Bicyclic carbocyclic nucleosides and oligomeric compounds prepared therefrom
The present invention provides novel bicyclic carbocyclic nucleosides and oligomeric compounds prepared therefrom. Incorporation of one or more of the bicyclic carbocyclic nucleosides into an oligomeric compound is expected to enhance one or more properties of the oligomeric compound. In certain embodiments, the oligomeric compounds provided herein hybridize to a portion of a target RNA resulting in modulation of normal function of the target RNA. In certain embodiments, bicyclic carbocyclic nucleosides are provided as monomers for use as antivirals.
1. A bicyclic carbocyclic nucleoside having Formula I:
wherein:
Bx is an optionally protected heterocyclic base moiety;
T 1 is a protected hydroxyl;
T 2 is a reactive phosphorus group capable of forming an internucleoside linkage selected from diisopropylcyanoethoxy phosphoramidite and H-phosphonate;
Q is halogen or O—[C(A 1 )(A 2 )]n-[(C═O) m —X] j —Z wherein Q is other than a protected hydroxyl group;
A 1 and A 2 are each, independently, H, halogen, C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl;
X is O, S or N(E 1 );
Z is H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C 2 -C 6 alkynyl or N(E 2 )(E 3 );
E 1 , E 2 and E 3 are each, independently, H, C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl;
n is from 1 to about 6;
m is 0 or 1;
j is 0 or 1 provided that when j is 1 then Z is other than halogen or N(E 2 )(E 3 );
L 1 and L 2 are each H or one of L 1 and L 2 is H and the other of L 1 and L 2 is C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl;
R 1 , R 2 , R 3 , R 4 , R 5 and R 6 are each H or one of R 1 , R 2 , R 3 , R 4 , R 5 and R 6 is F, CH 3 or OCH 3 and the remaining of R 1 , R 2 , R 3 , R 4 , R 5 and R 6 are each H;
each substituted group comprises one or more optionally protected substituent groups independently selected from halogen, OJ 1 , N(J 1 )(J 2 ), ═NJ 1 , SJ 1 , N 3 , OC(=G)J 1 , OC(=G)N(J 1 )(J 2 ) and C(=G)N(J 1 )(J 2 );
G is O, S or NJ 3 ; and
each J 1 , J 2 and J 3 is, independently, H or C 1 -C 6 alkyl.
2. The bicyclic carbocyclic nucleoside of claim 1 wherein one of L 1 and L 2 is H and the other of L 1 and L 2 is CH 3 .
3. The bicyclic carbocyclic nucleoside of claim 1 wherein L 1 and L 2 are each H.
4. The bicyclic carbocyclic nucleoside of claim 1 wherein L 1 , L 2 , R 1 , R 2 , R 3 , R 4 , R 5 and R 6 are each H.
5. The bicyclic carbocyclic nucleoside claim 1 wherein Q is F.
6. The bicyclic nucleoside of claim 1 wherein Q is O(CH 2 ) 2 —OCH 3 .
7. The bicyclic carbocyclic nucleoside of claim 1 wherein Bx is uracil, thymine, cytosine, 4-N-benzoylcytosine, 5-methylcytosine, 4-N-benzoyl-5-methylcytosine, adenine, 6-N-benzoyladenine, guanine or 2-N-isobutyrylguanine.
8. The bicyclic carbocyclic nucleoside of claim 1 wherein T 1 is O-4,4′-dimethoxytrityl and T 2 is diisopropylcyanoethoxy phosphoramidite.
