CA2335240C - Cyanine dyes and synthesis methods thereof - Google Patents
Cyanine dyes and synthesis methods thereof Download PDFInfo
- Publication number
- CA2335240C CA2335240C CA2335240A CA2335240A CA2335240C CA 2335240 C CA2335240 C CA 2335240C CA 2335240 A CA2335240 A CA 2335240A CA 2335240 A CA2335240 A CA 2335240A CA 2335240 C CA2335240 C CA 2335240C
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- Canada
- Prior art keywords
- group
- alkyl
- substituted
- compound
- heteroatom
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Expired - Lifetime
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- 239000000975 dye Substances 0.000 title claims abstract description 107
- ANRHNWWPFJCPAZ-UHFFFAOYSA-M thionine Chemical compound [Cl-].C1=CC(N)=CC2=[S+]C3=CC(N)=CC=C3N=C21 ANRHNWWPFJCPAZ-UHFFFAOYSA-M 0.000 title description 29
- 238000001308 synthesis method Methods 0.000 title description 2
- 125000001424 substituent group Chemical group 0.000 claims abstract description 58
- 150000001412 amines Chemical class 0.000 claims abstract description 52
- 125000002887 hydroxy group Chemical group [H]O* 0.000 claims abstract description 46
- 125000000217 alkyl group Chemical group 0.000 claims abstract description 33
- 125000004169 (C1-C6) alkyl group Chemical group 0.000 claims abstract description 28
- 238000000034 method Methods 0.000 claims abstract description 26
- 239000001257 hydrogen Substances 0.000 claims abstract description 20
- 229910052739 hydrogen Inorganic materials 0.000 claims abstract description 20
- 230000000269 nucleophilic effect Effects 0.000 claims abstract description 15
- 238000002372 labelling Methods 0.000 claims abstract description 9
- 150000003573 thiols Chemical class 0.000 claims abstract description 6
- 125000000923 (C1-C30) alkyl group Chemical group 0.000 claims description 53
- 150000001875 compounds Chemical class 0.000 claims description 51
- 125000005842 heteroatom Chemical group 0.000 claims description 49
- 125000001997 phenyl group Chemical group [H]C1=C([H])C([H])=C(*)C([H])=C1[H] 0.000 claims description 37
- 229910052717 sulfur Inorganic materials 0.000 claims description 28
- 229910052757 nitrogen Inorganic materials 0.000 claims description 26
- BDHFUVZGWQCTTF-UHFFFAOYSA-M sulfonate Chemical compound [O-]S(=O)=O BDHFUVZGWQCTTF-UHFFFAOYSA-M 0.000 claims description 26
- 238000006243 chemical reaction Methods 0.000 claims description 25
- 229910052760 oxygen Inorganic materials 0.000 claims description 23
- -1 indole compound Chemical class 0.000 claims description 21
- IJGRMHOSHXDMSA-UHFFFAOYSA-N Atomic nitrogen Chemical group N#N IJGRMHOSHXDMSA-UHFFFAOYSA-N 0.000 claims description 20
- 229910052736 halogen Inorganic materials 0.000 claims description 20
- 125000001434 methanylylidene group Chemical group [H]C#[*] 0.000 claims description 20
- 150000007942 carboxylates Chemical class 0.000 claims description 16
- 125000005843 halogen group Chemical group 0.000 claims description 16
- 150000002367 halogens Chemical group 0.000 claims description 16
- 125000003545 alkoxy group Chemical group 0.000 claims description 15
- 150000002431 hydrogen Chemical class 0.000 claims description 15
- NINIDFKCEFEMDL-UHFFFAOYSA-N Sulfur Chemical group [S] NINIDFKCEFEMDL-UHFFFAOYSA-N 0.000 claims description 13
- 150000001336 alkenes Chemical class 0.000 claims description 13
- 239000011593 sulfur Substances 0.000 claims description 13
- JUJWROOIHBZHMG-UHFFFAOYSA-N Pyridine Chemical compound C1=CC=NC=C1 JUJWROOIHBZHMG-UHFFFAOYSA-N 0.000 claims description 12
- 125000003729 nucleotide group Chemical group 0.000 claims description 12
- QVGXLLKOCUKJST-UHFFFAOYSA-N atomic oxygen Chemical compound [O] QVGXLLKOCUKJST-UHFFFAOYSA-N 0.000 claims description 11
- 239000001301 oxygen Substances 0.000 claims description 11
- SIKJAQJRHWYJAI-UHFFFAOYSA-N benzopyrrole Natural products C1=CC=C2NC=CC2=C1 SIKJAQJRHWYJAI-UHFFFAOYSA-N 0.000 claims description 10
- 238000005859 coupling reaction Methods 0.000 claims description 8
- 108090000765 processed proteins & peptides Proteins 0.000 claims description 8
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 claims description 7
- 230000008878 coupling Effects 0.000 claims description 7
- 238000010168 coupling process Methods 0.000 claims description 7
- 150000002430 hydrocarbons Chemical class 0.000 claims description 7
- PZOUSPYUWWUPPK-UHFFFAOYSA-N indole Natural products CC1=CC=CC2=C1C=CN2 PZOUSPYUWWUPPK-UHFFFAOYSA-N 0.000 claims description 7
- RKJUIXBNRJVNHR-UHFFFAOYSA-N indolenine Natural products C1=CC=C2CC=NC2=C1 RKJUIXBNRJVNHR-UHFFFAOYSA-N 0.000 claims description 7
- UMJSCPRVCHMLSP-UHFFFAOYSA-N pyridine Natural products COC1=CC=CN=C1 UMJSCPRVCHMLSP-UHFFFAOYSA-N 0.000 claims description 7
- NQRYJNQNLNOLGT-UHFFFAOYSA-N Piperidine Chemical class C1CCNCC1 NQRYJNQNLNOLGT-UHFFFAOYSA-N 0.000 claims description 6
- 150000001408 amides Chemical class 0.000 claims description 6
- 229930195733 hydrocarbon Natural products 0.000 claims description 6
- 239000000463 material Substances 0.000 claims description 6
- 102000004169 proteins and genes Human genes 0.000 claims description 6
- 108090000623 proteins and genes Proteins 0.000 claims description 6
- 230000001588 bifunctional effect Effects 0.000 claims description 5
- 239000012351 deprotecting agent Substances 0.000 claims description 4
- 102000039446 nucleic acids Human genes 0.000 claims description 4
- 150000007523 nucleic acids Chemical class 0.000 claims description 4
- 108020004707 nucleic acids Proteins 0.000 claims description 4
- 238000005935 nucleophilic addition reaction Methods 0.000 claims description 4
- 229920000642 polymer Polymers 0.000 claims description 4
- 102000004196 processed proteins & peptides Human genes 0.000 claims description 4
- 108090001008 Avidin Proteins 0.000 claims description 3
- 241000894006 Bacteria Species 0.000 claims description 3
- 108090001090 Lectins Proteins 0.000 claims description 3
- 102000004856 Lectins Human genes 0.000 claims description 3
- YNAVUWVOSKDBBP-UHFFFAOYSA-N Morpholine Natural products C1COCCN1 YNAVUWVOSKDBBP-UHFFFAOYSA-N 0.000 claims description 3
- 239000004480 active ingredient Substances 0.000 claims description 3
- 239000000427 antigen Substances 0.000 claims description 3
- 108091007433 antigens Proteins 0.000 claims description 3
- 102000036639 antigens Human genes 0.000 claims description 3
- 150000001720 carbohydrates Chemical class 0.000 claims description 3
- 235000014633 carbohydrates Nutrition 0.000 claims description 3
- 230000001413 cellular effect Effects 0.000 claims description 3
- 210000003527 eukaryotic cell Anatomy 0.000 claims description 3
- 239000007850 fluorescent dye Substances 0.000 claims description 3
- 150000004676 glycans Chemical class 0.000 claims description 3
- 229940088597 hormone Drugs 0.000 claims description 3
- 239000005556 hormone Substances 0.000 claims description 3
- 239000002523 lectin Substances 0.000 claims description 3
- 150000002632 lipids Chemical class 0.000 claims description 3
- 239000002207 metabolite Substances 0.000 claims description 3
- 239000002777 nucleoside Substances 0.000 claims description 3
- 125000003835 nucleoside group Chemical group 0.000 claims description 3
- 239000002773 nucleotide Substances 0.000 claims description 3
- 229920001542 oligosaccharide Polymers 0.000 claims description 3
- 150000002482 oligosaccharides Chemical class 0.000 claims description 3
- 229920001282 polysaccharide Polymers 0.000 claims description 3
- 239000005017 polysaccharide Substances 0.000 claims description 3
- 108020003175 receptors Proteins 0.000 claims description 3
- 102000005962 receptors Human genes 0.000 claims description 3
- 239000003053 toxin Substances 0.000 claims description 3
- 231100000765 toxin Toxicity 0.000 claims description 3
- 108700012359 toxins Proteins 0.000 claims description 3
- 210000002845 virion Anatomy 0.000 claims description 3
- WKBOTKDWSSQWDR-UHFFFAOYSA-N Bromine atom Chemical group [Br] WKBOTKDWSSQWDR-UHFFFAOYSA-N 0.000 claims description 2
- 150000004703 alkoxides Chemical class 0.000 claims description 2
- GDTBXPJZTBHREO-UHFFFAOYSA-N bromine Chemical group BrBr GDTBXPJZTBHREO-UHFFFAOYSA-N 0.000 claims description 2
- 229910052794 bromium Inorganic materials 0.000 claims description 2
- 125000004432 carbon atom Chemical group C* 0.000 claims description 2
- 239000000460 chlorine Substances 0.000 claims description 2
- 229910052801 chlorine Inorganic materials 0.000 claims description 2
- 125000001309 chloro group Chemical group Cl* 0.000 claims description 2
- PNDPGZBMCMUPRI-UHFFFAOYSA-N iodine Chemical group II PNDPGZBMCMUPRI-UHFFFAOYSA-N 0.000 claims description 2
- 125000006239 protecting group Chemical group 0.000 claims description 2
- 125000004178 (C1-C4) alkyl group Chemical group 0.000 claims 19
- 239000004215 Carbon black (E152) Substances 0.000 claims 4
- 238000004519 manufacturing process Methods 0.000 claims 3
- 102000008072 Lymphokines Human genes 0.000 claims 2
- 108010074338 Lymphokines Proteins 0.000 claims 2
- 230000002538 fungal effect Effects 0.000 claims 2
- 239000000758 substrate Substances 0.000 claims 2
- 229910052799 carbon Inorganic materials 0.000 claims 1
- 150000002780 morpholines Chemical class 0.000 claims 1
- 102220259596 rs146705057 Human genes 0.000 claims 1
- 239000002243 precursor Substances 0.000 abstract description 27
- 150000002475 indoles Chemical class 0.000 abstract description 12
- 125000000623 heterocyclic group Chemical group 0.000 abstract description 7
- 230000007246 mechanism Effects 0.000 abstract description 6
- 229940054051 antipsychotic indole derivative Drugs 0.000 abstract description 3
- QGKMIGUHVLGJBR-UHFFFAOYSA-M (4z)-1-(3-methylbutyl)-4-[[1-(3-methylbutyl)quinolin-1-ium-4-yl]methylidene]quinoline;iodide Chemical compound [I-].C12=CC=CC=C2N(CCC(C)C)C=CC1=CC1=CC=[N+](CCC(C)C)C2=CC=CC=C12 QGKMIGUHVLGJBR-UHFFFAOYSA-M 0.000 abstract 2
- 238000006073 displacement reaction Methods 0.000 abstract 1
- 125000004435 hydrogen atom Chemical class [H]* 0.000 abstract 1
- 230000002194 synthesizing effect Effects 0.000 abstract 1
- OKKJLVBELUTLKV-UHFFFAOYSA-N Methanol Chemical compound OC OKKJLVBELUTLKV-UHFFFAOYSA-N 0.000 description 48
- 239000000243 solution Substances 0.000 description 34
- 150000003839 salts Chemical class 0.000 description 30
- XAEFZNCEHLXOMS-UHFFFAOYSA-M potassium benzoate Chemical compound [K+].[O-]C(=O)C1=CC=CC=C1 XAEFZNCEHLXOMS-UHFFFAOYSA-M 0.000 description 29
- 125000003396 thiol group Chemical group [H]S* 0.000 description 24
- 239000007787 solid Substances 0.000 description 22
- 238000010992 reflux Methods 0.000 description 14
- 108010090804 Streptavidin Proteins 0.000 description 12
- 239000011541 reaction mixture Substances 0.000 description 12
- 239000011347 resin Substances 0.000 description 12
- 229920005989 resin Polymers 0.000 description 12
- RTZKZFJDLAIYFH-UHFFFAOYSA-N Diethyl ether Chemical compound CCOCC RTZKZFJDLAIYFH-UHFFFAOYSA-N 0.000 description 11
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 11
- YMWUJEATGCHHMB-UHFFFAOYSA-N Dichloromethane Chemical compound ClCCl YMWUJEATGCHHMB-UHFFFAOYSA-N 0.000 description 9
- 230000015572 biosynthetic process Effects 0.000 description 9
- 239000000203 mixture Substances 0.000 description 8
- 238000004366 reverse phase liquid chromatography Methods 0.000 description 8
- AVXURJPOCDRRFD-UHFFFAOYSA-N Hydroxylamine Chemical compound ON AVXURJPOCDRRFD-UHFFFAOYSA-N 0.000 description 7
- 239000003153 chemical reaction reagent Substances 0.000 description 7
- 238000003756 stirring Methods 0.000 description 7
- 238000003786 synthesis reaction Methods 0.000 description 7
- ZMANZCXQSJIPKH-UHFFFAOYSA-N Triethylamine Chemical compound CCN(CC)CC ZMANZCXQSJIPKH-UHFFFAOYSA-N 0.000 description 6
- 125000002496 methyl group Chemical group [H]C([H])([H])* 0.000 description 6
- SCVFZCLFOSHCOH-UHFFFAOYSA-M potassium acetate Chemical compound [K+].CC([O-])=O SCVFZCLFOSHCOH-UHFFFAOYSA-M 0.000 description 6
- 239000000126 substance Substances 0.000 description 6
- 239000000725 suspension Substances 0.000 description 6
- PEEHTFAAVSWFBL-UHFFFAOYSA-N Maleimide Chemical class O=C1NC(=O)C=C1 PEEHTFAAVSWFBL-UHFFFAOYSA-N 0.000 description 5
- 239000002904 solvent Substances 0.000 description 5
- 230000003595 spectral effect Effects 0.000 description 5
- 125000000472 sulfonyl group Chemical group *S(*)(=O)=O 0.000 description 5
- UMGDCJDMYOKAJW-UHFFFAOYSA-N thiourea Chemical compound NC(N)=S UMGDCJDMYOKAJW-UHFFFAOYSA-N 0.000 description 5
- AAAXMNYUNVCMCJ-UHFFFAOYSA-N 1,3-diiodopropane Chemical compound ICCCI AAAXMNYUNVCMCJ-UHFFFAOYSA-N 0.000 description 4
- IAZDPXIOMUYVGZ-UHFFFAOYSA-N Dimethylsulphoxide Chemical compound CS(C)=O IAZDPXIOMUYVGZ-UHFFFAOYSA-N 0.000 description 4
- 239000012298 atmosphere Substances 0.000 description 4
- LEQAOMBKQFMDFZ-UHFFFAOYSA-N glyoxal Chemical compound O=CC=O LEQAOMBKQFMDFZ-UHFFFAOYSA-N 0.000 description 4
- 239000002502 liposome Substances 0.000 description 4
- 229910000403 monosodium phosphate Inorganic materials 0.000 description 4
- 235000019799 monosodium phosphate Nutrition 0.000 description 4
- 239000000047 product Substances 0.000 description 4
- AJPJDKMHJJGVTQ-UHFFFAOYSA-M sodium dihydrogen phosphate Chemical compound [Na+].OP(O)([O-])=O AJPJDKMHJJGVTQ-UHFFFAOYSA-M 0.000 description 4
- JGVSIZVWGGQMPY-SNAWJCMRSA-N (e)-1,3,3-trimethoxyprop-1-ene Chemical compound CO\C=C\C(OC)OC JGVSIZVWGGQMPY-SNAWJCMRSA-N 0.000 description 3
- WEVYAHXRMPXWCK-UHFFFAOYSA-N Acetonitrile Chemical compound CC#N WEVYAHXRMPXWCK-UHFFFAOYSA-N 0.000 description 3
- KCXVZYZYPLLWCC-UHFFFAOYSA-N EDTA Chemical compound OC(=O)CN(CC(O)=O)CCN(CC(O)=O)CC(O)=O KCXVZYZYPLLWCC-UHFFFAOYSA-N 0.000 description 3
- ZMXDDKWLCZADIW-UHFFFAOYSA-N N,N-Dimethylformamide Chemical compound CN(C)C=O ZMXDDKWLCZADIW-UHFFFAOYSA-N 0.000 description 3
- KWYUFKZDYYNOTN-UHFFFAOYSA-M Potassium hydroxide Chemical compound [OH-].[K+] KWYUFKZDYYNOTN-UHFFFAOYSA-M 0.000 description 3
- 238000010521 absorption reaction Methods 0.000 description 3
- 125000004177 diethyl group Chemical group [H]C([H])([H])C([H])([H])* 0.000 description 3
- 238000001641 gel filtration chromatography Methods 0.000 description 3
- 125000001041 indolyl group Chemical group 0.000 description 3
- 238000007344 nucleophilic reaction Methods 0.000 description 3
- 235000011056 potassium acetate Nutrition 0.000 description 3
- 125000001436 propyl group Chemical group [H]C([*])([H])C([H])([H])C([H])([H])[H] 0.000 description 3
- QZAYGJVTTNCVMB-UHFFFAOYSA-N serotonin Chemical compound C1=C(O)C=C2C(CCN)=CNC2=C1 QZAYGJVTTNCVMB-UHFFFAOYSA-N 0.000 description 3
- 239000012265 solid product Substances 0.000 description 3
- 125000003088 (fluoren-9-ylmethoxy)carbonyl group Chemical group 0.000 description 2
- IHDBZCJYSHDCKF-UHFFFAOYSA-N 4,6-dichlorotriazine Chemical compound ClC1=CC(Cl)=NN=N1 IHDBZCJYSHDCKF-UHFFFAOYSA-N 0.000 description 2
- ORLGPUVJERIKLW-UHFFFAOYSA-N 5-chlorotriazine Chemical compound ClC1=CN=NN=C1 ORLGPUVJERIKLW-UHFFFAOYSA-N 0.000 description 2
- CSCPPACGZOOCGX-UHFFFAOYSA-N Acetone Chemical compound CC(C)=O CSCPPACGZOOCGX-UHFFFAOYSA-N 0.000 description 2
- NOWKCMXCCJGMRR-UHFFFAOYSA-N Aziridine Chemical class C1CN1 NOWKCMXCCJGMRR-UHFFFAOYSA-N 0.000 description 2
- LSNNMFCWUKXFEE-UHFFFAOYSA-M Bisulfite Chemical compound OS([O-])=O LSNNMFCWUKXFEE-UHFFFAOYSA-M 0.000 description 2
