Claims for Patent: 10,570,391

Summary for Patent: 10,570,391

Title:	RNAi agents, compositions and methods of use thereof for treating transthyretin (TTR) associated diseases
Abstract:	The present invention provides RNAi agents, e.g., double stranded RNAi agents, that target the transthyretin (TTR) gene and methods of using such RNAi agents for treating or preventing TTR-associated diseases.
Inventor(s):	Kallanthottathil G. Rajeev, Tracy Zimmermann, Muthiah Manoharan, Martin Maier, Satyanarayana KUCHIMANCHI, Klaus Charisse
Assignee:	Alnylam Pharmaceuticals Inc
Application Number:	US15/188,317
Patent Claims:	1. A double stranded RNAi agent comprising a sense strand complementary to an antisense strand, wherein said antisense strand comprises a region complementary to nucleotides 504 to 526 of the transthyretin (TTR) gene (SEQ ID NO:1), wherein each strand independently has 14 to 30 nucleotides, wherein said double stranded RNAi agent is represented by formula (III): sense: 5′ np -Na -(X X X)i-Nb - Y Y Y -Nb-(Z Z Z)j-Na - nq 3′ antisense: 3′ np′-Na′-(X′X′X′)k-Nb′-Y′Y′Y′-Nb′-(Z′Z′Z′)l-Na′- nq′ 5′ (III) wherein: i, j, k, and 1 are each independently 0 or 1, provided that at least one of i, j, k, and 1 is 1; p, p′, q, and q′ are each independently 0-6; each Na and Na′ independently represents an oligonucleotide sequence comprising 2-20 nucleotides which are modified, wherein the modifications on the nucleotides are 2′-O-methyl, 2′-fluoro or both; each Nb and Nb′ independently represents an oligonucleotide sequence comprising 1-10 nucleotides which are modified, wherein the modifications on the nucleotides are 2′-O-methyl, 2′-fluoro or both; each np, np′, nq, and nq′ independently represents an overhang nucleotide; XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides; and wherein the sense strand is conjugated to at least one ligand. 2. The RNAi agent of claim 1, wherein j is 1; or wherein 1 is 1; or wherein both j and 1 are 1. 3. The RNAi agent of claim 1, wherein XXX is complementary to X′X′X′, YYY is complementary to Y′Y′Y′, and ZZZ is complementary to Z′Z′Z′. 4. The RNAi agent of claim 1, wherein the YYY motif occurs at or near the cleavage site of the sense strand; or wherein the Y′Y′Y′ motif occurs at the 11, 12 and 13 positions of the antisense strand from the 5′-end. 5. The RNAi agent of claim 4, wherein the Y′ is 2′-O-methyl. 6. The RNAi agent of claim 1, wherein formula (III) is represented as formula (IIIa): sense: 5′ np -Na -Y Y Y -Nb -Z Z Z -Na-nq 3′ antisense: 3′ np′-Na′-Y′Y′Y′-Nb′-Z′Z′Z′-Na′nq′ 5′ (IIIa) wherein each Nb and Nb′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides; or wherein formula (III) is represented as formula (IIIb): sense: 5′ np -Na -X X X -Nb -Y Y Y -Na-nq 3′ antisense: 3′ np′-Na′-X′X′X′-Nb′-Y′Y′Y′-Na′-nq′ 5′ (IIIb) wherein each Nb and Nb′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides; or wherein formula (III) is represented as formula (IIIc): sense: 5′ np-Na-X X X -Nb-Y Y Y -Nb-Z Z Z-Na- nq 3′ antisense: 3′ np′-Na′-X′X′X′-Nb′-Y′Y′Y′-Nb′-Z′Z′ Z′-Na′-nq′ 5′ (IIIc) wherein each Nb and Nb′ independently represents an oligonucleotide sequence comprising 1-5 modified nucleotides and each Na and Na′ independently represents an oligonucleotide sequence comprising 2-10 modified nucleotides. 7. The RNAi agent of claim 1, wherein the sense strand and the antisense strand form a duplex region which is 15-30 nucleotide pairs in length. 8. The RNAi agent of claim 7, wherein the duplex region is 17-25 nucleotide pairs in length. 9. The RNAi agent of claim 1, wherein each strand independently has 19-25 nucleotides. 10. The RNAi agent of claim 1, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker. 11. The RNAi agent of claim 1, wherein the ligand is 12. The RNAi agent of claim 1, wherein the ligand is attached to the 3′ end of the sense strand. 13. The RNAi agent of claim 12, wherein the RNAi agent is conjugated to the ligand as shown in the following schematic wherein X is O or S. 14. The RNAi agent of claim 1 further comprising at least one phosphorothioate or methylphosphonate internucleotide linkage. 15. The RNAi agent of claim 14, wherein the phosphorothioate or methylphosphonate internucleotide linkage is at the 3′-terminal of one strand. 16. The RNAi agent of claim 15, wherein said strand is the antisense strand. 17. The RNAi agent of claim 1, wherein the Y nucleotides contain a 2′-fluoro modification and wherein the Y′ nucleotides contain a 2′-O-methyl modification. 18. The RNAi agent of claim 1, wherein p′=2. 19. The RNAi agent of claim 18, wherein q′=0, p=0, q=0, and p′ overhang nucleotides are complementary to the target mRNA. 20. The RNAi agent of claim 18, wherein at least one np′ is linked to a neighboring nucleotide via a phosphorothioate linkage. 