ArticleJournal of chemical information and modeling2025
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.
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Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13citing papers in PubMed
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Who cites it
13 citing papers in PubMed.
- Pushing the boundaries of virtual screening scale of combinatorial spaces with the V-SYNTHES approach.npj drug discovery · 2026Article
- Targeting the RNA-Binding Site of SARS-CoV-2 NSP13 by FRASE-bot in CACHE Challenge #2.Journal of chemical information and modeling · 2026Article
- Repurposing drug screen for the identification of helicase inhibitors from viruses of pandemic concern.SLAS discovery : advancing life sciences R & D · 2026Article
- Library Docking for Cannabinoid-2 Receptor Ligands.Journal of medicinal chemistry · 2026Article
- Automated Parallel Synthesis Accelerates Virtual Screening Hit Discovery.Journal of the American Chemical Society · 2026Article
- Library docking for Cannabinoid-2 Receptor ligands.bioRxiv : the preprint server for biology · 2026Article
- CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2.Journal of chemical information and modeling · 2026Article
- SARS-CoV-2 NSP8-Derived Peptide Effectively Suppresses the Activity of Helicase NSP13.Computational and structural biotechnology journal · 2026Article
- An efficient computational chemistry approach to generating negative data for drug discovery pipeline validation.Frontiers in bioinformatics · 2026Article
- Evaluating BindCraft for Generative Design of High-Affinity Peptides.ACS chemical biology · 2025Article
- Ultra-large library screening with an evolutionary algorithm in Rosetta (REvoLd).Communications chemistry · 2025Article
- A New Fragment-Based Pharmacophore Virtual Screening Workflow Identifies Potent Inhibitors of SARS-CoV-2 NSP13 Helicase.Journal of computational chemistry · 2025Article
- Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches.npj drug discovery · 2025Review
Corrections and comments
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Authors and funding
104 authors.
Oleksandra HerasymenkoStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Madhushika SilvaStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Abd Al-Aziz A Abu-SalehStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Ayaz AhmadSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Jesus Alvarado-HuayhuazCenter for Computational Sciences, Universidade Federal do Rio Grande - FURG, Rio Grande 96201-900, Brazil.
Oscar E A ArceCenter for Computational Sciences, Universidade Federal do Rio Grande - FURG, Rio Grande 96201-900, Brazil.
Roly J ArmstrongSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Cheryl ArrowsmithStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Kelly E BachtaDivision of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States.
Hartmut BeckBayer AG, Drug Discovery Sciences, Wuppertal, 42096, Germany.ORCID 0000-0002-7826-8467
Denes BertaDepartment of Physics and Astronomy, University College London, London WC1E 6BS, United Kingdom.ORCID 0000-0002-8299-3784
Mateusz K BieniekSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Vincent BlayDepartment of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California 95064, United States.ORCID 0000-0001-9602-2375
Albina BolotokovaStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Philip E BourneSchool of Data Science, University of Virginia, Charlottesville, Virginia 22904, United States of America.ORCID 0000-0002-7618-7292
Marko BreznikComputational Molecular Design, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2 + 4, Berlin 14195, Germany.
Peter J BrownUNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.
Aaron D G CampbellSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Emanuele CarosatiDepartment of Chemistry and Pharmaceutical Sciences, University of Trieste, Trieste 34127, Italy.ORCID 0000-0003-0657-5035
Irene ChauStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Daniel J ColeSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Ben CreeSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Wim DehaenDepartment of Organic Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
Katrin DenzingerComputational Molecular Design, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2 + 4, Berlin 14195, Germany.
Karina Dos Santos MachadoCenter for Computational Sciences, Universidade Federal do Rio Grande - FURG, Rio Grande 96201-900, Brazil.
Ian DunnDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.
Prasannavenkatesh DuraiKorea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea.ORCID 0000-0002-1538-8349
Kristina EdfeldtStructural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm 171 76, Sweden.
Aled EdwardsStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.ORCID 0000-0002-4782-6016
Darren FayneDCU Life Sciences Institute, Dublin City University, Dublin, D09 DXA0, Ireland.ORCID 0000-0003-2417-5406
Daniel FelfoldiDepartment of Physics and Astronomy, University College London, London WC1E 6BS, United Kingdom.ORCID 0000-0003-0774-0450
Kallie FristonSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Pegah GhiabiStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Elisa GibsonStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.ORCID 0000-0002-7112-337X
Judith GüntherBayer AG, Drug Discovery Sciences, Berlin 13353, Germany.ORCID 0000-0001-5794-8984
Anders GunnarssonStructure and Biophysics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, Gothenburg 431 50, Sweden.
