Oligonucleotide compounds for targeting huntingtin mRNA

Patent metadata

Field	Value
Publication number	US-9809817-B2
Application number	US-201615089319-A
Country	US
Kind code	B2
Filing date	Apr 1, 2016
Priority date	Apr 3, 2015
Publication date	Nov 7, 2017
Grant date	Nov 7, 2017

Abstract

This disclosure relates to novel huntingtin targets. Novel oligonucleotides for the treatment of Huntington's disease are also provided.

First claim

What is claimed is:

1. A vector for inhibiting the expression of HTT gene in a cell, said vector comprising a regulatory sequence operably linked to a nucleotide sequence that encodes a dsRNA molecule substantially complementary to 5′ CAGUAAAGAGAUUAA 3′ (SEQ ID NO:1), 5′ AUAUCAGUAAAGAGA 3′ (SEQ ID NO:2) or 5′ CUCAGGAUUUAAAAU 3′ (SEQ ID NO:3), wherein said dsRNA molecule is between 10 and 35 bases in length.

2. A cell comprising the vector of claim 1 .

3. A dsRNA molecule that is between 15 and 35 base pairs in length, comprising a region of complementarity which is substantially complementary to 5′ CAGUAAAGAGAUUAA 3′ (SEQ ID NO:1), 5′ AUAUCAGUAAAGAGA 3′ (SEQ ID NO:2) or 5′ CUCAGGAUUUAAAAU 3′ (SEQ ID NO:3), wherein the RNA molecule targets an HTT mRNA and comprises at least one modified nucleotide.

4. A pharmaceutical composition for inhibiting the expression of the HTT gene in an organism, comprising the dsRNA of claim 3 and a pharmaceutically acceptable carrier.

5. The dsRNA molecule of claim 3 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand comprises the region of complementarity which is substantially complementary to 5′ CAGUAAAGAGAUUAA 3′ (SEQ ID NO:1).

6. The dsRNA molecule of claim 3 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand comprises the region of complementarity which is substantially complementary to 5′ AUAUCAGUAAAGAGA 3′ (SEQ ID NO:2).

7. The dsRNA molecule of claim 3 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand comprises the region of complementarity which is substantially complementary to 5′ CUCAGGAUUUAAAAU 3′ (SEQ ID NO:3).

8. The dsRNA molecule of claim 3 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand is complementary to at least 10, 11, 12 or 13 contiguous nucleotides of SEQ ID NO:1, 2 or 3.

9. The dsRNA molecule of claim 3 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand contains no more than 3 mismatches with SEQ ID NO:1, 2 or 3.

10. The dsRNA molecule of claim 3 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand is fully complementary to SEQ ID NO:1, 2 or 3.

11. The dsRNA molecule of claim 3 , which is between 30 and 35 base pairs in length.

12. The dsRNA molecule of claim 3 , which is blunt-ended.

13. The dsRNA molecule of claim 3 , which comprises at least one single stranded nucleotide overhang.

14. The dsRNA molecule of claim 3 , wherein the at least one modified nucleotide is selected from the group consisting of a 2′-O-methyl modified nucleotide, a nucleotide comprising a 5′phosphorothioate group, and a terminal nucleotide linked to a cholesteryl derivative or dodecanoic acid bisdecylamide group.

15. The dsRNA molecule of claim 3 , wherein said modified nucleotide is selected from the group consisting of a 2′-deoxy-2′-fluoro modified nucleotide, a 2′-deoxy-modified nucleotide, a locked nucleotide, an abasic nucleotide, 2′-amino-modified nucleotide, 2′-alkyl-modified nucleotide, morpholino nucleotide, a phosphoramidate, a non-natural base comprising nucleotide, at least one 2′-O-methyl modified nucleotide and at least one nucleotide comprising a 5′phosphorothioate group.

16. The dsRNA molecule of claim 3 , wherein the dsRNA molecule comprises alternating 2′-methoxy-ribonucleotides and 2′-fluoro-ribonucleotides.

17. The dsRNA molecule of claim 3 , wherein the nucleotides at positions 2 and 14 from the 5′ end are not 2′-methoxy-ribonucleotides.

18. The dsRNA molecule of claim 3 , wherein the nucleotides are connected via phosphodiester or phosphorothioate linkages.

19. The dsRNA molecule of claim 3 , wherein the nucleotides at positions 1-6 from the 3′ end, or positions 1-7 from the 3′ end, are connected to adjacent nucleotides via phosphorothioate linkages.

20. A di-branched RNA compound comprising a dsRNA of claim 3 connected to another dsRNA by one or more moieties independently selected from a linker, a spacer and a branching point.

21. A method for inhibiting expression of HTT gene in a cell, the method comprising:
(a) introducing into the cell a double-stranded ribonucleic acid (dsRNA) of claim 3 ; and
(b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of the HTT gene, thereby inhibiting expression of the HTT gene in the cell.

22. A method of treating or managing Huntington's disease comprising administering to a patient in need of such treatment or management a therapeutically effective amount of said dsRNA of claim 3 .

23. The method of claim 21 , wherein said dsRNA is administered to the brain of the patient.

24. The method of claim 21 , wherein said dsRNA is administered by intrastriatal infusion.

25. The method of claim 21 , wherein the dsRNA causes a decrease in HTT gene mRNA in the striatum.

26. The method of claim 21 , where the dsRNA causes a decrease in HTT gene mRNA in the cortex.

27. The vector of claim 1 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand comprises the region of complementarity which is substantially complementary to 5′ CAGUAAAGAGAUUAA 3′ (SEQ ID NO:1).

28. The vector of claim 1 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand comprises the region of complementarity which is substantially complementary to 5′ AUAUCAGUAAAGAGA 3′ (SEQ ID NO:2).

29. The vector of claim 1 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand comprises the region of complementarity which is substantially complementary to 5′ CUCAGGAUUUAAAAU 3′ (SEQ ID NO:3).

30. The vector of claim 1 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand is complementary to at least 10, 11, 12 or 13 contiguous nucleotides of SEQ ID NO:1, 2 or 3.

31. The vector of claim 1 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand contains no more than 3 mismatches with SEQ ID NO:1, 2 or 3.

32. The vector of claim 1 , wherein the dsRNA comprises a sense strand and an antisense strand, wherein the antisense strand is fully complementary to SEQ ID NO:1, 2 or 3.

33. The vector of claim 1 , wherein the dsRNA is between 30 and 35 base pairs in length.

34. The vector of claim 1 , wherein the dsRNA blunt-ended.

35. The vector of claim 1 , wherein the dsRNA comprises at least one single stranded nucleotide overhang.

36. A method for inhibiting expression of HTT gene in a cell, the method comprising:
(a) introducing into the cell the vector of claim 1 ; and
(b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of the HTT gene, thereby inhibiting expression of the HTT gene in the cell.

37. A method of treating or managing Huntington's disease comprising administering to a patient in need of such treatment or management a therapeutically effective amount of the vector of claim 1 .

38. The method of claim 37 , whe

Assignees

• Univ Massachusetts

Inventors

• Khvorova Anastasia
• Aronin Neil
• Alterman Julia

Classifications

• A61P43/00

  Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00 · CPC title

• A61P25/14

  for treating abnormal movements, e.g. chorea, dyskinesia · CPC title

• C12N2310/3515

  Lipophilic moiety, e.g. cholesterol · CPC title

• A61K31/713

  Double-stranded nucleic acids or oligonucleotides · CPC title

• C12N2310/343

  having patterns, e.g. ==--==--==-- · CPC title