Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors

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.