Alexander HillischUCB, Monheim am Rhein 40789, Germany.
Douglas R HoustonSchool of Biological Sciences, University of Edinburgh, King's Buildings EH9 3BF, United Kingdom.ORCID 0000-0002-3469-1546
Jan Halborg JensenDepartment of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.ORCID 0000-0002-1465-1010
Rachel J HardingStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.ORCID 0000-0002-1134-391X
Kate S HarrisSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Laurent HofferDrug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.
Anders HognerMedicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 50, Sweden.ORCID 0000-0003-3823-4534
Joshua T HortonSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.ORCID 0000-0001-8694-7200
Scott HoulistonPrincess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2C4, Canada.
Judd F HultquistDivision of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States.
Ashley HutchinsonStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
John J IrwinPharmaceutical Chemistry, UCSF, 1700 fourth St, San Francisco California 94523, United States.
Marko JukičLaboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, Maribor SI-2000, Slovenia.ORCID 0000-0001-6083-5024
Shubhangi KandwalMolecular Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2 D02 R590, Ireland.
Andrea KarlovaDepartment of Computer Science, University College London, London OX3 7DQ, United Kingdom.
Vittorio L KatisCentre for Medicines Discovery, NDM Research Building, University of Oxford, Oxford OX3 7FZ, U.K.
Ryan P KichDivision of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States.ORCID 0009-0005-9833-6411
Dmitri KireevDepartment of Chemistry, University of Missouri, Columbia, Missouri 65211-7600, United States of America.ORCID 0000-0001-8479-8555
David KoesDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.ORCID 0000-0002-6892-6614
Nicole L InnissDepartment of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611 United States of America.
Uta LesselBoehringer Ingelheim Pharma GmbH & Co. KG Birkendorfer Str. 65, Biberach an der Riss 88397, Germany.ORCID 0000-0002-1698-6017
Sijie LiuComputational Molecular Design, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2 + 4, Berlin 14195, Germany.ORCID 0000-0001-8834-3881
Peter LoppnauStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Wei LuGalixir Technologies, Shanghai 200100, China.
Sam MartinoDepartment of Physics and Astronomy, University College London, London WC1E 6BS, United Kingdom.
Miles McGibbonDepartment of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
Jens MeilerCenter for Structural Biology, Vanderbilt University, South Nashville, Nashville, Tennessee 37240-0002, United States of America.
Akhila MettuDepartment of Chemistry, University of Missouri, Columbia, Missouri 65211-7600, United States of America.
Sam Money-KyrleDepartment of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California 95064, United States.
Rocco MorettiCenter for Structural Biology, Vanderbilt University, South Nashville, Nashville, Tennessee 37240-0002, United States of America.ORCID 0000-0003-2162-1116
Yurii S MorozChemspace, Kyiv 02094, Ukraine.
Charuvaka MuvvaKorea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea.
Joseph A NewmanCentre for Medicines Discovery, NDM Research Building, University of Oxford, Oxford OX3 7FZ, U.K.
Leon ObendorfComputational Molecular Design, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2 + 4, Berlin 14195, Germany.
Brooks PaigeDepartment of Computer Science, University College London, London OX3 7DQ, United Kingdom.
Amit PanditComputational Molecular Design, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2 + 4, Berlin 14195, Germany.
Keunwan ParkKorea Institute of Science and Technology, Seongbuk-gu, Seoul 02792, Republic of Korea.
Sumera PerveenStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Rachael PirieSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.ORCID 0000-0002-2449-3458
Gennady PodaLeslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada.
Mykola ProtopopovChemspace, Kyiv 02094, Ukraine.
Vera PütterNuvisan ICB GmBH, Berlin 13353, Germany.
Federico RicciUniversity of Messina, Messina 98122, Italy.
Natalie J RoperSchool of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom.
Edina RostaDepartment of Physics and Astronomy, University College London, London WC1E 6BS, United Kingdom.ORCID 0000-0002-9823-4766
Margarita RzhetskayaDivision of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States.
Yogesh SabnisUCB, Braine-L'Alleud 1420, Belgium.
