X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease

Günther, Sebastian; Reinke, Patrick Y. A.; Fernández-García, Yaiza; Lieske, Julia; Lane, Thomas J.; Ginn, Helen M.; Koua, Faisal H. M.; Ehrt, Christiane; Ewert, Wiebke; Oberthuer, Dominik; Yefanov, Oleksandr; Meier, Susanne; Lorenzen, Kristina; Krichel, Boris; Kopicki, Janine-Denise; Gelisio, Luca; Brehm, Wolfgang; Dunkel, Ilona; Seychell, Brandon; Gieseler, Henry; Norton-Baker, Brenna; Escudero-Pérez, Beatriz; Domaracky, Martin; Saouane, Sofiane; Tolstikova, Alexandra; White, Thomas A.; Hänle, Anna; Groessler, Michael; Fleckenstein, Holger; Trost, Fabian; Galchenkova, Marina; Gevorkov, Yaroslav; Li, Chufeng; Awel, Salah; Peck, Ariana; Barthelmess, Miriam; Schlünzen, Frank; Lourdu Xavier, P.; Werner, Nadine; Andaleeb, Hina; Ullah, Najeeb; Falke, Sven; Srinivasan, Vasundara; França, Bruno Alves; Schwinzer, Martin; Brognaro, Hévila; Rogers, Cromarte; Melo, Diogo; Zaitseva-Doyle, Joanna J.; Knoska, Juraj; Peña-Murillo, Gisel E.; Mashhour, Aida Rahmani; Hennicke, Vincent; Fischer, Pontus; Hakanpää, Johanna; Meyer, Jan; Gribbon, Philip; Ellinger, Bernhard; Kuzikov, Maria; Wolf, Markus; Beccari, Andrea R.; Bourenkov, Gleb; von Stetten, David; Pompidor, Guillaume; Bento, Isabel; Panneerselvam, Saravanan; Karpics, Ivars; Schneider, Thomas R.; Garcia-Alai, Maria Marta; Niebling, Stephan; Günther, Christian; Schmidt, Christina; Schubert, Robin; Han, Huijong; Boger, Juliane; Monteiro, Diana C. F.; Zhang, Linlin; Sun, Xinyuanyuan; Pletzer-Zelgert, Jonathan; Wollenhaupt, Jan; Feiler, Christian G.; Weiss, Manfred S.; Schulz, Eike-Christian; Mehrabi, Pedram; Karničar, Katarina; Usenik, Aleksandra; Loboda, Jure; Tidow, Henning; Chari, Ashwin; Hilgenfeld, Rolf; Uetrecht, Charlotte; Cox, Russell; Zaliani, Andrea; Beck, Tobias; Rarey, Matthias; Günther, Stephan; Turk, Dusan; Hinrichs, Winfried; Chapman, Henry N.; Pearson, Arwen R.; Betzel, Christian; Meents, Alke

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (M(pro)), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to M(pro). In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.