Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit

J Med Chem. 2016 May 26;59(10):4800-11. doi: 10.1021/acs.jmedchem.6b00012. Epub 2016 May 3.

Abstract

The acetyl post-translational modification of chromatin at selected histone lysine residues is interpreted by an acetyl-lysine specific interaction with bromodomain reader modules. Here we report the discovery of the potent, acetyl-lysine-competitive, and cell active inhibitor PFI-3 that binds to certain family VIII bromodomains while displaying significant, broader bromodomain family selectivity. The high specificity of PFI-3 for family VIII was achieved through a novel bromodomain binding mode of a phenolic headgroup that led to the unusual displacement of water molecules that are generally retained by most other bromodomain inhibitors reported to date. The medicinal chemistry program that led to PFI-3 from an initial fragment screening hit is described in detail, and additional analogues with differing family VIII bromodomain selectivity profiles are also reported. We also describe the full pharmacological characterization of PFI-3 as a chemical probe, along with phenotypic data on adipocyte and myoblast cell differentiation assays.

MeSH terms

  • Azabicyclo Compounds / chemical synthesis
  • Azabicyclo Compounds / chemistry
  • Azabicyclo Compounds / pharmacology*
  • Crystallography, X-Ray
  • DNA-Binding Proteins
  • Dose-Response Relationship, Drug
  • Humans
  • Models, Molecular
  • Molecular Probes / chemical synthesis
  • Molecular Probes / chemistry
  • Molecular Probes / pharmacology*
  • Molecular Structure
  • Nuclear Proteins / antagonists & inhibitors*
  • Nuclear Proteins / metabolism
  • Protein Processing, Post-Translational / drug effects
  • Pyridines / chemical synthesis
  • Pyridines / chemistry
  • Pyridines / pharmacology*
  • Structure-Activity Relationship
  • Substrate Specificity
  • Transcription Factors / antagonists & inhibitors*
  • Transcription Factors / metabolism

Substances

  • Azabicyclo Compounds
  • DNA-Binding Proteins
  • Molecular Probes
  • Nuclear Proteins
  • PBRM1 protein, human
  • PF-06687252
  • Pyridines
  • Transcription Factors