Karla J F SatchellDepartment of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611 United States of America.ORCID 0000-0003-3274-7611
Frederico Schmitt KremerOmixLab, Universidade Federal de Pelotas, Capão do Leão 96010-610, Brazil.
Thomas ScottCenter for Structural Biology, Vanderbilt University, South Nashville, Nashville, Tennessee 37240-0002, United States of America.
Almagul SeitovaStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
Casper SteinmannDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg 9220, Denmark.ORCID 0000-0002-5638-1346
Valerij TalagayevComputational Molecular Design, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2 + 4, Berlin 14195, Germany.ORCID 0000-0002-1907-9594
Olga O TarkhanovaChemspace, Kyiv 02094, Ukraine.
Natalie J TatumNewcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.ORCID 0000-0003-3878-9265
Dakota TreleavenConscience Medicines Network, Toronto, Ontario M5G 1L7 Canada.ORCID 0009-0006-6458-0042
Adriano Velasque WerhliCenter for Computational Sciences, Universidade Federal do Rio Grande - FURG, Rio Grande 96201-900, Brazil.
W Patrick WaltersRelay Therapeutics, Cambridge, Massachusetts 02141, United States.ORCID 0000-0003-2860-7958
Xiaowen WangDepartment of Chemistry, University of Missouri, Columbia, Missouri 65211-7600, United States of America.
Jude WellsDepartment of Computer Science, University College London, London OX3 7DQ, United Kingdom.
Geoffrey WellsDepartment of Pharmaceutical and Biological Chemistry, University College London, London WC1E 6BT, United Kingdom.ORCID 0000-0002-0253-911X
Yvonne WestermaierBoehringer Ingelheim RCV, Dr. Boehringer-Gasse 5-11, Vienna 1121, Austria.ORCID 0000-0002-0462-8650
Gerhard WolberComputational Molecular Design, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2 + 4, Berlin 14195, Germany.ORCID 0000-0002-5344-0048
Lars WortmannBoehringer Ingelheim Pharma GmbH & Co. KG Birkendorfer Str. 65, Biberach an der Riss 88397, Germany.ORCID 0000-0001-6514-947X
Jixian ZhangGalixir Technologies, Shanghai 200100, China.
Zheng ZhaoSchool of Data Science, University of Virginia, Charlottesville, Virginia 22904, United States of America.ORCID 0000-0003-1453-3230
Shuangjia ZhengShanghai Jiao Tong University, Shanghai 200030, China.
Matthieu SchapiraStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.ORCID 0000-0002-1047-3309
Funding
Targeting Viroporins and Coronavirus M ProteinU19AI171110 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Nevan J Krogan · 2022 to 2026
$103.4MResearch Project 1: Coronavirus antiviral lead development and combination testingU19AI171292 · NIAID · UNIV OF NORTH CAROLINA CHAPEL HILL · PI BARIC, RALPH S, WILLSON, TIMOTHY M · 2022 to 2022
$65.5MViral and Host Dynamics during Pediatric COVID-19 and Respiratory Virus Co-InfectionR01AI177498 · NIAID · NORTHWESTERN UNIVERSITY AT CHICAGO · PI Bria M Coates, Judd F Hultquist · 2024 to 2026
$2.4MNIAID NIH HHS R01 AI177498NIAID NIH HHS U19 AI171110NIAID NIH HHS U19 AI171292
Abstract
A critical assessment of computational hit-finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comprised of computational chemists and data scientists used protein structure and data from fragment-screening paired with advanced computational and machine learning methods to each predict up to 100 inhibitory ligands. Across all teams, 1957 compounds were predicted and were subsequently procured from commercial catalogs for biophysical assays. Of these compounds, 0.7% were confirmed to bind to Nsp13 in a surface plasmon resonance assay. The six best-performing computational workflows used fragment growing, active learning, or conventional virtual screening with and without complementary deep-learning scoring functions. Follow-up functional assays resulted in identification of two compound scaffolds that bound Nsp13 with a
Indexed as
Coronavirus RNA-Dependent RNA PolymeraseRNARNA HelicasesViral Nonstructural ProteinsBinding SitesDeep LearningLigandsCoronavirus RNA-Dependent RNA PolymeraseLigandsNS13 protein, SARS-CoV-2RNARNA HelicasesViral Nonstructural Proteins
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