AU2021277407A1 - Oligonucleotide compositions and methods thereof - Google Patents

Info

Publication number

AU2021277407A1

AU2021277407A1 AU2021277407A AU2021277407A AU2021277407A1 AU 2021277407 A1 AU2021277407 A1 AU 2021277407A1 AU 2021277407 A AU2021277407 A AU 2021277407A AU 2021277407 A AU2021277407 A AU 2021277407A AU 2021277407 A1 AU2021277407 A1 AU 2021277407A1

Authority

AU

Australia

Prior art keywords

independently

optionally substituted

heteroatoms

oligonucleotide

optionally

Prior art date

2020-05-22

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.)

Pending

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• 108091034117 Oligonucleotide Proteins 0.000 title claims abstract description 737
• 239000000203 mixture Substances 0.000 title claims abstract description 129
• 238000000034 method Methods 0.000 title claims abstract description 61
• 235000000346 sugar Nutrition 0.000 claims abstract description 517
• JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Chemical class Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 claims abstract description 202
• 150000008163 sugars Chemical class 0.000 claims abstract description 135
• 238000002360 preparation method Methods 0.000 claims abstract description 13
• 125000005842 heteroatom Chemical group 0.000 claims description 348
• -1 substituted Chemical class 0.000 claims description 293
• IJGRMHOSHXDMSA-UHFFFAOYSA-N Atomic nitrogen Chemical compound N#N IJGRMHOSHXDMSA-UHFFFAOYSA-N 0.000 claims description 198
• 125000004429 atom Chemical group 0.000 claims description 164
• 229910052698 phosphorus Inorganic materials 0.000 claims description 164
• 125000001931 aliphatic group Chemical group 0.000 claims description 156
• 229910052757 nitrogen Inorganic materials 0.000 claims description 155
• 238000012986 modification Methods 0.000 claims description 145
• 125000002619 bicyclic group Chemical group 0.000 claims description 144
• OAICVXFJPJFONN-UHFFFAOYSA-N Phosphorus Chemical compound [P] OAICVXFJPJFONN-UHFFFAOYSA-N 0.000 claims description 138
• 125000002950 monocyclic group Chemical group 0.000 claims description 138
• 239000011574 phosphorus Substances 0.000 claims description 137
• 125000003367 polycyclic group Chemical group 0.000 claims description 121
• 150000001875 compounds Chemical class 0.000 claims description 113
• 230000004048 modification Effects 0.000 claims description 110
• 108020004707 nucleic acids Proteins 0.000 claims description 102
• 102000039446 nucleic acids Human genes 0.000 claims description 102
• 150000007523 nucleic acids Chemical class 0.000 claims description 99
• 239000002777 nucleoside Substances 0.000 claims description 98
• 150000003839 salts Chemical class 0.000 claims description 83
• 239000000126 substance Substances 0.000 claims description 75
• 125000000623 heterocyclic group Chemical group 0.000 claims description 74
• 125000001072 heteroaryl group Chemical group 0.000 claims description 73
• 125000003118 aryl group Chemical group 0.000 claims description 70
• 229910019142 PO4 Inorganic materials 0.000 claims description 65
• 239000010452 phosphate Substances 0.000 claims description 65
• RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical compound [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 claims description 64
• NBIIXXVUZAFLBC-UHFFFAOYSA-K phosphate Chemical compound [O-]P([O-])([O-])=O NBIIXXVUZAFLBC-UHFFFAOYSA-K 0.000 claims description 63
• 125000003835 nucleoside group Chemical group 0.000 claims description 59
• 125000002496 methyl group Chemical group [H]C([H])([H])* 0.000 claims description 58
• 230000000694 effects Effects 0.000 claims description 52
• 150000003833 nucleoside derivatives Chemical group 0.000 claims description 50
• 125000000325 methylidene group Chemical group [H]C([H])=* 0.000 claims description 46
• 125000002015 acyclic group Chemical group 0.000 claims description 44
• 125000004433 nitrogen atom Chemical group N* 0.000 claims description 44
• 229910052760 oxygen Inorganic materials 0.000 claims description 42
• 229920006395 saturated elastomer Polymers 0.000 claims description 41
• 229910052717 sulfur Inorganic materials 0.000 claims description 41
• 125000003729 nucleotide group Chemical group 0.000 claims description 38