- 102400000967 Bradykinin Human genes 0.000 description 2
- 101800004538 Bradykinin Proteins 0.000 description 2
- 102400001370 Galanin Human genes 0.000 description 2
- 101800002068 Galanin Proteins 0.000 description 2
- QXZGBUJJYSLZLT-UHFFFAOYSA-N H-Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg-OH Natural products NC(N)=NCCCC(N)C(=O)N1CCCC1C(=O)N1C(C(=O)NCC(=O)NC(CC=2C=CC=CC=2)C(=O)NC(CO)C(=O)N2C(CCC2)C(=O)NC(CC=2C=CC=CC=2)C(=O)NC(CCCN=C(N)N)C(O)=O)CCC1 QXZGBUJJYSLZLT-UHFFFAOYSA-N 0.000 description 2
- OAKJQQAXSVQMHS-UHFFFAOYSA-N Hydrazine Chemical compound NN OAKJQQAXSVQMHS-UHFFFAOYSA-N 0.000 description 2
- GHAZCVNUKKZTLG-UHFFFAOYSA-N N-ethyl-succinimide Natural products CCN1C(=O)CCC1=O GHAZCVNUKKZTLG-UHFFFAOYSA-N 0.000 description 2
- HDFGOPSGAURCEO-UHFFFAOYSA-N N-ethylmaleimide Chemical compound CCN1C(=O)C=CC1=O HDFGOPSGAURCEO-UHFFFAOYSA-N 0.000 description 2
- XSQUKJJJFZCRTK-UHFFFAOYSA-N Urea Natural products NC(N)=O XSQUKJJJFZCRTK-UHFFFAOYSA-N 0.000 description 2
- 239000002253 acid Chemical class 0.000 description 2
- 150000001299 aldehydes Chemical class 0.000 description 2
- 230000004071 biological effect Effects 0.000 description 2
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- 125000003178 carboxy group Chemical group [H]OC(*)=O 0.000 description 2
- 238000004587 chromatography analysis Methods 0.000 description 2
- 239000013078 crystal Substances 0.000 description 2
- NZNMSOFKMUBTKW-UHFFFAOYSA-N cyclohexanecarboxylic acid Chemical compound OC(=O)C1CCCCC1 NZNMSOFKMUBTKW-UHFFFAOYSA-N 0.000 description 2
- 150000004891 diazines Chemical class 0.000 description 2
- 229940015043 glyoxal Drugs 0.000 description 2
- 150000004820 halides Chemical class 0.000 description 2
- RERZNCLIYCABFS-UHFFFAOYSA-N harmaline Chemical compound C1CN=C(C)C2=C1C1=CC=C(OC)C=C1N2 RERZNCLIYCABFS-UHFFFAOYSA-N 0.000 description 2
- 238000010438 heat treatment Methods 0.000 description 2
- UCMFXAIFSBSDAQ-UHFFFAOYSA-N hexanamide Chemical compound CCCCCC(N)=O.CCCCCC(N)=O UCMFXAIFSBSDAQ-UHFFFAOYSA-N 0.000 description 2
- 150000002463 imidates Chemical class 0.000 description 2
- 239000012948 isocyanate Substances 0.000 description 2
- 150000002513 isocyanates Chemical class 0.000 description 2
- 238000002955 isolation Methods 0.000 description 2
- 150000002540 isothiocyanates Chemical class 0.000 description 2
- 125000000956 methoxy group Chemical group [H]C([H])([H])O* 0.000 description 2
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- SLZIZIJTGAYEKK-CIJSCKBQSA-N molport-023-220-247 Chemical compound C([C@@H](C(=O)N[C@@H](C)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CC(O)=O)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CC=1N=CNC=1)C(=O)N[C@@H](CCCNC(N)=N)C(=O)N[C@@H](CO)C(=O)N[C@@H](CC=1C=CC=CC=1)C(=O)N[C@@H](CC=1N=CNC=1)C(=O)N[C@@H](CC(O)=O)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC=1C=CC(O)=CC=1)C(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C)C(N)=O)NC(=O)[C@H]1N(CCC1)C(=O)CNC(=O)[C@H](CC(C)C)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CC=1C=CC(O)=CC=1)NC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](CO)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)[C@H](CC=1C2=CC=CC=C2NC=1)NC(=O)CN)[C@@H](C)O)C1=CNC=N1 SLZIZIJTGAYEKK-CIJSCKBQSA-N 0.000 description 2
- 150000007530 organic bases Chemical class 0.000 description 2
- DDBREPKUVSBGFI-UHFFFAOYSA-N phenobarbital Chemical compound C=1C=CC=CC=1C1(CC)C(=O)NC(=O)NC1=O DDBREPKUVSBGFI-UHFFFAOYSA-N 0.000 description 2
- 239000000843 powder Substances 0.000 description 2
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- 125000002924 primary amino group Chemical class [H]N([H])* 0.000 description 2
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- 239000001488 sodium phosphate Substances 0.000 description 2
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- 235000011008 sodium phosphates Nutrition 0.000 description 2
- 159000000000 sodium salts Chemical class 0.000 description 2
- ULARYIUTHAWJMU-UHFFFAOYSA-M sodium;1-[4-(2,5-dioxopyrrol-1-yl)butanoyloxy]-2,5-dioxopyrrolidine-3-sulfonate Chemical compound [Na+].O=C1C(S(=O)(=O)[O-])CC(=O)N1OC(=O)CCCN1C(=O)C=CC1=O ULARYIUTHAWJMU-UHFFFAOYSA-M 0.000 description 2
- 238000006467 substitution reaction Methods 0.000 description 2
- 150000003461 sulfonyl halides Chemical class 0.000 description 2
- GKASDNZWUGIAMG-UHFFFAOYSA-N triethyl orthoformate Chemical compound CCOC(OCC)OCC GKASDNZWUGIAMG-UHFFFAOYSA-N 0.000 description 2
- LWIHDJKSTIGBAC-UHFFFAOYSA-K tripotassium phosphate Chemical compound [K+].[K+].[K+].[O-]P([O-])([O-])=O LWIHDJKSTIGBAC-UHFFFAOYSA-K 0.000 description 2
- RYFMWSXOAZQYPI-UHFFFAOYSA-K trisodium phosphate Chemical compound [Na+].[Na+].[Na+].[O-]P([O-])([O-])=O RYFMWSXOAZQYPI-UHFFFAOYSA-K 0.000 description 2
- 238000005406 washing Methods 0.000 description 2
- NWZSZGALRFJKBT-KNIFDHDWSA-N (2s)-2,6-diaminohexanoic acid;(2s)-2-hydroxybutanedioic acid Chemical compound OC(=O)[C@@H](O)CC(O)=O.NCCCC[C@H](N)C(O)=O NWZSZGALRFJKBT-KNIFDHDWSA-N 0.000 description 1
- IIZPXYDJLKNOIY-JXPKJXOSSA-N 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine Chemical compound CCCCCCCCCCCCCCCC(=O)OC[C@H](COP([O-])(=O)OCC[N+](C)(C)C)OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC IIZPXYDJLKNOIY-JXPKJXOSSA-N 0.000 description 1
- SIKJAQJRHWYJAI-UHFFFAOYSA-O 1H-indol-1-ium Chemical compound C1=CC=C2[NH2+]C=CC2=C1 SIKJAQJRHWYJAI-UHFFFAOYSA-O 0.000 description 1
- WAOPPELONVRRKQ-UHFFFAOYSA-N 1h-indol-1-ium;iodide Chemical compound [I-].C1=CC=C2[NH2+]C=CC2=C1 WAOPPELONVRRKQ-UHFFFAOYSA-N 0.000 description 1
- FLHJIAFUWHPJRT-UHFFFAOYSA-N 2,3,3-trimethylindole Chemical compound C1=CC=C2C(C)(C)C(C)=NC2=C1 FLHJIAFUWHPJRT-UHFFFAOYSA-N 0.000 description 1
- 102000040125 5-hydroxytryptamine receptor family Human genes 0.000 description 1
- 108091032151 5-hydroxytryptamine receptor family Proteins 0.000 description 1
- 238000001712 DNA sequencing Methods 0.000 description 1
- QOSSAOTZNIDXMA-UHFFFAOYSA-N Dicylcohexylcarbodiimide Chemical compound C1CCCCC1N=C=NC1CCCCC1 QOSSAOTZNIDXMA-UHFFFAOYSA-N 0.000 description 1
- BWGNESOTFCXPMA-UHFFFAOYSA-N Dihydrogen disulfide Chemical compound SS BWGNESOTFCXPMA-UHFFFAOYSA-N 0.000 description 1
- UFHFLCQGNIYNRP-UHFFFAOYSA-N Hydrogen Chemical compound [H][H] UFHFLCQGNIYNRP-UHFFFAOYSA-N 0.000 description 1
- QIVBCDIJIAJPQS-VIFPVBQESA-N L-tryptophane Chemical compound C1=CC=C2C(C[C@H](N)C(O)=O)=CNC2=C1 QIVBCDIJIAJPQS-VIFPVBQESA-N 0.000 description 1
- NQTADLQHYWFPDB-UHFFFAOYSA-N N-Hydroxysuccinimide Chemical compound ON1C(=O)CCC1=O NQTADLQHYWFPDB-UHFFFAOYSA-N 0.000 description 1
- 102400001103 Neurotensin Human genes 0.000 description 1
- 101800001814 Neurotensin Proteins 0.000 description 1
- 108091093037 Peptide nucleic acid Proteins 0.000 description 1
- ISWSIDIOOBJBQZ-UHFFFAOYSA-N Phenol Chemical compound OC1=CC=CC=C1 ISWSIDIOOBJBQZ-UHFFFAOYSA-N 0.000 description 1
- QIVBCDIJIAJPQS-UHFFFAOYSA-N Tryptophan Natural products C1=CC=C2C(CC(N)C(O)=O)=CNC2=C1 QIVBCDIJIAJPQS-UHFFFAOYSA-N 0.000 description 1
- BLGXFZZNTVWLAY-CCZXDCJGSA-N Yohimbine Natural products C1=CC=C2C(CCN3C[C@@H]4CC[C@@H](O)[C@H]([C@H]4C[C@H]33)C(=O)OC)=C3NC2=C1 BLGXFZZNTVWLAY-CCZXDCJGSA-N 0.000 description 1
- 239000000556 agonist Substances 0.000 description 1
- 229930013930 alkaloid Natural products 0.000 description 1
- 239000012080 ambient air Substances 0.000 description 1
- 150000001413 amino acids Chemical class 0.000 description 1
- 125000003277 amino group Chemical group 0.000 description 1
- 239000005557 antagonist Substances 0.000 description 1
- 239000007864 aqueous solution Substances 0.000 description 1
- 150000001540 azides Chemical class 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- 125000001797 benzyl group Chemical group [H]C1=C([H])C([H])=C(C([H])=C1[H])C([H])([H])* 0.000 description 1
- BLGXFZZNTVWLAY-UHFFFAOYSA-N beta-Yohimbin Natural products C1=CC=C2C(CCN3CC4CCC(O)C(C4CC33)C(=O)OC)=C3NC2=C1 BLGXFZZNTVWLAY-UHFFFAOYSA-N 0.000 description 1
- 230000000975 bioactive effect Effects 0.000 description 1
- QXZGBUJJYSLZLT-FDISYFBBSA-N bradykinin Chemical compound NC(=N)NCCC[C@H](N)C(=O)N1CCC[C@H]1C(=O)N1[C@H](C(=O)NCC(=O)N[C@@H](CC=2C=CC=CC=2)C(=O)N[C@@H](CO)C(=O)N2[C@@H](CCC2)C(=O)N[C@@H](CC=2C=CC=CC=2)C(=O)N[C@@H](CCCNC(N)=N)C(O)=O)CCC1 QXZGBUJJYSLZLT-FDISYFBBSA-N 0.000 description 1
- 210000004027 cell Anatomy 0.000 description 1
- 125000003636 chemical group Chemical group 0.000 description 1
- 239000007810 chemical reaction solvent Substances 0.000 description 1
- 239000012230 colorless oil Substances 0.000 description 1
- 238000007796 conventional method Methods 0.000 description 1
- 125000000596 cyclohexenyl group Chemical class C1(=CCCCC1)* 0.000 description 1
- 238000004163 cytometry Methods 0.000 description 1
- 238000013461 design Methods 0.000 description 1
- KZNICNPSHKQLFF-UHFFFAOYSA-N dihydromaleimide Natural products O=C1CCC(=O)N1 KZNICNPSHKQLFF-UHFFFAOYSA-N 0.000 description 1
- ATUOYWHBWRKTHZ-UHFFFAOYSA-N dimethylmethane Natural products CCC ATUOYWHBWRKTHZ-UHFFFAOYSA-N 0.000 description 1
- 230000002708 enhancing effect Effects 0.000 description 1
- 229960003133 ergot alkaloid Drugs 0.000 description 1
- 239000003797 essential amino acid Substances 0.000 description 1
- 235000020776 essential amino acid Nutrition 0.000 description 1
- 230000004634 feeding behavior Effects 0.000 description 1
- 238000000684 flow cytometry Methods 0.000 description 1
- 150000004675 formic acid derivatives Chemical class 0.000 description 1
- 239000012456 homogeneous solution Substances 0.000 description 1
- IKDUDTNKRLTJSI-UHFFFAOYSA-N hydrazine monohydrate Substances O.NN IKDUDTNKRLTJSI-UHFFFAOYSA-N 0.000 description 1
- 230000002209 hydrophobic effect Effects 0.000 description 1
- 238000003018 immunoassay Methods 0.000 description 1
- 239000000787 lecithin Substances 0.000 description 1
- 235000010445 lecithin Nutrition 0.000 description 1
- 229940067606 lecithin Drugs 0.000 description 1
- PCJGZPGTCUMMOT-ISULXFBGSA-N neurotensin Chemical compound C([C@@H](C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CC(C)C)C(O)=O)NC(=O)[C@H]1N(CCC1)C(=O)[C@H](CCCN=C(N)N)NC(=O)[C@H](CCCN=C(N)N)NC(=O)[C@H]1N(CCC1)C(=O)[C@H](CCCCN)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](CC=1C=CC(O)=CC=1)NC(=O)[C@H](CC(C)C)NC(=O)[C@H]1NC(=O)CC1)C1=CC=C(O)C=C1 PCJGZPGTCUMMOT-ISULXFBGSA-N 0.000 description 1
- 239000002858 neurotransmitter agent Substances 0.000 description 1
- 239000003921 oil Substances 0.000 description 1
- 239000003960 organic solvent Substances 0.000 description 1
- 229910000160 potassium phosphate Inorganic materials 0.000 description 1
- 235000011009 potassium phosphates Nutrition 0.000 description 1
- 239000001294 propane Substances 0.000 description 1
- 239000000376 reactant Substances 0.000 description 1
- 238000005057 refrigeration Methods 0.000 description 1
- 238000011160 research Methods 0.000 description 1
- 238000004007 reversed phase HPLC Methods 0.000 description 1
- 238000012552 review Methods 0.000 description 1
- 229940076279 serotonin Drugs 0.000 description 1
- 239000008247 solid mixture Substances 0.000 description 1
- 125000003107 substituted aryl group Chemical group 0.000 description 1
- 229960002317 succinimide Drugs 0.000 description 1
- 150000003871 sulfonates Chemical class 0.000 description 1
- 125000001273 sulfonato group Chemical group [O-]S(*)(=O)=O 0.000 description 1
- 238000010189 synthetic method Methods 0.000 description 1
- POHWAQLZBIMPRN-UHFFFAOYSA-N tert-butyl n-(3-aminopropyl)carbamate Chemical compound CC(C)(C)OC(=O)NCCCN POHWAQLZBIMPRN-UHFFFAOYSA-N 0.000 description 1
- YBRBMKDOPFTVDT-UHFFFAOYSA-N tert-butylamine Chemical compound CC(C)(C)N YBRBMKDOPFTVDT-UHFFFAOYSA-N 0.000 description 1
- 239000003981 vehicle Substances 0.000 description 1
- BLGXFZZNTVWLAY-SCYLSFHTSA-N yohimbine Chemical compound C1=CC=C2C(CCN3C[C@@H]4CC[C@H](O)[C@@H]([C@H]4C[C@H]33)C(=O)OC)=C3NC2=C1 BLGXFZZNTVWLAY-SCYLSFHTSA-N 0.000 description 1
- 229960000317 yohimbine Drugs 0.000 description 1
- AADVZSXPNRLYLV-UHFFFAOYSA-N yohimbine carboxylic acid Natural products C1=CC=C2C(CCN3CC4CCC(C(C4CC33)C(O)=O)O)=C3NC2=C1 AADVZSXPNRLYLV-UHFFFAOYSA-N 0.000 description 1
Classifications
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K49/00—Preparations for testing in vivo
- A61K49/001—Preparation for luminescence or biological staining
- A61K49/0013—Luminescence
- A61K49/0017—Fluorescence in vivo
- A61K49/0019—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules
- A61K49/0021—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules the fluorescent group being a small organic molecule
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K49/00—Preparations for testing in vivo
- A61K49/001—Preparation for luminescence or biological staining
- A61K49/0013—Luminescence
- A61K49/0017—Fluorescence in vivo
- A61K49/0019—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules
- A61K49/0021—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules the fluorescent group being a small organic molecule
- A61K49/0032—Methine dyes, e.g. cyanine dyes
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K49/00—Preparations for testing in vivo
- A61K49/001—Preparation for luminescence or biological staining
- A61K49/0013—Luminescence
- A61K49/0017—Fluorescence in vivo
- A61K49/005—Fluorescence in vivo characterised by the carrier molecule carrying the fluorescent agent
- A61K49/0052—Small organic molecules
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K49/00—Preparations for testing in vivo
- A61K49/001—Preparation for luminescence or biological staining
- A61K49/0013—Luminescence
- A61K49/0017—Fluorescence in vivo
- A61K49/005—Fluorescence in vivo characterised by the carrier molecule carrying the fluorescent agent
- A61K49/0056—Peptides, proteins, polyamino acids
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D209/00—Heterocyclic compounds containing five-membered rings, condensed with other rings, with one nitrogen atom as the only ring hetero atom
- C07D209/02—Heterocyclic compounds containing five-membered rings, condensed with other rings, with one nitrogen atom as the only ring hetero atom condensed with one carbocyclic ring
- C07D209/04—Indoles; Hydrogenated indoles
- C07D209/08—Indoles; Hydrogenated indoles with only hydrogen atoms or radicals containing only hydrogen and carbon atoms, directly attached to carbon atoms of the hetero ring
Landscapes
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- General Health & Medical Sciences (AREA)
- Epidemiology (AREA)
- Biomedical Technology (AREA)
- Animal Behavior & Ethology (AREA)
- Engineering & Computer Science (AREA)
- Public Health (AREA)
- Veterinary Medicine (AREA)
- Chemical & Material Sciences (AREA)
- Organic Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Indole Compounds (AREA)
- Plural Heterocyclic Compounds (AREA)
Abstract
A cyanine dye having formula (II), wherein R1-R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, and C0-C4 alkyl group having a hydrophilic substituent thereon. R11 and R12 are chosen to include a free or protected thiol, amine or hydroxyl substituent capable of reacting with a target molecule through a nucleophilic displacement mechanism. The dye is useful in labeling a variety of target molecules. Processes are described for synthesizing suitable heterocyclic and indole derivatives as precursors for the aforementioned cyanine dyes.
