Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain

J Med Chem. 2016 Feb 25;59(4):1350-6. doi: 10.1021/acs.jmedchem.5b00172. Epub 2015 Jul 15.

Abstract

Novel ligands of the CREBBP bromodomain were identified by fragment-based docking. The in silico discovered hits have been optimized by chemical synthesis into selective nanomolar compounds, thereby preserving the ligand efficiency. The selectivity for the CREBBP bromodomain over other human bromodomain subfamilies has achieved by a benzoate moiety which was predicted by docking to be involved in favorable electrostatic interactions with the Arg1173 side chain, a prediction that could be verified a posteriori by the high-resolution crystal structure of the CREBBP bromodomain in complex with ligand 6 and also by MD simulations (see Xu, M.; Unzue, A.; Dong, J.; Spiliotopoulos, D.; Nevado, C.; Caflisch, A. Discovery of CREBBP bromodomain inhibitors by high-throughput docking and hit optimization guided by molecular dynamics. J. Med. Chem. 2015, DOI: 10.1021/acs.jmedchem.5b00171).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Benzoates / chemistry*
  • Benzoates / pharmacology
  • CREB-Binding Protein / chemistry
  • CREB-Binding Protein / metabolism*
  • Drug Design*
  • Humans
  • Ligands
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Structure, Tertiary / drug effects
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / pharmacology

Substances

  • Benzoates
  • Ligands
  • Small Molecule Libraries
  • CREB-Binding Protein
  • CREBBP protein, human