RNA INTERFERENCE MEDIATED INHIBITION OF ISOCITRATE DEHYDROGENASE (IDH1) GENE EXPRESSION

• US 20140094503A1
• Filed: 06/01/2012
• Published: 04/03/2014
• Est. Priority Date: 06/06/2011
• Status: Active Grant

• Current Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Original Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Inventors: Brown, Duncan, Bartz, Steven, Ma, Yong
• Granted Patent: US 9,322,020 B2
• Time in Patent Office: Days
• US Class Current: 514/44.A
• 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: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C12N 15/1137 against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/317 with an inverted bond, e.g. a cap structure
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/332 Abasic residue
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2310/3533 Halogen
• CPC Class Codes: C12Y 101/01042 Isocitrate dehydrogenase (NADP+) (1.1.1.42)

Abstract

The present invention relates to compounds, compositions, and methods for the study, diagnosis, and treatment of traits, diseases and conditions that respond to the modulation of IDH1 and mutant IDH1 gene expression and/or activity, and/or modulate an IDH1 or mutant IDH1 gene expression pathway. Specifically, the invention relates to double-stranded nucleic acid molecules, including small nucleic acid molecules such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules, that are capable of mediating or that mediate RNA interference (RNAi) against IDH1 or mutant IDH1 gene expression.

Claims

1. An isolated double-stranded short interfering nucleic acid (siNA) molecule that inhibits the expression of IDH1 or mutant IDH1, wherein:

(a) the siNA comprises a sense strand and an antisense strand;

(b) each strand is independently 15 to 30 nucleotides in length; and

,

(c) at least one strand comprises at least a 15 nucleotide sequence selected from the group consisting of SEQ ID NOs;

1-506.

2. A double-stranded siNA molecule of claim 1, wherein:

the antisense strand comprises at least 15 nucleotides having sequence complementary to any of;

5. A double-stranded siNA molecule of claim 1, wherein the siNA comprises any of:

6. A double-stranded siNA molecule of claim 1, wherein at least one nucleotide is a chemically modified nucleotide.

9. A double-stranded siNA molecule of claim 1 comprising at least one phosphorothioate internucleotide linkage.

10. A double-stranded siNA molecule of claim 1 comprising a cap on the 3′

-end, 5′

-end, or both 3′ and

5′

ends of at least one strand.

11. A double-stranded siNA molecule of claim 1 comprising one or more 3′

-overhang nucleotides on one or both strands.

12. A double-stranded siNA molecule of claim 1, wherein the 5′

-end of the antisense strand is phosphorylated.

13. A double-stranded siNA molecule of claim 11, wherein the 3′

-overhang nucleotides on at least one strand are 2′

-O-methyl nucleotides.

15. A double-stranded siNA molecule of claim 6, wherein the at least one chemically modified nucleotide is a 2′

-deoxy-2′

-fluoro nucleotide.

16. A double-stranded siNA molecule of claim 6, wherein the at least one chemically modified nucleotide is a 2′

-deoxy nucleotide.

17. A double-stranded siNA molecule of claim 6, wherein the at least one chemically modified nucleotide is a 2′

-O-alkyl nucleotide.

38. A composition comprising a double-stranded siNA molecule of claim 1 in a pharmaceutically acceptable carrier or diluent.

39. A method of treating a human subject suffering from a condition that is mediated by the action or loss of action of IDH1 or mutant IDH 1, which comprises administering to said subject an effective amount of:

(a) a double-stranded siNA molecule according to claim 1;

or,

(b) a composition according to claim 38.

40. The method according to claim 39, wherein the condition is cancer.

3-4. -4. (canceled)

7-8. -8. (canceled)

14. (canceled)

18-23. -23. (canceled)

24. A double-stranded short interfering nucleic acid (siNA) molecule, comprising formula (A) having a sense strand and an antisense strand:

B—

N_X3—

(N)_X2B-3′

B(N)_X1—

N_X4—

[N3]-[N2]-[N1]-5′

 

 

(A)

wherein, the upper strand is the sense strand and the lower strand is the antisense strand of the double-stranded nucleic acid molecule;

wherein the antisense strand comprises at least a 15 nucleotide sequence of SEQ ID NO;

446, SEQ ID NO;

450, SEQ ID NO;

451, SEQ ID NO;

452, SEQ ID NO;

477, SEQ ID NO;

478, SEQ ID NO;

479, SEQ ID NO;

480, SEQ ID NO;

498, or SEQ ID NO;

502; and

the sense strand comprises a sequence having complementarity to the antisense strand;

each N is independently either a nucleotide that is unmodified or chemically modified, or a non-nucleotide;

each B is a terminal cap that is present or absent;

(N) represents overhanging nucleotides, each of which is independently unmodified or chemically modified;

X1 and X2 are independently integers from 0 to 4;

X3 is an integer from 15 to 30;

X4 is an integer from 12 to 27; and

,

[N1]-[N2]-[N3] are modified nucleotides or ribonucleotides, and wherein [N1]-[N2]-[N3] is selected from the groups consisting of;

(a) [N1] is a 2′

-deoxy-2′

-fluoro nucleotide, [N2] is a 2′

-deoxy-2′

-fluoro nucleotide, and [N3] is a 2′

-deoxy-2′

-fluoro nucleotide;

(b) [N1] is a 2′

-deoxy-2′

-fluoro nucleotide, [N2] is a 2′

-deoxy-2′

-fluoro nucleotide, and [N3] is a 2′

-deoxy nucleotide;

(c) [N1] is a 2′

-deoxy nucleotide, [N2] is a 2′

-deoxy-2′

-fluoro nucleotide, and [N3] is a 2′

-O-methyl nucleotide;

(d) [N1] is a 2′

-deoxy nucleotide, [N2] is a 2′

-deoxy-2′

-fluoro nucleotide, and [N3] is a 2′

-deoxy nucleotide; and

,

(e) [N1] is a ribonucleotide, [N2] is a ribonucleotide, and [N3] is a ribonucleotide.

25. A double-stranded siNA molecule according to claim 24, wherein:

(a) one or more pyrimidine nucleotides in N_X4 positions are independently 2′

-deoxy-2′

-fluoro nucleotides, 2′

-O-alkyl nucleotides, 2′

-deoxy nucleotides, ribonucleotides, or any combination thereof;

(b) one or more purine nucleotides in N_X4 positions are independently 2′

-deoxy-2′

-fluoro nucleotides, 2′

-O-alkyl nucleotides, 2′

-deoxy nucleotides, ribonucleotides, or any combination thereof;

(c) one or more pyrimidine nucleotides in N_X3 positions are independently 2′

-deoxy-2′

-fluoro nucleotides, 2′

-O-alkyl nucleotides, 2′

-deoxy nucleotides, ribonucleotides, or any combination thereof and,

(d) one or more purine nucleotides in N_X3 positions are independently 2′

-deoxy-2′

-fluoro nucleotides, 2′

-O-alkyl nucleotides, 2′

-deoxy nucleotides, ribonucleotides, or any combination thereof.

26. A double-stranded siNA molecule according to claim 24, wherein X1 is 2 and X2 is 2.

32. A double-stranded siNA molecule according to claim 24, wherein each X1 and X2=1 or 2;

X3=18, 19, 20, 21, 22, 23 or 24; and

, X4=15, 16, 17, 18, 19, 20, or 21.

37. A double-stranded siNA molecule according to claim 24, comprising one or more phosphorothioate internucleotide linkages.

27-31. -31. (canceled)

33-36. -36. (canceled)