Description
CYANINE DYES AND SYNTHESIS METHODS THEREOF
Field of the Invention This invention relates to the synthesis of cyanine dyes having nucleophilic reactive groups. Further, the present invention includes synthetic methods to produce free reactive thiol, amine or hydroxyl groups from protected sub stituents, the nucleophilic groups capable of nucleophilic addition to target molecules.
Background of the Invention Cyanine dyes are now recognized to have widespread application as fluorescent probes which can be conjugated to a variety of biological molecules, thus finding applications in DNA sequencing, flow cytometry and immunoassays.
Cyanine dyes are characterized by strong spectral absorption bands with the absorption being tunable over a large spectral range by synthetic design.
In addition to the spectral characteristics of a cyanine dye, a practical dye is characterized by also being stable during isolation and purification, yet be reactive for covalent bonding with a target molecule under conditions which will not degrade the target molecule. Prior art cyanine dyes having reactive groups capable of covalently bonding a target molecule have all been limited in their utility either by structural stability or the reaction conditions required for coupling of the dye and target molecules.
An iodo acetyl moiety attached to a cyanine dye is capable of covalently reacting with a sulthydryl group of a target molecule. The iodo acetyl group is limited in its utility by the sulfhydryl groups being present in only a small class of proteins. Other reactive moieties have included sulfonic acid, carboxylates, and sulfonates (for example see, Anal. Biochem. 243, 15-27: 1996; Bioconj. Chem.
4, 105-111: 1993; 8, 751-756: 1997; Cytometry 10, 3-10: 1989; 10, 11-19: 1989;
U.S. Patent 5,106,990; and J. Chem. Soc. Perkin Transactions 1, 143-7: 1998).
Such moieties remain reactive during the course of subsequent chemical transformations and purification or are limited by the reaction conditions for bonding to a target molecule.
U.S. Patent 5,627,027 is directed to a method for labeling proteins, cells, nucleic acid and DNA with a cyanine dye, as well as the reaction therebetween.
The cyanine dye specified is limited in the position of a reactive group within the dye and its identity is limited to isothiocyanate, isocyanate, monochlorotriazine, dichlorotriazine, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, aziridine, sulfonyl halide, acid halide, hydroxy succinimide ester, hydroxy sulfosuccinimide ester, imido ester, glyoxal and aldehyde. The method still further requires forming a covalent bond between the reactive group on the dye, and an amine or hydroxyl group on the material being labeled utilizing an electrophilic mechanism for coupling the dye and material being labeled.
U.S. Patent 5,486,616 is directed to particular cyanine dye structures which are water soluble, and capable of reacting with amino, hydroxy or sulthydryl groups through a reactive moiety. The dye structures including at least one sulfonic acid or sulfonate moiety attached directly to a benzyl portion of the dye utilizing an electrophilic mechanism for coupling the dye and material being labeled.
Field of the Invention This invention relates to the synthesis of cyanine dyes having nucleophilic reactive groups. Further, the present invention includes synthetic methods to produce free reactive thiol, amine or hydroxyl groups from protected sub stituents, the nucleophilic groups capable of nucleophilic addition to target molecules.
Background of the Invention Cyanine dyes are now recognized to have widespread application as fluorescent probes which can be conjugated to a variety of biological molecules, thus finding applications in DNA sequencing, flow cytometry and immunoassays.
Cyanine dyes are characterized by strong spectral absorption bands with the absorption being tunable over a large spectral range by synthetic design.
In addition to the spectral characteristics of a cyanine dye, a practical dye is characterized by also being stable during isolation and purification, yet be reactive for covalent bonding with a target molecule under conditions which will not degrade the target molecule. Prior art cyanine dyes having reactive groups capable of covalently bonding a target molecule have all been limited in their utility either by structural stability or the reaction conditions required for coupling of the dye and target molecules.
An iodo acetyl moiety attached to a cyanine dye is capable of covalently reacting with a sulthydryl group of a target molecule. The iodo acetyl group is limited in its utility by the sulfhydryl groups being present in only a small class of proteins. Other reactive moieties have included sulfonic acid, carboxylates, and sulfonates (for example see, Anal. Biochem. 243, 15-27: 1996; Bioconj. Chem.
4, 105-111: 1993; 8, 751-756: 1997; Cytometry 10, 3-10: 1989; 10, 11-19: 1989;
U.S. Patent 5,106,990; and J. Chem. Soc. Perkin Transactions 1, 143-7: 1998).
Such moieties remain reactive during the course of subsequent chemical transformations and purification or are limited by the reaction conditions for bonding to a target molecule.
U.S. Patent 5,627,027 is directed to a method for labeling proteins, cells, nucleic acid and DNA with a cyanine dye, as well as the reaction therebetween.
The cyanine dye specified is limited in the position of a reactive group within the dye and its identity is limited to isothiocyanate, isocyanate, monochlorotriazine, dichlorotriazine, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, aziridine, sulfonyl halide, acid halide, hydroxy succinimide ester, hydroxy sulfosuccinimide ester, imido ester, glyoxal and aldehyde. The method still further requires forming a covalent bond between the reactive group on the dye, and an amine or hydroxyl group on the material being labeled utilizing an electrophilic mechanism for coupling the dye and material being labeled.
U.S. Patent 5,486,616 is directed to particular cyanine dye structures which are water soluble, and capable of reacting with amino, hydroxy or sulthydryl groups through a reactive moiety. The dye structures including at least one sulfonic acid or sulfonate moiety attached directly to a benzyl portion of the dye utilizing an electrophilic mechanism for coupling the dye and material being labeled.
U.S. Patent 5,268,486 discloses water soluble dyes which contain reactive moieties including isothiocyanate, isocyanate, monochlorotriazine, dichlorotriazine, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, maleimide, aziridine, sulfonyl halide, acid halide, hydroxysuccinimide ester, hydroxysulfosuccinimide ester, imido ester, hydrazine, azidonitrophenyl, azide, 3-(2-pyridyl dithio)-proprionamide, glyoxal and aldehyde. These dyes are chosen to label target molecules containing amino-, hydroxy- and sulfhydryl groups.
In view of the prior art, it is apparent that there exists a need for a wider range of indole derivatives which will allow the facile synthesis of stable cyanine dyes with suitably positioned reactive groups for covalent attachment to target molecules. The cyanine dyes should allow covalent bonding to target molecules under conditions which will not degrade the target molecules. They should be stable, easily formed, purified and reactive under conditions of attachment to target molecules. This invention describes the facile synthesis of new, stable indole precursors derived from indoles. These precursors allow the facile synthesis of cyanine dyes with protected thiol, amine or hydroxyl groups. The protected groups can be deprotected to yield free thiol, amine or hydroxyl groups which can be covalently attached to target molecules via a nucleophilic mechanism.
In view of the prior art, it is apparent that there exists a need for a cyanine dye having a more generic utility. A need exists for a cyanine dye which is water soluble and contains at least one reactive moiety capable of labeling a range of substances in addition to compounds containing amino, hydroxy and sulfhydryls through covalent bonding with target molecules under conditions which will not degrade a target molecule.
Prior coupling reactions have been carried out by an electrophilic mechanism. Thus, there further exists a need for a generic class of cyanine dyes which are capable of coupling to a target molecule by a nucleophilic mechanism.
Detailed Description of the Invention The present invention relates to a class of nitrogen containing heterocyclics of the formula:
R
R2 oil - - - -Y
(1) N
wherein Y1 is selected from a group consisting of:
RIO R9 RIO R.
9 Rio /P9 Pe ----S\1(F40 eRio , and Re wherein RI, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, a Co-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, I
hydroxyl, substituted amines and quaternary amines, optionally, at least one of RI-R4 is the Co-Ca alkyl group having the hydrophilic substituent;
wherein R9, R91, R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the 5 heteroatom is 0, N or S; and wherein R11 is selected from a group consisting of ¨R13-00..21%=.... --12,..e.NH
.%..._.
rei3 , ''''Rle."'"''S NI-42 , R n¨NH2 , ¨Rik.e..N.,...R13 .,,x.,.
R'i3 ......)1.."... sS R13, cr.......(........IR
¨R13 Q = . S
Z W , "'"""1:213 0 = H3 .
.o.,.,S 0 NO2 S ¨
'..-. Cr-. \ 12,3 ¨R/n 0 ¨Rn µ 0 = NO2 ' _ s20/( ek =
¨R13 ¨R13 0 .
0 s,..)\N,/%"===.....
¨R-13 H
OCH3 _____K( sõA,R,===="\
S¨
X
=
0 ¨R73 =
I =
and ¨R13-0¨Si(CH3)3 wherein R13, R'13, R"13 and R"'13 are each independently C1-C30 alkyl. Q
is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen.
Prior to the present invention it has been difficult to synthesize N
substituted heterocyclics and indoles in particular with hydrocarbon moieties containing protected nucleophilic groups. The present invention describes a facile reaction between bifunctional hydrocarbons containing the moiety XR13Q where X is chlorine, bromine or iodine, R13 is C1-C30 alkyl and Q is sulfur, nitrogen or oxygen; and nitrogen containing heterocyclics which leads to heterocyclics having protected nucleophilic groups in the primary position on the new N-substituent or a moiety which can be converted to a protected nucleophilic group such as a thiol, amine or alcohol. The new reaction proceeds by heating a solid mixture of the precursors at elevated temperature for a short period of time. The product is purified using conventional chromatography. Alternatively the reaction proceeds by heating a suitable suspension of solid nitrogen containing heterocyclic in a suitable reagent solution. The product from the latter method can be purified using conventional methods.
In view of the prior art, it is apparent that there exists a need for a wider range of indole derivatives which will allow the facile synthesis of stable cyanine dyes with suitably positioned reactive groups for covalent attachment to target molecules. The cyanine dyes should allow covalent bonding to target molecules under conditions which will not degrade the target molecules. They should be stable, easily formed, purified and reactive under conditions of attachment to target molecules. This invention describes the facile synthesis of new, stable indole precursors derived from indoles. These precursors allow the facile synthesis of cyanine dyes with protected thiol, amine or hydroxyl groups. The protected groups can be deprotected to yield free thiol, amine or hydroxyl groups which can be covalently attached to target molecules via a nucleophilic mechanism.
In view of the prior art, it is apparent that there exists a need for a cyanine dye having a more generic utility. A need exists for a cyanine dye which is water soluble and contains at least one reactive moiety capable of labeling a range of substances in addition to compounds containing amino, hydroxy and sulfhydryls through covalent bonding with target molecules under conditions which will not degrade a target molecule.
Prior coupling reactions have been carried out by an electrophilic mechanism. Thus, there further exists a need for a generic class of cyanine dyes which are capable of coupling to a target molecule by a nucleophilic mechanism.
Detailed Description of the Invention The present invention relates to a class of nitrogen containing heterocyclics of the formula:
R
R2 oil - - - -Y
(1) N
wherein Y1 is selected from a group consisting of:
RIO R9 RIO R.
9 Rio /P9 Pe ----S\1(F40 eRio , and Re wherein RI, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, a Co-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, I
hydroxyl, substituted amines and quaternary amines, optionally, at least one of RI-R4 is the Co-Ca alkyl group having the hydrophilic substituent;
wherein R9, R91, R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the 5 heteroatom is 0, N or S; and wherein R11 is selected from a group consisting of ¨R13-00..21%=.... --12,..e.NH
.%..._.
rei3 , ''''Rle."'"''S NI-42 , R n¨NH2 , ¨Rik.e..N.,...R13 .,,x.,.
R'i3 ......)1.."... sS R13, cr.......(........IR
¨R13 Q = . S
Z W , "'"""1:213 0 = H3 .
.o.,.,S 0 NO2 S ¨
'..-. Cr-. \ 12,3 ¨R/n 0 ¨Rn µ 0 = NO2 ' _ s20/( ek =
¨R13 ¨R13 0 .
0 s,..)\N,/%"===.....
¨R-13 H
OCH3 _____K( sõA,R,===="\
S¨
X
=
0 ¨R73 =
I =
and ¨R13-0¨Si(CH3)3 wherein R13, R'13, R"13 and R"'13 are each independently C1-C30 alkyl. Q
is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen.
