Oligonucleotide Compositions and Related Methods - Patent application

Abstract

The present disclosure features useful oligonucleotide compositions and methods related thereto.The present disclosure encompasses the recognition that structural elements of oligonucleotides, such as base sequence, chemical modifications (e.g., sugar modifications, bases and / or internucleotide linkages) or patterns thereof, can have significant effects on oligonucleotide properties and activity.The present disclosure also provides a method for treating disorders in which deamination of adenosine in mRNA, for example, results in therapeutic outcomes in subjects in need thereof.

Claims

1. Oligonucleotide, 5'-N １ N ０ N －１ -3' is included, N －１ , N ０ and N １ Each of them is independently a nucleoside, (a) N ０ The nucleic acid base is BA, and BA is 【Chemistry 1】 Either BA comprises ring BA or its tautomers, and ring BA is of formula BA-III-e: 【Chemistry 2】 (In the formula, X １ is -N(-)- or -C(-)=, W Ｘ２ and W Ｘ６ each of which is, independently, O, S or Se, R Ｂ４ These are halogen, -CN, -NO ２ or -L Ｂ４ -R Ｂ４１ And R Ｂ４１ is R', R Ｂ５ These are halogen, -CN, -NO ２ or -L Ｂ５ -R Ｂ５１ And R Ｂ５１ is -R', -N(R') ２ , -OR' or -SR', L Ｂ４ and L Ｂ５ Each of them is independent of L Ｂ And, Each L Ｂ These are independently, optionally substituted divalent carbon atoms having covalent bonds or 0 to 6 heteroatoms. １～１０ A saturated or partially unsaturated chain, in which one or more methylene units are optionally and independently -Cy-, -O-, -S-, -N(R')-, -C(O)-, -C(S)-, -C(NR')-, -C(O)N(R')-, -N(R')C(O)N(R')-, -N(R')C(O)O-, -S(O)-, -S(O) ２ -, -S(O) ２ It is replaced by N(R')-, -C(O)S-, or -C(O)O-, Each -Cy- is independently an optionally substituted 3- to 20-membered monocyclic, bicyclic, or polycyclic ring having 0 to 10 heteroatoms. Each R' is independently -R, -C(O)R, -C(O)OR, -C(O)N(R) ２ or -SO ２ R is, and Each R is independently -H or C １～２０ Aliphatic carbon atoms containing 1 to 10 heteroatoms １～２０ Heteroliphatic, C ６～２０ Ariel, C ６～２０ Aryl aliphatic carbon atoms containing 1 to 10 heteroatoms ６～２０ The group is an optionally substituted group selected from aryl heteroaliphatic groups, 5-20 membered heteroaryl groups having 1-10 heteroatoms, and 3-20 membered heterocyclines having 1-10 heteroatoms, or The two R groups may, either selectively and independently, form a covalent bond together, or Two or more R groups on the same atom may, optionally and independently, together with the atom, form an optionally substituted 3-20 member monocyclic, bicyclic, or polycyclic ring having 0-10 heteroatoms in addition to the atom, or Two or more R groups on two or more atoms, optionally and independently, together with their intercalating atoms, form optionally substituted 3-30 member monocyclic, bicyclic, or polycyclic rings having 0-10 heteroatoms in addition to the intercalating atoms. It has a structure, and (b) N ０ The sugar contains a 2'-OR modification, where R is optionally substituted with C. １～６ Oligonucleotides are aliphatic organisms.

2. N ０ The nucleic acid bases are, 【Transformation 3】 【Chemistry 4】 【Transformation 5】 and 【Transformation 6】 An oligonucleotide according to claim 1, selected from the following.

3. N ０ The oligonucleotide according to claim 2, wherein the sugar is a 2'-OMe modified sugar.

4. The oligonucleotide according to claim 1, comprising one or more 2'-F modified sugars.

5. The oligonucleotide according to claim 1, having a length of approximately 10 to 200 nucleic acid bases.

6. (i) containing about 1 to 50 sugars having 2'-F modification, or about 5% to 100% of the sugars in the oligonucleotide containing 2'-F modification; (ii) Containing about 1 to 50 sugars having 2'-OMe modification, or about 5% to 100% of the sugars in the oligonucleotide contain 2'-OMe modification. (iii) containing about 1 to 50 sugars having 2'-MOE modification, or about 5% to 100% of the sugars in the oligonucleotide containing 2'-MOE modification; and / or (iv) comprising one or more 2'-F blocks and one or more isolated blocks, wherein each sugar in each 2'-F block is independently a 2'-F modified sugar, and each sugar in each isolated block is independently a sugar other than a 2'-F modified sugar. Optionally, (a) The oligonucleotide contains two or more 2'-F blocks, (b) Two or more isolation blocks are present in the oligonucleotide. (c) Each isolated block independently contains a 2'-OR modified sugar, where R is not -H; optionally, each sugar in each isolated block independently is a 2'-OR modified sugar or a bicyclic sugar, where R is optionally substituted with C １～６ It is aliphatic; each sugar in the optionally separated block is independently a 2'-OMe or 2'-MOE modified sugar, and / or (d) Each 2'-F block contains approximately 1, 2, 3, 4, or 5 2'-F modified sugars. The oligonucleotide according to claim 1.

