Compositions for modulating C9ORF72 expression

• US 10,443,052 B2
• Filed: 10/15/2013
• Issued: 10/15/2019
• Est. Priority Date: 10/15/2012
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: Ionis Pharmaceuticals, Inc.
• Inventors: Freier, Susan M.
• Primary Examiner(s): McGarry, Sean
• Application Number:
  US14/436,024
• Publication Number:
  US 20150259679A1
• Time in Patent Office: 2,191 Days
• Field of Search: None
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/16 Anti-Parkinson drugs
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C12N 15/113 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 when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/313 Phosphorodithioates
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/3233 Morpholino-type ring
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: C12N 2310/3533 Halogen

Abstract

Disclosed herein are compositions and methods for reducing expression of C90RF72 mRNA and protein in an animal with C90RF72 specific inhibitors. Such methods are useful to treat, prevent, or ameliorate neurodegenerative diseases in an individual in need thereof. Such C90RF72 specific inhibitors include antisense compounds. Examples of neurodegenerative diseases that can be treated, prevented, and ameliorated with the administration C90RF72 specific inhibitors include amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), corticalbasal degeneration syndrome (CBD), atypical Parkinsonian syndrome, and olivopontocerellar degeneration (OPCD).

Claims

1. A compound comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising at least 8 contiguous nucleobases of SEQ ID NO:

300 or SEQ ID NO;

301, wherein the modified oligonucleotide comprises at least one modification selected from a modified sugar, a sugar surrogate, and a modified internucleoside linkage.

2. The compound of claim 1, wherein the nucleobase sequence of the modified oligonucleotide is 100% complementary to an equal length portion of a C9ORF72 nucleic acid.

3. The compound of claim 2, wherein the C9ORF72 nucleic acid has the nucleobase sequence of SEQ ID NO:

2.

4. The compound of claim 1, wherein the modified oligonucleotide is a single-stranded oligonucleotide.

5. The compound of claim 4, wherein the single-stranded modified oligonucleotide is a gapmer.

6. The compound of claim 1, wherein at least one internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

7. The compound of claim 6, wherein each internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

8. The compound of claims 6, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

9. The compound of claim 7, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

10. The compound of claim 1, wherein at least one nucleobase of the modified oligonucleotide is a modified nucleobase.

11. The compound of claim 10, wherein the modified nucleobase is a 5-methylcytosine.

12. The compound of claim 1, wherein at least one nucleoside of the modified oligonucleotide comprises a modified sugar.

13. The compound of claim 12, wherein each nucleoside of the modified oligonucleotide comprises a modified sugar.

14. The compound of claim 12, wherein at least one modified sugar is a bicyclic sugar.

15. The compound of claim 14, wherein each bicyclic sugar comprises a chemical bridge between the 4′

and 2′

positions of the sugar, wherein each chemical bridge is independently selected from;

4′

-CH(R)—

O-2′ and

4′

-(CH₂)₂—

O-2′

, wherein each R is independently selected from H, C₁-C₆ alkyl, and C₁-C₆ alkoxy.

16. The compound of claim 15, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is methyl.

17. The compound of claim 15, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is H.

18. The compound of claim 15, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is —

CH₂—

O—

CH₃.

19. The compound of claim 12, wherein at least one modified sugar comprises a 2′

-O-methoxyethyl group.

20. The compound of claim 12, wherein at least one modified sugar comprises a 2′

-O-methyl group.

21. The compound of claim 1, wherein the compound comprises a conjugate group.

22. A composition comprising a compound according to claim 1 and a pharmaceutically acceptable carrier or diluent.

23. The compound of claim 13, wherein each modified sugar comprises a 2′

-O-methoxyethyl group or a 2′

-O-methyl group.

24. The compound of claim 1, wherein the at least one nucleoside of the modified oligonucleotide comprises a sugar surrogate.

25. The compound of claim 24, wherein at least one sugar surrogate is a morpholino or a peptide nucleic acid.

26. A double-stranded compound comprising the compound of claim 1.

27. The double-stranded compound of claim 26, wherein the double-stranded compound comprises a conjugate group.

28. A modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising at least 8 contiguous nucleobases of SEQ ID NO:

300 or SEQ ID NO;

301,

wherein the modified oligonucleotide comprises at least one modification selected from a modified sugar, a sugar surrogate, and a modified internucleoside linkage.

