Amyloid precursor protein (APP) RNAi agent compositions and methods of use thereof

Patent metadata

Field	Value
Publication number	US-11034957-B2
Application number	US-202016925286-A
Country	US
Kind code	B2
Filing date	Jul 9, 2020
Priority date	Dec 19, 2018
Publication date	Jun 15, 2021
Grant date	Jun 15, 2021

Abstract

The disclosure relates to double stranded ribonucleic acid (dsRNAi) agents and compositions targeting the APP gene, as well as methods of inhibiting expression of an APP gene and methods of treating subjects having an APP-associated disease or disorder, such as cerebral amyloid angiopathy (CAA) and early onset familial Alzheimer disease (EOFAD or eFAD), using such dsRNAi agents and compositions.

First claim

We claim:

1. A double stranded ribonucleic acid (RNAi) agent for inhibiting expression of an amyloid precursor protein (APP) gene, comprising:
(a) a sense strand comprising the nucleotide sequence of 5′-GGCUACGAAAAUCCAACCUAA-3′ (SEQ ID NO: 2735), wherein the sense strand comprises one or more lipophilic moieties conjugated to one or more non-terminal nucleotide positions excluding positions 9-12, wherein the 5′ terminal G of SEQ ID NO: 2735 is position 1; and
(b) an antisense strand comprising the nucleotide sequence of 5′-UUAGGUTGGAUTUUCGUAGCCGU-3′ (SEQ ID NO:2743);
wherein the double stranded RNAi agent comprises at least one modified nucleotide.

2. The double stranded RNAi agent of claim 1 , wherein the sense strand and the antisense strand each are 30 nucleotides or less in length.

3. The double stranded RNAi agent of claim 1 , wherein a plurality of the nucleotides of the sense strand, the antisense strand, or both the sense strand and the antisense strand are modified nucleotides.

4. The double stranded RNAi agent of claim 3 , wherein substantially all of the nucleotides of the sense strand, the antisense strand, or both the sense strand and the antisense strand are modified nucleotides.

5. The double stranded RNAi agent of claim 1 , wherein the at least one modified nucleotide is selected from the group consisting of a 2′-O-methyl modification, a 2′-deoxy modification, a glycol nucleic acid (GNA), and a 2′-fluoro modification.

6. The double stranded RNAi agent of claim 1 , further comprising 6-8 phosphorothioate internucleotide linkages.

7. The double stranded RNAi agent of claim 1 , wherein at least one strand comprises a 3′ overhang of at least 2 nucleotides or the antisense strand comprises a 3′ overhang of at least 2 nucleotides.

8. The double stranded RNAi agent of claim 1 , wherein the one or more non-terminal nucleotide positions of the sense strand have the following structure:

wherein B is a nucleotide base or a nucleotide base analog.

9. The double stranded RNAi agent of claim 1 , wherein the antisense strand comprises one or more lipophilic moieties conjugated to one or more non-terminal nucleotide positions.

10. The double stranded RNAi agent of claim 1 , wherein the one or more lipophilic moieties are conjugated to any of positions 4-8 of the sense strand counting from the 5′ end of the sense strand.

11. The double stranded RNAi agent of claim 1 , further comprising a phosphate or a phosphate mimic or a 5′-vinyl phosphonate (VP) group at the 5′-end of the antisense strand.

12. The double stranded RNAi agent of claim 1 , further comprising a 5′-vinyl phosphonate (VP) group at the 5′-end of the antisense strand.

13. The double stranded RNAi agent of claim 1 , wherein the one or more lipophilic moieties is one lipophilic moiety conjugated to one nucleotide position selected from the group consisting of positions 4, 6, 7, and 8 of the sense strand counting from the 5′-end of the sense strand.

14. The double stranded RNAi agent of claim 1 , wherein the one or more lipophilic moieties are only conjugated to one or more of positions 5, 6, 7, 15, and 17 on the sense strand.

