, DharmaFECT, and PBS are to be added to cells. Particles and PBS are to be added at a volume of 25ul to 75ul of complete media for a total of lOOul/well.
  • Total RNA is then purified from individual samples using Qiagen RNEasy columns on a QiaCube (Qiagen) automated RNA purification system as suggested by the manufacturer. Qiashredders and on- column DNase I (Qiagen) digestion steps are also conducted as suggested by the manufacturer (included in automated RNA preparation protocol). Following RNA purification, total RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad).
  • cDNA is then added to SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ realtime qPCR machines (BioRad).
  • qPCR quantitative real-time qPCR
  • Included in all qPCR experiments are pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p-dehydrogenase (GAPDH), glucose phosphate isomerase (GPI), and hydroxymethylbilane synthase (HMBS), as well as pre-designed and pre- validated primers specific for the apolipoprotein B gene (ApoB).
  • GPDH glyceraldehydes-3-p-dehydrogenase
  • GPI glucose phosphate isomerase
  • HMBS hydroxymethylbilane synthase
  • Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ⁇ Ct-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of ApoB mRNA expression to the geometric mean of the three housekeeping genes.
  • RNA purification and on- column DNase I (Qiagen) digestion steps are also conducted (included in automated RNA preparation protocol).
  • total RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad).
  • cDNA is then added to SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ real-time qPCR machines (BioRad).
  • qPCR experiments include pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p- dehydrogenase (GAPDH), glucose phosphate isomerase (GPI), and hydroxymethylbilane synthase (HMBS), as well as pre-designed and pre-validated primers specific for the apolipoprotein B gene (ApoB). Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer.
  • GPDH glyceraldehydes-3-p- dehydrogenase
  • GPI glucose phosphate isomerase
  • HMBS hydroxymethylbilane synthase
  • Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer.
  • Cryopreserved mouse primary hepatocytes are thawed and grown in William's Media with 10% fetal bovine serum (according to the manufacturer's protocol) at 37 0 C and 5% CO2 for 24 hours. Thawed cells in suspension are then counted and plated at a density of 35,000 cells/well in 96-well collagen- 1 coated plates (Becton Dickenson) using a proprietary mixture of media supplements (CellzDirect- Thawing/Plating Supplement Pack). Cells are allowed to settle and attach to the collagen- 1 substrate for 48 hours as media is replaced after 24 and 48 hours.
  • DharmaFECT transfection reagent #6 is used to transfect naked inhibitory dsRNA into primary mouse hepatocytes as a positive control for mRNA knockdown. All DharmaFECT reagents are to be made up according to the manufacturer' s suggested protocol and added at 100 ⁇ l /well, and all experiments are performed in triplicate.
  • FVII inhibitory dsRNA which has the following sequence: sense 5'- GGAUC AUCUC AAGUCUUACT*T-3' (SEQ ID NO: 64) and antisense 5'- GUAAGACUUGAGAUGAUCCT*T -3' (SEQ ID NO: 65); bold letters denote 2'-F-modified nucleotides and asterisks represent phosphorothioate linkages, as well as SiGenome 5, which has the following sequence: sense 5'- UGGUUUACAUGUCGACUAA- 3' (SEQ ID NO: 66) are loaded into particles as described previously.
  • RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad). cDNA is then be added to
  • SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ real-time qPCR machines (BioRad). Included in all qPCR experiments are pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p-dehydrogenase (GAPDH), Cyclophillin A, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase (YWHAZ), as well as predesigned and pre- validated primers specific for the mouse Factor VII mRNA sequence.
  • GPDH glyceraldehydes-3-p-dehydrogenase
  • Cyclophillin A Cyclophillin A
  • YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase
  • Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ⁇ Ct-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of FVII mRNA expression to the geometric mean of the three housekeeping genes mentioned above.
  • Example 24 Factor VII Inhibition in vivo
  • a total of 48 female C57bl mice are injected intravenously in the tail vein with 200 ⁇ l of particles loaded with FVII inhibitory dsRNA at 0.5mg/kg inhibitory dsRNA.
  • the FVII inhibitory dsRNA has the following sequences: sense 5'- GGAUC AUCUCA AGUCUUACT*T-3' (SEQ ID NO: 64) and antisense 5'-
  • GUAAGACUUGAGAUGAUCCT*T -3' (SEQ ID NO: 65); bold letters denote 2'-F-modified nucleotides and asterisks represent phosphrothioate linkages, and the SiGenome 5 inhibitory dsRNA, which has the sequence: sense 5'-UGGUUUACAUGUCGACUAA- 3' (SEQ ID NO: 66) are loaded into particles as described previously.
  • SiGenome 5 inhibitory dsRNA which has the sequence: sense 5'-UGGUUUACAUGUCGACUAA- 3' (SEQ ID NO: 66) are loaded into particles as described previously.
  • six animals are sacrificed at 4 hours, 1 day, 3 days, 7 days, 10 days, 14 days, 21 days, and 28 days following injection and livers are removed and stored at 4°C in RNA Later solution (Ambion) for subsequent mRNA purification and analysis.
  • a total of 12 non-injected na ⁇ ve animals are also sacrificed and livers are removed for use as control animals in
  • livers are removed from RNALater storage solution and 20 mg tissue samples are dissected, weighed and placed into 600 ⁇ l RLT lysis buffer (Qiagen) with b-mercaptoethanol (BME). Tissues are then lysed using a Tissue Lyser (Qiagen) at 30 hertz for 2 minutes. Total RNA is then purified from individual samples using Qiagen RNEasy columns on a QiaCube (Qiagen) automated RNA purification system as suggested by the manufacturer. Qiashredders and on-column DNase I (Qiagen) digestion steps are also conducted (included in automated RNA preparation protocol).
  • RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad). cDNA is added to SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ real-time qPCR machines (BioRad).
  • qPCR quantitative real-time qPCR
  • qPCR experiments include pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p-dehydrogenase (GAPDH), Cyclophillin A, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase (YWHAZ), as well as pre-designed and pre-validated primers specific for the mouse Factor VII mRNA sequence.
  • Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ⁇ Ct-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of FVII mRNA expression to the geometric mean of the three selected housekeeping genes.
  • Example 25 Angiotensinogen Inhibition in Mouse AML12 Cells
  • Mouse AML12 cells are grown in DMEM with 10% fetal bovine serum, insulin/transferring/selenium , 2mM 1-glutamine, and penicillin/streptomycin at 37 0 C and 5% CO2. Cells are seeded in 96-well plastic plates at -50,000 cells/well and allowed to settle overnight. The following day, when cells have reached > 90% confluency, therapeutic particles, DharmaFECT, and PBS are added to cells. Chimerasomes and PBS are added at a volume of 25 ⁇ l to 75 ⁇ l of complete media for a total of 100 ⁇ l /well.
  • Angiotensinogen inhibitory dsRNA which has the following sequence: sense 5'- UGUUGUUC AGAUUUGCCUCCGCACC-3' (SEQ ID NO: 67) and antisense 5'-
  • Total RNA is purified from individual samples using Qiagen RNEasy columns on a QiaCube (Qiagen) automated RNA purification system. Qiashredders and on-column DNase I (Qiagen) digestion steps are also conducted (included in automated RNA preparation protocol). Following RNA purification, total RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad).
  • RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad).
  • cDNA is added to SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ real-time qPCR machines (BioRad). Included in all qPCR experiments are pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p-dehydrogenase (GAPDH), Cyclophillin A, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase (YWHAZ), as well as pre-designed and pre-validated primers specific for angiotensinogen mRNA.
  • GPDH glyceraldehydes-3-p-dehydrogenase
  • Cyclophillin A Cyclophillin A
  • YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase
  • Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ⁇ Ct-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of angiotensinogen mRNA expression to the geometric mean of the three housekeeping genes, GAPDH, Cyclophilin A, and YWHAZ.
  • the instant example describes a general method for measuring the endotoxin level in therapeutic particle preparations.
  • Endotoxin measurement is based on the Limulus Amebocyte Lysate Pyrogent Plus Single Test Kit (Lonza, US License No. 1701, Catalog No. N289-06).
  • the endotoxin vial is reconstituted with 1.0 ml of LAL reagent water (Lonza #W50-640) and vortexed for at least 15 minutes.
  • Endotoxin is diluted with the LAL reagent water to a concentration of lEU/ml.
  • 0.25 ml of an endotoxin standard that contains twice the labeled minimum sensitivity is used.
  • 0.23 ml of LAL reagent water is used.
  • sample serial dilutions are prepared in duplicates, beginning with a 1:4 dilution and end with a 1:64 dilution of sample:LAL reagent water. 0.25 ml of each sample is added to the test vial. Mix the samples by tilting and gently swirling the vial until the contents are in solution. Each vial of sample is incubated for 60 minutes (+/- 2 minutes) at 37°C (+/- I 0 C). At the end of the incubation period, each vial is carefully removed and inverted 180 degrees. A positive reaction is characterized by the formation of a firm gel that remains intact momentarily when the tube is inverted, which should be observed in the positive sample control vial. A negative test is characterized by the absence of solid clot after inversion. The lysate may show an increase in turbidity or viscosity. This is considered a negative result.
  • the endotoxin concentration is calculated by the multiple of the lysate sensitivity and the geometric mean of the endpoint:
  • Results from an endotoxin analysis of mFVII-containing therapeutic particles are shown below. The results indicate that there are no endotoxin contamination in the therapeutic particles.

Abstract

Chimeric therapeutics are disclosed that include a modified viral core protein and a nucleic acid bound to the modified viral core protein. In some embodiments, the nucleic acid may be substantially homologous to a specific gene target. In some embodiments, the nucleic acid bound to the modified viral core protein is substantially non-immunogenic.

Description

CHIMERIC THERAPEUTICS, COMPOSITIONS, AND METHODS FOR USING SAME
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of and priority to U.S. Provisional Application
No. 61/103,835, filed October 8, 2008; the disclosure of which is incorporated herein by reference in its entirety.
BACKGROUND
[0002] Gene silencing using nucleic acids such as interfering RNA has emerged as a powerful tool, and the potential for therapeutic applications using nucleic acids for gene modulation, e.g. silencing and knockdown of disease targets, is extensive.
[0003] Effective therapeutics that include nucleic acids such as interfering RNA may require stability in order to reach target cells or targets before the therapeutic is degraded or excreted. For example, such therapeutics must get into the target cells, link up with a intracellular target, and exert a therapeutic effect. In order to be effective, such therapeutics should exert enough of an effect to improve the health of the person taking it. Further, therapeutics that include nucleic acid should be effective without causing significant toxic effects in for example, tissues. [0004] Many proposed therapeutic agents have not been successful because of a limited ability to reach the target tissue. Further, some agents can be taken up by cells, and therefore may not allow efficient drug accumulation at a target site in a patient. Other proposed agents are unsuccessful because of premature loss of efficacy once administered, due for example, to rapid clearance and/or rapid metabolism. For example, protein and nucleic acid therapeutics are typically administered intravenously due to their instability at a high pH in e.g. the stomach after oral administration.
[0005] Viral core proteins, such as wild type hepatitis C, human papilloma virus type 6 Ll and L2, and/or cowpea chlorotic mottle virus coat protein may form a capsid with a terminal tail and/or an inward facing surface. However, such wild type viral core proteins may be unsuitable for use in therapeutics in part because of uncertainty in binding properties with e.g. a nucleic acid that targets a specific gene of interest. [0006] As such, there is an on-going need for nucleic acid based therapeutics that are long lasting and provide effective treatment for diseases and disorders associated with gene targets.
SUMMARY
[0007] The present disclosure is generally directed, at least in part, to chimeric therapeutics, e.g. chimeric proteins that may include a protein and a nucleic acid, and/or particles and/or compositions that include the disclosed therapeutic chimerics. [0008] In an embodiment, a protein capable of forming a capsid is provided that includes a structural core portion chosen from the structural core portion of a HPV, SV40, CCMV, DGNNV, TBSV, Norwalk Virus, and HCV; and a modified portion capable of binding to a nucleic acid with a binding affinity that allows release of said nucleic acid when said protein bound to said polynucleotide is administered in vivo. For example, a modified portion may be a modified C-terminal tail portion and/or a modified N-terminal tail portion, for example, a modified tail portion comprises about 4 to about 30 lysines, or may include a lysine domain of about 4 to about 30 lysines, or about 5 to about 20 lysines in length. In some embodiments, a modified tail portion comprises a histidine tag of about 1 to about 10 histidines in length. Modified tail portions may further comprise a linker segment. Also disclosed herein are nucleic acids encoding disclosed proteins.
[0009] In another embodiment, disclosed is a chimeric therapeutic comprising a modified viral core protein chosen from HPV, SV40, CCMV, DGNNV, TBSV, Norwalk Virus, and HCV, having a modified tail portion; and a nucleic acid bound to said modified viral core protein.
[0010] The nucleic acid bound to a modified viral core protein of a disclosed chimeric therapeutic may have a binding affinity of about 50 nM to about 500 nM, at 2OmM NaHCO3, and a pH of 9.5, or about 55 nM to about 400 nM, at 2OmM NaHCO3, and a pH of 9.5, and/or about 50 nM to about 500 nM, at 2OmM (CH2OH)3CNH2, and a pH of 7.7. In some embodiments, the nucleic acid of a disclosed chimeric therapeutic is substantially bound to the modified viral core protein by Coulombic interactions.
[0011] The disclosed chimeric therapeutics, compositions, and/or particles may be substantially free of nuclease and/or substantially free of endogenous nucleic acids. [0012] In some embodiments, a disclosed chimeric therapeutic and/or particle having a nucleic acid bound to a viral core protein may be substantially protected from serum degradation when administered in vivo, for example, a nucleic acid bound to a viral core protein may be substantially protected from serum degradation for at least two weeks when a disclosed therapeutic chimeric and/or particle and/or composition is exposed at 370C to a composition comprising a 1:1 weight ratio of human serum to water.
[0013] Disclosed viral core proteins may include a modified structural core portion comprises a conjugation site allowing attachment of a chemical linker moiety and/or a modified structural core portion may comprise one or more stability modifications [0014] Disclosed viral core proteins may include a modified tail portion that comprises about 10 to about 35 amino acids. In some embodiments, a modified tail portion comprises truncations, substitutions and/or additions of amino acids as compared to a wild type tail portion. For example, a modified tail portion may include about 4 to about 30 lysines, e.g., may include a lysine domain of about 5 to about 20 lysines, e.g. about 9 lysines. In some embodiments, a disclosed modified tail portion may comprise a histidine tag of about 1 to about 10 histidines, e.g. about 5 to about 6 histidines. Disclosed modified tail portions may further comprise a linker segment comprising about 1 to about 20 amino acids.
[0015] The chimeric therapeutics disclosed herein may include a nucleic acid that is e.g., an inhibiting nucleic acid, and/or is chemically modified, e.g. has a thiophosphate linkage. Contemplated nucleic acids that may e.g. form part of disclosed chimeric therapeutics, particles and/or compositions include double stranded RNA, antisense nucleic acid, hairpin RNA, and microRNA. In some embodiments, a contemplated nucleic acid may be about 25 to about 44 bases in length, or about 10 to about 30 bases in length, or about 19 to about 23 bases in length.
[0016] Disclosed herein are compositions that include disclosed particles and/or chimeric therapeutics and a pharmaceutically acceptable carrier.
[0017] For example, disclosed herein is a therapeutic composition that includes a particle formed from a plurality of disclosed chimeric therapeutics, wherein the particle further comprises a coating; and a pharmaceutically acceptable excipient. In another embodiment, a therapeutic composition is provided that comprises: a particle formed from at least: i) a first discrete number of modified viral core proteins; and ii) a second discrete number of nucleic acids each bound to one of said modified viral core protein. In some embodiments, the nucleic acids bound to said modified viral core proteins may be substantially nonimmunogenic. In other embodiments, disclosed particles may include optionally, a coating associated with said particle and/or a pharmaceutically acceptable excipient. The first discrete number may be about, for example, 150 to about 600, for example, the first discrete number may be about 500, or about 343, or about 164, or about 313, or about 336, or about 510, or about 171. The second discrete number may be about, for example, 2 to about 60, or about 8 to about 20, or about 14 to about 18.
[0018] In another embodiment, a therapeutic particle is provided that includes a plurality of viral core proteins each comprising a structural core portion and a modified tail portion, wherein the structural core portions form a capsid; and the modified tail portions are substantially disposed within said capsid; and a plurality of nucleic acids, bound to said modified tail portion, wherein the nucleic acids are resistant to degradation with a nuclease when said particle is placed in an aqueous solution. For example, a particle comprises about 180 to about 250 viral core proteins, or about 170 to about 190 viral core proteins. In another embodiment, the particle includes about 3 to about 50 nucleic acids, or about 6 to about 28 nucleic acids. A chemical linker moiety, in some embodiments, may be bound to the capsid, e.g., a chemical linker moiety may be formed by contacting said capsid with PE-maleimide.
[0019] A coating may be provided, in some embodiments, that is e.g., associated with a disclosed particle, and may include one or more lipids. For example, in an embodiment, at least one lipid molecule may be covalently bound through lipid linker moiety to one of the viral core proteins that form e.g., the particle. Disclosed coatings may include, cholesterol or one or more neutral lipids. Claims appended to this disclosure are incorporated by reference and form part of this disclosure.
BRIEF DESCRIPTION OF THE DRAWINGS [0020] FIGURE 1 is a schematic depicting phosphatidyl ethanolamine (PE) conjugation to an exemplary lipid linker moiety.
[0021] FIGURE 2 is a schematic depicting conjugating a maleimide-containing linker on a lipid, to a sulfhydryl-containing protein.
[0022] FIGURE 3 is a flow diagram depicting the construction of a therapeutic particle. [0023] FIGURE 4 depicts results from a capsid stability assay. [0024] FIGURE 5 is a quantitative representation of the results of a nuclease protection assay.
[0025] FIGURE 6 is a quantitative representation of the results of a serum stability assay.
[0026] FIGURE 7 is line graph depicting the binding curve for K9 mutants. [0027] FIGURE 8 is a line graph depicting the binding curves for K7 and KI l mutants.
[0028] FIGURE 9 depicts a chromatogram obtained by a purification method.
[0029] FIGURE 10 depicts a particle size measurement.
DETAILED DESCRIPTION
[0030] The present disclosure is generally directed, at least in part, to chimeric therapeutics, e.g. a therapeutic that includes a nucleic acid, e.g. an inhibitory nucleic acid, bound to a modified protein, and particles and/or compositions that include such chimeric therapeutics.
[0031] Before further description of the present invention, certain terms employed in the specification, examples and appended claims are collected here. These definitions should be read in light of the remainder of the disclosure and understood as by a person of skill in the art. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art.
Definitions
[0032] The term "amphipathic lipid" refers, in part, to any suitable material wherein the hydrophobic portion of the lipid material orients into a hydrophobic phase, while the hydrophilic portion orients toward the aqueous phase. Hydrophilic characteristics derive from the presence of polar or charged groups such as carbohydrates, phosphate, carboxylic, sulfato, amino, sulfhydryl, nitro, hydroxyl, and other like groups. Hydrophobicity can be conferred by the inclusion of apolar groups that include, but are not limited to, long chain saturated and unsaturated aliphatic hydrocarbon groups and such groups substituted by one or more aromatic, cycloaliphatic or heterocyclic group(s). Examples of amphipathic compounds include, but are not limited to, phospholipids, aminolipids and sphingolipids. Representative examples of phospholipids include, but are not limited to, phosphatidylcholine such as egg phosphatidylcholine or hydrogenated soy phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, phosphatidic acid, pahnitoyloleoyl phosphatidylcholine, lysophosphatidylcholine, lysophosphatidylethanolamine, dipalmitoylphosphatidylcholine, dioleoylphosphatidylcholine, distearoylphosphatidylcholine, phosphatidyl glycerol, monosialoganlgolioside, spingomyelin, dimyristoylphosphatidylcholine, and dilinoleoylphosphatidylcholine. Other compounds lacking in phosphorus, such as sphingolipid, glycosphingolipid families, diacylglycerols, and β-acyloxyacids, are also within the group designated as amphipathic lipids. Additionally, the amphipathic lipid described above can be mixed with other lipids including triglycerides and sterols.
[0033] The term "anionic lipid" refers to any lipid that is negatively charged at physiological pH. These lipids include, but are not limited to, phosphatidylglycerols, cardiolipins, diacylphosphatidylserines, diacylphosphatidic acids, N-dodecanoyl phosphatidylethanolamines, N-succinyl phosphatidylethanolamines, N- glutarylphosphatidylethanolamines, lysylphosphatidylglycerols, palmitoyloleyolphosphatidylglycerol (POPG), and other anionic modifying groups joined to neutral lipids.
[0034] The term "cationic lipid" refers to any of a number of lipid species that carry a net positive charge at a selected pH, such as physiological pH (e.g., pH of about 7.0). Examples of cationic lipids include, but are not limited to, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), dioctadecyldimethylammonium (DODMA), distearyldimethylammonium (DSDMA), N-(l-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N-(l-(2,3-dioleoyloxy)propyl)- N,N,N-trimethylammonium chloride (DOTAP), 3-(N-(N',N'-dimethylaminoethane)- carbamoyl)cholesterol (DC-Choi), N-( 1 ,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N- hydroxyethyl ammonium bromide (DMRIE), l,2-dilinoleyloxy-N,N-dimethylaminopropane (DLinDMA), l,2-dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA), and mixtures thereof. In certain embodiments, anionic lipids can be neutral on the surface with an internal negative charge.
[0035] An "effective amount" or "therapeutically effective amount" of a therapeutic, composition or particle contemplated herein is an amount sufficient to produce a desired effect, e.g., inhibition of expression of a target in comparison to the normal expression level detected in the absence of administration. The therapeutically effective amount will vary depending upon the subject and disease condition being treated, the rate of target transcript turnover, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like. For example, certain compositions of the present invention may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.
[0036] The term "gene" refers to a nucleic acid (e.g., DNA or RNA) sequence that comprises partial length or entire length coding sequences necessary for the production of a polypeptide or precursor polypeptide.
[0037] The term "inhibitory nucleic acid" refers to a single-stranded or double- stranded RNA, siRNA (small interfering RNA), shRNA (short hairpin RNA), or antisense RNA, or a portion thereof, or an analog or mimetic thereof, that when administered to a mammal results in a decrease (e.g., by 10%, 25%, 50%, 75%, 90%, 95%, or 100%) in the expression of a target.
Typically, an inhibitory nucleic acid comprises or corresponds to at least a portion of a target nucleic acid or gene, or an ortholog thereof, or comprises at least a portion of the complementary strand of a target nucleic acid or gene. An inhibitory nucleic acid typically has substantial or complete identity or homology (e.g. 60%, 70%, 80%, 85%, 90%, 95%, 99% or
100%) to the target nucleic acid.
[0038] The term "lipid" refers to a group of organic compounds that include, but are not limited to, esters of fatty acids and are characterized by being insoluble in water, but soluble in many organic solvents. They are usually divided into at least three classes: (1) "simple lipids," which include fats and oils as well as waxes; (2) "compound lipids," which include phospholipids and glycolipids; and (3) "derived lipids" such as steroids.
[0039] The term "modulation" is art-recognized and refers to up regulation (i.e., activation or stimulation), down regulation (i.e., inhibition or suppression) of a response, or the two in combination or apart.
[0040] The term "neutral lipid" refers to any of a number of lipid species that exist either in an uncharged or neutral zwitterionic form at a selected pH. At physiological pH, such lipids include, for example, diacylphosphatidylcholine, diacylphosphatidylethanolamine, ceramide, sphingomyelin, cephalin, cholesterol, cerebrosides, and diacylglycerols. [0041] The term "nucleic acid" as used herein refers to a polymer containing at least two deoxyribonucleotides or ribonucleotides in either single- or double- stranded form and includes DNA and RNA. DNA may be in the form of, e.g., antisense molecules, plasmid DNA, pre- condensed DNA, a PCR product, vectors (Pl, PAC, BAC, YAC, artificial chromosomes), expression cassettes, chromosomal DNA, or derivatives and combinations of these groups. RNA may be in the form of inhibitory RNA, mRNA, tRNA, rRNA, tRNA, vRNA, and combinations thereof. Nucleic acids include nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, and which have similar binding properties as the reference nucleic acid. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2'-O-methyl ribonucleotides, and peptide-nucleic acids (PNAs). "Nucleotides" contain a deoxyribose (DNA) or ribose (RNA), a sugar, a nitrogenous base, and a phosphate group or analog thereof. Nucleotides are linked together through the phosphate groups. "Bases" include purines and pyrimidines, which further include natural compounds adenine, thymine, guanine, cytosine, uracil, inosine, and natural analogs, and synthetic derivatives of purines and pyrimidines, which include, but are not limited to, modifications which place new reactive groups such as, but not limited to, amines, alcohols, thiols, carboxylates, and alkylhalides.
[0042] A "patient," "subject" or "host" to be treated by a disclosed method may mean either a human or non-human animal.
[0043] The term "pharmaceutically acceptable excipient" is art-recognized and refers to a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent, involved in carrying or transporting any subject composition or component thereof from one organ, or portion of the body, to another organ, or portion of the body. Each excipient must be "acceptable" in the sense of being compatible with the subject composition and its components and not injurious to the patient. Some examples of materials which may serve as pharmaceutically acceptable excipients include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21) other non-toxic compatible substances employed in pharmaceutical formulations.
[0044] The term "portion" when used in reference to a protein refers to fragments of that protein.
[0045] "Target" refers to a nucleic acid or variants thereof required for expression of a polypeptide that is the site or potential site of therapeutic intervention by a therapeutic agent; or a non-peptide entity including a microorganism, virus, bacterium, or single cell parasite (wherein the entire genome of a virus may be regarded as a target); and/or a naturally occurring interfering RNA or microRNA or precursor thereof. For example, target may refer to the sequence of nucleotides corresponding to the portion of a gene's coding mRNA. [0046] "Serum- stable" in relation to nucleic acid-lipid particles means that the particle is not significantly degraded after exposure to a serum or nuclease assay that would significantly degrade free DNA or RNA. Suitable assays include, for example, a standard serum assay, a DNase assay, or an RNase assay.
Chimeric Therapeutics [0047] The chimeric therapeutics disclosed herein may be capable of forming a particle, which may be a particle, e.g. a nanoparticle, for example, a plurality of disclosed chimeric therapeutics may self- assemble in to a particle or capsid. Such therapeutic chimerics may include a modified viral core protein with a nucleic acid associated with, e.g. bound to, the modified viral core protein. The nucleic acid may be bound to the modified viral core protein by substantially Coulombic forces, or in another embodiment, by Coulombic forces and/or hydrogen bonding. [0048] Nucleic acids associated with a disclosed viral core protein may be, e.g., substantially homologous to a target, e.g. a target gene. In some embodiments, the nucleic acid, when bound to the modified viral core protein, may be substantially non-immunogenic. For example, a nucleic acid bound to a modified viral core protein may be substantially less immunogenic as compared to an identical unbound nucleic acid.
[0049] In another embodiment, a chimeric therapeutic is provided that includes an e.g. modified viral core protein and a nucleic acid bound to the modified viral core protein (e.g., to a modified tail portion of the viral core protein) with a binding affinity that allows release of the nucleic acid when the chimeric therapeutic is administered in vivo. [0050] The nucleic acid of a chimeric therapeutic, wherein bound to a disclosed modified viral core protein, may be resistant in an aqueous solution to degradation with a nuclease, e.g. benzoase. For example, a nucleic acid bound to a disclosed modified viral core protein at 1.9 units/nmole, 100 unit/nmole, 500 units/nmole or 945 units/nmole and incubated for 1 hour at room temperature does not substantially degrade as compared to an identical, but unbound, nucleic acid. In other embodiments, a nucleic acid bound to a disclosed modified viral core protein is substantially protected from serum degradation in vivo or in vitro, for example, when a chimeric therapeutic is exposed at 370C to a composition comprising a 1:1 weight ratio of human serum to water.
[0051] Disclosed chimeric therapeutics may be substantially free of nuclease and/or may be substantially free of endogenous nucleic acids.
[0052] Also provided herein is a therapeutic multiplex that includes a plurality of capsids, such as disclosed herein, for example, wherein each capsid comprises a viral core protein having a structural core portion and a tail portion, and a nucleic acid bound to said tail portion. A coating may substantially surround two or more of capsids, e.g. may surround about six capsids.
