10
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Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kautsar SA, Kim H, Leao TF, Masschelein J, Rees ER, Reher R, Reker D, Schwaller P, Segler M, Skinnider MA, Walker AS, Willighagen EL, Zdrazil B, Ziemert N, Goss RJM, Guyomard P, Volkamer A, Gerwick WH, Kim HU, Müller R, van Wezel GP, van Westen GJP, Hirsch AKH, Linington RG, Robinson SL, Medema MH. Artificial intelligence for natural product drug discovery. Nat Rev Drug Discov 2023; 22:895-916. [PMID: 37697042 DOI: 10.1038/s41573-023-00774-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2023] [Indexed: 09/13/2023]
Abstract
Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.
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Affiliation(s)
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Neha Garg
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - David Meijer
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Marina Gorostiola González
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
- ONCODE institute, Leiden, The Netherlands
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Florian Huber
- Center for Digitalization and Digitality, Hochschule Düsseldorf, Düsseldorf, Germany
| | - Stefan Leopold-Messer
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany
| | - Tristan de Rond
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Jena, Germany
- Pharmaceuticals R&D, Bayer AG, Berlin, Germany
| | - Marcy J Balunas
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles", Université Paris-Saclay, CNRS, BioCIS, Orsay, France
| | - Doris A van Bergeijk
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Chase M Clark
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Chao Du
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Francesca Grisoni
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | | | - Willem Jespers
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Drug Bioinformatics, Medical Faculty, Saarland University, Homburg, Germany
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Hyunwoo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University Seoul, Goyang-si, Republic of Korea
| | - Tiago F Leao
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Joleen Masschelein
- Center for Microbiology, VIB-KU Leuven, Heverlee, Belgium
- Department of Biology, KU Leuven, Heverlee, Belgium
| | - Evan R Rees
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Raphael Reher
- Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, Marburg, Germany
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Daniel Reker
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Philippe Schwaller
- Laboratory of Artificial Chemical Intelligence, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Michael A Skinnider
- Adapsyn Bioscience, Hamilton, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Barbara Zdrazil
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, UK
| | - Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), Institute for Bioinformatics and Medical Informatics (IBMI), University of Tuebingen, Tuebingen, Germany
| | | | - Pierre Guyomard
- Bonsai team, CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Université de Lille, Villeneuve d'Ascq Cedex, France
| | - Andrea Volkamer
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Center for infection research (DZIF), Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, The Netherlands
| | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands.
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.
- Department of Pharmacy, Saarland University, Saarbrücken, Germany.
- German Center for infection research (DZIF), Braunschweig, Germany.
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany.
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Serina L Robinson
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Dübendorf, Switzerland.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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18
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Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, et alGordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 2020; 370:eabe9403. [PMID: 33060197 PMCID: PMC7808408 DOI: 10.1126/science.abe9403] [Show More Authors] [Citation(s) in RCA: 494] [Impact Index Per Article: 98.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/12/2020] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.
