Manufacture of antisense oligomers and conjugates targeting PCSK9
The present invention relates to oligomeric compounds and conjugates thereof that target Proprotein Convertase Subtilisin/Kexin type 9 (PCSK9) PCSK9 mRNA in a cell, leading to reduced expression of PCSK9. Reduction of PCSK9 expression is beneficial for a range of medical disorders, such as hypercholesterolemia and related disorders.
1. A method of manufacturing a compound consisting of an antisense oligomer that is 16 contiguous nucleotides in length, the method comprising chemically synthesizing the compound using sequential solid phase oligonucleotide synthesis, wherein the sequence of the antisense oligomer is 100% complementary to the sequence of SEQ ID NO: 31, wherein the antisense oligomer is a gapmer comprising at least one LNA unit, and wherein the antisense oligomer targets mRNA encoding PCSK9.
2. The method of claim 1 , wherein the antisense oligomer is an intermediate.
3. The method of claim 1 , wherein the sequence of the antisense oligomer is SEQ ID NO: 26.
4. The method of claim 1 , wherein the LNA is oxy-LNA, thio-LNA, amino-5 LNA, 5′-methyl-LNA, ENA, cET, cMOE or a combination thereof.
5. The method of claim 1 , wherein the LNA is a stereoisomer in the beta-D-configuration or the alpha-L configuration.
6. The method of claim 1 , wherein the antisense oligomer comprises at least one cET unit.
7. The method of claim 1 , wherein the antisense oligomer comprises six or seven LNA units.
8. The method of claim 7 , wherein every LNA unit in the antisense oligomer is a beta-D-oxy LNA unit or every LNA unit in the antisense oligomer is an alpha-L-oxy-LNA unit.
9. The method of claim 7 , wherein every LNA unit in the antisense oligomer is a stereoisomer in the same configuration.
10. The method of claim 1 , wherein the sequence of the antisense oligomer comprises at least one phosphorothioate, phosphorodithioate, or boranophosphate internucleoside linkage.
11. The method of claim 10 , wherein all the internucleoside linkages are phosphorothioate.
12. The method of claim 10 , wherein one or more of the inernucleoside linkages comprises a chiral center in the R conformation and/or in the S conformation.
13. The method of claim 1 , wherein the sequence of the antisense oligomer is SEQ ID NO: 2.
14. The method of claim 1 , wherein the sequence of the antisense oligomer is SEQ ID NO: 3.
15. The method of claim 1 , wherein the compound and an oligomer of SEQ ID NO:31 can form a duplex with increased thermal stability with respect to a corresponding duplex comprising the corresponding antisense oligomer without LNA.
16. A method of manufacturing an antisense oligonucleotide conjugate comprising covalently attaching at least one non-nucleotide or non-polynucleotide moiety covalently to an antisense oligomer that is 16 contiguous nucleotides in length directly or via a linker positioned between the antisense oligomer sequence and the non-nucleotide or non-polynucleotide moiety, wherein the sequence of the antisense oligomer is 100% complementary to the sequence of SEQ ID NO: 31, wherein the antisense oligomer is a gapmer comprising at least one LNA unit, and wherein the antisense oligonucleotide conjugate targets mRNA encoding PCSK9.
17. The method of claim 16 , wherein the non-nucleotide or non-polynucleotide moiety is a liver targeting moiety that is attached to the 5′-end or to the 3′-end of the antisense oligomer.
18. The method of claim 17 , wherein the liver targeting moiety is linked to the antisense oligomer via a linker.
19. The method of claim 18 , wherein the linker is a biocleavable linker.
20. The method of claim 17 , wherein the liver targeting moiety comprises a carbohydrate conjugate moiety comprising a carbohydrate or a carbohydrate group.
21. The method of claim 20 , wherein the carbohydrate is selected from the group consisting of galactose, lactose, N-acetylgalactosamine (GalNAc), mannose, mannose-6-phosphate, and combinations thereof.
22. The method of claim 20 , wherein the carbohydrate conjugate moiety is not a linear carbohydrate polymer.
23. The method of claim 20 , wherein the carbohydrate conjugate moiety is a carbohydrate group comprising 1 2, 3, or 4 carbohydrate moieties.
