Compositions and methods for modulating apolipoprotein (a) expression

• US 9,957,504 B2
• Filed: 08/28/2015
• Issued: 05/01/2018
• Est. Priority Date: 05/01/2013
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: Ionis Pharmaceuticals, Inc.
• Inventors: Prakash, Thazha P., Seth, Punit P., Swayze, Eric E., Graham, Mark J.
• Primary Examiner(s): McIntosh, III, Traviss C
• Application Number:
  US14/839,580
• Publication Number:
  US 20160090596A1
• Time in Patent Office: 977 Days
• Field of Search: None
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61K 47/549 Sugars, nucleosides, nucleotides or nucleic acids
• CPC Class Codes: A61K 47/59 obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• 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 15/1137 against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/113 targeting other non-coding nucleic acids, e.g. antagomirs
• CPC Class Codes: C12N 2310/17 Immunomodulatory nucleic acids
• CPC Class Codes: C12N 2310/31 of the backbone
• 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 2310/3231 having an additional ring, e.g. LNA, ENA
• 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 2310/351 : Conjugate
• CPC Class Codes: C12N 2310/3511 : intercalating or cleaving agent
• CPC Class Codes: C12N 2310/3513 : Protein; Peptide
• CPC Class Codes: C12N 2310/3515 : Lipophilic moiety, e.g. cholesterol
• CPC Class Codes: C12N 2310/3525 : MOE, methoxyethoxy
• CPC Class Codes: C12N 2310/353 : linked to the nucleic acid via an atom other than carbon
• CPC Class Codes: C12N 2320/32 : Special delivery means, e.g. tissue-specific
• CPC Class Codes: C12Y 301/03048 : Protein-tyrosine-phosphatase (3.1.3.48)

Abstract

Provided herein are oligomeric compounds with conjugate groups targeting apoplipoprotein (a) [apo(a)]. In certain embodiments, the apo(a) targeting oligomeric compounds are conjugated to N-Acetylgalactosamine. Also disclosed herein are conjugated oligomeric compounds targeting apo(a) for use in decreasing apo(a) to treat, prevent, or ameliorate diseases, disorders or conditions related to apo(a) and/or Lp(a). Certain diseases, disorders or conditions related to apo(a) and/or Lp(a) include inflammatory, cardiovascular and/or metabolic diseases, disorders or conditions. The conjugated oligomeric compounds disclosed herein can be used to treat such diseases, disorders or conditions in an individual in need thereof.

Claims

1. A compound comprising a modified oligonucleotide and a conjugate group, wherein the modified oligonucleotide consists of 12 to 30 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion of nucleobases 1 to 3900 or 3921 to 6489 of SEQ ID NO:

1; and

wherein the conjugate group comprises;

2. The compound of claim 1, wherein the modified oligonucleotide consists of 20 linked nucleosides.

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

4. The compound of claim 3, wherein at least one modified sugar is a bicyclic sugar.

5. The compound of claim 3, wherein at least one modified sugar comprises a 2′

-O-methoxyethyl, a constrained ethyl, a 3′

-fluoro-HNA or a 4′

-(CH₂)_n—

O-2′

bridge, wherein n is 1 or 2.

6. The compound of claim 3, wherein at least one modified sugar is 2′

-O-methoxyethyl.

7. The compound of claim 1, wherein at least one nucleoside comprises a modified nucleobase.

8. The compound of claim 7, wherein the modified nucleobase is a 5-methylcytosine.

9. The compound of claim 1, wherein the conjugate group is linked to the modified oligonucleotide at the 5′

end of the modified oligonucleotide.

10. The compound of claim 1, wherein the conjugate group is linked to the modified oligonucleotide at the 3′

end of the modified oligonucleotide.

11. The compound of claim 1, wherein each internucleoside linkage of the modified oligonucleotide is selected from a phosphodiester internucleoside linkage and a phosphorothioate internucleoside linkage.

12. The compound of claim 11, wherein the modified oligonucleotide comprises at least 5 phosphodiester internucleoside linkages.

13. The compound of claim 11, wherein the modified oligonucleotide comprises at least two phosphorothioate internucleoside linkages.

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

15. The compound of claim 1, wherein the modified oligonucleotide is double stranded.

16. The compound of claim 1, wherein the modified oligonucleotide comprises:

a gap segment consisting of linked deoxynucleosides;

a 5′

wing segment consisting of linked nucleosides;

a 3′

wing segment consisting of linked nucleosides;

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.

17. The compound of claim 16, wherein each internucleoside linkage in the gap segment of the modified oligonucleotide is a phosphorothioate linkage.

18. The compound of claim 17, wherein the modified oligonucleotide further comprises at least one phosphorothioate internucleoside linkage in each wing segment.

19. The compound of claim 2, wherein the nucleobase sequence of the modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of any of SEQ ID NOs:

12-57, 59-130, 133, 134.

20. The compound of claim 19, wherein each internucleoside linkage in the gap segment of the modified oligonucleotide is a phosphorothioate linkage.

21. The compound of claim 20, wherein the modified oligonucleotide further comprises at least one phosphorothioate internucleoside linkage in each wing segment.

22. The compound of claim 19, wherein the modified oligonucleotide comprises:

a gap segment consisting of ten linked deoxynucleosides;

a 5′

wing segment consisting of five linked nucleosides;

a 3′

wing segment consisting of five linked nucleosides;

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment, wherein each nucleoside of each wing segment comprises a 2′

-O-methoxyethyl sugar, wherein each internucleoside linkage in the gap segment is a phosphorothioate linkage and wherein each cytosine residue is a 5-methylcytosine.

23. The compound of claim 22, wherein the modified oligonucleotide further comprises at least one phosphorothioate internucleoside linkage in each wing segment.

