title: Covalent docking of large libraries for the discovery of chemical probes.
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/).
authors.affiliation: Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Nir
authors.initials: N
authors.lastname: London
authors.affiliation: Chemistry and Chemical Biology Graduate Program, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Rand M
authors.initials: RM
authors.lastname: Miller
authors.affiliation: 1] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA. [2] Howard Hughes Medical Institute, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Shyam
authors.initials: S
authors.lastname: Krishnan
authors.affiliation: 1] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA. [2] Howard Hughes Medical Institute, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Kenji
authors.initials: K
authors.lastname: Uchida
authors.affiliation: 1] Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA. [2] Faculty of Pharmacy, University of Toronto, Toronto, Canada. [3] Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada.
authors.forename: John J
authors.initials: JJ
authors.lastname: Irwin
authors.affiliation: Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Oliv
authors.initials: O
authors.lastname: Eidam
authors.affiliation: 1] Faculty of Pharmacy, University of Toronto, Toronto, Canada. [2] Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada. [3] Clermont Université, UMR 1071 INSERM-Université d'Auvergne, Clermont-Ferrand, France.
authors.forename: Lucie
authors.initials: L
authors.lastname: Gibold
authors.affiliation: Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Cimermančič
authors.affiliation: 1] Clermont Université, UMR 1071 INSERM-Université d'Auvergne, Clermont-Ferrand, France. [2] INRA, USC 2018, Clermont-Ferrand, France. [3] Service de Bactériologie, Centre Hospitalier Universitaire, Clermont-Ferrand, France.
authors.forename: Richard
authors.initials: R
authors.lastname: Bonnet
authors.affiliation: 1] Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA. [2] Faculty of Pharmacy, University of Toronto, Toronto, Canada. [3] Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada.
authors.forename: Brian K
authors.initials: BK
authors.lastname: Shoichet
authors.affiliation: 1] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA. [2] Howard Hughes Medical Institute, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Jack
authors.initials: J
authors.lastname: Taunton
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D019556:COS Cells; D003545:Cysteine / Q000737:chemistry / Q000378:metabolism; D055808:Drug Discovery; D006090:Gram-Negative Bacteria / Q000187:drug effects / Q000201:enzymology / Q000254:growth & development; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D053616:Janus Kinase 3 / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D008024:Ligands; D062105:Molecular Docking Simulation; D015335:Molecular Probes / Q000737:chemistry* / Q000494:pharmacology; D011485:Protein Binding; D047428:Protein Kinase Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D038744:Ribosomal Protein S6 Kinases, 90-kDa / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D012694:Serine / Q000737:chemistry / Q000378:metabolism; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000494:pharmacology; D065093:beta-Lactamase Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D001618:beta-Lactamases / Q000737:chemistry / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D015335:Molecular Probes; D047428:Protein Kinase Inhibitors; D011994:Recombinant Proteins; D054852:Small Molecule Libraries; D065093:beta-Lactamase Inhibitors; D012694:Serine; C507933:JAK3 protein, human; D053616:Janus Kinase 3; D038744:Ribosomal Protein S6 Kinases, 90-kDa; C116919:mitogen and stress-activated protein kinase 1; C069330:ribosomal protein S6 kinase, 90kDa, polypeptide 3; C048795:AmpC beta-lactamases; D001618:beta-Lactamases; D003545:Cysteine