Prior to the present invention it has been difficult to synthesize N
substituted heterocyclics and indoles in particular with hydrocarbon moieties containing protected nucleophilic groups. The present invention describes a facile reaction between bifunctional hydrocarbons containing the moiety XR13Q where X is chlorine, bromine or iodine, R13 is C1-C30 alkyl and Q is sulfur, nitrogen or oxygen; and nitrogen containing heterocyclics which leads to heterocyclics having protected nucleophilic groups in the primary position on the new N-substituent or a moiety which can be converted to a protected nucleophilic group such as a thiol, amine or alcohol. The new reaction proceeds by heating a solid mixture of the precursors at elevated temperature for a short period of time. The product is purified using conventional chromatography. Alternatively the reaction proceeds by heating a suitable suspension of solid nitrogen containing heterocyclic in a suitable reagent solution. The product from the latter method can be purified using conventional methods.
Chemicals containing the indole nucleus occur widely throughout the animal and plant kingdoms and are components of chemicals found in the human body. For example, the essential amino acid tryptophan (which occurs in many peptides and bioactive proteins) contains an indole nucleus and is the biochemical precursor to serotonin which is the important neurotransmitter involved in learning, memory, depression and feeding behavior. Many naturally occurring alkaloids containing the indole nucleus such as Harmaline, Cinchera, Yohimbine, Rauwolfi a and Ergot alkaloids have widely differing impacts on biological activities. Indole containing chemicals have been used in industrial applications as dye components and biochemical labeling reagents.
The new and facile chemistry described in this application enables the synthesis of many new derivatives of indole containing chemicals by providing a vehicle to add a wide variety of chemical groups to an indole nucleus allowing researchers in the life sciences access to a broader variety of biologically active molecules and labeling reagents for target molecules. For example, long chain hydrocarbons may be added to indole chemicals giving them hydrophobic qualities or alternatively linker molecules may be added that will enable the various biological activities of the indoles to be covalently attached to reporter systems or to be used as the reporter molecule in various biological systems.
This chemistry can also be used to synthesize new indole derivatives having interesting and beneficial pharmaceutical properties. In research, new derivatives that act as agonists or antagonists to the various sub classes of serotonin receptors may be formed. New derivatives may also lead to new labeling reagents and alternative methods of attaching labeling reagents, such as cyanine dyes, to target molecules.
The new heterocyclic derivatives synthesized lby the above methods can be converted to cyanine dyes using conventional chemistry.
These heterocyclics are operative as precursors for a generic class of cyanine dyes having a protected reactive group for nucleophilic covalent attachment to target molecules. The precursor. (1) is condensed to form a fluorescent cyanine dye through a polymethine linkage.
RI, R2, R3 and R4 are optionally such that two of these adjacent R groups are fused to form a ring structure. The resulting ring structure also optionally being fimctionalized to modify solubility and spectral properties.
The polymethine linkage being formed by reacting two equivalents of precursor (1) in the presence of a molecule illustratively including trialkyl orthof9rmate, dialkyl amides, and trialkoxy alkene in the presence of a base.
Preferably, the base is an organic base. The linkage reaction proceeds under ambient air in a refluxing organic solvent, although it proceeds at a slower rate without solvent reflux. The organic base illustratively includes pyridine, phenol and an alkoxide, morpholine, piperidine, t-butylamine, and triethylamine and an amine. The polymethine linkage is a conjugated system having 3, 5, 7 or more linear carbon atoms therein.
The polymethine linkage between two molecules of precursor (1) is appreciated to include linear chains, as well as also cyclo-aliphatics, substituted aryl and heterocyclic ring structures coupled to the conjugate system of the polymethine chain. For instance, a bisaldehyde is more reactive towards the precursors of the present invention than formates, amides or alkoxyalkenes and reaction does not require the presence of a base. Instead, reaction occurs in the presence of an alcohol (J. Org. Chem. 60, 2391-2395: 1995). A 1-formy1-3-(hydroxymethylene)cyclohex-1-ene derivative thus yields a heptamethine linkage.
Thus, it is appreciated that modification and extension of the conjugate bonding across the chain will affect the absorption characteristics of the dye.
Further, it is appreciated that additional reactive groups or solubility enhancing moieties are readily coupled to the polymethine linkage.
The resulting cyanine dye has the formula:
Ri Re - - -y *- (2) R4 R11 R12 Re wherein RI, R2, R3, R4, R59 R69 R79 and RS are each independently selected from a group consisting of hydrogen, C1-C30 alkyl group, a Co-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein Yi and Y2 are each independently selected from a group consisting of:
.1, Pe _ Ra / Rio R. .
X, \ r R, ____, /
PG
_,, <. . .
,x wherein R9, R's, R10, and R'10 are each independently selected from a group consisting of CI-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is 0, N or S;
wherein R11 and R12 are each independently selected from a group 5 consisting of C1-C30 alkyl, phenyl substituted CI-C30, C1-C30 having a protected substituent selected from a group consisting of:
H
¨.,...N.õ , ¨R,3¨Q ¨13 . --R13--"S NI12 . R1ky R13¨NH2 .
H ---R
.13 ..)L.
¨Rikyõ. M N
R.(3 ItS
o o IP
¨RA
7. .
. .
¨R13 =i3 ¨RS 0 NO2 s...........H
µ
..," =
¨R13 0 ¨R13 \ 0 , NO2 .
)Lo--R13 ¨Ri3 0 rs)Lo s 0 .
H
s OCH3 ¨ S¨"¨S
/S S
¨R13 R,3¨R13 X
¨12;
and ¨R13-0¨Si(CH03 wherein R13, R'13, R"13 and R"13 are each independently C1-C30 alkyl; Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen;
L is selected from a group consisting of: methine, a methine group having a substituent C1-C6 alkyl group and a substituted C1-C6 alkyl group having a phenyl, hydroxyl, sulfonyl, a halogen atom, a heteroatorn substituted phenyl and a C1-C4 alkoxyl where n is 1, 2, 3 or greater.
R1-R8 are optionally such that two of these adjacent R groups are fused to form a ring structure. The resulting ring structure optionally is functionalized to modify solubility and spectral properties.
In order to increase the water solubility of the resulting dye (2), the RI, R2, R3, R4, R5, R6, R7, Rs, R9, R91, Rio, R101, Rii and R12 groups are each optionally selected from well known polar and charged moieties. Preferably, each precursor molecule (1) contains at least one hydrophilic moiety in order to impart water solubility.
n The dr moieties oililustratively are useful in organic -11dr -substituted amino, -quaternary amino, -sulfonate and -carboxylate. It is 5appreciated that hydrophilic micoori ar precursors cYsol:xenYt' systems.
A dye (2) is reactive towards a target molecule upon formation of a thiol, amine or hydroxyl moiety. The thiol, amine or hydroxyl moiety is characterized by a lone pair of electrons sterically and electronically amenable to bonding with a reactant which is reactive towards target molecules. The reaction of a dye (2) with a deprotecting agent converts the substituent into a reactive thiol, amine or hydroxyl substituent. Deprotecting agents are well known to the art. (Theodora W. Greene and Peter G.M. Wuts, Protective Groups in Organic Synthesis, 2nd edition (1991) 277-308.) It is appreciated that an amine or hydroxyl substituent in fact optionally need not be protected, but instead are stable under synthesis conditions and are isolated as such. Thus, an amine or hydroxyl substituent operates as a reactive nucleophilic substituent without the occurrence of an intermediate deprotecting reaction.
It is appreciated that the dyes of the present invention are also amenable to isolation in deprotected form of free thiols. A free thiol containing dye of the present invention results upon reacting a dye (2) with a deprotecting agent and isolating the free thiol therefrom. The resulting free thiol, depending on its specific identity, has a shelf life of more than one month. As with other reactive thiols, free thiol cyanine dyes of the present invention are best maintained under conditions suitable to prevent the formation of disulfide linkages. These conditions illustratively include refrigeration, darkness and storage under an inert atmosphere. Alternatively, nitrogen containing heterocyclics identical to (1) except that R11 is selected from the group consisting of RI4SH, R14NH2 and are formed directly wherein R14 is a C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonyl, or halogen atom or a heteroatom substituted phenyl.
The reaction chemistry to produce a free thiol dye precursor analog to (1) proceeds in a similar fashion to the formation of protected heterocyclics (1).
For example, a cationic nitrogen-containing heterocyclic and a halogenated thiol are able to react via a metatheses reaction to create a free thiol dye precursor.
The amine or hydroxyl moiety are produced by analogous type reactions. A free thiol precursor thereafter is reacted in a manner similar to precursor (1) to form a polymethine linkage therebetween. The resulting c:yanine dye compound is identical to that of (2) except that R11 and R12 are each independently RiaSH, RI4NH2 or RI40H when R14 is a C3-C30 alkyl or C3-C30 alkyl having a phenyl, hydroxyl, sulfonyl, or halogen atom or a heteroatom substituted phenyl.
A commercial package of the present invention includes a compound of Formula (1) with instructions and optionally reagents fin converting the precursor (1) to a dye compound (2) and further instructions for the use of the dye compound (2) as a dye or hapten. It is appreciated that a free thiol, amine or hydroxyl analog of a compound (1) is also operative herein. Alternatively, a commercial package includes a compound (2) as an active ingredient together with instructions for the use thereof as a dye or hapten in labeling a target molecule. It is also appreciated that a free thiol, amine or hydroxyl analog of a compound (2) is also operative herein.
The addition of a reactive form of a dye (2) to a target molecule proceeds under conventional nucleophilic reaction conditions. The solvent for the nucleophilic reaction is dictated by the identity of the target molecule.
Since many target molecules of interest are of a biological nature, water is often the nucleophilic reaction solvent.
A target molecule which is coupled with a dye of the present invention illustratively includes organic molecules, polymers, silaceous materials, natural and synthetic: lipid vesicles, amino acids, peptide nucleic acids, peptides, nucleic acids, nucleotides, nucleosides, DNA, RNA, proteins, carbohydrates, oligosaccharides, polysaccharides, antibodies, cellular receptors, antigens, haptens, lectins, avidins, streptavidins, lyrnpholcines, hormones, metabolites, toxins, virions, bacteria, fimgal components, esinophils, eukaryotic cells, and derivatives thereof.
A dye (2) of the present invention in which neither R11 or R12 is CI-Cm, having a heteroatom containing substituent finds utility as a physi-sorbed, fluorescent dye. Alternatively, a dye of the present invention lacking a heteroatom within R11 or R12 is coupled to a target molecule through a hydrophilic moiety of R1-R8 or a pendant reactive moiety extending from the polymethine linkage.
14.1 A compound according to another aspect of the invention comprises an indole nucleus having substituents wherein the substituents at indole positions 1-7 are each independently selected from a group consisting of hydrogen and CI -C30 alkyl, wherein at least one of the substituents at positions 1-7 is Ci-C30 alkyl and at least one of the substituents at positions 1-7 is C1-C30 alkyl having a phenyl, hydroxyl, carboxyl, sulfonyl, amine, thiol or halogen atom or a heteroatom substituted phenyl.
According to yet another aspect of the invention, the the indole position 2 substituent is methyl and the indole position 1 substituent is selected from CI-Cm alkyl and C1-C30 alkyl, having a phenyl, hydroxyl, carboxyl, sulfonyl, amine, thiol or halogen atom or a heteroatom substituted phenyl, and at least one of the substituents at positions 3-7 is C0-C30 alkyl.
In order to more fully demonstrate the advantages arising from the present invention, the following examples are set forth. It is to be understood that the following is by way of example only and not intended as a limitation on the scope of the invention.
5 Example 1 - Dye precursor 143-S-Acetylthiopropy11-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (5).
To a 250 rnL round bottom flask with magnetic stir bar is added 2,3,3-trimethy1-5-sulfo-3H-indolium, potassium salt (3) (7.21 mmol) and 3-bromo-1-10 thioacetylpropane (4) (25.88 mmol). The mixture is stirred and heated at for 20 min. The residue is cooled to 20 C and washed with diethyl ether. The solid is purified by Reversed Phase Chromatography to give 143-S-Acetylthio-propy1]-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (5) as a solid.
Example 2 - Dye precursor 143-S-Acetylthiopropy11-2,3,3-trimethy1-5-15 hydroxyl-6-benzo-311-indolium, inner salt (7).
The procedure of Example 1 is repeated except 2,3,3-trimethy1-5-hydroxy1-6-benz-indolium, potassium salt (6) is substituted for (3). A solid product 143-S-Acetylthiopropy1)-2,3,3-trimethyl-5-hydroxyl-6-benzo-indolitun, inner salt (7) is isolated.
Example 3- Dye precursor 1-14-S-benzoylbutyI]-3-methy1-4-carboxyl benzoxizolium, inner salt (10).
The procedure of Example 1 is repeated except 3-methyl-4-carboxyl benzoxizolium, sodium salt (8) is substituted for (3) and 4-bromo- 1 -S-benzoylbutane (9) is substituted for (4). A solid product 144-S-benzoylbuty1]-methy1-4-carboxyl benzoxizolium, inner salt (10) is isolated.
Example 4- Dye precursor 1-[3-S-t-butylpropy11-3-methyl-5-sulfo-benzoimidazolium, inner salt (13).
The procedure of Example 1 is repeated except 3-methy1-5-sulfo-benzoimidazolium (11) and 3-bromo-1-S-t-butyl propane (12) is substituted for (4). A solid product 143-S-t-butylpropy1]-3-methy1-5-sulfo-benzoimidazolium, inner salt (13) is isolated.
Example 5- Cyanine-3 dyes derived from (5).
A solution of (5) (2.68 mmol) and 1-ethy1-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (14) (2.68 mmol) is heated to reflux in pyridine (70 mL) and triethyl orthoformate (24.0 znmol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The solvents are removed under reduced pressure and the solid is azeotroped two times with methanol. The solid is purified by Reversed Phase Chromatography and the isolated products are passed over an AG50W-X4, 200-400 mesh K+ form, column to give 1-[3-S-acetylthiopropy1]-2-[341 -ethyl-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1-propenyl] -3,3-dimethy1-5-sulfo-3H-indoliurn, potassium salt (15), 143-S-AcetylthiopropylF
2434143-S-acetylthiopropy1]-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indol-2-ylidene]-1-propeny1J-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (16), and 1 -ethy1-24341-ethy1-1, 3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1-propeny1]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (17) as solids.
Examples 6-10 - Cyanine-3 dyes derived from (7), (10) and (13).
The procedure of Example 5 is repeated with (7), (10) and (13) substituted for (5) and the 1-ethyl-analogs of (7), (10) and (13) substituted for (14).
The resulting solid compounds which are isolated in purified form are summarized in Table 1.
Example 11 - Cyanine-5 dyes derived from (5).
A solution of (5) (1.60 mmol), (14) (1.60 mmol) and potassium acetate (3.56 mmol) in methanol (50 mL) is heated to reflux and 1,3,3-trimethoxypropene (21.0 mmol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The methanol is removed under reduced pressure and the solid is purified by Reversed Phase Chromatography to give 143-S-Acetylthiopropyli-2-[541-ethy1-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indol-2-ylidene]-1,3-pentadieny1]-3,3-dimethy1-5-sulfo-3H-indolium, potassium salt (29), 1-[3-S-Acetylthiopropy1]-24341-[5-S-acetylthiopropyl]-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidenej-1,3-pentadienyl]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (30) and I-ethyl-245-[ 1 -ethy1-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1,3-pentadieny1J-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (31) as solids.
Example 12 - Dye precursor S-(3-lodopropyl)isothiourea (32).
Thiourea (14 mmol) is added to a solution of 1,3-diiodopropane (340 mmol) in anhydrous methanol (300 mL) and stirred under an atmosphere of nitrogen at 60 C for 4 hours. The solution is cooled to 4 C overnight during which time excess 1,3-diiodopropane separates to the bottom of the flask as a colorless oil. The excess 1,3-diiodopropane is removed by pipette and the remaining methanol solution is evaporated in vacuo and the residue is suspended in dichloromethane, filtered, and washed with additional dichloromethane to give S-(3-Iodopropypisothiourea (32) as a powder.
Example 13 - Dye precursor 1-13-Isothiouronylpropy11-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (33).
A solution of (32) (0.36 mmol) and 2,3,3-trimethylindoleniniurn-5-sulfonate, potassium salt (3) (0.46 mmol) are placed in a flask and heated to 148 C with stirring for 15 minutes under an atmosphere ofnitrogen. The reaction mixture is cooled to room temperature and the residue is crystallized from methanol to give 143-isothiouronylpropy1]-2,3,3-trimethy1-5-sulfo-3H-indolitun, inner salt (33) as a powder.
Example 14- Cyanine-3 dyes derived from (33).
A solution of (33) (0.022 mmol) and 1-ethy1-2,3,3-trimethy1-5-sulfo-3H-, indolium, inner salt (14) (0.022 mmol) are dissolved in N,N-dimethylformamide containing 50 uL of triethylamine and the mixture is heated to 60 C as triethylorthofonnate (4 x 10 uL, 4 x 0.06 mmol) is added in four portions over hours. The solution is heated at 60 C for an additional hour, cooled to room temperature, washed 3 times with diethyl ether, and the resulting precipitate is purified by reverse phase HPLC to give isolated 143-Isothiouronylpropy1]-243-[1-ethy1-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1-propenylj-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (34), 143-Isothiouronylpropy1]-2-[34143-isothiouronylpropy1]-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indol-2-ylidene]-1-propeny1]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (35) and 1-ethy1-24341-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene1-1-propeny1]-3,3-dimethy1-5-sulfo-3H-indolium, potassium salt (17) as solids.