Viral Core Proteins
[0053] Any viral core protein that is capable, together with other viral core proteins, of self-assembling into a capsid is suitable for use in the disclosed therapeutics. Non-limiting examples of self-assembling core proteins include human and duck Hepatitis B Virus core protein, Hepatitis C Virus core protein (HCV), Human Papillomavirus (HPV), Simian Virus 40 (SV40), Cowpea Chlorotic Mottle Virus (CCMV), Dragon Grouper Nervous Necrosis Virus (DGNNV), Tomato Bushy Stunt Virus (TBSV), and Norwalk Virus. It may be appreciated that different strains of viral proteins may have slight variations in sequences, and that any strain can be utilized. Exemplary sequences of HPV, SV40, CCMV, DGNNV, TBSV, Norwalk Virus, and HCV are listed below. [0054] Human Papillomavirus (HPV) Type 16 Ll Sequence (Swiss-Prot Accession #
P03101): (SEQ ID NO: 1)
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIH LPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGI SGHPLLNKLDDTENASAYAANAGVDNRECI SMDYK QTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSI CKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDA QIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAI STSETTYKNTNFKEYLRHGEEYDLQFIFQLCK ITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFS ADLDQFPLGRKFLLQLGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKL
[0055] Simian Virus 40 (SV40) VPl sequence (Uni-Prot Accession # P03087): (SEQ ID
NO: 2)
MKMAPTKRKGSCPGAAPKKPKEPVQVPKLVIKGGIEVLGVKTGVDSFTEVECFLNPQMGNPDEHQKGLSKSLAAEK QFTDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQKTHENGAGKPIQGSNF HFFAVGGEPLELQGVLANYRTKYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKNENTRYFGTYT GGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNTSGTQQWKGLPRYFKITLRKRSVKNPYPI SFLLSDLINRRTQRVDGQPMIGMSSQVEEVRVYEDTEELPGDPDMIRYIDEFGQTTTRMQ
[0056] Cowpea Chlorotic Mottle Virus (CCMV) (Uni-prot Accession # P03601): (SEQ
ID NO: 3) MSTVGTGKLTRAQRRAAARKNKRNTRVVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPN ELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTA DLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY
[0057] Dragon Grouper Nervous Necrosis Virus (DGNNV) (GenBank Accession # AF245004): (SEQ ID NO: 4)
MVRKGEKKLAKPPTTKAANPQPRRRANNRRRSNRTDAPVSKASTVTGFGRGTNDVHLSGMSRISQAVLPAGTGTDG YVVVDATIVPDLLPRLGHAARIFQRYAVETLEFEIQPMCPANTGGGYVAGFLPDPTDNDHTFDALQATRGAVVAKW WESRTVRPQYTRTLLWTSSGKEQRLTSPGRLILLCVGNNTDVVNVSVLCRWSVRLSVPSLETPEETTAPIMTQGSL YNDSLSTNDFKS ILLGSTPLDIAPDGAVFQLDRPLS IDYSLGTGDVDRAVYWHLKKFAGNAGTPAGWFRWGIWDNF NKTFTDGVAYYSDEQPRQILLPVGTVCTRVDSEN [0058] Tomato Bushy Stunt Virus (TBSV) (Swiss-Prot Accession # Pl 1689): (SEQ ID
NO: 5)
MAMVKRNNNTGMIPVSTKQLLALGAAAGATALQGFVKNNGMAIVEGAVDLTKRAYKAVRRRGGKKQQMIN
HVGGTGGAIMAPVAVTRQLVGSKPKFTGRTSGSVTVTHREYLSQVNNSTGFQVNGGIVGNLLQLNPLNGT LFSWLPAIASNFDQYTFNSVVLHYVPLCSTTEVGRVAIYFDKDSEDPEPADRVELANYSVLKETAPWAEA
MLRVPTDKIKRFCDDSSTSDHKLIDLGQLGIATYGGAGTNAVGDIFI SYSVTLYFPQPTNTLLSTRRLDL
INCTVSNLPSVVTFTSTGITSATVHCVRATRQNDVSLI
[0059] Norwalk Virus (Swiss-Prot Accession # Q83884): (SEQ ID NO: 6) MMMASKDATSSVDGASGAGQLVPEVNASDPLAMDPVAGSSTAVATAGQVNPIDPWIINNFVQAPQGEFTI SPNNTPGDVLFDLSLGPHLNPFLLHLSQMYNGWVGNMRVRIMLAGNAFTAGKI IVSCIPPGFGSHNLTIA QATLFPHVIADVRTLDPIEVPLEDVRNVLFHNNDRNQQTMRLVCMLYTPLRTGGGTGDSFVVAGRVMTCP SPDFNFLFLVPPTVEQKTRPFTLPNLPLSSLSNSRAPLPI SSMGI SPDNVQSVQFQNGRCTLDGRLVGTT PVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPD TFVPHLGS IQANGIGSGNYVGVLSWI SPPSHPSGSQVDLWKIPNYGSS ITEATHLAPSVYPPGFGEVLVF FMSKMPGPGAYNLPCLLPQEYI SHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASS GPQQLPINGVFVFVSWVSRFYQLKPVGTASSARGRLGLRR
[0060] Hepatitis C Virus core protein consensus sequence (HCV) (from Kunkel et al., 2001): (SEQ ID NO: 7)
MSTNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRSW AQPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFADLMGYIPLVGAPLGGVARALA HGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPASA
[0061] A modified viral core protein contemplated herein may include a structural core protein and a tail portion. For example, a modified viral core protein for use in the disclosed therapeutics may include a modified structural core portion and a tail portion, e.g., a carboxyl terminal tail portion and/or a N-terminal tail portion, or may include a structural core portion and a modified tail portion, or may include a modified structural core portion and a modified tail portion, e.g., a modified structural core portion and/or modified tail portion as compared to the wild-type viral core protein, such as discussed above. In some embodiments, the structural core portions of modified viral core proteins may form a capsid, and the tail portion of the modified viral core proteins may be substantially disposed within the capsid. In other embodiments, an inward facing surface of formed capsid may act as modification location.
[0062] For example, a modified viral core protein, e.g., a modified HPV core protein may include a modified structural core portion and a modified C-terminal tail portion. Such modifications can include alterations, truncations and/or mutations, etc. to the structural core portion and/or the modified tail portion of the viral core protein. Such modifications may enhance the structural and functional characteristics of the HPV C-protein and may provide more effective therapeutics, e.g., a modified viral core protein is bound to a nucleic acid, e.g., an inhibitory nucleic acid. In other embodiments, a modified e.g. C-terminal or N-terminal tail portion of a viral core protein (e.g. HPV) may provide a therapeutic that is substantially free of endogenous nucleic acids and/or substantially free of nuclease. These modifications to viral core protein can be made or engineered according to any method known in the art, including without limitation genetic engineering, chemical modifications, etc.
[0063] Modification to the viral core protein, for example, a viral core protein with a modified tail portion, may also optimize binding and release of a nucleic acid bound to a viral core protein. For example, the binding affinity of a nucleic acid bound to a disclosed modified viral core protein may be about 50 nM to about 500 nM, or about 55 nM to about 400 nM, at 2OmM NaHCO3, and a pH of 9.5, or may be about 50 nM to about 500 nM, or about 55 nM to about 400 nM, at 2OmM (CH2OH)3CNH2, and a pH of 7.7.
[0064] Disclosed viral core proteins can be expressed and purified using common molecular biology and biochemistry techniques. For example, recombinant expression vectors can be used which can be engineered to carry a viral core protein gene into a host cell to provide for expression of the viral core protein. Such vectors, for example, can be introduced into a host cell by transfection means including, but not limited to, heat shock, calcium phosphate, DEAE-dextran, electroporation or liposome-mediated transfer. Recombinant expression vectors include, but are not limited to, Escherichia coli based expression vectors such as BL21 (DE3) pLysS, COS cell-based expression vectors such as CDM8 or pDC201, or CHO cell-based expression vectors such as pED vectors. A C-protein gene coding region, for example, can be linked to one of any number of promoters in an expression vector that can be activated in the chosen cell line. In an embodiment, a cassette (capsid gene and promoter) is carried by a vector that contains a selectable marker such that cells receiving the vector can be identified.
[0065] For example, promoters to express the capsid proteins within a cell line can be drawn from those that are functionally active within the host cell. Such promoters can include, but are not limited to, a T7 promoter, a CMV promoter, a SV40 early promoter, a herpes TK promoter, and others known in recombinant DNA technology. Inducible promoters can be used, and include promoters such as metallothionine promoter (MT), mouse mammary tumor virus promoter (MMTV), and others known to those skilled in the art. Exemplary selectable markers and their attendant selection agents can be drawn, for example, from the group including, but not limited to, ampicillin, kanamycin, aminoglycoside phosphotransferase/G418, hygromycin-B phosphotransferase/hygromycin-B, and amplifiable selection markers such as dihydrofolate reductase/methotrexate and others known to skilled practitioners.
[0066] A variety of eukaryotic, prokaryotic, insect, plant and yeast expression vector systems (e.g., vectors which contain the necessary elements for directing the replication, transcription, and translation of viral core protein coding sequences) can be utilized by those skilled in the art to express viral core protein coding sequences. These include but are not limited to microorganisms such as bacteria transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing the capsid protein coding sequences; yeast transformed with recombinant yeast expression vectors containing the capsid protein coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the capsid protein coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing the capsid protein coding sequences.
A. Modified Tail Portions
[0067] Various modifications of the terminal tails of the disclosed viral core protein are contemplated. For example, the C-terminal tail of HPV core protein, can be engineered to, for example, provide appropriate properties for binding a nucleic acid to the modified viral core protein. For example, a therapeutic chimeric is provided that includes a viral core protein with a modified tail portion and a nucleic acid associated with, e.g., bound to the modified tail portion. HPV
[0068] Wild type HPV is typically a non-enveloped, dsDNA virus that forms about a 60 nm diameter capsid. The capsid is typically formed by 72 pentamers of the major virus coat protein, Ll, in association with the minor virus coat protein, L2. The Ll protein is 531 amino acids of which the C-terminal 31 amino acids are disordered in the crystal structure of the capsid and typically project toward the interior of the capsid. This C-terminal portion of the HPV viral core protein, in some embodiments, functions as a nucleic acid binding domain of the HPV virion.
SEQ ID NO: 8: HPV C-terminal tail amino acid sequence 501 to 531
KAKPKFTLGKRKATPTTSSTSTTAKRKKRKL [0069] This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a HPV structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
SV40
[0070] Wild type SV40 forms an about 45 nm diameter, non-enveloped virus that in some embodiments is highly similar to HPV. The outer shell of the capsid is typically formed by pentamers of the major capsid protein VPl while proteins VP2 and VP3 form a bridge between the outer shell and the dsDNA viral genome. The VPl protein is typically about 364 amino acids of which the first N-terminal 21 amino acids are disordered in the crystal structure.
SEQ ID NO: 9: SV40 N-terminal tail amino acid sequence 1 to 21 MKMAPTKRKGSCPGAAPKKPK
[0071] This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions. For example, the first 21 amino acid tail may be removed and replaced by polylysine domains as discussed below.
CCMV
[0072] CCMV is a 28 nm diameter virus composed of 180 capsid protein subunits. The capsid protein is typically about 190 amino acids of which the first N-terminal 26 amino acids are disordered in the crystal structure and may interact with the viral RNA. (G. Vriend, BJ. M. Verduin, M. A. Hemminga, /. MoI. Biol, 191, 453-460 (1986)). Removal of these residues followed by replacement with polylysine segments plus linker regions, may, in some embodiments, serve as alternative nucleic acid binding domains. SEQ ID NO: 10: CCMV N-terminal tail amino acid sequence 1 to 26
MSTVGTGKLTRAQRRAAARKNKRNTR
[0073] This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
DGNNV
[0074] Wild type DGNNV is a 27 nm diameter non-enveloped virus composed of 180 capsid protein subunits. The capsid protein is typically about 338 amino acids of which the first 25 N-terminal amino acids are known to bind to the RNA genome of the virus. It is possible, in some embodiments, to e.g. remove and/or alter the first 25 amino acids of the capsid protein and e.g., replace it with a modified tail portion to construct alternative nucleic acid binding domains.
SEQ ID NO: 11: CCMV N-terminal tail amino acid sequence 1 to 25 MVRKGEKKLAKPPTTKAANPQPRRR
[0075] This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
TBSV [0076] Wild type TBSV is a 34 nm diameter virus composed of 180 capsid protein subunits. The capsid protein is typically about 388 amino acids of which the first 65 N- terminal amino acids are known to bind to the RNA genome of the virus. In some embodiments, up to 52 amino acids from the N-terminus of the capsid protein may be removed and/or altered and e.g., replaced with a modified tail portion to construct alternative nucleic acid binding domains.
SEQ ID NO: 12: TBSV N-terminal tail amino acid sequence 1 to 52 MAMVKRNNNTGMIPVSTKQLLALGAAAGATALQGFVKNNGMAIVEGAVDLTK
[0077] This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions. Norwalk Virus
[0078] Wild type Norwalk virus is a 38 nm virus composed of 180 capsid protein subunits. The capsid protein is typically about 530 amino acids of which the first 27 N- terminal amino acids is presumed to hang inside the viral capsid and are either all or partially disordered in the crystal structure. Deletion of the first 20 amino acids of the capsid protein followed by insertion of a poly-lysine region with varying linkers, could provide an alternative nucleic-acid binding domain. SEQ ID NO: 13: Norwalk virus N-terminal tail amino acid sequence 1 to 20
MMMASKDATSSVDGASGAGQ
[0079] This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions.
HCV
[0080] Wild type HCV is an enveloped virus that is 60 nm in diameter. The core protein
(P21) is cleaved from a P23 precursor by a signal peptidase in the endoplasmic reticulum. There has been some debate as to the exact length of the P21 protein following cleavage, but a recent report has shown that cleavage occurs following residue 177 (Ogino, et al., J. Biol. Chem., 281, 27679-27691, (2006)). The RNA binding domain of the sequence has been located to the first 75 N-terminal amino acids (Santolini, et al., J. Virol, 68, 3631-3641, (1994)). Since there is no structural information available for the core protein of the HCV capsid, one can posit that removal of a subset of the first N-terminal 75 amino acids (perhaps the first 20) of the core protein and replacement with varying poly-lysine domains followed by variable linker regions could serve as an alternative nucleic acid binding domain.
SEQ ID NO: 14: HCV N-terminal tail amino acid sequence 1 to 20 MSTNPKPQRKTKRNTNRRPQ [0081] This wild type tail can be modified, truncated, and/or mutated to provide a modified tail portion, that, together with a structural core portion, provides a complete viral core protein for use in the disclosed therapeutic chimerics, particles, and compositions. Poly-Lysine Tail
[0082] In some embodiments, a modified tail portion, e.g., a modified C-terminal tail portion and/or a modified N-terminal tail portion may include a modification that includes one or more poly-lysines. For example, the modified tail portion may include about 4 to about 30 lysines, or about 5 to about 20 lysines, e.g., about 7, 8, 9, or 10 lysines. [0083] In some embodiments, the modified tail portion may include one or more lysine domains. For example, each poly-lysine domain may comprise about one to about thirty lysine residues. In some embodiments the poly-lysine domain may comprise about 5 lysine residues to about 20 lysine residues. When more than one polylysine domain is present, the poly-lysine domains can be separated by about 1 to about 20 amino acid residues. In some embodiments, where more than one polylysine domain is present the each poly-lysine domain can comprise about 4 lysine residues to about 20 lysine residues (or any specific amino acid length disposed with the range). In some embodiments, at least four or at least five consecutive lysine residues are included in a modified C-terminal and/or N-terminal tail portion.
[0084] Poly-lysines and poly-lysine domains and/or a polyhistidine tag can form part of a modified C-terminal tail and/or N-terminal tail separately or in combination. A polyhistidine tag may, in some embodiments, facilitate purification of the proteins.
[0085] Exemplary modified C-terminal and/or N-terminal tail portions include those having e.g., 5 lysines (K5), 7 lysines (K7), 9 lysines (K9), 10 lysines (KIO), 11 lysines (KU), 13 lysines (K13), or 20 lysines (K20). Other exemplary modified tail portions include those with a poly-lysine region with nine lysines alternating with a poly-alanine region with nine alanines (KA9), a poly-lysine region with nine lysines alternating with a poly- glycine region with nine glycines (KG9) and a poly-lysine region with nine lysines interrupted by a sequence of at least four amino acids between the fourth and fifth lysines (K4-5). In some embodiments, an about four amino acid stretch between the fourth and fifth lysines of the K4-5 tail may be amino acids Ser-Gln-Ser-Pro. For example, a modified tail portion may be represented by: KLAAA [ KKKKK ] 1LE [ H ] 3 SEQ ID NO: 15 wherein i is an integer from 4 to 21, and j is an integer from 0 to 10. For example, i may be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20; j may be 0, 1, 2, 3, 4, 5 or more. Such modified tail portion may form part of a modified viral core protein. For example, exemplary modified viral core proteins provided herein include:
Modified HPV K5 (SEQ ID NO: 16)
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIH LPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGI SGHPLLNKLDDTENASAYAANAGVDNRECI SMDYK QTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSI CKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDA QIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAI STSETTYKNTNFKEYLRHGEEYDLQFIFQLCK ITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFS ADLDQFPLGRKFLLQLGLDKLAAAKKKKKLEHHHHHH
Modified SV40 K5 (SEQ ID NO: 17) HHHHHHELKKKKKAAALKDEPVQVPKLVIKGGIEVLGVKTGVDSFTEVECFLNPQMGNPDEHQKGLSKSLAAEKQF TDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQKTHENGAGKPIQGSNFHF FAVGGEPLELQGVLANYRTKYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKNENTRYFGTYTGG ENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNTSGTQQWKGLPRYFKITLRKRSVKNPYPI SF LLSDLINRRTQRVDGQPMIGMSSQVEEVRVYEDTEELPGDPDMIRYIDEFGQTTTRMQ Modified CCMV K5 (SEQ ID NO: 18)
HHHHHHELKKKKKAAALKDVVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITI SLPNELSSERN KQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLY SSAALTEGDVIVHLEVEHVRPTFDDSFTPVY
Modified DGNNV K5 (SEQ ID NO: 19) HHHHHHELKKKKKAAALKDANNRRRSNRTDAPVSKASTVTGFGRGTNDVHLSGMSRISQAVLPAGTGTDGYVVVDA TIVPDLLPRLGHAARIFQRYAVETLEFEIQPMCPANTGGGYVAGFLPDPTDNDHTFDALQATRGAVVAKWWESRTV RPQYTRTLLWTSSGKEQRLTSPGRLILLCVGNNTDVVNVSVLCRWSVRLSVPSLETPEETTAPIMTQGSLYNDSLS TNDFKS ILLGSTPLDIAPDGAVFQLDRPLS IDYSLGTGDVDRAVYWHLKKFAGNAGTPAGWFRWGIWDNFNKTFTD GVAYYSDEQPRQILLPVGTVCTRVDSEN Modified TBSV K5 (SEQ ID NO: 20)
HHHHHHELKKKKKAAALKDRAYKAVRRRGGKKQQMINHVGGTGGAIMAPVAVTRQLVGSKPKFTGRTSGSVTVTHR EYLSQVNNSTGFQVNGGIVGNLLQLNPLNGTLFSWLPAIASNFDQYTFNSVVLHYVPLCSTTEVGRVAIYFDKDSE DPEPADRVELANYSVLKETAPWAEAMLRVPTDKIKRFCDDSSTSDHKLIDLGQLGIATYGGAGTNAVGDIFISYSV TLYFPQPTNTLLSTRRLDLAGALVTASGPGYLLVSRTATVLTMTFRATGTFVI SGTYRCLTATTLGLAGGVNVNS I TVVDNIGTDSAFFINCTVSNLPSVVTFTSTGITSATVHCVRATRQNDVSLI
Modified Norwalk Virus K5 (SEQ ID NO: 21) HHHHHHELKKKKKAAALKDLVPEVNASDPLAMDPVAGSSTAVATAGQVNPIDPWIINNFVQAPQGEFTI SPNNTPGDVLFDLSLGPHLNPFLLHLSQMYNGWVGNMRVRIMLAGNAFTAGKI IVSCIPPGFGSHNLTIA QATLFPHVIADVRTLDPIEVPLEDVRNVLFHNNDRNQQTMRLVCMLYTPLRTGGGTGDSFVVAGRVMTCP SPDFNFLFLVPPTVEQKTRPFTLPNLPLSSLSNSRAPLPI SSMGI SPDNVQSVQFQNGRCTLDGRLVGTT PVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPD TFVPHLGS IQANGIGSGNYVGVLSWI SPPSHPSGSQVDLWKIPNYGSS ITEATHLAPSVYPPGFGEVLVF FMSKMPGPGAYNLPCLLPQEYI SHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCV PNGASS GPQQLPINGVFVFVSWVSRFYQLKPVGTASSARGRLGLRR
Modified HCV K5: (SEQ ID NO: 22)
HHHHHHELKKKKKAAALKDDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRSWA QPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFADLMGYIPLVGAPLGGVARALAH GVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPASA
[0086] In other embodiments, a modified tail portion may be formed from alternating lysines, for example, a modified tail portion can include the sequence represented by;
DKLAA [ AK ] PLE [ H ] D (SEQ ID NO: 23) wherein p is an integer from 5 to 12, and j is an integer from 0 to 10. For example, p may be 5, 6, 7, 8, 9, 10, 11, or 12; j may be 0, 1, 2, 3, 4, 5 or more.
[0087] In some embodiments, mutations creating e.g., various poly-lysine domains of differing lengths can be engineered using any methods known in the art. In one embodiment, the core protein gene can be amplified via PCR and various numbers of lysine (or other) residues can be added.
Poly-Arginine Tail
[0088] In some embodiments, a modified tail portion includes one or more arginines. For example, the modified tail portion may include about 4 to about 30 arginines, or about 5 to about 20 arginines, e.g. about 7, 8, 9, or 10 arginines.
[0089] In some embodiments, the modified tail portion may include one or more arginine domains. When more than one poly-arginine domain is present, the poly-arginine domains can be separated by about 1 to about 20 amino acid residues. For example, each poly-arginine domain may comprise about one to about thirty arginine residues. In some embodiments, when more than one poly-arginine domain is present, the each poly-arginine domain can comprise about 4 arginine residues to about 20 arginine residues (or any specific amino acid length disposed with the range). In some embodiments, a modified C-terminal tail and/or N-terminal tail includes at least four or at least five consecutive arginine residues. In another embodiment, a modified C-terminal tail and/or N-terminal tail may include both arginines and lysines, e.g., may include both arginine and lysine domains.
[0090] Poly-arginine domains and/or a poly histidine tag can be added to the C-terminal tails separately or in combination. A poly histidine tag may, in some embodiments, facilitate purification of the proteins. Exemplary modified tail portions may include for example, 5 arginines (R5), 7 arginines (R7), 9 arginines (R9), 11 arginines (RI l), 13 arginines (R13), or 20 arginines (R20). Such modified tail portions may be represented by:
DKLAAA [ R ] qLE [ H ] : (SEQ ID NO: 24) wherein q is an integer from 4 to 21 or more, and j is an integer from 0 to 10. For example, q may be 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20; j may be 0, 1, 2, 3, 4, 5 or more.
[0091] Exemplary modified viral core proteins that include such modified tail portions include:
Modified HPV R5 (SEQ ID NO: 25) MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIH LPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGI SGHPLLNKLDDTENASAYAANAGVDNRECI SMDYK QTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSI CKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDA QIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAI STSETTYKNTNFKEYLRHGEEYDLQFIFQLCK ITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFS ADLDQFPLGRKFLLQLGLDKLAAARRRRRLEHHHHHH
Modified SV40 R5 (SEQ ID NO: 26)
HHHHHHELRRRRRAAALKDEPVQVPKLVIKGGIEVLGVKTGVDSFTEVECFLNPQMGNPDEHQKGLSKSLAAEKQF TDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQKTHENGAGKPIQGSNFHF FAVGGEPLELQGVLANYRTKYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKNENTRYFGTYTGG ENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNTSGTQQWKGLPRYFKITLRKRSVKNPYPI SF LLSDLINRRTQRVDGQPMIGMSSQVEEVRVYEDTEELPGDPDMIRYIDEFGQTTTRMQ
Modified CCMV R5 (SEQ ID NO: 27)
HHHHHHELRRRRRAAALKDVVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITI SLPNELSSERN KQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLY SSAALTEGDVIVHLEVEHVRPTFDDSFTPVY
Modified DGNNV R5 (SEQ ID NO: 28)
HHHHHHELRRRRRAAALKDANNRRRSNRTDAPVSKASTVTGFGRGTNDVHLSGMSRISQAVLPAGTGTDGYVVVDA TIVPDLLPRLGHAARIFQRYAVETLEFEIQPMCPANTGGGYVAGFLPDPTDNDHTFDALQATRGAVVAKWWESRTV RPQYTRTLLWTSSGKEQRLTSPGRLILLCVGNNTDVVNVSVLCRWSVRLSVPSLETPEETTAPIMTQGSLYNDSLS TNDFKS ILLGSTPLDIAPDGAVFQLDRPLS IDYSLGTGDVDRAVYWHLKKFAGNAGTPAGWFRWGIWDNFNKTFTD GVAYYSDEQPRQILLPVGTVCTRVDSEN Modified TBSV R5 (SEQ ID NO: 29)
HHHHHHELRRRRRAAALKDRAYKAVRRRGGKKQQMINHVGGTGGAIMAPVAVTRQLVGSKPKFTGRTSGSVTVTHR EYLSQVNNSTGFQVNGGIVGNLLQLNPLNGTLFSWLPAIASNFDQYTFNSVVLHYVPLCSTTEVGRVAIYFDKDSE DPEPADRVELANYSVLKETAPWAEAMLRVPTDKIKRFCDDSSTSDHKLIDLGQLGIATYGGAGTNAVGDIFISYSV TLYFPQPTNTLLSTRRLDLAGALVTASGPGYLLVSRTATVLTMTFRATGTFVI SGTYRCLTATTLGLAGGVNVNS I TVVDNIGTDSAFFINCTVSNLPSVVTFTSTGITSATVHCVRATRQNDVSLI
Modified Norwalk Virus R5 (SEQ ID NO: 30)
HHHHHHELRRRRRAAALKDLVPEVNASDPLAMDPVAGSSTAVATAGQVNPIDPWIINNFVQAPQGEFTI SPNNTPGDVLFDLSLGPHLNPFLLHLSQMYNGWVGNMRVRIMLAGNAFTAGKI IVSCIPPGFGSHNLTIA QATLFPHVIADVRTLDPIEVPLEDVRNVLFHNNDRNQQTMRLVCMLYTPLRTGGGTGDSFVVAGRVMTCP SPDFNFLFLVPPTVEQKTRPFTLPNLPLSSLSNSRAPLPI SSMGI SPDNVQSVQFQNGRCTLDGRLVGTT PVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPD TFVPHLGS IQANGIGSGNYVGVLSWI SPPSHPSGSQVDLWKIPNYGSS ITEATHLAPSVYPPGFGEVLVF FMSKMPGPGAYNLPCLLPQEYI SHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCV PNGASS GPQQLPINGVFVFVSWVSRFYQLKPVGTASSARGRLGLRR
Modified HCV R5 (SEQ ID NO: 31)
HHHHHHELRRRRRAAALKDDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRSWA QPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFADLMGYIPLVGAPLGGVARALAH GVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPASA
Truncation Mutations
[0092] In some embodiments, a modified tail portion includes one or more truncation mutations. For example, the modified tail portion may include truncations of about 3 to about 50 amino acids, about 5 to about 40 amino acids, e.g. about 10, about 20, or about 30 amino acids or more. Some modified tail portions may or may not include a histidine tag.