29. The modified oligonucleotide of claim 28, wherein the nucleobase sequence of the oligonucleotide is 100% complementary to an equal length portion of a C9ORF72 nucleic acid.

30. The modified oligonucleotide of claim 29, wherein the C9ORF72 nucleic acid has the nucleobase sequence of SEQ ID NO:

2.

31. The modified oligonucleotide of claim 28, wherein at least one internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

32. The modified oligonucleotide of claim 28, wherein each internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.

33. The modified oligonucleotide of claims 31, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

34. The modified oligonucleotide of claim 32, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

35. The modified oligonucleotide of claim 28, wherein at least one modified sugar is a bicyclic sugar.

36. The modified oligonucleotide of claim 35, wherein each bicyclic sugar comprises a chemical bridge between the 4′

and 2′

positions of the sugar, wherein each chemical bridge is independently selected from;

4′

-CH(R)—

O-2′ and

4′

-(CH₂)₂—

O-2′

, wherein each R is independently selected from H, C₁-C₆ alkyl, and C₁-C₆ alkoxy.

37. The modified oligonucleotide of claim 36, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is methyl.

38. The modified oligonucleotide of claim 36, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is H.

39. The modified oligonucleotide of claim 36, wherein at least one chemical bridge is 4′

-CH(R)—

O-2′ and

wherein R is —

CH₂—

O—

CH₃.

40. The modified oligonucleotide of claims 28, wherein at least one modified sugar comprises a 2′

-O-methoxyethyl group.

41. The modified oligonucleotide of claim 28, wherein at least one modified sugar comprises a 2′

-O-methyl group.

42. A composition comprising a modified oligonucleotide according to claim 28 and a pharmaceutically acceptable carrier or diluent.

43. A compound comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising at least 8 contiguous nucleobases that are 100% complementary to an equal length portion of nucleobases 1552-1572 of SEQ ID NO:

2, wherein the nucleobase sequence of the modified oligonucleotide is at least 90% complementary to an equal length portion of SEQ ID NO;

2, and wherein the modified oligonucleotide comprises at least one modification selected from a modified sugar, a sugar surrogate, and a modified internucleoside linkage.

44. The compound of claim 43, wherein the nucleobase sequence of the modified oligonucleotide is 100% complementary to an equal length portion of SEQ ID NO:

2.

45. The compound of claim 44, wherein the modified oligonucleotide is a single-stranded oligonucleotide.

46. The compound of claim 45, wherein at least one internucleoside linkage is a modified internucleoside linkage.

47. The compound of claim 46, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

48. The compound of claim 46, wherein each internucleoside linkage of the single-stranded modified oligonucleotide is a phosphorothioate internucleoside linkage or a phosphodiester internucleoside linkage.

49. The compound of claim 45, wherein at least one nucleoside of the single-stranded modified oligonucleotide comprises a modified sugar.

50. The compound of claim 49, wherein at least one modified sugar comprises a 2′

-O-methyl group.

51. The compound of claim 49, wherein at least one modified sugar comprises a 2′

-O-methyoxyethyl group.

52. The compound of claim 49, wherein at least one modified sugar comprises a 2′

-O-methyl group and at least one modified sugar comprises a 2′

-O-methoxyethyl group.

53. The compound of claim 45, wherein the single-stranded modified oligonucleotide is a gapmer.

54. The compound of claim 53, wherein the gapmer is a 5-10-5 gapmer.

55. The compound of claim 54, wherein each nucleoside of the 5′

wing and each nucleoside of the 3′

wing of the gapmer comprises a modified sugar.

56. The compound of claim 55, wherein each modified sugar comprises a 2′

-O-methyl group or a 2′

-O-methyoxyethyl group.

57. The compound of claim 43, wherein the compound comprises a conjugate group.

58. A modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising at least 8 contiguous nucleobases that are 100% complementary to an equal length portion of nucleobases 1552-1572 of SEQ ID NO:

2, wherein the nucleobase sequence of the modified oligonucleotide is at least 90% complementary to an equal length portion of SEQ ID NO;

2, and wherein the modified oligonucleotide comprises at least one modification selected from a modified sugar, a sugar surrogate, and a modified internucleoside linkage.

