WO2022204430A1 - Double-stranded sirna having patterned chemical modifications - Google Patents

Double-stranded sirna having patterned chemical modifications Download PDF

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Publication number
WO2022204430A1
WO2022204430A1 PCT/US2022/021790 US2022021790W WO2022204430A1 WO 2022204430 A1 WO2022204430 A1 WO 2022204430A1 US 2022021790 W US2022021790 W US 2022021790W WO 2022204430 A1 WO2022204430 A1 WO 2022204430A1
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Prior art keywords
formula
sirna molecule
nucleotides
length
ribonucleoside
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English (en)
French (fr)
Inventor
Matthew Hassler
Daniel Curtis
Bruno GODINHO
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Atalanta Therapeutics Inc
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Atalanta Therapeutics Inc
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Priority to CA3214660A priority Critical patent/CA3214660A1/en
Priority to JP2023558979A priority patent/JP2024511473A/ja
Priority to EP22776673.0A priority patent/EP4313075A4/en
Priority to AU2022242899A priority patent/AU2022242899A1/en
Priority to US18/283,666 priority patent/US20240182892A1/en
Priority to CN202280037397.4A priority patent/CN117597133A/zh
Publication of WO2022204430A1 publication Critical patent/WO2022204430A1/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/713—Double-stranded nucleic acids or oligonucleotides
    • C—CHEMISTRY; METALLURGY
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/315—Phosphorothioates
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/321—2'-O-R Modification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/322—2'-R Modification
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/341—Gapmers, i.e. of the type ===---===
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/343—Spatial arrangement of the modifications having patterns, e.g. ==--==--==--
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/344—Position-specific modifications, e.g. on every purine, at the 3'-end
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/346—Spatial arrangement of the modifications having a combination of backbone and sugar modifications
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3515—Lipophilic moiety, e.g. cholesterol

