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bioRxiv · 10.1101/2022.12.16.520794

The H163A Mutation Unravels an Oxidized Conformation of the SARS-CoV-2 Main Protease and Opens a New Avenue for Anti-Viral Therapeutic Design

Tran, N.·Dasari, S.·Barwell, S.·McLeod, M.·Kalyaanamoorthy, S.·Holyoak, T.·Ganesan, A.
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Abstract

The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpros susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of a new Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrated a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild-type enzyme. We show that other point mutations can also significantly shift the equilibrium towards this state by altering conformational free energies. New therapeutic strategies against SARS-CoV-2 can be explored by understanding how H163 modulates this equilibrium.

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Tran, N., Dasari, S., Barwell, S., McLeod, M., Kalyaanamoorthy, S., Holyoak, T., Ganesan, A.. 2022-12-16. The H163A Mutation Unravels an Oxidized Conformation of the SARS-CoV-2 Main Protease and Opens a New Avenue for Anti-Viral Therapeutic Design. https://doi.org/10.1101/2022.12.16.520794

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