Granted Patent B2

US 12,503,455 · App. 18/155,528 · Granted Dec 23, 2025

Inventors: Gnanasambandam Kumaravel (Lexington, MA); Jennifer C. Petter (Stow, MA); Jonathan Craig Blain (Melrose, MA); Donovan Noel Chin (Lexington, MA); Chao Fang (Lexington, MA); Herschel Mukherjee (Somerville, MA); Neil Kubica (Swampscott, MA)

Assignee: Arrakis Therapeutics, Inc.

C07D401/14A61K9/0019A61K9/0053A61K31/522A61K31/65A61K39/395A61K47/545A61K47/6809A61P25/28A61P43/00C07D217/26C07D401/12C07D495/04C12N15/115C12Q1/6816G01N33/5008

Abstract

Claims (33)

1 . A method of determining the three-dimensional structure, binding site of a ligand of interest, or accessibility of a nucleotide in a target nucleic acid, comprising: contacting the target nucleic acid with a compound of Formula I or a pharmaceutically acceptable salt thereof; irradiating the compound; determining whether covalent modification of a nucleotide of the nucleic acid has occurred; and optionally deriving the pattern of nucleotide modification, the three-dimensional structure, ligand binding site, or other structural information about the nucleic acid; wherein the compound of Formula I is of the following structure:

or a pharmaceutically acceptable salt thereof; wherein:

Ligand is a small molecule RNA binder selected from the group consisting of a heteroaryldihydropyrimidine (HAP), a macrolide, an alkaloid, an aminoglycoside, a tetracycline, a SMN2 ligand, a pleuromutilin, theophylline or an analogue thereof, ribocil or an analogue thereof, a substituted anthracene, a substituted triptycene, an oxazolidinone, and CPNQ or an analogue thereof; wherein Ligand may be optionally substituted with one or more substituents;

T 1 is a bivalent tethering group selected from a C 1-20 bivalent straight or branched hydrocarbon chain wherein 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of the chain are independently and optionally replaced with a natural or non-natural amino acid, —O—, —C(O)—, —C(O)O—, —OC(O)—, —N(R)—, —C(O)N(R)—, —(R)NC(O)—, —OC(O)N(R)—, —(R)NC(O)O—, —N(R)C(O)N(R)—, —S—, —SO—, —SO 2 —, —SO 2 N(R)—, —(R)NSO 2 —, —C(S)—, —C(S)O—, —OC(S)—, —C(S)N(R)—, —(R)NC(S)—, —(R)NC(S)N(R)—, or -Cy-; and 1-20 of the methylene units of the chain are independently and optionally replaced with —OCH 2 CH 2 —;

wherein each -Cy- is independently a bivalent optionally substituted 3-8 membered saturated or partially unsaturated monocyclic carbocyclic ring, optionally substituted phenylene, an optionally substituted 4-8 membered saturated or partially unsaturated monocyclic heterocyclic ring having 1-3 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, an optionally substituted 5-6 membered monocyclic heteroaromatic ring having 1-4 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, an optionally substituted 8-10 membered bicyclic or bridged bicyclic saturated or partially unsaturated heterocyclic ring having 1-5 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, or an optionally substituted 8-10 membered bicyclic or bridged bicyclic heteroaromatic ring having 1-5 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur;

each R is independently hydrogen or an optionally substituted group selected from the group consisting of C 1-6 aliphatic, a 3-8 membered saturated or partially unsaturated monocyclic carbocyclic ring, phenyl, an 8-10 membered bicyclic aromatic carbocyclic ring, a 4-8 membered saturated or partially unsaturated monocyclic heterocyclic ring having 1-2 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, a 5-6 membered monocyclic heteroaromatic ring having 1-4 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, and an 8-10 membered bicyclic heteroaromatic ring having 1-5 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur; and

R mod is a the group consisting of

2 . The method of claim 1 , wherein Ligand is selected from the group consisting of an optionally substituted heteroaryldihydropyrimidine (HAP), erythromycin, azithromycin, berberine, palmatine, a paromomycin, a neomycin, a kanamycin, doxycycline, oxytetracycline, pleuromutilin, theophylline or an analogue thereof, ribocil or an analogue thereof, LMI070 (NVS-SM1), a substituted triptycene, linezolid, tedizolid, and CPNQ or an analogue thereof; wherein Ligand may be optionally substituted with 1, 2, 3, or 4 substituents.

