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

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

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.
PMID: 33811162 DOI: 10.1126/science.abf7945
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 (Mpro), 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 Mpro 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.

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