Hepatitis D virus (HDV) iRNA compositions and methods of use thereof

• US 10,640,770 B2
• Filed: 05/10/2017
• Issued: 05/05/2020
• Est. Priority Date: 11/10/2014
• Status: Active Grant

• Current Assignee: Alnylam Pharmaceuticals Incorporated
• Original Assignee: Alnylam Pharmaceuticals Incorporated
• Inventors: Hinkle, Gregory, Sepp-Lorenzino, Laura, Jadhav, Vasant, Maier, Martin, Manoharan, Muthiah, Milstein, Stuart, Shulga Morskaya, Svetlana, Rajeev, Kallanthottathil G., Xu, Huilei
• Primary Examiner(s): McGarry, Sean
• Application Number:
  US15/591,558
• Publication Number:
  US 20170349901A1
• Time in Patent Office: 1,091 Days
• Field of Search: None
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61K 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61P 1/16 for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
• CPC Class Codes: A61P 31/02 Local antiseptics
• CPC Class Codes: A61P 31/14 for RNA viruses
• CPC Class Codes: A61P 31/20 for DNA viruses
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C12N 15/1131 against viruses
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/335 Modified T or U
• CPC Class Codes: C12N 2310/3515 Lipophilic moiety, e.g. cholesterol
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2310/3533 Halogen

Abstract

The present invention relates to RNAi agents, e.g., double-stranded RNAi agents, targeting the hepatitis D virus (HDV) genome, and methods of using such RNAi agents to inhibit expression of one or more HBV genes and methods of treating subjects having an HDV infection and/or HDV-associated disorder.

Claims

1. A double stranded ribonucleic acid (RNAi) agent for inhibiting expression of hepatitis D virus (HDV) in a cell, wherein said double stranded RNAi agent comprises a sense strand and an antisense strand forming a double-stranded region,

wherein the sense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from the nucleotide sequence of 5′

-AAGAAGAUCAAGAAACUUGAA-3′

(SEQ ID NO;

1963), and the antisense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from the nucleotide sequence of 5′

-UUCAAGUUUCUUGAUCUUCUU-3′

(SEQ ID NO;

2141),

wherein substantially all of the nucleotides of said sense strand and substantially all of the nucleotides of said antisense strand are modified nucleotides,

wherein said sense strand is conjugated to a ligand attached at the 3′

-terminus, and

wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.

2. The double stranded RNAi agent of claim 1, wherein all of the nucleotides of said sense strand and all of the nucleotides of said antisense strand are modified nucleotides.

3. The double stranded RNAi agent of claim 1, wherein at least one of said modified nucleotides is selected from the group consisting of a 3′

-terminal deoxy-thymine (dT) nucleotide, a 2′

-O-methyl modified nucleotide, a 2′

-fluoro modified nucleotide, a 2′

-deoxy-modified nucleotide, a locked nucleotide, an unlocked nucleotide, a conformationally restricted nucleotide, a constrained ethyl nucleotide, an abasic nucleotide, a 2′

-amino-modified nucleotide, a 2′

-O-allyl-modified nucleotide, 2′

-C-alkyl-modified nucleotide, 2′

-hydroxly-modified nucleotide, a 2′

-methoxyethyl modified nucleotide, a 2′

-O-alkyl-modified nucleotide, a morpholino nucleotide, a phosphoramidate, a non-natural base comprising nucleotide, a tetrahydropyran modified nucleotide, a 1,5-anhydrohexitol modified nucleotide, a cyclohexenyl modified nucleotide, a nucleotide comprising a phosphorothioate group, a nucleotide comprising a methylphosphonate group, a nucleotide comprising a 5′

-phosphate, and a nucleotide comprising a 5′

-phosphate mimic.

4. The double stranded RNAi agent of any claim 1, wherein at least one strand comprises a 3′

overhang of at least 1 nucleotide;

or at least 2 nucleotides.

