Molecular Characterization of Ebselen Binding Activity to SARS-CoV-2 Main Protease

TL;DR

This study uses molecular simulations to analyze how Ebselen binds to SARS-CoV-2 main protease, revealing a new binding site and potential allosteric effects that could inform drug design against COVID-19.

Contribution

It uncovers a second, stronger binding site for Ebselen on Mpro and elucidates its allosteric effects, advancing understanding of its inhibitory mechanism.

Findings

Ebselen binds strongly to a newly identified site on Mpro.

A second binding site exhibits higher affinity than the catalytic site.

Binding induces allosteric changes that may inhibit enzymatic activity.

Abstract

The Coronavirus Disease (COVID-19) pandemic caused by the SARS-coronavirus 2 (SARS-CoV-2) urgently calls for the design of drugs directed against this new virus. Given its essential role in proteolytic processing, the main protease Mpro has been identified as an attractive candidate for drugs against SARS-CoV-2 and similar coronaviruses. Recent high-throughput screening studies have identified a set of existing, small-molecule drugs as potent Mpro inhibitors. Amongst these, Ebselen (2-Phenyl-1,2-benzoselenazol-3-one), a glutathione peroxidase mimetic seleno-organic compound, is particularly attractive. Recent experiments suggest that its effectiveness is higher than that of other molecules that also act at the enzyme catalytic site. By relying on extensive simulations with all-atom models, in this study we examine at a molecular level the potential of Ebselen to decrease Mpro catalytic activity. Our results indicate that Ebselen exhibits a distinct affinity for the catalytic site cavity of Mpro. In addition, our molecular models reveal a second, previously unkown binding site for Ebselen in the dimerization region localized between the II and III domains of the protein. A detailed analysis of the free energy of binding indicates that the affinity of Ebselen to this second binding site is in fact significantly larger than that to the catalytic site. A strain analysis indicates that Ebselen bound between the II-III domains exerts a pronounced allosteric effect that regulates catalytic site access through surface loop interactions, and induces a displacement and reconfiguration of water hotspots, including the catalytic water, which could interfere with normal enzymatic function. Taken together, these findings provide a framework for the future design of more potent and specific Mpro inhibitors, based on the Ebselen scaffold, that could lead to new therapeutic strategies for COVID-19.