24. The method of claim 23 , wherein the carbohydrate moieties are identical or non-identical.
25. The method of claim 23 , wherein the carbohydrate moieties are non-identical.
26. The method of claim 20 , wherein the carbohydrate conjugate moiety comprises at least one asialoglycoprotein receptor targeting conjugate moiety.
27. The method of claim 26 , wherein the asialoglycoprotein receptor targeting conjugate moiety comprises a GalNAc cluster.
28. The method of claim 26 , wherein the asialoglycoprotein receptor targeting conjugate moiety comprises a monovalent, divalent, trivalent, or tetravalent GalNAc cluster.
29. The method of claim 27 , wherein the GalNAc cluster is a trivalent GalNAc cluster.
30. The method of claim 29 , wherein each GalNAc in the trivalent GalNAc cluster is attached to a branch point group via a spacer.
31. The method of claim 30 , wherein the branch point group comprises di-lysine.
32. The method of claim 30 , wherein the spacer comprises a PEG spacer.
33. The method of claim 18 , wherein the linker comprises a C6 to C12 amino alkyl group or a biocleavable phosphate nucleotide linker comprising between 1 to 6 nucleotides.
34. The method of claim 29 , wherein the trivalent GalNAc cluster comprises Conj 2a:
35. The method of claim 16 , wherein the non-nucleotide or non-polynucleotide moiety is covalently attached to the antisense oligomer via a covalent bond.
36. The method of claim 16 , wherein the antisense oligonucleotide conjugate is SEQ ID NO: 18.
37. The method of claim 16 , wherein the antisense oligonucleotide conjugate is SEQ ID NO: 19.
38. The method of claim 16 , wherein covalently attaching the at least one non-nucleotide or non-polynucleotide moiety to the antisense oligomer comprises:
(i) chemically synthesizing the antisense oligomer; and,
(ii) adding by chemical synthesis or conjugation the at least one non-nucleotide or non-polynucleotide moiety to the antisense oligonucleotide conjugate.
39. The method of claim 38 , wherein adding by chemical synthesis or conjugation the at least one non-nucleotide or non-polynucleotide moiety to the antisense oligonucleotide conjugate comprises:
(i) incorporating by chemical synthesis or conjugation at least one non-nucleotide or non-polynucleotide moiety to the antisense oligonucleotide conjugate;
(ii) incorporating by chemical synthesis or conjugation at least one linker to the antisense oligonucleotide conjugate;
(iii) incorporating by chemical synthesis or conjugation at least one branching point to the antisense oligonucleotide conjugate;
(iv) incorporating by chemical synthesis or conjugation at least one spacer to the antisense oligonucleotide conjugate; or,
(v) a combination thereof.
40. The method of claim 39 , wherein at least one linker is interposed between the antisense oligomer and a branching point.
41. The method of claim 39 , wherein at least one branching point is interposed between a linker and at least one non-nucleotide or non-polynucleotide moiety.
42. The method of claim 39 , wherein at least one, two, or three non-nucleotide or non-polynucleotide moieties are attached to a branching point.
43. The method of claim 39 , wherein at least one PEG spacer is interposed between each of the one, two, or three non-nucleotide or non-polynucleotide moieties and a branching point.
44. A method of manufacturing an antisense oligonucleotide conjugate of SEQ ID NO: 18
wherein
a superscript L identifies a beta-D-oxy LNA unit,
a Me C identifies a 5-methylcytosine unit,
a subscript s identifies a phosphorothioate internucleoside linkage,
and wherein
is a Conj 2a asialoglycoprotein receptor targeting conjugate moiety
and wherein the antisense oligonucleotide conjugate targets mRNA encoding PCSK9, the method comprising covalently attaching the Conj 2a asialoglycoprotein receptor targeting conjugate moiety to the 5′ end of an antisense oligomer of SEQ ID NO: 2.
45. A method of manufacturing an antisense oligonucleotide conjugate of SEQ ID NO: 19
wherein
a superscript L identifies a beta-D-oxy LNA unit,
a Me C identifies a 5-methylcytosine unit,
a subscript s identifies a phosphorothioate internucleoside linkage,
and wherein
is a Conj 2a asialoglycoprotein receptor targeting conjugate moiety
and wherein the antisense oligonucleotide conjugate targets mRNA encoding PCSK9, the method comprising covalently attaching the Conj 2a asialoglycoprotein receptor targeting conjugate moiety to the 5′ end of an antisense oligomer of SEQ ID NO: 3.