5. The double stranded RNAi agent of claim 1, wherein the double-stranded region is 15-30 nucleotide pairs in length;

17-23 nucleotide pairs in length;

17-25 nucleotide pairs in length;

23-27 nucleotide pairs in length;

19-21 nucleotide pairs in length;

or 21-23 nucleotide pairs in length.

6. The double stranded RNAi agent of claim 1, wherein each strand is independently 15-30 nucleotides in length;

or 19-30 nucleotides in length.

7. The double stranded RNAi agent of claim 1, wherein the ligand is

8. The double stranded RNAi agent of claim 1, wherein the RNAi agent is conjugated to the ligand as shown in the following schematic

9. The double stranded RNAi agent of claim 1, wherein said RNAi agent is AD-70260.1.

11. A composition comprising two or more of the double stranded RNAi agents independently selected from the agents of claim 1 or 9.

14. A pharmaceutical composition comprising the double stranded RNAi agent of claim 1 or 10, or the composition of claim 12.

15. A method of inhibiting Hepatitis D virus (HDV) gene expression in a cell, the method comprising:

(a) contacting the cell with the double stranded RNAi agent of claim 1 or 10, or the composition of claim 12; and

(b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of an HDV gene, thereby inhibiting expression of the HDV gene in the cell.

16. A method of treating a subject having a Hepatitis D virus (HDV) infection, comprising administering to the subject a therapeutically effective amount of the double stranded RNAi agent of claim 1 or 10, or the composition of claim 12, thereby treating said subject.

17. The method of claim 16, wherein the double stranded RNAi agent is administered at a weight based dose of about 0.01 mg/kg to about 10 mg/kg or about 0.5 mg/kg to about 50 mg/kg;

a weight based dose of about 10 mg/kg to about 30 mg/kg;

a weight based dose of 3 mg/kg;

a weight based dose of about 10 mg/kg;

or a fixed dose of about 50 mg to 200 mg.

18. The method of claim 16, wherein the double stranded RNAi agent is administered subcutaneously;

or intravenously.

19. The method of claim 16, further comprising administering to the subject an additional therapeutic agent.

20. The double stranded RNAi agent of claim 1, wherein

the sense strand comprises 5′

-asAfsgaagauCfaAfgaAfaCfuugasa-3′

(SEQ ID NO;

     2319) and the antisense strand comprises 5′

-usUfscaaguuUfcUfugAfuCfuucusu-3′

(SEQ ID NO;

     2497),

wherein a, c, g, and u are 2′

-O-methyladenosine-3′

-phosphate, 2′

-O-methylcytidine-3′

-phosphate, 2′

-O-methylguanosine-3′

-phosphate, and 2′

-O-methyluridine-3′

-phosphate, respectively;

Af, Cf, Gf, and Uf are 2′

-fluoroadenosine-3′

-phosphate, 2′

-fluorocytidine-3′

-phosphate, 2′

-fluoroguanosine-3′

-phosphate, and 2′

-fluorouridine-3′

-phosphate, respectively; and

s is a phorphorothioate linkage.

22. A pharmaceutical composition comprising the composition of claim 11.

23. A method of inhibiting Hepatitis D virus (HDV) gene expression in a cell, the method comprising:

(a) contacting the cell with the composition of claim 11; and

(b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of an HDV gene, thereby inhibiting expression of the HDV gene in the cell.

24. A method of treating a subject having a Hepatitis D virus (HDV) infection, comprising administering to the subject a therapeutically effective amount of the pharmaceutical composition of claim 14, thereby treating said subject.

10. A double stranded RNAi agent for inhibiting expression of hepatitis D virus (HDV) in a cell, wherein said double stranded RNAi agent comprises a sense strand and an antisense strand forming a double-stranded region, wherein said sense strand comprises the nucleotide sequence of 5′

-AAGAAGAUCAAGAAACUUGAA-3′

(SEQ ID NO;

1963), and the antisense strand comprises the nucleotide sequence of 5′

-UUCAAGUUUCUUGAUCUUCUU-3′

(SEQ ID NO;

2141),

wherein substantially all of the nucleotides of said sense strand and substantially all of the nucleotides of said antisense strand are modified nucleotides,

wherein said sense strand is conjugated to a ligand attached at the 3′

-terminus, and

wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.

