WO2021081026A1 - Complement component c3 irna compositions and methods of use thereof - Google Patents

Complement component c3 irna compositions and methods of use thereof Download PDF

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WO2021081026A1
WO2021081026A1 PCT/US2020/056563 US2020056563W WO2021081026A1 WO 2021081026 A1 WO2021081026 A1 WO 2021081026A1 US 2020056563 W US2020056563 W US 2020056563W WO 2021081026 A1 WO2021081026 A1 WO 2021081026A1
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nucleotide
nucleotides
ome
antisense strand
strand
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French (fr)
Inventor
Mark Keating
James D. MCININCH
Kristina YUCIUS
Charalambos KAITTANIS
Adam CASTORENO
Sarah SOLOMON
Elane FISHILEVICH
Mark K. SCHLEGEL
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Alnylam Pharmaceuticals Inc
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Alnylam Pharmaceuticals Inc
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Priority to CA3158320A priority Critical patent/CA3158320A1/en
Priority to AU2020369515A priority patent/AU2020369515A1/en
Priority to JP2022523709A priority patent/JP7676377B2/ja
Priority to CN202080083674.6A priority patent/CN115176004A/zh
Priority to IL292360A priority patent/IL292360A/en
Priority to EP20803407.4A priority patent/EP4048793A1/en
Priority to KR1020227017181A priority patent/KR20220084399A/ko
Priority to BR112022007540A priority patent/BR112022007540A2/pt
Priority to MX2022004726A priority patent/MX2022004726A/es
Application filed by Alnylam Pharmaceuticals Inc filed Critical Alnylam Pharmaceuticals Inc
Publication of WO2021081026A1 publication Critical patent/WO2021081026A1/en
Priority to US17/721,530 priority patent/US12365896B2/en
Anticipated expiration legal-status Critical
Priority to US18/594,132 priority patent/US12258565B2/en
Priority to JP2025075152A priority patent/JP2025131567A/ja
Priority to US19/236,016 priority patent/US20260049312A1/en
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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • 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
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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
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/66—General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
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    • C12N2310/00—Structure or type of the nucleic acid
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
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    • C12N2310/3125—Methylphosphonates
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    • C12N2310/00—Structure or type of the nucleic acid
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    • C12N2310/315—Phosphorothioates
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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
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
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    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate

Definitions

  • the present invention provides iRNA compositions which affect the RNA-induced silencing complex (RISC)-mediated cleavage of RNA transcripts of a gene encoding complement component C3.
  • RISC RNA-induced silencing complex
  • the complement component C3 may be within a cell, e.g., a cell within a subject, such as a human subject.
  • the antisense strand comprises at least 15 contiguous nucleotides differing by nor more than 0, 1, 2, or 3 nucleotides from any one of the antisense strand nucleotide sequences of a duplex selected from the group consisting of AD-565541.2, AD-564742, AD-567304, AD-568978, AD-569164, AD-569272.2, AD-569765.2, AD-564730.2, AD-567315, AD-564745.2, AD-571715.2, AD-570714, AD-571826, AD-572041.2, AD-572039.2, AD-572387, AD-568586.2, AD-566837.2, AD-566444.2, AD-567700.2, AD-567814.2, AD-568003.2, AD-569164.2, AD- 569763.2, AD-565281.2, AD-571539.2, AD-572389.2, AD-567315.2, AD-571752.2, AD-568026.2, AD-571298, AD-57
  • substantially all of the nucleotides of the sense strand; substantially all of the nucleotides of the antisense strand comprise a modification; or substantially all of the nucleotides of the sense strand and substantially all of the nucleotides of the antisense strand comprise a modification. In one embodiment, all of the nucleotides of the sense strand comprise a modification; all of the nucleotides of the antisense strand comprise a modification; or all of the nucleotides of the sense strand and all of the nucleotides of the antisense strand comprise a modification.
  • the present invention provides iRNA compositions which effect the RNA-induced silencing complex (RISC)-mediated cleavage of RNA transcripts of a complement component C3 gene.
  • the gene may be within a cell, e.g., a cell within a subject, such as a human.
  • RISC RNA-induced silencing complex
  • the use of these iRNAs enables the targeted degradation of mRNAs of the corresponding gene (complement component C3 gene) in mammals.
  • the iRNAs of the invention have been designed to target the human complement component C3 gene, including portions of the gene that are conserved in the complement component C3 orthologs of other mammalian species.