Linker Segment Mutations
[0093] A linker segment may be optionally present between e.g. a modified core portion and a modified tail portion. In some embodiments, the linker segment is about 3 amino acids to about 15 amino acids in length (or any specific amino acid length disposed with the range) and can link e.g. a poly-lysine and/or a polyarginine domain to an amino acid corresponding to the end of a structural core portion of a corresponding viral core protein, for example, to provide flexibility to a modified tail portion. In some embodiments, an e.g., poly-lysine and/or poly arginine domain can be followed by a poly-histidine tag and/or followed by an Xhol restriction site. The poly-histidine tag can include, in some embodiments, at least six histidine residues added to the C-terminal tail. For example, such linker segments may be represented by one of: [ SAG ] 3 (SEQ ID NO: 32)
[ TAG ] , (SEQ ID NO: 33)
[ GAG ] t (SEQ ID NO: 34) wherein r, s and t are, each independently, integers from 1 to 6 or more. [0094] Exemplary viral core proteins that include a linker segment can be represented by:
HPV Linker 1 K9 (SEQ ID NO: 35)
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIH LPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGI SGHPLLNKLDDTENASAYAANAGVDNRECI SMDYK QTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSI CKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDA QIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAI STSETTYKNTNFKEYLRHGEEYDLQFIFQLCK ITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFS ADLDQFPLGRKFLLQLGLSAGSAGKKKKKKKKKLEHHHHHH
SV40 Linker 1 K9 (SEQ ID NO: 36) HHHHHHELKKKKKKKKKGASGASEPVQVPKLVIKGGIEVLGVKTGVDSFTEVECFLNPQMGNPDEHQKGLSKSLAA EKQFTDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQKTHENGAGKPIQGS NFHFFAVGGEPLELQGVLANYRTKYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKNENTRYFGT YTGGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNTSGTQQWKGLPRYFKITLRKRSVKNPY PISFLLSDLINRRTQRVDGQPMIGMSSQVEEVRVYEDTEELPGDPDMIRYIDEFGQTTTRMQ CCMV Linker 1 K9 (SEQ ID NO: 37)
HHHHHHELKKKKKKKKKGASGASVVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAAEAKVTSAITISLPNELS SERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLT IYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY
DGNNV Linker 1 K9 (SEQ ID NO: 38) HHHHHHELKKKKKKKKKGASGASANNRRRSNRTDAPVSKASTVTGFGRGTNDVHLSGMSRISQAVLPAGTGTDGYV VVDATIVPDLLPRLGHAARIFQRYAVETLEFEIQPMCPANTGGGYVAGFLPDPTDNDHTFDALQATRGAVVAKWWE SRTVRPQYTRTLLWTSSGKEQRLTSPGRLILLCVGNNTDVVNVSVLCRWSVRLSVPSLETPEETTAPIMTQGSLYN DSLSTNDFKS ILLGSTPLDIAPDGAVFQLDRPLS IDYSLGTGDVDRAVYWHLKKFAGNAGTPAGWFRWGIWDNFNK TFTDGVAYYSDEQPRQILLPVGTVCTRVDSEN TBSV Linker 1 K9 (SEQ ID NO: 39)
HHHHHHELKKKKKKKKKGASGASRAYKAVRRRGGKKQQMINHVGGTGGAIMAPVAVTRQLVGS KPKFTGRTSGSVTVTHREYLSQVNNSTGFQVNGGIVGNLLQLNPLNGTLFSWLPAIASNFDQY TFNSVVLHYVPLCSTTEVGRVAIYFDKDSEDPEPADRVELANYSVLKETAPWAEAMLRVPTDK IKRFCDDSSTSDHKLIDLGQLGIATYGGAGTNAVGDIFI SYSVTLYFPQPTNTLLSTRRLDLA GALVTASGPGYLLVSRTATVLTMTFRATGTFVISGTYRCLTATTLGLAGGVNVNSITVVDNIG TDSAFFINCTVSNLPSVVTFTSTGITSATVHCVRATRQNDVSLI Norwalk Virus Linker 1 K9 (SEQ ID NO: 40)
HHHHHHELKKKKKKKKKGASGASLVPEVNASDPLAMDPVAGSSTAVATAGQVNPIDPWIINNFVQAPQGEFTI SPNNTPGDVLFDLSLGPHLNPFLLHLSQMYNGWVGNMRVRIMLAGNAFTAGKI IVSCIPPGFGSHNLTIA QATLFPHVIADVRTLDPIEVPLEDVRNVLFHNNDRNQQTMRLVCMLYTPLRTGGGTGDSFVVAGRVMTCP SPDFNFLFLVPPTVEQKTRPFTLPNLPLSSLSNSRAPLPI SSMGI SPDNVQSVQFQNGRCTLDGRLVGTT PVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPD TFVPHLGS IQANGIGSGNYVGVLSWI SPPSHPSGSQVDLWKIPNYGSS ITEATHLAPSVYPPGFGEVLVF FMSKMPGPGAYNLPCLLPQEYI SHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCV PNGASS GPQQLPINGVFVFVSWVSRFYQLKPVGTASSARGRLGLRR
HCV Linker 1 K9 (SEQ ID NO: 41)
HHHHHHELKKKKKKKKKGASGASDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEG RSWAQPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFADLMGYIPLVGAPLGGVAR ALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPASA
[0095] In some embodiments, the modification of the tail portion may allow a nucleic acid to bind to the tail portion with a binding affinity that may allow release of the nucleic acid when the chimeric therapeutic (e.g. viral core protein bound to a nucleic acid) is administered e.g. in vivo. For example, a modified tail portion that includes lysine may bind a nucleic acid using substantially Coulombic forces only, such that the nucleic acid may, in some embodiments, be released when exposed to a ionic solution e.g. a salt solution.
[0096] In another embodiment, the disclosed chimeric therapeutics, e.g. that do not include a modified tail portion with a substantial number of arginines such as those arranged as in a wild type tail portion, may be substantially free of endogenous nucleic acids. B. Modified Structural Core
[0097] The structural core of a modified viral core protein may be modified to e.g., (a) strengthen and promote assembly of the viral core protein, e.g. HPV core protein monomers, into a capsid; (b) enhance and promote a coating of one or more capsids with a layer comprising a lipid , (c) facilitate the attachment of other moieties, e.g., chemical modifiers and/or targeting agents; and/or (d) facilitate the disassembly of the entire capsid in the bloodstream following administration. HPV
[0098] The wild type HPV Ll protein is 531 amino acids of which the first 500 amino acids may form a structural core. Provided herein is a structural core portion based on amino acid 1-500 of SEQ ID NO: 1, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid. An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 42, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 42 and additionally, a modified or unmodified tail portion, e.g. a modified tail portion such as those described above.
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIH LPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGI SGHPLLNKLDDTENASAYAANAGVDNRECI SMDYK QTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSI CKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKXXXSTANLASSNYFPTPSGSMVTSDA QIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAI STSETTYKNTNFKEYLRHGEEYDLQFIFQLCK ITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFS
ADLDQFPLGRKFLLQLGL (SEQ ID NO: 42) wherein the X, at a given location is selected from:
X at 280 : X = S , C X at 281 : X = G , C
X at 282 : X = S , C
SV40
[0099] The wild type SV40 protein is 364 amino acids of which the carboxyl 343 amino acids may form a structural core. Provided herein is a structural core portion based on amino acid 22-364 of SEQ ID NO: 2, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid. An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 43, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 43 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above. EPVQVPKLVIKGGIEVLGVKTGVDSFTEVECFLNPQMGNPDEHQKGLSKSLAAEKQFTDDSPDKEQLPCYSVARIP LPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQXXHENGAGKPIQGSNFHFFAVGGEPLELQGVLANYRT KYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKNENTRYFGTYTGGENVPPVLHITNTATTVLLD EQGVGPLCKADSLYVSAVDICGXXTNTSGTQQWKGLPRYFKITLRKRSVKNPYPI SFLLSDLINRRTQRVDGQPMI GMSSQVEEVRVYEDTEELPGDPDMiRYiDEFGQTTTRMQ (SEQ ID NO: 43)
wherein the X, at a give location, is selected from:
X at 137 : X = K , C
X at 138 : X = T , C X at 272 : X = L , C
X at 273 : X = F , C
CCMV
[0100] The wild type CCMV protein is 190 amino acids of which the carboxyl 164 amino acids may form a structural core. Provided herein is a structural core portion based on amino acid 27-190 of SEQ ID NO: 3, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid. An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 44, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 44and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
VVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAAXXXKVTSAITISLPNELSSERNKQLKVGRVLLWLGLLPSVS GTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTADLTIYLYSSAALTEGDVIVHLEVEHV RPTFDDSFTPVY (SEQ ID NO: 44) wherein the X, at a given location is selected from:
X at 62 : X = A , C X at 63 : X = E , C X at 64 : X = A , C
DGNNV
[0101] The wild type DGNNV protein is 338 amino acids of which the carboxyl 313 amino acids may form a structural core. Provided herein is a structural core portion based on amino acid 26-373 of SEQ ID NO: 4, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid. An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 45. One of skill in the art would understand that cysteine residues may be mutated into a most apical solvent-exposed surface of the capsid protein. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 45 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
ANNRRRSNRTDAPVSKASTVTGFGRGTNDVHLSGMSRISQAVLPAGTGTDGYVVVDATIVPDLLPRLGHAARIFQR YAVETLEFEIQPMCPANTGGGYVAGFLPDPTDNDHTFDALQATRGAVVAKWWESRTVRPQYTRTLLWTSSGKEQRL TSPGRLILLCVGNNTDVVNVSVLCRWSVRLSVPSLETPEETTAPIMTQGSLYNDSLSTNDFKS ILLGSTPLDIAPD GAVFQLDRPLS IDYSLGTGDVDRAVYWHLKKFAGNAGTPAGWFRWGIWDNFNKTFTDGVAYYSDEQPRQILLPVGT vcTRVDSEN (SEQ ID NO: 45)
TBSV
[0102] The wild type TBSV protein is 388 amino acids of which the carboxyl 336 amino acids form a structural core. Provided herein is a structural core portion based on amino acid 53-388 of SEQ ID NO: 5, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid. An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 46, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 46 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
RAYKAVRRRGGKKQQMINHVGGTGGAIMAPVAVTRQLVGSKPKFTGRTSGSVTVTHREYLSQVNNSTGFQVNGGIV
GNLLQLNPLNGTLFSWLPAIASNFDQYTFNSVVLHYVPLCSTTEVGRVAIYFDKDSEDPEPADRVELANYSVLKET APWAEAMLRVPTDKIKRFCDDSSTSDHKLIDLGQLGIATYGGAGTNAVGDIFI SYSVTLYFPQPTNTLLSTRRLDL
NLPSvvTFTSTGiTSATVHCVRATRQNDVSLi (SEQ ID NO: 46) wherein the X, at a given location is selected from: X at 343 : X = I , C
X at 344 : X = G , C X at 345 : X = T , C
Norwαlk Virus
[0103] The wild type Norwalk Virus protein is 530 amino acids of which the carboxyl 510 amino acids form a structural core. Provided herein is a structural core portion based on amino acid 21-530 of SEQ ID NO: 6, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid. An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 47, where X, independently for each occurrence, represents a modified amino acid. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 47 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above.
LVPEVNASDPLAMDPVAGSSTAVATAGQVNPIDPWIINNFVQAPQGEFTISPNNTPGDVLFDLSLGPHLNPFLLHL SQMYNGWVGNMRVRIMLAGNAFTAGKI IVSCIPPGFGSHNLTIAQATLFPHVIADVRTLDPIEVPLEDVRNVLFHN NDRNQQTMRLVCMLYTPLRTGGGTGDSFVVAGRVMTCPSPDFNFLFLVPPTVEQKTRPFTLPNLPLSSLSNSRAPL PISSMGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLG GCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGS IQANGXXXGNYVGVLSWI SPPSHXXXSQVDLWKIPNYGSS IT EATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYI SHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAY
PDGFLTCVPNGASSGPQQLPiNGVFVFvswvsRFYQLKPVGTASSARGRLGLRR (SEQ ID NO: 47) wherein the X, at a given location is selected from:
X at 364 X = I, C X at 365 X = G, C X at 366 X = S, C X at 382 X = P, C X at 383 X = S, C X at 384 X = G, C
HCV [0104] It is postulated that the carboxyl 171 amino acids may form a structural core of HCV. One of skill in the art may understand that a structural core portion may be based on amino acid 21-191 of SEQ ID NO: 7, that includes one or more of a stability modifications that alter the ability of the capsid to assemble or disassemble and/or one or more modification that promote the attachment of a lipid. An exemplary modified structural core protein is, in some embodiments, represented by SEQ ID NO: 48. One of skill in the art would understand that cysteine residues may be mutated into a most apical solvent-exposed surface of the capsid protein. It is understood that a contemplated viral core protein may include a structural portion represented by SEQ ID NO: 48 and additionally, a modified or unmodified tail portion, e.g. a modified N-terminal tail portion such as those described above. DVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRSWAQPGYPWPLYGNEGCGWAGW LLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFAE
SFSiFLLALLSCLTVPASA (SEQ ID NO: 48) Capsid Assembly Modifications
[0105] The various viral capsids are typically approximate spherical macromolecular assemblies composed of monomers of core proteins. For example, the CCMV capsid is comprised of 180 capsid protein subunits. The intermolecular interactions between dimers that stabilize the assembly can be formed by e.g., disulfide bonds, salt bridges, and hydrophobic interactions. In some embodiments, the structural core portion may include mutation of interacting amino acid side chains to either stabilize or destabilize the interactions and therefore, the capsid assembly. The stabilizing and destabilizing mutations can be introduced singly and in combination to fine-tune capsid stability. [0106] For example, expressed viral core proteins in solution may form a dimer that is naturally stabilized by salt bridges, hydrophobic interactions, and covalent inter- and intramolecular disulfide bonds. In some embodiments, intra-molecular bonds may be engineered so that viral core protein stability can be tuned to a desired level. Additionally, inter-molecular disulfide bonds can be engineered so as to affect the stability of the capsid. Specific salt bridges between dimers that help form the capsid can also be mutated to cysteines so that disulfide bonds form and stabilize the capsid structure.
Capsid Disassembly Modifications
[0107] In order to facilitate the breakdown of the entire capsid, various alterations or mutations may be made on the structural core (which may form the outer surface of the capsid) that may introduce blood protease recognition sequences, e.g., protease recognition sites at hinge and loop regions. The protease may recognize and cleave this loop thereby promoting disassembly.
[0108] Exemplary blood protease recognition sequences include for example, thrombin (SEQ ID NO: 49) and factor Xa (SEQ ID NO: 50.) GPGAPGLVPRGS (SEQ ID NO: 49)
GPASGPGIEGRA (SEQ ID NO: 50)
[0109] These sequences can be inserted into the spike, hinge, and/or loop regions of the viral core proteins. Capsid Conjugate Site Modifications
[0110] The structural core portion of the viral core protein may be modified to include a conjugation site that allows the attachment of a chemical linker, e.g. a lipid linker moiety. For example, either of the amino acids cysteine or lysine may be placed in the structural core in such a way so that when formed in a capsid these modifications protrude away from the capsid surface toward the plasma membrane.
[0111] In an embodiment, such modifications may permit the addition of one or more lipid linker moieties which can serve to promote or facilitate a lipid layer. In another embodiment, such a modification may permit the addition {e.g. the attachment of) one or more targeting agents, as described below.
[0112] Cysteine mutations can also be introduced at other locations in the viral protein. The choice of lysine or cysteine at each position is dependent of the orientation and geometry of each amino acid as judged from the crystal structure of the viral capsid protein. Exemplary modified structural portions, with a wild type terminal tail, are provided below: HPV attachment mutant S280C (SEQ ID NO: 51)
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIH LPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGI SGHPLLNKLDDTENASAYAANAGVDNRECI SMDYK QTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSI CKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGCGSTANLASSNYFPTPSGSMVTSDA QIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAI STSETTYKNTNFKEYLRHGEEYDLQFIFQLCK ITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFS ADLDQFPLGRKFLLQLGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKL
SV40 attachment mutant K137C (SEQ ID NO: 52) MKMAPTKRKGSCPGAAPKKPKEPVQVPKLVIKGGIEVLGVKTGVDSFTEVECFLNPQMGNPDEHQKGLSKSLAAEK QFTDDSPDKEQLPCYSVARIPLPNINEDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQCTHENGAGKPIQGSNF HFFAVGGEPLELQGVLANYRTKYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKNENTRYFGTYT GGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNTSGTQQWKGLPRYFKITLRKRSVKNPYPI SFLLSDLINRRTQRVDGQPMIGMSSQVEEVRVYEDTEELPGDPDMIRYIDEFGQTTTRMQ
CCMV attachment mutant A62C (SEQ ID NO: 53)
MSTVGTGKLTRAQRRAAARKNKRNTRVVQPVIVEPIASGQGKAIKAWTGYSVSKWTASCAACEAKVTSAITISLPN ELSSERNKQLKVGRVLLWLGLLPSVSGTVKSCVTETQTTAAASFQVALAVADNSKDVVAAMYPEAFKGITLEQLTA DLTIYLYSSAALTEGDVIVHLEVEHVRPTFDDSFTPVY TBSV attachment mutants G344C (SEQ ID NO: 54)
MAMVKRNNNTGMIPVSTKQLLALGAAAGATALQGFVKNNGMAIVEGAVDLTKRAYKAVRRRGGKKQQMIN
HVGGTGGAIMAPVAVTRQLVGSKPKFTGRTSGSVTVTHREYLSQVNNSTGFQVNGGIVGNLLQLNPLNGT
LFSWLPAIASNFDQYTFNSVVLHYVPLCSTTEVGRVAIYFDKDSEDPEPADRVELANYSVLKETAPWAEA MLRVPTDKIKRFCDDSSTSDHKLIDLGQLGIATYGGAGTNAVGDIFI SYSVTLYFPQPTNTLLSTRRLDL
INCTVSNLPSVVTFTSTGITSATVHCVRATRQNDVSLI
Norwalk Virus attachment mutant P382C sequence: (SEQ ID NO: 55)
MMMASKDATSSVDGASGAGQLVPEVNASDPLAMDPVAGSSTAVATAGQVNPIDPWIINNFVQAPQGEFTI SPNNTPGDVLFDLSLGPHLNPFLLHLSQMYNGWVGNMRVRIMLAGNAFTAGKI IVSCIPPGFGSHNLTIA
QATLFPHVIADVRTLDPIEVPLEDVRNVLFHNNDRNQQTMRLVCMLYTPLRTGGGTGDSFVVAGRVMTCP
SPDFNFLFLVPPTVEQKTRPFTLPNLPLSSLSNSRAPLPI SSMGI SPDNVQSVQFQNGRCTLDGRLVGTT
PVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPD
TFVPHLGS IQANGIGSGNYVGVLSWI SPPSHCSGSQVDLWKIPNYGSS ITEATHLAPSVYPPGFGEVLVF FMSKMPGPGAYNLPCLLPQEYI SHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASS
GPQQLPINGVFVFVSWVSRFYQLKPVGTASSARGRLGLRR
[0113] In a one embodiment, a chemical linker, e.g. a bifunctional linker, may bind another moiety to a particle formed from viral core proteins that include a modified structure core portion, e.g. that include one or more cysteine residues. Exemplary chemical linkers include moieties such as those formed by contacting a cysteine residue with a maleimide containing compound such as phosphoethanolamine-maleimide (PE-maleimide or PE- mal). Phospholipids, for example, may be directly linked through a chemical linker to a modified structural core portion e.g. to link a lipid molecule and/or a targeting agent. [0114] In another embodiment, cysteine residues may be engineered into the structural core portion region to provide a covalent linker to a modified viral core protein. For example, a S- protein may guide the coating of the lipid layer or lipid/cholesterol layer. Contemplated S- proteins for attaching to a disclosed capsid or particle may be modified to have cysteines as well to complement the disulfide bridge formation between C-protein monomers. Alternatively, a S-protein can be replaced by a peptide such as a transmembrane engineered peptide. An exemplary transmembrane engineered peptide may have e.g., a flexible region that ends with a cysteine so as to form disulfide bridges with the cage, with the opposite end comprising primarily of hydrophobic residues. A non-limiting example of such a S-protein transmembrane engineered peptide has the amino acid sequence: CARGARGARGARG I LGVF I LLYM (SEQ ID NO: 56) [0115] Although specific modified viral core protein sequences are disclosed, one of skill in the art would recognize that nucleic acid and amino acid sequences about 75% to about 99% identical, about 80% to about 95% identical, about 85% to about 90% identical, or about 95% to about 99% identical, or any specific percent identity disposed within these ranges, to disclosed viral core proteins capable of forming a capsid and capable of binding a nucleic acid are within the scope of the present invention.
Compositions and Particles
[0116] Provided herein are therapeutic compositions that include particles formed from a plurality of chimeric therapeutics as described above. Such particles may include a coating, or alternatively, a set of particles may be associated with each other, and such set of particles may include a coating over the set. Therapeutic compositions may include a pharmaceutically acceptable excipient.
[0117] For example, provided herein is a therapeutic composition comprising a particle formed from at least: i) a first discrete number of modified viral core proteins; and ii) a second discrete number of nucleic acids each bound to one of said modified viral core proteins. For example, not all of the first discrete number of modified viral core proteins may be associated or bound to a nucleic acid. It will be appreciated that in some embodiments, a particle may include different modified viral core proteins, e.g., those with different modified tail portions, or a particle may be, e.g., formed from all the same modified viral core proteins. In some embodiments, only a portion of modified viral core proteins are bound to a nucleic acid. The formed particles may include a coating associated with a given particle or may include a coating associated with or surrounding several particles.
[0118] In some embodiments, the first discrete number of modified viral core proteins is about the number necessary to form a capsid from a disclosed viral core protein, e.g. about 170 to about 200 modified viral core proteins, or about 180 modified viral core proteins, for e.g. a CCMV capsid.
[0119] The second discrete number of nucleic acids, wherein each nucleic acid is bound to one of the viral core proteins, is about for example, 2 to about 60, about 8 to about 20, or about 14 to about 18, e.g. about 15, 16, or 17 nucleic acids. For example, in an exemplary embodiment, if a disclosed particle is formed from 180 modified viral core proteins, about 14 to about 18 of those modified viral core proteins are bound to a nucleic acid. In an embodiment, a given particle can include e.g. about 8 to about 20 of the same nucleic acid, or one or more nucleic acids may be substantially different, e.g. directed to a different area of a gene target or to a different gene target.
[0120] Also contemplated herein is a therapeutic particle that includes a plurality of viral core proteins each comprising a structural core portion and a modified tail portion, wherein said structural core portions form a capsid; and said modified tail portions are substantially disposed within said capsid; and a plurality of nucleic acids, bound to a modified tail portion of one of the viral core proteins. In some embodiments, the number of nucleic acids bound to a modified tail portion is less than that number of viral core proteins present in the particle. [0121] Throughout the specification, particles contemplated herein may be referred to as "capsids," "particles," "therapeutic particles," and "therapeutic chimeric particles."
[0122] Disclosed particles may further, in some embodiments, comprise a partial or substantially complete coating disposed on the particle that includes one or more lipids. For example, at least one lipid molecule may covalently bound through a chemical linker moiety, e.g. a lipid linker moiety, to a viral core protein, e.g., to a structural core portion of a disclosed viral core protein. For example, the lipid may be attached via bond or chemical linker moiety, to an engineered location on the structural core portion of the viral core protein.
[0123] Also contemplated herein, in an embodiment, is a therapeutic multiplex comprising two or more capsids, e.g., a plurality of capsids, for example, about 3 to about 12, e.g. 4, 5, or 6 capsids, each capsid comprising a disclosed modified viral core protein having, e.g., a modified structural core portion and a modified tail portion, and a nucleic acid bound to said tail portion, and a coating at least partially surrounding the two or more capsids.
[0124] Contemplated lipid linker moieties may include those formed from contacting e.g. a succinimidyl derivative such as succinimidyl-4-(p-maleimidophenyl)butyrate (SMPB) or m- maleimidobenzoyl-N-hydroxysuccinimide ester with a structural core portion of the viral core protein.
[0125] A disclosed particle (or set of particles) may have a layer or coating comprising one or more lipids, e.g., a neutral lipid, an anionic lipid, and/or a cationic lipid. For example, a neutral lipid and/or an amphipathic lipid, for example, a phospholipid such as phophatidyl serine, may be covalently bonded to a lipid linker moiety. Such covalently bound lipid molecules may guide the placement of a coating, e.g. that may include one more neutral lipids, and/or may include an anionic lipid that is surface neutral, such as POPG.
[0126] Exemplary phospholipids suitable for use include, but are not limited to, hydrogenated soy phosphatidylcholine (HSPC), egg phosphatidylcholine (EPC), phosphatidyl ethanolamine (PE), phosphatidyl glycerol (PG), phosphatidyl inositol (PI), monosialogangolioside, spingomyelin (SPM), distearoylphosphatidylcholine (DSPC), dimyristoylphosphatidylcholine (DMPC), or dimyristoylphosphatidylglycerol (DMPG).
[0127] In some embodiments, particles contemplated herein include one or more lipids including one, two, or more of lipids such as palmitoyloleoylphosphatidylglycerol (POPG), hydrogenated soy phosphatidylcholine (HSPC). Contemplated lipids include PEG- phospholipids, including poly(ethylene glycol) -derivatized distearoylphosphatidylethanolamine (PEG-DSPE) and/or poly(ethylene glycol)-derivatized ceramides (PEG-CER).
[0128] Provided herein are particles that may include a coating comprising one or more lipids and cholesterol, for example, may include various amounts of cholesterol, HSPC or
POPG. The lipid composite material can be about 5% to about 40% cholesterol, about 10% to about 80% HSPC and/or about 5% to about 80% POPG, or any specific percentage within said ranges. In some embodiments, a coating may comprise, for example, (a) about 20% cholesterol and about 80 % HSPC; (b) about 50% cholesterol and about 50 % HSPC; (c) about 20% cholesterol and about 20 % HSPC and about 60% POPG; (d) about 50% cholesterol and about 50% POPG; (e) 20% cholesterol and 80 % POPG; or (f) about 10 % Cholesterol and about 15% HSPC and about 65% POPG. In an embodiment, a coating may include about 20% Cholesterol, about 20 % HSPC and about 60% POPG.
[0129] A coating composition may have a mass value of the particle of about 10% to about 60%, about 10% to about 50%, about 15 to about 40%, about 20% to about 35% of the total protein (w/w), or any specific percentage with the recited ranges. For example, a lipid coating composition may coat a particle at a mass value of about 30% (w/w).
[0130] In some embodiments, a coating may be modified to enhance e.g. the ability of the particles to enter target cells and/or to at least partially evade the immune system in vivo. For example, cholesterol-tagged or lipid-tagged polyethylene glycol (PEG) and/or protein transduction domains (PTD) may form part of a coating. Non-limiting examples of suitable PTDs are the Human Immunodeficiency Virus (HIV) transactivator of transcription (Tat) peptide and/or poly-arginine (poly-Arg). For example, a cholesterol-tagged PEG may be anchored into a lipid coating and/or cholesterol tagged PTDs may be anchored into a coating. Suitable ratios of protein: lipid for the coating process may range, in an embodiment, from approximately 1:1 protein:lipid (w:w) to approximately 1:30 protein:lipid (w:w).
[0131] In an exemplary embodiment, a disclosed particle that includes a lipid coating may be generally prepared by 1) first mixing a modified viral core protein with an nucleic acid of choice; 2) placing the core protein in a buffered solution, e.g., phosphate, citrate, tris, sodium buffer, causing particles to be formed that substantially encapsulate the nucleic acid; 3) adding sonicated phospholipids solution to the mixture which may bind with modified sites on the viral core protein; 4) adding cholesterol or lipid-tagged polyethylene glycol to the mixture; and 5) purifying the system by centrifugation or size exclusion chromatography. In a exemplary embodiment, formation of a disclosed particle is shown pictorially in Figure 3.
[0132] To prevent premature formation of a capsid or particle, the viral core proteins may be maintained in any suitable chemical denaturant or denaturing agent known in the art (e.g., urea, guanidine hydrochloride (GuHCl), sodium dodecyl sulfate (SDS)) in a concentration of about IM to about 6M, about 1.5M to about 5M, about 1.75M to about 4.5M, or any integer disposed within said ranges. For example, the chemical denaturant may be urea, which may be present in e.g. a concentration of about 2M to about 6M, about 3M to about 5M, about 3.5M to about 4.5M, e.g. about 4M, or any integer disposed within said ranges. To trigger a self- assembly reaction of a capsid or particle, the ionic strength of the solution can be raised to a final concentration of about 50 mM to about 600 mM using e.g. a salt, e.g. NaCl. The final concentration can be about 100 mM to about 550 mM, about 150 mM to about 500 mM, about 200 to about 450 mM, about 250 mM to about 400 mM or about 300 mM to about 350 mM, or any integer disposed within said ranges. The final ionic concentration of the solution may be directly related to the amount of chemical denaturant present in the solution. In addition to salt and chemical denaturant concentrations, temperature may facilitate self-assembly of the capsid. A temperature of about 25° C to about 105° C, about 40 ° C to about 90 ° C or about 55° C to about 75° C (or any specific temperature within the recited ranges) may trigger self-assembly of the capsid. In another embodiment, reducing agents such as DTT or beta-mercaptoethanol may be used to facilitate self-assembly of a capsid. [0133] After incubating the mixture, the presence of fully formed particles may be verified using standard biochemical analyses known in the art.
[0134] Particles disclosed herein may be substantially non-replicating. For example, the viral core proteins may be designed so that once the particle starts to disintegrate, they are degraded quickly so as to limit any potential immune response. Disclosed particles do not substantially incorporate any attenuated wild type virus.
Targeting Agents
[0135] Various targeting agents can be incorporated into e.g. a coating layer of the disclosed particles, e.g. incorporated or bound to a lipid layer or lipid/cholesterol layer coat to direct the particle to a tissue or cell target. Alternatively, a targeting agent may be bound directly, e.g. chemically linked, directly or through a chemical linker moiety, to a disclosed particle.
[0136] An exemplary targeting agent may be an antibody. For example, exposed sulfhydryl groups on the heavy chain of an antibody can be used to link the antibody to e.g. a free sulfate group on a coating comprising one or more lipids. Alternatively, a lipid can be attached to antibodies through different chemical means, such as reacting an activated lipid such as PE-maleimide to activated free amines of an antibody with agents such as Traut' s Reagent.
[0137] A reduced antibody heavy chain-light chain complex above can also be attached directly to the naked particle. For example, the modified viral core protein may incorporate cysteine residues with reactive sulfhydryl groups as described above which then can be linked with the partially disassociated antibody chains.