59. The modified oligonucleotide of claim 58, wherein the nucleobase sequence of the modified oligonucleotide is 100% complementary to an equal length portion of SEQ ID NO:

2.

60. The compound of claim 59, wherein the modified oligonucleotide is a single-stranded oligonucleotide.

61. The compound of claim 60, wherein at least one internucleoside linkage is a modified internucleoside linkage.

62. The compound of claim 61, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

63. The compound of claim 61, wherein each internucleoside linkage of the modified oligonucleotide is a phosphorothioate internucleoside linkage or a phosphodiester internucleoside linkage.

64. The compound of claim 60, wherein at least one nucleoside of the single-stranded oligonucleotide comprises a modified sugar.

65. The compound of claim 64, wherein at least one modified sugar comprises a 2′

-O-methyl group.

66. The compound of claim 64, wherein at least one modified sugar comprises a 2′

-O-methyoxyethyl group.

67. The compound of claim 64, wherein at least one modified sugar comprises a 2′

-O-methyl group and at least one modified sugar comprises a 2′

-O-methoxyethyl group.

68. The modified oligonucleotide of claim 60, wherein the single-stranded modified oligonucleotide is a gapmer.

69. The compound of claim 68, wherein the gapmer is a 5-10-5 gapmer.

70. The compound of claim 69, wherein each nucleoside of the 5′

wing and each nucleoside of the 3′

wing of the gapmer comprises a modified sugar.

71. The compound of claim 70, wherein each modified sugar comprises a 2′

-O-methyl group or a 2′

-O-methyoxyethyl group.

72. A compound comprising a single-stranded modified oligonucleotide consisting of 20 linked nucleosides and having a nucleobase sequence comprising at least 8 contiguous nucleobases of SEQ ID NO:

300 or SEQ ID NO;

301, wherein the nucleobase sequence of the modified oligonucleotide is 100% complementary to an equal length portion of SEQ ID NO;

2, wherein each internucleoside linkage is a phosphorothioate internucleoside linkage or a phosphodiester internucleoside linkage, wherein the single-stranded modified oligonucleotide is a 5-10-5 gapmer, wherein each nucleoside of the 5′

wing and each nucleoside of the 3′

wing comprises a modified sugar; and

wherein each modified sugar comprises a 2′

-O-methyl group or a 2′

-O-methyoxyethyl group.

73. The compound of claim 72, wherein the modified oligonucleotide comprises at least 9 contiguous nucleobases of SEQ ID NO:

300.

74. The compound of claim 72, wherein the modified oligonucleotide comprises at least 10 contiguous nucleobases of SEQ ID NO:

300.

75. The compound of claim 72, wherein the modified oligonucleotide comprises at least 9 contiguous nucleobases of SEQ ID NO:

301.

76. The compound of claim 72, wherein the modified oligonucleotide comprises at least 10 contiguous nucleobases of SEQ ID NO:

301.

77. The compound of claim 72, wherein the compound comprises a conjugate group.

78. A single-stranded modified oligonucleotide consisting of 20 linked nucleosides and having a nucleobase sequence comprising at least 8 contiguous nucleobases of SEQ ID NO:

300 or SEQ ID NO;

301, wherein the nucleobase sequence of the modified oligonucleotide is 100% complementary to an equal length portion of SEQ ID NO;

2, wherein each internucleoside linkage is a phosphorothioate internucleoside linkage or a phosphodiester internucleoside linkage, wherein the single-stranded modified oligonucleotide is a 5-10-5 gapmer, wherein each nucleoside of the 5′

wing and each nucleoside of the 3′

wing comprises a modified sugar; and

wherein each modified sugar comprises a 2′

-O-methyl group or a 2′

-O-methyoxyethyl group.

79. The compound of claim 78, wherein the modified oligonucleotide comprises at least 9 contiguous nucleobases of SEQ ID NO:

300.

80. The compound of claim 78, wherein the modified oligonucleotide comprises at least 10 contiguous nucleobases of SEQ ID NO:

300.

81. The compound of claim 78, wherein the modified oligonucleotide comprises at least 9 contiguous nucleobases of SEQ ID NO:

301.

82. The compound of claim 78, wherein the modified oligonucleotide comprises at least 10 contiguous nucleobases of SEQ ID NO:

301.