21. The RNAi agent of claim 18, wherein q′=0, p=0, q=0, and p′ overhang nucleotides are non-complementary to the target mRNA. 22. The RNAi agent of claim 1, wherein the double stranded RNAi agent comprises a double stranded RNAi agent selected from the group consisting of AD-51546 (5′-UfgGfGfAfuUfuCfAfUfgUfaAfcCfAfAfgAfL96-3′ (SEQ ID NO: 2210) and 5′-uCfuugGfuUfaCfaugAfaAfuccCfasUfsc-3′ (SEQ ID NO: 2216)), and AD-51547 (5′-UfgGfgAfuUfuCfAfUfgUfaacCfaAfgAfL96-3′ (SEQ ID NO: 2211) and 5′-uCfuUfgGfUfUfaCfaugAfaAfuCfcCfasUfsc-3′ (SEQ ID NO: 2217)), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, and U; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C and U; s is a phosphorothioate linkage; and L96 is a GalNAc3 ligand. 23. The RNAi agent of claim 1, wherein each of the sense strand and the antisense strand independently have 21 to 23 nucleotides. 24. The RNAi agent of claim 1, wherein the sense strand has a total of 21 nucleotides and the antisense strand has a total of 23 nucleotides. 25. The RNAi agent of claim 1, wherein the Z nucleotides contain a 2′-O-methyl modification. 26. The RNAi agent of claim 1, wherein the RNAi agent is AD-51547 (5′-UfgGfgAfuUfuCfAfUfgUfaacCfaAfgAfL96-3′ (SEQ ID NO: 2211) and 5′-uCfuUfgGfUfUfaCfaugAfaAfuCfcCfasUfsc-3′ (SEQ ID NO: 2217)), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, and U; Af, Gf, Cf, and Uf are 2′-fluoro A, G, C and U; s is a phosphorothioate linkage; and L96 is a GalNAc3 ligand. 27. An isolated cell containing the RNAi agent of claim 1. 28. A pharmaceutical composition comprising the RNAi agent of claim 1. 29. A double stranded RNAi agent for inhibiting expression of TTR in a cell, wherein said double stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region; wherein the sense strand comprises the nucleotide sequence 5′-UGGGAUUUCAUGUAACCAAGA 3′ (SEQ ID NO:2211) and the antisense strand comprises the nucleotide sequence 5′-UCUUGGUUACAUGAAAUCCCAUC-3′ (SEQ ID NO:2217); wherein substantially all of the nucleotides of said sense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification; wherein substantially all of the nucleotides of said antisense strand comprise a modification selected from the group consisting of a 2′-O-methyl modification and a 2′-fluoro modification; and wherein said sense strand is conjugated to one or more GalNAc derivatives attached through a branched bivalent or trivalent linker at the 3′-terminus. 30. A method of inhibiting expression of a transthyretin (TTR) in a cell comprising contacting said cell with the RNAi agent of claim 1 in an amount effective to inhibit expression of said TTR in said cell, thereby inhibiting expression of said transthyretin (TTR) in said cell. 31. A method of treating a TTR-associated disease in a subject, comprising administering to said subject a therapeutically effective amount of the RNAi agent of claim 1, thereby treating said TTR-associated disease in said subject. 32. The method of claim 31, wherein said subject is a human. 33. The method of claim 31, wherein said subject carries a TTR gene mutation that is associated with the development of a TTR-associated disease. 34. The method of claim 31, wherein said TTR-associated disease is selected from the group consisting of senile systemic amyloidosis (SSA), systemic familial amyloidosis, familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy (FAC), leptomeningeal/Central Nervous System (CNS) amyloidosis, and hyperthyroxinemia. 35. The method of claim 31, wherein said subject has a TTR-associated amyloidosis and said method reduces an amyloid TTR deposit in said subject. 36. The method of claim 31, wherein said RNAi agent is administered to the subject subcutaneously. 37. A kit for performing the method of claim 30 or 31, comprising a) said RNAi agent, and b) instructions for use. 38. The kit for performing the method of claim 37, further comprising means for administering said RNAi agent to said subject. 39. A method of inhibiting production of TTR protein in a cell, comprising contacting the cell with the RNAi agent of claim 1, thereby inhibiting production of TTR protein in the cell. 40. The method of claim 39, wherein the cell is within a subject. 41. The method of claim 40, wherein the subject is a human subject. 42. The method of claim 41, wherein said subject carries a TTR gene mutation that is associated with the development of a TTR-associated disease. 43. The method of claim 42, wherein the subject has a TTR-associated amyloidosis and the method reduces an amyloid TTR deposit in the subject. 44. A method of inhibiting production of an amyloid TTR deposit in a subject carrying a mutation that is associated with development of a TTR-associated amyloidosis, comprising administering to the subject the RNAi agent of claim 1, thereby inhibiting production of the amyloid TTR deposit in the subject. 45. The method of claim 44, wherein the subject is a human subject.