Example 15- Bonding of dye (15) to a target nucleotide derivative.
To a 2 mL vial with a stir bar is added (15) (1.58 pmol), 5-[3-[3-[2,5-dihydro-2,5-dioxo-1H-pyrrole]propanamido]-l-propynyli-2'-deoxycytidine triphosphate (36) (5.0 pmol) in 50 mM sodium dihydrogenphosphate pH 7.0 - 7.5 (250 pL). To the stirred solution is added 1M hydroxylamine pH 7.0 - 7.5 (250 pL) and the resulting solution is stirred at room temperature for 1 hour. The reaction mixture is purified to give 5-(343-(34143-thiopropyli-24341-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidenei-1-propenyli-3,3-dimethy1-5-sulfo-3H-indolium]-2,5-pyrrolidindione]propanamido]-1-propyny1]-2'-deoxycytidine triphosphate (37).
Example 16- Bonding of dye (28) to a target nucleotide derivative.
The procedure of Example 15 is repeated with (28) substituted for (15).
The reaction mixture is purified to give 5-[3434341-[3-thiopropy1]-24341-ethyl-3-methyl-5-sulfo-benz-imidazol-2-ylidene]-1-propeny1]-3,3 dimethy1-5-hydroxy1-6-benz-indolitun]-2,5-pyrrolidindione]propanamidoi-1-propynyl}2'-deoxycytidine triphosphate (38).
Example 17- Bonding of dye (29) to a target nucleotide derivative.
The procedure of Example 15 is repeated with (29) substituted for (15).
The reaction mixture is purified to give 543-[343-143-thiopropy1}-24541-ethyl-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1,3-pentadienyl]-3,3-dimethy1-5-su1fo-3H-indolium1-2,5-pyrro1idindionejpropanamido]-1-propyny11-2'-deoxycytidine triphosphate (39).
Example 18 - Dye precursor 1-13-Isothiouronylpropy11-2,3,3-trimethyl-3H-5 indolium iodide (41).
To a 50 mL round bottom flask is added 2,3,3-trimethylindolenine (14.4 mmol) and 1,3-diiodopropane (72.7 mmol) and the mixture is stirred at 60 C
under an atmosphere of nitrogen for 16 hours. The resulting solid is recrystallized 10 from ethanol to give 1[3-iodopropy1]-2,3,3-trimethy1-3H-indolium iodide (40) as crystals.
To a 100 mL round bottom flask is added (40) (4.38 mmol), thiourea (4.5 mmol), and methanol (30 mL). The solution is stirred at 60 C for 5 hours, evaporated in vacuo, the residue is dissolved in water (20 mL) and washed with 15 dichloromethane (3 x 6 mL) and cooled to 4 C overnight, and the resulting crystals are filtered and washed with acetone to give 143-isothiouronylpropy1]-2,3,3-trimethy1-3H-indolium iodide (41).
Example 19 - Cyanine-3 dyes derived from (41).
To a 25 mL round bottom flask is added (41) (1.0 mmol), (14) (1.5 mmol), 20 and pyridine (10 mL). The solution is heated to reflux and triethyl orthoformate (4 x 166 uL, 4 x 1.0 mmol) is added in four portions over one hour. The solution is heated at reflux for an additional hour, cooled to room temperature, the evaporated in vacuo, and the residue is washed with ethyl ether (3 x 25 mL), and purified by C18 reverse phase chromatography to give isolated 143-isothiouronylpropy1]-24341-ethy1-1,3-dihydro-3,3-diunethyl-5-sulfo-2H-indol-2-ylidenel-1-propeny1]-3,3-dimethyl-3H-indolium, inner salt (42), 143-isothiouronylpropylj-2-[34143 -isothiouronylpropyl] -1,3 -dihydro-3,3-dimethyl-2H-indo1-2-ylidene]-1-propenyl] -3,3-dimethy1-3H-indolium iodide (43) and 1-ethyl-2-[3-[1 -ethyl-1,3 -dihydro-3 ,3 -dimethy1-5-sulfo-2H-indo1-2-ylidene]-1-propeny11-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (17) as solids.
Example 20- Cyanine-5 dyes derived from (41).
A solution of (41) (0.28 mmol) and (14) (0.28 mmol) and potassium acetate (0.28 mmol) in methanol (2 mL) is heated to reflux and 1,3,3-trimethoxypropene (160 uL, 1.17 mmol) is added via syringe over 2 hour in four equal portions. A suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The methanol is removed under reduced pressure and the solid is purified by C18 Reversed Phase Chromatography to give 143-isothiouronylpropy1]-24541-ethy1-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadieny11-3,3-dimethy1-3H-indolium, inner salt (44), the related di-isothiouronyl-propyl and diethyl inner salts as solids.
Example 21 - Bonding of dye (42) to a target nucleotide derivative.
To a 2 mL vial with a stir bar is added 143-isothiouronylpropy1]-24341-ethy1-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indol-2-ylidenej-1-propenyli-3,3-dimethyl-3H-indolium, inner salt (42) (81=01) in 0.1 M potassium hydroxide (1.0 mL). The solution is stirred at room temperature for 1 hour to form the free thiol of (42). Thereafter, (36) (15 gmol) is added to the thiol in aqueous solution.
The reaction mixture is purified to give 54343434143-thiopropyl]-24311-ethy1-1,3-, dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1-propeny11-3,3-dimethy1-3H-indoliumi-2,5-pyrrolidindionejpropanamido]-1-propynyl]-2'-deoxycytidine triphosphate (45).
Example 22- Bonding of dye (44) to a target nucleotide derivative.
The procedure of Example 21 is repeated with (44) substituted for (42).
The reaction mixture is purified to give 54343434143-thiopropyli-24541-ethy1-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadienyl]-3,3-dimethyl-3H-indolium]-2,5-pyrrolidindione]propanamidoi-1-propynyl]-2'-deoxycytidine triphosphate (46).
Example 23 - Bonding of dye (15) to a target nucleotide derivative.
To a 5 mL vial with a stir bar is added (15) (19 mop, 543-[iodoacetamido]-1-propynyli-2'-deoxycytidine triphosphate (47) (30.0 p.mol) in rnM sodium dihydrogenphosphate pH 7.0 - 7.5 (250 pL). To the stirred solution 1M hydroxylamine pH 7.0 - 7.5 (250 1.) is added. The resulting solution is stirred at room temperature for 4 hours to react the free thiol of (15) with (47).
The reaction mixture is purified to give 5434143-thiopropyli-24341-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-211-indol-2-ylidenei-1-propenyl]-3,3-dimethyl-5-sulfo-3H-indoliumjacetamido-1-propynyl]-2'-deoxycytidine triphosphate (48).
Example 24- Bonding of dye (29) to a target nucleotide derivative.
The procedure of Example 23 is repeated with (29) substituted for (15).
The reaction mixture is purified to give 54341-[thiopropy1]-2-[541-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadieny1]-3,3-dimethyl-5-sulfo-3H-indoliumiacetamido-1-propyny11-2'-deoxycytidine triphosphate (49).
Example 25- Dye precursor 1-[N-F3-(tert-butyloxycarbonylamino) propyllhexanamide]-2,3,3-trimethyl-5-sulfo-3H-indolium, inner salt (51).
To a 100 inL round bottom flask with a stir bar is added 1-N-{5-carboxypenty1}-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (50) (1.70 nunol) and 40 inL of N,N-dimethylfonnamide. The mixture is heated at 50 C until a homogeneous solution is obtained. To this solution is added 1,3-dicyclohexylcarbodiimide (2.30 mmol), N-hydroxysuccinimide (2.34 mmol) and t-butyl N-(3-aminopropyl)carbamate (2.29 mmol). The reaction mixture is heated at 50 C for 30 min and then room temperature 16 hours. The reaction mixture is filtered, the solvents are removed under reduced pressure and the solid is azeotroped two times with methanol. The solid is purified by Reversed Phase Chromatography to give 1-M-[-3-(tert-butyloxycarbonylamino)propyl]
hexanamide]-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (51) as a solid.
Example 26 - Cyanine-3 dyes derived from (51).
A solution of (51) (0.291 mmol) and (14) (0.281 mmol) is heated to reflux in pyridine (30 mL) and triethyl orthofonnate (2.4 mmol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 4 hours and cooled to room temperature. The solvents are removed under reduced pressure and the solid is azeotroped two times with methanol.
The purple solid is purified by Reversed Phase Chromatography and the isolated products are passed over an AG50W-X4, 200-400 mesh K+ form, column to give 1-4N43-(tert-butyloxycarbonylamino)-propylihexanamide]-2-1341-ethyl-.1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1-propenylj-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (52), 14N-[3-(tert-butyloxycarbonyl-amino) propyl]hexanamide)-24341-N43-(tert-butyloxycarbonylamino)-propyl]hexanamidel-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1-propenyl]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (53) and the related diethyl salt as solids.
Example 27- Cyanine-5 dyes derived from (51).
A solution of (51) (0.291 mmol) and (14) (0.292 mmol) and potassium acetate (78 mg, 0.79 mmol) in methanol (15 mL) is heated to reflux and 1,3,3-trimethoxypropene (0.5 mL, 3.64 nunol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The methanol is removed under reduced pressure and the solid is purified by Reversed Phase Chromatography to give 1-[1=1-13-(tert-butyloxycarbonylamino)propyThexanamide]-24541-ethyl-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1,3-pentadienylj-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (54), 1-N-[3-(tert-butyloxycarbonyl-amino)propyl]hexanamide]-24541-[1143-(tert-butyloxycarbonylamino)propy1]-hexanamidei-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidenel-1,3-pentadienylj-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (55) and the related diethyl salt as solids.
Example 28 - Bonding of dye (44) to a target nucleotide derivative.
To a2 mL vial with a stir bar is added (44) (17 mop and 1 M potassium phosphate (4.0 mL) and methanol (2 mL) and the resulting solution is stirred at room temperature for 1 hour to give 143-thiopropy1]-24541-ethyl-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene)-1,3-pentadienylj-3,3-ciimethyl-3H-indolium, inner salt (56). To this solution is added (36) (34 p.mol) and the reaction mixture is stirred for 1 hour and then purified to give 5-(343434143-thiopropy1]-24541-ethy1-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidenei-1,3-5 pentadienyli-3,3-dimethy1-3H-indolium1-2,5-pyrrolidindione]propanamido1-1-propyny13-2'-deoxycytidine triphosphate (46).
Example 29- Bonding dye (15) with streptavidin.
Streptavidin (15 mg) is dissolved in 1 mL 0.1M sodium phosphate buffer, pH 7Ø Sulfosuccinimidy141N-maleimidomethylj cyclohexane- 1 -carboxylate (9 10 mg) in 0.2 mL dimethylsulfoxide is added to the streptavidin solution at room temperature, mixed for 1 hour and purified by gel filtration chromatography to give maleimide derivatized streptavidin. To a 1.5 mL solution of maleimide derivatized streptavidin (3.5 mg) in 0.1M sodium phosphate, 5 rnM EDTA buffer, pH 6.0, 1 mg of Cyanine 3 Dye (15) is added followed by 0.15 mL of 1M
15 hydroxylamine pH 7Ø The solution is mixed at room temperature for 1 hour and then 20 p.L of 0.1M N-ethylmaleimide is added and the mixture is stored at 4 C
for 16 hours. The mixture is purified by gel filtration chromatography to give streptavidin modified with Cyanine 3 Dye (15).
Example 30 - Bonding dye 16 with streptavidin.
20 Streptavidin (15 mg) is dissolved in 1 mL 0.1M sodium phosphate buffer, pH 7Ø Sulfosuccinimidyl 4[N-maleimidomethyll cyclohexane- 1 -carboxylate (9 mg) in 0.2 mL dimethylsulfoxide is added to the streptavidin solution at room temperature, mixed for 1 hour and purified by gel filiration chromatography to give maleimide derivatized streptavidin. To a 1.5 mL solution of maleimide derivatized streptavidin (3.5 mg) in 0.1M sodium phosphate, 5 mM EDTA buffer, pH 6.0, 1 mg of Cyanine 3 Dye (16) is added followed by 0.15 mL of 1M
hydroxylamine pH 7Ø The solution is mixed at room temperature for 1 hour and then 20 AL of 0.1M N-ethylmaleimide is added and the mixture is stored at 4 C
for 16 hours. The mixture is purified by gel filtration chromatography to give streptavidin modified with Cyanine 3 Dye (16).
Example 31 - Bonding of dye (15) with neurotensin on resin.
Fmoc-Neurotensin on Resin (Wang polymer) 100 mg (substitution 0.6 mmol/g) is swelled in dimethy formatnide (DMF) for 30 minutes where Fmoc has the structure:
414111, (57) O
Fmoc is removed by reaction with 25% Piperidine/DMF (about 20 ml x 3 min, wash with DMF, and 20 ml x 20 min). Resin is washed with DMF 7 x 20 ml (1 min each washing step). 25 mg of (N4gamma-malemidobutryloxy]succinimide ester (Sulfo-GMBS) in DMF (15 ml) is added and mixed with resin 24 hours.
After reaction the resin is washed 7 x 20 ml of DMF. Cyanine (15) (10 mg) solution in DMF/methanol (15 ml) is added along with 5 ml 1 M solution of hydroxylamine in water. Reaction is performed overnight. After washing with DMF (7 x 20 ml) and methanol (3 x 30 ml) resin is dried. Labeled peptide is cleaved from resin with Reagent K (92.5% TFA/2.5% EDT/2.5% water/2.5% TIS) ml for 2 hours. Crude peptide is precipitated with cold diethyl ether and centrifuged. Precipitate is dissolved in 50% Acetonitrile/water and lyophilized.
Example 32- Bonding of dye (15) with galanin on resin.
5 Fmoc-Galinin on Resin is swelled as in Example 31. Orthogonal protection on Lys 25 ((4,4-dimethy1-2,6 dioxocyclohex-1-ylidene)ethyl-Dde) is removed by reaction with 2% hydrazine hydrate (2 x 20 ml, 2 min). Resin is washed 6 times with DMF (20 m1). 25 mg of Sulfo-GMBS in DMF (15 ml) is added and mixed with resin for 24 hours. After reaction the resin was washed 7 x 10 20 ml of DMF, (15) (10 mg) solution in DMF/Me0H (15 ml) is added along with 5 ml 1 M solution of hydroxylamine in water. Reaction is performed overnight.
Labeled galanin is purified and isolated as per Example 32.
Example 33- Bonding of dye (29) with a native peptide - bradykinin.
Bradylcinin (3 mg) dissolved in 1 ml of 50 mM sodium dihydrogen phosphate pH 7.5, and added sulfoGMBS (3.4 mg), mixed for 2 hours in room temperature. To the reaction mixture is added 1 ml of solution (5.8 mg) of (29) in sodium dihydrogen phosphate pH 7.5 and 0.5 ml 1 M hydroxylamine (pH 7), and mixed overnight. Labeled peptide is lyophilized.
Example 34- Bonding of dye (29) with liposomes.
The procedure of Example 33 is repeated with the substitution of liposomes as per Example 1 of U.S. Patent 4,089,801 for bradykinin, where the liposome includes lecithin and amyloglucoside therein. A labeled liposome is purified therefrom.
F
....___ Example 35- Bonding of 1-13-N-acetylaminopropy1J-2-[5-1-[ethy1-1,3 dihydro-3,3-dimethy1-5-sulfo-211-indol-2-ylidene]-1,3-pentadieny11-3,3-dimethyl-5-sulfo-3II-indolium, potassium salt (58) to a target nucleotide derivative.
The dye (58) is prepared as per Examples 1 and 11 using the amine analog to the dye precursor (5). The dye (58) is combined with (36) as per Example 28 to yield the amine analog to (46).
Those skilled in the art will appreciate from the foregoing description and examples that the broad teaching of the present invention can be implemented in a variety of forms. Therefore, while this invention has been described in connection with particular examples thereof, the true scope of the invention should not be so limited since other modifications will become apparent to one skilled in the art upon review of the specification and the following claims.
. .
