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

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 IC(50)s in the low-nanomolar range and EC(50)s in the low-micromolar range. Here, we present nine crystal structures of Mpro 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.

Automated summary

This study optimized an existing FDA-approved chemical scaffold, perampanel, to noncovalently bind and inhibit M-pro, achieving IC(50)s in the low-nanomolar range and EC(50)s in the low-micromolar range. The research presented nine crystal structures of Mpro bound to a series of perampanel analogs, providing detailed structural insights into their mechanism of action and structure-activity relationship. These insights reveal strategies for rational inhibitor design efforts in the context of active-site flexibility and potential resistance mechanisms.