3 . The method of claim 1 , wherein T 1 is selected from a C 1-10 bivalent straight or branched hydrocarbon chain wherein 1, 2, 3, 4, or 5 methylene units of the chain are independently and optionally replaced with a natural or non-natural amino acid, —O—, —C(O)—, —C(O)O—, —OC(O)—, —N(R)—, —C(O)N(R)—, —(R)NC(O)—, —OC(O)N(R)—, —(R)NC(O)O—, —N(R)C(O)N(R)—, —S—, —SO—, —SO 2 —, —SO 2 N(R)—, —(R)NSO 2 —, —C(S)—, —C(S)O—, —OC(S)—, —C(S)N(R)—, —(R)NC(S)—, —(R)NC(S)N(R)—, or -Cy-; and 1, 2, 3, 4, or 5, of the methylene units of the chain are independently and optionally replaced with —OCH 2 CH 2 —.

4 . The method of claim 1 , wherein

R mod is selected from the group consisting of

5 . The method of claim 1 , wherein R mod is

6 . The method of claim 1 , wherein the method determines the binding site of a ligand of interest.

7 . The method of claim 1 , wherein the method comprises the step of deriving the pattern of nucleotide modification, the three-dimensional structure, ligand binding site, or other structural information about the nucleic acid.

8 . A method of determining the three-dimensional structure, binding site of a ligand of interest, or accessibility of a nucleotide in a target nucleic acid, comprising: contacting the target nucleic acid with a of Formula II or a pharmaceutically acceptable salt thereof; irradiating the compound; determining whether covalent modification of a nucleotide of the nucleic acid has occurred; and optionally deriving the pattern of nucleotide modification, the three-dimensional structure, ligand binding site, or other structural information about the nucleic acid;

wherein the of Formula II is of the following structure:

or a pharmaceutically acceptable salt thereof; wherein:

Ligand is a small molecule RNA binder selected from the group consisting of a heteroaryldihydropyrimidine (HAP), a macrolide, an alkaloid, an aminoglycoside, a tetracycline, a SMN2 ligand, a pleuromutilin, theophylline, ribocil, a substituted anthracene, a substituted triptycene, an oxazolidinone, and CPNQ; wherein Ligand may be optionally substituted with one or more substituents;

T 1 is a bivalent tethering group selected from a C 1-20 bivalent straight or branched hydrocarbon chain wherein 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of the chain are independently and optionally replaced with a natural or non-natural amino acid, —O—, —C(O)—, —C(O)O—, —OC(O)—, —N(R)—, —C(O)N(R)—, —(R)NC(O)—, —OC(O)N(R)—, —(R)NC(O)O—, —N(R)C(O)N(R)—, —S—, —SO—, —SO 2 —, —SO 2 N(R)—, —(R)NSO 2 —, —C(S)—, —C(S)O—, —OC(S)—, —C(S)N(R)—, —(R)NC(S)—, —(R)NC(S)N(R)—, or -Cy-; and 1-20 of the methylene units of the chain are independently and optionally replaced with —OCH 2 CH 2 —;

wherein each -Cy- is independently a bivalent optionally substituted 3-8 membered saturated or partially unsaturated monocyclic carbocyclic ring, optionally substituted phenylene, an optionally substituted 4-8 membered saturated or partially unsaturated monocyclic heterocyclic ring having 1-3 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, an optionally substituted 5-6 membered monocyclic heteroaromatic ring having 1-4 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, an optionally substituted 8-10 membered bicyclic or bridged bicyclic saturated or partially unsaturated heterocyclic ring having 1-5 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, or an optionally substituted 8-10 membered bicyclic or bridged bicyclic heteroaromatic ring having 1-5 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur;

each R is independently hydrogen or an optionally substituted group selected from the group consisting of C 1-6 aliphatic, a 3-8 membered saturated or partially unsaturated monocyclic carbocyclic ring, phenyl, an 8-10 membered bicyclic aromatic carbocyclic ring, a 4-8 membered saturated or partially unsaturated monocyclic heterocyclic ring having 1-2 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, a 5-6 membered monocyclic heteroaromatic ring having 1-4 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur, and, or an 8-10 membered bicyclic heteroaromatic ring having 1-5 heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur;

