High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors

Abstract

A new coronavirus (SARS-CoV-2) has been identified as the etiologic agent for the COVID-19 outbreak. Currently, effective treatment options remain very limited for this disease; therefore, there is an urgent need to identify new anti-COVID-19 agents. In this study, we screened over 6,000 compounds that included approved drugs, drug candidates in clinical trials, and pharmacologically active compounds to identify leads that target the SARS-CoV-2 papain-like protease (PLpro). Together with main protease (Mpro), PLpro is responsible for processing the viral replicase polyprotein into functional units. Therefore, it is an attractive target for antiviral drug development. Here we discovered four compounds, YM155, cryptotanshinone, tanshinone I and GRL0617 that inhibit SARS-CoV-2 PLpro with IC50 values ranging from 1.39 to 5.63 μmol/L. These compounds also exhibit strong antiviral activities in cell-based assays. YM155, an anticancer drug candidate in clinical trials, has the most potent antiviral activity with an EC50 value of 170 nmol/L. In addition, we have determined the crystal structures of this enzyme and its complex with YM155, revealing a unique binding mode. YM155 simultaneously targets three “hot” spots on PLpro, including the substrate-binding pocket, the interferon stimulating gene product 15 (ISG15) binding site and zinc finger motif. Our results demonstrate the efficacy of this screening and repurposing strategy, which has led to the discovery of new drug leads with clinical potential for COVID-19 treatments.

Structural biology of SARS-CoV-2 and implications for therapeutic development

“…79 ). YM155, an anticancer drug candidate in clinical trials, has also been shown to inhibit SARS-CoV-2 PL pro and has potent antiviral activity (halfmaximal effective concentration (EC 50 ) of 170 nM) 80 . YM155 achieves such a strong inhibition by simultaneously recognizing three hotspots in PL pro .…”

HERC5 and the ISGylation Pathway: Critical Modulators of the Antiviral Immune Response

“…Following PL pro -UbV complex formation, PL pro deubiquitylation, deISGylation and protease activities were significantly hindered and viral progeny were much less infectious [98]. Smallmolecule inhibitor screens have subsequently identified the substrate-binding pocket and the ISG15 binding site of PL pro as important determinants of viral fitness and could serve as attractive targets for antiviral drug development [136][137][138][139][140][141][142]. For example, the small molecule GRL0617 is one of the most promising SARS-CoV-2 inhibitors currently being studied that sterically blocks the binding of ISG15 and ubiquitin to PL pro [137,142].…”

Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332

“…The replication of SARS-CoV-2 relies on two polyproteins pp1a and pp1ab, which are encoded by the 5’ two-thirds of the viral genome (Cui et al, 2020 ). Both pp1a and pp1ab are co-translationally cleaved into 16 mature nonstructural proteins (nsps) by the two viral cysteine proteases, the main protease (M pro , also called 3C like protease, 3CLpro) and the papain like protease (PLpro) (Jin et al, 2020 ; Zhao et al, 2021 ). SARS-CoV-2 M pro processes the two polyproteins through at least 11 cleavage sites.…”