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

• Published in: Scientific reports Vol. 12; no. 1; p. 2505
• Main Authors: Rossetti, Giacomo G., Ossorio, Marianna A., Rempel, Stephan, Kratzel, Annika, Dionellis, Vasilis S., Barriot, Samia, Tropia, Laurence, Gorgulla, Christoph, Arthanari, Haribabu, Thiel, Volker, Mohr, Peter, Gamboni, Remo, Halazonetis, Thanos D.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 15.02.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/535/1266; 631/92/507; 631/92/613; Cell culture; Coronaviruses; COVID-19; Crystallography; Humanities and Social Sciences; Inhibitors; Life cycles; multidisciplinary; Proteinase; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Tissue culture; X-ray crystallography
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-06306-4

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 IC 50 value of 1 μM 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.