T 2 is a covalent bond or a bivalent tethering group selected from a C 1-20 bivalent straight or branched hydrocarbon chain wherein 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of the chain are independently and optionally replaced with a natural or non-natural amino acid, —O—, —C(O)—, —C(O)O—, —OC(O)—, —N(R)—, —C(O)N(R)—, —(R)NC(O)—, —OC(O)N(R)—, —(R)NC(O)O—, —N(R)C(O)N(R)—, —S—, —SO—, —SO 2 N(R)—, —(R)NSO 2 —, —C(S)—, —C(S)O—, —OC(S)—, —C(S)N(R)—, —(R)NC(S)—, —(R)NC(S)N(R)—, or -Cy-; and 1-20 of the methylene units of the chain are independently and optionally replaced with —OCH 2 CH 2 —;

R CG is a click-ready group selected from the group consisting of an azide, an alkyne, 4-dibenzocyclooctynol (DIBO) gem-difluorinated cyclooctynes (DIFO or DFO), biarylazacyclooctynone (BARAC), bicyclononyne (BCN), a strained cyclooctyne, an oxime, and oxanorbornadiene; or a pull-down group selected from the group consisting of a hapten, a 14 C, a 32 P, and a 3 H radiolabel; and

R mod is a photoactivatable group selected from the group consisting of

wherein Y − is a pharmaceutically acceptable anion.

9 . The method of claim 8 , wherein Ligand is selected from the group consisting of an optionally substituted heteroaryldihydropyrimidine (HAP), erythromycin, azithromycin, berberine, palmatine, a paromomycin, a neomycin, a kanamycin, doxycycline, oxytetracycline, pleuromutilin, theophylline, ribocil, LMI070 (NVS-SM1), a substituted triptycene, linezolid, tedizolid, and CPNQ; wherein Ligand may be optionally substituted with 1, 2, 3, or 4 substituents.

10 . The method of claim 8 , wherein T 1 is selected from a C 1-10 bivalent straight or branched hydrocarbon chain wherein 1, 2, 3, 4, or 5 methylene units of the chain are independently and optionally replaced with a natural or non-natural amino acid, —O—, —C(O)—, —C(O)O—, —OC(O)—, —N(R)—, —C(O)N(R)—, —(R)NC(O)—, —OC(O)N(R)—, —(R)NC(O)O—, —N(R)C(O)N(R)—, —S—, —SO—, —SO 2 —, —SO 2 N(R)—, —(R)NSO 2 —, —C(S)—, —C(S)O—, —OC(S)—, —C(S)N(R)—, —(R)NC(S)—, —(R)NC(S)N(R)—, or -Cy-; and 1, 2, 3, 4, or 5, of the methylene units of the chain are independently and optionally replaced with —OCH 2 CH 2 —.

11 . The method of claim 8 , wherein R mod is selected from the group consisting of

12 . The method of claim 8 , wherein R mod is

13 . The method of claim 8 , wherein R CG is an azide, an alkyne, 4-dibenzocyclooctynol (DIBO) gem-difluorinated cyclooctynes (DIFO or DFO), biarylazacyclooctynone (BARAC), bicyclononyne (BCN), or biotin.

14 . The method of claim 8 , wherein R CG is an azide or an alkyne.

15 . The method of claim 8 , wherein the method determines the binding site of a ligand of interest.

16 . The method of claim 8 , wherein the method comprises the step of deriving the pattern of nucleotide modification, the three-dimensional structure, ligand binding site, or other structural information about the nucleic acid.

Assignments (1)

Continuity (3)

References Cited (357)