Discovery of Pyrrolo[3,2- d]pyrimidin-4-one Derivatives as a New Class of Potent and Cell-Active Inhibitors of P300/CBP-Associated Factor Bromodomain

J Med Chem. 2019 May 9;62(9):4526-4542. doi: 10.1021/acs.jmedchem.9b00096. Epub 2019 Apr 30.

Abstract

Herein, we report the discovery of a series of new P300/CBP-associated factor (PCAF) bromodomain (BRD) inhibitors, which were obtained through a hit discovery process and subsequent structure-based optimization and structure-activity relationship analyses toward a retrieved hit compound (12). Among these inhibitors, ( R, R)-36n is the most potent one with an IC50 of 7 nM in homogeneous time-resolved fluorescence assay and a KD of 78 nM in isothermal titration calorimetry assay. This compound also exhibited activity against GCN5 and FALZ, but weak or no activity against other 29 BRD proteins and 422 kinases, indicating considerable selectivity. X-ray cocrystal structure analysis revealed the molecular interaction mode and the precise stereochemistry required for bioactivity. Cellular activity, preliminary RNA-seq analysis, and pharmacokinetic properties were also examined for this compound. Collectively, this study provides a versatile tool molecule to explore molecular mechanisms of PCAF BRD regulation and also offers a new lead compound for drug discovery targeting PCAF.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Drug Discovery
  • Enzyme Inhibitors / chemical synthesis
  • Enzyme Inhibitors / pharmacokinetics
  • Enzyme Inhibitors / pharmacology*
  • Gene Expression / drug effects
  • HEK293 Cells
  • Humans
  • Male
  • Mice
  • Microsomes, Liver / metabolism
  • Molecular Structure
  • Protein Domains / drug effects*
  • Pyrimidinones / chemical synthesis
  • Pyrimidinones / pharmacokinetics
  • Pyrimidinones / pharmacology*
  • Pyrroles / chemical synthesis
  • Pyrroles / pharmacokinetics
  • Pyrroles / pharmacology*
  • Rats, Sprague-Dawley
  • Stereoisomerism
  • Structure-Activity Relationship
  • p300-CBP Transcription Factors / antagonists & inhibitors*
  • p300-CBP Transcription Factors / chemistry

Substances

  • Enzyme Inhibitors
  • Pyrimidinones
  • Pyrroles
  • p300-CBP Transcription Factors
  • p300-CBP-associated factor