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The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease

Norman Tran1, Sathish Dasari2, Sarah A E Barwell1

  • 1Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.

Nature Communications
|September 12, 2023
PubMed

Insights

The SARS-CoV-2 main protease (Mpro) can change shape due to oxidation. A specific mutation (H163A) reveals a protective oxidized state, offering new therapeutic targets for COVID-19.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Virology

Background:

  • The SARS-CoV-2 main protease (Mpro) is crucial for viral replication and a key therapeutic target.
  • Mpro undergoes redox-associated conformational changes influenced by cellular oxidation.
  • The precise mechanisms and functional impact of these Mpro conformational changes remain unclear.

Purpose of the Study:

  • To investigate the structural and mechanistic basis of Mpro conformational changes induced by oxidation.
  • To explore the role of specific residues, like H163, in modulating Mpro's redox-dependent behavior.
  • To identify potential therapeutic strategies targeting Mpro's conformational flexibility.

Main Methods:

  • X-ray crystallography of an Mpro point mutant (H163A).
  • Metadynamics simulations to model conformational transitions.
  • Analysis of free energy changes associated with Mpro mutations.

Main Results:

  • The crystal structure of H163A Mpro revealed an oxidized conformation with a disulfide bond involving the catalytic cysteine.
  • Metadynamics simulations proposed a mechanism for H163-mediated redox modulation.
  • Point mutations were shown to significantly alter the equilibrium towards the oxidized state by modifying conformational free energies.
  • The study suggests that wild-type Mpro exists in an equilibrium between oxidized and reduced states.

Conclusions:

  • Mpro can adopt a protected oxidized conformation under oxidative stress, potentially involving H163.
  • Understanding H163's role in modulating Mpro redox equilibrium opens new research avenues for COVID-19 therapeutics.
  • Targeting Mpro's redox-sensitive conformational changes represents a promising strategy for antiviral drug development.

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