, a, a u.) 3..3 a a Cyanine-3 dyes derived from precursors (7), (10),(13) and the 1-ethyl analogs thereof in terms of dye formula (2) Example Compound # RI R2 112 R4 R5 Ro. R7 RI Yi Y2 RI t R12 6 (18) H OH -C., He H OH -C4H4--C(C2H 5)2- -C(C2H5)2- C3H6SC(0)CH 3 C2H 5 (7) + I -Et(7) (19) H OH -C4HE H OH -C41-14--C(C3H 5)2- -C( C2115 )2- C3 HaSC(0)CH3 C31-1SC(0)CH3 P
(20) H OH . -C4H4- H OH -C4F14- -C(C2H5)2- -C(C21.15)2- C2H5 C2H5 N, w w 0, N, 1 7 (21) COO H H
10+ 1-Et(10) (22) COY H H
(23) coo- H H H
H
COO" H
COO' H H
H
H H
H
H
-o--o-cc:HH:sc(o)cals C2 H 5 C4HISC(0)C6H5 CASCOOK CO
C2Fis o iv o o o F-, COiv ii 8 (24) H SO; H H H SO; H H -N(CH3)- -N(CH3)-C41-IsSC(CH3)3 C21-15 i , q 13 + 1-Et(I0) (25) H so; H H H SO; H H
-N(CH))- -N(CH3)- C4HiSC(CH3)3 C.FIRSC(CH3)3 Ø
(26) H SO; H H H SO; H H -N(CH3)- -N(CH3)- C21-15 P
1 rn 9 (19) (23) 7 + 1-Et(10) a (27) H OH -C.He COO. H H H
-C(C2Hi)2- -0- C3H6SC(0)CH3 C21-Is (19) (7) + 1-Et(13) (26) (28) H OH -C41-14- H SO; El H
-C(C21-15)2- -N(CH3)- C3H,,SC(0)CH3 C21-15 oo n co) o a *Note: In Examples 6-10 L is CH and n is 1.
---I-, cm u3 ca f.A3 ,
The new and facile chemistry described in this application enables the synthesis of many new derivatives of indole containing chemicals by providing a vehicle to add a wide variety of chemical groups to an indole nucleus allowing researchers in the life sciences access to a broader variety of biologically active molecules and labeling reagents for target molecules. For example, long chain hydrocarbons may be added to indole chemicals giving them hydrophobic qualities or alternatively linker molecules may be added that will enable the various biological activities of the indoles to be covalently attached to reporter systems or to be used as the reporter molecule in various biological systems.
This chemistry can also be used to synthesize new indole derivatives having interesting and beneficial pharmaceutical properties. In research, new derivatives that act as agonists or antagonists to the various sub classes of serotonin receptors may be formed. New derivatives may also lead to new labeling reagents and alternative methods of attaching labeling reagents, such as cyanine dyes, to target molecules.
The new heterocyclic derivatives synthesized lby the above methods can be converted to cyanine dyes using conventional chemistry.
These heterocyclics are operative as precursors for a generic class of cyanine dyes having a protected reactive group for nucleophilic covalent attachment to target molecules. The precursor. (1) is condensed to form a fluorescent cyanine dye through a polymethine linkage.
RI, R2, R3 and R4 are optionally such that two of these adjacent R groups are fused to form a ring structure. The resulting ring structure also optionally being fimctionalized to modify solubility and spectral properties.
The polymethine linkage being formed by reacting two equivalents of precursor (1) in the presence of a molecule illustratively including trialkyl orthof9rmate, dialkyl amides, and trialkoxy alkene in the presence of a base.
Preferably, the base is an organic base. The linkage reaction proceeds under ambient air in a refluxing organic solvent, although it proceeds at a slower rate without solvent reflux. The organic base illustratively includes pyridine, phenol and an alkoxide, morpholine, piperidine, t-butylamine, and triethylamine and an amine. The polymethine linkage is a conjugated system having 3, 5, 7 or more linear carbon atoms therein.
The polymethine linkage between two molecules of precursor (1) is appreciated to include linear chains, as well as also cyclo-aliphatics, substituted aryl and heterocyclic ring structures coupled to the conjugate system of the polymethine chain. For instance, a bisaldehyde is more reactive towards the precursors of the present invention than formates, amides or alkoxyalkenes and reaction does not require the presence of a base. Instead, reaction occurs in the presence of an alcohol (J. Org. Chem. 60, 2391-2395: 1995). A 1-formy1-3-(hydroxymethylene)cyclohex-1-ene derivative thus yields a heptamethine linkage.
Thus, it is appreciated that modification and extension of the conjugate bonding across the chain will affect the absorption characteristics of the dye.
Further, it is appreciated that additional reactive groups or solubility enhancing moieties are readily coupled to the polymethine linkage.
The resulting cyanine dye has the formula:
Ri Re - - -y *- (2) R4 R11 R12 Re wherein RI, R2, R3, R4, R59 R69 R79 and RS are each independently selected from a group consisting of hydrogen, C1-C30 alkyl group, a Co-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein Yi and Y2 are each independently selected from a group consisting of:
.1, Pe _ Ra / Rio R. .
X, \ r R, ____, /
PG
_,, <. . .
,x wherein R9, R's, R10, and R'10 are each independently selected from a group consisting of CI-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is 0, N or S;
wherein R11 and R12 are each independently selected from a group 5 consisting of C1-C30 alkyl, phenyl substituted CI-C30, C1-C30 having a protected substituent selected from a group consisting of:
H
¨.,...N.õ , ¨R,3¨Q ¨13 . --R13--"S NI12 . R1ky R13¨NH2 .
H ---R
.13 ..)L.
¨Rikyõ. M N
R.(3 ItS
o o IP
¨RA
7. .
. .
¨R13 =i3 ¨RS 0 NO2 s...........H
µ
..," =
¨R13 0 ¨R13 \ 0 , NO2 .
)Lo--R13 ¨Ri3 0 rs)Lo s 0 .
H
s OCH3 ¨ S¨"¨S
/S S
¨R13 R,3¨R13 X
¨12;
and ¨R13-0¨Si(CH03 wherein R13, R'13, R"13 and R"13 are each independently C1-C30 alkyl; Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen;
L is selected from a group consisting of: methine, a methine group having a substituent C1-C6 alkyl group and a substituted C1-C6 alkyl group having a phenyl, hydroxyl, sulfonyl, a halogen atom, a heteroatorn substituted phenyl and a C1-C4 alkoxyl where n is 1, 2, 3 or greater.
R1-R8 are optionally such that two of these adjacent R groups are fused to form a ring structure. The resulting ring structure optionally is functionalized to modify solubility and spectral properties.
In order to increase the water solubility of the resulting dye (2), the RI, R2, R3, R4, R5, R6, R7, Rs, R9, R91, Rio, R101, Rii and R12 groups are each optionally selected from well known polar and charged moieties. Preferably, each precursor molecule (1) contains at least one hydrophilic moiety in order to impart water solubility.
n The dr moieties oililustratively are useful in organic -11dr -substituted amino, -quaternary amino, -sulfonate and -carboxylate. It is 5appreciated that hydrophilic micoori ar precursors cYsol:xenYt' systems.
A dye (2) is reactive towards a target molecule upon formation of a thiol, amine or hydroxyl moiety. The thiol, amine or hydroxyl moiety is characterized by a lone pair of electrons sterically and electronically amenable to bonding with a reactant which is reactive towards target molecules. The reaction of a dye (2) with a deprotecting agent converts the substituent into a reactive thiol, amine or hydroxyl substituent. Deprotecting agents are well known to the art. (Theodora W. Greene and Peter G.M. Wuts, Protective Groups in Organic Synthesis, 2nd edition (1991) 277-308.) It is appreciated that an amine or hydroxyl substituent in fact optionally need not be protected, but instead are stable under synthesis conditions and are isolated as such. Thus, an amine or hydroxyl substituent operates as a reactive nucleophilic substituent without the occurrence of an intermediate deprotecting reaction.
It is appreciated that the dyes of the present invention are also amenable to isolation in deprotected form of free thiols. A free thiol containing dye of the present invention results upon reacting a dye (2) with a deprotecting agent and isolating the free thiol therefrom. The resulting free thiol, depending on its specific identity, has a shelf life of more than one month. As with other reactive thiols, free thiol cyanine dyes of the present invention are best maintained under conditions suitable to prevent the formation of disulfide linkages. These conditions illustratively include refrigeration, darkness and storage under an inert atmosphere. Alternatively, nitrogen containing heterocyclics identical to (1) except that R11 is selected from the group consisting of RI4SH, R14NH2 and are formed directly wherein R14 is a C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonyl, or halogen atom or a heteroatom substituted phenyl.
The reaction chemistry to produce a free thiol dye precursor analog to (1) proceeds in a similar fashion to the formation of protected heterocyclics (1).
For example, a cationic nitrogen-containing heterocyclic and a halogenated thiol are able to react via a metatheses reaction to create a free thiol dye precursor.
The amine or hydroxyl moiety are produced by analogous type reactions. A free thiol precursor thereafter is reacted in a manner similar to precursor (1) to form a polymethine linkage therebetween. The resulting c:yanine dye compound is identical to that of (2) except that R11 and R12 are each independently RiaSH, RI4NH2 or RI40H when R14 is a C3-C30 alkyl or C3-C30 alkyl having a phenyl, hydroxyl, sulfonyl, or halogen atom or a heteroatom substituted phenyl.
A commercial package of the present invention includes a compound of Formula (1) with instructions and optionally reagents fin converting the precursor (1) to a dye compound (2) and further instructions for the use of the dye compound (2) as a dye or hapten. It is appreciated that a free thiol, amine or hydroxyl analog of a compound (1) is also operative herein. Alternatively, a commercial package includes a compound (2) as an active ingredient together with instructions for the use thereof as a dye or hapten in labeling a target molecule. It is also appreciated that a free thiol, amine or hydroxyl analog of a compound (2) is also operative herein.
The addition of a reactive form of a dye (2) to a target molecule proceeds under conventional nucleophilic reaction conditions. The solvent for the nucleophilic reaction is dictated by the identity of the target molecule.
Since many target molecules of interest are of a biological nature, water is often the nucleophilic reaction solvent.
A target molecule which is coupled with a dye of the present invention illustratively includes organic molecules, polymers, silaceous materials, natural and synthetic: lipid vesicles, amino acids, peptide nucleic acids, peptides, nucleic acids, nucleotides, nucleosides, DNA, RNA, proteins, carbohydrates, oligosaccharides, polysaccharides, antibodies, cellular receptors, antigens, haptens, lectins, avidins, streptavidins, lyrnpholcines, hormones, metabolites, toxins, virions, bacteria, fimgal components, esinophils, eukaryotic cells, and derivatives thereof.
A dye (2) of the present invention in which neither R11 or R12 is CI-Cm, having a heteroatom containing substituent finds utility as a physi-sorbed, fluorescent dye. Alternatively, a dye of the present invention lacking a heteroatom within R11 or R12 is coupled to a target molecule through a hydrophilic moiety of R1-R8 or a pendant reactive moiety extending from the polymethine linkage.
14.1 A compound according to another aspect of the invention comprises an indole nucleus having substituents wherein the substituents at indole positions 1-7 are each independently selected from a group consisting of hydrogen and CI -C30 alkyl, wherein at least one of the substituents at positions 1-7 is Ci-C30 alkyl and at least one of the substituents at positions 1-7 is C1-C30 alkyl having a phenyl, hydroxyl, carboxyl, sulfonyl, amine, thiol or halogen atom or a heteroatom substituted phenyl.
According to yet another aspect of the invention, the the indole position 2 substituent is methyl and the indole position 1 substituent is selected from CI-Cm alkyl and C1-C30 alkyl, having a phenyl, hydroxyl, carboxyl, sulfonyl, amine, thiol or halogen atom or a heteroatom substituted phenyl, and at least one of the substituents at positions 3-7 is C0-C30 alkyl.
In order to more fully demonstrate the advantages arising from the present invention, the following examples are set forth. It is to be understood that the following is by way of example only and not intended as a limitation on the scope of the invention.
5 Example 1 - Dye precursor 143-S-Acetylthiopropy11-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (5).
To a 250 rnL round bottom flask with magnetic stir bar is added 2,3,3-trimethy1-5-sulfo-3H-indolium, potassium salt (3) (7.21 mmol) and 3-bromo-1-10 thioacetylpropane (4) (25.88 mmol). The mixture is stirred and heated at for 20 min. The residue is cooled to 20 C and washed with diethyl ether. The solid is purified by Reversed Phase Chromatography to give 143-S-Acetylthio-propy1]-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (5) as a solid.
Example 2 - Dye precursor 143-S-Acetylthiopropy11-2,3,3-trimethy1-5-15 hydroxyl-6-benzo-311-indolium, inner salt (7).
The procedure of Example 1 is repeated except 2,3,3-trimethy1-5-hydroxy1-6-benz-indolium, potassium salt (6) is substituted for (3). A solid product 143-S-Acetylthiopropy1)-2,3,3-trimethyl-5-hydroxyl-6-benzo-indolitun, inner salt (7) is isolated.
Example 3- Dye precursor 1-14-S-benzoylbutyI]-3-methy1-4-carboxyl benzoxizolium, inner salt (10).
The procedure of Example 1 is repeated except 3-methyl-4-carboxyl benzoxizolium, sodium salt (8) is substituted for (3) and 4-bromo- 1 -S-benzoylbutane (9) is substituted for (4). A solid product 144-S-benzoylbuty1]-methy1-4-carboxyl benzoxizolium, inner salt (10) is isolated.
Example 4- Dye precursor 1-[3-S-t-butylpropy11-3-methyl-5-sulfo-benzoimidazolium, inner salt (13).
The procedure of Example 1 is repeated except 3-methy1-5-sulfo-benzoimidazolium (11) and 3-bromo-1-S-t-butyl propane (12) is substituted for (4). A solid product 143-S-t-butylpropy1]-3-methy1-5-sulfo-benzoimidazolium, inner salt (13) is isolated.
Example 5- Cyanine-3 dyes derived from (5).
A solution of (5) (2.68 mmol) and 1-ethy1-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (14) (2.68 mmol) is heated to reflux in pyridine (70 mL) and triethyl orthoformate (24.0 znmol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The solvents are removed under reduced pressure and the solid is azeotroped two times with methanol. The solid is purified by Reversed Phase Chromatography and the isolated products are passed over an AG50W-X4, 200-400 mesh K+ form, column to give 1-[3-S-acetylthiopropy1]-2-[341 -ethyl-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1-propenyl] -3,3-dimethy1-5-sulfo-3H-indoliurn, potassium salt (15), 143-S-AcetylthiopropylF
2434143-S-acetylthiopropy1]-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indol-2-ylidene]-1-propeny1J-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (16), and 1 -ethy1-24341-ethy1-1, 3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1-propeny1]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (17) as solids.
Examples 6-10 - Cyanine-3 dyes derived from (7), (10) and (13).
The procedure of Example 5 is repeated with (7), (10) and (13) substituted for (5) and the 1-ethyl-analogs of (7), (10) and (13) substituted for (14).
The resulting solid compounds which are isolated in purified form are summarized in Table 1.
Example 11 - Cyanine-5 dyes derived from (5).
A solution of (5) (1.60 mmol), (14) (1.60 mmol) and potassium acetate (3.56 mmol) in methanol (50 mL) is heated to reflux and 1,3,3-trimethoxypropene (21.0 mmol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The methanol is removed under reduced pressure and the solid is purified by Reversed Phase Chromatography to give 143-S-Acetylthiopropyli-2-[541-ethy1-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indol-2-ylidene]-1,3-pentadieny1]-3,3-dimethy1-5-sulfo-3H-indolium, potassium salt (29), 1-[3-S-Acetylthiopropy1]-24341-[5-S-acetylthiopropyl]-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidenej-1,3-pentadienyl]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (30) and I-ethyl-245-[ 1 -ethy1-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1,3-pentadieny1J-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (31) as solids.
Example 12 - Dye precursor S-(3-lodopropyl)isothiourea (32).
Thiourea (14 mmol) is added to a solution of 1,3-diiodopropane (340 mmol) in anhydrous methanol (300 mL) and stirred under an atmosphere of nitrogen at 60 C for 4 hours. The solution is cooled to 4 C overnight during which time excess 1,3-diiodopropane separates to the bottom of the flask as a colorless oil. The excess 1,3-diiodopropane is removed by pipette and the remaining methanol solution is evaporated in vacuo and the residue is suspended in dichloromethane, filtered, and washed with additional dichloromethane to give S-(3-Iodopropypisothiourea (32) as a powder.
Example 13 - Dye precursor 1-13-Isothiouronylpropy11-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (33).
A solution of (32) (0.36 mmol) and 2,3,3-trimethylindoleniniurn-5-sulfonate, potassium salt (3) (0.46 mmol) are placed in a flask and heated to 148 C with stirring for 15 minutes under an atmosphere ofnitrogen. The reaction mixture is cooled to room temperature and the residue is crystallized from methanol to give 143-isothiouronylpropy1]-2,3,3-trimethy1-5-sulfo-3H-indolitun, inner salt (33) as a powder.
Example 14- Cyanine-3 dyes derived from (33).
