Article
Author: Loboda, Jure  ; Hinrichs, Winfried  ; Reinke, Patrick Y. A.  ; Turk, Vito  ; Sekirnik, Andreja  ; Dretnik, Klemen  ; Usenik, Aleksandra  ; Herrmann, Alexander  ; Ebert, Gregor  ; Lieske, Julia  ; Lindič, Nataša  ; Meents, Alke  ; Karničar, Katarina  ; Ewert, Wiebke  ; Tsuge, Hideaki  ; Turk, Dušan  ; Falke, Sven  ; Chapman, Henry N.  ; Günther, Sebastian 
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.