Chemical Proteomic Profiling of Bromodomains Enables the Wide-Spectrum Evaluation of Bromodomain Inhibitors in Living Cells

J Am Chem Soc. 2019 Jul 24;141(29):11497-11505. doi: 10.1021/jacs.9b02738. Epub 2019 Jul 9.

Abstract

Bromodomains, epigenetic "readers" of lysine acetylation marks, exist in different nuclear proteins with diverse biological functions in chromatin biology. Malfunctions of bromodomains are associated with the pathogenesis of human diseases, such as cancer. Bromodomains have therefore emerged as therapeutic targets for drug discovery. Given the high structural similarity of bromodomains, a critical step in the development of bromodomain inhibitors is the evaluation of their selectivity to avoid off-target effects. While numerous bromodomain inhibitors have been identified, new methods to evaluate the inhibitor selectivity toward endogenous bromodomains in living cells remain needed. Here we report the development of a photoaffinity probe, photo-bromosporine (photo-BS), that enables the wide-spectrum profiling of bromodomain inhibitors in living cells. Photo-BS allowed light-induced cross-linking of recombinant bromodomains and endogenous bromodomain-containing proteins (BCPs) both in vitro and in living cells. The photo-BS-induced labeling of the bromodomains was selectively competed by the corresponding bromodomain inhibitors. Proteomics analysis revealed that photo-BS captured 28 out of the 42 known BCPs from the living cells. Assessment of the two bromodomain inhibitors, bromosporine and GSK6853, resulted in the identification of known as well as previously uncharacterized bromodomain targets. Collectively, we established a chemical proteomics platform to comprehensively evaluate bromodomain inhibitors in terms of their selectivity against endogenous BCPs in living cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbamates / chemistry*
  • Carbamates / pharmacology
  • Cell Cycle Proteins / antagonists & inhibitors
  • Cell Cycle Proteins / chemistry
  • Chromosomal Proteins, Non-Histone / antagonists & inhibitors
  • Chromosomal Proteins, Non-Histone / chemistry
  • Cross-Linking Reagents / chemistry
  • Drug Evaluation, Preclinical / methods*
  • HEK293 Cells
  • Humans
  • Mass Spectrometry / methods
  • Photoaffinity Labels / chemistry*
  • Protein Domains*
  • Proteins / antagonists & inhibitors
  • Proteins / chemistry*
  • Proteins / metabolism
  • Proteomics / methods*
  • Pyridazines / chemistry*
  • Pyridazines / pharmacology
  • Recombinant Proteins / chemistry
  • Transcription Factors / antagonists & inhibitors
  • Transcription Factors / chemistry
  • Triazoles / chemistry*
  • Triazoles / pharmacology

Substances

  • BAZ2A protein, human
  • BRD4 protein, human
  • Carbamates
  • Cecr2 protein, human
  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone
  • Cross-Linking Reagents
  • Photoaffinity Labels
  • Proteins
  • Pyridazines
  • Recombinant Proteins
  • Transcription Factors
  • Triazoles
  • bromosporine