7. 5'-N ２ N １ N ０ N －１ N －２ -3' is included, N ２ , N １ , N ０ , N －１ and N －２ Each of these is independently a nucleoside, and when the oligonucleotide is aligned with the target nucleic acid, N ０ This is the opposite side of the target adenosine; N １ The sugars are natural DNA sugars, 2'-F modified sugars, and 2'-OR modified sugars (wherein R is optionally substituted C). １～６ It is either an aliphatic or bicyclic sugar; N －１ The sugars are natural DNA sugars, 2'-F modified sugars, and 2'-OR modified sugars (wherein R is optionally substituted C). １～６ It is either an aliphatic or bicyclic sugar; N ２ and N １ The nucleotide bonds between them are natural phosphate bonds, PS nucleotide bonds (e.g., phosphorothioate nucleotide bonds), or PN nucleotide bonds (e.g., phosphorylguanidine nucleotide bonds such as n001); N １ and N ０ The nucleotide bonds between them are natural phosphate bonds, PS nucleotide bonds (e.g., phosphorothioate nucleotide bonds), or PN nucleotide bonds (e.g., phosphorylguanidine nucleotide bonds such as n001); N ０ and N －１ The nucleotide bonds between them are natural phosphate bonds, PS nucleotide bonds (e.g., phosphorothioate nucleotide bonds) or PN nucleotide bonds (e.g., phosphorylguanidine nucleotide bonds such as n001); and / or N －１ and N －２ The nucleotide bonds between them are natural phosphate bonds, PS nucleotide bonds (e.g., phosphorothioate nucleotide bonds), or PN nucleotide bonds (e.g., phosphorylguanidine nucleotide bonds such as n001). The oligonucleotide according to claim 1.

8. 5'-N ２ N １ N ０ N －１ N －２ N －３ -3' is included, N －３ It is independently a nucleoside, and N －２ and N －３ The oligonucleotide according to claim 1, wherein the nucleotide bond between is a natural phosphate bond, a PS nucleotide bond (e.g., a phosphorothioate nucleotide bond), or a PN nucleotide bond (e.g., a phosphorylguanidine nucleotide bond such as n001).

9. N －２ and N －３ The oligonucleotide according to claim 1, wherein the nucleotide bond between is a natural phosphate bond or a PS nucleotide bond (e.g., a phosphorothioate nucleotide bond).

10. The oligonucleotide according to claim 1, comprising one or more PN bonds.

11. An oligonucleotide, wherein at the position of the modified nucleotide bond, -O ５ -P Ｌ (R ＣＡ )-O ３ - (In the formula, P Ｌ is P or P (=W), W is O, S, or W Ｎ And, R ＣＡ This is an asymmetric auxiliary portion that is optionally substituted or capped, or includes such a portion. O ５ is the oxygen bonded to the 5'-carbon of the sugar, and O ３ (This is the oxygen atom bonded to the 3'-carbon of the sugar.) An oligonucleotide identical in all other respects to the oligonucleotide described in claim 1, except that the bond has a specific structure.

12. It is a phosphoramidite, The nucleic acid base of the phosphoramidite is the nucleic acid base described in claim 1 or a tautomer thereof, and the nucleic acid base or tautomer thereof is optionally substituted or protected; or The nucleic acid bases of the phosphoramidite are or contain a ring BA, and the ring BA has the structure of BA-I, BA-I-a, BA-I-b, BA-I-c, BA-I-d, BA-II, BA-II-a, BA-II-b, BA-II-c, BA-II-d, BA-III, BA-III-a, BA-III-b, BA-III-c, BA-III-d, BA-III-e, BA-IV, BA-IV-a, BA-IV-b, BA-V, BA-V-a, BA-V-b, or BA-VI or a tautomer of the ring BA, and the nucleic acid bases are optionally substituted or protected. The phosphoramidite wherein the sugar of the phosphoramidite is optionally the sugar described in claim 1, and the sugar is optionally protected.

