Identifying new therapeutic agents

Patent metadata

Field	Value
Publication number	US-10989710-B2
Application number	US-201816227828-A
Country	US
Kind code	B2
Filing date	Dec 20, 2018
Priority date	Dec 28, 2010
Publication date	Apr 27, 2021
Grant date	Apr 27, 2021

Abstract

Disclosed herein are methods for identifying novel drug candidates.

First claim

What is claimed is:

1. A method of modulating the activity of K-Ras, said method comprising contacting a compound and a presenter protein under suitable conditions to produce a complex, wherein the complex binds to K-Ras and the compound has the formula:

wherein:
the compound comprises between 18 and 30 ring atoms, wherein each of the ring atoms is selected from the group consisting of oxygen, nitrogen, carbon, sulfur, and phosphorus;
each L is independently a bond or a bivalent substituted or unsubstituted portion of the compound;
the TIS is a Target Interacting Site that contacts one or more corresponding interacting sites on K-Ras; and
the PIS is a Presenter Interacting Site that contacts one or more corresponding interacting sites on the presenter protein, and wherein the PIS comprises the formula selected from the formulas consisting of (A), (B) and (C):

wherein:
J is hydrogen or (C1-C2) alkyl;
K is (C1-C4)-straight or branched alkyl, benzyl or cyclohexylmethyl; or
wherein J and K may be taken together to form a 5-7 membered heterocyclic ring which may contain an O, S, SO or SO 2 substituent therein;
the stereochemistry at carbon position 1 is R or S;
X is selected from —NH—, —N(alkyl)-, —O—, —C(O)—, —CHOH—, —CH═, or —CH 2 —;
Y is selected from —C(O)NH—, —C(O)N(alkyl)-, —C(O)O—, —C(O)C(O)—, —C(O)CHOH—, —C(O)CH═, —C(O)CH 2 —, and —S(O) 2 ; and
represents a single or a double bond; and the points of attachment to the rest of the compound are through a terminus of each L; and

wherein:
each X is independently selected from —NH—, —N(alkyl)-, —O—, —C(O)—, —CHOH—, or —CH 2 —; and
the points of attachment to the rest of the compound is by a covalent bond to a terminus of each L; and

wherein:
X is selected from —NH—, —N(alkyl)-, —O—, —C(O)—, —CHOH—, or —CH 2 —,
R 1 is selected from (C1-C6)-alkyl, (C1-C6)-alkenyl, (C1-C6)-alkynyl, aryl, (C3-C7)-carbocyclyl, —(C1-C4 alkylene)-aryl, and —(C1-C4 alkylene)-(C3-C7) carbocyclyl;
each R 2 is independently selected from halo, —C≡N, C1-C4 alkyl, ═O, C 3 -C 7 cycloalkyl, C 1 -C 4 alkyl, —OH, —O—(C 1 -C 4 alkyl), —SH, —S—(C 1 -C 4 alkyl), —(C 1 -C 4 alkyl)-N(R b )(R b ), —N(R b )(R b ), —O—(C 1 -C 4 alkyl)-N(R b )(R b ), —(C 1 -C 4 alkyl)-O—(C 1 -C 4 alkyl)-N(R b )(R b ), —C(O)—N(R b )(R b ), —(C 1 -C 4 alkyl)-C(O)—N(R b )(R b ), —O-(heteroaryl), —O-(heterocycle), —O-phenyl, -heteroaryl, -heterocycle, and -phenyl, wherein:
each R b is independently selected from hydrogen, and —C 1 -C 4 alkyl; or two R b are taken together with the nitrogen atom to which they are bound to form a 4- to 8-membered saturated heterocycle optionally comprising one additional heteroatom selected from N, S, S(═O), S(═O) 2 , and 0,
any alkyl substituent is optionally further substituted with one or more of —OH, —O—(C 1 -C 4 alkyl), halo, —NH 2 , —NH(C 1 -C 4 alkyl), or —N(C 1 -C 4 alkyl) 2 ; and
any carbon atom on a phenyl, cycloalkyl, heteroaryl or heterocycle substituent is optionally further substituted with one or more of —(C 1 -C 4 alkyl), —(C 1 -C 4 fluoroalkyl), —OH, —O—(C 1 -C 4 alkyl), —O—(C 1 -C 4 fluoroalkyl), halo, —NH 2 , —NH(C 1 -C 4 alkyl), or —N(C 1 -C 4 alkyl) 2 ;
m is 0, 1, 2 or 3; and
the points of attachment to the rest of the compound is by a covalent bond to a terminus of each L;
wherein each L is independently selected from a bond and a linear chain of up to 10 atoms, independently selected from carbon, nitrogen, oxygen, sulfur or phosphorous atoms, wherein each atom in the chain is optionally substituted with one or more substituents independently selected from alkyl, alkenyl, alkynyl, aryl, heteroaryl, chloro, iodo, bromo, fluoro, hydroxy, alkoxy, aryloxy, carboxy, amino, alkylamino, dialkylamino, acylamino, carboxamido, cyano, oxo, thio, alkylthio, arylthio, acylthio, alkylsulfonate, arylsulfonate, phosphoryl, and sulfonyl, and wherein any two atoms in the chain may be taken together with the substituents bound thereto to form a ring, wherein the ring may be further substituted and/or fused to one or more optionally substituted carbocyclic, heterocyclic, aryl or heteroaryl rings; and
wherein when the PIS has formula (A) the presenter protein is a member of the FKBP family, and when the PIS has formula (B) or (C), the presenter protein is a member of the cyclophilin family.

2. The method of claim 1 , wherein the presenter protein is a member of the FKBP family.

3. The method of claim 2 , wherein the PIS has the structure of formula (A).

4. The method of claim 1 , wherein the presenter protein is a member of the cyclophilin family.

5. The method of claim 4 , wherein the PIS has the structure of formula (B) or (C).

6. The method of claim 1 , wherein the complex binds K-Ras with at least a two-fold increase in affinity relative to the affinity of the compound for K-Ras in the absence of the presenter protein.

Assignees

• Revolution Medicines Inc

Inventors

• Verdine Gregory L
• White David W
• Armistead David M
• Palestrant Deborah J
• Chow Brian Y
• Varma Chris K
• Sowa Mathew Edward

Classifications

• G01N33/68 Primary

  involving proteins, peptides or amino acids {(involving lipoproteins G01N33/92)} · CPC title

• G01N2500/04

  Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A) · CPC title

• G01N33/6848

  Methods of protein analysis involving mass spectrometry · CPC title

• C40B30/04

  by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding · CPC title

• G01N33/5308 Primary

  for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites · CPC title