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Affiliation(s)
- David E Gordon
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joseph Hiatt
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, cedex 15, France
| | - Svenja Ulferts
- Institute for Clinical and Experimental Pharmacology and Toxicology I, University of Freiburg, 79104 Freiburg, Germany
| | - Hannes Braberg
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Alexander S Jureka
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jeffrey Z Guo
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Robyn M Kaake
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Tristan W Owens
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Meghna Gupta
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Sergei Pourmal
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Erron W Titus
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Merve Cakir
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael McGregor
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Zeynep Cakir
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Gwendolyn Jang
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Ziyang Zhang
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Dmitry Kuchenov
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
| | - Manisha Ummadi
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Beril Tutuncuoglu
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ujjwal Rathore
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Maya Modak
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Paige Haas
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kelsey M Haas
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Zun Zar Chi Naing
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ernst H Pulido
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ying Shi
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Danish Memon
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eirini Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alistair Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Correa Marrero
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - David Burke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, cedex 15, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, cedex 15, France
| | - Jesus A Silvas
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Caleigh M Azumaya
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Christian Billesbølle
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Axel F Brilot
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Melody G Campbell
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Amy Diallo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Miles Sasha Dickinson
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Devan Diwanji
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Nadia Herrera
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Nick Hoppe
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Huong T Kratochvil
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yanxin Liu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Gregory E Merz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Michelle Moritz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Henry C Nguyen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Carlos Nowotny
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Cristina Puchades
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Alexandrea N Rizo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Amber M Smith
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ming Sun
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Beam Therapeutics, Cambridge, MA 02139, USA
| | - Iris D Young
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jianhua Zhao
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Daniel Asarnow
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Justin Biel
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Alisa Bowen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Julian R Braxton
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jen Chen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Cynthia M Chio
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Un Seng Chio
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ishan Deshpande
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Loan Doan
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Bryan Faust
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Sebastian Flores
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Mingliang Jin
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kate Kim
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Victor L Lam
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Fei Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Junrui Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yen-Li Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yang Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Xi Liu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Megan Lo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kyle E Lopez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Arthur A Melo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Frank R Moss
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Phuong Nguyen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Joana Paulino
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Komal Ishwar Pawar
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jessica K Peters
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Thomas H Pospiech
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Maliheh Safari
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Smriti Sangwan
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kaitlin Schaefer
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Paul V Thomas
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Aye C Thwin
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Raphael Trenker
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Eric Tse
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Tsz Kin Martin Tsui
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Feng Wang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Natalie Whitis
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Zanlin Yu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kaihua Zhang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yang Zhang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Fengbo Zhou
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Daniel Saltzberg
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Anthony J Hodder
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Amber S Shun-Shion
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Daniel M Williams
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Suzannah Rihn
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Mir M Khalid
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Parinaz Fozouni
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Camille R Simoneau
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - David Wu
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Mohd Anisul Karim
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Maya Ghoussaini
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Francesco Berardi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari 'ALDO MORO', Via Orabona, 4 70125, Bari, Italy
| | - Sebastian Weigang
- Institute of Virology, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | - Maxime Chazal
- Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France
| | - Jisoo Park
- Department of Medicine, University of California, San Diego, CA 92093, USA
| | - James Logue
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Marisa McGrath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Haupt
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Matthew Elliott
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Fiona Brown
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Kerry A Burness
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Elaine Reid
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Mark Dorward
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Stuart G Wilkinson
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Anna Geyer
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Daniel M Giesel
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Carla Baillie
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Samantha Raggett
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Hannah Leech
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Nicola Goodman
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Abigail L Lind
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Kafi R Hemphill
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | | | - Jennifer Oki
- Synthego Corporation, Redwood City, CA 94063, USA
| | - Kevin Holden
- Synthego Corporation, Redwood City, CA 94063, USA
| | | | - Katherine S Pollard
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Andrej Sali
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - David A Agard
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - James S Fraser
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Adam Frost
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Natalia Jura
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Tanja Kortemme
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- The University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA 94158, USA
| | - Aashish Manglik
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Daniel R Southworth
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Robert M Stroud
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, CA 92093, USA
- Department to Bioengineering, University of California, San Diego, CA 92093, USA
| | - Carmen Abate
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari 'ALDO MORO', Via Orabona, 4 70125, Bari, Italy
| | - Nolwenn Jouvenet
- Institute of Virology, Medical Center-University of Freiburg, 79104 Freiburg, Germany
- Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France
| | - Georg Kochs
- Institute of Virology, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | - Brian Shoichet
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Kevan M Shokat
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert Grosse
- Institute for Clinical and Experimental Pharmacology and Toxicology I, University of Freiburg, 79104 Freiburg, Germany.
- Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Oren S Rosenberg
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA.
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Kliment A Verba
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA.
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, cedex 15, France.
| | - Andrew A Peden
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA.
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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