Chimeric oligonucleoside compounds

• US 6,060,456 A
• Filed: 10/27/1997
• Issued: 05/09/2000
• Est. Priority Date: 11/16/1993
• Status: Expired due to Fees

• Current Assignee: Genta Incorporated
• Original Assignee: Genta Incorporated
• Inventors: Giachetti, Cristina, Lebedev, Alexandre V., Reynolds, Mark A., Arnold, Lyle J. Jr.
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US08/960,111
• Time in Patent Office: 925 Days
• Field of Search: 435/6, 435/91.1, 514/44.1, 536/22.1, 536/23.1, 536/25.3, 536/24.1, 536/24.2, 536/24.3, 536/24.31, 536/24.32, 536/24.33
• US Class Current: 514/44.00A
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61K 48/00 Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• 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: C12N 15/1131 against viruses

Abstract

Chimeric oligonucleoside compounds, and methods of preparing and formulating the same, are disclosed. The compounds and compositions are useful in activating RNaseH-mediated cleavage of target ribonucleic acid sequences, and in treating disease conditions relating to such sequences.

Claims

1. An oligonucleoside compound for effecting RNaseH-mediated cleavage of a target ribonucleic acid sequence, comprising an RNaseH-activating region and a non-RNaseH-activating region, wherein

the RNaseH-activating region comprises a segment of at least three consecutive 2'"'"'-unsubstituted nucleosides linked by charged internucleoside linkage structures,

the non-RNaseH-activating region comprises a segment of at least two linked nucleosides, at least one linkage in said non-RNaseH-activating region being chirally-selected,

and wherein the base sequence of the oligonucleoside compound is complementary to a target region of the target ribonucleic acid sequence.

2. The oligonucleoside compound of claim 1 wherein said RHaseH-activating region comprises between five and about nine consecutive linked nucleosides.

3. The oligonucleoside compound of claim 2 wherein the charged linkage structures in said RNaseH-activating region are selected from the group consisting of phosphodiester linkages, phosphorodithioate linkages and phosphorothioate linkages.

4. The oligonucleoside compound of claim 3 wherein said RNaseH-activating region comprises a plurality of phosphorothioate linkages.

5. The oligonucleoside compound of claim 2 wherein said chirally selected linkage in the non-RNase-activating region comprises at least four linked nucleosides, and further comprises a plurality of R_p -selected linkage structures.

6. The oligonucleoside compound of claim 5 wherein the segment of chirally-selected linkage structures in said non-RNaseH-activating region comprises a mixed chiral linkage sequence including at least two different linkage structures, at least one of which is asymmetric.

7. The oligonucleoside compound of claim 6 wherein said different linkage structures in the mixed chiral linkage sequence are selected from the group consisting of:

R_p -methylphosphonate and phosphodiester linkages;

R_p -methylphosphonate and racemic methylphosphonate linkages;

R_p -methylphosphonate and phosphorothioate linkages;

R_p -methylphosphonate and phosphorodithioate linkages; and

R_p -methylphosphonate and alkylphosphonothioate linkages.

8. The oligonucleoside compound of claim 6 wherein said different linkage structures in the mixed chiral linkage sequence are selected from the group consisting of

9. The oligonucleoside compound of claim 6 wherein one or both of the nucleosides linked by said different linkage structures in the mixed chiral linkage sequence are 2'"'"'-substituted nucleosides.

10. The oligonucleoside compound of claim 9 wherein said 2'"'"'-substituents are selected from the group consisting of alkoxy, allyloxy and halo substituents.

11. The oligonucleoside compound of claim 1 wherein said RNaseH-activating region is at one terminal portion of the compound and said non-RNaseH-activating region is at the other terminal portion of the compound.

12. The oligonucleoside compound of claim 1 comprising a second non-RNaseH-activating region, and wherein said RNaseH-activating region is flanked in the compound by the first and second non-RNaseH-activating regions.

13. The oligonucleoside compound of claim 1 wherein said target ribonucleic acid sequence is associated with a disease condition in a subject animal, and wherein the target ribonucleic acid sequence contains an RNA target base different from an RNA non-target base occurring in the corresponding position of a non-target ribonucleic acid sequence of the subject animal, the oligonucleoside compound further comprising a targeting oligonucleoside base positioned in the RNaseH-activating region of the compound, or at the first nucleoside outside the 5'"'"'-end of the RNaseH-activating region, such that the targeting oligonucleoside base is complementary to the RNA target base upon hybridization of the compound to the target ribonucleic acid sequence.

14. The oligonucleoside compound of claim 13 wherein said RNaseH-activating region contains from 3 to about 6 deoxynucleosides.

15. The oligonucleoside compound of claim 13 wherein said targeting oligonucleoside base is positioned at the first, second or third nucleoside from the 5'"'"'-end of the RNaseH-activating region.

16. The oligonucleoside compound of claim 13 wherein the charged linkage structures in said RNaseH-activating region are selected from the group consisting of phosphodiester linkages, phosphorodithioate linkages and phosphorothioate linkages.

