LNA-G process

Patent metadata

Field	Value
Publication number	US-11591594-B2
Application number	US-202016812233-A
Country	US
Kind code	B2
Filing date	Mar 6, 2020
Priority date	Aug 24, 2015
Publication date	Feb 28, 2023
Grant date	Feb 28, 2023

Abstract

Recent advancements in LNA oligonucleotides include the use of amine linkers to link an LNA antisense oligonucleotide to a conjugate group. For example please see WO2014/I18267. The present invention originates from the identification of a problem when de-protecting LNA oligonucleotides which comprise an aliphatic amine group and DMF protected LNA G nucleoside, which results in the production of a +28 Da impurity. This problem is solved by using acyl protection groups on the exocyclic nitrogen of the LNA-G residue, rather than the standard DMF protection group.

First claim

The invention claimed is:

1. A method of preparing a LNA oligonucleotide comprising the steps of:
a) incorporating at least one LNA-G monomer comprising an acyl protected exocyclic nitrogen into an oligonucleotide, wherein the acyl protection group on the exocyclic nitrogen of the LNA-G monomer(s) is isobutyryl (iBu);
b) incorporating at least one optionally protected aliphatic amine group into the oligonucleotide; and,
c) deprotecting the acyl protected exocyclic nitrogen of the at least one LNA-G monomer by removal of the acyl protection group,
wherein steps a) and b) can occur in either order.

2. The method according to claim 1 wherein the optionally protected aliphatic amine group is a primary or secondary amine.

3. The method according to claim 1 , wherein the optionally protected aliphatic amine group is a non nucleosidic amine group.

4. The method according to claim 1 , wherein the optionally aliphatic amine group is selected from the group consisting of an amino alkyl, alkylamino alkyl, piperidine, piperazine, pyrrolidine and imidazole.

5. The method according to claim 1 , wherein the optionally aliphatic amine group is selected from the group consisting of 5′-TFA-Amino-Modifier-C5-CE Phosphoramidite, 5′-TFA-Amino-Modifier C6-CE Phosphoramidite, 11-(trifluoroacetamido)-3,6,9-trioxaundecan-1-yl-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite, 5-TFA-Amino-Modifier-C12-CE Phosphoramidite, Amino-Modifier C2-dT-CE Phosphoramidite, Amino-Modifier C6-dA-CE Phosphoramidite, Amino-Modifier C6-dA-CE Phosphoramidite, Amino-Modifier C6-dT-CE Phosphoramidite, N2-Amino-Modifier C6 dG, Fmoc Amino-Modifier C6 dT, 3′-Amino-Modifier C7 CPG 1000, 3′-Amino-Modifier C6-dC CPG, 3′-Amino-Modifier C6-dC CPG, 3′-PT-Amino-Modifier C6 CPG, 3′-Amino-Modifier C6-dT CPG, PC 5′-Amino-Modifier-CE Phosphoramidite, 5′-Amino-Modifier C6-PDA, 5′-Amino-Modifier C12-PDA, 5′-Amino-Modifier TEG PDA, Amino-Modifier Serinol and 3′-Amino-Modifier Serinol CPG.

6. The method according to claim 1 , wherein the optionally protected aliphatic amine group is an amino hexyl linker.

7. The method according to claim 1 , wherein the aliphatic amine group is incorporated into the oligonucleotide via the incorporation of an amino-modified monomer.

8. The method according to claim 7 , wherein the aliphatic amino-modified monomer is a phosphoramidite, a H phosphonate or a phosphotriester monomer.

9. The method according to claim 7 , wherein the amino-modified monomer is a phosphoramidite.

10. The method according to claim 1 , wherein, if present, other G residues incorporated into the oligonucleotide also comprise an acyl protection group.

11. The method according to claim 1 , wherein the LNA-G monomer(s), and optionally when present other G monomers, is a phosphoramidite, a H-phosphonate or a phosphotriester monomer.

12. The method according to claim 1 , wherein the LNA-G monomer(s), and optionally when present other G monomers, is a phosphoramidite.

13. The method according to claim 1 , wherein the LNA-G monomer comprises a 2′-O—CH 2 -4′ biradical in the furanose ring.

14. The method according to claim 1 , wherein step c) further comprises deprotection of the aliphatic amine group.

15. The method according to claim 1 , wherein step c) comprises deprotection of the oligonucleotide performed in the presence of ammonia.

16. The method according to claim 1 , wherein step c) is followed by an additional step (d) which comprises incorporating a conjugate group onto the aliphatic primary amine group.

17. The method according to claim 16 , wherein the conjugate group is a non-nucleotide moiety, selected from the group consisting of a lipid, a sterol, a carbohydrate, a peptide and a protein.

18. The method according to claim 1 , wherein at least steps a)-c) are performed on a solid support and are followed by the cleavage of the oligonucleotide from the solid support which may be performed during step c) or subsequent to step c).

19. The method according to claim 1 , wherein the acyl protection group(s) is isobutyryl and the aliphatic primary amine group(s) is an aminohexyl linker.

20. The method of claim 15 wherein the deprotection of the oligonucleotide is performed in a solution of ammonium hydroxide.

21. An LNA oligonucleotide which comprises at least one LNA-G monomer comprising an acyl protected exocyclic nitrogen and at least one optionally protected aliphatic amine group, wherein said LNA oligonucleotide is attached to a solid support, and wherein the acyl protection group on the acyl protected exocyclic nitrogen of the LNA-G monomer(s) is isobutyryl (iBu).

Assignees

• Roche Innovation Ct Copenhagen As

Inventors

• Hansen Dennis Jul
• Hoernschemeyer Joerg
• Ravn Jacob
• Rosenbohm Christoph

Classifications

• C12N2310/3231

  having an additional ring, e.g. LNA, ENA · CPC title

• C12N15/111 Primary

  General methods applicable to biologically active non-coding nucleic acids · CPC title

• C12N2310/311

  Phosphotriesters · CPC title

• C12N2330/30

  chemically synthesised · CPC title

• C07H21/00

  Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids · CPC title