5′-cyclo-phosphonate modified nucleotides
Described are 5′-cyclo-phosphonate modified nucleotides, and oligonucleotides, such as interference (RNAi) agents, containing 5′-cyclo-phosphonate modified nucleotides. The RNAi agents having either double-stranded or single-stranded oligonucleotides described herein comprising 5′cyclo-phosphonate modified nucleotides are useful in modulating gene expression as well as therapeutic, diagnostic, target validation, and genomic discovery applications. The RNAi agents and single-stranded antisense oligonucleotides comprising 5′-cyclo-phosphonate modified nucleotides are useful in the treatment of diseases or conditions that respond to inhibition of gene expression or activity in a cell, tissue, or organism.
1. A compound having Formula A:
wherein:
Cyclo is
X′ is
X″ comprises a substituent derived from a phosphate or phosphorothioate moiety of an RNAi agent;
D is O or S;
X is a 9-purinyl or 1-pyrimidinyl base;
Z is H, —OH, F, OCH 3 , —O—(CH 2 ) 2 —OCH 3 or halogen;
Y 1 , Y 2 , Y 3 , and Y 4 are each, independently, H, halogen, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl,
J is O r S; and
K and L are each independently selected from OH, OR 16 , SR 16 , or NR 16 , wherein R 16 is selected from H, C 1 -C 10 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, aryl, or
wherein R 14 is selected from H or C 1 -C 4 alkyl optionally substituted with one to three substituents independently selected from SH, S—(C1-C4 alkyl), amino, hydroxyl, oxo or —NH—C═(NH)NH 2 , and R 15 is selected from H, or C 1 -C 18 alkyl.
2. The compound of claim 1 , having Formula I or Formula II:
wherein,
Q is a divalent moiety selected from O, S, N(R 30 ), or C(R 31 )(R 32 ), wherein R 30 is H, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and R 31 and R 32 are each, independently, H, halogen, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl; and
A a substituent derived from a phosphate or phosphorothioate moiety of an RNAi agent.
3. The compound of claim 2 wherein Q is O.
4. The compound of claim 1 , wherein Cyclo is:
5. The compound of claim 1 , wherein the RNAi agent is double-stranded.
6. The compound of claim 1 , wherein X is 1-uracilyl, 1-thyminyl, 1-cytosinyl, 5-methyl-1-cytosinyl, 9-adeninyl, 9-guaninyl, or 9-inosinyl.
7. A composition comprising the compound of claim 1 .
8. A composition comprising an RNAi agent, wherein the RNAi agent comprises the compound of claim 1 .
9. The composition of claim 8 , wherein the RNAi agent is double stranded.
10. A compound having the structure of Formula I-b or Formula II-b:
wherein,
D is O or S;
X is a 9-purinyl or 1-pyrimidinyl base:
Z is H, —OH, F, OCH 3 , —O—(CH 2 ) 2 —OCH 3 or halogen;
Y 1 , Y 2 , Y 3 , and Y 4 are each, independently, H, halogen, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl,
J is O or S;
K and L are each independently selected from OH, OR 16 , SR 16 , or NR 16 , wherein R 16 is selected from H, C 1 -C 10 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, aryl, or
wherein R 14 is selected from H or C 1 -C 4 alkyl optionally substituted with one to three substituents independently selected from SH, S—(C1-C4 alkyl), amino, hydroxyl, oxo or —NH—C═(NH)NH 2 , and R 15 is selected from H, or C 1 -C 18 alkyl;
Q is a divalent moiety selected from O, S, N(R 30 ), or C(R 31 )(R 32 ), wherein R 30 is H, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl, and R 31 and R 32 are each, independently, H, halogen, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, or C 2 -C 6 alkynyl; and
A comprises a substituent derived from a phosphate or phosphorothioate moiety of an RNAi agent; and
G 1 , G 2 , G 3 and G 4 are each H.
11. The compound of claim 10 , wherein Q is O.
12. A compound having Formula I-b-5 or Formula II-b-5:
wherein,
D is O or S,
X is a 9-purinyl or 1-pyrimidinyl base;
Z is H, —OH, F, OCH 3 , —O—(CH 2 ) 2 —OCH 3 or halogen;
Y 1 , Y 2 , Y 3 , and Y 4 are each, independently, H, halogen, C 1 -C 6 alkyl, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, or C 2 -C 6 alkynyl;
J is O or S;
K and L are each independently selected from OH, OR 16 , SR 16 , or NR 16 , wherein R 16 is selected from H, C 1 -C 10 alkyl, C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, aryl, or
wherein R 14 is selected from H or C 1 -C 4 alkyl optionally substituted with one to three substituents independently selected from SH, S—(C1-C4 alkyl), amino, hydroxyl, oxo or —NH—C═(NH)NH 2 , and R 15 is selected from H, or C 1 -C 18 alkyl; and
G 1 , G 2 , G 3 and G 4 are each independently selected from the group consisting of H, F, halogen, C 1 -C 6 alkyl, CN, CH 2 (R 33 ), CH 2 —O—(R 33 ), C(═O)(R 33 ), C(═S)(R 33 ), or (R 34 )(R 33 ), wherein R 33 is O(R 35 ), S(R 35 ), or N(R 35 )(R 36 ), wherein R 34 , R 35 , and R 36 are each independently selected from H, halogen, or C 1 -C 6 alkyl.
13. The compound of claim 12 , wherein the compound has the following structure:
14. A compound having Formula III-b or Formula IV-b:
wherein:
X is a 9-purinyl or 1-pyrimidinyl base;
Z is H, —OH, F, OCH 3 , —O—(CH 2 ) 2 —OCH 3 or halogen;
J and J′ are each independently O or S; and
comprises a substituent derived from an RNAi agent.
15. The compound of claim 1 , wherein the compound has the formula selected from the group consisting of:
or a pharmaceutically acceptable salt thereof.
16. A composition comprising the RNAi agent of claim 1 and a pharmaceutically acceptable excipient.
17. A method of inhibiting expression of a target nucleic acid in a subject in need thereof, the method comprising administering to the subject a therapeutic amount of an RNAi agent of claim 1 .
18. A method of treating a disease or disorder in a subject in need thereof, the method comprising administering a therapeutic amount of the composition of claim 8 to a subject in need of treatment thereof.
19. A method of inhibiting expression of a target nucleic acid in a subject in need thereof, the method comprising administering to the subject a therapeutic amount of a composition of claim 8 .