17. The oligonucleoside compound of claim 16 wherein said RNaseH-activating region comprises a plurality of phosphorothioate linkages.

18. The oligonucleoside compound of claim 14 wherein said segment chirally selected linkage in the non-RNase-activating region comprises at least four linked nucleosides, and further comprises a plurality of R_p -selected linkage structures.

19. The oligonucleoside compound of claim 18 wherein the segment of chirally-selected linkage structures in said non-RNaseH-activating region comprises a mixed chiral linkage sequence including at least two different linkage structures, at least one of which is asymmetric.

20. The oligonucleoside compound of claim 19 wherein one or both of the nucleosides linked by said different linkage structures in the mixed chiral linkage sequence are 2'"'"'-substituted nucleosides.

21. The oligonucleoside compound of claim 20 wherein said 2'"'"'-substituents are selected from the group consisting of alkoxy, allyloxy and halo substituents.

22. The oligonucleoside compound of claim 13 wherein said RNaseH-activating region is at one terminal portion of the compound and said non-RNaseH-activating region is at the other terminal portion of the compound.

23. The oligonucleoside compound of claim 13 wherein a second non-RNaseH-activating region, and wherein said RNaseH-activating region is flanked in the compond by the first and second non-RNaseH-activating regions.

37. A pharmaceutical composition comprising an effective amount of an oligonucleoside compound of claim 13 and a pharmaceutically acceptable carrier.

24. An oligonucleoside compound for effecting RNaseH-mediated cleavage of a target ribonucleic acid sequence, wherein said target ribonucleic acid sequence is associated with a disease condition in a subject animal, and wherein the target ribonucleic acid sequence contains an RNA target base different from an RNA non-target base occurring in the corresponding position of a non-target ribonucleic acid sequence of the subject animal, said oligonucleoside compound comprising

a base sequence complementary to a target region of the target ribonucleic acid sequence containing said RNA target base,

an RNaseH-activating region comprising a segment of from 3 to about 6 consecutive 2'"'"'-unsubstituted nucleosides linked by charged intemucleoside linkage structures, including a targeting oligonucleoside base positioned at the first, second or third nucleoside from the 5'"'"'-end of the RNaseH-activating region, such that the targeting oligonucleoside base is complementary to the RNA target base upon hybridization of the compound to the target ribonucleic acid sequence, and

a non-RNaseH-activating region comprising a segment of at least two linked nucleosides, at least one of the linkages in said non-RNaseH-activating region being chirally selected.

25. The oligonucleoside compound of claim 24 wherein the charged linkage structures in said RNaseH-activating region are selected from the group consisting of phosphodiester linkages, phosphorodithioate linkages and phosphorothioate linkages.

26. The oligonucleoside compound of claim 25 wherein said RNaseH-activating region comprises a plurality of phosphorothioate linkages.

27. The oligonucleoside compound of claim 24 wherein said segment of linked nucleosides in the non-RNase-activating region comprises at least four linked nucleosides.

28. The oligonucleoside compound of claim 27 wherein said segment of linked nucleosides in the non-RNase-activating region further comprises a plurality of R_p -selected linkage structures.

29. The oligonucleoside compound of claim 28 wherein the segment of chirally-selected linkage structures in said non-RNaseH-activating region comprises a mixed chiral linkage sequence including at least two different linkage structures, at least one of which is asymmetric.

30. The oligonucleoside compound of claim 29 wherein said different linkage structures in the mixed chiral linkage sequence are selected from the group consisting of:

R_p -methylphosphonate and phosphodiester linkages;

R_p -methylphosphonate and racemic methylphosphonate linkages;

R_p -methylphosphonate and phosphorothioate linkages;

R_p -methylphosphonate and phosphorodithioate linkages; and

R_p -methylphosphonate and alkylphosphonothioate linkages.

31. The oligonucleoside compound of claim 29 wherein said different linkage structures in the mixed chiral linkage sequence are selected from the group consisting of

32. The oligonucleoside compound of claim 24 wherein one or more of the nucleosides in said non-RNaseH-activating region are 2'"'"'-substituted nucleosides.

33. The oligonucleoside compound of claim 32 wherein one or more of the nucleosides in said non-RNaseH-activating region are 2'"'"'-substituted nucleosides.

34. The oligonucleoside compound of claim 32 wherein said 2'"'"'-substituents are selected from the group consisting of alkoxy, allyloxy and halo substituents.

35. The oligonucleoside compound of claim 26 wherein said RNaseH-activating region is at one terminal portion of the compound and said non-RNaseH-activating region is at the other terminal portion of the compound.

36. The oligonucleoside compound of claim 26 comprising a second non-RNaseH-activating region, and wherein said RNaseH-activating region is flanked in the compound by the first and second non-RNaseH-activating regions.

38. A pharmaceutical composition comprising an effective amount of an oligonucleoside compound of claim 29 and a pharmaceutically acceptable carrier.