5'-END DERIVATIVES

• US 20130323836A1
• Filed: 04/22/2011
• Published: 12/05/2013
• Est. Priority Date: 04/22/2010
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Manoharan, Muthiah, Rajeev, Kallanthottathil G., Zlatev, Ivan, Swayze, Eric E., Prakash, Thazha P., Lima, Walter F.
• Granted Patent: US 9,725,479 B2
• Time in Patent Office: Days
• US Class Current: 435/375
• CPC Class Codes: C07H 17/02 Heterocyclic radicals containing only nitrogen as ring hetero atoms
• CPC Class Codes: C07H 19/067 with ribosyl as the saccharide radical
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• 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 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/344 Position-specific modifications, e.g. on every purine, at the 3'-end
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy

Abstract

The present invention provides compounds of formula (1). Another aspect of the invention relates to a method of inhibiting the expression of a gene in call, the method comprising (a) contacting an oligonucleotide of the invention with the cell; and (b) maintaining the cell from step (a) for a time sufficient to obtain degradation of the mRNA of the target gene.

Claims

1-3. -3. (canceled)

4. A compound represented by the following formulas:

5. The compound of claim 4, represented by the following formulas:

9. The compound of claim 4 wherein Y′

and Y″

are independently for each occurrence (CH₂)_nOH, (CH₂)_nSCH₃, (CH₂)_nSH, COR₁₀₀, (CH₂)_nCOR₁₀₀, (CH₂)_nNQ₁Q₂, OP(Z₁₀)(Y₁₀)NQ₁Q₂, OP(Z₁₀)(X₁₀)Y₁₀, linear or branched alkyl, aryl, heteroaryl, or heterocyclic.

10. The compound of claim 4 wherein n is 1-4.

12. The compound of claim 4 wherein R₁₀₀ is OH or alkoxy.

18. The compound of claim 4 wherein Z₁ is oligonucleotide.

19. An oligonucleotide comprising at least one compound of claim 18.

21. The oligonucleotide of claim 19 wherein the oligonucleotide comprises:

1-20 first-type regions, each first-type region independently comprising 1-20 contiguous nucleosides wherein each nucleoside of each first-type region comprises a first-type modification;

0-20 second-type regions, each second-type region independently comprising 1-20 contiguous nucleosides wherein each nucleoside of each second-type region comprises a second-type modification; and

0-20 third-type regions, each third-type region independently comprising 1-20 contiguous nucleosides wherein each nucleoside of each third-type region comprises a third-type modification,

wherein the first-type modification, the second-type modification, and the third-type modification are each independently selected from 2′

-F, 2′

-OCH₃, 2′

-0(CH₂)2OCH₃, BNA, F—

HNA, 2′

-H and 2′

-OH.

22. The oligonucleotide of claim 19, wherein the oligonucleotide comprises at least one non-phosphodiester internucleoside linkage.

23. The oligonucleotide of claim 22, wherein the non-phosphodiester internucleoside linkage is selected from a group consisting of phosphorothioate, phosphorodithioate, H-phosphonate, alkyl-phosphonate, phosphoramidate internucleoside linkage, and any combinations thereof.

24. The oligonucleotide of claim 19, wherein the oligonucleotide comprises one or more regions of alternating 2′

-F and 2′

-OMe modified nucleotides.

25. The oligonucleotide of claim 19, wherein the oligonucleotide comprises one or more regions of alternating non-phosphodiester internucleoside linkage and phosphodiester internucleoside linkage.

26. The oligonucleotide of claim 19, wherein the oligonucleotide comprises one or more alternating regions of (2′

-F)—

(PS)-(2′

-OMe)-(PO).

27. The oligonucleotide of claim 19, wherein the oligonucleotide comprises at least one ligand conjugate.

29. The oligonucleotide of claim 19, wherein the oligonucleotide is double stranded comprising first strand and second strand.

33. The oligonucleotide of claim 19, wherein the oligonucleotide is single stranded.

34. The oligonucleotide of claim 33, wherein the single-stranded oligonucleotide is a single-stranded siRNA.

36. The oligonucleotide of claim 19, wherein the oligonucleotide is an antisense, an antagomir, a microRNA, a pre-microRNA, an antimir, a ribozyme or an aptamer.

37. A method of inhibiting the expression of a target gene in a cell, the method comprising contacting the cell with the oligonucleotide of claim 19.

38. The method of claim 37, wherein the target gene is selected from the group consisting of Factor VII, Eg5, PCSK9, TPX2, apoB, SAA, TTR, RSV, PDGF beta gene, Erb-B gene, Src gene, CR gene, GRB2 gene, RAS gene, MEK gene, JNK gene, RAF gene, Erk1/2 gene, PCNA(p21) gene, MYB gene, JUN gene, FOS gene, BCL-2 gene, Cyclin D gene, VEGF gene, EGFR gene, Cyclin A gene, Cyclin E gene, WNT-1 gene, beta-catenin gene, c-MET gene, PKC gene, NFKB gene, STAT3 gene, survivin gene, Her2/Neu gene, topoisomerase I gene, topoisomerase II alpha gene, p73 gene, p21(WAF1/CIP1) gene, p27(KIP1) gene, PPM1D gene, RAS gene, caveolin I gene, MIB I gene, MTAI gene, M68 gene, mutations in tumor suppressor genes, p53 tumor suppressor gene, and combinations thereof.

6-8. -8. (canceled)

11. (canceled)

13-17. -17. (canceled)

20. (canceled)

28. (canceled)

30-32. -32. (canceled)

35. (canceled)