Conjugated antisense compounds and their use

• US 9,181,549 B2
• Filed: 12/30/2014
• Issued: 11/10/2015
• Est. Priority Date: 05/01/2013
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Prakash, Thazha P., Seth, Punit P., Swayze, Eric E.
• Primary Examiner(s): McIntosh, III, Traviss C
• Application Number:
  US14/586,751
• Publication Number:
  US 20150126718A1
• Time in Patent Office: 315 Days
• Field of Search: None
• US Class Current: 1/1
• 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. In certain embodiments, the oligomeric compounds are conjugated to N-Acetylgalactosamine.

Claims

1. A compound having the formula (XXVI):

2. The compound of claim 1, wherein the conjugate linker comprises an amine, an amide, an ester, an ether, a pyrrolidine, ethylene glycol, a polyamide, or a disulfide bond.

3. The compound of claim 1, wherein the conjugate linker has the formula:

4. The compound of claim 1, wherein T₂ has the formula:

5. The compound of claim 4, wherein T₂ has the formula:

6. The compound of claim 5, wherein the oligomeric compound is a modified oligonucleotide.

7. The compound of claim 6, wherein the modified oligonucleotide consists of 15 to 24 linked nucleosides wherein at least one nucleoside is a modified nucleoside.

8. The compound of claim 6, wherein the modified oligonucleotide comprises at least one modified nucleoside selected from among:

a 2′

-MOE nucleoside, a 2′

-OMe nucleoside, a 2′

-F nucleoside, a (4′

-CH₂—

O-2′

) bicyclic nucleoside, a (4′

-(CH₂)₂-O-2′

) bicyclic nucleoside, a (4′

-C(CH₃)H—

O-2′

) bicyclic nucleoside; and

a morpholino.

9. The compound of claim 8, wherein the modified oligonucleotide has a gapmer sugar motif comprising:

a 5′

-region consisting of 2-8 linked 5′

-region nucleosides, wherein each 5′

-region nucleoside is a modified nucleoside;

a 3′

-region consisting of 2-8 linked 3′

-region nucleosides, wherein each 3′

-region nucleoside is a modified nucleoside; and

a central region between the 5′

-region and the 3′

-region consisting of 5-10 linked central region nucleosides, each independently selected from among;

a modified nucleoside and an unmodified deoxynucleoside, wherein the 5′

-most central region nucleoside is an unmodified deoxynucleoside and the 3′

-most central region nucleoside is an unmodified deoxynucleoside.

10. The compound of claim 9, wherein the modified oligonucleotide has a chemical motif selected from among:

MsMy(Ds)_0-1(DsDs)_(3-5)MsM

MsMy(Ds)_0-1(DsDs)_(3-5)MyMsM

MsMy(Ds)_0-1(DsDs)_(3-5)MyMyMsM

MsMy(Ds)_0-1(DsDs)_(3-5)MyMyMyMsM

MsMyMy(Ds)_0-1(DsDs)_(3-5)MsM

MsMyMy(Ds)_0-1(DsDs)_(3-5)MyMsM

MsMyMy(Ds)_0-1(DsDs)_(3-5)MyMyMsM

MsMyMy(Ds)_0-1(DsDs)_(3-5)MyMyMyMsM

MsMyMyMy(Ds)_0-1(DsDs)_(3-5)MsM

MsMyMyMy(Ds)_0-1(DsDs)_(3-5)MyMsM

MsMyMyMy(Ds)_0-1(DsDs)_(3-5)MyMyMsM

MsMyMyMy(Ds)_0-1(DsDs)_(3-5)MyMyMyMsM

MsMyMyMyMy(Ds)_0-1(DsDs)_(3-5)MsM

MsMyMyMyMy(Ds)_0-1(DsDs)_(3-5)MyMsM

MsMyMyMyMy(Ds)_0-1(DsDs)_(3-5)MyMyMsM; and

MsMyMyMyMy(Ds)_0-1(DsDs)_(3-5)MyMyMyMsM;

wherein each M is independently a modified nucleoside, each D is a deoxynucleoside;

each s is a phosphorothioate internucleoside linkage, and each y is independently either a phosphodiester internucleoside linkage or a phosphorothioate internucleoside linkage, provided that at least one y is a phosphodiester internucleotide linkage.

11. The compound of claim 9, wherein the 5′

-region consists of 2-5 linked 5′

-region nucleosides;

the 3′

-region consists of 2-5 linked 3′

-region nucleosides; and

the central region consists of 8-10 central region nucleosides.

12. The compound of claim 11, wherein each internucleoside linkage of the modified oligonucleotide is either a phosphorothioate internucleoside linkage or a phosphodiester internucleoside linkage.

13. The compound of claim 11, wherein the modified oligonucleotide is attached to the remainder of the compound at the 5′

-end of the modified oligonucleotide.

14. The compound of claim 13, wherein the modified oligonucleotide is single-stranded.

15. The compound of claim 14, wherein the modified oligonucleotide is complementary to a target nucleic acid.

16. The compound of claim 15, wherein the target nucleic acid is selected from among:

mRNA, pre-mRNA, micro-RNA, and long non-coding RNA.

17. A compound having the formula:

18. The compound of claim 17, wherein X is S.

19. The compound of claim 17, wherein T₄ is an oligomeric compound, and wherein the oligomeric compound is a modified oligonucleotide.

20. The compound of claim 19, wherein the modified oligonucleotide is a gapmer.

21. The compound of claim 20, wherein the modified oligonucleotide activates RNase H when bound to a complementary target nucleic acid.

22. The compound of claim 21, wherein the at least one modified nucleoside is a modified nucleoside selected from a 2′

-F nucleoside, a 2′

-OCH₃ nucleoside, a 2′

-O(CH₂)₂OCH₃ nucleoside, a 2′

-OC(CH₃)H-4′

nucleoside, and a 2′

-OCH₂-4′

nucleoside.

23. The compound of claim 22, wherein the modified nucleoside is a 2′

-O(CH₂)₂OCH₃ nucleoside.

24. A compound having the formula:

25. The compound of claim 24, wherein X is S.

26. The compound of claim 24, wherein T₄ is an oligomeric compound, and wherein the oligomeric compound is a modified oligonucleotide.

27. The compound of claim 26, wherein the modified oligonucleotide is a gapmer.

28. The compound of claim 27, wherein the modified oligonucleotide activates RNase H when bound to a complementary target nucleic acid.

29. The compound of claim 28, wherein the at least one modified nucleoside is a modified nucleoside selected from a 2′

-F nucleoside, a 2′

-OCH₃ nucleoside, a 2′

-O(CH₂)₂OCH₃ nucleoside, a 2′

-OC(CH₃)H-4′

nucleoside, and a 2′

-OCH₂-4′

nucleoside.

30. The compound of claim 29, wherein the modified nucleoside is a 2′

-O(CH₂)₂OCH₃ nucleoside.