24. The compound of claim 22, wherein the internucleoside linkages are phosphorothioate linkages between nucleosides 1-2, nucleosides 6-16 and nucleosides 18-20 of the modified oligonucleotide, wherein nucleosides 1-20 are positioned 5′

to 3′

.

25. The compound of claim 22, wherein the 2nd, 3rd, 4th, and 5th internucleoside linkage from the 5′

-end is a phosphodiester internucleoside linkage, wherein the 3rd and 4th internucleoside linkage from the 3′

-end is a phosphodiester internucleoside linkage, and wherein each remaining internucleoside linkage is a phosphorothioate internucleoside linkage.

26. A composition comprising the compound of claim 1, or a salt thereof, and a pharmaceutically acceptable carrier or diluent.

27. A composition comprising the compound of claim 22, or a salt thereof, and a pharmaceutically acceptable carrier or diluent.

28. The compound of claim 2, wherein the nucleobase sequence of the modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of any of SEQ ID NOs:

12-56, 62-98, 100-130, 133, 134.

29. A compound comprising a modified oligonucleotide and a conjugate group, wherein the modified oligonucleotide consists of 12 to 30 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion of nucleobases in SEQ ID NO:

1;

with the proviso that if the modified oligonucleotide consists of 20 contiguous nucleobases, the 20 contiguous nucleobases are not at least 80% complementary to an equal length portion of nucleobases 3901 to 3920 of SEQ ID NO;

1; and

wherein the conjugate group comprises;

30. The compound of claim 29, wherein the modified oligonucleotide consists of 20 linked nucleosides.

31. The compound of claim 29, wherein the modified oligonucleotide comprises at least one modified sugar.

32. The compound of claim 31, wherein at least one modified sugar is a bicyclic sugar.

33. The compound of claim 31, wherein at least one modified sugar comprises a 2′

-O-methoxyethyl, a constrained ethyl, a 3′

-fluoro-HNA or a 4′

-(CH₂)_n—

O-2′

bridge, wherein n is 1 or 2.

34. The compound of claim 31, wherein at least one modified sugar is 2′

-O-methoxyethyl.

35. The compound of claim 29, wherein at least one nucleoside comprises a modified nucleobase.

36. The compound of claim 35, wherein the modified nucleobase is a 5-methylcytosine.

37. The compound of claim 29, wherein the conjugate group is linked to the modified oligonucleotide at the 5′

end of the modified oligonucleotide.

38. The compound of claim 29, wherein the conjugate group is linked to the modified oligonucleotide at the 3′

end of the modified oligonucleotide.

39. The compound of claim 29, wherein each internucleoside linkage of the modified oligonucleotide is selected from a phosphodiester internucleoside linkage and a phosphorothioate internucleoside linkage.

40. The compound of claim 39, wherein the modified oligonucleotide comprises at least 5 phosphodiester internucleoside linkages.

41. The compound of claim 39, wherein the modified oligonucleotide comprises at least two phosphorothioate internucleoside linkages.

42. The compound of claim 29, wherein the modified oligonucleotide is single-stranded.

43. The compound of claim 29, wherein the modified oligonucleotide is double stranded.

44. The compound of claim 29, wherein the modified oligonucleotide comprises:

a gap segment consisting of linked deoxynucleosides;

a 5′

wing segment consisting of linked nucleosides;

a 3′

wing segment consisting of linked nucleosides;

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.

45. The compound of claim 44, wherein each internucleoside linkage in the gap segment of the modified oligonucleotide is a phosphorothioate linkage.

46. The compound of claim 45, wherein the modified oligonucleotide further comprises at least one phosphorothioate internucleoside linkage in each wing segment.

47. The compound of claim 30, wherein the nucleobase sequence of the modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of any of SEQ ID NOs:

12-57, 59-130, 133, 134.

48. The compound of claim 47, wherein each internucleoside linkage in the gap segment of the modified oligonucleotide is a phosphorothioate linkage.

49. The compound of claim 48, wherein the modified oligonucleotide further comprises at least one phosphorothioate internucleoside linkage in each wing segment.

50. The compound of claim 47, wherein the modified oligonucleotide comprises:

a gap segment consisting of ten linked deoxynucleosides;

a 5′

wing segment consisting of five linked nucleosides;

a 3′

wing segment consisting of five linked nucleosides;

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment, wherein each nucleoside of each wing segment comprises a 2′

-O-methoxyethyl sugar, wherein each internucleoside linkage in the gap segment is a phosphorothioate linkage and wherein each cytosine residue is a 5-methylcytosine.

51. The compound of claim 50, wherein the modified oligonucleotide further comprises at least one phosphorothioate internucleoside linkage in each wing segment.

52. The compound of claim 50, wherein the internucleoside linkages are phosphorothioate linkages between nucleosides 1-2, nucleosides 6-16 and nucleosides 18-20 of the modified oligonucleotide, wherein nucleosides 1-20 are positioned 5′

to 3′

.

53. The compound of claim 50, wherein the 2nd, 3rd, 4th, and 5th internucleoside linkage from the 5′

-end is a phosphodiester internucleoside linkage, wherein the 3rd and 4th internucleoside linkage from the 3′

-end is a phosphodiester internucleoside linkage, and wherein each remaining internucleoside linkage is a phosphorothioate internucleoside linkage.

54. The compound of claim 30, wherein the nucleobase sequence of the modified oligonucleotide comprises at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of any of SEQ ID NOs:

12-56, 62-98, 100-130, 133, 134.

55. A composition comprising the compound of claim 29, or a salt thereof, and a pharmaceutically acceptable carrier or diluent.

56. A composition comprising the compound of claim 50, or a salt thereof, and a pharmaceutically acceptable carrier or diluent.