Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

  • bioRxiv. 2020 Nov 24;2020.11.24.393405. doi: 10.1101/2020.11.24.393405.
Marion Schuller  1 ,  Galen J Correy  2 ,  Stefan Gahbauer  3 ,  Daren Fearon  4 ,  Taiasean Wu  5  6 ,  Roberto Efraín Díaz  2  7 ,  Iris D Young  2  8 ,  Luan Carvalho Martins  9 ,  Dominique H Smith  10 ,  Ursula Schulze-Gahmen  8 ,  Tristan W Owens  8 ,  Ishan Deshpande  8 ,  Gregory E Merz  8 ,  Aye C Thwin  8 ,  Justin T Biel  8 ,  Jessica K Peters  8 ,  Michelle Moritz  8 ,  Nadia Herrera  8 ,  Huong T Kratochvil  8 ,  QCRG Structural Biology Consortium ,   Anthony Aimon  4 ,  James M Bennett  11 ,  Jose Brandao Neto  4 ,  Aina E Cohen  12 ,  Alexandre Dias  4 ,  Alice Douangamath  4 ,  Louise Dunnett  4 ,  Oleg Fedorov  11 ,  Matteo P Ferla  13 ,  Martin Fuchs  14 ,  Tyler J Gorrie-Stone  4 ,  James M Holton  15  16  12 ,  Michael G Johnson  17 ,  Tobias Krojer  11  18 ,  George Meigs  15  16 ,  Ailsa J Powell  4 ,  Johannes Gregor Matthias Rack ,   Victor L Rangel  11  18  19 ,  Silvia Russi  12 ,  Rachael E Skyner  4 ,  Clyde A Smith  12 ,  Alexei S Soares  20 ,  Jennifer L Wierman  12 ,  Kang Zhu  1 ,  Natalia Jura  21 ,  Alan Ashworth  10 ,  John Irwin  3 ,  Michael C Thompson  22 ,  Jason E Gestwicki  3  5 ,  Frank von Delft  4  11  18  23 ,  Brian K Shoichet  3 ,  James S Fraser  2 ,  Ivan Ahel  1
Affiliations
  • 1. Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
  • 2. Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA.
  • 3. Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA.
  • 4. Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom.
  • 5. Institute for Neurodegenerative Disease, University of California San Francisco, CA, USA.
  • 6. Chemistry and Chemical Biology Graduate Program, University of California San Francisco, CA, USA.
  • 7. Tetrad Graduate Program, University of California San Francisco, CA, USA.
  • 8. Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA.
  • 9. Biochemistry Department, Institute for Biological Sciences, Federal University of Minas Gerais. Belo Horizonte, Brazil.
  • 10. Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA, USA.
  • 11. Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK.
  • 12. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA.
  • 13. Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK.
  • 14. National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA.
  • 15. Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA.
  • 16. Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • 17. ChemPartner Corporation, South San Francisco, CA, USA.
  • 18. Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK.
  • 19. School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, São Paulo, Brazil.
  • 20. Photon Sciences, Brookhaven National Laboratory, Upton, NY, USA.
  • 21. Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA, USA.
  • 22. Department of Chemistry and Chemical Biology, University of California Merced, CA, USA.
  • 23. Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa.
PMID: 33269349 DOI: 10.1101/2020.11.24.393405
Abstract

The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated Antiviral ADP-ribosylation signalling. This enzyme is a promising Antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse Fragment Libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

Products