Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors

• Published in: Journal of medicinal chemistry 2024-05, Vol.67 (9), p.7048-7067
• Main Authors: Falke, Sven, Lieske, Julia, Herrmann, Alexander, Loboda, Jure, Karničar, Katarina, Günther, Sebastian, Reinke, Patrick Y. A., Ewert, Wiebke, Usenik, Aleksandra, Lindič, Nataša, Sekirnik, Andreja, Dretnik, Klemen, Tsuge, Hideaki, Turk, Vito, Chapman, Henry N., Hinrichs, Winfried, Ebert, Gregor, Turk, Dušan, Meents, Alke
• Format: Article
• Language: English
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/acs.jmedchem.3c02351

Emerging RNA viruses, including SARS-CoV-2, continue to be a major threat. Cell entry of SARS-CoV-2 particles via the endosomal pathway involves cysteine cathepsins. Due to ubiquitous expression, cathepsin L (CatL) is considered a promising drug target in the context of different viral and lysosome-related diseases. We characterized the anti-SARS-CoV-2 activity of a set of carbonyl- and succinyl epoxide-based inhibitors, which were previously identified as inhibitors of cathepsins or related cysteine proteases. Calpain inhibitor XII, MG-101, and CatL inhibitor IV possess antiviral activity in the very low nanomolar EC50 range in Vero E6 cells and inhibit CatL in the picomolar Ki range. We show a relevant off-target effect of CatL inhibition by the coronavirus main protease α-ketoamide inhibitor 13b. Crystal structures of CatL in complex with 14 compounds at resolutions better than 2 Å present a solid basis for structure-guided understanding and optimization of CatL inhibitors toward protease drug development.