Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease

Abstract

There is a clinical need for direct-acting antivirals targeting SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, to complement current therapeutic strategies. The main protease (M^pro) is an attractive target for antiviral therapy. However, the vast majority of protease inhibitors described thus far are peptidomimetic and bind to the active-site cysteine via a covalent adduct, which is generally pharmacokinetically unfavorable. We have reported the optimization of an existing FDA-approved chemical scaffold, perampanel, to bind to and inhibit M^pro noncovalently with IC₅₀s in the low-nanomolar range and EC₅₀s in the low-micromolar range. Here, we present nine crystal structures of M^pro bound to a series of perampanel analogs, providing detailed structural insights into their mechanism of action and structure-activity relationship. These insights further reveal strategies for pursuing rational inhibitor design efforts in the context of considerable active-site flexibility and potential resistance mechanisms.

Keywords: 3CL M(pro); 3CL main protease; SARS-CoV-2; X-ray crystallography; drug design; enzyme kinetics; protease inhibitor.