Definitions

  • the sense strand includes a structure represented by Formula S2, wherein Formula S2 is, in the 5’-to-3’ direction:
  • the sense strand includes a structure represented by Formula S3, wherein Formula S3 is, in the 5’-to-3’ direction:
  • Formula S3 wherein A represents a 2’-0-Me ribonucleoside, B represents a 2’-F ribonucleoside, O represents a phosphodiester internucleoside linkage, and S represents a phosphorothioate internucleoside linkage.
  • the sense strand includes a structure represented by Formula S5, wherein Formula S5 is, in the 5’-to-3’ direction:
  • the sense strand includes a structure represented by Formula VII, wherein Formula VII is, in the 5’-to-3’ direction:
  • the length of the sense strand is 29 nucleotides. In some embodiments, the length of the sense strand is 30 nucleotides.
  • the antisense strand is 20 nucleotides in length and the sense strand is 17 nucleotides in length.
  • the antisense strand is 22 nucleotides in length and the sense strand is 22 nucleotides in length.
  • the antisense strand is 27 nucleotides in length and the sense strand is 17 nucleotides in length.
  • the antisense strand is 27 nucleotides in length and the sense strand is 22 nucleotides in length.
  • the antisense strand is 27 nucleotides in length and the sense strand is 23 nucleotides in length.
  • the antisense strand is 29 nucleotides in length and the sense strand is 14 nucleotides in length.
  • the antisense strand is 29 nucleotides in length and the sense strand is 21 nucleotides in length.
  • the antisense strand is 30 nucleotides in length and the sense strand is 17 nucleotides in length.
  • the ds-sRNA molecule also features a central block of about 11 to 13 modified ribonucleosides linked by phosphodiester internucleoside linkages flanked on the 5’ end and the 3’ end, or on the 5’ end only, by a block of 2 to 5 modified ribonucleosides linked by phosphorothioate internucleoside linkages.
  • antisense strand refers to the strand of the siRNA duplex that contains some degree of complementarity to the target gene.
  • sense strand refers to the strand of the siRNA duplex that contains complementarity to the antisense strand.
  • a benzyl group can be unsubstituted or substituted with one or more suitable substituents.
  • the substituent may replace an H of the phenyl component and/or an H of the methylene (-CH2-) component.
  • triazole refers to heterocyclic compounds with the formula (C 2 H3N3), having a five-membered ring of two carbons and three nitrogens, the positions of which can change resulting in multiple isomers.
  • guide RNAs refers to nucleic acids that have sequence complementarity to a specific sequence in the genome immediately or 1 base pair upstream of the protospacer adjacent motif (PAM) sequence as used in CRISPR/Cas9 gene editing systems.
  • PAM protospacer adjacent motif
  • amino acid refers to a molecule containing amine and carboxyl functional groups and a side chain specific to the amino acid.
  • a proper Watson-Crick base pair is referred to in this context as a “match,” while each unpaired nucleotide, and each incorrectly paired nucleotide, is referred to as a “mismatch.”
  • Alignment for purposes of determining percent nucleic acid sequence complementarity can be achieved in various ways that are within the capabilities of one of skill in the art, for example, using publicly available computer software such as BLAST, BLAST-2, or Megalign software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal complementarity over the full length of the sequences being compared.
  • the siRNA molecules disclosed herein may be branched siRNA molecules.
  • the siRNA molecule may not be branched, or may be di-branched, tri-branched, or tetra-branched, connected through a linker.
  • Each main branch may be further branched to allow for 2, 3, 4, 5, 6, 7, or 8 separate RNA single- or double-strands.
  • the branch points on the linker may stem from the same atom, or separate atoms along the linker.
  • any carbon or oxygen atom of the linker is optionally replaced with a nitrogen atom, bears a hydroxyl substituent, or bears an oxo substituent.
  • the linker is a poly-ethylene glycol (PEG) linker.
  • PEG linkers suitable for use with the disclosed compositions and methods include linear or non-linear PEG linkers. Examples of non-linear PEG linkers include branched PEGs, linear forked PEGs, or branched forked PEGs.
  • the linker has a structure of Formula L4, as is shown below:
  • the antisense strand has complementarity sufficient to hybridize to a region of any of the following genes: APOE, BIN1 , C1QA, C3, C90RF72,
  • E5. The siRNA molecule of E1 or E3, wherein j is from 1 to 5.
  • E17 The siRNA molecule of E16, wherein k is from 1 to 5.
  • siRNA molecule of any one of E1-E29, wherein the sense strand includes a structure represented by Formula III, wherein Formula III is, in the 5’-to-3’ direction:
  • Formula S1 wherein A represents a 2’-0-Me ribonucleoside, B represents a 2’-F ribonucleoside, O represents a phosphodiester internucleoside linkage, and S represents a phosphorothioate internucleoside linkage.
  • E51 The siRNA molecule of E47, wherein j is from 1 to 3.
  • E102 The siRNA molecule of E91 or E90, wherein j is 6.
  • E145 The siRNA molecule of E130, wherein n is from 1 to 4.
  • E152 The siRNA molecule of E130, wherein n is 5.
  • E177 The siRNA molecule of E176, wherein at least 50% of the ribonucleosides are 2’-0-Me ribonucleosides.
  • E204 The siRNA molecule of E203, wherein at least 40% of the internucleoside linkages are phosphodiester linkages or phosphorothioate linkages.
  • E207 The siRNA molecule of E206, wherein at least 70% of the internucleoside linkages are phosphodiester linkages or phosphorothioate linkages.
  • E216 The siRNA molecule of E215, wherein the nucleobase is an adenine, uracil, guanine, thymine, or cytosine.
  • E217 The siRNA molecule of E215 or E216, wherein the 5’ phosphorus stabilizing moiety is (E)- vinylphosphonate represented by Formula X.
  • siRNA molecule of E239 wherein the length of the sense strand is 27 nucleotides.

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PCT/US2022/021790 2021-03-24 2022-03-24 Double-stranded sirna having patterned chemical modifications Ceased WO2022204430A1 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
CA3214660A CA3214660A1 (en) 2021-03-24 2022-03-24 Double-stranded sirna having patterned chemical modifications
JP2023558979A JP2024511473A (ja) 2021-03-24 2022-03-24 パターン化化学修飾を有する二本鎖ｓｉｒｎａ
EP22776673.0A EP4313075A4 (en) 2021-03-24 2022-03-24 DOUBLE-STRANDED SIRNA WITH PATTERNED CHEMICAL MODIFICATIONS
AU2022242899A AU2022242899A1 (en) 2021-03-24 2022-03-24 Double-stranded sirna having patterned chemical modifications
US18/283,666 US20240182892A1 (en) 2021-03-24 2022-03-24 Double-stranded sirna having patterned chemical modifications
CN202280037397.4A CN117597133A (zh) 2021-03-24 2022-03-24 具有模式化化学修饰的双链siRNA

