Selective and Cell-Active PBRM1 Bromodomain Inhibitors Discovered through NMR Fragment Screening

J Med Chem. 2022 Oct 27;65(20):13714-13735. doi: 10.1021/acs.jmedchem.2c00864. Epub 2022 Oct 13.

Abstract

PBRM1 is a subunit of the PBAF chromatin remodeling complex that uniquely contains six bromodomains. PBRM1 can operate as a tumor suppressor or tumor promoter. PBRM1 is a tumor promoter in prostate cancer, contributing to migratory and immunosuppressive phenotypes. Selective chemical probes targeting PBRM1 bromodomains are desired to elucidate the association between aberrant PBRM1 chromatin binding and cancer pathogenesis and the contributions of PBRM1 to immunotherapy. Previous PBRM1 inhibitors unselectively bind SMARCA2 and SMARCA4 bromodomains with nanomolar potency. We used our protein-detected NMR screening pipeline to screen 1968 fragments against the second PBRM1 bromodomain, identifying 17 hits with Kd values from 45 μM to >2 mM. Structure-activity relationship studies on the tightest-binding hit resulted in nanomolar inhibitors with selectivity for PBRM1 over SMARCA2 and SMARCA4. These chemical probes inhibit the association of full-length PBRM1 to acetylated histone peptides and selectively inhibit growth of a PBRM1-dependent prostate cancer cell line.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Carcinogens
  • Chromatin
  • DNA Helicases / metabolism
  • DNA-Binding Proteins / metabolism
  • Histones* / metabolism
  • Humans
  • Male
  • Nuclear Proteins / metabolism
  • Prostatic Neoplasms* / drug therapy
  • Protein Domains
  • Transcription Factors / metabolism

Substances

  • Histones
  • Chromatin
  • Carcinogens
  • SMARCA4 protein, human
  • DNA Helicases
  • Nuclear Proteins
  • Transcription Factors
  • PBRM1 protein, human
  • DNA-Binding Proteins