Method for rapidly evaluating performance of short interfering RNA with novel chemical modifications

1. A method for evaluating a novel chemical modification in a siRNA oligomer, said method comprising:

a) providing a siRNA oligomer with 1 or more sugar un-modified universal base containing nucleosides;

b) obtaining position-specific knockdown data to create a baseline data;

c) providing a siRNA oligomer with 1 or more sugar modified universal base containing nucleosides;

d) obtaining position-specific knockdown data; and

e) comparing the position-specific knockdown data from step d) to the baseline data,

wherein a change in the position-specific knockdown data from step d) relative to the baseline data is indicative of siRNA knockdown function.

2. A siRNA which contains a 2′-sugar modification(s) at positions 3, 5, 6, 8, 15, 17 and 19 wherein the 2′-sugar modification(s) is represented in Formula B,

wherein, p is 0, 1, 2 or 3;

Ring K is aryl, heterocyclyl or a (C 3 -C 8 )cycloalkyl;

R 1 is independently selected from: OH, COOH, CF 3 , NO 2 , halo, (C 1 -C 6 )alkyl, O(C 1 -C 6 ) alkyl, aryl, O-aryl, heteroaryl, O-heteroaryl, heterocyclyl or O-heterocyclyl, wherein said alkyl, aryl, heteroaryl and heterocyclyl is optionally substituted with from one to three substituents selected from halo and (C 1 -C 6 )alkyl;

R 2 is selected from: a canonical or universal base; and R 3 is selected from H and (C 1 -C 6 ) alkyl;

or a pharmaceutically acceptable salt or stereoisomer thereof.

3. A siRNA which contains a 2′-sugar modification(s) at positions 3, 5, 6, 8, 15, 17 or 19 wherein the 2′-sugar modification(s) is represented in Formula B,

wherein, p is 0, 1, 2 or 3;

Ring K is aryl, heterocyclyl or a (C 3 -C 8 )cycloalkyl, with the proviso that when aryl is phenyl, then p is not 0;

R 1 is independently selected from: OH, COOH, CF 3 , NO 2 , halo, (C 1 -C 6 )alkyl, O(C 1 -C 6 )alkyl, aryl, O-aryl, heteroaryl, O-heteroaryl, heterocyclyl or O-heterocyclyl, wherein said alkyl, aryl, heteroaryl and heterocyclyl is optionally substituted with from one to three substituents selected from halo and (C 1 -C 6 )alkyl;

R 2 is selected from: a canonical or universal base; and

R 3 is selected from H and (C 1 -C 6 )alkyl;

or a pharmaceutically acceptable salt or stereoisomer thereof.

4. The method of claim 1 , wherein the evaluation of the position-specific knockdown data comprises detecting target mRNA degradation.

5. The siRNA of claim 3 , wherein p is 0, 1, or 2.

6. The siRNA of claim 3 , wherein p is 0 or 1.

7. The siRNA of claim 3 , wherein p is 0.

8. The siRNA of claim 3 , wherein K is phenyl, naphthyl, or pyridyl.

9. The siRNA of claim 8 , wherein K is phenyl.

10. The siRNA of claim 3 , wherein R 1 is OH, COOH, CF 3 , NO 2 , halo, (C 1 -C 6 )alkyl, O(C 1 -C 6 ) alkyl, phenyl, O-phenyl, O-pyranyl or oxadiazolyl, wherein said alkyl, phenyl, and oxadiazolyl is optionally substituted with one to three substituents selected from halo and (C 1 -C 4 )alkyl.

