Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with k inact /K I = 9,600 M −1 s −1 , achieves sub-μM EC 50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.
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Brian C. Sanders, Suman Pokhrel, Audrey D. Labbe et al.. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nature Communications. (2023). https://doi.org/10.1038/s41467-023-37254-w Brian C. Sanders, Suman Pokhrel, Audrey D. Labbe, Irimpan I. Mathews, Connor J. Cooper, Russell B. Davidson, Gwyndalyn Phillips, Kevin L. Weiss, Qiu Zhang, Hugh O’Neill, Manat Kaur, Jurgen G. Schmidt, Walter Reichard, Surekha Surendranathan, Jyothi Parvathareddy, Lexi Phillips, Christopher Rainville, David E. Sterner, Desigan Kumaran, Babak Andi, Gyorgy Babnigg, Nigel W. Moriarty, Paul D. Adams, Andrzej Joachimiak, Brett L. Hurst, Suresh Kumar, Tauseef R. Butt, Colleen B. Jonsson, Lori Ferrins, Soichi Wakatsuki, Stephanie Galanie, Martha S. Head, Jerry M. Parks
1grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA 2grid.168010.e0000000419368956Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA USA 3grid.445003.60000 0001 0725 7771Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA USA 4grid.511397.80000 0004 0452 8128Stanford Synchrotron Radiation Lightsource, Menlo Park, CA USA 5grid.135519.a0000 0004 0446 2659Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN USA 6grid.168010.e0000000419368956Department of Structural Biology, Stanford University School of Medicine, Stanford, CA USA 7grid.148313.c0000 0004 0428 3079B-11 Bioenergy and Biome Sciences, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA 8grid.267301.10000 0004 0386 9246Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN USA 9grid.267301.10000 0004 0386 9246Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN USA 10grid.53857.3c0000 0001 2185 8768Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT USA 11grid.281189.b0000 0004 6108 4308Progenra Inc., Malvern, PA USA 12grid.202665.50000 0001 2188 4229Biology Department, Brookhaven National Laboratory, Upton, NY USA 13grid.202665.50000 0001 2188 4229Center for BioMolecular Structure, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY USA 14grid.170205.10000 0004 1936 7822Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL USA 15grid.187073.a0000 0001 1939 4845Biosciences Division, Argonne National Laboratory, Argonne, IL USA 16grid.184769.50000 0001 2231 4551Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA USA 17grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA USA 18grid.187073.a0000 0001 1939 4845Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL USA 19grid.170205.10000 0004 1936 7822Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL USA 20grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA 21grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN USA 22grid.135519.a0000 0004 0446 2659Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN USA 23grid.417993.10000 0001 2260 0793Present Address: Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA 24grid.417886.40000 0001 0657 5612Present Address: Computational and Data Sciences, Center for Research Acceleration by Digital Innovation, Amgen, Inc., Thosand Oaks, CA, USA