9. An oligomeric compound comprising at least one bicyclic carbocyclic nucleoside having Formula II:
wherein independently for each bicyclic carbocyclic nucleoside of Formula II
Bx is an optionally protected heterocyclic base moiety;
one of T 3 and T 4 is an internucleoside linking group attaching the bicyclic nucleoside to the remainder of one of the 5′ or 3′ end of the oligomeric compound and the other of T 3 and T 4 is hydroxyl, a protected hydroxyl, a 5′ or 3′ terminal group or an internucleoside linking group attaching the bicyclic nucleoside to the remainder of the other of the 5′ or 3′ end of the oligomeric compound;
Q is halogen or O—[C(A 1 )(A 2 )] n -[(C═O) m —X] j —Z wherein Q is other than a protected hydroxyl group;
A 1 and A 2 are each, independently, H, halogen, C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl;
X is O, S or N(E 1 );
Z is H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C 2 -C 6 alkynyl or N(E 2 )(E 3 );
E 1 , E 2 and E 3 are each, independently, H, C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl;
n is from 1 to about 6;
m is 0 or 1;
j is 0 or 1 provided that when j is 1 then Z is other than halogen or N(E 2 )(E 3 );
L 1 and L 2 are each H or one of L 1 and L 2 is H and the other of L 1 and L 2 is C 1 -C 6 alkyl, or substituted C 1 -C 6 alkyl;
R 1 , R 2 , R 3 , R 4 , R 5 and R 6 are each H or one of R 1 , R 2 , R 3 , R 4 , R 5 and R 6 is F, CH 3 or OCH 3 and the remaining of R 1 , R 2 , R 3 , R 4 , R 5 and R 6 are each H;
each substituted group comprises one or more optionally protected substituent groups independently selected from halogen, OJ 1 , N(J 1 )(J 2 ), ═NJ 1 , SJ 1 , N 3 , OC(=G)J 1 , OC(=G)N(J 1 )(J 2 ) and C(=G)N(J 1 )(J 2 );
G is O, S or NJ 3 ;
each J 1 , J 2 and J 3 is, independently, H or C 1 -C 6 alkyl; and
wherein said oligomeric compound comprises from 8 to 40 monomeric subunits linked by internucleoside linking groups and wherein at least some of the heterocyclic base moieties are capable of hybridizing to a nucleic acid molecule.
10. The oligomeric compound of claim 9 wherein one of L 1 and L 2 is H and the other of L 1 and L 2 is CH 3 for each bicyclic carbocyclic nucleoside having Formula II.
11. The oligomeric compound of claim 9 wherein L 1 and L 2 are each H for each bicyclic carbocyclic nucleoside having Formula II.
12. The oligomeric compound of claim 9 wherein L 1 , L 2 , R 1 , R 2 , R 3 , R 4 , R 5 and R 6 are each H for each bicyclic carbocyclic nucleoside having Formula II.
13. The oligomeric compound of claim 9 wherein Q is F for each bicyclic carbocyclic nucleoside having Formula II.
14. The oligomeric compound of claim 9 wherein Q is O(CH 2 ) 2 —OCH 3 for each bicyclic carbocyclic nucleoside having Formula II.
15. The oligomeric compound of claim 9 wherein each Bx is, independently, uracil, thymine, cytosine, 5-methylcytosine, adenine or guanine.
16. The oligomeric compound of claim 9 wherein one T 3 and or one T 4 is a terminal group.
17. The oligomeric compound of claim 9 wherein one T 3 or one T 4 is a conjugate group that may include a bifunctional linking moiety.
18. The oligomeric compound of claim 9 comprising a first region consisting of from 2 to 5 modified nucleosides, a second region consisting of from 2 to 5 modified nucleosides and a gap region consisting of from 6 to 14 monomer subunits located between the first and second region wherein at least one of the monomer subunits in the gap region or at least one of the modified nucleosides in the first region is a bicyclic carbocyclic nucleoside having Formula II.
19. The oligomeric compound of claim 18 wherein the gap region comprises from about 8 to about 10 monomer subunits.
20. The oligomeric compound of claim 18 wherein each monomer subunit in the gap region other than bicyclic carbocyclic nucleosides of Formula II is a β-D-2′-deoxyribonucleoside.
21. The oligomeric compound of claim 18 wherein each modified nucleoside in the first and second region is, independently, a bicyclic nucleoside comprising a bicyclic furanosyl sugar moiety or a modified nucleoside comprising a furanosyl sugar moiety having at least one substituent group.
22. The oligomeric compound of claim 18 wherein each modified nucleoside in the first and second region is, independently, a bicyclic nucleoside comprising a 4′-CH((S)—CH 3 )—O-2′ bridge or a 2′-O-methoxyethyl substituted nucleoside.
23. The oligomeric compound of claim 18 wherein each monomer subunit in the gap region is a β-D-2′-deoxyribonucleoside.
24. The oligomeric compound of claim 9 wherein each internucleoside linking group is, independently, a phosphodiester internucleoside linking group or a phosphorothioate internucleoside linking group.
25. A method of inhibiting gene expression comprising contacting a cell with an oligomeric compound of claim 9 wherein said oligomeric compound is complementary to a target RNA.
26. The method of claim 25 wherein said target RNA is selected from mRNA, pre-mRNA and micro RNA.
27. The method of claim 25 further comprising detecting the levels of target RNA.
28. An in vitro method of inhibiting gene expression comprising contacting one or more cells or a tissue with an oligomeric compound of claim 9 .