11. The siRNA of claim 3 , wherein R 2 is adenine, guanine, uracil, or cytosine.

12. The siRNA of claim 3 , wherein R 2 is a universal base.

13. The siRNA of claim 12 , wherein R 2 is a hydrogen atom or inosine.

14. The siRNA of claim 3 , wherein R 3 is H and CH 3 .

15. The siRNA of claim 14 , wherein R 3 is H.

16. The siRNA of claim 3 , wherein the siRNA contains a 2′-sugar modification at position 8, 15, or 19.

17. The siRNA of claim 3 , wherein the 2′-sugar modifications are at positions 8, 15, and 19.

18. The siRNA of claim 3 , wherein the 2′-sugar modification is selected from the group consisting of:

1,4-Anhydro-2-O-benzyl-D-ribitol;

1,4-Anhydro-2-O-(4-tert-butylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(4-methylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2-fluorobenzyl)-D-ribitol;

1,4-Anhydro-2-O-(4-fluorobenzyl)-D-ribitol;

1,4-Anhydro-2-O-(3-trifluoromethylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(4-trifluoromethylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2-fluoro-4-trifluoromemylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(3,5-ditrifluoromethylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2,6-difiuoromethylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2,4-difluoromethylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2-difluoromethoxybenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2-fluoro-4-chloromethylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2-chloromethylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(3-chloro-5-trifluoromethoxybenzyl)-D-ribitol;

1,4-Anhydro-2-O-(4-methoxybenzyl)-D-ribitol;

1,4-Anhydro-2-O-(3-methoxybenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2-methoxybenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2-methylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(3,5-dimethylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(4-isopropylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(4-phenylbenzyl)-D-ribitol;

1,4-Anhydro-2-O-(2-naphthyl)-D-ribitol;

1,4-Anhydro-2-O-(3-nitrobenzyl)-D-ribitol;

1,4-Anhydro-2-O-[(4-tetrahydropyran-4-yl)benzyl]-D-ribitol;

1,4-Anhydro-2-O-[(5-methyl-1,2,4-oxadiazol-3-yl)benzyl]-D -ribitol;

1,4-Anhydro-2-O-[(5-methyl-1,3,4-oxadiazol-2-yl)benzyl]-D -ribitol;

1,4-Anhydro-2-O-benzyl]-D-arabinitol;

1,4-Anhydro-2-O-(2-methylbenzyl)-D-ribitol;

2′-O-benzylinosine;

2′-O-(2-methylbenzyl) inosine;

2′-O-(2-naphthyl) inosine;

2′-O-(2-diiluoromethoxybenzyl) inosine;

2′-O-(3-methoxybenzyl)inosine;

2′-O-(pyridin-2-ylmethyl)inosine;

2′-O-(pyridin-3-ylmethyl)inosine;

2′-O-(pyridin-4-ylmethyl)inosine;

2′-O-(4-bromobenzyl)inosine;

9-(2-O-benzyl-b-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one 2′-O-[(4-pyridin-4-yl)benzyl]inosine;

2′-O-[4-(5-methyl-1,3,4-oxadiazol-2-yl)benzyl]inosine;

2′-O-[4-(oxazol-2-yl)benzyl]inosine;

2′-O-[4-(thiazol-2-yl)benzyl]inosine;

2′-O-[4-(furan-2-yl)benzyl]inosine;

2′-O-[4-(2-methoxypyridin-3-yl)benzyl]inosine;

2′-O-[4-(2-methylpyrazol-4-yl)benzyl]inosine;

2′-O-[4-(1-methylpyrol-2-yl)benzyl]inosine;

2′-O-[4-(5-methyl-1,2,4-oxadiazol-3-yl)benzyl]inosine;

2′-O-{4-[2-(pyrrolidin-1-yl)pyrimidin-5-yl]benzyl }inosine;

2′-O-[4-(2-methoxypyridin-5-yl)benzyl)]inosine;

2′-O-[4-(3-fluoropyridin-5-yl)benzyl]inosine;

2′-O-(2-bromobenzyl) inosine;

2′-O-(pyridyn-4-ylmethyl) inosine;

2′-O-[2-(2-methoxypyridin-5-yl)benzyl]inosine;

N-acetyl-2′-O-benzyladenosine;

2-O-benzyluridine;

2′-O-benzylguanosine; and

N-Acetyl-2′-O-benzylcytidine;

or a pharmaceutically acceptable salt or stereoisomer thereof.