ArticleProtein science : a publication of the Protein Society2023
Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.
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Article in Protein science : a publication of the Protein Society, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24citing papers in PubMed
7.7field-weighted citation impact, top 2% of its field
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Who cites it
24 citing papers in PubMed, 40 citations in OpenAlex.
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- The Selectivity Implications of Docking Libraries with Greater and Lesser Similarities to Bio-like Molecules.Journal of medicinal chemistry · 2026Article
- The architecture of computational antiviralism: a multi-scale framework from molecular targeting to viral ecosystem engineering.Molecular diversity · 2026Review
- Discovery of Covalent Ligands with AlphaFold3.Journal of the American Chemical Society · 2026Article
- The selectivity implications of docking libraries with greater and lesser similarities to bio-like molecules.bioRxiv : the preprint server for biology · 2026Article
- Discovery of Coronavirus Main Protease Inhibitors with Enhanced Brain Exposure and Potent Oral Efficacy in SARS-CoV-2 and MERS Infection Models.Journal of medicinal chemistry · 2026Article
- Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds.Journal of enzyme inhibition and medicinal chemistry · 2025Review
- Large Library Docking and Biophysical Analysis of Small-Molecule TMPRSS2 Inhibitors.Journal of medicinal chemistry · 2025Article
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- A Database for Large-Scale Docking and Experimental Results.Journal of chemical information and modeling · 2025Article
- Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MScience advances · 2025Article
- Rapid traversal of vast chemical space using machine learning-guided docking screens.Nature computational science · 2025Article
- DTBind: A Mechanism-Driven Deep Learning Framework for Accurate Prediction of Drug-Target Molecular Recognition.Research (Washington, D.C.) · 2025Article
- Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds.Journal of chemical information and modeling · 2024Article
- Identifying Artifacts from Large Library Docking.Journal of medicinal chemistry · 2024Article
- Phytochemicals in Drug Discovery-A Confluence of Tradition and Innovation.International journal of molecular sciences · 2024Review
- Identifying Artifacts from Large Library Docking.bioRxiv : the preprint server for biology · 2024Article
- Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking.Journal of chemical information and modeling · 2024Article
- On the origins of SARS-CoV-2 main protease inhibitors.RSC medicinal chemistry · 2024Review
- Article
Corrections and comments
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Authors and funding
31 authors at 6 institutions in 2 countries.
Elissa A FinkDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Conner BardineDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Stefan GahbauerDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Isha SinghDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Tyler C DetomasiDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Kris WhiteDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Shuo GuDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Xiaobo WanDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Jun ChenDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Beatrice AryDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Isabella GlennDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Joseph O'ConnellDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Henry O'DonnellDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Pavla FajtováSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, San Diego, California, USA.
Jiankun LyuDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Seth VigneronDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Nicholas J YoungDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Ivan S KondratovEnamine Ltd., Kyïv, Ukraine.
Arghavan AlisoltaniDivision of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Lacy M SimonsDivision of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Ramon Lorenzo-RedondoDivision of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Egon A OzerDivision of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Judd F HultquistDivision of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Anthony J O'DonoghueSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, San Diego, California, USA.
Yurii S MorozNational Taras Shevchenko University of Kyïv, Kyïv, Ukraine.
Jack TauntonDepartment of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA.
Adam R RensloDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
John J IrwinDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
Adolfo García-SastreDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Brian K ShoichetDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.ORCID 0000-0002-6098-7367
Charles S CraikDepartment of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.
University of California, San Francisco · USNorthwestern University · USIcahn School of Medicine at Mount Sinai · USUniversity of California San Diego · USNational Academy of Sciences of Ukraine · UATaras Shevchenko National University of Kyiv · UA
Funding
Targeting Viroporins and Coronavirus M ProteinU19AI171110 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Nevan J Krogan · 2022 to 2026
$103.4MNIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00014 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI GARCIA-SASTRE, ADOLFO · 2021 to 2025
$62.6MSARS-CoV adaptations through a Systems Biology Lens (SYBIL)U19AI135972 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Adolfo Garcia-Sastre · 2018 to 2026
$27.2MDevelopment and Testing of New Computational Methods for Ligand Discovery and MechanismR35GM122481 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Brian K Shoichet · 2017 to 2026
$8.5MResearch Training in Chemistry and Chemical BiologyT32GM145460 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Jason E Gestwicki · 2022 to 2026
$3.1MUltra-large library docking for ligand discoveryR01GM133836 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI IRWIN, JOHN J. · 2019 to 2022
$1.6MAssessing the Risk of SARS-CoV-2 Remdesivir ResistanceR21AI163912 · NIAID · NORTHWESTERN UNIVERSITY AT CHICAGO · PI HULTQUIST, JUDD F · 2021 to 2022
$440kNIAID NIH HHS 75N93021C00014NIAID NIH HHS R21 AI163912NIAID NIH HHS U19 AI135972NIAID NIH HHS U19AI135972NIAID NIH HHS U19 AI171110NIAID NIH HHS U19AI171110NIGMS NIH HHS R01 GM133836NIGMS NIH HHS R35 GM122481NIGMS NIH HHS T32 GM145460NIH HHS R21AI163912NIH HHS R35GM122481
Abstract
Antiviral therapeutics to treat SARS-CoV-2 are needed to diminish the morbidity of the ongoing COVID-19 pandemic. A well-precedented drug target is the main viral protease (M
Indexed as
COVID-19Antiviral AgentsCoronavirus 3C ProteasesHumansMolecular Docking SimulationPandemicsProtease InhibitorsSARS-CoV-2Viral Nonstructural Proteins3C-like proteinase, SARS-CoV-2Antiviral AgentsCoronavirus 3C ProteasesProtease InhibitorsViral Nonstructural Proteinsdiscoverydockinganti-viralmajor proteaseSARS-COV-2structure-based inhibitor
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