X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease PMID: 33811162

Target-related Cytokines

2026-09-23

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease

Science. 2021 May 7;372(6542):642-646. doi: 10.1126/science.abf7945.

Sebastian Günther ^# ¹ , Patrick Y A Reinke ^# ² , Yaiza Fernández-García ³ , Julia Lieske ² , Thomas J Lane ² , Helen M Ginn ⁴ , Faisal H M Koua ² , Christiane Ehrt ⁵ , Wiebke Ewert ² , Dominik Oberthuer ² , Oleksandr Yefanov ² , Susanne Meier ⁶ ⁷ , Kristina Lorenzen ⁸ , Boris Krichel ⁹ , Janine-Denise Kopicki ⁹ , Luca Gelisio ² , Wolfgang Brehm ² , Ilona Dunkel ¹⁰ , Brandon Seychell ¹¹ , Henry Gieseler ⁶ ⁷ , Brenna Norton-Baker ¹² ¹³ , Beatriz Escudero-Pérez ³ , Martin Domaracky ² , Sofiane Saouane ¹⁴ , Alexandra Tolstikova ² , Thomas A White ² , Anna Hänle ² , Michael Groessler ² , Holger Fleckenstein ² , Fabian Trost ² , Marina Galchenkova ² , Yaroslav Gevorkov ² ¹⁵ , Chufeng Li ² , Salah Awel ² , Ariana Peck ¹⁶ , Miriam Barthelmess ² , Frank Schlünzen ² , P Lourdu Xavier ² ¹² , Nadine Werner ¹⁷ , Hina Andaleeb ¹⁷ , Najeeb Ullah ¹⁷ , Sven Falke ¹⁷ , Vasundara Srinivasan ¹⁷ , Bruno Alves França ¹⁷ , Martin Schwinzer ¹⁷ , Hévila Brognaro ¹⁷ , Cromarte Rogers ⁶ ⁷ , Diogo Melo ⁶ ⁷ , Joanna J Zaitseva-Doyle ⁶ ⁷ , Juraj Knoska ² , Gisel E Peña-Murillo ² , Aida Rahmani Mashhour ² , Vincent Hennicke ² , Pontus Fischer ² , Johanna Hakanpää ¹⁴ , Jan Meyer ¹⁴ , Philip Gribbon ¹⁸ , Bernhard Ellinger ¹⁸ , Maria Kuzikov ¹⁸ , Markus Wolf ¹⁸ , Andrea R Beccari ¹⁹ , Gleb Bourenkov ²⁰ , David von Stetten ²⁰ , Guillaume Pompidor ²⁰ , Isabel Bento ²⁰ , Saravanan Panneerselvam ²⁰ , Ivars Karpics ²⁰ , Thomas R Schneider ²⁰ , Maria Marta Garcia-Alai ²⁰ , Stephan Niebling ²⁰ , Christian Günther ²⁰ , Christina Schmidt ⁸ , Robin Schubert ⁸ , Huijong Han ⁸ , Juliane Boger ²¹ , Diana C F Monteiro ²² , Linlin Zhang ²¹ ²³ , Xinyuanyuan Sun ²¹ ²³ , Jonathan Pletzer-Zelgert ⁵ , Jan Wollenhaupt ²⁴ , Christian G Feiler ²⁴ , Manfred S Weiss ²⁴ , Eike-Christian Schulz ¹² , Pedram Mehrabi ¹² , Katarina Karničar ²⁵ ²⁶ , Aleksandra Usenik ²⁵ ²⁶ , Jure Loboda ²⁵ , Henning Tidow ⁶ ²⁷ , Ashwin Chari ²⁸ , Rolf Hilgenfeld ²¹ ²³ , Charlotte Uetrecht ⁹ , Russell Cox ²⁹ , Andrea Zaliani ¹⁸ , Tobias Beck ⁶ ¹¹ , Matthias Rarey ⁵ , Stephan Günther ³ , Dusan Turk ²⁵ ²⁶ , Winfried Hinrichs ¹⁷ ³⁰ , Henry N Chapman ² ⁶ ³¹ , Arwen R Pearson ⁶ ⁷ , Christian Betzel ⁶ ¹⁷ , Alke Meents ¹

Affiliations

1. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany. [email protected] [email protected].
2. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
3. Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany.
4. Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
5. Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany.
6. Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
7. Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany.
8. European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany.
9. Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany.
10. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.
11. Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany.
12. Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
13. Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, USA.
14. Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
15. Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany.
16. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
17. Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany.
18. Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany.
19. Dompé Farmaceutici SpA, 67100 L'Aquila, Italy.
20. EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany.
21. Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany.
22. Hauptmann Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
23. German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany.
24. Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
25. Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
26. Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia.
27. Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.
28. Research Group for Structural Biochemistry and Mechanisms, Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
29. Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167 Hannover, Germany.
30. Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany.
31. Universität Hamburg, Department of Physics, Luruper Chaussee 149, 22761 Hamburg, Germany.
# Contributed equally.

Abstract

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main Protease (M^pro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to M^pro In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed Antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.