Discovery of CHD1 Antagonists for PTEN-Deficient Prostate Cancer

J Med Chem. 2024 Nov 28;67(22):20056-20075. doi: 10.1021/acs.jmedchem.4c01172. Epub 2024 Nov 7.

Abstract

CHD1 is a chromodomain-helicase DNA-binding protein that preferentially recognizes di- and trimethylated lysine 4 on histone H3 (H3K4me2/3). Genetic studies have established CHD1 as a synthetic lethal target in phosphatase and tensin homologue (PTEN)-deficient cancers. Despite this attractive therapeutic link, no inhibitors or antagonists of CHD1 have been reported to date. Herein, we report the discovery of UNC10142, a first-in-class small molecule antagonist of the tandem chromodomains of CHD1 that binds with an IC50 of 1.7 ± 0.2 μM. A cocrystal structure revealed a unique binding mode and competition pull-down experiments in cell lysates confirmed endogenous target engagement. Treatment of PTEN-deficient prostate cancer cells with UNC10142 led to a dose-dependent reduction in viability while PTEN-intact prostate cancer cells were unaffected, phenocopying genetic loss of CHD1. Overall, this study demonstrates the ligandability of the CHD1 chromodomains and suggests more potent and selective antagonists could translate to compounds of therapeutic value in PTEN-deficient cancers.

MeSH terms

  • Antineoplastic Agents / chemistry
  • Antineoplastic Agents / pharmacology
  • Cell Line, Tumor
  • Crystallography, X-Ray
  • DNA Helicases
  • DNA-Binding Proteins* / antagonists & inhibitors
  • DNA-Binding Proteins* / metabolism
  • Drug Discovery
  • Humans
  • Male
  • PTEN Phosphohydrolase* / deficiency
  • PTEN Phosphohydrolase* / metabolism
  • Prostatic Neoplasms* / drug therapy
  • Prostatic Neoplasms* / metabolism
  • Prostatic Neoplasms* / pathology
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology
  • Structure-Activity Relationship

Substances

  • PTEN Phosphohydrolase
  • CHD1 protein, human
  • PTEN protein, human
  • DNA-Binding Proteins
  • Antineoplastic Agents
  • Small Molecule Libraries
  • DNA Helicases