Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors

  • J Med Chem. 2024 May 9;67(9):7048-7067. doi: 10.1021/acs.jmedchem.3c02351.
Sven Falke  1 ,  Julia Lieske  1 ,  Alexander Herrmann  2 ,  Jure Loboda  3 ,  Katarina Karničar  3  4 ,  Sebastian Günther  1 ,  Patrick Y A Reinke  1 ,  Wiebke Ewert  1 ,  Aleksandra Usenik  3  4 ,  Nataša Lindič  3 ,  Andreja Sekirnik  3 ,  Klemen Dretnik  3  5 ,  Hideaki Tsuge  6 ,  Vito Turk  3 ,  Henry N Chapman  1  7  8 ,  Winfried Hinrichs  9 ,  Gregor Ebert  2  10 ,  Dušan Turk  3  4 ,  Alke Meents  1
Affiliations
  • 1. Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.
  • 2. Institute of Virology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Munich, Germany.
  • 3. Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
  • 4. Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia.
  • 5. The Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia.
  • 6. Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.
  • 7. Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
  • 8. Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
  • 9. Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany.
  • 10. Institute of Virology, Technical University of Munich, Trogerstraße 30, 81675 Munich, Germany.
PMID: 38630165 DOI: 10.1021/acs.jmedchem.3c02351
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 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.