Covalent docking of large libraries for the discovery of chemical probes

• Published in: Nature chemical biology Vol. 10; no. 12; pp. 1066 - 1072
• Main Authors: London, Nir, Miller, Rand M, Krishnan, Shyam, Uchida, Kenji, Irwin, John J, Eidam, Oliv, Gibold, Lucie, Cimermančič, Peter, Bonnet, Richard, Shoichet, Brian K, Taunton, Jack
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.12.2014; Nature Publishing Group
• Subjects: 631/114/2248; 631/326; 631/80/86; 631/92/96; Animals; Bacterial Proteins - antagonists & inhibitors; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; beta-Lactamase Inhibitors - chemistry; beta-Lactamase Inhibitors - pharmacology; beta-Lactamases - chemistry; beta-Lactamases - genetics; Biochemical Engineering; Biochemistry; Bioorganic Chemistry; Cell Biology; Chemical bonds; Chemistry; Chemistry/Food Science; COS Cells; Crystal structure; 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; Life Sciences; Ligands; Molecular Docking Simulation; Molecular Probes - chemistry; Molecular Probes - pharmacology; Probes; Protein Binding; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - pharmacology; Proteins; 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; RHEUMATOID-ARTHRITIS; DESIGN; LIGANDS; REACTIVITY; KINASE INHIBITORS; GENERATION; OPTIMIZATION; ELECTROPHILES; PREDICTION; TOOL
• ISSN: 1552-4450; 1552-4469
• DOI: 10.1038/nchembio.1666

A modification of the in silico screening tool, DOCK, allows for identification of compounds that covalently modify catalytic and noncatalytic protein nucleophiles to modulate the activities of bacterial β-lactamase and the kinases RSK2, MSK1 and JAK3. 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/ ).