13. A method for preparing an oligonucleotide or composition, comprising coupling the -OH group of the oligonucleotide or nucleoside with the phosphoramidite or compound described in claim 12.

14. A method for modifying a target adenosine in a target nucleic acid, comprising contacting the target nucleic acid with an oligonucleotide according to any one of claims 1 to 11, or A method for deaminating a target adenosine in a target nucleic acid, comprising contacting the target nucleic acid with an oligonucleotide according to any one of claims 1 to 11, or A method for producing a product of a specific nucleic acid or restoring or increasing its level, comprising contacting a target nucleic acid with an oligonucleotide described in any one of claims 1 to 11, wherein the target nucleic acid comprises a target adenosine, and the specific nucleic acid differs from the target nucleic acid in that the specific nucleic acid has I or G instead of the target adenosine, or A method for reducing the level of a target nucleic acid product, comprising contacting the target nucleic acid with an oligonucleotide according to any one of claims 1 to 11, wherein the target nucleic acid comprises a target adenosine, or A method for regulating protein-protein interactions in a system in which a protein is translated from its coding RNA, comprising contacting the coding RNA with an oligonucleotide according to any one of claims 1 to 11, wherein adenosine in the coding RNA is edited, and a protein is translated from the edited mRNA ("edited protein"), and the edited protein differs from an unedited protein in terms of amino acid residues involved in the protein-protein interaction, or A method for regulating the interaction of a protein with a drug in a system in which a protein is translated from its coding RNA, comprising contacting the coding RNA with an oligonucleotide according to any one of claims 1 to 11, wherein adenosine in the coding RNA is edited, and a protein is translated from the edited mRNA ("edited protein"), and the edited protein differs from the unedited protein in terms of amino acid residues involved in the protein-drug interaction, or A method for regulating the interaction of a protein with a drug in a system in which a protein is translated from its coding RNA, comprising administering an oligonucleotide according to any one of claims 1 to 11 to the system, wherein adenosine in the coding RNA is edited, and a protein is translated from the edited mRNA ("edited protein"), and the edited protein differs from the unedited protein in terms of amino acid residues involved in the protein-drug interaction, or A method for regulating the interaction between a protein and its partner protein in a system, comprising administering to the system an oligonucleotide according to any one of claims 1 to 11, wherein the oligonucleotide can edit adenosine in the nucleic acid encoding the protein or its partner protein, and the edited nucleic acid encodes a protein different from the protein encoded by the unedited nucleic acid at at least one amino acid residue involved in the interaction between the protein and its partner protein, or A method for regulating the level, structure and / or activity of a nucleic acid and / or a product encoded by it in a system, comprising contacting the nucleic acid with an oligonucleotide according to any one of claims 1 to 11, wherein adenosine in the nucleic acid is edited, or A method for regulating the level, structure and / or activity of a nucleic acid and / or a product encoded by it in a system, comprising administering to the system an oligonucleotide according to any one of claims 1 to 11, wherein adenosine in the nucleic acid is edited, or A method for editing transcripts in immune cells, comprising administering an effective amount of an oligonucleotide according to any one of claims 1 to 11 to the immune cells, or A method for delivering an oligonucleotide to a system, comprising administering a conjugate of the oligonucleotide to the system together with an additional chemical part or a salt thereof, or A method for improving the editing level of an oligonucleotide, comprising incorporating any one of claims 1 to 13 or a structural element described in this disclosure.

15. An oligonucleotide for preventing or treating a pathological condition, disorder, or disease, which is administered or delivered in an effective amount to a subject who is susceptible to or suffering from such condition, according to any one of claims 1 to 11.

16. Use of an oligonucleotide according to any one of claims 1 to 11 for modifying mRNA splicing, wherein the target adenosine of mRNA is edited, used, or Use of an oligonucleotide according to any one of claims 1 to 11 for silencing protein expression, wherein the target adenosine of the protein-encoding mRNA is edited, used, or Use of an oligonucleotide according to any one of claims 1 to 11 for repairing a nonsense mutation, wherein the target adenosine of the RNA is edited so as to repair the nonsense mutation. Use of an oligonucleotide according to any one of claims 1 to 11 for repairing a missense mutation, wherein the target adenosine of RNA is edited to repair the missense mutation, or Use of an oligonucleotide according to any one of claims 1 to 11 for editing a target adenosine in a codon, or Use of an oligonucleotide according to any one of claims 1 to 11 for editing a target adenosine in an upstream ORF.

17. Oligonucleotides, compositions, phosphoramidites, compounds, agents, methods, or uses as described herein or in any one of the exemplary embodiments 1 to 2597.

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