  • NM_000064.3 (GI:726965399; SEQ ID NO:1); mouse C3, the amino acid and nucleotide sequence of which may be found in, for example, GenBank Accession No. NM_009778.3 (GI:773669943; SEQ ID NO:2); and rat C3, the amino acid and nucleotide sequence of which may be found in, for example, GenBank Accession No. NM_016994.2 (GI:158138560; SEQ ID NO:3).
  • C3 also includes Macaca fascicularis C3, the amino acid and nucleotide sequence of which may be found in, for example, GenBank Accession No.
  • cleavage region refers to a region that is located immediately adjacent to the cleavage site.
  • the cleavage site is the site on the target at which cleavage occurs.
  • the cleavage region comprises three bases on either end of, and immediately adjacent to, the cleavage site.
  • the cleavage region comprises two bases on either end of, and immediately adjacent to, the cleavage site.
  • the sense and antisense strands are selected from any one of duplexes AD-1181519, AD-569268, or AD-570714.
  • the dulex is AD-570714.
  • an “iRNA” includes ribonucleotides with chemical modifications. Such modifications may include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a dsRNA molecule, are encompassed by “iRNA” for the purposes of this specification and claims.
  • an agent for use in the methods and compositions of the invention is a single-stranded antisense oligonucleotide molecule that inhibits a target mRNA via an antisense inhibition mechanism.
  • treating refers to a beneficial or desired result, such as reducing at least one sign or symptom of a complement component C3-associated disorder, e.g., hemolysis in a subject.
  • Treatment also includes a reduction of one or more sign or symptoms associated with unwanted complement component C3 expression, e.g., hemolysis; diminishing the extent of unwanted complement component C3 activation or stabilization; amelioration or palliation of unwanted complement component C3 activation or stabilization.
  • Treatment can also mean prolonging survival as compared to expected survival in the absence of treatment.
  • complement component C3-associated disease or “C3-associated disease,” is a disease or disorder that would benefit from reduction in complement component C3 expression.
  • Patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Patent Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, the entire contents of each of which are hereby incorporated herein by reference.
  • RNA molecules can include N- (acetylaminocaproyl)-4-hydroxyprolinol (Hyp-C6-NHAc), N-(caproyl-4-hydroxyprolinol (Hyp-C6), N-(acetyl-4-hydroxyprolinol (Hyp-NHAc), thymidine-2'-0-deoxythymidine (ether), N- (aminocaproyl)-4-hydroxyprolinol (Hyp-C6-amino), 2-docosanoyl-uridine-3"- phosphate, inverted base dT(idT) and others.
  • the asymmetric blunt end at the 5’-end of the antisense strand and 3’-end overhang of the antisense strand favor the guide strand loading into RISC process.
  • the dsRNAi agent is a double ended bluntmer of 19 nucleotides in length, wherein the sense strand contains at least one motif of three 2’-F modifications on three consecutive nucleotides at positions 7, 8, 9 from the 5’end.
  • the antisense strand contains at least one motif of three 2’-O-methyl modifications on three consecutive nucleotides at positions 11, 12, 13 from the 5’end.
  • the sense strand of the dsRNAi agent may contain at least one motif of three identical modifications on three consecutive nucleotides at the cleavage site of the strand; and the antisense strand may have at least one motif of three identical modifications on three consecutive nucleotides at or near the cleavage site of the strand.
  • the alternating motif in the sense strand may start with “AABBAABB” from 5’ to 3’ of the strand and the alternating motif in the antisense strand may start with “BBAABBAA” from 5’ to 3’ of the strand within the duplex region, so that there is a complete or partial shift of the modification patterns between the sense strand and the antisense strand.
  • the phosphorothioate or methylphosphonate internucleotide linkage modification may occur on any nucleotide of the sense strand, antisense strand, or both strands in any position of the strand.
  • the internucleotide linkage modification may occur on every nucleotide on the sense strand or antisense strand; each internucleotide linkage modification may occur in an alternating pattern on the sense strand or antisense strand; or the sense strand or antisense strand may contain both internucleotide linkage modifications in an alternating pattern.
  • each Na’ independently represents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
  • Each of X′, Y′ and Z′ may be the same or different from each other.
  • a cyclic carrier may be a carbocyclic ring system, i.e., all ring atoms are carbon atoms, or a heterocyclic ring system, i.e., one or more ring atoms may be a heteroatom, e.g., nitrogen, oxygen, sulfur.
  • the cyclic carrier may be a monocyclic ring system, or may contain two or more rings, e.g. fused rings.
