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Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance
Ala M Shaqra1, Sarah N Zvornicanin1, Qiu Yu J Huang1
1Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, US.
Abstract:
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 (Mpro) of SARS-CoV-2, an essential enzyme that promotes viral maturation. We solved nine high-resolution cocrystal structures of SARS-CoV-2 Mpro bound to substrate peptides and six structures with cleavage products. These structures enabled us to define the substrate envelope of Mpro, 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 Mpro inhibitors. Our results suggest strategies for developing robust inhibitors against SARS-CoV-2 that will retain longer-lasting efficacy against this evolving viral pathogen.
Insights
To combat SARS-CoV-2 evolution, researchers studied the main protease (Mpro) structure. This work identifies vulnerable sites to develop long-lasting COVID-19 antiviral drugs resistant to mutations.
Area of Science:
- Virology
- Structural Biology
- Drug Discovery
Background:
- Coronaviruses, like SARS-CoV-2, rapidly evolve, causing severe disease and mortality.
- While vaccines are effective, new antiviral treatments targeting essential viral enzymes are crucial.
- Antiviral drug resistance is a significant challenge in treating viral infections.
Purpose of the Study:
- To preemptively address drug resistance in SARS-CoV-2 protease inhibitors.
- To understand the substrate recognition of the SARS-CoV-2 main protease (Mpro).
- To identify sites vulnerable to mutations that could confer resistance to Mpro inhibitors.
Main Methods:
- Determined nine high-resolution cocrystal structures of SARS-CoV-2 Mpro with substrate peptides.
- Solved six structures of Mpro with cleavage products.
- Analyzed structural data to define the substrate envelope and recognition elements.
Main Results:
- Defined the substrate envelope of SARS-CoV-2 Mpro, revealing critical recognition sites.
- Mapped key interactions between Mpro and its substrates.
- Identified evolutionarily vulnerable sites within Mpro susceptible to resistance mutations.
Conclusions:
- Structural insights into Mpro provide a foundation for designing next-generation SARS-CoV-2 antivirals.
- Strategies can be developed to create robust inhibitors with durable efficacy against evolving SARS-CoV-2 variants.
- Understanding Mpro's substrate envelope is key to overcoming antiviral resistance.
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