• 125000004432 carbon atom Chemical group C* 0.000 claims description 36
• 230000008878 coupling Effects 0.000 claims description 35
• 125000000956 methoxy group Chemical group [H]C([H])([H])O* 0.000 claims description 35
• 238000010168 coupling process Methods 0.000 claims description 34
• 238000005859 coupling reaction Methods 0.000 claims description 34
• 229910052799 carbon Inorganic materials 0.000 claims description 33
• 125000005647 linker group Chemical group 0.000 claims description 32
• 239000002773 nucleotide Substances 0.000 claims description 32
• NINIDFKCEFEMDL-UHFFFAOYSA-N Sulfur Chemical compound [S] NINIDFKCEFEMDL-UHFFFAOYSA-N 0.000 claims description 25
• QVGXLLKOCUKJST-UHFFFAOYSA-N atomic oxygen Chemical compound [O] QVGXLLKOCUKJST-UHFFFAOYSA-N 0.000 claims description 25
• 239000001301 oxygen Substances 0.000 claims description 25
• 239000011593 sulfur Substances 0.000 claims description 25
• 125000004169 (C1-C6) alkyl group Chemical group 0.000 claims description 24
• 125000003161 (C1-C6) alkylene group Chemical group 0.000 claims description 24
• 125000004450 alkenylene group Chemical group 0.000 claims description 24
• 229910052736 halogen Inorganic materials 0.000 claims description 24
• 150000002367 halogens Chemical class 0.000 claims description 24
• 230000000295 complement effect Effects 0.000 claims description 20
• 229910052739 hydrogen Inorganic materials 0.000 claims description 20
• 239000001257 hydrogen Substances 0.000 claims description 20
• 125000000449 nitro group Chemical group [O-][N+](*)=O 0.000 claims description 19
• 238000002515 oligonucleotide synthesis Methods 0.000 claims description 18
• 230000014509 gene expression Effects 0.000 claims description 14
• 125000002887 hydroxy group Chemical group [H]O* 0.000 claims description 14
• 241001465754 Metazoa Species 0.000 claims description 13
• 108020004999 messenger RNA Proteins 0.000 claims description 13
• 150000001450 anions Chemical class 0.000 claims description 12
• 108090000623 proteins and genes Proteins 0.000 claims description 12
• 239000003795 chemical substances by application Substances 0.000 claims description 11
• 238000010511 deprotection reaction Methods 0.000 claims description 11
• XUIMIQQOPSSXEZ-UHFFFAOYSA-N Silicon Chemical compound [Si] XUIMIQQOPSSXEZ-UHFFFAOYSA-N 0.000 claims description 10
• 125000003277 amino group Chemical group 0.000 claims description 10
• 150000001720 carbohydrates Chemical group 0.000 claims description 10
• 229910052710 silicon Inorganic materials 0.000 claims description 10
• 239000010703 silicon Substances 0.000 claims description 10
• 239000008186 active pharmaceutical agent Substances 0.000 claims description 9
• 229910052711 selenium Inorganic materials 0.000 claims description 9
• 239000002253 acid Substances 0.000 claims description 8
• 125000004435 hydrogen atom Chemical class [H]* 0.000 claims description 8
• 210000000056 organ Anatomy 0.000 claims description 8
• 239000007787 solid Substances 0.000 claims description 8
• 241000282414 Homo sapiens Species 0.000 claims description 7
• 239000003937 drug carrier Substances 0.000 claims description 7
• 239000008194 pharmaceutical composition Substances 0.000 claims description 7
• 230000008685 targeting Effects 0.000 claims description 6
• YNAVUWVOSKDBBP-UHFFFAOYSA-N Morpholine Chemical group C1COCCN1 YNAVUWVOSKDBBP-UHFFFAOYSA-N 0.000 claims description 5
• 238000000746 purification Methods 0.000 claims description 5
• 102000004169 proteins and genes Human genes 0.000 claims description 4
• 230000002829 reductive effect Effects 0.000 claims description 4
• 238000005987 sulfurization reaction Methods 0.000 claims description 4
• 238000000099 in vitro assay Methods 0.000 claims description 3
• ZOXJGFHDIHLPTG-UHFFFAOYSA-N Boron Chemical compound [B] ZOXJGFHDIHLPTG-UHFFFAOYSA-N 0.000 claims description 2
• 229910052796 boron Inorganic materials 0.000 claims description 2
• WFDIJRYMOXRFFG-UHFFFAOYSA-N Acetic anhydride Chemical compound CC(=O)OC(C)=O WFDIJRYMOXRFFG-UHFFFAOYSA-N 0.000 claims 2
• 238000002955 isolation Methods 0.000 claims 2
• 230000009435 amidation Effects 0.000 claims 1
• 238000007112 amidation reaction Methods 0.000 claims 1