15. The double stranded RNAi agent of claim 1 , wherein the sense strand comprises the modified nucleotide sequence of 5′-gsgscua(Chd)gadAadAuccaaccusasa-3′ (SEQ ID NO:2734) and the antisense strand comprises the modified nucleotide sequence of 5′-VPusUfsaggu(Tgn)ggaudTuUfcdGuagccsgsu-3′ (SEQ ID NO:2742), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, and U; s is a phosphorothioate linkage; Uf is 2′-fluoro U; dA, dG, and dT are 2′-deoxy A, G, and T; (Chd) is 2′-O-hexadecyl-cytidine-3′-phosphate; (Tgn) is Thymidine-glycol nucleic acid (GNA)S-Isomer; and VP is 5′-vinyl phosphonate.

16. A pharmaceutical composition for inhibiting expression of an APP gene comprising the double stranded RNAi agent of claim 15 .

17. The double stranded RNAi agent of claim 1 , wherein:
the sense strand consists of the modified nucleotide sequence of 5′-gsgscua(Chd)gadAadAuccaaccusasa-3′ (SEQ ID NO:2734) and;
the antisense strand consists of the modified nucleotide sequence of 5′-VPusUfsaggu(Tgn)ggaudTuUfcdGuagccsgsu-3′ (SEQ ID NO:2742),
wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, and U; s is a phosphorothioate linkage; Uf is 2′-fluoro U; dA, dG, and dT are 2′-deoxy A, G, and T; (Chd) is 2′-O-hexadecyl-cytidine-3′-phosphate; (Tgn) is Thymidine-glycol nucleic acid (GNA)S-Isomer; and VP is 5′-vinyl phosphonate.

18. A pharmaceutical composition for inhibiting expression of an amyloid precursor protein (APP) gene comprising the double stranded RNAi agent of claim 17 .

19. A method of inhibiting expression of an amyloid precursor protein (APP) gene in a cell, the method comprising:
(a) contacting the cell with the pharmaceutical composition of claim 16 ; and
(b) maintaining the cell of step (a) in contact with the pharmaceutical composition for a time sufficient to degrade mRNA transcripts of the APP gene, thereby inhibiting expression of the APP gene in the cell.

20. The method of claim 19 , wherein the APP expression is inhibited by at least about 30%.

21. The method of claim 19 , wherein the cell is within a subject.

22. The method of claim 21 , wherein the pharmaceutical composition is administered to the subject intrathecally.

23. The method of claim 21 , wherein the subject suffers from an APP-associated disorder.

24. The method of claim 23 , wherein the APP-associated disorder is selected from the group consisting of a cerebral amyloid angiopathy (CAA), an early onset familial Alzheimer disease (EOFAD), and an Alzheimer's disease (AD).

25. A method of inhibiting expression of an amyloid precursor protein (APP) gene in a cell, the method comprising:
(a) contacting the cell with the pharmaceutical composition of claim 18 ; and
(b) maintaining the cell of step (a) in contact with the pharmaceutical composition for a time sufficient to obtain degradation of the mRNA transcript of an APP gene, thereby inhibiting expression of the APP gene in the cell.

26. The method of claim 25 , wherein the APP expression is inhibited by at least about 30%.

27. The method of claim 26 , wherein the cell is within a subject.

28. The method of claim 27 , wherein the pharmaceutical composition is administered to the subject intrathecally.

29. The method of claim 27 , wherein the subject suffers from an APP-associated disorder.

30. The method of claim 29 , wherein the APP-associated disease is cerebral amyloid angiopathy (CAA), early onset familial Alzheimer disease (EOFAD), or Alzheimer's disease (AD).

Assignees

• Alnylam Pharmaceuticals Inc

Inventors

• Milstein Stuart
• Brown Kirk
• Nair Jayaprakash
• Maier Martin
• Jadhav Vasant
• Keating Mark
• Castoreno Adam
• Haslett Patrick
• Soundarapandian Mangala Meenakshi
• Fitzgerald Kevin

Classifications

• C12N2310/3533

  Halogen · CPC title

• C12N2310/3521

  Methyl · CPC title

• C12N2310/3515

  Lipophilic moiety, e.g. cholesterol · CPC title

• C12N2310/322

  2'-R Modification · CPC title

• C12N2310/321

  2'-O-R Modification · CPC title