[0138] Antibodies suitable for use as targeting agents include antibodies directed to cell surface antigens which cause the antibody-particle complex to be internalized, either directly or indirectly. Specific non-limiting examples of suitable antibodies include antibodies to CD 19, CD20, CD22, CD33 and CD74. CD33 and CD22 are over-expressed on lymphomas and binding to these antigens caused endocytosis and thereby internalization of the antibody- particle complex. Methods for incorporating monoclonal antibodies to CD22 into the lipid coating can be found in U.S. Patent Publication No. 20070269370, which is incorporated herein by reference. [0139] In some embodiments, a coating of a particle, or the particle itself, may be modified, to enhance e.g. the ability of the particles to enter target cells and/or to at least partially evade the immune system in vivo. For example, a large polymer {e.g. PEG), cholesterol-tagged or lipid-tagged polyethylene glycol (PEG) and/or protein transduction domains (PTD) may form part of a coating, and/or may be covalently linked through a bond or a chemical linker moiety to the coating and/or to specific site(s) (e.g. cysteine sites) on the modified structural core portion of the viral core protein. Non-limiting examples of suitable PTDs are the Human Immunodeficiency Virus (HIV) transactivator of transcription (Tat) peptide and/or poly- arginine (poly-Arg). In an embodiment, the particles and/or coatings may be modified by attaching a PEG. For example, one or more cholesterol-tagged PEGs may be anchored into a lipid coating or particle, and/or one or more cholesterol tagged PTD may be anchored into a coating or particle. In some embodiments, The particle and/or coating may be modified, e.g., covalently bonded through a chemical linker, to e.g. a carbohydrate and/or a sugar (e.g. branched sugar) moiety. [0140] Antibody mimetics and/or peptide mimetics that include complementarity determining region (CDR) subunits may also be, in some embodiments, associated with or bound to (e.g. via linker) to a coating or particle disclosed herein.
[0141] In another embodiment, an targeting agent that binds FcRN, s-protein or other moiety can be bound or associated with either a coating, e.g. a lipid coating, or may be bound directly to a modified viral core. Such targeting agents include those in US Patent Application 20070254831
Nucleic Acids
[0142] The therapeutic chimerics, particles and compositions disclosed here include at least one nucleic acid substantially homologous to a particular target bound to, or associated with, a viral core protein. In certain embodiments, an nucleic acid molecule, when bound to a viral core protein, is "substantially non-immunogenic" i.e., does not elicit, induce, or invoke a substantial immune response, for example, a humoral and/or a cellular immune response in a mammalian subject, such as a human subject. In other embodiments, an inhibitory nucleic acid molecule that is not bound to the viral core protein, e.g. when substantially released in vivo from a therapeutic disclosed herein, may be substantially non-immunogenic, or may have immunogenic properties. [0143] Exemplary nucleic molecules that may form part of the e.g., disclosed therapeutics, particles and/or compositions disclosed herein include inhibitory nucleic acids. [0144] Inhibitory nucleic acid molecules include an inhibitory double-stranded RNA, i.e., a "interfering RNA" or "iRNA" of about 10 to about 60, about 15 to about 50, about 15 to about 40, about 15 to about 30, or about 15 to about 20 nucleotides in length. In some embodiments, an inhibitory double stranded RNA is about 25 to about 45, about 27 to about 40, about 30 to about 40, about 33 to about 40, or about 36 to about 40 nucleotides in length. In other embodiments, an inhibitory double stranded RNA is about 15 to about 30, about 15 to about 25, about 19 to about 25, about 19 to about 23, or about 19 to about 21 nucleotides in length. In yet other embodiments, an inhibitory double stranded RNA is about 20 to about 24 or about 21 to about 22 or to about 23 nucleotides in length. An inhibitory double stranded RNA may be transcribed from a transcriptional cassette in a DNA plasmid. Such inhibitory double stranded RNA reduces, inhibits or silences expression of a target gene by mediating the degradation of mRNAs, which are complementary to the sequence of an inhibitory RNA. [0145] An inhibitory double stranded RNA can be formed by two complementary strands or by a single, self-complementary strand. The relationship between a target mRNA and the sense strand of an inhibitory RNA is that of identity. The sense strand of an inhibitory RNA is also called a passenger strand, if present. The relationship between a target mRNA (a sense strand) and the antisense strand of an inhibitory RNA is that of complementarity. The antisense strand of an inhibitory RNA is also called a guide strand. Exemplary inhibitory double stranded RNA duplex may comprise 3' overhangs of about 1 to about 4 nucleotides, for example of about 2 to about 3 nucleotides, and 5' phosphate termini. In other embodiments, an inhibitory double stranded RNA duplex may have no overhangs on one or both ends (blunt ends). Some exemplary inhibitory double stranded RNAs may lack a terminal phosphate. [0146] Examples of inhibitory double stranded RNA molecules include, without limitation, a double- stranded polynucleotide molecule assembled from two separate oligonucleotides, wherein one strand is the sense strand and the other is the complementary antisense strand; a double-stranded polynucleotide molecule assembled from a single oligonucleotide, where the sense and antisense regions are linked by a nucleic acid-based or non-nucleic acid-based linker; a double- stranded polynucleotide molecule with a hairpin secondary structure having self- complementary sense and antisense regions; and a circular single-stranded polynucleotide molecule with two or more loop structures and a stem having self-complementary sense and antisense regions, where the circular polynucleotide may be processed in vivo or in vitro to generate an active inhibitory double- stranded RNA molecule.
[0147] The sequence of an inhibitory double- stranded RNA to be delivered by the present invention must have a sufficient identity to a target nucleic acid in order to mediate target- specific RNA interference. In an exemplary embodiment, an inhibitory double-stranded RNA has an identity of at least about 85%, 90%, 95%, or 100% to the desired target nucleic acid. The identity of a double- stranded RNA molecule to a predetermined nucleic acid target molecule, e.g., an mRNA target molecule, may be determined as follows: I= n/L x 100: wherein I is the identity in percent, n is the number of identical nucleotides in the double- stranded portion of the dsRNA and the target and L is the length of the sequence overlap of the double-stranded portion of the dsRNA and the target.
[0148] Alternatively, the identity of a double-stranded RNA molecule to the target sequence may also be defined to include a 3' overhang, particularly an overhang having a length from 1-3 nucleotides, with a sequence identity of at least about 50%, about 70% , or about 85% or more to the target sequence. For example, the nucleotides from the 3' overhang and up to 2 nucleotides from the 5' and/or 3' terminus of the double strand may be modified without significant loss of activity.
[0149] Inhibitory nucleic acids may include one or more mismatch motifs or mismatch regions, which refer to a portion of an nucleic acid sequence that does not have 100% complementary to its target sequence. A nucleic acid may have at least one, two, three, four, five, six, or more mismatch regions. The mismatch regions may be contiguous or may be separated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more nucleotides. The mismatch motifs or regions may comprise a single nucleotide or may comprise two, three, four, five, or more nucleotides. [0150] Inhibitory double stranded RNA contemplated herein may be sufficiently identical or sufficiently complementary, e.g. substantially homologous to a target nucleic acid, e.g., a target mRNA, such that the inhibitory double stranded RNA silences production of protein encoded by the target mRNA. In one embodiment, a contemplated inhibitory double stranded RNA may be identical or exactly complementary (excluding the RRMS containing subunit(s)) to a target RNA, e.g., the target RNA and the inhibitory double stranded RNA anneal, e.g., to form a hybrid made of Watson-Crick base pairs in the region of exact identity or complementarity. For example, a sufficiently identical or sufficiently complementary target RNA may include an internal region (e.g., of at least 10 nucleotides) that is exactly identical or complementary to a target. Moreover, in some instances, an inhibitory double stranded RNA may specifically discriminate a single-nucleotide difference, for example, mediating RNA interference if exact identity or complementary is found in the region of the single-nucleotide difference (e.g., within 7 nucleotides of the single-nucleotide difference).
Selecting and Optimizing Inhibitory Nucleic Acid Molecule Sequences
[0151] Suitable inhibitory double stranded RNA sequences that target a gene of interest may be identified using any means known in the art. Typically, methods such as gene walking or the methods described in Elbashir et al., Nature 411:494-498 (2001) and Elbashir et al., EMBO J 20: 6877-6888 (2001) are combined with rational design rules set forth in Reynolds et al., Nature Biotech. 22:326-330 (2004), each of which are incorporated herein by reference.
[0152] Typically, a sequence within about 50 to about 100 nucleotides 3' of the AUG start codon of a transcript from the target gene of interest is scanned for dinucleotide sequences (e.g., AA, CC, GG, or UU) (see, e.g., Elbashir, et al, EMBO J 20: 6877-6888 (2001)). The nucleotides immediately 3' to the dinucleotide sequences are identified as potential inhibitory double stranded RNA target sequences. Typically, the 19, 21, 23, 25, 27, 29, 31, 33, 35, 38, 40, 42, or more nucleotides immediately 3' to the dinucleotide sequences are identified as potential inhibitory double stranded RNA target sites. The dinucleotide sequence may be, for example, an AA sequence and the 19 to about 40 nucleotides immediately 3' to the AA dinucleotide are identified as a potential inhibitory double stranded RNA target site. Typically, inhibitory double stranded RNA target sites are spaced at different positions along the length of the target gene. To further enhance silencing efficiency of an inhibitory double stranded RNA sequences, potential inhibitory double stranded RNA target sites may be analyzed to identify sites that do not contain regions of homology to other coding sequences. For example, in some embodiments, a suitable inhibitory double stranded RNA target site of about 21 base pairs may not have more than 16-17 contiguous base pairs of homology to other coding sequences. If inhibitory double stranded RNA sequences are to be expressed from an RNA Pol III promoter, inhibitory double stranded RNA target sequences lacking more than 4 contiguous A's or T's may be selected. [0153] Once a potential inhibitory double stranded RNA sequence has been identified, the sequence may be analyzed using a variety of criteria known in the art. For example, to enhance their silencing efficiency, inhibitory double stranded RNA sequences may be analyzed by a rational design algorithm to identify sequences that have one or more of the following features: (1) G/C content of about 25% to about 60% G/C; (2) at least 2 or 3 A/Us at positions 15-19 of the sense strand; (3) no internal repeats; (4) an A at position 19 of the sense strand; (5) an A at position 3 of the sense strand; (6) a U at position 10 of the sense strand; (7) an A at position 14 of the sense strand; (8) no G/C at position 19 of the sense strand; and (9) no G at position 13 of the sense strand. Inhibitory double stranded RNA design tools that incorporate algorithms that assign suitable values of each of these features and are useful for selection of inhibitory double stranded RNA can be found at, e.g., http://boz094.ust.hk/RNAi/siRNA. One of skill in the art will appreciate that sequences with one or more of the foregoing characteristics may be selected for further analysis and testing as potential inhibitory double stranded RNA sequences. Inhibitory double stranded RNA sequences complementary to target nucleic acid sites may also be designed. Techniques for selecting target sequences for inhibitory RNAs are provided by Tuschl, T. et al., "The siRNA User Guide," revised May 6, 2004, available on the Rockefeller University web site; by Technical Bulletin #506, "siRNA Design Guidelines," Ambion Inc. at Ambion's web site; and by other web-based design tools at, for example, the Invitrogen, Dharmacon, Integrated DNA Technologies, Genscript, or Proligo web sites. For example, initial search parameters can include G/C contents between 35% and 55% and siRNA lengths between 19 and 27 nucleotides. The target sequence may be located in the coding region or in the 5' or 3' untranslated regions of the mRNA.
[0154] Additionally, potential inhibitory double stranded RNA target sequences with one or more of the following criteria can often be eliminated as inhibitory double stranded RNA: (1) sequences comprising a stretch of 4 or more of the same base in a row; (2) sequences comprising homopolymers of Gs (i.e., to reduce possible non-specific effects due to structural characteristics of these polymers; (3) sequences comprising triple base motifs (e.g., GGG, CCC, AAA, or TTT); (4) sequences comprising stretches of 7 or more G/Cs in a row; and (5) sequence comprising direct repeats of 4 or more bases within the candidates resulting in internal fold-back structures. However, one of skill in the art will appreciate that sequences with one or more of the foregoing characteristics may still be selected for further analysis and testing as potential inhibitory double stranded RNA sequences. The importance of various criteria can vary greatly. For instance, a C base at position 10 of the sense strand may make a minor contribution to duplex functionality. In contrast, the absence of a C at position 3 of the sense strand is may be very important.
[0155] With respect to criteria for selecting an inhibitory double stranded RNA, GC content, as well as a high number of AU in positions 15-19 of the sense strand, may be important for easement of the unwinding of an inhibitory double stranded RNA duplex. Duplex unwinding has been shown to be crucial for inhibitory double stranded RNA functionality in vivo. The internal structure is measured in terms of the melting temperature (Tm) of the single strand of inhibitory double stranded RNA, which is the temperature at which 50% of the molecules will become denatured.
[0156] It should be noted that all of the aforementioned criteria regarding sequence position specifics are with respect to the 5' end of the sense strand. Reference is made to the sense strand, because most databases contain information that describes the information of the mRNA. An inhibitory nucleic acid molecule contemplated herein may be a variety of lengths. The aforementioned criteria may assume an inhibitory nucleic acid molecule of at least 19 nucleotides in length so that it is important to keep the aforementioned criteria applicable to the correct bases. It is understood that a person skilled in the art will know how to apply the aforementioned criteria to inhibitory nucleic acid molecules of varying lengths.
[0157] In addition to gene walking and sequence analysis and optimization, as described above, various algorithms well-known in the art can be utilized to select an inhibitory dsRNA sequence. Exemplary algorithms for selecting inhibitory RNA sequences are disclosed in Naito et al, Nucleic Acids Res 33: W589-591, 2005, Henschel et al, Nucleic Acids Res 32: Wl 13- 120, 2004, Naito et al, Nucleic Acids Res 32: W124-129, 2004 (for mammalian- specific interfering RNAs) and Naito et al, Nucleic Acids Res 34: W448-450, 2006 (for viral- specific interfering RNAs), each of which is incorporated herein by reference. In some embodiments, a person skilled in the art may use one or more algorithms to select an inhibitory RNA sequence. Further, a person skilled in the art will appreciate the use of multiple parameters and algorithms in selecting and optimizing an inhibitory RNA sequence.
[0158] Inhibitory double stranded RNA selected according to the aforementioned criteria or one of the aforementioned algorithms are also, for example, useful in the simultaneous screening and functional analysis of multiple genes and gene families using high throughput strategies, as well as in direct gene suppression or silencing. Useful applications for inhibitory nucleic acid molecules include, but are not limited to, target validation, gene functional analysis, research and drug discovery, gene therapy and therapeutics. Methods for using inhibitory nucleic acid molecules including inhibitory double-stranded RNA molecules in these applications are well known to persons of skill in the art.
[0159] Inhibitory double stranded RNA molecules contemplated herein may be applicable across a broad range of species, including but not limited to all mammalian species, such as humans, dogs, horses, cats, cows, mice, hamsters, chimpanzees and gorillas, as well as other species and organisms such as bacteria, viruses, insects, plants and C. elegans. [0160] Also contemplated herein are nucleic acids applicable for use for silencing a broad range of genes, including but not limited to the roughly 45,000 genes of a human genome.
Analysis of Inhibitory Nucleic Acid Molecules
[0161] Potential inhibitory double stranded RNA target sequences may be further analyzed based on inhibitory double stranded RNA duplex asymmetry as described in, e.g., Khvorova et al., Cell, 115:209-216 (2003); and Schwarz et al., Cell, 115: 199-208 (2003). Potential inhibitory double stranded RNA target sequences may be further analyzed based on secondary structure at the mRNA target site as described in, e.g., Luo et al., Biophys. Res. Commun., 318:303-310 (2004). For example, mRNA secondary structure may be modeled using the Mfold algorithm (available at http://www.bioinfo.rpi.edu/applications/mfold/rna/forml.cgi) to select inhibitory double stranded RNA sequences which favor accessibility at the mRNA target site where less secondary structure in the form of base-pairing and stem-loops is present.
[0162] Once a potential inhibitory double stranded RNA sequence has been identified, the sequence may be analyzed for the presence of any immunostimulatory properties, e.g., using an in vitro cytokine assay or an in vivo animal model. Motifs in the sense and/or antisense strand of the inhibitory double stranded RNA sequence such as GU-rich motifs (e.g., 5'-GU-3', 5'- UGU-3', 5'-GUGU-3', 5'-UGUGU-3', etc.) may also provide an indication of whether the sequence may be immunostimulatory. If an inhibitory double stranded RNA molecule is found to be immunostimulatory, it may, in certain embodiments, be modified to decrease its immunostimulatory properties. The detectable immune response may comprise production of a cytokine or growth factor such as, e.g., TNF-α, IFN-CC, IFN-β, IFN-γ, IL-6, IL- 12, or a combination thereof. As a non-limiting example, an inhibitory double stranded RNA identified as being immunostimulatory can be modified to decrease its immuno stimulatory properties by replacing at least one (but less than about 30%) of the nucleotides on the sense and/or antisense strand with modified nucleotides such as 2'0Me nucleotides (e.g., 2'OMe-guanosine, 2'0Me- uridine, 2'OMe-cytosine, and/or 2'OMe-adenosine), as described in further detail herein.
[0163] Suitable in vitro assays for detecting an immune response include, but are not limited to, the double monoclonal antibody sandwich immunoassay technique of David et al. (U.S. Pat. No. 4,376,110); monoclonal-polyclonal antibody sandwich assays (Wide et al., in Kirkham and Hunter, eds., Radioimmunoassay Methods, E. and S. Livingstone, Edinburgh (1970)); the "Western blot" method of Gordon et al. (U.S. Pat. No. 4,452,901); immunoprecipitation of labeled ligand (Brown et al, J. Biol. Chem. 255:4980-4983 (1980)); enzyme-linked immunosorbent assays (ELISA) as described, for example, by Raines et al., J. Biol. Chem. 257:5154-5160 (1982); immunocytochemical techniques, including the use of fluorochromes (Brooks et al., Clin. Exp. Immunol. 39:477 (1980)); and neutralization of activity (Bowen-Pope et al, Proc. Natl. Acad. Sci. USA 81:2396-2400 (1984)). In addition to the immunoassays described above, a number of other immunoassays are available, including those described in U.S. Pat. Nos. 3,817,827; 3,850,752; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; and 4,098,876.
Generating Inhibitory Nucleic Acid Molecules [0164] Inhibitory nucleic acid molecules may be provided in several forms including, e.g., as one or more isolated RNA duplexes, e.g. siRNA, longer double- stranded RNA (dsRNA) or RNA transcribed from a transcriptional cassette in a DNA plasmid. Inhibitory nucleic acid molecules, such as inhibitory double stranded RNAs may also be chemically synthesized. The inhibitory double stranded RNA sequences may have overhangs (e.g., 3' or 5' overhangs as described in Elbashir et al, Genes Dev. 15:188 (2001) or Nykanen et al, Cell 107:309 (2001), or may lack overhangs (i.e., to have blunt ends).
[0165] Exemplary RNA population may be used to provide long precursor RNAs, or long precursor RNAs that have substantial or complete identity to a selected target sequence may be used to make the inhibitory dsRNA. For example, the RNAs can be isolated from cells or tissue, synthesized, and/or cloned according to methods well known to those of skill in the art. The RNA may be a mixed population (obtained from cells or tissue, transcribed from cDNA, subtracted, selected etc.), or may e.g. represent a single target sequence. RNA may be naturally occurring, (e.g., isolated from tissue or cell samples), synthesized in vitro (e.g., using T7 or SP6 polymerase and PCR products or a cloned cDNA), or chemically synthesized.
[0166] For example, to form a long dsRNA, for synthetic RNAs, the complement is transcribed in vitro and hybridized to form a dsRNA. If a naturally occurring RNA population is used, the RNA complements are also provided (e.g., to form dsRNA for digestion by E. coli RNAse III or Dicer), e.g., by transcribing cDNAs corresponding to the RNA population, or by using RNA polymerases. The precursor RNAs are then hybridized to form double stranded RNAs for digestion. [0167] Alternatively, one or more DNA plasmids encoding one or more inhibitory dsRNA templates are used to provide the inhibitory dsRNA. Inhibitory dsRNA can, in some embodiments, be transcribed as sequences that automatically fold into duplexes with hairpin loops from DNA templates in plasmids having RNA polymerase III transcriptional units, for example, based on the naturally occurring transcription units for small nuclear RNA U6 or human RNase P RNA Hl (see, Brummelkamp, et al, Science 296:550 (2002); Donze, et al, Nucleic Acids Res. 30:e46 (2002); Paddison, et al, Genes Dev. 16:948 (2002); Yu, et al, PNAS USA 99:6047 (2002); Lee, et al., Nat. Biotech. 20:500 (2002); Miyagishi, et al., Nat. Biotech. 20:497 (2002); Paul, et al., Nat. Biotech. 20:505 (2002); and Sui, et al., PNAS USA 99:5515 (2002)). Typically, a transcriptional unit or cassette will contain an RNA transcript promoter sequence, such as an Hl-RNA or a U6 promoter, operably linked to a template for transcription of a desired inhibitory dsRNA sequence and a termination sequence, comprised of 2-3 uridine residues and a polythymidine (T5) sequence (polyadenylation signal) (Brummelkamp, Science, supra). The selected promoter may e.g. provide for constitutive or inducible transcription. Compositions and methods for DNA-directed transcription of RNA interference molecules is described in detail in U.S. Pat. No. 6,573,099. The transcriptional unit is incorporated into a plasmid or DNA vector from which the interfering RNA is transcribed. Plasmids suitable for in vivo delivery of genetic material for therapeutic purposes are described in detail in U.S. Pat. Nos. 5,962,428 and 5,910,488, and such plasmids may provide for transient or stable delivery of a target cell. It will be apparent to those of skill in the art that plasmids originally designed to express desired gene sequences can be modified to contain a transcriptional unit cassette for transcription of inhibitory dsRNA. [0168] Methods for isolating RNA, synthesizing RNA, hybridizing nucleic acids, making and screening cDNA libraries, and performing PCR are well known in the art (see, e.g., Gubler and Hoffman, Gene 25:263-269 (1983); Sambrook et al., supra; Ausubel et al., supra), as are PCR methods (see U.S. Pat. Nos. 4,683,195 and 4,683,202; PCR Protocols: A Guide to Methods and Applications (Innis et al., eds, 1990)). Expression libraries are also well known to those of skill in the art. Additional basic texts disclosing the general methods of use in this invention include Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed. 1989); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 1994)). [0169] In an exemplary embodiment, a inhibitory nucleic acid molecules are chemically synthesized. The single stranded molecules that comprise a modified inhibitory nucleic acid molecule may be synthesized using any of a variety of techniques known in the art, such as those described in Usman et al., J. Am. Chem. Soc. 109:7845 (1987); Scaringe et al., Nuc. Acids Res. 18:5433 (1990); Wincott et al, Nuc. Acids Res. 23:2677-2684 (1995); and Wincott et al., Methods MoI. Bio. 74:59 (1997). The synthesis of oligonucleotides makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end and phosphoramidites at the 3'-end. As a non-limiting example, small scale syntheses may be conducted on an Applied Biosystems synthesizer using a 0.2 μmol scale protocol with a 2.5 min. coupling step for 2'-O-methylated nucleotides. Alternatively, syntheses at the 0.2 μmol scale may be performed on a 96- well plate synthesizer from Protogene (Palo Alto, Calif.).
However, a larger or smaller scale of synthesis is also within the scope of the present invention. Suitable reagents for oligonucleotide synthesis, methods for RNA deprotection, and methods for RNA purification are known to those of skill in the art.
[0170] Alternatively, an inhibitory dsRNA may be synthesized via a tandem synthesis technique, wherein both strands are synthesized as a single continuous oligonucleotide fragment or strand separated by a cleavable linker that is subsequently cleaved to provide separate fragments or strands that hybridize to form the inhibitory dsRNA duplex. For example, a linker can be a polynucleotide linker or a non-nucleotide linker. A tandem synthesis of modified inhibitory dsRNA may be readily adapted to both multiwell/multiplate synthesis platforms as well as large scale synthesis platforms employing batch reactors, synthesis columns, and the like. Alternatively, the modified inhibitory dsRNA can be assembled from two distinct oligonucleotides, wherein one oligonucleotide comprises the sense strand and the other comprises the antisense strand of the inhibitory dsRNA. For example, each strand can be synthesized separately and joined together by hybridization or ligation following synthesis and/or deprotection. In certain other instances, the modified inhibitory dsRNA can be synthesized as a single continuous oligonucleotide fragment, wherein the self-complementary sense and antisense regions hybridize to form an inhibitory dsRNA duplex having hairpin secondary structure.
Modifying Inhibitory Nucleic Acid Molecule Sequences
[0171] Inhibitory dsRNAs described herein may comprise at least one modified nucleotide in the sense and/or antisense strand. Exemplary contemplated modifications include the introduction of phosphorothioate linkages and 2'-substitutions on the ribose unit, e.g., 2'-deoxy, 2'-deoxy-2'-fluoro, 2'-O-methyl, 2'-O-methoxyethyl (2'-0-MOE), 2'-O-aminopropyl (2'-0-AP), 2'-O-dimethylaminoethyl (2'-0-DMAOE), 2'-O-dimethylaminopropyl (2'-0-DMAP), 2'-O- dimethylaminoethyloxyethyl (2'-0-DMAEOE), 2'-O-N-methylacetamido (2'-0-NMA) substitutions, 5-C-methyl, 2'-methoxyethyl, 4'-thio, 2'-amino, or 2'-C-allyl group. Modified nucleotides having a Northern conformation such as those described in, e.g., Saenger, Principles of Nucleic Acid Structure, Springer- Verlag Ed. (1984), are also suitable for use in an inhibitory dsRNA of the present invention. Such modified nucleotides include, without limitation, locked nucleic acid (LNA) nucleotides (e.g., 2'-O, 4'-C-methylene-(D-ribofuranosyl) nucleotides), 2'-methoxyethoxy (MOE) nucleotides, 2'-methyl-thio-ethyl nucleotides, 2'-deoxy- 2'-fluoro nucleotides, 2'-deoxy-2'-chloro nucleotides, and 2'-azido nucleotides. In certain instances, the inhibitory dsRNA includes one or more G-clamp nucleotides. A G-clamp nucleotide refers to a modified cytosine analog wherein the modifications confer the ability to hydrogen bond both Watson-Crick and Hoogsteen faces of a complementary guanine nucleotide within a duplex (see, e.g., Lin et al., J. Am. Chem. Soc. 120:8531-8532 (1998)). In addition, nucleotides having a nucleotide base analog such as, for example, C-phenyl, C- naphthyl, other aromatic derivatives, inosine, azole carboxamides, and nitroazole derivatives such as 3-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole (see, e.g., Loakes, Nucl. Acids Res. 29:2437-2447 (2001)) can be incorporated into the inhibitory dsRNA. [0172] In an embodiment, a cholesterol moiety (e.g., on the 3'-end of the sense strand), a T- modification (e.g., a 2'-O-methyl or 2'-deoxy-2'-fluoro-modification), and a phosphorothioate (e.g., on the 3'-most one or two nucleotides of the sense and antisense strands) may be present in the same inhibitory dsRNA. [0173] In an embodiment, 2'- substitutions may be made to the 5' nucleotide of a 5'-UA-3' dinucleotide, a 5'-UG-3' dinucleotide, a 5'-CA-3' dinucleotide, a 5'-UU-3' dinucleotide, or a 5'- CC-3' dinucleotide on the sense strand and, optionally, also on the antisense strand of the inhibitory dsRNA, or to all pyrimidine-base comprising nucleotides. For example, the 5'-most pyrimidines in substantially occurrences of the sequence motifs 5'-UA-3', 5'-CA-3', 5'-UU-3', and 5'-UG-3' may be 2'-modified nucleotides, or for example, substantially all pyrimidines in the sense strand are 2'-modified nucleotides, and 5'-most pyrimidines in substantially all occurrences of the sequence motifs 5'-UA-3' and 5'-CA-3', e.g. all pyrimidines in the sense strand are 2'-modified nucleotides, and the 5'-most pyrimidines in all occurrences of the sequence motifs 5'-UA-3', 5'-CA-3', 5'-UU-3', and 5'-UG-3' are 2'-modified nucleotides in the antisense strand.
