1. Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design.
- Author
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Rut W, Lv Z, Zmudzinski M, Patchett S, Nayak D, Snipas SJ, El Oualid F, Huang TT, Bekes M, Drag M, and Olsen SK
- Subjects
- Amino Acid Sequence, Betacoronavirus isolation & purification, Binding Sites, COVID-19, Catalytic Domain, Coronavirus 3C Proteases, Coronavirus Infections pathology, Coronavirus Infections virology, Crystallography, X-Ray, Cysteine Endopeptidases genetics, Cysteine Endopeptidases metabolism, Humans, Kinetics, Molecular Dynamics Simulation, Oligopeptides chemistry, Oligopeptides metabolism, Pandemics, Pneumonia, Viral pathology, Pneumonia, Viral virology, Protease Inhibitors metabolism, Recombinant Proteins biosynthesis, Recombinant Proteins chemistry, Recombinant Proteins isolation & purification, SARS-CoV-2, Substrate Specificity, Ubiquitins metabolism, Viral Nonstructural Proteins genetics, Viral Nonstructural Proteins metabolism, Betacoronavirus enzymology, Drug Design, Protease Inhibitors chemistry, Viral Nonstructural Proteins antagonists & inhibitors
- Abstract
Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro. We determined crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro that reveals their inhibitory mechanisms and provides a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Together, this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)
- Published
- 2020
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