  • the cyclic carrier may be a fully saturated ring system, or it may contain one or more double bonds.
  • the ligand may be attached to the polynucleotide via a carrier.
  • T1 is at the cleavage site of the sense strand. In one example, T1 is at position 11 from the 5’ end of the sense strand, when the sense strand is 19-22 nucleotides in length, and n 2 is 1. In an exemplary embodiment, T1 is at the cleavage site of the sense strand at position 11 from the 5’ end of the sense strand, when the sense strand is 19-22 nucleotides in length, and n 2 is 1, In one embodiment, T2’ starts at position 6 from the 5’ end of the antisense strand. In one example, T2’ is at positions 6-10 from the 5’ end of the antisense strand, and q 4 is 1.
  • n 4 is 0, B3 is 2’-OMe, n 5 is 3, B1’ is 2’-OMe or 2’-F, q 1 is 9, T1’ is 2’-F, q 2 is 1, B2’ is 2’-OMe or 2’-F, q 3 is 4, T2’ is 2’-F, q 4 is 1, B3’ is 2’-OMe or 2’-F, q 5 is 6, T3’ is 2’-F, q 6 is 1, B4’ is 2’-OMe, and q 7 is 1; with two phosphorothioate internucleotide linkage modifications within positions 1-5 of the sense strand (counting from the 5’-end of the sense strand), and two phosphorothioate internucleotide linkage modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage modifications within positions 18-23 of the antisense strand (counting from the 5’-end of the antisense strand).
  • B1 is 2’-OMe or 2’-F
  • n 1 8 T1 is 2’F
  • n 2 3
  • B2 is 2’-OMe
  • n 3 7
  • n 4 is 0,
  • B3 is 2’OMe
  • n 5 3
  • B1’ is 2’-OMe or 2’-F
  • q 1 9
  • T1’ is 2’-F
  • q 2 1, B2’ is 2’-OMe or 2’-F
  • q 4 1, B3’ is 2’-OMe or 2’-F
  • q 5 6
  • T3’ is 2’-F
  • q 7 1
  • B1 is 2’-OMe or 2’-F
  • n 1 8 T1 is 2’F
  • n 2 3
  • B2 is 2’-OMe
  • n 3 7
  • n 4 0,
  • B3 2’OMe
  • n 5 3
  • B1’ is 2’-OMe or 2’-F
  • q 1 9
  • T1’ is 2’-F
  • q 2 1, B2’ is 2’-OMe or 2’-F
  • q 3 5, T2’ is 2’-F
  • q 4 1, B3’ is 2’-OMe or 2’-F
  • q 5 5
  • T3’ 2’-F
  • q 7 is 1; optionally with at least 2 additional TT at the 3’-end of the antisense strand.
  • the RNAi agent also comprises a 5’-P.
  • B1 is 2’-OMe or 2’-F
  • n 1 8
  • T1 is 2’F
  • n 2 3
  • B2 is 2’-OMe
  • n 3 7, n 4 is 0,
  • B3 is 2’-OMe
  • n 5 3
  • B1’ is 2’-OMe or 2’-F
  • q 1 9
  • T1’ is 2’-F
  • q 2 1, B2’ is 2’-OMe or 2’-F
  • q 3 4, T2’ is 2’-F, q 4 is 2,
  • B3’ is 2’-OMe or 2’-F
  • q 5 5
  • T3’ is 2’-F
  • q 7 1; with two phosphorothioate internucleotide linkage modifications within position 1-5 of the sense strand (counting from the 5’-end of the sense strand
  • the RNAi agent also comprises a 5’- VP (e.g., a 5’-E-VP, 5’-Z-VP, or combination thereof) and a targeting ligand.
  • a 5’-VP e.g., a 5’-E-VP, 5’-Z-VP, or combination thereof
  • the 5’-VP is at the 5’-end of the antisense strand
  • the targeting ligand is at the 3’-end of the sense strand.
  • the GalNAc or GalNAc derivative is attached to an iRNA agent of the invention via a trivalent linker.
  • the double stranded RNAi agents of the invention comprise one or more GalNAc or GalNAc derivative attached to the iRNA agent.
  • the GalNAc may be attached to any nucleotide via a linker on the sense strand or antsisense strand.
  • the GalNac may be attached to the 5’-end of the sense strand, the 3’ end of the sense strand, the 5’-end of the antisense strand, or the 3’ – end of the antisense strand.
  • Acids Res., 1990, 18:3777 a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14:969), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36:3651), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264:229), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277:923).
