ArticleCommunications biology2022
Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.
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Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26citing papers in PubMed
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Who cites it
26 citing papers in PubMed, 57 citations in OpenAlex.
- Discovery of novel druggable binding pockets on SARS-CoV-2 PLpro via fragment screening and insights for structure-based inhibitor design.The Journal of biological chemistry · 2026Article
- Structural analysis of the flexibility of the Ubl2 domain within the papain-like protease of SARS-CoV-2.Acta crystallographica. Section F, Structural biology communications · 2026Article
- Structural Basis and Inhibitor Development of SARS-CoV-2 Papain-like Protease.Molecules (Basel, Switzerland) · 2026Review
- Chasing allosteric inhibition of the SARS-CoV-2 PLpro via molecular dynamics simulations with flooding fragments (MDFFr).Journal of computer-aided molecular design · 2025Article
- Onion-Mitochondria Inhibit Lipopolysaccharide-Induced Acute Lung Injury by Shaping Lung Macrophage Mitochondrial Function.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Structural and functional insights into Ubl domain-mediated regulation of SARS-CoV-2 PLpro.Biology direct · 2025Article
- Virucidal Potential of 3,3',4,4',5,5'-Hexahydroxy-Viruses · 2025Article
- Statine-based peptidomimetics as SARS-CoV-2 Papain-like protease inhibitors: in Silico and in vitro studies.Scientific reports · 2025Article
- Integrating Molecular Dynamics, Molecular Docking, and Machine Learning for Predicting SARS-CoV-2 Papain-like Protease Binders.Molecules (Basel, Switzerland) · 2025Article
- Identification of naturally occurring drug-resistant mutations of SARS-CoV-2 papain-like protease.Nature communications · 2025Article
- Synergistic Antiviral Activity of European Black Elderberry Fruit Extract and Quinine Against SARS-CoV-2 and Influenza A Virusa.Nutrients · 2025Article
- Development of a Fluorescence Polarization Assay for the SARS-CoV-2 Papain-like Protease.ACS pharmacology & translational science · 2025Article
- Analysis of Structures of SARS-CoV-2 Papain-like Protease Bound with Ligands Unveils Structural Features for Inhibiting the Enzyme.Molecules (Basel, Switzerland) · 2025Review
- Unveiling the mechanism of action of a novel natural dual inhibitor of SARS-CoV-2 Mpro and PLpro with molecular dynamics simulations.Natural products and bioprospecting · 2025Article
- Effects of Phenolic Acids Produced from Food-Derived Flavonoids and Amino Acids by the Gut Microbiota on Health and Disease.Molecules (Basel, Switzerland) · 2024Review
- Identification and Ranking of Binding Sites from Structural Ensembles: Application to SARS-CoV-2.Viruses · 2024Article
- Advances in the Search for SARS-CoV-2 MPathogens (Basel, Switzerland) · 2024Review
- An expanded trove of fragment-bound structures for the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data.Structure (London, England : 1993) · 2024Article
- Comparative metabolomics analysis ofHeliyon · 2024Article
- Arylamines QSAR-Based Design and Molecular Dynamics of New Phenylthiophene and Benzimidazole Derivatives with Affinity for the C111, Y268, and H73 Sites of SARS-CoV-2 PLpro Enzyme.Pharmaceuticals (Basel, Switzerland) · 2024Article
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Authors and funding
51 authors at 10 institutions in 5 countries.
Vasundara SrinivasanDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany. vasundara.srinivasan@chemie.uni-hamburg.de.ORCID 0000-0002-8895-5885
Hévila BrognaroDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
Prince R PrabhuDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
Edmarcia Elisa de SouzaDepartment of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.
Sebastian GüntherCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0002-7329-6653
Patrick Y A ReinkeCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Thomas J LaneHamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.ORCID 0000-0003-2627-4432
Helen GinnDiamond Light Source Ltd. Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
Huijong HanEuropean XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany.
Wiebke EwertCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0001-8626-4864
Janina SprengerCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Faisal H M KouaCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0001-8371-9587
Sven FalkeDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
Nadine WernerDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
Hina AndaleebDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
Najeeb UllahDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.ORCID 0000-0003-0900-5927
Bruno Alves FrancaDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
Mengying WangDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
Angélica Luana C BarraDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.ORCID 0000-0003-0457-7758
Markus PerbandtDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.ORCID 0000-0001-7517-8522
Martin SchwinzerDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
Christina SchmidtEuropean XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany.ORCID 0000-0002-6662-1294
Lea BringsEuropean XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany.
Kristina LorenzenEuropean XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany.
Robin SchubertEuropean XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany.ORCID 0000-0002-6213-2872
Rafael Rahal Guaragna MachadoDepartment of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.
Erika Donizette CandidoDepartment of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.ORCID 0000-0002-9132-569X
Danielle Bruna Leal OliveiraDepartment of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.ORCID 0000-0002-0534-0886
Edison Luiz DurigonDepartment of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.
Stephan NieblingEuropean Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0001-6582-5984
Angelica Struve GarciaEuropean Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Oleksandr YefanovCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Julia LieskeCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0002-5439-5082
Luca GelisioCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0001-7832-6201
Martin DomarackyCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0003-4624-023X
Philipp MiddendorfCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Michael GroesslerCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Fabian TrostCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0001-5628-598X
Marina GalchenkovaCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Aida Rahmani MashhourCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Sofiane SaouanePhoton Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0002-7260-9021
Johanna HakanpääPhoton Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany.
Markus WolfFraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee114, 22525, Hamburg, Germany.
Maria Garcia AlaiEuropean Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany.
Dusan TurkDepartment of Biochemistry & Molecular & Structural Biology, Jozef Stefan Institute, Jamova 39, 1 000, Ljubljana, Slovenia.ORCID 0000-0003-0205-6609
Arwen R PearsonHamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.ORCID 0000-0001-8499-7490
Henry N ChapmanHamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
Winfried HinrichsInstitute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.ORCID 0000-0002-0435-4565
Carsten WrengerDepartment of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.ORCID 0000-0001-5987-1749
Alke MeentsCenter for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.ORCID 0000-0001-6078-4095
Christian BetzelDepartment of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany. christian.betzel@uni-hamburg.de.ORCID 0000-0002-3879-5019
Universität Hamburg · DEUniversidade de São Paulo · BREuropean X-Ray Free-Electron Laser · DEEuropean Molecular Biology Laboratory · DEBahauddin Zakariya University · PKDeutsches Elektronen-Synchrotron DESY · DEDiamond Light Source · GBFraunhofer Institute for Translational Medicine and Pharmacology · DEJožef Stefan Institute · SIUniversität Greifswald · DE
Funding
No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.
Indexed as
Antiviral AgentsCOVID-19 Drug TreatmentAllosteric SiteCoronavirus Papain-Like ProteasesHumansPapainPeptide HydrolasesSARS-CoV-2Antiviral AgentsCoronavirus Papain-Like ProteasesPapainpapain-like protease, SARS-CoV-2Peptide Hydrolases
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