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

• Published in: Scientific reports 2022-02, Vol.12 (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: Article
• Language: English
• Subjects: Binding Sites; Coronavirus 3C Proteases - antagonists & inhibitors; Coronavirus 3C Proteases - genetics; Coronavirus 3C Proteases - metabolism; COVID-19 - pathology; COVID-19 - virology; Crystallography, X-Ray; Humans; Molecular Conformation; Molecular Docking Simulation; Nitriles - chemistry; Nitriles - metabolism; Nitriles - pharmacology; Protease Inhibitors - chemistry; Protease Inhibitors - metabolism; Protease Inhibitors - pharmacology; Quinazolines - chemistry; Quinazolines - metabolism; Quinazolines - pharmacology; Recombinant Proteins - biosynthesis; Recombinant Proteins - chemistry; Recombinant Proteins - isolation & purification; SARS-CoV-2 - enzymology; SARS-CoV-2 - isolation & purification; SARS-CoV-2 - physiology; Virus Replication - drug effects
• ISSN: 2045-2322
• DOI: 10.1038/s41598-022-06306-4

M , 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 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 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 and were considered not useful for further development. The compounds of the second chemotype bound to and enhanced the melting temperature of M . The most active compound from this chemotype inhibited M in vitro with an IC value of 1 μM and suppressed replication of the SARS-CoV-2 virus in tissue culture cells. Its mode of binding to M 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.