  • RNA interference has also shown success with local delivery to the CNS by direct injection (Dorn, G., et al. (2004) Nucleic Acids 32:e49; Tan, PH., et al (2005) Gene Ther.12:59-66; Makimura, H., et al (2002) BMC Neurosci.3:18; Shishkina, GT., et al (2004) Neuroscience 129:521-528; Thakker, ER., et al (2004) Proc. Natl. Acad. Sci. U.S.A. 101:17270-17275; Akaneya,Y., et al (2005) J. Neurophysiol.93:594-602).
  • the constructs can include viral sequences for transfection, if desired.
  • the construct can be incorporated into vectors capable of episomal replication, e.g. EPV and EBV vectors.
  • Constructs for the recombinant expression of an iRNA will generally require regulatory elements, e.g., promoters, enhancers, etc., to ensure the expression of the iRNA in target cells.
  • regulatory elements e.g., promoters, enhancers, etc.
  • a single dose of the pharmaceutical compositions of the invention is administered quarterly (i.e., about every three months). In other embodiments of the invention, a single dose of the pharmaceutical compositions of the invention is administered twice per year (i.e., about once every six months).
  • treatment of a subject with a prophylactically or therapeutically effective amount, as appropriate, of a composition can include a single treatment or a series of treatments.
  • Emulsions are often biphasic systems comprising two immiscible liquid phases intimately mixed and dispersed with each other.
  • the complement component C3 gene may be a wild-type complement component C3 gene, a mutant complement component C3 gene, or a transgenic complement component C3 gene in the context of a genetically manipulated cell, group of cells, or organism.
  • “Inhibiting expression of a complement component C3 gene” includes any level of inhibition of a complement component C3 gene, e.g., at least partial suppression of the expression of a complement component C3 gene.
  • the expression of the complement component C3 gene may be assessed based on the level, or the change in the level, of any variable associated with complement component C3 gene expression, e.g., complement component C3 mRNA level or complement component C3 protein level.
  • expression level is determined by the method provided in Example 2 using, e.g., a 10nM siRNA concentration, in the species matched cell line.
  • the expression levels of complement component C3 mRNA may be monitored using a membrane blot (such as used in hybridization analysis such as northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See U.S. Patent Nos.5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are incorporated herein by reference.
  • the determination of complement component C3 expression level may also comprise using nucleic acid probes in solution.
  • the cell may be contacted with the siRNA in vitro or in vivo, i.e., the cell may be within a subject.
  • a cell suitable for treatment using the methods of the invention may be any cell that expresses a complement component C3 gene, e.g., a liver cell, a brain cell, a gall bladder cell, a heart cell, or a kidney cell, but preferably a liver cell.
  • the present invention further provides methods of treatment in a subject in need thereof, e.g., a subject diagnosed with a complement component C3-associated disorder, such as, cold agglutinin disease (CAD), warm autoimmune hemolytic anemia, and paroxysmal nocturnal hemoglobinuria (PNH), lupis nephritis (LN), bullous pemphigoid, pemphigus, e.g., pemphigus vulgaris (PV) and pemphigus foliaceus (PF), or C3 glomerulopathy.
  • CAD cold agglutinin disease
  • PNH paroxysmal nocturnal hemoglobinuria
  • LN paroxysmal nocturnal hemoglobinuria
  • LN lupis nephritis
  • bullous pemphigoid e.g., pemphigus vulgaris (PV) and pemphigus foliaceus (PF)
  • C3 glomerulopathy
  • kits for performing any of the methods of the invention include one or more dsRNA agent(s) and instructions for use, e.g., instructions for administering a prophylactically or therapeutically effective amount of a dsRNA agent(s).
  • the dsRNA agent may be in a vial or a pre-filled syringe.
  • RNA Synthesis Source of reagents Where the source of a reagent is not specifically given herein, such reagent can be obtained from any supplier of reagents for molecular biology at a quality/purity standard for application in molecular biology.
  • siRNA Design siRNAs targeting the human complement component C3 (C3) gene (human: NCBI refseqID NM_000064.3; NCBI GeneID: 718) were designed using custom R and Python scripts.
  • the human NM_000064.3 REFSEQ mRNA has a length of 5148 bases.
  • RNA isolation was performed using DYNABEADS. Briefly, cells are lysed in 10 ⁇ l of Lysis/Binding Buffer containing 3 ⁇ L of beads per well are mixed for 10 minutes on an electrostatic shaker. The washing steps are automated on a Biotek EL406, using a magnetic plate support.

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