[0174] The inhibitory dsRNA may include one or more chemical modifications such as terminal cap moieties, phosphate backbone modifications, and the like. Examples of terminal cap moieties include, without limitation, inverted deoxy abasic residues, glyceryl modifications, 4',5'-methylene nucleotides, l-(β-D-erythrofuranosyl) nucleotides, 4'-thio nucleotides, carbocyclic nucleotides, 1,5-anhydrohexitol nucleotides, L- nucleotides, OC- nucleotides, modified base nucleotides, threo-pentofuranosyl nucleotides, acyclic 3',4'-seco nucleotides, acyclic 3,4-dihydroxybutyl nucleotides, acyclic 3,5-dihydroxypentyl nucleotides, 3'-3'-inverted nucleotide moieties, 3'-3'-inverted abasic moieties, 3'-2'-inverted nucleotide moieties, 3'-2'-inverted abasic moieties, 5'-5'-inverted nucleotide moieties, 5'-5'-inverted abasic moieties, 3'-5'-inverted deoxy abasic moieties, 5'-amino-alkyl phosphate, l,3-diamino-2-propyl phosphate, 3-aminopropyl phosphate, 6-aminohexyl phosphate, 1,2-aminododecyl phosphate, hydroxypropyl phosphate, 1,4-butanediol phosphate, 3'-phosphoramidate, 5'-phosphoramidate, hexylphosphate, aminohexyl phosphate, 3'-phosphate, 5'-amino, 3'-phosphorothioate, 5'- phosphorothioate, phosphorodithioate, and bridging or non-bridging methylphosphonate or 5'- mercapto moieties (see, e.g., U.S. Pat. No. 5,998,203; Beaucage et αl., Tetrahedron 49:1925 (1993)). Non-limiting examples of phosphate backbone modifications (i.e., resulting in modified internucleotide linkages) include phosphorothioate, phosphorodithioate, methylphosphonate, phosphotriester, morpholino, amidate, carbamate, carboxymethyl, acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal, thioformacetal, and alkylsilyl substitutions (see, e.g., Hunziker et al., Nucleic Acid Analogues: Synthesis and Properties, in Modern Synthetic Methods, VCH, 331-417 (1995); Mesmaeker et al., Novel Backbone Replacements for Oligonucleotides, in Carbohydrate Modifications in Antisense Research, ACS, 24-39 (1994)). Such exemplary chemical modifications can occur e.g., at the 5'-end and/or 3'-end of the sense strand, antisense strand, or both strands of the inhibitory dsRNA. [0175] The sense and/or antisense strand may include, for example, a 3'-terminal overhang having about 1 to about 4 (e.g.,. 1, 2, 3, or 4) 2'-deoxy ribonucleotides and/or any combination of modified and unmodified nucleotides. Additional examples of modified nucleotides and types of chemical modifications that can be introduced into the modified inhibitory dsRNA are described, e.g., in UK Patent No. GB 2,397,818 B and U.S. Patent Publication Nos. 20040192626 and 20050282188.
[0176] Modified inhibitory dsRNA described herein may include one or more non- nucleotides in one or both strands of the inhibitory dsRNA. As used herein, the term "non- nucleotide" refers to any group or compound that can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their activity. The group or compound is abasic in that it does not contain a commonly recognized nucleotide base such as adenosine, guanine, cytosine, uracil, or thymine and therefore lacks a base at the 1 '-position.
[0177] Chemical modification of the inhibitory dsRNA may include attaching a conjugate to the chemically-modified inhibitory dsRNA. The conjugate may be attached at the 5' and/or 3'-end of the sense and/or antisense strand of the chemically-modified inhibitory dsRNA via a covalent attachment such as, e.g., a biodegradable linker. The conjugate may also be attached to the chemically-modified inhibitory dsRNA, e.g., through a carbamate group or other linking group (see, e.g., U.S. Patent Publication Nos. 20050074771, 20050043219, and 20050158727). In certain instances, the conjugate is a molecule that facilitates the delivery of the chemically- modified inhibitory dsRNA into a cell. Examples of conjugate molecules suitable for attachment to a chemically-modified inhibitory dsRNA include, without limitation, steroids such as cholesterol, glycols such as polyethylene glycol (PEG), human serum albumin (HSA), fatty acids, carotenoids, terpenes, bile acids, folates (e.g., folic acid, folate analogs and derivatives thereof), sugars (e.g., galactose, galactosamine, N-acetyl galactosamine, glucose, mannose, fructose, fucose, etc.), phospholipids, peptides, ligands for cellular receptors capable of mediating cellular uptake, and combinations thereof (see, e.g., U.S. Patent Publication Nos. 20030130186, 20040110296, and 20040249178; U.S. Pat. No. 6,753,423). Other examples include the lipophilic moiety, vitamin, polymer, peptide, protein, nucleic acid, small molecule, oligosaccharide, carbohydrate cluster, intercalator, minor groove binder, cleaving agent, and cross-linking agent conjugate molecules described in U.S. Patent Publication Nos. 20050119470 and 20050107325. Yet other examples include the 2'-O-alkyl amine, 2'-O- alkoxyalkyl amine, polyamine, C5-cationic modified pyrimidine, cationic peptide, guanidinium group, amidininium group, cationic amino acid conjugate molecules described in U.S. Patent Publication No. 20050153337. Additional examples include the hydrophobic group, membrane active compound, cell penetrating compound, cell targeting signal, interaction modifier, and steric stabilizer conjugate molecules described in U.S. Patent Publication No. 20040167090. Further examples include the conjugate molecules described in U.S. Patent Publication No. 20050239739. The type of conjugate used and the extent of conjugation to the chemically- modified inhibitory dsRNA molecule may be evaluated for improved pharmacokinetic profiles, bioavailability, and/or stability of the inhibitory dsRNA. As such, one skilled in the art can screen chemically-modified inhibitory dsRNA having various conjugates attached thereto to identify ones having improved properties using any of a variety of well-known in vitro cell culture or in vivo animal models.
[0178] In some embodiments, the introduction of modifications into inhibitory dsRNAs may enhance stabilization towards degradation in biological environments and may improve pharmacological properties, e.g. pharmacodynamic properties. Other suitable modifications to a sugar, base, or backbone of an inhibitory dsRNA are described in PCT Publication No. WO 2004/064737. For example, an inhibitory dsRNA can include a non-naturally occurring base, such as the bases described in PCT Publication No. WO 2004/094345 and/or may include a non-naturally occurring sugar, such as a non-carbohydrate cyclic carrier molecule. Exemplary features of non-naturally occurring sugars for use in inhibitory dsRNAs are described in PCT Publication No. WO 2004/094595. [0179] An inhibitory dsRNA may include, in some embodiments, an internucleotide linkage (e.g., the chiral phosphorothioate linkage) useful for increasing nuclease resistance. In addition, or in the alternative, an inhibitory dsRNA may include, for example, a ribose mimic for increased nuclease resistance. An inhibitory dsRNA may include ligand-conjugated monomer subunits and monomers for oligonucleotide synthesis, and/or may be complexed with an amphipathic moiety. The sense and antisense sequences of an inhibitory dsRNA may be palindromic, and/or may have non-canonical pairings, such as between the sense and antisense sequences of the iRNA duplex. Examples of these modifications are described in PCT Publication No. WO 2004/080406 and U.S. Patent Publication No. 2005/0107325. Enhanced Nuclease Resistance
[0180] An inhibitory dsRNA, e.g., an inhibitory dsRNA that targets ApoB, may be modified to enhance resistance to nucleases. For example, increased resistance may include identifying cleavage sites and modifying such sites to inhibit cleavage. For example, the dinucleotides 5'-UA-3', 5'-UG-3\ 5'-CA-3\ 5'-UU-3', or 5'-CC-3' can serve as cleavage sites, as described in PCT Publication No. WO 2005/115481.
[0181] For increased nuclease resistance and/or binding affinity to the target, an inhibitory dsRNA, e.g., the sense and/or antisense strands of the inhibitory dsRNA, may include, for example, 2'-modified ribose units and/or phosphorothioate linkages. For example, the 2' hydroxyl group (OH) can be modified or replaced with a number of different "oxy" or "deoxy" substituents.
[0182] Examples of "oxy"-2' hydroxyl group modifications include alkoxy or aryloxy (OR, e.g., R=H, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar); polyethyleneglycols (PEG), 0(CH2CH2O)nCH2CH2OR; "locked" nucleic acids (LNA) in which the 2' hydroxyl is connected, e.g., by a methylene bridge, to the 4' carbon of the same ribose sugar; 0-AMINE (AMINE=NH2; alkylamino, dialkylamino, heterocyclyl, arylamino, diaryl amino, heteroaryl amino, or diheteroaryl amino, ethylene diamine, polyamino) and aminoalkoxy, 0(CH2)nAMINE, (e.g., AMINE=NH2; alkylamino, dialkylamino, heterocyclyl, arylamino, diaryl amino, heteroaryl amino, or diheteroaryl amino, ethylene diamine, polyamino). It is noteworthy that oligonucleotides containing only the methoxyethyl group (MOE), (OCH2CH2OCH3, a PEG derivative), exhibit nuclease stabilities comparable to those modified with the robust phosphorothioate modification. The integer n may be any integer, e.g. 0 to 10. [0183] "Deoxy" modifications include hydrogen (i.e. deoxyribose sugars, which are of particular relevance to the overhang portions of partially dsRNA); halo (e.g., fluoro); amino (e.g. NH2; alkylamino, dialkylamino, heterocyclyl, arylamino, diaryl amino, heteroaryl amino, diheteroaryl amino, or amino acid); NH(CH2CH2NH)nCH2CH2-AMINE (AMINE=NH2; n=0 to 10), alkylamino, dialkylamino, heterocyclyl, arylamino, diaryl amino, heteroaryl amino, or diheteroaryl amino), -NHC(O)R (R=alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), cyano; mercapto; alkyl-thio-alkyl; thioalkoxy; and alkyl, cycloalkyl, aryl, alkenyl and alkynyl, which may be optionally substituted with e.g., an amino functionality. Exemplary substitutents include 2'-methoxyethyl, 2'-OCH3, 2'-O-allyl, 2'-C-allyl, and 2'-fluoro. [0184] In an exemplary embodiment, 2' modifications may be used in combination with one or more phosphate linker modifications (e.g., phosphorothioate).
[0185] All the pyrimidines of an inhibitory dsRNA may carry a 2'-modification which may have enhanced resistance to endonucleases. In some embodiments, enhanced nuclease resistance may also be achieved by modifying the 5' nucleotide, resulting, for example, in at least one 5'-uridine-adenine-3' (5'-UA-3') dinucleotide wherein the uridine is a 2'-modified nucleotide; at least one 5'-uridine-guanine-3' (5'-UG-3') dinucleotide, wherein the 5'-uridine is a 2'-modified nucleotide; at least one 5'-cytidine-adenine-3' (5'-CA-3') dinucleotide, wherein the 5'-cytidine is a 2'-modified nucleotide; at least one 5'-uridine-uridine-3' (5'-UU-3') dinucleotide, wherein the 5'-uridine is a 2'-modified nucleotide; or at least one 5'-cytidine-cytidine-3' (5'-CC- 3') dinucleotide, wherein the 5'-cytidine is a 2'-modified nucleotide. The inhibitory dsRNA may include, in some embodiments, at least 2, at least 3, at least 4 or at least 5 of such dinucleotides. For example, 5'-most pyrimidines in substantially all occurrences of the sequence motifs 5'-UA-3', 5'-CA-3', 5'-UU-3', and 5'-UG-3' may be 2'-modified.
[0186] The inclusion of furanose sugars in the oligonucleotide backbone may, in some embodiments, decrease endonucleolytic cleavage. For example, an inhibitory dsRNA may be further modified by including a 3' cationic group, or by inverting the nucleoside at the 3'- terminus with a 3'-3' linkage. In another alternative, the 3'-terminus may be blocked with an aminoalkyl group, e.g., a 3' C5-aminoalkyl dT, or other 3' conjugates such as naproxen or ibuprofen, small alkyl chains, aryl groups, or heterocyclic conjugates or modified sugars (D- ribose, deoxyribose, glucose etc.). In another embodiment, a 5' conjugate may be included, such as naproxen or ibuprofen, may inhibit exonucleolytic cleavage by sterically blocking the exonuclease from binding to the 5'-end of oligonucleotide.
[0187] In some embodiments, an inhibitory dsRNA may have increased resistance to nucleases when a duplexed inhibitory dsRNA includes a single- stranded nucleotide overhang on at least one end. In exemplary instances, the nucleotide overhang includes 1 to 4, e.g. about 2 to 3, unpaired nucleotides. For example, an unpaired nucleotide of the single- stranded overhang that is directly adjacent to the terminal nucleotide pair contains a purine base, and the terminal nucleotide pair is a G-C pair, or at least two of the last four complementary nucleotide pairs are G-C pairs. In further instances, a nucleotide overhang may have 1 or 2 unpaired nucleotides, and in an exemplary instance a nucleotide overhang is 5'-GC-3', for example on the 3'-end of the antisense strand. In one instance, the inhibitory dsRNA includes the motif 5'- CGC-3' on the 3'-end of the antisense strand, such that a 2-nt overhang 5'-GC-3' is formed.
[0188] For example, an inhibitory dsRNA may include monomers which have been modified so as to inhibit degradation, e.g., by nucleases, e.g., endonucleases or exonucleases, found in the body of a subject. These monomers are referred to herein as NRMs, or Nuclease Resistance promoting Monomers or modifications. In many cases these modifications will modulate other properties of the inhibitory dsRNA as well, e.g., the ability to interact with a protein, e.g., a transport protein, e.g., serum albumin, or a member of the RISC, or the ability of the first and second sequences to form a duplex with one another or to form a duplex with another sequence, e.g., a target molecule.
[0189] Modifications that may be useful for producing inhibitory dsRNA that invoke nuclease resistance may include one or more of the following chemical and/or stereochemical modifications of the sugar, base, and/or phosphate backbone:
[0190] (1) chiral (Sp) thioates, e.g., that include nucleotide dimers with a particular chiral form of a modified phosphate group containing a heteroatom at the nonbridging position, e.g., Sp or Rp, at the position X, where this is the position normally occupied by the oxygen. The atom at X may be for example, selected from S, Se, Nr2, or Br3. For example, when X is S, the linkage may be an enriched or chirally pure Sp linkage.
[0191] (2) attachment of one or more cationic groups to the sugar, base, and/or the phosphorus atom of a phosphate or modified phosphate backbone moiety, for example, NRMs including monomers at the terminal position derivatized at a cationic group. In an embodiment, a 5'-end of an antisense sequence has a terminal —OH or phosphate group so that a NRM is not used at the 5'-end of an antisense sequence. The group should be attached at a position on the base which minimizes interference with H bond formation and hybridization, e.g., away form the face which interacts with the complementary base on the other strand, e.g., at the 5' position of a pyrimidine or a 7-position of a purine.
[0192] (3) nonphosphate linkages at the termini, for example a NRM that includes non- phosphate linkages, e.g., a linkage of 4 atoms which confers greater resistance to cleavage than does a phosphate bond. Examples include 3' CH2-NCH3-O-CH2-S' and 3' CH2-NH-(O=)-CH2-
5'. [0193] (4) 3'-bridging thiophosphates and 5'-bridging thiophosphates.
[0194] (5) L-RNA, 2'-5' linkages, inverted linkages, a-nucleosides, e.g. L nucleosides and dimeric nucleotides derived from L-nucleosides; 2'-5' phosphate, non-phosphate and modified phosphate linkages (e.g., thiophosphates, phosphoramidates and boronophosphates); dimers having inverted linkages, e.g., 3'-3' or 5'-5' linkages; monomers having an alpha linkage at the I' site on the sugar, e.g., the structures described herein having an alpha linkage;
[0195] (6) conjugate groups, e.g., a targeting moiety or a conjugated ligand described herein conjugated with the monomer, e.g., through the sugar, base, or backbone;
[0196] (7) abasic linkages, e.g., an abasic monomer as described herein (e.g., a nucleobaseless monomer); an aromatic or heterocyclic or polyheterocyclic aromatic monomer as described herein; and
[0197] (8) 5'-phosphonates and 5'-phosphate prodrugs. For example, NRM's may include monomers, e.g. at the terminal position, e.g., the 5' position, in which one or more atoms of the phosphate group is derivatized with a protecting group, which protecting group or groups, may be removed as a result of the action of a component in the subject's body, e.g., a carboxyesterase or an enzyme present in the subject's body.
[0198] In some embodiments, one or more different NRM modifications may be introduced into an inhibitory dsRNA or into a sequence of an inhibitory dsRNA. An NRM modification can be used more than once in a sequence or in an inhibitory dsRNA. As some NRMs interfere with hybridization the total number incorporated should be such that acceptable levels of inhibitory dsRNA duplex formation are maintained. For example, NRM modifications may be introduced into the terminal cleavage site or in the cleavage region of a sequence (a sense strand or sequence) which does not target a desired sequence or gene in the subject, which may reduce off-target silencing.
[0199] Nuclease resistant modifications may include those placed only at the terminus and others which may be placed at any position. Such modifications may inhibit hybridization, and in some embodiments, modifications are used only in terminal regions. A NRM can be used anywhere in a sense sequence, provided that sufficient hybridization between the two sequences of the inhibitory dsRNA is maintained. In some instances it is desirable to put a NRM at the cleavage site or in the cleavage region of a sequence which does not target a subject sequence or gene, as it can minimize off-target silencing.
[0200] In most cases, any nuclease-resistance promoting modifications will be distributed differently depending on whether the sequence will target a sequence in the subject (often referred to as an antisense sequence) or will not target a sequence in the subject (often referred to as a sense sequence). If a sequence is to target a sequence in the subject, modifications which interfere with or inhibit endonuclease cleavage should not be inserted in the region which is subject to RISC mediated cleavage, e.g., the cleavage site or the cleavage region (As described in Elbashir et al., 2001, Genes and Dev. 15: 188, hereby incorporated by reference). Such modifications may be introduced into the terminal regions, e.g., at the terminal position or within 2, 3, 4, or 5 positions of the terminus, of a sequence which targets or a sequence which does not target a sequence in the subject.
[0201] Inhibitory dsRNA may, in some embodiments, include a 5' phosphorylate or include a phosphoryl analog at the 5' prime terminus. Possible 5'-phosphate modifications of the antisense strand include those which are compatible with RISC mediated gene silencing. Suitable modifications include: 5'-monophosphate ((HO)2(O)P-O-S'); 5'-diphosphate ((HO)2(O)P-O-P(HO)(O)-O-5'); 5'-triphosphate ((HO)2(O)P-O-(HO)(O)P-O-P(HO)(O)- 0-5'); 5'-guanosine cap (7-methylated or non-methylated) (7m-G-O-5'-(HO)(O)P-O- (H0)(0)P-0-P(H0)(0)-0-5'); 5'-adenosine cap (Appp), and any modified or unmodified nucleotide cap structure (N-O-5'-(HO)(O)P-O-(HO)(O)P-O-P(HO)(O)-O-5'); 5'- monothiophosphate (phosphorothioate; (HO)2(S)P- 0-5'); 5'-monodithiophosphate (phosphorodithioate; (HO)(HS)(S)P-O-5'), 5'-phosphorothiolate ((HO)2(O)P-S-5'); any additional combination of oxygen/sulfur replaced monophosphate, diphosphate and triphosphates (e.g. 5'-alpha-thiotriphosphate, 5'-gamma-thiotriphosphate, etc.), 5'- phosphoramidates ((HO)2(O)P-NH-5', (HO)(NH2)(O)P--O-5'), 5'-alkylphosphonates (R=alkyl=methyl, ethyl, isopropyl, propyl, etc., e.g. RP(0H)(0)-0-5'-, (OH)2(O)P-5'-CH2-), 5'-alkyletherphosphonates (R=alkylether=methoxymethyl (MeOCH2-), ethoxymethyl, etc., e.g. RP(0H)(0)-0-5'-).
[0202] In some embodiments, a sense strand can be modified in order to inactivate the sense strand and prevent formation of an active RISC, thereby potentially reducing off-target effects, for example, by a modification which prevents 5'-phosphorylation of the sense strand, e.g., by modification with a 5'-O-methyl ribonucleotide (see Nykanen et al., (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309-321.) Other modifications which prevent phosphorylation can also be used, e.g., simply substituting the 5'-OH by H rather than O-Me. Alternatively, a large bulky group may be added to the 5'-phosphate turning it into a phosphodiester linkage.
[0203] More detailed and specific modifications for an inhibitory dsRNA, such as phosphate group and/or sugar group modifications, replacement of the phosphate group and/or ribophosphate backbone, terminal modifications or base modifications, as well as preferred inhibitory dsRNA formula, can be found in U.S. Patent Publication No. 2007/0275914.
^Evaluation of candidate inhibitory nucleic acid molecule
[0204] A candidate inhibitory dsRNA may be evaluated for its ability to downregulate target gene expression. For example, a candidate inhibitory dsRNA may be contacted with a cell that expresses the target gene either endogenously or because it has been transfected with a construct from which the gene can be expressed. The level of target gene expression prior to and following contact with the candidate inhibitory dsRNA can be compared, e.g. on an mRNA or protein level. If it is determined that the amount of RNA or protein expressed from the target gene is lower following contact with the inhibitory dsRNA, then it can be concluded that the inhibitory dsRNA downregulates target gene expression. The level of target RNA or protein in the cell can be determined by any method desired. For example, the level of target RNA can be determined by Northern blot analysis, reverse transcription coupled with polymerase chain reaction (RT-PCR), or RNAse protection assay. The level of protein can be determined, for example, by Western blot analysis. [0205] A functional assay can also be used in some embodiments, to evaluate a modified candidate inhibitory dsRNA. A functional assay can be applied to determine if the modification alters the ability of the molecule to silence gene expression. For example, a cell, e.g., a mammalian cell, such as a mouse or human cell, can be co-transfected with a plasmid expressing a fluorescent protein, e.g., GFP, and a candidate inhibitory dsRNA homologous to the transcript encoding the fluorescent protein (see, e.g., WO 00/44914). For example, a modified inhibitory dsRNA homologous to the GFP mRNA can be assayed for the ability to inhibit GFP expression by monitoring for a decrease in cell fluorescence, as compared to a control cell, in which the transfection did not include the candidate inhibitory dsRNA, e.g., controls with no inhibitory dsRNA added and/or controls with a non-modified inhibitory dsRNA added. Efficacy of the candidate inhibitory dsRNA on gene expression can be assessed by comparing cell fluorescence in the presence of the modified and unmodified inhibitory dsRNA molecules.
Stability Testing, Modification, and Retesting of inhibitory nucleic acid molecules [0206] A candidate inhibitory dsRNA may be evaluated with respect to stability, e.g., its susceptibility to cleavage by an endonuclease or exonuclease, such as when the inhibitory dsRNA is introduced into the body of a subject. For example, methods can be employed to e.g., identify sites that are susceptible to modification, particularly cleavage, e.g., cleavage by a component found in the body of a subject. [0207] When sites susceptible to cleavage are identified, a further inhibitory dsRNA can be designed and/or synthesized wherein the potential cleavage site is made resistant to cleavage, e.g. by introduction of a 2'-modification on the site of cleavage, e.g. a 2'-O-mathyl group. This further inhibitory dsRNA can be retested for stability, and this process may be iterated until an inhibitory dsRNA is found exhibiting the desired stability. [0208] For example, a candidate inhibitory dsRNA, e.g., a modified inhibitory dsRNA, may be scanned for a selected property by e.g. exposing the inhibitory dsRNA or modified inhibitory dsRNA and a control molecule to the appropriate conditions and evaluating for the presence of the selected property. For example, resistance to a degradent can be evaluated as follows. A candidate modified inhibitory dsRNA {e.g., a control molecule, usually the unmodified form) can be exposed to degradative conditions, e.g., exposed to a milieu, which includes a degradative agent, e.g., a nuclease. For example, one can use a biological sample, e.g., one that is similar to a milieu, which might be encountered, in therapeutic use, e.g., blood or a cellular fraction, e.g., a cell-free homogenate or disrupted cells. The candidate and control could then be evaluated for resistance to degradation by any of a number of approaches. For example, the candidate and control may be labeled, e.g. prior to exposure, with, e.g., a radioactive or enzymatic label, or a fluorescent label, such as Cy3 or Cy5. Control and modified inhibitory dsRNA can be incubated with the degradative agent, and optionally a control, e.g., an inactivated, e.g., heat inactivated, degradative agent. A physical parameter, e.g., size, of the modified and control molecules are then determined. They can be determined by a physical method, e.g., by polyacrylamide gel electrophoresis or a sizing column, to assess whether the molecule has maintained its original length, or assessed functionally.
Alternatively, Northern blot analysis can be used to assay the length of an unlabeled modified molecule.
In Vivo Testing
[0209] An inhibitory dsRNA identified as being capable of inhibiting target gene expression can be tested for functionality in vivo in an animal model (e.g., in a mammal, such as in mouse or rat). For example, the inhibitory dsRNA can be administered to an animal, and the inhibitory dsRNA evaluated with respect to its biodistribution, stability, and its ability to inhibit target gene expression.
[0210] For example, an inhibitory dsRNA can be administered directly to the target tissue, such as by injection, or an inhibitory dsRNA can be administered to the animal model in the same manner that it would be administered to a human. An inhibitory dsRNA can also be evaluated for its intracellular distribution. Such evaluation may include determining whether the inhibitory dsRNA was taken up into the cell and/or may include determining the stability (e.g., the half-life) of the inhibitory dsRNA. In an exemplary embodiment, an evaluation of an inhibitory dsRNA in vivo can be facilitated by use of an inhibitory dsRNA conjugated to a traceable marker (e.g., a fluorescent marker such as fluorescein; a radioactive label, such as 35S, 32P, 33P, or 3H; gold particles; or antigen particles for immunohistochemistry).
[0211] In some embodiments, an inhibitory dsRNA useful for monitoring biodistribution can lack gene silencing activity in vivo. For example, the inhibitory dsRNA can target a gene not present in the animal (e.g., an inhibitory dsRNA injected into mouse can target luciferase), or an inhibitory dsRNA can have a non-sense sequence, which does not target any gene, e.g., any endogenous gene). Localization/biodistribution of the inhibitory dsRNA can be monitored, e.g. by a traceable label attached to the inhibitory dsRNA, such as a traceable agent described above.
[0212] Inhibitory dsRNA may be evaluated with respect to its ability to modulate, e.g. down regulate a given target gene expression. Levels of target gene expression in vivo can be measured, for example, by in situ hybridization, or by the isolation of RNA from tissue prior to and following exposure to the inhibitory dsRNA. Where the animal needs to be sacrificed in order to harvest the tissue, an untreated control animal will serve for comparison. Target mRNA can be detected by any desired method, including but not limited to RT-PCR, Northern blot, branched-DNA assay, or RNAase protection assay. Alternatively, or additionally, target gene expression can be monitored by performing Western blot analysis on tissue extracts treated with the inhibitory dsRNA.
[0213] In one example, a candidate inhibitory dsRNA homologous to an endogenous mouse gene, e.g., a maternally expressed gene, such as c-mos, can be injected into an immature mouse oocyte to assess the ability of the inhibitory dsRNA to inhibit gene expression in vivo (see, e.g., WO 01/36646). A phenotype of the oocyte, e.g., the ability to maintain arrest in metaphase II, can be monitored as an indicator that the inhibitory dsRNA is inhibiting expression. For example, cleavage of c-mos mRNA by the inhibitory dsRNA may cause the oocyte to exit metaphase arrest and initiate parthenogenetic development (Colledge et al. Nature 370: 65-68, 1994; Hashimoto et al. Nature, 370:68-71, 1994). The effect of a modified inhibitory dsRNA on target RNA levels may be verified by, for example, a Northern blot to assay for a decrease in the level of target mRNA, or by Western blot to assay for a decrease in the level of target protein, as compared to a negative control. Such controls may include e.g. cells in which no inhibitory dsRNA is added and/or cells in which a non-modified inhibitory dsRNA is added.
Targets
[0214] Disclosed chimeric therapeutics, particles and/or compositions include a nucleic acid, for example a RNA, as described above. In one embodiment, a nucleic acid is targeted to specific gene target, such as apoB, for example, a provided nucleic acid is substantially homologous to a region of the apoB gene, for example, a mammalian (e.g. human or mouse) apoB gene. In other embodiments, chimeric therapeutics, particles and/or compositions include a nucleic acid targeted to one or more of: prothrombin, FIX, angiotensinogen, renin (see US20070270365), TFPI (see US7022672), CCR5, HCV (see US20070149470), SYK (see US 7173015), RANKL, IL-23 (see WO2004/094636), Complement C3 (see US20070178068), Factor H, IL-4Ralpha (see US 2005014333), RBP4, glucagon/glucagon receptor (see US2008/0113372), ghrelin (see US20080140056), GOAT, gastrin, PTPlB, leptin, PCSK-9, IGF-IR, cMet, DR4, DR5, VEGF-A, HGF, sclerostin, and/or myostatin.
[0215] Provided herein are methods for delivering, in vivo or in vitro, a nucleic acid targeting a particular target to a cell, e.g. by contacting a composition, therapeutic or particle disclosed herein with a cell. Also provided here are in vitro and in vivo methods for modulating, e.g., downregulating or silencing the transcription and translation of particular targets. In some embodiments, administered compositions, particles or therapeutics disclosed herein may localize in the liver or to the gut, e.g., the intestine, such as to the jejunum of the intestine after administration to a patient.