A solution of (33) (0.022 mmol) and 1-ethy1-2,3,3-trimethy1-5-sulfo-3H-, indolium, inner salt (14) (0.022 mmol) are dissolved in N,N-dimethylformamide containing 50 uL of triethylamine and the mixture is heated to 60 C as triethylorthofonnate (4 x 10 uL, 4 x 0.06 mmol) is added in four portions over hours. The solution is heated at 60 C for an additional hour, cooled to room temperature, washed 3 times with diethyl ether, and the resulting precipitate is purified by reverse phase HPLC to give isolated 143-Isothiouronylpropy1]-243-[1-ethy1-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1-propenylj-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (34), 143-Isothiouronylpropy1]-2-[34143-isothiouronylpropy1]-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indol-2-ylidene]-1-propeny1]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (35) and 1-ethy1-24341-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene1-1-propeny1]-3,3-dimethy1-5-sulfo-3H-indolium, potassium salt (17) as solids.
Example 15- Bonding of dye (15) to a target nucleotide derivative.
To a 2 mL vial with a stir bar is added (15) (1.58 pmol), 5-[3-[3-[2,5-dihydro-2,5-dioxo-1H-pyrrole]propanamido]-l-propynyli-2'-deoxycytidine triphosphate (36) (5.0 pmol) in 50 mM sodium dihydrogenphosphate pH 7.0 - 7.5 (250 pL). To the stirred solution is added 1M hydroxylamine pH 7.0 - 7.5 (250 pL) and the resulting solution is stirred at room temperature for 1 hour. The reaction mixture is purified to give 5-(343-(34143-thiopropyli-24341-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidenei-1-propenyli-3,3-dimethy1-5-sulfo-3H-indolium]-2,5-pyrrolidindione]propanamido]-1-propyny1]-2'-deoxycytidine triphosphate (37).
Example 16- Bonding of dye (28) to a target nucleotide derivative.
The procedure of Example 15 is repeated with (28) substituted for (15).
The reaction mixture is purified to give 5-[3434341-[3-thiopropy1]-24341-ethyl-3-methyl-5-sulfo-benz-imidazol-2-ylidene]-1-propeny1]-3,3 dimethy1-5-hydroxy1-6-benz-indolitun]-2,5-pyrrolidindione]propanamidoi-1-propynyl}2'-deoxycytidine triphosphate (38).
Example 17- Bonding of dye (29) to a target nucleotide derivative.
The procedure of Example 15 is repeated with (29) substituted for (15).
The reaction mixture is purified to give 543-[343-143-thiopropy1}-24541-ethyl-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1,3-pentadienyl]-3,3-dimethy1-5-su1fo-3H-indolium1-2,5-pyrro1idindionejpropanamido]-1-propyny11-2'-deoxycytidine triphosphate (39).
Example 18 - Dye precursor 1-13-Isothiouronylpropy11-2,3,3-trimethyl-3H-5 indolium iodide (41).
To a 50 mL round bottom flask is added 2,3,3-trimethylindolenine (14.4 mmol) and 1,3-diiodopropane (72.7 mmol) and the mixture is stirred at 60 C
under an atmosphere of nitrogen for 16 hours. The resulting solid is recrystallized 10 from ethanol to give 1[3-iodopropy1]-2,3,3-trimethy1-3H-indolium iodide (40) as crystals.
To a 100 mL round bottom flask is added (40) (4.38 mmol), thiourea (4.5 mmol), and methanol (30 mL). The solution is stirred at 60 C for 5 hours, evaporated in vacuo, the residue is dissolved in water (20 mL) and washed with 15 dichloromethane (3 x 6 mL) and cooled to 4 C overnight, and the resulting crystals are filtered and washed with acetone to give 143-isothiouronylpropy1]-2,3,3-trimethy1-3H-indolium iodide (41).
Example 19 - Cyanine-3 dyes derived from (41).
To a 25 mL round bottom flask is added (41) (1.0 mmol), (14) (1.5 mmol), 20 and pyridine (10 mL). The solution is heated to reflux and triethyl orthoformate (4 x 166 uL, 4 x 1.0 mmol) is added in four portions over one hour. The solution is heated at reflux for an additional hour, cooled to room temperature, the evaporated in vacuo, and the residue is washed with ethyl ether (3 x 25 mL), and purified by C18 reverse phase chromatography to give isolated 143-isothiouronylpropy1]-24341-ethy1-1,3-dihydro-3,3-diunethyl-5-sulfo-2H-indol-2-ylidenel-1-propeny1]-3,3-dimethyl-3H-indolium, inner salt (42), 143-isothiouronylpropylj-2-[34143 -isothiouronylpropyl] -1,3 -dihydro-3,3-dimethyl-2H-indo1-2-ylidene]-1-propenyl] -3,3-dimethy1-3H-indolium iodide (43) and 1-ethyl-2-[3-[1 -ethyl-1,3 -dihydro-3 ,3 -dimethy1-5-sulfo-2H-indo1-2-ylidene]-1-propeny11-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (17) as solids.
Example 20- Cyanine-5 dyes derived from (41).
A solution of (41) (0.28 mmol) and (14) (0.28 mmol) and potassium acetate (0.28 mmol) in methanol (2 mL) is heated to reflux and 1,3,3-trimethoxypropene (160 uL, 1.17 mmol) is added via syringe over 2 hour in four equal portions. A suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The methanol is removed under reduced pressure and the solid is purified by C18 Reversed Phase Chromatography to give 143-isothiouronylpropy1]-24541-ethy1-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadieny11-3,3-dimethy1-3H-indolium, inner salt (44), the related di-isothiouronyl-propyl and diethyl inner salts as solids.
Example 21 - Bonding of dye (42) to a target nucleotide derivative.
To a 2 mL vial with a stir bar is added 143-isothiouronylpropy1]-24341-ethy1-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indol-2-ylidenej-1-propenyli-3,3-dimethyl-3H-indolium, inner salt (42) (81=01) in 0.1 M potassium hydroxide (1.0 mL). The solution is stirred at room temperature for 1 hour to form the free thiol of (42). Thereafter, (36) (15 gmol) is added to the thiol in aqueous solution.
The reaction mixture is purified to give 54343434143-thiopropyl]-24311-ethy1-1,3-, dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1-propeny11-3,3-dimethy1-3H-indoliumi-2,5-pyrrolidindionejpropanamido]-1-propynyl]-2'-deoxycytidine triphosphate (45).
Example 22- Bonding of dye (44) to a target nucleotide derivative.
The procedure of Example 21 is repeated with (44) substituted for (42).
The reaction mixture is purified to give 54343434143-thiopropyli-24541-ethy1-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadienyl]-3,3-dimethyl-3H-indolium]-2,5-pyrrolidindione]propanamidoi-1-propynyl]-2'-deoxycytidine triphosphate (46).
Example 23 - Bonding of dye (15) to a target nucleotide derivative.
To a 5 mL vial with a stir bar is added (15) (19 mop, 543-[iodoacetamido]-1-propynyli-2'-deoxycytidine triphosphate (47) (30.0 p.mol) in rnM sodium dihydrogenphosphate pH 7.0 - 7.5 (250 pL). To the stirred solution 1M hydroxylamine pH 7.0 - 7.5 (250 1.) is added. The resulting solution is stirred at room temperature for 4 hours to react the free thiol of (15) with (47).
The reaction mixture is purified to give 5434143-thiopropyli-24341-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-211-indol-2-ylidenei-1-propenyl]-3,3-dimethyl-5-sulfo-3H-indoliumjacetamido-1-propynyl]-2'-deoxycytidine triphosphate (48).
Example 24- Bonding of dye (29) to a target nucleotide derivative.
The procedure of Example 23 is repeated with (29) substituted for (15).
The reaction mixture is purified to give 54341-[thiopropy1]-2-[541-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadieny1]-3,3-dimethyl-5-sulfo-3H-indoliumiacetamido-1-propyny11-2'-deoxycytidine triphosphate (49).
Example 25- Dye precursor 1-[N-F3-(tert-butyloxycarbonylamino) propyllhexanamide]-2,3,3-trimethyl-5-sulfo-3H-indolium, inner salt (51).
To a 100 inL round bottom flask with a stir bar is added 1-N-{5-carboxypenty1}-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (50) (1.70 nunol) and 40 inL of N,N-dimethylfonnamide. The mixture is heated at 50 C until a homogeneous solution is obtained. To this solution is added 1,3-dicyclohexylcarbodiimide (2.30 mmol), N-hydroxysuccinimide (2.34 mmol) and t-butyl N-(3-aminopropyl)carbamate (2.29 mmol). The reaction mixture is heated at 50 C for 30 min and then room temperature 16 hours. The reaction mixture is filtered, the solvents are removed under reduced pressure and the solid is azeotroped two times with methanol. The solid is purified by Reversed Phase Chromatography to give 1-M-[-3-(tert-butyloxycarbonylamino)propyl]
hexanamide]-2,3,3-trimethy1-5-sulfo-3H-indolium, inner salt (51) as a solid.
Example 26 - Cyanine-3 dyes derived from (51).
A solution of (51) (0.291 mmol) and (14) (0.281 mmol) is heated to reflux in pyridine (30 mL) and triethyl orthofonnate (2.4 mmol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 4 hours and cooled to room temperature. The solvents are removed under reduced pressure and the solid is azeotroped two times with methanol.
The purple solid is purified by Reversed Phase Chromatography and the isolated products are passed over an AG50W-X4, 200-400 mesh K+ form, column to give 1-4N43-(tert-butyloxycarbonylamino)-propylihexanamide]-2-1341-ethyl-.1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1-propenylj-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (52), 14N-[3-(tert-butyloxycarbonyl-amino) propyl]hexanamide)-24341-N43-(tert-butyloxycarbonylamino)-propyl]hexanamidel-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1-propenyl]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (53) and the related diethyl salt as solids.
Example 27- Cyanine-5 dyes derived from (51).
A solution of (51) (0.291 mmol) and (14) (0.292 mmol) and potassium acetate (78 mg, 0.79 mmol) in methanol (15 mL) is heated to reflux and 1,3,3-trimethoxypropene (0.5 mL, 3.64 nunol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The methanol is removed under reduced pressure and the solid is purified by Reversed Phase Chromatography to give 1-[1=1-13-(tert-butyloxycarbonylamino)propyThexanamide]-24541-ethyl-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene]-1,3-pentadienylj-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (54), 1-N-[3-(tert-butyloxycarbonyl-amino)propyl]hexanamide]-24541-[1143-(tert-butyloxycarbonylamino)propy1]-hexanamidei-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidenel-1,3-pentadienylj-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (55) and the related diethyl salt as solids.
Example 28 - Bonding of dye (44) to a target nucleotide derivative.
To a2 mL vial with a stir bar is added (44) (17 mop and 1 M potassium phosphate (4.0 mL) and methanol (2 mL) and the resulting solution is stirred at room temperature for 1 hour to give 143-thiopropy1]-24541-ethyl-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidene)-1,3-pentadienylj-3,3-ciimethyl-3H-indolium, inner salt (56). To this solution is added (36) (34 p.mol) and the reaction mixture is stirred for 1 hour and then purified to give 5-(343434143-thiopropy1]-24541-ethy1-1,3-dihydro-3,3-dimethy1-5-sulfo-2H-indo1-2-ylidenei-1,3-5 pentadienyli-3,3-dimethy1-3H-indolium1-2,5-pyrrolidindione]propanamido1-1-propyny13-2'-deoxycytidine triphosphate (46).
Example 29- Bonding dye (15) with streptavidin.
Streptavidin (15 mg) is dissolved in 1 mL 0.1M sodium phosphate buffer, pH 7Ø Sulfosuccinimidy141N-maleimidomethylj cyclohexane- 1 -carboxylate (9 10 mg) in 0.2 mL dimethylsulfoxide is added to the streptavidin solution at room temperature, mixed for 1 hour and purified by gel filtration chromatography to give maleimide derivatized streptavidin. To a 1.5 mL solution of maleimide derivatized streptavidin (3.5 mg) in 0.1M sodium phosphate, 5 rnM EDTA buffer, pH 6.0, 1 mg of Cyanine 3 Dye (15) is added followed by 0.15 mL of 1M
15 hydroxylamine pH 7Ø The solution is mixed at room temperature for 1 hour and then 20 p.L of 0.1M N-ethylmaleimide is added and the mixture is stored at 4 C
for 16 hours. The mixture is purified by gel filtration chromatography to give streptavidin modified with Cyanine 3 Dye (15).
Example 30 - Bonding dye 16 with streptavidin.
20 Streptavidin (15 mg) is dissolved in 1 mL 0.1M sodium phosphate buffer, pH 7Ø Sulfosuccinimidyl 4[N-maleimidomethyll cyclohexane- 1 -carboxylate (9 mg) in 0.2 mL dimethylsulfoxide is added to the streptavidin solution at room temperature, mixed for 1 hour and purified by gel filiration chromatography to give maleimide derivatized streptavidin. To a 1.5 mL solution of maleimide derivatized streptavidin (3.5 mg) in 0.1M sodium phosphate, 5 mM EDTA buffer, pH 6.0, 1 mg of Cyanine 3 Dye (16) is added followed by 0.15 mL of 1M
hydroxylamine pH 7Ø The solution is mixed at room temperature for 1 hour and then 20 AL of 0.1M N-ethylmaleimide is added and the mixture is stored at 4 C
for 16 hours. The mixture is purified by gel filtration chromatography to give streptavidin modified with Cyanine 3 Dye (16).
Example 31 - Bonding of dye (15) with neurotensin on resin.
Fmoc-Neurotensin on Resin (Wang polymer) 100 mg (substitution 0.6 mmol/g) is swelled in dimethy formatnide (DMF) for 30 minutes where Fmoc has the structure:
414111, (57) O
Fmoc is removed by reaction with 25% Piperidine/DMF (about 20 ml x 3 min, wash with DMF, and 20 ml x 20 min). Resin is washed with DMF 7 x 20 ml (1 min each washing step). 25 mg of (N4gamma-malemidobutryloxy]succinimide ester (Sulfo-GMBS) in DMF (15 ml) is added and mixed with resin 24 hours.
After reaction the resin is washed 7 x 20 ml of DMF. Cyanine (15) (10 mg) solution in DMF/methanol (15 ml) is added along with 5 ml 1 M solution of hydroxylamine in water. Reaction is performed overnight. After washing with DMF (7 x 20 ml) and methanol (3 x 30 ml) resin is dried. Labeled peptide is cleaved from resin with Reagent K (92.5% TFA/2.5% EDT/2.5% water/2.5% TIS) ml for 2 hours. Crude peptide is precipitated with cold diethyl ether and centrifuged. Precipitate is dissolved in 50% Acetonitrile/water and lyophilized.
Example 32- Bonding of dye (15) with galanin on resin.
5 Fmoc-Galinin on Resin is swelled as in Example 31. Orthogonal protection on Lys 25 ((4,4-dimethy1-2,6 dioxocyclohex-1-ylidene)ethyl-Dde) is removed by reaction with 2% hydrazine hydrate (2 x 20 ml, 2 min). Resin is washed 6 times with DMF (20 m1). 25 mg of Sulfo-GMBS in DMF (15 ml) is added and mixed with resin for 24 hours. After reaction the resin was washed 7 x 10 20 ml of DMF, (15) (10 mg) solution in DMF/Me0H (15 ml) is added along with 5 ml 1 M solution of hydroxylamine in water. Reaction is performed overnight.
Labeled galanin is purified and isolated as per Example 32.
Example 33- Bonding of dye (29) with a native peptide - bradykinin.
Bradylcinin (3 mg) dissolved in 1 ml of 50 mM sodium dihydrogen phosphate pH 7.5, and added sulfoGMBS (3.4 mg), mixed for 2 hours in room temperature. To the reaction mixture is added 1 ml of solution (5.8 mg) of (29) in sodium dihydrogen phosphate pH 7.5 and 0.5 ml 1 M hydroxylamine (pH 7), and mixed overnight. Labeled peptide is lyophilized.
Example 34- Bonding of dye (29) with liposomes.
The procedure of Example 33 is repeated with the substitution of liposomes as per Example 1 of U.S. Patent 4,089,801 for bradykinin, where the liposome includes lecithin and amyloglucoside therein. A labeled liposome is purified therefrom.
F
....___ Example 35- Bonding of 1-13-N-acetylaminopropy1J-2-[5-1-[ethy1-1,3 dihydro-3,3-dimethy1-5-sulfo-211-indol-2-ylidene]-1,3-pentadieny11-3,3-dimethyl-5-sulfo-3II-indolium, potassium salt (58) to a target nucleotide derivative.
The dye (58) is prepared as per Examples 1 and 11 using the amine analog to the dye precursor (5). The dye (58) is combined with (36) as per Example 28 to yield the amine analog to (46).
Those skilled in the art will appreciate from the foregoing description and examples that the broad teaching of the present invention can be implemented in a variety of forms. Therefore, while this invention has been described in connection with particular examples thereof, the true scope of the invention should not be so limited since other modifications will become apparent to one skilled in the art upon review of the specification and the following claims.
. .
