8A4W

Crystal structure of human cathepsin L with covalently bound Cathepsin L inhibitor IV

Summary for 8A4W

• Entry DOI: 10.2210/pdb8a4w/pdb
• Related: 7ZS7 7ZVF 7ZXA 8A4U 8A4V
• Descriptor: Cathepsin L, N-(1-naphthylsulfonyl)-(L)-isoleucyl-(L)-tryptophanol, DI(HYDROXYETHYL)ETHER, ... (8 entities in total)
• Functional Keywords: cystein protease, drug target, lysosome, virus cell entry, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 4
• Total formula weight: 99905.95

Authors

Falke, S.,Lieske, J.,Guenther, S.,Reinke, P.Y.A.,Ewert, W.,Loboda, J.,Karnicar, K.,Usenik, A.,Lindic, N.,Sekirnik, A.,Chapman, H.N.,Hinrichs, W.,Turk, D.,Meents, A. (deposition date: 2022-06-13, release date: 2023-07-05, Last modification date: 2024-10-23)

Primary citation

Falke, S.,Lieske, J.,Herrmann, A.,Loboda, J.,Karnicar, K.,Gunther, S.,Reinke, P.Y.A.,Ewert, W.,Usenik, A.,Lindic, N.,Sekirnik, A.,Dretnik, K.,Tsuge, H.,Turk, V.,Chapman, H.N.,Hinrichs, W.,Ebert, G.,Turk, D.,Meents, A.
Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors.
J.Med.Chem., 67:7048-7067, 2024

PubMed Abstract: 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 EC range in Vero E6 cells and inhibit CatL in the picomolar 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.

PubMed: 38630165
DOI: 10.1021/acs.jmedchem.3c02351

Experimental method

X-RAY DIFFRACTION (1.4 Å)