[0216] Also provided herein are methods of treating a disease or disorder characterized by e.g., a particular target expression, e.g. target misexpression, including, but not limited to those diseases and disorders associated with misexpression, and that include administering to a patient in need thereof an effective amount of a disclosed composition, therapeutic, or particle. Such methods can further include administration (e.g., concurrently or consecutively) with conventional agents used to treat such diseases or disorders. [0217] Various methodologies, such as those described herein (gene walks, algorithm computation) can be utilized to select candidate nucleic acids targeting particular targets. For example, nucleic acids targeting specific targets may be identified using the methods set forth herein.
[0218] In other embodiments, contemplated nucleic acids, e.g. RNAs targeting specific gene targets include those recited in the following patents and patent applications, hereby incorporated by reference, and targeting the following genes: VEGF (see U.S. Patent 7,176,304), HIFl (see U.S. Patent Publication No. 20080188430), SARS (see U.S. Patent Publication No. 20070270360), HDAC (see U.S. Patent Publication No. 20070185049); Nogo and Nogo Receptor (see U.S. Patent Publication No. 20070185043), WHN (see U.S. Patent Publication No. 20070179104), PCSK9 (see U.S. Patent Publication No. 20070173473), CETP (see U.S. Patent Publication No. 20070173467), XIAP (see U.S. Patent Publication No. 20070093437), CHK-I (see U.S. Patent Publication No. 20060216747), HR (see U.S. Patent Publication No. 20060160757), CDK2 (see U.S. Patent Publication No. 20060142225), PGF (see U.S. Patent Publication No. 20050267058), PTP-IB (see U.S. Patent Publication No. 20060025361), TGF-beta and TGF-beta Receptor (see U.S. Patent Publication No. 20050287128), STAT3 (see U.S. Patent Publication No. 20050196781), GAB2 (see U.S. Patent Publication No. 20050196767), ICAM (see U.S. Patent Publication No. 20050187174), BCL-2 (see U.S. Patent Publication No. 20050176025), ADAM33 (see U.S. Patent Publication No. 20050164968), EZH2 (see U.S. Patent Publication No. 20050159382), PCNA (see U.S. Patent Publication No. 20050158735), c-SRC (see U.S. Patent Publication No. 20040101850), Notch2 (see U.S. Patent Publication No. 20040101847), IL22 (see U.S. Patent Publication No. 20040097447), Adam9 (see U.S. Patent Publication No. 20040092466), PIM-I (see U.S. Patent Publication No. 20040092463), TNFSF14 (see U.S. Patent Publication No. 20040096835), MAGE-Dl (see U.S. Patent Publication No. 20040110702), CDlD (see U.S. Patent Publication No. 20040110700), SEDL (see U.S. Patent Publication No. 20040110160), NRF (see U.S. Patent Publication No. 20040110156), BAF53 (see U.S. Patent Publication No. 20040110147), MALTl (see U.S. Patent Publication No. 20040110145), CDK9 (see U.S. Patent Publication No. 20040110140), PAKl (see U.S. Patent Publication No. 20040102623), KU86 (see U.S. Patent Publication No. 20040102404), and PPMlB (see U.S. Patent Publication No. 20040102397).. [0219] Contemplated nucleic acids include those targeting targets associated with viral infections, for example, those nucleic acids targeting the following viruses and recited in the following patent applications: Influenza Virus (see U.S. Patent Publication No. 20070197460), HCV (see U.S. Patent Publication No. 20080207542), RSV (see U.S. Patent Publication No. 20060287267), and HIV (see U.S. Patent Publication No. 20050191618), wherein each patent and patent application is incorporated by reference.
Administration and Dosage
[0220] Disclosed chimeric therapeutics, compositions and/or particles may be administered to a patient by any conventional route. These include, but are not limited to, the systemic routes, e.g. subcutaneous, intradermal, intramuscular or intravenous route, and mucosal routes, e.g. oral, nasal, pulmonary or anogenital route. For example, an intratumoral route may be used in e.g. the treatment of solid tumors. When the treatment of genetic diseases is involved, the choice of the route of administration will depend on the nature of the disease; for example, particles and/or compositions may be administered via a pulmonary route in the case of cystic fibrosis (e.g. wherein the particles are formulated in aerosol form) or e.g. via intravenous route in the case of hemophilia.. [0221] For example, disclosed particles may be administered a composition that comprises a biocompatible aqueous solution. Contemplated solutions may include water and/or saline, and may optionally contain pharmaceutical excipients known to those skilled in the art, for example, buffers, stabilizing molecules, preservatives, sugars, amino acids, proteins, carbohydrates and vitamins, and the like. [0222] The administration of disclosed particles or compositions can be carried out at a single dose or at a dose repeated once or several times after a certain time interval. The appropriate dosage varies according to various parameters, for example the therapeutically effective dosage is dictated by and directly dependent on the individual treated, the mode of administration, the unique characteristics of the nucleic acid and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals. Appropriate doses can be established by persons skilled in the art of pharmaceutical dosing such as physicians. The particles can be included in a container, pack, or dispenser together with instructions for administration.
[0223] In some embodiments, the particles and compositions disclosed herein may allow for sustained release of a nucleic acid, e.g. an inhibitory nucleic acid, to e.g. a specific body target site, e.g., the liver. For example, in some embodiments, the disclosed compositions and/or particles may allow for release of a nucleic acid over about 1 day to about 7 days or more, e.g. about 1 day to about 3 days or more, or about 1 day to about 3 weeks or more.
[0224] In an embodiment, long-term storage stability of disclosed particles may be increased and/or enhanced by for example, freezing and lyophilizing particles disclosed herein in the presence of one or more protective agents such as sucrose, mannitol, trehalose or the like. Upon rehydration of the lyophilized particles, the suspension may, for example, retain essentially all nucleic acid previously encapsulated and/or may retain substantially the same particle size. Rehydration may be accomplished by e.g., adding purified or sterile water or 0.9% sodium chloride injection or 5% dextrose solution followed by gentle swirling of the suspension. EXAMPLES
[0225] The examples which follow are intended in no way to limit the scope of the invention but are provided to illustrate different features of the present invention, including preparation and use of the therapeutics contemplated herein. Many other embodiments of this invention will be apparent to one skilled in the art. Example 1
A. HPV S280C His-tagged protein
[0226] A HPV S280C His-tagged protein is cloned into the Ndel/Xhol restriction sites of vector pET21b (Novagen). This plasmid is transformed into E. coli BL21 (DE3) pLysS cells (Stratagene) for protein expression. The amino acid sequence of the His-tagged HPV S280C protein is depicted below:
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIH LPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGI SGHPLLNKLDDTENASAYAANAGVDNRECI SMDYK QTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSI CKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGCGSTANLASSNYFPTPSGSMVTSDA QIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAI STSETTYKNTNFKEYLRHGEEYDLQFIFQLCK ITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFS
ADLDQFPLGRKFLLQLGLKAKPKFTLGKRKATPTTSSTSTTAKRKKRKLLEHHHHHH (SEQ ID NO: 57)
B. Poly-lysine Tail Mutants
[0227] DNA fragment containing the HPV K5 construct is synthesized via PCR using the HPV K5 template and primers. The HPV K5 template consists of the HPV nucleic acid sequence cloned into the Ndel/Xhol restriction sites of vector pET22b. PCR primers are designed to introduce 5 lysine residues to the HPV tail portion. Each PCR reaction is composed of 12.5 μl of 5X GC polymerase buffer (Finnzyme), 1.25 μl of a 1OmM dNTP mixture, 1.5 μl of 5 μM forward primer, 1.5 μl of 5 μM reverse primer, 0.6 μl of Stratagene mini-prepped template, 0.8 μl of2 unit/μl Phusion Hot Start polymerase (Finnzyme), and 44.25 μl of water. The PCR reaction consists of a one-time incubation at 980C for 1 minute, followed by incubation at 98°C for 25 seconds, incubation at 70°C for 30 seconds, and incubation at 72°C for 1 minute and 10 seconds. These last three steps are repeated 24 times followed by a final incubation at 72°C for 7 minutes. [0228] The PCR product and a pET22b vector are both digested with restriction enzymes Ndel and Xhol at 370C for 2 hours. The digested products are run on an agarose gel, the bands excised, and purified via gel extraction (Stratagene). Ligation reaction is composed of 5 μl of digested and purified PCR product, 1 μl of digested and purified pET22b vector, 1 μl of T4 DNA ligase buffer (NEB), 1 μl of T4 DNA ligase (NEB), and 2 μl of water and is incubated at room temperature for 12 hours.
[0229] The ligation reaction is transformed into XLI Blue E. coli cells (Stratagene) and the resulting colonies are grown in IX LB broth and the plasmid purified via mini-prep (Stratagene). The purified plasmid is sequenced (see below) and transformed into E. coli BL21 (DE3) pLysS cells (Stratagene) for protein expression. This strategy can be used for proteins containing from 0 to 30 lysine residues.
C. Modified Structural Core Mutants:
[0230] DNA fragment containing the SV40 K137C construct is synthesized via PCR using the SV40 K137C template . Each PCR reaction consists of 5 μl of 1OX Pfu Turbo polymerase buffer (Stratagene), 1 μl of a 10 mM dNTP mixture, 1.5 μl of 5 μM forward primer, 1.5 μl of 5 μM reverse primer, 1 μl of Stratagene mini-prepped template, 1 μl of 2.5 unit/μl Pfu Turbo polymerase (Stratagene), and 39 μl of water. The PCR reaction consists of a one-time incubation at 98°C for 1 minute, followed by incubation at 98°C for 30 seconds, incubation at 64-72°C (depending on primer Tm) for 1 minute, and incubation at 72°C for 6 minutes. These last three steps are repeated 20 times.
[0231] The PCR product is digested with the restriction enzyme Dpnl at 37°C for 1.5 hours to rid the reaction of any un-mutated template. The digested product is run on a 1% agarose gel, the bands excised, and purified via gel extraction (Stratagene).
[0232] The PCR product is then transformed into E. coli BL21 (DE3) PlysS cells (Stratagene) and the resulting colonies are grown in IX LB broth and the plasmid purified via mini-prep (Stratagene). The purified plasmid is then sequenced to confirm the change in nucleic acid sequence. This strategy can be applied to single amino acid changes or the deletion or insertion of multiple amino acid residues such as the removal of a poly-histidine tag. Example 2
[0233] Various wild type and modified core proteins described herein can be expressed and purified according to Protocol 1 or Protocol 2 as follows:
Protocol 1:
[0234] A pET-lla vector containing the full-length HPV-protein gene, is transformed into E. coli DE3 cells and grown at 370C in LB media, fortified with 2-4% glucose, trace elements and 200 μg/mL carbenicillin. Protein expression is induced by the addition of 2mM IPTG (isopropyl-beta-D-thiogalactopyranoside). Cells are harvested by pelleting after three hours of induction. SDS-PAGE is used to assess expression of C-protein.
[0235] HPV protein is purified from E. coli by resuspending in a solution of 50 mM Tris- HCl, pH 7.4, ImM EDTA, 5 mM DTT, ImM AEBSF, O.lmg/mL DNasel and 0.1 mg/mL RNase. Cells are then lysed by passage through a French pressure cell. The suspension is centrifuged at 2600OxG for one hour. The pellet is discarded and solid sucrose added to the supernatant to a final concentration of 0.15 M and centrifuged at 10000OxG for one hour. The pellet is discarded and solid (NH4)ISO4 is then added to a final concentration of 40% saturation, stirred for one hour and then centrifuged for one hour at 2600OxG. The pellet is resuspended in a solution of 100 mM Tris-HCI at pH 7.5, 100 mM NaCl, 50 rnM sucrose and 2 mM DTT (Buffer A) and loaded onto a Sepharose CL-4B (Phannacia Biotech, Piscataway, NJ) column (5 cm diameter X 95 cm) equilibrated with Buffer A. and the column eluted at 2mL/minute. Using this purification scheme, HPV viral capsids are separated from large aggregates and from soluble proteins of lower molecular weight. The fractions are pooled according to chromatographic profile and SDS-PAGE analysis and the solution concentrated by ultrafiltration using Diaflo YM 100 ultrafiltration membrane (Amicon, Beverly, MA) to about 10 mg/mL. Concentrated HPV protein is dialyzed against 50 mM Tris-HCI, pH 7.5 and 0.15 M sucrose. The solution is then adjusted to pH 9.5 with ION NaOH and urea added to a final concentration of 3.5 M. The solution is then filtered using a Millex-HA 0.45 urn pore size filter unit (Millipore, Bedford, MA) and applied to a column (6.0 cm diameter X 60 cm) of Superdex 75 (Pharmacia Biotech, Piscataway, NJ) equilibrated with 100 mM sodium bicarbonate, pH 9.5, containing 2 mM DTT. The column is eluted at 5 niL/minute. The fractions containing dimeric protein as assessed by SDS-PAGE are pooled. These procedures can be used for the expression and purification of all core protein mutants. Alternately, the expression of this protein can be done in yeast cells according to methods well known to persons skilled in the art.
Protocol 2: [0236] All protein constructs containing a C-terminal 6-histidine tag are purified as follows:
[0237] The pET vector containing the gene for HPV His-tagged protein is kept in BL21 (DE3) PlysS cells for expression. The starter culture can be inoculated from a colony on an IX Luria Broth (IXLB) agar plate or from a 10% glycerol stock, stored at -80 0C. The IXLB is autoclaved in a 2 L flask and cooled. 100 mg of ampicillin (Amp) is added to the IXLB. A started culture is inoculated and allowed to grow for up to 24 hours with shaking at 200 rpm at 37 0C.
[0238] Fifteen 2 L flasks with 0.8 L of 2X yeast-tryptone (2XYT) broth is autoclaved and 1 mL of 100 mg/mL Amp is added to each flask. 50 mL of starter culture is then added to each flask. The culture is incubated at 37 0C, while shaking at 200 rpm until the optical density (OD) at 600 nm reaches 0.4-0.6. This process should take approximately 2 hours. When the OD reaches 0.4-0.6, the culture is induced with 1 mL of 1 M IPTG. Shaking is continued for 4 more hours until OD reaches 2.0 or greater. The cells are harvested by centrifuging in 500 mL centrifuge bottles at 11300 g for 8 minutes. The bacterial pellets are transferred into two 50 mL conical tubes. Each tube is labeled with date/construct/prep number and frozen at -200C. [0239] Two 50 ml tubes (approximately 20 mL each) of cell paste are thawed and the following steps are applied to each tube. 40 mL resuspension buffer (5 M urea, 50 mM NaHCO3 (pH 9.5), 10 mM imidazole) is added into each tube. The cells are suspended by continuous pipetting and poured into a 400 mL beaker. More resuspension buffer is added until there is -100 mL total cell resuspension in the beaker. The beaker containing resuspended cells is placed in an ice bath and sonicated for 5 minutes using a Branson probe sonifier (pulse mode at approximately 40% duty cycling and power setting of 5). The cell mixture should be sonicated in several intervals, and allowed to rest on ice in-between, if it appears that the sample is heating to higher than room temperature. The cell lysate is diluted 2 fold to 200 mL total, and 200 μL of 100 mg/mL DNaseis added to the suspension. This suspension is stirred while on ice for 10 minutes. The sonication step is repeated for 5 more minutes while on ice. The lysate is transferred to six 50 rnL plastic centrifuge tubes, and centrifuged at 32000 g for 45 minutes. Supernatant is discarded.
[0240] For purification, a 50 rnL Ni2+-NTA agarose (Qiagen) column is washed and equilibrated in the resuspension buffer. A full 12 L cell growth is lysed for each run of the column. The centrifuged lysate from 12 L worth of cells is combined and diluted to 500 mL with resuspension buffer. The centrifuged cell lysate is loaded onto the column, and the protein solution is allowed to sink to the top of the nickel matrix. 50 mL of resuspension buffer is passed through the column. An optional salt wash can be performed by washing the column with 250 mL of NaCl wash buffer (5 M urea, 50 mM NaHCO3 (pH 9.5), 20 mM imidazole, 250 mM NaCl). This salt wash reduces the A260/A280 ratio of the final purified protein by a value of 0.1 A.U.. The column is washed with 250 mL of wash buffer (5 M Urea, 50 mM NaHCO3 (pH 9.5), 20 mM imidazole), and 200 mL of elution buffer (5 M Urea, 2 mM NaHCO3 (pH 9.5), 250 mM imidazole) is through the column. Fractions are collected at every 5 mL, which should yield 5 to 8 fractions that contain protein. [0241] The presence and/or concentration of protein is detected by measuring the absorbance of the fractions. SDS polyacrylamide gel electrophoresis (SDS PAGE) analysis is performed on the proteins to determine purity. Fractions containing protein are pooled, and transferred to dialysis tubing. Dialysis is performed in 4 L of storage buffer (5 M Urea, 2 mM NaHCO3 (pH 9.5)) for at least 4 hours at 4 0C. The protein can then be concentrated in an Amicon stirred cell concentrator (Millipore) to a final protein concentration of up to 75 mg/ml. A 12 L cell growth yields approximately 500 mg of pure protein. Pure dialyzed protein can be stored at -80 0C for 6-8 months.
Example 3
[0242] Conjugation of phospholipids via a SMPB (succinimidyl-4-(p-maleimidophenyl) butyrate) intermediate is depicted schematically in Figure 1.
[0243] 100 μmoles of phosphatidyl ethanolamine (PE) is dissolved in 5 mL of argon- purged, anhydrous methanol containing 100 μmoles of triethylamine (TEA). The solution is maintained under an argon or nitrogen atmosphere. The reaction can also be done in dry chloroform. 50 mg of SMPB (Pierce) is added to the PE solution and mixed well to dissolve. [0244] The solution is maintained under an argon or nitrogen atmosphere while the reaction proceeds for 2 hours at room temperature. Methanol is removed from the reaction solution by rotary evaporation and the solids are redissolved in chloroform (5 mL). The water-soluble reaction by-products is extracted from the chloroform with an equal volume of 1% NaCl. Extraction is performed twice. The MPB-PE derivative is purified by chromatography on a column of silicic acid (Martin FJ et al., Immuno specific targeting of liposomes to cells: A novel and efficient method for covalent attachment of Fab' fragments via disulfide bonds. Biochemistry, 1981; 20:4229-38). Chloroform is removed from the MBP-PE by rotary evaporation, and the derivative is stored at -20 0C under a nitrogen atmosphere until use. Example 4
[0245] Conjugation of a maleimide-containing linker to a sulfhydryl-containing protein is depicted schematically in Figure 2.
[0246] The sulfhydryl-containing protein is dissolved in TRIS *HC1 buffer (pH = 8.0, 100 mM) to obtain a concentration of 1 mM). The solution is purged under a nitrogen or argon atmosphere for 20 minutes. The maleimide-containing linker is dissolved in the same buffer as above, and purged under a nitrogen or argon atmosphere for 20 minutes, to obtain a 10-fold molar excess.
[0247] The two solutions are combined and purged under a nitrogen or argon atmosphere for an additional 20 minutes. The reaction is allowed to proceed for 6 hours at room temperature.
Example 5
[0248] The instant example describes a general method for forming a therapeutic particle containing inhibitory dsRNA .
[0249] The protein is allowed to thaw to 25 0C. The inhibitory dsRNA-containing solution is added to the protein solution at a molar ratio of 9.58:1 or 9.42: 1 for non-modified or modified inhibitory dsRNA, respectively. The solution is mixed for 1 hour at 25 0C. BME is added at a molar ratio of 3: 1 to the protein to protect cysteine functional groups. This reaction is incubated for 1 hour at 25 0C. A 2:1 volume ratio of 10 mM NaCl solution is added to reaction mixture containing protein and inhibitory dsRNA. The solution is kept in a water bath set to 25 0C for 48 hours. [0250] To functionalize protein with maleimide-terminated lipid, 2X molar excess of PE- MAL (l,2-Dipalmitoyl-sn-Glycero-3-Phosphoethanolamine-N-[4-(p-maleimidophenyl)- butyramide] (Sodium Salt)) predissolved in 400 μL DMF (dimethylformamide) is added dropwise to the protein and inhibitory dsRNA-containing solution, and allowed to react for 10 minutes.
[0251] To make lipid coating material, cholesterol (Avanti Lipids, Alabaster, AL, USA), HSPC (L-α-Phosphatidylcholine, Hydrogenated (Soy), Avanti Lipids, Alabaster, AL, USA) and POPG (l-Palmitoyl-2-Oleoyl-sft-Glycero-3-[Phospho-rac-(l -glycerol)] (Sodium Salt), Avanti Lipids, Alabaster, AL, USA) in dry power forms are premixed in a 3:1:1 molar ratio, respectively, in a glass beaker. The mixture is predissolved and homogenized with 2.0 mL of chloroform. Once homogenized, the chloroform is allowed to evaporate (20 to 30 minutes on a hot plate set to 50 0C). When dry, 0.5X PBS pH 9.5 (phosphate buffered saline with 5 mM NaHCO3) is added to make the lipid coating material at a concentration of 2 mg/mL. This solution is sonicated for at least 3.0 min at 62 0C. [0252] The lipid coating material is added immediately after sonication to the solution containing functionalized protein and inhibitory dsRNA at a mass ratio of 5: 1 protein:lipid coating material. The material is allowed to cool to 25 0C.
[0253] The chimeric protein for forming the capsid is purified via FPLC (fast performance liquid chromatography) (Amersham Pharmacia). The large FPLC column (Pharmacia XK- 16 16mm x 700mm) is ran at 1.0 niL/min using 0.5X PBS pH 9.5 buffer as the mobile phase, and Sepharose CL-4B (Amersham Pharmacia) matrix as the stationary phase. Fractions containing therapeutic particles are collected and combined (typically eluting at 70 mL based on the stationary phase and column configuration described above). Protein concentration is determined using the Agilent 2100 Bioanalyzer system. Samples are diluted 1:1 with 0.5X PBS pH 9.5 and ran on a Protein 80 chip in triplicates as described by manufacturer.
[0254] Example of Chromatogram obtained by the purification method described above is shown in Figure 9. Example of particle size measurement as determined by the instrument is shown in Figure 10. Example 6
[0255] The instant example describes two general methods for quantifying the inhibitory dsRNA contained within the therapeutic particle.
[0256] The first method describes SDS Extraction of inhibitory dsRNA from a therapeutic particle. A standard curve of inhibitory dsRNA is generated for concentrations of 175, 250, 350, 500, 700 nM; samples are prepared in triplicates. 100 μL of the therapeutic particle is mixed with 5 μL of 10% SDS solution. The solution is heated at 7O0C for 30 minutes and cooled to room temperature. 30 μL of a 75% glycerol stock is added to the particle/SDS solution. The lysed particles and the inhibitory dsRNA standards are run on a 15% urea-PAGE gel (Biorad 161-1135) at 230 V for 35 minutes in IX TBE buffer. The gel is then stained with SYBR Green II (140 mL of water and 4 μL of stock SYBR Green II) on an orbiting platform for 30 minutes. The stained gel is scanned on a Typhoon Trio using 488 nm excitation with a 526 nm SP filter and the PMT set at 350 V. Using the Image Quant TL (V 7.0) software, the densitometry of the bands is measured and the concentration of the inhibitory dsRNA is determined using a standard curve.
[0257] The second method describes extraction using phenol/chloroform. A standard curve of inhibitory dsRNA is generated for concentrations of 175, 250, 350, 500, 700 nM; samples are prepared in triplicates. 100 μL of therapeutic particles are mixed with 100 μL of phenol: chloroform (95:5) solution. These solutions are vortexed for 5 minutes and spun at 13,000 g for 60 seconds. 50 μL of aqueous solution is mixed with 15 μL of a 75% glycerol stock. The lysed particles and the inhibitory dsRNA standards are run on a 15% urea-PAGE gel (Biorad 161-1135) at 230 V for 35 minutes in IX TBE buffer. The gel is stained with SYBR Green II (140 mL of water and 4 μL of stock SYBR Green II) on an orbiting platform for 30 minutes. The stained gel is scanned on a Typhoon Trio using 488 nm excitation with a 526 nm SP filter and the PMT set at 350 V. Using the Image Quant TL (V 7.0) software, the densitometry of the bands is measured and the concentration of the inhibitory dsRNA is determined using a standard curve. Example 7
[0258] The instant example describes two general methods for analyzing the lipid contained as part of the therapeutic particles.
[0259] The first example is a NMR- Analysis (dry extraction). 30 mL of the therapeutic particle is dried under vacuum in a speedvac. The resulting material is scraped into a 10 mL glass beaker. 3 mL of water and 3 mL of chloroform are added to the solids. This solution is sonicated for 20 seconds and the mixture is incubated for 30 minutes at room temperature. The solution is centrifuged and the chloroform layer is isolated and filtered through a glass plug. The chloroform is removed under vacuum and the NMR spectrum is measured of the material. [0260] The second example is a NMR- Analysis (wet extraction). 30 mL of the therapeutic particles is mixed with 10 mL of chloroform. The solution is sonicated for 20 seconds and the mixture is incubated for 30 minutes at room temperature. The solution is centrifuged and the chloroform layer is isolated and filtered through a glass plug. The chloroform is removed under vacuum and the NMR spectrum is measured of the material. Example 8 Protein Quantification
[0261] Protein analysis is done according to Agilent Protein 80 Assay Protocol (Protein 80 kit 5067-1515; protocol revision 04/2007). Samples are diluted 1:1 in 0.5X phosphate buffered saline (PBS, Fisher Scientific BP3994, 5mM NaHCO3, pH 9.5) and analyzed. The Chips are run on an Agilent 2100 Bioanalyzer and protein concentration is obtained. Example 9
[0262] Methods of providing targeting of particles are described. [0263] To modify the antibodies, antibodies at a concentration of 4 mg/mL in 1 X PBS buffer pH 7.4 are treated with 20 mole equivalents of Traut's reagent, 2-iminothiolane HCI, for 1 hour. The antibodies are purified via column chromatography (8 x 200 rnm) G-50 (Amersham Pharmacia) in 0.25X PBS buffer pH 7.4.
[0264] One mole equivalent of purified coated particle is treated with 200 mole equivalents of PE-maleimide lipid (1,2-Dipalrnitoyl-sra-Glycero 3-Phosphoethanolamine-N-[4-(p- maleimidophenyl)-butyramide] (Sodium Salt)) (dissolved in DMF). Following 30 minutes of incubation, 1 mole equivalent of the particle is treated with 30 mole equivalents of the modified antibodies. The reaction is allowed to proceed overnight. Excess antibodies are removed via a packed column (16 x 200 mm) packed with Sepharose CL-4B matrix with the isocratic mobile phase (0.25X PBS pH7.4). This gives a typical yield of about 60 % and has about 20-30 antibodies per particle as determined by SDS-PAGE gels.
Example 10 HPV K5 protein-RNA complex via electrophoresis of labeled inhibitory dsRNA and HPV K5 protein
[0265] Inhibitory dsRNA that is 3 '-labeled with Dy547 is purchased from Dharmacon (Lafayette,CO). Labeled and unlabelled inhibitory dsRNA solutions are diluted to 4 μM in 4 M Urea, 10 mM Hepes, pH 8.15. To label the protein, 3 μM of the HPV K5 protein is incubated with 30μM maleimido-cy5 (Pierce) in 4 M Urea, 10 mM Hepes, pH 8.15 for 1 hour. Labeled and unlabeled protein solutions are diluted to 3 μM in 4M Urea.
[0266] To allow the binding reaction to take place, 15 μL of the HPV K5 protein is mixed with 5 μL inhibitory dsRNA and incubated for 10 minutes. Labeled and unlabeled RNA and protein are used in separate binding reactions. Samples are run on a 1.5% TAE-agarose gel for 35 minutes at 110 volts. [0267] A typhoon phosphoimager(GE) is used to visualize the cy5- only, DY547-only and cy5/DY547 labeled RNA protein complexes. Filters are employed to separately detect Dy547 and cy5 fluorescent labels. To image all fluorescence on the gel, cy5-filtered and dy547- filtered images are overlayed
Example 11 [0268] Transmission Electron Microscopy and Dynamic Light Scattering are utilized to assess and validate formation of the therapeutic particle.
[0269] Transmission Electron microscopy (TEM) is a useful tool to examine the morphological characteristics of small (sub-micrometer) particles, including therapeutic particles. The negative staining process involves surrounding particles with electron-dense chemicals thus revealing the structure, size, and surface topology of individual particles as the contrast between the stain (dark) and the specimen (light). One "drop" of particle (100 μg/ml) in PBS is placed on multiple formvar coated copper mesh TEM grids (Electron Microscopy Sciences) followed by one drop of 1% PTA solution (phosphotungstic acid in water, pH adjusted to 7.0 with IN NaOH). After 2 minutes, excess liquid is blotted with filter paper. TEM grids are then allowed to air dry for approximately 10 minutes. Grids are then examined using standard transmission electron microscopy (TEM). Photographs are taken at multiple magnifications (5000X - 1,000,000X) using an attached digital camera. Multiple particle constructs are used for these experiments, including particles with and without attached anti- CD22 antibodies as well as naked particles lacking a lipid coat. [0270] Dynamic Light Scattering (DLS) is a useful tool to examine the size characteristics of small (sub-micrometer) particles in solution. Solutions of purified therapeutic particles are analyzed to validate that the predicted material is obtained. Results indicate that select fractions purified from a size exclusion column are in fact very monodispersed.