• 230000032050 esterification Effects 0.000 claims 1
• 238000005886 esterification reaction Methods 0.000 claims 1
• 125000003473 lipid group Chemical group 0.000 claims 1
• FAIAAWCVCHQXDN-UHFFFAOYSA-N phosphorus trichloride Chemical compound ClP(Cl)Cl FAIAAWCVCHQXDN-UHFFFAOYSA-N 0.000 claims 1
• 238000005516 engineering process Methods 0.000 abstract description 35
• 239000002585 base Substances 0.000 description 109
• 235000021317 phosphate Nutrition 0.000 description 64
• 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 54
• 230000007935 neutral effect Effects 0.000 description 50
• ISAKRJDGNUQOIC-UHFFFAOYSA-N Uracil Chemical compound O=C1C=CNC(=O)N1 ISAKRJDGNUQOIC-UHFFFAOYSA-N 0.000 description 42
• OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 42
• 125000000217 alkyl group Chemical group 0.000 description 41
• RWQNBRDOKXIBIV-UHFFFAOYSA-N thymine Chemical compound CC1=CNC(=O)NC1=O RWQNBRDOKXIBIV-UHFFFAOYSA-N 0.000 description 40
• QJGQUHMNIGDVPM-UHFFFAOYSA-N nitrogen group Chemical group [N] QJGQUHMNIGDVPM-UHFFFAOYSA-N 0.000 description 36
• 108020004414 DNA Proteins 0.000 description 35
• UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 description 32
• 108091032973 (ribonucleotides)n+m Proteins 0.000 description 31
• 208000035475 disorder Diseases 0.000 description 28
• 125000001424 substituent group Chemical group 0.000 description 27
• 201000010099 disease Diseases 0.000 description 26
• 125000001997 phenyl group Chemical group [H]C1=C([H])C([H])=C(*)C([H])=C1[H] 0.000 description 26
• YIMATHOGWXZHFX-WCTZXXKLSA-N (2r,3r,4r,5r)-5-(hydroxymethyl)-3-(2-methoxyethoxy)oxolane-2,4-diol Chemical compound COCCO[C@H]1[C@H](O)O[C@H](CO)[C@H]1O YIMATHOGWXZHFX-WCTZXXKLSA-N 0.000 description 21
• GFFGJBXGBJISGV-UHFFFAOYSA-N Adenine Chemical compound NC1=NC=NC2=C1N=CN2 GFFGJBXGBJISGV-UHFFFAOYSA-N 0.000 description 20
• 229940104302 cytosine Drugs 0.000 description 20
• 229940035893 uracil Drugs 0.000 description 20
• 229940113082 thymine Drugs 0.000 description 19
• HMFHBZSHGGEWLO-UHFFFAOYSA-N alpha-D-Furanose-Ribose Natural products OCC1OC(O)C(O)C1O HMFHBZSHGGEWLO-UHFFFAOYSA-N 0.000 description 18
• PYMYPHUHKUWMLA-LMVFSUKVSA-N Ribose Natural products OC[C@@H](O)[C@@H](O)[C@@H](O)C=O PYMYPHUHKUWMLA-LMVFSUKVSA-N 0.000 description 17
• 239000003814 drug Substances 0.000 description 17
• 125000001495 ethyl group Chemical group [H]C([H])([H])C([H])([H])* 0.000 description 15
• 229930024421 Adenine Natural products 0.000 description 14
• NYHBQMYGNKIUIF-UUOKFMHZSA-N Guanosine Chemical compound C1=NC=2C(=O)NC(N)=NC=2N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O NYHBQMYGNKIUIF-UUOKFMHZSA-N 0.000 description 14
• 229960000643 adenine Drugs 0.000 description 14
• OIRDTQYFTABQOQ-KQYNXXCUSA-N adenosine Chemical compound C1=NC=2C(N)=NC=NC=2N1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O OIRDTQYFTABQOQ-KQYNXXCUSA-N 0.000 description 14
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• 125000004437 phosphorous atom Chemical group 0.000 description 13
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• ASJSAQIRZKANQN-CRCLSJGQSA-N 2-deoxy-D-ribose Chemical class OC[C@@H](O)[C@@H](O)CC=O ASJSAQIRZKANQN-CRCLSJGQSA-N 0.000 description 11
• 125000000304 alkynyl group Chemical group 0.000 description 11
• 125000001797 benzyl group Chemical group [H]C1=C([H])C([H])=C(C([H])=C1[H])C([H])([H])* 0.000 description 11
• ZRALSGWEFCBTJO-UHFFFAOYSA-N guanidine group Chemical group NC(=N)N ZRALSGWEFCBTJO-UHFFFAOYSA-N 0.000 description 11
• 125000001183 hydrocarbyl group Chemical group 0.000 description 11
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• CHJJGSNFBQVOTG-UHFFFAOYSA-N N-methyl-guanidine Natural products CNC(N)=N CHJJGSNFBQVOTG-UHFFFAOYSA-N 0.000 description 9
• 108091093037 Peptide nucleic acid Proteins 0.000 description 9
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• NYHBQMYGNKIUIF-UHFFFAOYSA-N D-guanosine Natural products C1=2NC(N)=NC(=O)C=2N=CN1C1OC(CO)C(O)C1O NYHBQMYGNKIUIF-UHFFFAOYSA-N 0.000 description 7
• HMFHBZSHGGEWLO-SOOFDHNKSA-N D-ribofuranose Chemical compound OC[C@H]1OC(O)[C@H](O)[C@@H]1O HMFHBZSHGGEWLO-SOOFDHNKSA-N 0.000 description 7
• 230000008901 benefit Effects 0.000 description 7
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