Title: Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design.
Authors: Rut, Wioletta; Lv, Zongyang; Zmudzinski, Mikolaj; Patchett, Stephanie; Nayak, Digant; Snipas, Scott J; El Oualid, Farid; Huang, Tony T; Bekes, Miklos; Drag, Marcin; Olsen, Shaun K
Published In Sci Adv, (2020 10)
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.
PubMed ID: 33067239
MeSH Terms: Amino Acid Sequence; Betacoronavirus/enzymology*; 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; Drug Design*; Humans; Kinetics; Molecular Dynamics Simulation; Oligopeptides/chemistry; Oligopeptides/metabolism; Pandemics; Pneumonia, Viral/pathology; Pneumonia, Viral/virology; Protease Inhibitors/chemistry*; Protease Inhibitors/metabolism; Recombinant Proteins/biosynthesis; Recombinant Proteins/chemistry; Recombinant Proteins/isolation & purification; SARS-CoV-2; Substrate Specificity; Ubiquitins/metabolism; Viral Nonstructural Proteins/antagonists & inhibitors*; Viral Nonstructural Proteins/genetics; Viral Nonstructural Proteins/metabolism