Chiral control

• US 9,982,257 B2
• Filed: 07/12/2013
• Issued: 05/29/2018
• Est. Priority Date: 07/13/2012
• Status: Active Grant

• Current Assignee: WAVE Life Sciences Ltd.
• Original Assignee: WAVE Life Sciences Ltd.
• Inventors: Butler, David, Iwamoto, Naoki, Meena, Svrzikapa, Nenad, Verdine, Gregory L., Zlatev, Ivan
• Primary Examiner(s): Chong, Kimberly
• Application Number:
  US14/414,614
• Publication Number:
  US 20150211006A1
• Time in Patent Office: 1,782 Days
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07C 317/28 with sulfone or sulfoxide groups bound to acyclic carbon atoms of the carbon skeleton
• CPC Class Codes: C07D 295/088 to an acyclic saturated chain
• CPC Class Codes: C07H 1/02 Phosphorylation
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C12N 15/11 DNA or RNA fragments; Modified forms thereof DNA or RNA not used in recombinant technology, C07H21/00; Non-coding nucleic acids having a biological activity
• 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 2310/11 Antisense
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/31 of the backbone
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2330/30 chemically synthesised
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes

Abstract

The present invention relates to chirally controlled oligonucleotides, chirally controlled oligonucleotide compositions, and the method of making and using the same. The invention specifically encompasses the identification of the source of certain problems with prior methodologies for preparing chiral oligonucleotides, including problems that prohibit preparation of fully chirally controlled compositions, particularly compositions comprising a plurality of oligonucleotide types. In some embodiments, the present invention provides chirally controlled oligonucleotide compositions. In some embodiments, the present invention provides methods of making chirally controlled oligonucleotides and chirally controlled oligonucleotide compositions.

Claims

1. A chirally controlled oligonucleotide composition comprising a plurality of oligonucleotides of at least one type, wherein each type is defined by:

1) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone X-moieties (—

X-L-R¹);

wherein;

the oligonucleotides of the at least one type comprise one or more phosphorothioate triester internucleotidic linkages and one or more phosphate diester linkage;

the oligonucleotides of the at least one type comprise at least two consecutive modified internucleotidic linkages; and

oligonucleotides of the at least one oligonucleotide type comprise one or more modified internucleotidic linkages independently having the structure of formula (I);

2. The composition of claim 1, wherein the oligonucleotides are cleaved from a solid support.

3. The composition of claim 2, wherein the oligonucleotides comprise one or more modified internucleotide linkages independently having the structure of formula I-b:

4. The composition of claim 3, wherein the oligonucleotides are at least 15 nucleotide units in length.

5. The composition of claim 3, wherein the composition contains predetermined levels of at least two oligonucleotide types.

9. A pharmaceutical composition comprising a therapeutically effective amount of a composition of claim 1 and a pharmaceutically acceptable excipient.

10. The composition of claim 4, wherein the oligonucleotides comprise one or more modified internucleotide linkages independently having the structure of formula I-b wherein -L-R¹ is not hydrogen.

11. The composition of claim 3, wherein the oligonucleotides comprise one or more modified nucleobases.

12. The composition of claim 3, wherein the oligonucleotides comprise one or more modified sugars.

13. The composition of claim 4, wherein the oligonucleotides comprise one or more modified sugars.

14. The composition of claim 10, wherein the oligonucleotides comprise one or more modified sugars.

15. The composition of claim 3, wherein the oligonucleotides comprise one or more 2′

-modified sugars.

16. The composition of claim 4, wherein the oligonucleotides comprise one or more 2′

-modified sugars.

17. The composition of claim 10, wherein the oligonucleotides comprise one or more 2′

-modified sugars.

18. The composition of claim 3, wherein the oligonucleotides comprise one or more 2′

-F modifications.

19. The composition of claim 4, wherein the oligonucleotides comprise one or more 2′

-F modifications.

20. The composition of claim 10, wherein the oligonucleotides comprise one or more 2′

-F modifications.

21. The composition of claim 3, wherein the oligonucleotides comprise one or more 2′

-OR′

modifications, wherein R′

is independently optionally substituted C₁-C₆ aliphatic.

