Covalent docking of large libraries for the discovery of chemical probes

Nat Chem Biol. 2014 Dec;10(12):1066-72. doi: 10.1038/nchembio.1666. Epub 2014 Oct 26.

Abstract

Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules. We apply this method prospectively to discover reversible covalent fragments that target distinct protein nucleophiles, including the catalytic serine of AmpC β-lactamase and noncatalytic cysteines in RSK2, MSK1 and JAK3 kinases. We identify submicromolar to low-nanomolar hits with high ligand efficiency, cellular activity and selectivity, including what are to our knowledge the first reported reversible covalent inhibitors of JAK3. Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization. As covalent virtual screening may have broad utility for the rapid discovery of chemical probes, we have made the method freely available through an automated web server (http://covalent.docking.org/).

Publication types

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

MeSH terms

  • Animals
  • Bacterial Proteins / antagonists & inhibitors
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • COS Cells
  • Cysteine / chemistry
  • Cysteine / metabolism
  • Drug Discovery
  • Gram-Negative Bacteria / drug effects
  • Gram-Negative Bacteria / enzymology
  • Gram-Negative Bacteria / growth & development
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Janus Kinase 3 / antagonists & inhibitors
  • Janus Kinase 3 / chemistry
  • Janus Kinase 3 / genetics
  • Ligands
  • Molecular Docking Simulation*
  • Molecular Probes / chemistry*
  • Molecular Probes / pharmacology
  • Protein Binding
  • Protein Kinase Inhibitors / chemistry*
  • Protein Kinase Inhibitors / pharmacology
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Ribosomal Protein S6 Kinases, 90-kDa / antagonists & inhibitors
  • Ribosomal Protein S6 Kinases, 90-kDa / chemistry
  • Ribosomal Protein S6 Kinases, 90-kDa / genetics
  • Serine / chemistry
  • Serine / metabolism
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / pharmacology
  • beta-Lactamase Inhibitors / chemistry*
  • beta-Lactamase Inhibitors / pharmacology
  • beta-Lactamases / chemistry
  • beta-Lactamases / genetics

Substances

  • Bacterial Proteins
  • Ligands
  • Molecular Probes
  • Protein Kinase Inhibitors
  • Recombinant Proteins
  • Small Molecule Libraries
  • beta-Lactamase Inhibitors
  • Serine
  • JAK3 protein, human
  • Janus Kinase 3
  • Ribosomal Protein S6 Kinases, 90-kDa
  • mitogen and stress-activated protein kinase 1
  • ribosomal protein S6 kinase, 90kDa, polypeptide 3
  • AmpC beta-lactamases
  • beta-Lactamases
  • Cysteine