12. A composition for inhibiting expression of hepatitis D virus (HDV) in a cell, said composition comprising

(a) a first double-stranded RNAi agent comprising a first sense strand and a first antisense strand forming a double-stranded region,

wherein substantially all of the nucleotides of said first sense strand and substantially all of the nucleotides of said first antisense strand are modified nucleotides,

wherein said first sense strand is conjugated to a ligand attached at the 3′

-terminus, and

wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker; and

(b) a second double-stranded RNAi agent comprising a second sense strand and a second antisense strand forming a double-stranded region,

wherein substantially all of the nucleotides of said second sense strand and substantially all of the nucleotides of said second antisense strand are modified nucleotides,

wherein said second sense strand is conjugated to a ligand attached at the 3′

-terminus, and

wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker;

wherein the first sense strand comprises the nucleotide sequence of 5′

-AAGAAGAUCAAGAAACUUGAA-3′

(SEQ ID NO;

1963), and the second sense strand comprises the nucleotide sequence of any one of the sense strands of a duplex selected from the group consisting of

AD-70260.1, AD-70232.1, AD-70249.1, AD-70244.1, AD-70272.1, AD-70228.1, AD-70255.1, AD-70278.1, AD-70295.1, AD-67200.1, AD-67211.1, AD-67199.1, AD-67202.1, AD-67208.1, AD-67210.1, AD-70259.1, AD-70267.1, AD-70271.1, AD-70268.1, AD-70269.1, AD-70256.1, AD-70257.1, and AD-70275.1, and

wherein the first antisense strand comprises the nucleotide sequence of 5′

-UUCAAGUUUCUUGAUCUUCUU-3′

(SEQ ID NO;

2141), and the second antisense strand comprises the nucleotide sequence of any one of the antisense strands of a duplex selected from the group consisting of AD-70260.1, AD-70232.1, AD-70249.1, AD-70244.1, AD-70272.1, AD-70228.1, AD-70255.1, AD-70278.1, AD-70295.1, AD-67200.1, AD-67211.1, AD-67199.1, AD-67202.1, AD-67208.1, AD-67210.1, AD-70259.1, AD-70267.1, AD-70271.1, AD-70268.1, AD-70269.1, AD-70256.1, AD-70257.1, and AD-70275.1.

13. A double stranded RNAi agent comprising a sense strand and an antisense strand, wherein the sense strand comprises the nucleotide sequence of SEQ ID NO:

1963, and the antisense strand comprises the nucleotide sequence of SEQ ID NO;

2141.

21. A double stranded ribonucleic acid (RNAi) agent for inhibiting expression of hepatitis D virus (HDV) in a cell, wherein said double stranded RNAi agent comprises a sense strand and an antisense strand forming a double-stranded region,

wherein the sense strand comprises 5′

-asAfsgaagauCfaAfgaAfaCfuugasa-3′

(SEQ ID NO;

     2319) and the antisense strand comprises 5′

-usUfscaaguuUfcUfugAfuCfuucusu-3′

(SEQ ID NO;

     2497),

wherein a, c, g, and u are 2′

-O-methyladenosine-3′

-phosphate, 2′

-O-methylcytidine-3′

-phosphate, 2′

-O-methylguanosine-3′

-phosphate, and 2′

-O-methyluridine-3′

-phosphate, respectively;

Af, Cf, Gf, and Uf are 2′

-fluoroadenosine-3′

-phosphate, 2′

-fluorocytidine-3′

-phosphate, 2′

-fluoroguanosine-3′

-phosphate, and 2′

-fluorouridine-3′

-phosphate, respectively; and

s is a phorphorothioate linkage, and

wherein the 3′

end of the sense strand is conjugated to a ligand as shown in the following schematic