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/).
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Computational methods supported by US National Institutes of Health (NIH) grant GM59957, and the web portal was supported by NIH GM71896. This work was also supported by the Ministère de la Recherche et de la Technologie, the Institut national de la santé et de la recherche médicale (UMR Inserm U1071), the Institut National de la Recherche Agronomique (USC-2018) and the Centre Hospitalier Régional Universitaire de Clermont-Ferrand, France (to R.B.). We thank M. Fischer and D. Shaya for help with X-ray data collection, A. O'Donoghue (UCSF) for protease substrates, P. Coffino and S. Menant (UCSF) for the proteasome and the PA26 complex sample, X. Ouyang (Nanyang Technological University) for the r.m.s. calculation software used for the β-lactam benchmark, and S. Barelier for reading of this manuscript. N.L. was supported by an EMBO long-term fellowship (ALTF 1121-2011) and the University of California–San Francisco Program for Breakthrough Biomedical Research, which is funded in part by the Sandler Foundation. S.K. was supported by a fellowship from the California Tobacco-Related Disease Research Program (no. 19FT-0091). P.C. was supported by Howard Hughes Medical Institute Predoctoral Fellowship.
J.T., R.M.M. and S.K. have filed patent applications on cyanoacrylamide kinase inhibitors (licensed to Principia Biopharma, of which J.T. is a cofounder).
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London, N., Miller, R., Krishnan, S. et al. Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol 10, 1066–1072 (2014). https://doi.org/10.1038/nchembio.1666
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