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US202163165543P 2021-03-24 2021-03-24
US63/165,543 2021-03-24

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AU (1) AU2022242899A1 (https=)
CA (1) CA3214660A1 (https=)
WO (1) WO2022204430A1 (https=)

Cited By (5)

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Publication number Priority date Publication date Assignee Title
WO2024073595A3 (en) * 2022-09-28 2024-05-16 Atalanta Therapeutics, Inc. Compositions and methods for treatment of huntington's disease
WO2024169770A1 (zh) * 2023-02-17 2024-08-22 苏州时安生物技术有限公司 一种抑制SCN9A基因表达的siRNA、其药物组合物及用途
WO2025085593A1 (en) * 2023-10-18 2025-04-24 University Of Massachusetts Oligonucleotides with ethylene glycol modification
WO2025108284A1 (en) * 2023-11-20 2025-05-30 Shanghai Argo Biopharmaceutical Co., Ltd. Compositions and methods for inhibiting expression of sodium voltage-gated channel alpha subunit 9 (scn9a)
WO2025196505A2 (en) 2024-03-22 2025-09-25 Takeda Pharmaceutical Company Limited Compositions and methods for inhibiting cytochrome p450 family 7 subfamily a member 1 (cyp7a1) expression

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US20190024082A1 (en) * 2017-06-23 2019-01-24 University Of Massachusetts Two-tailed self-delivering sirna
US20200385737A1 (en) * 2019-03-29 2020-12-10 University Of Massachusetts OLIGONUCLEOTIDE-BASED MODULATION OF C9orf72
US20210024926A1 (en) * 2015-04-03 2021-01-28 University Of Massachusetts Fully stabilized asymmetric sirna

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US10125369B2 (en) * 2012-12-05 2018-11-13 Alnylam Pharmaceuticals, Inc. PCSK9 iRNA compositions and methods of use thereof
EA201792263A1 (ru) * 2015-04-13 2018-08-31 Элнилэм Фармасьютикалз, Инк. КОМПОЗИЦИИ НА ОСНОВЕ iRNA ПРОТИВ АНГИОПОЭТИН-ПОДОБНОГО БЕЛКА 3 (ANGPTL3) И СПОСОБЫ ИХ ПРИМЕНЕНИЯ
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US20150267200A1 (en) * 2002-02-20 2015-09-24 Sirna Therapeutics, Inc. RNA INTERFERENCE MEDIATED INHIBITION OF GENE EXPRESSION USING CHEMICALLY MODIFIED SHORT INTERFERING NUCLEIC ACID (siNA)
US20210024926A1 (en) * 2015-04-03 2021-01-28 University Of Massachusetts Fully stabilized asymmetric sirna
US20190024082A1 (en) * 2017-06-23 2019-01-24 University Of Massachusetts Two-tailed self-delivering sirna
US20200385737A1 (en) * 2019-03-29 2020-12-10 University Of Massachusetts OLIGONUCLEOTIDE-BASED MODULATION OF C9orf72

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Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2024073595A3 (en) * 2022-09-28 2024-05-16 Atalanta Therapeutics, Inc. Compositions and methods for treatment of huntington's disease
WO2024169770A1 (zh) * 2023-02-17 2024-08-22 苏州时安生物技术有限公司 一种抑制SCN9A基因表达的siRNA、其药物组合物及用途
WO2025085593A1 (en) * 2023-10-18 2025-04-24 University Of Massachusetts Oligonucleotides with ethylene glycol modification
WO2025108284A1 (en) * 2023-11-20 2025-05-30 Shanghai Argo Biopharmaceutical Co., Ltd. Compositions and methods for inhibiting expression of sodium voltage-gated channel alpha subunit 9 (scn9a)
WO2025196505A2 (en) 2024-03-22 2025-09-25 Takeda Pharmaceutical Company Limited Compositions and methods for inhibiting cytochrome p450 family 7 subfamily a member 1 (cyp7a1) expression
US12553050B2 (en) 2024-03-22 2026-02-17 Takeda Pharmaceutical Company Limited Compositions and methods for inhibiting cytochrome P450 family 7 subfamily a member 1 (CYP7A1) expression

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US20240182892A1 (en) 2024-06-06
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JP2024511473A (ja) 2024-03-13
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AU2022242899A1 (en) 2023-11-09
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