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Covalent docking of large libraries for the discovery of chemical probes

Nature Chemical Biology volume 10, pages 1066–1072 (2014)Cite this article

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An Erratum to this article was published on 17 February 2015

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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/).

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Figure 1: Overview of the DOCKovalent methodology.
Figure 2: Boronic acid inhibitors of AmpC predicted by virtual screening.
Figure 3: Cyanoacrylamide inhibitors of RSK2 and MSK1 predicted by covalent docking.
Figure 4: Reversible covalent JAK3 inhibitors discovered via docking.

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  • 22 December 2014

    In the version of this article initially published, the scaffold structure shown for compounds 33 and 34 was incorrect in Figure 4a, with a nitrogen atom misplaced within the five-membered ring moiety. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

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.

Author information

Author notes

  1. Nir London, Rand M Miller and Shyam Krishnan: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, California, USA

    Nir London, John J Irwin, Oliv Eidam & Brian K Shoichet

  2. Chemistry and Chemical Biology Graduate Program, University of California–San Francisco, San Francisco, California, USA

    Rand M Miller

  3. Department of Cellular and Molecular Pharmacology, University of California–San Francisco, San Francisco, California, USA

    Shyam Krishnan, Kenji Uchida, Peter Cimermančič & Jack Taunton

  4. Howard Hughes Medical Institute, University of California–San Francisco, San Francisco, California, USA

    Shyam Krishnan, Kenji Uchida & Jack Taunton

  5. Faculty of Pharmacy, University of Toronto, Toronto, Canada

    John J Irwin, Lucie Gibold & Brian K Shoichet

  6. Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada

    John J Irwin, Lucie Gibold & Brian K Shoichet

  7. Clermont Université, UMR 1071 INSERM–Université d'Auvergne, Clermont-Ferrand, France

    Lucie Gibold & Richard Bonnet

  8. INRA, USC 2018, Clermont-Ferrand, France

    Richard Bonnet

  9. Service de Bactériologie, Centre Hospitalier Universitaire, Clermont-Ferrand, France

    Richard Bonnet

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Contributions

B.K.S. and J.T. directed the project. N.L. designed the algorithms, wrote the covalent docking code and executed the docking simulations. N.L. performed β-lactamase assays and crystallography with help from O.E. J.J.I. designed and implemented the DOCKovalent web tool. P.C. performed the proteasome experiments. L.G. and R.B. performed bacterial cell culture experiments. R.M.M. executed synthetic chemistry, kinase assays, crystallography and cell-based assays for RSK2 and MSK1. S.K. and K.U. performed synthetic chemistry for JAK3, S.K. performed JAK1 and JAK3 kinase assays. N.L., R.M.M., B.K.S. and J.T. wrote the paper. All authors contributed to the manuscript in its final form.

Corresponding authors

Correspondence to Brian K Shoichet or Jack Taunton.

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Competing interests

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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Supplementary Results, Supplementary Tables 1–11, Supplementary Figures 1–17 and Supplementary Notes 1 and 2. (PDF 7163 kb)

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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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