22. The composition of claim 4, wherein the oligonucleotides comprise one or more 2′

-OR′

modifications, wherein R′

is independently optionally substituted C₁-C₆ aliphatic.

23. The composition of claim 10, wherein the oligonucleotides comprise one or more 2′

-OR′

modifications, wherein R′

is independently optionally substituted C₁-C₆ aliphatic.

24. The composition of claim 3, wherein the oligonucleotides comprise one or more locked nucleic acid moieties.

25. The composition of claim 4, wherein the oligonucleotides comprise one or more locked nucleic acid moieties.

26. The composition of claim 10, wherein the oligonucleotides comprise one or more locked nucleic acid moieties.

27. The composition of claim 4, wherein the oligonucleotides comprise at least one Rp modified internucleotidic linkage and at least one Sp modified internucleotidic linkage.

28. The composition of claim 27, wherein the oligonucleotides comprise at least one phosphorothioate diester linkage.

29. The composition of claim 28, wherein the oligonucleotides comprise one or more modified nucleobases.

30. The composition of claim 28, wherein the oligonucleotides comprise one or more modified sugars.

31. The composition of claim 28, wherein the oligonucleotides comprise one or more 2′

-modified sugars.

32. The composition of claim 28, wherein the oligonucleotides comprise one or more 2′

-F modifications.

33. The composition of claim 28, wherein the oligonucleotides comprise one or more 2′

-OR′

modifications, wherein R′

is independently optionally substituted C₁-C₆ aliphatic.

34. The composition of claim 28, wherein the oligonucleotides comprise one or more locked nucleic acid moieties.

35. The composition of claim 1, wherein oligonucleotides of at least one oligonucleotide type comprise at least two individual internucleotidic linkages having different P-modifications relative to one another.

36. The composition of claim 35, wherein the oligonucleotides are cleaved from a solid support.

37. The composition of claim 36, wherein the oligonucleotides comprise one or more modified nucleobases.

38. The composition of claim 36, wherein the oligonucleotides comprise one or more modified sugars.

39. The composition of claim 36, wherein the oligonucleotides comprise one or more 2′

-modified sugars.

40. The composition of claim 36, wherein the oligonucleotides comprise one or more 2′

-F modifications.

41. The composition of claim 36, wherein the oligonucleotides comprise one or more 2′

-OR′

modifications, wherein R′

is independently optionally substituted C₁-C₆ aliphatic.

42. The composition of claim 36, wherein the oligonucleotides comprise one or more locked nucleic acid moieties.

6. A chirally controlled oligonucleotide comprising one or more modified internucleotide linkages independently having the structure of formula I:

7. The chirally controlled oligonucleotide of claim 6, comprising at least 5, at least 6, or at least 7 consecutive modified internucleotidic linkages, and at least one of the consecutive modified internucleotidic linkages is not a phosphorothioate diester linkage.

8. The chirally controlled oligonucleotide of claim 7, wherein the chirally controlled oligonucleotide is at least 15 nucleotide units in length.

43. A chirally controlled oligonucleotide composition comprising a plurality of oligonucleotides of the same type, wherein the type is defined by:

1) base sequence;

2) pattern of backbone linkages;

3) pattern of backbone chiral centers; and

4) pattern of backbone X-moieties (—

X-L-R¹);

wherein;

the oligonucleotides of the same type comprise one or more phosphorothioate triester internucleotidic linkages and one or more phosphate diester linkage;

the oligonucleotides of the same type comprise at least two consecutive modified internucleotidic linkages; and

oligonucleotides of the same type comprise one or more modified internucleotidic linkages independently having the structure of formula (I);

44. The composition of claim 43, wherein the oligonucleotides comprise one or more modified internucleotide linkages independently having the structure of formula I-b:

45. The composition of claim 44, wherein the oligonucleotides are at least 15 nucleotide units in length.

46. The composition of claim 45, wherein the oligonucleotides are cleaved from a solid support.

47. The composition of claim 46, wherein the oligonucleotides comprise-one or more modified nucleobases.

48. The composition of claim 46, wherein the oligonucleotides comprise one or more modified sugars.