[0271] ELISA is a useful tool in determining the ability of the particles to bind various bioactive agents. Protein constructs (3 mg/ml) are mixed with 20OuM of RNA at a ratio of 6.25 protein dimers per RNA duplex and incubated for 15 minutes. This mixture is then diluted 1:1 with a buffer containing 30 mM Sodium, Hepes pH 7.5, and 60 mM NaCI in order to encapsulate RNA. Encapsulation is allowed to proceed overnight at room temperature. The samples are loaded on a 1.0 % agarose gel containing ethidium bromide, run for 40 minutes at 100 Volts, and visualized on a Molecular Dynamics Typhoon imager.
Example 12
[0272] The following assays describe the effectiveness and efficiency of various lipid particles.
A. Fluorescent Particle Binding Assay (Anti-CD22 Targeted vs. Non-targeted Therapeutic Particles)
[0273] 96-well ELISA plates are coated overnight with either 50 μL of mCD22Ig protein or 2% BSA (w/v) in 0.1 M borate buffered saline at a concentration of 50 ug/ml. Plates are washed 3 times in Tris buffered saline (TBS). All wells are then blocked with 2% BSA in TBS for 1 hour, followed by 3 TBS rinses. Anti-CD22 targeted particle constructs and non-targeted particle constructs (no antibody) containing 4% DiI embedded within the lipid coat are incubated in triplicates, at multiple concentrations, in buffer containing 2% BSA and 0.1% tween in TBS for 4 hours. Wells are rinsed 4 times in TBS and plates are read using a Typhoon Molecular Imager (Molecular Dynamics). Background wells contain mCD22Ig (from original plating) and TBS. The readings are conducted in TBS. B. Particle Binding ELISA (Anti-CD22 Targeted vs. Non-targeted Therapeutic Particles)
[0274] 96-well ELISA plates are coated overnight with either 50 μL of mCD22Ig protein or 2% BSA (w/v) in 0.1 M borate buffered saline at a concentration of 50 μg/ml. Plates are washed 3 times in Tris buffered saline (TBS). All wells are then blocked with 2% BSA in TBS for 1 hour, followed by 3 TBS rinses. Anti-CD22 targeted particle constructs and non-targeted particle constructs are incubated in triplicates, at multiple concentrations, in buffer containing 2% BSA and 0.1% tween in TBS for 4 hours. Wells are then rinsed 3 times in TBS followed by incubation with antibodies against (1) rabbit-anti HBV core protein (AbCam), (2) mouse anti-HBV core protein (GenTex), or (3) no antibody in 2% BSA and 0.1% tween in TBS for 1 hour. Wells are rinsed 3 times again in TBS followed by 1 hour incubation in (1) goat anti- rabbit conjugated to alkaline phosphatase, (2) goat anti-mouse Fc region conjugated to alkaline phosphatase, or (3) no antibodies in 2% BSA and 0.1% tween in TBS. All wells are rinsed 3 times in TBS, one time in PBS, and incubated in DDAO-phosphate (1:100,000) in PBS. Primary antibodies (rabbit-anti HBV core protein (AbCam) or mouse anti-HBV core protein (GenTex)) are omitted in background control wells. Readings are conducted using Cy5 excitation/emission settings on a Typhoon Molecular Imager. Anti-core protein antibodies are used to detect the presence of therapeutic particles. Non-targeted particle binding data are normalized to the % of anti-CD22 targeted particle binding.
[0275] Additional ELISA assays are conducted to measure the amount of mouse-anti CD22 antibody present on targeted cages versus non-targeted cages. Same protocol as above are used except for the omission of the primary antibodies. For these experiments, only goat anti-mouse Fc region specific antibodies are used to detect the presence of cages. DDAO-phosphate is used as the fluorescent substrate (see above) and all analyses are conducted in the same manner. Anti-core protein antibodies (blue columns) and goat-antimouse antibodies (red columns) are used to detect the presence of particles or anti-CD22 antibody on the surface of particles (respectively). Non-targeted particle binding data are normalized to the % of anti- CD22 targeted particle binding. C. Fluorescent Cell Assays Cell Growth
[0276] B Cell (BCLI and Ramos) and T cell lines (Jurkat and HH) are purchased from ATCC and grown at 37 0C (5% CO2) in RPMI medium with 10% fetal bovine serum, supplements and antibiotics. Cells grown under these conditions consistently exhibit "normal" growth characteristics. All cell experiments are conducted while cells are exhibiting log-phase growth characteristics.
Anti-CD22 Targeted vs. Non-targeted Fluorescent Particle Binding to Cells
[0277] 9 mL of Ramos cells (from cultures at a density of 1,000,000 cells/mL) are drawn from T75 culture flasks into 3 sterile 15 mL conical tubes (3 mL each), spun down, and re- suspended in 3 mL of complete RPMI medium. Cells are incubated with 3 mL (-60 nM ) of fluorescent anti-CD22 targeted cages, non-targeted cages (both with 3% DiI embedded in the lipid coat), or an equal volume of "media only" at 37 0C at a concentration of 400,000 cages/cell for 2 hours. Cells are then spun down and rinsed 2 times in 5 mL of complete media. Cells are rinsed again 3 times in 5 mL sterile PBS, spun down and resuspended in 150 μl of PBS. To fix the cells, 150 μl of 2% paraformaldehyde is slowly added to the cells. Cells are allowed to fix for 10 minutes, and 100 μl of cell suspension is added to each well of a 96- well plate in triplicates. Plates are spun down using a clinical centrifuge. To detect fluorescence, a Typhoon Molecular Imager is used with Cy3 excitation/emission settings. Background fluorescence of "cells alone" is included for comparison.
Anti-CD22 Targeted vs. Non-targeted Fluorescent Particle Internalization
[0278] Adherent BCLI cells are plated onto glass coverslips (Fisher Scientific) in sterile 24- well tissue culture plates 12 hours prior to experimentation. Cells are allowed to grow to semi- confluency (cell density estimated at 200,000 cells/well) in complete RPMI media (see Cell Growth above). Prior to experiments, cells are rinsed with once with media and 500 μl of media is added to each well. Following experimental incubations (see below) adherent cells are rinsed once in media, 3 times in PBS, resuspended in 150 μl PBS. To fix the cells, 150 μl of 2% paraformaldehyde is slowly added to the tubes. [0279] A total of 200,000 suspension cells (Ramos, Jurkat, and HH Cells) are added to sterile 24-well tissue culture plates. Media volumes are adjusted (upwards) to 500 μl. Following experimental incubations (see below) suspension cells are sequentially pelleted and rinsed once in media and 3 times in PBS. Cells are then resuspended in 150 μl PBS. To fix the cells, 150 μl of 2% paraformaldehyde is slowly added to the tubes.
[0280] For experimental incubations, cells (adherent and suspension) are incubated with fluorescent anti-CD22 targeted particles, non-targeted particles (both with 3% DiI embedded in the lipid coat), or an equal volume of "media only" at 37 0C at multiple particle concentrations [300,000 cages/cell (-30 nM), 100,000 cages/cell (~10nM), 30,000 cages/cell (-3 nM), 10,000 cages/cell (-1 nM), 3000 cages/cell (-300 pM), and 1000 cages/cell (-100 pM)] in 500 μl media for 2 hours. Following rinses and fixation (see above), cells are coverslipped in 5 % n- propyl gallate in glycerol (w/v) and sealed under cover-slips using nail polish. Internalized fluorescent particles are quantified using standard fluorescence microscopy. Two-hundred cells are counted per coverslip and the percentage of cells with internalized particles is quantified.
D. Competition Assay using Anti-CD22 Targeted Particles in the Presence of "Free anti- CD22"
[0281] Particle constructs are generated using standard procedures. Following antibody attachment to the particle, removal of free antibodies from the particles was not conducted. This results in the presence of free antibody (>10: 1) in targeted particle preparations. Fluorescent internalization experiments are conducted using BCLl cells and identical experimental conditions as stated above. Experimental incubations for this experiment included the comparison between identical concentrations of purified targeted particles and non-purified targeted particles. Particle concentrations for all experiments are determined by quantifying core protein concentration, so free antibody does not effect concentration calculations. Analysis of internalized particles in these experiments is identical to those mentioned above.
Example 13 Stability assay
[0282] The purpose of this assay is to assess the stability of capsids formed by core proteins with destabilizing and/or stabilizing mutations. This assay can compare the relative stabilities of various capsids with that of the wild type capsid. [0283] Capsids are formed in the presence of fluorescently-labeled RNA molecules. The core protein is incubated with the RNA at a ratio of 10:1 protein:RNA and then 70 mM NaCl is added at a 1:1 ratio to the protein/RNA mixture to initiate capsid formation. Capsid formation can be confirmed by light scattering and/or size-exclusion chromatography. The pre-formed capsids are incubated in 4M urea at a temperature of 55 0C to force degradation of the capsids. Aliquots of the capsids are taken at various time points and analyzed on a 1% agarose gel. The gel analysis reveals the amount of RNA that is present as free molecules or inside the intact capsid and as such serves as a gauge of intact capsid present at the various time points. The amount of RNA in the intact capsid band can be quantified by densitometry and plotted over time. Figure 4 depicts results from a capsid stability assay performed using a HBV(hepatitis B) core protein.
Example 14 Benzonase protection assay
[0284] The purpose of this assay is to determine if the K9 core protein protects the encapsulated inhibitory dsRNA molecules from the benzonase nuclease. [0285] Free RNA (50 nM) or core-protein encapsulated RNA (150 nM) is injected into IX benzonase cleavage buffer with varying amounts of benzonase (range = 1.9 units/nmole to 945 units/nmole). A sample is prepared with no benzonase as a negative control. The mixture is incubated for 1 hour at room temperature. The samples are run on a 1.0% TAE-agarose gel containing ethidium bromide. The gel is imaged and the intensity of the RNA bands is determined.
[0286] Figure 5 depicts results from a benzonase protection assay performed using a HBV K9 protein. Free RNA band is degraded at about 20 units/nmol. RNA associated with the HBV K9 protein does not degrade at any nuclease concentrations tested, indicating that the RNA is effectively protected. This assay shows that RNA is significantly protected against nuclease activity by encapsulation with K9 core protein. Example 15 Serum protection assay
[0287] The purpose of this assay is to determine if the RNA inside of particles is protected from serum degradation. Degradation is compared to two control samples: free RNA and empty particles with RNA added after assembly. The second control is to determine whether particles protect RNA from serum degradation by some mechanism other than encapsulation. [0288] Equal volumes of each RNA sample is mixed with human serum. The total volume of sample and serum is between 2-4 mL. Freeze several aliquots of sample and serum immediately for time zero time points, and place the remaining samples at 37 0C. Multiple 50 μL aliquots are removed from samples at regular intervals, labeled and froze at - 8O0C. To process the samples, 10% SDS is added to achieve a final concentration of 0.7% SDS. The mixture is incubated at room temperature for 5 minutes. Samples are ran at 200 V for 30 minutes on a 1.0% TAE-agarose gel containing ethidium bromide. The lifetime of the RNAs is quantitated to determine the amount of protection.
[0289] Figure 6 depicts results from a serum protection assay using HBV K9 protein. Figure 6 demonstrates that the control samples, using Hep B particles had degraded by the first time point (1 day) while the particle -protected (Hep B) RNA survived without appreciable degradation for the duration of the experiment, 4 days. These results indicate that the particle protects the RNA cargo from serum degradation. Additional experiments indicate that RNA stability is achieved at 14 days without the degradation of the RNA payload. Free RNA, in the presence and absence of empty particle, is completely degraded by 1 day.
[0290] The control samples are degraded by the first time point (1 day) while the particle- protected RNA survived without appreciable degradation for the duration of the experiment, 4 days. These results indicate that the particle protects the RNA cargo from serum degradation. Additional experiments indicate that RNA stability is achieved at 14 days without the degradation of the RNA payload. Free RNA, in the presence and absence of empty particle, is completely degraded by 1 day.
Example 16 Binding affinity
[0291] The following assays determine the Kd, for HPV K5 mutant with fluorescent inhibitory dsRNA. Below is the sequence of fluorescent inhibitory dsRNA that was used in these experiments. Siglo Cyclophilin B:
DY547-GGAAAGACUGUUCCAAAAAUUUUCCUUUCUGACAAGGUUUUU-P (SEQ ID NO:58)
A. [0292] A solution of 20 nM fluorescent duplex (Siglo cycB, RNA from Dharmacon) in 10 rnM Tris is referred to as f-RNA buffer. HPV K5 protein stock is diluted to 6 μM in f-RNA buffer. The dilution is performed quickly and on ice, so that particle assembly is less apt to form. Successive dilutions of HPV K5 is made in f-RNA buffer. The RNA-protein dilutions are removed from ice and allowed to sit at room temperature for 5 minutes.
[0293] The reactions are run on a gel under the following conditions: 15 μL of the samples in duplicates are loaded per lane on a 1.5% TAE-agarose gel and the gel is run at 200 V for 35 minutes and documented on a Molecular Dynamics Typhoon scanner.
[0294] The assay is performed using the HBV K9 mutant protein. Figure 7 indicates that fluorescent inhibitory dsRNA binds to a HBV (Hep B) K9 mutant protein with a Kd of 115 nM. This is a tight affinity, which is characteristic of RNA-protein interactions. This tight binding affinity is well below the concentrations of RNA and protein used for assembly of particles. Therefore, these data suggests that during assembly the RNA binding sites of K9 protein are saturated with RNA. B.
[0295] A solution of 2OnM fluorescent duplex (Siglo cycB, RNA from Dharmacon) in 20 mM Sodium Bicarbonate, pH 9.5, is prepared. HPV K5 protein stock is diluted to 40 μM in the same buffer. Successively diluting the 40 μM protein in 20 mM Sodium Bicarbonate, pH 9.5, generated a range of protein concentrations. RNA and protein solutions are mixed 1:1 and allowed to bind at room temperature for 5 minutes. The final protein concentration in the binding reactions ranges three orders magnitude, from 20 μM to 20 nM. A 1/5 volume of 6X RNA loading buffer (xylene cyanol in 55% glycerol 20 mM Tris, pH 7.7) is added. The samples are then loaded on a 1.0% TAE-agarose gel (13cmxl6cm), at 80 μL/lane. The gel is run for 180 V for 35 minutes and documented on a Molecular Dynamics Typhoon scanner. [0296] The assay is performed using the HBV K7 and KI l mutant proteins. Figure 8 indicates that fluorescent inhibitory dsRNA bound to HBV K7 with a Kd of 370 nM and to Kl 1 with a Kd of 69 nM. This is a tight affinity which is characteristic of RNA-protein interactions. The increase affinity observed for KI l relative to K9 and K7 is attributable to the larger number of cationic residues at the C-terminal end of this protein. As with the mutant K9, the affinity is high enough to fully saturate the RNA binding sites for both mutants during the process of particle assembly. Table 2 provides a summary of HBV K7, K9, and KI l mutant binding conditions as well as the Kd values.
Table 2
Figure imgf000081_0001
Example 17
[0297] The following examples demonstrate the ability of therapeutic particles to encapsulate inhibitory dsRNA, effectively delivering the encapsulated inhibitory dsRNA to a cell and the ability of the encapsulated inhibitory dsRNA to silence or down regulate the activity of a particular gene of interest. A.
[0298] C 166 cells stably expressing the enhanced green fluorescent protein (eGFP) are grown at 370C, 5% CO2, in DMEM media with 10% fetal bovine serum and supplements. Cell stocks are grown in T25, T75, or T125 flasks and transferred to 24-well plates for experimentation. Cells are also grown on glass coverslips in 24-well plates when microscopy is to be performed. Cells grown under these conditions consistently exhibit "normal" growth characteristics and doubling times.
B. Lipid Particles Containing Red Fluorescent Inhibitory dsRNA Enter Cells
[0299] C166 cells are grown on glass coverslips in 24-well plates. Cells are plated onto coverslips 24 hours prior to the addition of lipid particles containing inhibitory dsRNA. 100 μl of lipid particles containing 3 nM final concentration of red- fluorescent inhibitory dsRNA directed against Cyclophilin B (SEQ ID NO:58) are added to 1 mL of media and incubated at 370C for 4 hours. Control cells are incubated in 100 μl of PBS (no lipid particles present). Cells are rinsed 3 times in cold PBS and fixed in 1% paraformaldehyde in PBS. Hoescht 33342 (1: 10,000) is added for the visualization of cell nuclei, and coverslips are mounted onto glass slides (cells facing down). Slides are visualized using standard fluorescence microscopy.
Microscope settings are held constant for both experimental and control slides. Lipid particles containing red fluorescent inhibitory dsRNA enter eGFP-expressing C 166 cells when incubated at 3 nM for 4 hours, thus staining these cells red.
C. Lipid Particles Containing Inhibitory dsRNA Directed Against eGFP Inhibit eGFP mRNA Expression In Vitro [0300] C166 cells are grown on glass coverslips in 24-well plates. Cells are plated onto coverslips 24 hours prior to the addition of lipid particles. 250 μl of lipid particles containing inhibitory dsRNA directed against eGFP (eGFP- 19) with the following sequences:
GCUGACCCUGAAGUUCAUC-dTdT (SEQ ID NO:59) dTdT-CGACUGGGACUUCAAGUAG (SEQ ID NO:60) are added to 1 rnL of media and incubated at 37 0C for 24 and 48 hours. The final concentration of inhibitory dsRNA within the particle is 10 nM. Control cells are incubated in 250 μl of PBS (no lipid particles present). Cells are rinsed 3 times in cold PBS and homogenized using buffer RLT (Qiagen) with 0.1% BME. Three wells are used for each experimental condition at each time point. RNA is purified using the RNEasy kit (Qiagen) as recommended by the manufacturer, including an on-column DNAse digestion step. RNA is quantified on the Nanodrop (Thermofisher). 1 μg of total RNA is reverse transcribed using iScript reverse transcriptase (BioRad) as recommended by the manufacturer. Quantitative polymerase chain reactions (qPCR) are performed using cDNA, SybrGreen master mix (BioRad) as recommended by the manufacturer, and prequalified primer sets designed using Beacon Designer 6.0 (Premier Biosoft). eGFP gene inhibition is quantified using the ΔΔCt method by comparing eGFP expression levels in each sample to the geometric mean of 3 housekeeping genes in the same sample. All samples are run in triplicates.
D. Lipid Particles Containing Inhibitory dsRNA Directed Against eGFP Inhibit eGFP Protein Expression In Vitro. [0301] C166 cells are grown on glass coverslips in 24-well plates. Cells are plated onto coverslips 24 hours prior to the addition of lipid particles. lOOμl of lipid particles red- fluorescent inhibitory dsRNA directed against eGFP (F-eGFP 19 with the following sequence:
DY547-GCUGACCCUGAAGUUCAUC-dTdT (SEQ ID NO:61) dTdT-CGACUGGGACUUCAAGUAG (SEQ ID NO:60) are added to 1 niL of media and allowed to sit at 37 0C for 18 hours. The final concentration of inhibitory dsRNA within the particle is 10 nM. Control cells are incubated in lOOμl of PBS (no lipid particles present). Cells are rinsed 3 times in cold PBS and fixed in 1% paraformaldehyde in PBS. Hoescht 33342 (1:10,000) is added for the visualization of cell nuclei, and coverslips are mounted onto glass slides (cells facing down) in 5 % n-propyl gallate in glycerol. Slides are visualized using confocal microscopy. Microscope gain and PMT settings are held constant for both experimental and control conditions. Lipid particles containing red fluorescent inhibitory dsRNA directed against eGFP can enter cells and inhibit eGFP protein expression after an 18 hour incubation. eGFP (green) expression is reduced in cells incubated with lipid particles loaded with inhibitory dsRNA (red).
E. Lipid Particles Containing Inhibitory dsRNA Directed Against eGFP Inhibit eGFP mRNA Expression In Vivo.
[0302] Female C57BL/6-Tg(ACTb-eGFP)10sb/J mice (~8 weeks old) are treated with 200 μl of lipid particles loaded with a total of -620 ng inhibitory dsRNA (eGFP 19 of SEQ ID NO:59 and SEQ ID NO:60) through tail injections. The mice are sacrificed 24 or 48 hours later. 20 animals are injected with lipid particles loaded with inhibitory dsRNA, and 20 animals are injected with 200 μl of PBS alone. 16 animals are sacrificed from each group at 24- 48 hours, and 4 animals from each group are sacrificed at 48 hours. RNA is harvested from the liver, kidney, heart, lung, spleen, and pancreas using RNA later storage solution (Ambion). RNA is purified from -25 mg of tissue from each organ using the RNEasy total RNA purification kit and DNAse digestion is conducted on column. 1 μg of total RNA is reverse transcribed using the iScript reverse transcription kit. Equal amounts of cDNA are added to qPCR reactions. Levels of eGFP are normalized to the geometric mean of 3 housekeeping genes and percent inhibition is calculated using the ΔΔCt method. All qPCR samples are run in triplicates.
F. Lipid Particles Containing Inhibitory dsRNA Directed Against eGFP Inhibit eGFP Protein Expression In Vivo.
[0303] A female C57BL/6-Tg(ACTb-eGFP)10sb/J mouse (-9 weeks old) is injected with 200 μL of lipid particles loaded with a total of -40 ng siGlo-conjugated inhibitory dsRNA (F- eGFP 19 of SEQ ID NO:61 and SEQ ID NO: 60). The mouse is sacrificed 24 hours later. A total of 1 animal received 200 μL lipid particles containing inhibitory dsRNA in PBS and 3 naive animals (female animals from the same litter) received no injection. Liver tissue is harvested and immediately placed in 4% paraformaldehyde in PBS and stored at 4 0C. 16 μm frozen sections are cut at -20 0C on a cryostat, covers lipped in 5% n-propyl gallate in glycerol, and viewed using a confocal microscope. All PMT and gain settings are held constant for both experimental and control liver sections. Lipid particles containing red fluorescent inhibitory dsRNA directed against eGFP reduce eGFP protein expression in the mouse liver in vivoG. Lipid Particles Containing Inhibitory dsRNA Directed Against eGFP Knock Down eGFP Expression In Vivo. [0304] For each mouse liver from the above experiment, 75 μg of tissue is homogenized and extracted in 1.5 mL of PBS-T using a Tissue Lyser (Qiagen). The extract is spun for 10 minutes at 12 g, 40C. Supernatant is decanted into a fresh 2 mL tube. This centrifugation and decanting step is repeated to produce approximately 1 mL of clear liver protein extract. Liver protein extract is stored at -8O0C. [0305] Liver extract is diluted 1 : 1 with PBS and tested for protein concentration with a DC protein assay (BioRad) in a 96-well format. Final calculated protein concentrations are in the range of 2.5 to 3 mg/mL and vary from each other with a standard deviation of 0.2 mg/mL.
[0306] Liver extracts are diluted 1:10 in PBS and tested for eGFP fluorescence on a fluorescent spectrophotometer. To determine relative levels of eGFP fluorescence from individual liver extracts, 100 μL of 1 : 10 diluted extract is loaded into a 96 well plate and read on a Turner fluorescent plate reader. Each sample is read in duplicates. To determine inhibition, eGFP fluorescence is compared between livers treated with or without inhibitory dsRNA.
Example 18 [0307] To demonstrate in vitro knockdown of ApoB protein by ApoB2 loaded therapeutic particles, ApoAl protein expression is monitored for normalization of protein expression. In both cases, ApoB and ApoAl, protein expression is quantified via ELISA.
[0308] HepG2 cells grown in HepG2 media are plated overnight on coated 96-well plates. The volume of cells per well is 100 uL. A therapeutic particle stock containing 171 nM ApoB2 inhibitory dsRNA is prepared at a ratio of 4.5 inhibitory dsRNA's per particle. [0309] Cells are approximately 60% confluent at the beginning of the experiment. Media is replaced with HEPG2 media containing 20% stock therapeutic particles. Cells are incubated with particles or control (HepG2 containing 20% of vehicle) at 370C. After 48 hours, the media is replaced with HepG2 media and allowed to incubate 24, 48 or 72 hours. [0310] At the three time points for both particle-containing and control conditions, media from three wells are harvested for analysis of ApoB and ApoAl levels.
[0311] Both ApoB and ApoAl levels are detected by ELISA. For ELISA analysis of ApoBl, antibodies are immobilized on high binding polystyrene 96 well plates (Corning Costar cat#3590). The capturing antibody is Apolipoprotein B antibody BlGl (cat# GTX27616), diluted 1 :2000 in 0. IM sodium bicarbonate pH 9.6. To block further attachment to the plastic wells, PBS-BSA (PBS + lOmg/ml BSA) is applied. Samples are prepared in HepG2 conditioned media diluted 1:10 in PBS-O. IXBSA (PBS + lmg/ml BSA). A standard is generated by serial dilution of an ApoB standard (Alerchek). The detection antibody is an ApoB-Horse Radish Peroxidase antibody conjugate (Genetex cat # GTX40047), diluted 1:1000 in PBS-BSA. Each well is measured in triplicates. Between capture antibody, block, sample, and detection antibody applications, wells are washed 3 times with 200 uL of PBST (PBS containing 0.1% TWEEN 20). HRP is detected with ULTRA-TMB reagent (Thermofisher).
[0312] For the ELISA analysis of ApoAl, an ApoAl ELISA kit is purchased from Alerchek (cat# Cardiocheck Apolipoprotein Al) and used according to manufacturer's directions. ApoAl and ApoB levels are determined. The ratio of ApoB to ApoAl (ApoB/ApoAl) is also determined.
Example 19
[0313] Anti-CD22 Targeted Particles loaded with Doxorubicin are evaluated for their ability to Target and Kill CD-22 Expressing Cells [0314] B cells (Ramos), and T cells (Jurkat) are added to sterile 96-well plates containing 500,000 cells/ml in early log growth phase. Multiple concentrations (lOpM, 10OpM, InM, 1OnM, and 10OnM) of both CD22-targeted particles and non-targeted particles loaded with doxorubicin are added to the cells along with complete media (see previously). Cells are assayed for viability using Trypan Blue exclusion at multiple time points (12hr, 24Hr, 36hr, 48hr, 60hr, and 72hr). Cell viability is normalized to cell viability at the beginning of the experiments for each cell line and is expressed as a % of "normal". Cell density is also calculated and plotted across each time point for each concentration. All experiments at individual concentrations are conducted in triplicates for each time point.
Example 20 [0315] Anti-CD22 Targeted Particles loaded with Doxorubicin are evaluated for their ability to Reduce Tumor Growth, in vivo.
[0316] Female athymic BALB/c nu/nu mice (Harlan Sprague-Dawley), 7-9 weeks of age are maintained on a normal diet ad libitum and under pathogen-free conditions. Raji or Ramos cells are harvested in logarithmic growth phase and 2.5-5.0 x 106 cells are injected subcutaneously into both sides of the abdomen of each mouse. Studies are initiated 3 weeks after implantation, when tumors are 100-300 mm . Experimental groups consist of untreated, doxorubicin alone, naked particles loaded with doxorubicin, and particles loaded with doxorubicin and coated with HB 22.7.
[0317] Tumor volume is calculated by the formula for hemiellipsoids (DeNardo GL, Kukis DL, Shen S, et al., Clin Cancer Res 1997;3:71-79). Initial tumor volume is defined as the volume on the day prior to treatment. Mean tumor volume is calculated for each group on each day of measurement; tumors that have completely regressed are considered to have a volume of zero. Tumor responses are categorized as follows: C, cure (tumor disappeared and did not regrow by the end of the 84 day study); CR, complete regression (tumor disappeared for at least 7 days, but later regrew); PR, partial regression (tumor volume decreased by 50% or more for at least 7 days, then regrew).
[0318] Differences in response among treatment groups are evaluated using the Kruskall Walis rank sum test with the response ordered as none, PR, CR, and Cure. Survival time is also evaluated using the Kruskall Walis test. Tumor volume is compared at 3 time points: month 1 (day 26-29), month 2 (day 55-58), and at the end of the study (day 84). If an animal is sacrificed due to tumor-related causes, the last volume is carried forward and used in the analysis of later time points. Analysis of variance is used to test for differences among treatment groups. P-values are two-tailed and represent the nominal p-values. Protection for multiple comparisons is provided by testing only within subsets of groups found to be statistically significantly different. Example 21
ApoB Inhibition in vitro Using Human HepG2 Cells
[0319] HepG2 cells (human hepatocellular carcinoma cell line- ATCC) are grown in DMEM with 10% fetal bovine serum, 2mM 1-glutamine, and penicillin/streptomycin at 37 0C and 5% CO2. Cells are seeded in 96-well poly-lysine coated plates at -50,000 cells/well and allowed to settle overnight. The following day, when cells have reached >90% confluency, viral core protein particles as prepared as above, DharmaFECT, and PBS are to be added to cells. Particles and PBS are to be added at a volume of 25ul to 75ul of complete media for a total of lOOul/well. All experimental conditions are performed using triplicate wells (n= 3) of 96 well plates. ApoB inhibitory dsRNA with the following sequences, sense 5'- GUCAUC ACACUGAAUACCAAU-3' (SEQ ID NO: 62) and antisense 5'- AUUGGUAUUCAGUGUGAUGACAC-S' (SEQ ID NO: 63), are loaded in particles as described previously.
