Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease

Günther, Sebastian; Reinke, Patrick Y. A.; Oberthuer, Dominik; Yefanov, Oleksandr; Ginn, Helen; Meier, Susanne; Lane, Thomas J.; Lorenzen, Kristina; Gelisio, Luca; Brehm, Wolfgang; Dunkel, Illona; Domaracky, Martin; Saouane, Sofiane; Lieske, Julia; Ehrt, Christiane; Koua, Faisal; Tolstikova, Alexandra; White, Thomas A.; Groessler, Michael; Fleckenstein, Holger; Trost, Fabian; Galchenkova, Marina; Gevorkov, Yaroslav; Li, Chufeng; Awel, Salah; Peck, Ariana; Xavier, P. Lourdu; Barthelmess, Miriam; Schlünzen, Frank; Werner, Nadine; Andaleeb, Hina; Ullah, Najeeb; Falke, Sven; Franca, Bruno Alves; Schwinzer, Martin; Brognaro, Hévila; Seychell, Brandon; Gieseler, Henry; Melo, Diogo; Zaitsev-Doyle, Jo J.; Norton-Baker, Brenna; Knoska, Juraj; Esperanza, Gisel; Mashhour, Aida Rahmani; Guicking, Filip; Hennicke, Vincent; Fischer, Pontus; Rogers, Cromarte; Monteiro, Diana C. F.; Hakanpää, Johanna; Meyer, Jan; Noei, Heshmat; Gribbon, Phil; Ellinger, Bernhard; Kuzikov, Maria; Wolf, Markus; Zhang, Linlin; Sun, Xinyuanyuan; Pletzer-Zelgert, Jonathan; Wollenhaupt, Jan; Feiler, Christian; Weiss, Manfred; Schulz, Eike-Christian; Mehrabi, Pedram; Schmidt, Christina; Schubert, Robin; Han, Huijong; Krichel, Boris; Fernández-García, Yaiza; Escudero-Pérez, Beatriz; Günther, Stephan; Turk, Dusan; Uetrecht, Charlotte; Beck, Tobias; Tidow, Henning; Chari, Ashwin; Zaliani, Andrea; Rarey, Matthias; Cox, Russell; Hilgenfeld, Rolf; Chapman, Henry N.; Pearson, Arwen R.; Betzel, Christian; Meents, Alke

Here we present the crystal structure of SARS-CoV-2 main protease (Mpro) covalently bound to 2-methyl-1-tetralone. This complex was obtained by co-crystallization of Mpro with HEAT (2-(((4-hydroxyphenethyl)amino)methyl)-3,4-dihydronaphthalen-1(2H)-one) in the framework of a large X-ray crystallographic screening project of Mpro against a drug repurposing library, consisting of 5632 approved drugs or compounds in clinical phase trials. Further investigations showed that HEAT is cleaved by Mpro in an E1cB-like reaction mechanism into 2-methylene-1-tetralone and tyramine. The catalytic Cys145 subsequently binds covalently in a Michael addition to the methylene carbon atom of 2-methylene-1-tetralone. According to this postulated model HEAT is acting in a pro-drug-like fashion. It is metabolized by Mpro, followed by covalent binding of one metabolite to the active site. The structure of the covalent adduct elucidated in this study opens up a new path for developing non-peptidic inhibitors.