Non-covalent SARS-CoV-2 Mpro inhibitors developed from in silico screen hits

M-pro, the main protease of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is essential for the viral life cycle. Accordingly, several groups have performed in silico screens to identify M-pro inhibitors that might be used to treat SARS-CoV-2 infections. We selected more than five hundred compounds from the top-ranking hits of two very large in silico screens for on-demand synthesis. We then examined whether these compounds could bind to M-pro and inhibit its protease activity. Two interesting chemotypes were identified, which were further evaluated by characterizing an additional five hundred synthesis on-demand analogues. The compounds of the first chemotype denatured M-pro and were considered not useful for further development. The compounds of the second chemotype bound to and enhanced the melting temperature of M-pro. The most active compound from this chemotype inhibited M-pro in vitro with an IC50 value of 1 mu M and suppressed replication of the SARS-CoV-2 virus in tissue culture cells. Its mode of binding to M-pro was determined by X-ray crystallography, revealing that it is a non-covalent inhibitor. We propose that the inhibitors described here could form the basis for medicinal chemistry efforts that could lead to the development of clinically relevant inhibitors.

Automated summary

A potential M-pro inhibitor for treating SARS-CoV-2 infections has been identified and its efficacy and mode of action have been further characterized.