Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance

The authors determined crystal structures of the main protease (Mpro) of SARS-CoV-2 bound to substrate peptides. These structures define the substrate envelope and enable identification of sites that may be susceptible to drug resistance. Coronaviruses can evolve and spread rapidly to cause severe disease morbidity and mortality, as exemplified by SARS-CoV-2 variants of the COVID-19 pandemic. Although currently available vaccines remain mostly effective against SARS-CoV-2 variants, additional treatment strategies are needed. Inhibitors that target essential viral enzymes, such as proteases and polymerases, represent key classes of antivirals. However, clinical use of antiviral therapies inevitably leads to emergence of drug resistance. In this study we implemented a strategy to pre-emptively address drug resistance to protease inhibitors targeting the main protease (M-pro) of SARS-CoV-2, an essential enzyme that promotes viral maturation. We solved nine high-resolution cocrystal structures of SARS-CoV-2 M-pro bound to substrate peptides and six structures with cleavage products. These structures enabled us to define the substrate envelope of M-pro, map the critical recognition elements, and identify evolutionarily vulnerable sites that may be susceptible to resistance mutations that would compromise binding of the newly developed M-pro inhibitors. Our results suggest strategies for developing robust inhibitors against SARS-CoV-2 that will retain longer-lasting efficacy against this evolving viral pathogen.

Automated summary

The study determined the crystal structures of SARS-CoV-2 main protease (Mpro) bound to substrate peptides, defining the substrate envelope and identifying sites susceptible to drug resistance. These findings provide insights for developing robust inhibitors against SARS-CoV-2 and preventing drug resistance.