Mechanism and inhibition of the papain‐like protease, PLpro, of SARS‐CoV‐2

Abstract

The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, noncovalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model.

Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay

“…PL pro in complex with ubiquitin propargylamide was utilized (Klemm et al, 2020). In addition to this, four other crystal structures of SARS-CoV-2 that were available on the RCSB PDB were evaluated.…”

“…Several crystal structures of the SARS-CoV-2 PL pro were obtained from the RCSB Protein Data Bank (PDB ID: 6xaa, 6w9c, 6wuu, 6wx4, and 7jrn) (Berman et al, 2000;Klemm et al, 2020;Osipiuk et al, 2020;Rut et al, 2020;Sacco et al, 2020). The SARS-CoV PL pro (PDB ID: 4mm3) and MERS-CoV PL pro (PDB ID: 4rf0) were also used for comparison in this study (Bailey-Elkin et al, 2014;Ratia et al, 2014).…”

Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors

“…Computational methods applied to toxicology have been proved, over the years, and through numerous works, as powerful methods in guiding the drug discovery of molecules capable of efficiently binding to biological targets, like proteins. These interactions can be exploited towards the discovery of antidotes to toxic proteins, drugs against pathogens, or modulators in the human body [19,[31][32][33]. It is also possible to use cheminformatics aiming clarification and explanation of obtained or existing experimental results [15,34,35].…”

A pocket guide on how to structure SARS-CoV-2 drugs and therapies

“…Structures of SARS-CoV-2 PLpro in complex with ubiquitin-propargylamide and ISG15 C-terminal domainpropargylamide have revealed how PLpro accommodates human ubiquitin and ISG15 onto the PLpro 'palm' domain which, via either the 'finger' (for ubiquitin; Figure 4A) or 'thumb' (for ISG15; Figure 4B) domains, channel the ubiquitin/ISG15 C-terminal domains into the catalytic site for cleavage [71]. Nsp3 is a major antiviral target with inhibitors of this multi-faceted proteolytic activity including disulfiram, mycophenolic acid, thiopurine analogues (6-mercaptopurine and 6-thioguanine) [72,73], pyrimidine derived 'compound 6' [74] and tashinones derived from Salvia miltiorrhiza [75].…”