[0320] On Day 0 (24 hours after seeding cells on 96-well poly-1-lysine coated plastic plates), therapeutic particles and PBS are added to individual wells and incubated at 37 degrees Celsius for 72 hours. After incubations are completed, media is removed from each well and 150ul RLT lysis buffer (Qiagen) with b-mercaptoethanol (BME) is added to lyse the cells and stabilize RNA (as indicated by the manufacturer). Following lysis, the entire volume of lysate is added to 450ul of RLT lysis buffer with BME for a total of 600ul lysis solution. Total RNA is then purified from individual samples using Qiagen RNEasy columns on a QiaCube (Qiagen) automated RNA purification system as suggested by the manufacturer. Qiashredders and on- column DNase I (Qiagen) digestion steps are also conducted as suggested by the manufacturer (included in automated RNA preparation protocol). Following RNA purification, total RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad). cDNA is then added to SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ realtime qPCR machines (BioRad). Included in all qPCR experiments are pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p-dehydrogenase (GAPDH), glucose phosphate isomerase (GPI), and hydroxymethylbilane synthase ( HMBS), as well as pre-designed and pre- validated primers specific for the apolipoprotein B gene (ApoB). Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ΔΔCt-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of ApoB mRNA expression to the geometric mean of the three housekeeping genes.
Example 22
ApoB inhibition in vitro Using Mouse AML 12 Cells
[0321] AML12 cells (mouse hepatocyte cell line- ATCC) are grown in DMEM with 10% fetal bovine serum, 2mM 1-glutamine, insulin/transferring/selenium, and penicillin/streptomycin at 370C and 5% CO2 (as recommended by ATCC). Cells are seeded in 96-well plastic plates at -50,000 cells/well and allowed to settle overnight. The following day, when cells reach > 90% confluency, therapeutic particles and PBS are added to cells. Particles and PBS will be added at a volume of 25 μl to 75 μl of complete media for a total of 100 μl/well. All experimental conditions are performed using triplicate wells (n= 3) of 96 well plates. ApoB inhibitory dsRN A has the following sequence: sense 5'-
GUCAUC ACACUGAAUACCAAU-3' (SEQ ID NO: 62) and antisense 5'- AUUGGUAUUCAGUGUGAUGACAC-3' (SEQ ID NO: 63).
[0322] On Day 0 (24 hours after seeding cells on 96-well plastic plates), particles and PBS are added to individual wells and incubated at 37 0C for 72 and 96 hours. After incubations are complete, media is removed from each well and 150 μl RLT lysis buffer (Qiagen) with b- mercaptoethanol (BME) is added to lyse the cells and stabilize the RNA. Following lysis, the entire volume of lysate is added to 450 μl of RLT lysis buffer with BME for a total of 600 μl lysis solution. Total RNA is then purified from individual samples using Qiagen RNEasy columns on a QiaCube (Qiagen) automated RNA purification system. Qiashredders and on- column DNase I (Qiagen) digestion steps are also conducted (included in automated RNA preparation protocol). Following RNA purification, total RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad). cDNA is then added to SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ real-time qPCR machines (BioRad). Included in all qPCR experiments are pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p- dehydrogenase (GAPDH), glucose phosphate isomerase (GPI), and hydroxymethylbilane synthase ( HMBS), as well as pre-designed and pre-validated primers specific for the apolipoprotein B gene (ApoB). Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ΔΔCt-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of ApoB mRNA expression to the geometric mean of the three housekeeping genes (GAPDH, GPI, and HMBS). Example 23: Factor VII Inhibition in vitro Using Primary Mouse Hepatocytes
[0323] Cryopreserved mouse primary hepatocytes (Cellz Direct) are thawed and grown in William's Media with 10% fetal bovine serum (according to the manufacturer's protocol) at 370C and 5% CO2 for 24 hours. Thawed cells in suspension are then counted and plated at a density of 35,000 cells/well in 96-well collagen- 1 coated plates (Becton Dickenson) using a proprietary mixture of media supplements (CellzDirect- Thawing/Plating Supplement Pack). Cells are allowed to settle and attach to the collagen- 1 substrate for 48 hours as media is replaced after 24 and 48 hours. 48 hours after plating the cells, therapeutic particles, DharmaFECT, and PBS are added at a volume of 25 μl to 75 μl of complete media for a total of 100 μl /well. All experimental conditions are to be performed using triplicate wells (n= 3) in 96 well plates. DharmaFECT transfection reagent #6 is used to transfect naked inhibitory dsRNA into primary mouse hepatocytes as a positive control for mRNA knockdown. All DharmaFECT reagents are to be made up according to the manufacturer' s suggested protocol and added at 100 μl /well, and all experiments are performed in triplicate. FVII inhibitory dsRNA, which has the following sequence: sense 5'- GGAUC AUCUC AAGUCUUACT*T-3' (SEQ ID NO: 64) and antisense 5'- GUAAGACUUGAGAUGAUCCT*T -3' (SEQ ID NO: 65); bold letters denote 2'-F-modified nucleotides and asterisks represent phosphorothioate linkages, as well as SiGenome 5, which has the following sequence: sense 5'- UGGUUUACAUGUCGACUAA- 3' (SEQ ID NO: 66) are loaded into particles as described previously. [0324] After incubations are completed, media is removed from each well and 150 μl RLT lysis buffer (Qiagen) with b-mercaptoethanol (BME) is added to lyse the cells and stabilize RNA. Following lysis, the entire volume of lysate is added to 450 μl of RLT lysis buffer with BME for a total of 600 μl lysis solution. Total RNA is then purified from individual samples using Qiagen RNEasy columns on a QiaCube (Qiagen) automated RNA purification system. Qiashredders and on-column DNase I (Qiagen) digestion steps are also conducted (included in automated RNA preparation protocol). Following RNA purification, total RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad). cDNA is then be added to
SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ real-time qPCR machines (BioRad). Included in all qPCR experiments are pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p-dehydrogenase (GAPDH), Cyclophillin A, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase (YWHAZ), as well as predesigned and pre- validated primers specific for the mouse Factor VII mRNA sequence. Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ΔΔCt-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of FVII mRNA expression to the geometric mean of the three housekeeping genes mentioned above.
Example 24: Factor VII Inhibition in vivo
[0325] A total of 48 female C57bl mice are injected intravenously in the tail vein with 200 μl of particles loaded with FVII inhibitory dsRNA at 0.5mg/kg inhibitory dsRNA. The FVII inhibitory dsRNA has the following sequences: sense 5'- GGAUC AUCUCA AGUCUUACT*T-3' (SEQ ID NO: 64) and antisense 5'-
GUAAGACUUGAGAUGAUCCT*T -3' (SEQ ID NO: 65); bold letters denote 2'-F-modified nucleotides and asterisks represent phosphrothioate linkages, and the SiGenome 5 inhibitory dsRNA, which has the sequence: sense 5'-UGGUUUACAUGUCGACUAA- 3' (SEQ ID NO: 66) are loaded into particles as described previously. For the following study, six animals are sacrificed at 4 hours, 1 day, 3 days, 7 days, 10 days, 14 days, 21 days, and 28 days following injection and livers are removed and stored at 4°C in RNA Later solution (Ambion) for subsequent mRNA purification and analysis. A total of 12 non-injected naϊve animals are also sacrificed and livers are removed for use as control animals in this study.
[0326] After the completion of the study, livers are removed from RNALater storage solution and 20 mg tissue samples are dissected, weighed and placed into 600 μl RLT lysis buffer (Qiagen) with b-mercaptoethanol (BME). Tissues are then lysed using a Tissue Lyser (Qiagen) at 30 hertz for 2 minutes. Total RNA is then purified from individual samples using Qiagen RNEasy columns on a QiaCube (Qiagen) automated RNA purification system as suggested by the manufacturer. Qiashredders and on-column DNase I (Qiagen) digestion steps are also conducted (included in automated RNA preparation protocol). [0327] Following RNA purification, total RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad). cDNA is added to SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ real-time qPCR machines (BioRad). Included in all qPCR experiments are pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p-dehydrogenase (GAPDH), Cyclophillin A, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase (YWHAZ), as well as pre-designed and pre-validated primers specific for the mouse Factor VII mRNA sequence. Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ΔΔCt-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of FVII mRNA expression to the geometric mean of the three selected housekeeping genes.
Example 25: Angiotensinogen Inhibition in Mouse AML12 Cells [0328] Mouse AML12 cells are grown in DMEM with 10% fetal bovine serum, insulin/transferring/selenium , 2mM 1-glutamine, and penicillin/streptomycin at 37 0C and 5% CO2. Cells are seeded in 96-well plastic plates at -50,000 cells/well and allowed to settle overnight. The following day, when cells have reached > 90% confluency, therapeutic particles, DharmaFECT, and PBS are added to cells. Chimerasomes and PBS are added at a volume of 25 μl to 75 μl of complete media for a total of 100 μl /well. All experimental conditions were performed using triplicate wells (n= 3) of 96 well plates. DharmaFECT transfection reagent #6 is used to transfect naked inhibitory dsRNA into HepG2 cells as a positive control. All DharmaFECT reagents are to be made up according to the manufacturer's suggested protocol and added at 100 μl/well, and all experiments are performed in triplicates. Angiotensinogen inhibitory dsRNA, which has the following sequence: sense 5'- UGUUGUUC AGAUUUGCCUCCGCACC-3' (SEQ ID NO: 67) and antisense 5'-
ACAACAAGUCUAAACGGAGGCGUGG -3' (SEQ ID NO: 68), and the SiGenome 5, which has the following sequence: sense 5'-UGGUUUACAUGUCGACUAA- 3' (SEQ ID NO: 66), are loaded into particles as described previously.
[0329] On Day 0 (24 hours after seeding cells on 96-well poly-1-lysine coated plastic plates), therapeutic particles, PBS, and DharmaFECT are added to individual wells and incubated at 370C for 72 hours (unless indicated otherwise). After incubations are completed, media is removed from each well and 150 μl RLT lysis buffer (Qiagen) with b- mercaptoethanol (BME) is added to lyse the cells and stabilize the RNA. Following lysis, the entire volume of lysate is added to 450 μl of RLT lysis buffer with BME for a total of 600 μl lysis solution. Total RNA is purified from individual samples using Qiagen RNEasy columns on a QiaCube (Qiagen) automated RNA purification system. Qiashredders and on-column DNase I (Qiagen) digestion steps are also conducted (included in automated RNA preparation protocol). Following RNA purification, total RNA is quantified using a Nanodrop spectrophotometer (ThermoFisher) and equal amounts of RNA (as suggested by the manufacturer) are reverse transcribed for every sample within each experiment into cDNA using the iScript reverse transcriptase kit (BioRad). cDNA is added to SybrGreen qPCR master mix (BioRad-as recommended by the manufacturer) and quantitative real-time qPCR (qPCR) is performed using the 96-well plate format on MyIQ real-time qPCR machines (BioRad). Included in all qPCR experiments are pre-designed and pre- validated primers for 3 housekeeping genes, glyceraldehydes-3-p-dehydrogenase (GAPDH), Cyclophillin A, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase (YWHAZ), as well as pre-designed and pre-validated primers specific for angiotensinogen mRNA. Standard thermal cycler protocols are used to perform qPCR reactions for a total of 40 cycles as suggested by the manufacturer. All qPCR data is analyzed using the ΔΔCt-based algorithm included in the BioRad iQ5 software package, which incorporates the normalization of angiotensinogen mRNA expression to the geometric mean of the three housekeeping genes, GAPDH, Cyclophilin A, and YWHAZ.
Example 26
[0330] The instant example describes a general method for measuring the endotoxin level in therapeutic particle preparations.
[0331] Endotoxin measurement is based on the Limulus Amebocyte Lysate Pyrogent Plus Single Test Kit (Lonza, US License No. 1701, Catalog No. N289-06). The endotoxin vial is reconstituted with 1.0 ml of LAL reagent water (Lonza #W50-640) and vortexed for at least 15 minutes. Endotoxin is diluted with the LAL reagent water to a concentration of lEU/ml. For a positive control, 0.25 ml of an endotoxin standard that contains twice the labeled minimum sensitivity is used. For a negative control, 0.23 ml of LAL reagent water is used.
[0332] Five sample serial dilutions are prepared in duplicates, beginning with a 1:4 dilution and end with a 1:64 dilution of sample:LAL reagent water. 0.25 ml of each sample is added to the test vial. Mix the samples by tilting and gently swirling the vial until the contents are in solution. Each vial of sample is incubated for 60 minutes (+/- 2 minutes) at 37°C (+/- I0C). At the end of the incubation period, each vial is carefully removed and inverted 180 degrees. A positive reaction is characterized by the formation of a firm gel that remains intact momentarily when the tube is inverted, which should be observed in the positive sample control vial. A negative test is characterized by the absence of solid clot after inversion. The lysate may show an increase in turbidity or viscosity. This is considered a negative result.
[0333] The endotoxin concentration is calculated by the multiple of the lysate sensitivity and the geometric mean of the endpoint:
(Antilogio (Mean (Logio Endpoint 1; Logio Endpoint 2)))"1 x lysate sensitivity.
[0334] Results from an endotoxin analysis of mFVII-containing therapeutic particles are shown below. The results indicate that there are no endotoxin contamination in the therapeutic particles.
Figure imgf000094_0001
[0335] Sensitivity calculation:
(Antilogio (Mean (Logio 0.125; Logio I)))"1 x 0.06 EU/mL = 0.170 EU/mL References
[0336] All publications and patents mentioned herein, including those items listed below, are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.
US20060292174; US20070269370; U.S.S.N. 12/082154 Equivalents
[0337] While specific embodiments of the subject invention have been discussed, the above specification is illustrative and not restrictive. Many variations of the invention will become apparent to those skilled in the art upon review of this specification. The full scope of the invention should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations.
[0338] Unless otherwise indicated, all numbers expressing quantities of ingredients, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term "about." Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention.
[0339] The terms "a" and "an" and "the" used in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. Recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g. "such as") provided herein is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention otherwise claimed. No language in the specification should be construed as indicating any non-claimed element essential to the practice of the invention. [0340] What is claimed is:

Claims

CLAIMS L A protein capable of forming a capsid comprising: a structural core portion chosen from the structural core portion of a HPV, SV40, CCMV, DGNNV, TBSV, Norwalk Virus, and HCV a modified portion capable of binding to a nucleic acid with a binding affinity that allows release of said nucleic acid when said protein bound to said polynucleotide is administered in vivo.
2. The protein of claim 1, wherein said modified portion is a modified C-terminal tail portion and/or a modified N-terminal tail portion.
3. The protein of claim 1 or 2, wherein the modified tail portion comprises about 4 to about 30 lysines.
4. The protein of any one of claims 1-3, wherein the modified tail portion comprises a lysine domain of about 4 to about 30 lysines.
5. The protein of claim 4, wherein said lysine domain is about 5 to about 20 lysines in length.
6. The protein of any one of claims 1-5, wherein the modified tail portion comprises a histidine tag of about 1 to about 10 histidines in length.
7. The protein of any one of claims 1-6, wherein the modified tail portion further comprises a linker segment.
8. The protein of any one of claims 1-7, wherein the protein is chosen from SEQ ID NO: 16 - SEQ ID NO: 23, SEQ ID NO: 25 - SEQ ID NO: 31, SEQ ID NO: 35 - SEQ ID NO: 48; SEQ ID NO: 51 - SEQ ID NO: 55, and SEQ ID NO: 57.
9. The protein of any one of claims 1-7, wherein the modified tail portion is chosen from SEQ ID NO: 15 and SEQ ID NO: 24, optionally including a linker segment chosen from SEQ ID NO: 32 - SEQ ID NO: 34.
10. A nucleic acid encoding the protein of any one of claims 1-9.
11. A chimeric therapeutic comprising: a modified viral core protein chosen from HPV, SV40, CCMV, DGNNV, TBSV, Norwalk Virus, and HCV, having a modified tail portion; and a nucleic acid bound to said modified viral core protein.
12. The chimeric therapeutic of claim 11, wherein the modified viral core protein has a modified structural core portion and a modified tail portion.
13. The chimeric therapeutic of claim 11 or 12, wherein said nucleic acid is bound to said modified tail portion.
14. The chimeric therapeutic of any one of claims 11-13, wherein said nucleic acid bound to said modified tail portion is substantially less immunogenic as compared to an identical unbound nucleic acid.
15. The chimeric therapeutic of any one of claims 11-14, wherein said nucleic acid bound to said modified viral core protein is bound with a binding affinity that allows release of said nucleic acid when said chimeric therapeutic is administered in vivo.
16. The chimeric therapeutic of any one of claims 11-15, wherein said nucleic acid bound to said modified viral core protein is resistant in an aqueous solution to degradation with a nuclease.
17. The chimeric therapeutic of any one of claims 11-16, wherein the binding affinity of said nucleic acid bound to said modified viral core protein is about 50 nM to about 500 nM, at 2OmM NaHCO3, and a pH of 9.5.
18. The chimeric therapeutic of any one of claims 11-17, wherein the binding affinity of said nucleic acid bound to said modified viral core protein is about 55 nM to about 400 nM, at 2OmM NaHCO3, and a pH of 9.5.
19. The chimeric therapeutic of any one of claims 11-18, wherein the binding affinity of said nucleic acid bound to said modified viral core protein is about 50 nM to about 500 nM, at 2OmM (CH2OH)3CNH2, and a pH of 7.7.
20. The chimeric therapeutic of any one of claims 11-19, wherein said nucleic acid bound to said modified viral core protein is bound substantially by Coulombic interactions.
21. The chimeric therapeutic of any one of claims 11-20, wherein said chimeric therapeutic is substantially free of nuclease.
22. The chimeric therapeutic of any one of claims 11-21, wherein said chimeric therapeutic is substantially free of endogenous nucleic acids.
23. The chimeric therapeutic of any one of claims 11-22, wherein said nucleic acid bound to said viral core protein is substantially protected from serum degradation when administered in vivo.
24. The chimeric therapeutic of any one of claims 11-23, wherein said nucleic acid bound to said viral core protein is substantially protected from serum degradation for at least two weeks when said therapeutic chimeric is exposed at 37 0C to a composition comprising a 1:1 weight ratio of human serum to water.
25. The chimeric therapeutic of any one of claims 11-24, wherein said modified structural core portion comprises a conjugation site allowing attachment of a chemical linker moiety.
26. The chimeric therapeutic of any one of claims 11-25, wherein said modified structural core portion comprises one or more stability modifications.
27. The chimeric therapeutic of any one of claims 11-26, wherein modified tail portion comprises about 10 to about 35 amino acids.
28. The chimeric therapeutic of any one of claims 11-27, wherein the modified tail portion comprises truncations, substitutions and/or additions of amino acids as compared to a wild type tail portion.
29. The chimeric therapeutic of claim 27 or 28, wherein the modified tail portion comprises about 4 to about 30 lysines.
30. The chimeric therapeutic of any one of claim 27-29 wherein the modified tail portion comprises a lysine domain of about 4 to about 30 lysines.
31. The chimeric therapeutic of claim 30, wherein said lysine domain is about 5 to about 20 lysines.
32. The chimeric therapeutic of claim 31, wherein said lysine domain is 9 lysines.
33. The chimeric therapeutic of any one of claims 27-32, wherein the modified tail portion further comprises a histidine tag of about 1 to about 10 histidines.
34. The chimeric therapeutic of any one of claims 27-33, wherein the modified tail portion further comprises a histidine tag of about 5 to about 6 histidines.
35. The chimeric therapeutic of any one of claims 27-34, wherein the modified tail portion further comprises a linker segment comprising about 1 to about 20 amino acids.
36. The chimeric therapeutic of any one of claims 11-35, wherein the tail portion is chosen from SEQ ID NO: 15 and SEQ ID NO: 24, optionally including a linker segment chosen from SEQ ID NO: 32 - SEQ ID NO: 34.
37. The chimeric therapeutic of any one of claims 11-36, wherein the modified viral core protein is chosen from SEQ ID NO: 16 - SEQ ID NO: 23, SEQ ID NO: 25 - SEQ ID NO: 31, SEQ ID NO: 35 - SEQ ID NO: 48; SEQ ID NO: 51 - SEQ ID NO: 55, and SEQ ID NO: 57.
38. The chimeric therapeutic of any one of claims 11-37, wherein said nucleic acid is an inhibiting nucleic acid.
39. The chimeric therapeutic of any one of claims 11-38, wherein the nucleic acid is chemically modified.
40. The chimeric therapeutic of claim 39, wherein said nucleic acid comprises at least one of: a thiophosphate linkage.
41. The chimeric therapeutic of any one of claims 11-40, wherein said nucleic acid is a double stranded RNA.
42. The chimeric therapeutic of any one of claims 11-40, wherein said nucleic acid is an antisense nucleic acid.
43. The chimeric therapeutic of any one of claims 11-40, wherein said nucleic acid is a hairpin RNA.
44. The chimeric therapeutic of any one of claims 11-40, wherein said nucleic acid is microRNA.
45. The chimeric therapeutic of any one of claims 11-44, wherein said nucleic acid is about 25 to about 44 bases in length.
46. The chimeric therapeutic of any one of claims 11-44, wherein said nucleic acid is about 10 to about 30 bases in length.
47. The chimeric therapeutic of any one of claims 11-44, wherein said nucleic acid is about 19 to about 23 bases in length.
48. A therapeutic composition comprising a particle formed from a plurality of chimeric therapeutics of any one of claims 11-47, wherein said particle further comprises a coating; and a pharmaceutically acceptable excipient.
49. The therapeutic composition of claim 48, wherein the particle is a modified icosahedral or is substantially spherical.
50. A therapeutic composition comprising: a) a particle formed from at least: i) a first discrete number of modified viral core proteins; and ii) a second discrete number of nucleic acids each bound to one of said modified viral core proteins; wherein said nucleic acids bound to said modified viral core proteins are substantially nonimmunogenic; and iii) optionally, a coating associated with said particle; and b) a pharmaceutically acceptable excipient.
51. The therapeutic composition of claim 50, wherein said first discrete number is about 500, or about 343, or about 164, or about 313, or about 336, or about 510, or about 171.
52. The therapeutic composition of claim 50 or 51, wherein said second discrete number is about 2 to about 60.
53. The therapeutic composition of claim 52, wherein said second discrete number is about 8 to about 20.
54. The therapeutic composition of any one of claims 50-53, wherein said second discrete number is about 14 to about 18.
55. The therapeutic composition of any one of claims 50-54, wherein said coating comprises one or more lipids.
56. The therapeutic composition of claim 55, wherein at least one lipid molecule is covalently bound through lipid linker moiety to one of said viral core proteins.
57. The therapeutic composition of any one of claims 50-56, wherein said coating comprises cholesterol.
58. The therapeutic composition of any one of claims 55-57, wherein said coating comprises one or more neutral lipids.
59. The therapeutic composition of any one of claims claim 50-58, wherein said coating comprises HSPC and/or POPG.
60. The therapeutic composition of any one of claims 50-59 wherein said therapeutic composition is substantially free of nuclease.
61. The therapeutic composition of any one of claims 50-60, wherein said nucleic acids are substantially protected from serum degradation.
62. The therapeutic composition of any one of claims 50-61, wherein said nucleic acids are substantially protected from serum degradation for at least two weeks when said particle is exposed at 37 0C to a composition comprising a 1:1 weight ratio of human serum to water.
63. The therapeutic composition of any one of claims 50-62, wherein the binding affinity of said nucleic acids to said viral core proteins is about 50 nM to about 500 nM, at 2OmM NaHCO3, and a pH of 9.5.
64. The therapeutic composition of any one of claims 50-63, wherein said nucleic acids are bound to a modified tail portion of said viral core proteins with a binding affinity that allows release of said nucleic acid when said therapeutic composition is administered in-vivo.
65. The therapeutic composition of claim 64, wherein the modified tail portion comprises a lysine domain of about 4 to about 30 lysines.
66. The therapeutic composition of claim 65, wherein said lysine domain is 9 lysines.
67. The therapeutic composition of any one of claims 64-66, wherein the modified tail portion further comprises a histidine tag of about 1 to about 10 histidines.
68. The therapeutic composition of any one of claims 64-67, wherein the modified tail portion further comprises a linker segment comprising about 1 to about 20 amino acids.
69. The therapeutic composition of any one of claims 64-68, wherein the modified tail portion is chosen from SEQ ID NO: 15 and SEQ ID NO: 24, optionally including a linker segment chosen from SEQ ID NO: 32 - SEQ ID NO: 34.
70. The therapeutic composition of any one of claims 50-69, wherein the modified viral core protein is chosen from SEQ ID NO: 16 - SEQ ID NO: 23, SEQ ID NO: 25 - SEQ ID NO: 31, SEQ ID NO: 35 - SEQ ID NO: 48; SEQ ID NO: 51 - SEQ ID NO: 55, and SEQ ID NO: 57.
71. A therapeutic particle comprising: a plurality of viral core proteins each comprising a structural core portion and a modified tail portion, wherein said structural core portions form a capsid; and said modified tail portions are substantially disposed within said capsid; and a plurality of nucleic acids, bound to said modified tail portion, wherein said nucleic acids are resistant to degradation with a nuclease when said particle is placed in an aqueous solution.
72. The therapeutic particle of claim 71, wherein said nucleic acids bound to said modified tail portion are substantially non-immunogenic.
73. The therapeutic particle of claim 71 or 72, wherein said nucleic acids bound to said modified tail portion is bound with a binding affinity that allows release of said nucleic acids when said therapeutic particle is administered in vivo.
74. The therapeutic particle of any one of claims 71-73, wherein said particle comprises about 3 to about 50 nucleic acids.
75. The therapeutic particle of any one of claims 71-74, wherein said particle comprises about 6 to about 28 nucleic acids.
76. The therapeutic particle of any one of claims 71-75, wherein said particle is resistant to serum degradation in an aqueous serum solution.
77. The therapeutic particle of any one of claims 71-76, wherein a chemical linker moiety is bound to said capsid.
78. The therapeutic particle of claim 77, wherein said chemical linker moiety is formed by contacting said capsid with PE-maleimide.
79. The therapeutic particle of any one of claims 71-78, further comprising a coating.
80. The therapeutic particle of claim 79 wherein said coating comprises one or more lipids.
81. The therapeutic particle of claim 79 or 80, wherein the coating comprises cholesterol.
82. The therapeutic particle of claim 80, wherein said coating comprises a neutral lipid.
83. The therapeutic particle of any one of claims 80-82, wherein said coating further comprises HSPC and/or POPG.
84. The therapeutic particle of any one of claims 71-83, wherein said viral core proteins are hepatitis B viral core proteins.
85. The therapeutic particle of any one of claims 71-84, wherein the modified tail portion comprises a lysine domain of about 4 to about 30 lysines.
86. The therapeutic particle of claim 85 wherein said lysine domain is 9 lysines.
87. The therapeutic particle any one of claims 71-86, wherein the modified tail portion further comprises a histidine tag of about 1 to about 10 histidines.
88. The therapeutic composition of any one of claims 71-87, wherein the modified tail portion further comprises a linker segment comprising about 1 to about 20 amino acids.
89. The therapeutic particle of any one of claims 71-88, wherein the modified tail portion is chosen from SEQ ID NO: 15 and SEQ ID NO: 24, optionally including a linker segment chosen from SEQ ID NO: 32 - SEQ ID NO: 34.
90. The therapeutic particle of any one of claims 71-89 wherein the modified viral core protein is chosen from SEQ ID NO: 16 - SEQ ID NO: 23, SEQ ID NO: 25 - SEQ ID NO: 31, SEQ ID NO: 35 - SEQ ID NO: 48; SEQ ID NO: 51 - SEQ ID NO: 55, and SEQ ID NO: 57.
91. A pharmaceutically acceptable composition comprising a plurality of the therapeutic particles of any of claims 71-90 and a pharmaceutically acceptable excipient.
92. A method of regulating gene expression in a cell comprising administering to the cell a therapeutic particle or composition of any one of claims 50-91.
93. A method of treating a disease associated with a target in a patient in need thereof comprising administering to said patient a pharmaceutically effective amount of a composition comprising the therapeutic particles or compositions of any one of claims 50-91.
94. A therapeutic particle comprising: a plurality of modified viral core proteins chosen from SEQ ID NO: 16 - SEQ ID NO: 23, SEQ ID NO: 25 - SEQ ID NO: 31, SEQ ID NO: 35 - SEQ ID NO: 48; SEQ ID NO: 51 - SEQ ID NO: 55, and SEQ ID NO: 57, and wherein said nucleic acid is bound to one of said modified viral core proteins.
95. The therapeutic particle of claim 94, comprising a plurality of said nucleic acids each bound to one of said modified viral core proteins.
96. The therapeutic particle of claim 94 or 95, further comprising a coating comprising a lipid composition.
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