, a, a u.) 3..3 a a Cyanine-3 dyes derived from precursors (7), (10),(13) and the 1-ethyl analogs thereof in terms of dye formula (2) Example Compound # RI R2 112 R4 R5 Ro. R7 RI Yi Y2 RI t R12 6 (18) H OH -C., He H OH -C4H4--C(C2H 5)2- -C(C2H5)2- C3H6SC(0)CH 3 C2H 5 (7) + I -Et(7) (19) H OH -C4HE H OH -C41-14--C(C3H 5)2- -C( C2115 )2- C3 HaSC(0)CH3 C31-1SC(0)CH3 P
(20) H OH . -C4H4- H OH -C4F14- -C(C2H5)2- -C(C21.15)2- C2H5 C2H5 N, w w 0, N, 1 7 (21) COO H H
10+ 1-Et(10) (22) COY H H
(23) coo- H H H
H
COO" H
COO' H H
H
H H
H
H
-o--o-cc:HH:sc(o)cals C2 H 5 C4HISC(0)C6H5 CASCOOK CO
C2Fis o iv o o o F-, COiv ii 8 (24) H SO; H H H SO; H H -N(CH3)- -N(CH3)-C41-IsSC(CH3)3 C21-15 i , q 13 + 1-Et(I0) (25) H so; H H H SO; H H
-N(CH))- -N(CH3)- C4HiSC(CH3)3 C.FIRSC(CH3)3 Ø
(26) H SO; H H H SO; H H -N(CH3)- -N(CH3)- C21-15 P
1 rn 9 (19) (23) 7 + 1-Et(10) a (27) H OH -C.He COO. H H H
-C(C2Hi)2- -0- C3H6SC(0)CH3 C21-Is (19) (7) + 1-Et(13) (26) (28) H OH -C41-14- H SO; El H
-C(C21-15)2- -N(CH3)- C3H,,SC(0)CH3 C21-15 oo n co) o a *Note: In Examples 6-10 L is CH and n is 1.
---I-, cm u3 ca f.A3 ,
Claims (37)
1. A compound of the formula:
wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 is selected from a group consisting of:
wherein R13, R'13, R"13 and R"'13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen-hydrogen or oxygen, X is a halogen and Y is a halogen.
wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 is selected from a group consisting of:
wherein R13, R'13, R"13 and R"'13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen-hydrogen or oxygen, X is a halogen and Y is a halogen.
2. The compound of claim 1 wherein R13 comprises more than two carbon atoms.
3. The compound of claim 1 wherein at least one of 121-R4 is the C1-C4 alkyl group having the hydrophilic substituent.
4. A compound of the formula:
wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of: hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 is selected from a group consisting of R14SH, R14NH2 and R14OH;
and wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl.
wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of: hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 is selected from a group consisting of R14SH, R14NH2 and R14OH;
and wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl.
5. The compound of claim 4 wherein at least one of R1-R4 is the C1-C4 alkyl group having the hydrophilic substituent.
6. A process for preparing wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is 0, N or S; and wherein R11 is selected from a group consisting of:
wherein R13, R'13, R"13 and R"'13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen-hydrogen or oxygen, X is a halogen and Y is a halogen, which comprises reacting an indole compound with XR13Q moiety of a bifunctional hydrocarbon wherein X is chlorine, bromine or iodine, R13 is C1-C30 alkyl and Q is sulfur, nitrogen or oxygen.
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is 0, N or S; and wherein R11 is selected from a group consisting of:
wherein R13, R'13, R"13 and R"'13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen-hydrogen or oxygen, X is a halogen and Y is a halogen, which comprises reacting an indole compound with XR13Q moiety of a bifunctional hydrocarbon wherein X is chlorine, bromine or iodine, R13 is C1-C30 alkyl and Q is sulfur, nitrogen or oxygen.
7. The process of claim 6 wherein Q is sulfur.
8. The process of claim 6 wherein said bifunctional hydrocarbon is a thiol.
9. The process of claim 6 wherein said bifunctional hydrocarbon is an amine.
10. The process of claim 6 wherein said bifunctional hydrocarbon is an alcohol.
11. The process of claim 6 wherein Q is protected by a protecting group.
12. A dye compound of the formula:
wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, R'9, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of C30 alkyl, phenyl substituted C1-C30 alkyl and C1-C30 alkyl having a protected substituent selected from a group consisting of:
wherein R13, R'13, R"13 and R"13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen and at least one of R11 and R12 is the C1-C30 having the protected substituent; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C6 alkyl group, and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3.
wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, R'9, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of C30 alkyl, phenyl substituted C1-C30 alkyl and C1-C30 alkyl having a protected substituent selected from a group consisting of:
wherein R13, R'13, R"13 and R"13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen and at least one of R11 and R12 is the C1-C30 having the protected substituent; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C6 alkyl group, and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3.
13. The dye compound of claim 12 wherein at least one of R1-R8 is the C1-C4 alkyl group having the hydrophilic substituent.
14. The dye compound of claim 12 wherein both R11 and R12 are the C1-C30 alkyl having the protected substituent.
15. The dye compound of claim 12 wherein only one of R11 and R12 is the C1-alkyl having the protected substituent.
16. A dye compound of the formula:
wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines, such that at least one of R1-R8 is the C1-C4 alkyl group having the hydrophilic substituent;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, W9, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of and nucleophilic substituent: R14SH, R14NH2 or R14OH
wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C30 alkyl group and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is at least 1.
wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines, such that at least one of R1-R8 is the C1-C4 alkyl group having the hydrophilic substituent;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, W9, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of and nucleophilic substituent: R14SH, R14NH2 or R14OH
wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C30 alkyl group and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is at least 1.
17. The dye compound of claim 16 wherein R11 and R12 are both the nucleophilic substituents.
18. The dye compound of claim 16 wherein only one of R11 and R12 is the nucleophilic substituent.
19. A process for preparing wherein R1- R4, are all the same, R5 - R8 are all the same and each group of and R5 - R8 is independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines, wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, R'9, R10, and R'10 are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of C30 alkyl, phenyl substituted C1-C30 alkyl and C1-C30 alkyl having a protected substituent selected from a group consisting of:
wherein R13, R'13, R"13 and R"13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen and at least one of R11 and R12 is the C1-C30 having the protected substituent; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C30 alkyl group, and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3, which comprises reacting compounds wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are all the same and R1 is selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 in the substrate (1) is as defined for compound (2);
with a molecule selected from the group consisting of: trialkyl orthoformate, dialkyl amide, trialkoxy alkene and C3-C12 bisaldehyde wherein any alkyl and alkoxy groups of said molecule are independently C1-C6 and any alkene is C3 or C5 or a molecule that is C3-C12 bisaldehyde, wherein said bisaldehyde is not C3-C12 bisaldehyde with alkyl and alkoxy groups being C1-C6 and alkene being C3 or C5, wherein, when the compound is reacted with the molecule selected from the group of:
trialkyl orthoformate, dialkyl amide, trialkoxy alkene, and C3-C12 bisaldehyde wherein the alkyl and alkoxy groups of said molecule are independently C1-C6 and the alkene is C3 or C5, the reaction is in the presence of a base; and wherein, when the compound is reacted with the molecule that is a C3-C12 bisaldehyde, wherein the bisaldehyde is other than alkyl and alkoxy groups being C1-C6 and the alkene being C3 or C5, the reaction is in the presence of alcohol.
wherein R9, R'9, R10, and R'10 are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of C30 alkyl, phenyl substituted C1-C30 alkyl and C1-C30 alkyl having a protected substituent selected from a group consisting of:
wherein R13, R'13, R"13 and R"13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen and at least one of R11 and R12 is the C1-C30 having the protected substituent; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C30 alkyl group, and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3, which comprises reacting compounds wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are all the same and R1 is selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 in the substrate (1) is as defined for compound (2);
with a molecule selected from the group consisting of: trialkyl orthoformate, dialkyl amide, trialkoxy alkene and C3-C12 bisaldehyde wherein any alkyl and alkoxy groups of said molecule are independently C1-C6 and any alkene is C3 or C5 or a molecule that is C3-C12 bisaldehyde, wherein said bisaldehyde is not C3-C12 bisaldehyde with alkyl and alkoxy groups being C1-C6 and alkene being C3 or C5, wherein, when the compound is reacted with the molecule selected from the group of:
trialkyl orthoformate, dialkyl amide, trialkoxy alkene, and C3-C12 bisaldehyde wherein the alkyl and alkoxy groups of said molecule are independently C1-C6 and the alkene is C3 or C5, the reaction is in the presence of a base; and wherein, when the compound is reacted with the molecule that is a C3-C12 bisaldehyde, wherein the bisaldehyde is other than alkyl and alkoxy groups being C1-C6 and the alkene being C3 or C5, the reaction is in the presence of alcohol.
20. A process for preparing wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines; such that at least one of R1-R8 is the C1-C4 alkyl group having the hydrophilic substituent;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, R19, R10, and RI10 are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of and nucleophilic substituent: R14SH, R14NH2 or R14OH;
wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C6 alkyl group and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3, which comprises reacting compounds wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R91, R10, and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 in the substrate (1) is as defined for compound (2);
with a molecule selected from the group consisting of: trialkyl orthoformate, dialkyl amide, trialkoxy alkene and C3-C12 bisaldehyde, wherein any alkyl and alkoxy groups of said molecule are independently C1-C6 and any alkene is C3 or C5 Or a molecule that is C3-C12 bisaldehyde, wherein said bisaldehyde is not C3-C12 bisaldehyde with alkyl and alkoxy groups being C1-C6 and alkene being C3 or C5, wherein, when the compound is reacted with the molecule selected from the group of:
trialkyl orthoformate, dialkyl amide, trialkoxy alkene, and C3-C12 bisaldehyde wherein the alkyl and alkoxy groups of said molecule are independently C1-C6 and the alkene is C3 or C5, the reaction is in the presence of a base;
wherein, when the compound is reacted with the molecule that is a C3-C12 bisaldehyde, wherein the bisaldehyde is other than alkyl and alkoxy groups being C1-C6 and the alkene being C3 or C5, the reaction is in the presence of alcohol.
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, R19, R10, and RI10 are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of and nucleophilic substituent: R14SH, R14NH2 or R14OH;
wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C6 alkyl group and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3, which comprises reacting compounds wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R91, R10, and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 in the substrate (1) is as defined for compound (2);
with a molecule selected from the group consisting of: trialkyl orthoformate, dialkyl amide, trialkoxy alkene and C3-C12 bisaldehyde, wherein any alkyl and alkoxy groups of said molecule are independently C1-C6 and any alkene is C3 or C5 Or a molecule that is C3-C12 bisaldehyde, wherein said bisaldehyde is not C3-C12 bisaldehyde with alkyl and alkoxy groups being C1-C6 and alkene being C3 or C5, wherein, when the compound is reacted with the molecule selected from the group of:
trialkyl orthoformate, dialkyl amide, trialkoxy alkene, and C3-C12 bisaldehyde wherein the alkyl and alkoxy groups of said molecule are independently C1-C6 and the alkene is C3 or C5, the reaction is in the presence of a base;
wherein, when the compound is reacted with the molecule that is a C3-C12 bisaldehyde, wherein the bisaldehyde is other than alkyl and alkoxy groups being C1-C6 and the alkene being C3 or C5, the reaction is in the presence of alcohol.
21. The process of claim 19 wherein the base is selected from a group consisting of: pyridine, C1-C4 alkoxide, C1-C4 substituted morpholine, piperidine and an amine.
22. A process for coupling said compound of claim 12 to a target molecule which comprises:
reacting said compound (2) wherein R11 or R12 comprises a heteroatom containing protected substituent, with a deprotecting agent wherein the heteroatom is selected from a group consisting of: sulfur, nitrogen and oxygen; and introducing said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).
reacting said compound (2) wherein R11 or R12 comprises a heteroatom containing protected substituent, with a deprotecting agent wherein the heteroatom is selected from a group consisting of: sulfur, nitrogen and oxygen; and introducing said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).
23. A process for coupling a compound of claim 16 to a target molecule which comprises:
reacting said compound (2) wherein R or R12 comprises amine or hydroxyl with said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).
reacting said compound (2) wherein R or R12 comprises amine or hydroxyl with said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).
24. A process for coupling a compound of claim 16 to a target molecule which comprises:
reacting said compound (2) wherein R11 or R12 comprises a thiol with said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).
reacting said compound (2) wherein R11 or R12 comprises a thiol with said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).
25. The process of claim 23 wherein said target molecule is selected from a group consisting of: organic molecules, polymers, silaceous materials, natural and synthetic: lipid vesicles, peptides, nucleic acids, nucleotides, nucleosides, DNA, RNA, proteins, carbohydrates, oligosaccharides, polysaccharides, antibodies, cellular receptors, antigens, haptens, lectins, avidins, streptavidins, lymphokines, hormones, metabolites, toxins, virions, bacteria, fungal components, esinophils, eukaryotic cells, and derivatives thereof.
26. A compound (2) as claimed in claim 12 for use as a fluorescent dye.
27. Use of a compound (2) as claimed in claim 12 for labeling a target molecule.
28. A commercial package comprising a compound (2) according to claim 12 as the active ingredient together with instruction for the use thereof as a dye or hapten.
29. A commercial package comprising a compound (2) according to claim 16 as the active ingredient together with instruction for the use thereof as a dye or hapten.
30. The process of claim 24 wherein said target molecule is selected from a group consisting of: organic molecules, polymers, silaceous materials, natural and synthetic: lipid vesicles, peptides, nucleic acids, nucleotides, nucleosides, DNA, RNA, proteins, carbohydrates, oligosaccharides, polysaccharides, antibodies, cellular receptors, antigens, haptens, lectins, avidins, streptavidins, lymphokines, hormones, metabolites, toxins, virions, bacteria, fungal components, esinophils, eukaryotic cells, and derivatives thereof.
31. The dye compound of claim 15 wherein the C1-C30 alkyl having the protected substituent is a sulfur containing moiety.
32. The dye compound of claim 15 wherein the R11 or R12 group lacking the protected C1-C30 protected substituent is the C1-C30 alkyl.
33. The dye compound of claim 16 wherein one of R11 or R12 is R14SH and the other of R11 or R12 is R14H.
34. A compound of the formula (1) wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 is selected from a group consisting of:
wherein R13, R'13, R"13 and R'"13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen-hydrogen or oxygen, X is a halogen and Y is a halogen;
wherein at least two adjacent R groups of R1-R4, R9', R9, R10 and R10' are fused to form a ring structure.
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 is selected from a group consisting of:
wherein R13, R'13, R"13 and R'"13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen-hydrogen or oxygen, X is a halogen and Y is a halogen;
wherein at least two adjacent R groups of R1-R4, R9', R9, R10 and R10' are fused to form a ring structure.
35. A compound of the formula wherein Y1 is selected from a group consisting of:
wherein R1, R2, R35 and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9', R9, R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 is selected from a group consisting of R14SH, R14NH2 and R14OH;
wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl; and wherein at least two adjacent R groups of R1-R4, are fused to form a ring structure.
wherein R1, R2, R35 and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9', R9, R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 is selected from a group consisting of R14SH, R14NH2 and R14OH;
wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl; and wherein at least two adjacent R groups of R1-R4, are fused to form a ring structure.
36. A dye compound of the formula:
wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, W9, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of C 1' C30 alkyl, phenyl substituted C1-C30 alkyl and C1-C30 alkyl having a protected substituent selected from a group consisting of:
wherein R13, R'13, R"13 and R"'13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen and at least one of R11 and R12 is the C1-C30 alkyl having the protected substituent; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C30 alkyl group and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3, wherein at least two adjacent R groups of R1-R8, are fused to form a ring structure.
wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, W9, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of C 1' C30 alkyl, phenyl substituted C1-C30 alkyl and C1-C30 alkyl having a protected substituent selected from a group consisting of:
wherein R13, R'13, R"13 and R"'13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen and at least one of R11 and R12 is the C1-C30 alkyl having the protected substituent; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C30 alkyl group and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3, wherein at least two adjacent R groups of R1-R8, are fused to form a ring structure.
37. A dye compound of the formula:
wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines; such that at least one of R1-R12, R9' and R10' is the C1-C4 alkyl group having a hydrophilic substituent;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, R19, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted Ci-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of and nucleophilic substituent: R14SH, R14NH2 or R14OH;
wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C6 alkyl group and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3 wherein at least two adjacent R groups of R1-R8 are fused to form a ring structure.
wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group and a C1-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines; such that at least one of R1-R12, R9' and R10' is the C1-C4 alkyl group having a hydrophilic substituent;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, R19, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted Ci-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of and nucleophilic substituent: R14SH, R14NH2 or R14OH;
wherein R14 is selected from a group consisting of: C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonate, halogen atom or a heteroatom substituted phenyl; and L is selected from a group consisting of: methine, a methine group having a substituent C1-C6 alkyl group and a methine substituted with a C1-C30 alkyl group having a phenyl, hydroxyl, sulfonate, a halogen atom, a heteroatom substituted phenyl or a C1-C4 alkoxyl where n is 1, 2 or 3 wherein at least two adjacent R groups of R1-R8 are fused to form a ring structure.
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