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      In vitro study of Hesperetin and Hesperidin as inhibitors of zika and chikungunya virus proteases

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          Abstract

          The potential outcome of flavivirus and alphavirus co-infections is worrisome due to the development of severe diseases. Hundreds of millions of people worldwide live under the risk of infections caused by viruses like chikungunya virus (CHIKV, genus Alphavirus), dengue virus (DENV, genus Flavivirus), and zika virus (ZIKV, genus Flavivirus). So far, neither any drug exists against the infection by a single virus, nor against co-infection. The results described in our study demonstrate the inhibitory potential of two flavonoids derived from citrus plants: Hesperetin (HST) against NS2B/NS3 pro of ZIKV and nsP2 pro of CHIKV and, Hesperidin (HSD) against nsP2 pro of CHIKV. The flavonoids are noncompetitive inhibitors and the determined IC 50 values are in low µM range for HST against ZIKV NS2B/NS3 pro (12.6 ± 1.3 µM) and against CHIKV nsP2 pro (2.5 ± 0.4 µM). The IC 50 for HSD against CHIKV nsP2 pro was 7.1 ± 1.1 µM. The calculated ligand efficiencies for HST were > 0.3, which reflect its potential to be used as a lead compound. Docking and molecular dynamics simulations display the effect of HST and HSD on the protease 3D models of CHIKV and ZIKV. Conformational changes after ligand binding and their effect on the substrate-binding pocket of the proteases were investigated. Additionally, MTT assays demonstrated a very low cytotoxicity of both the molecules. Based on our results, we assume that HST comprise a chemical structure that serves as a starting point molecule to develop a potent inhibitor to combat CHIKV and ZIKV co-infections by inhibiting the virus proteases.

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          AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

          AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. Copyright 2009 Wiley Periodicals, Inc.
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            AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.

            We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique. (c) 2009 Wiley Periodicals, Inc.
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              Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: Writing – original draft
                Role: InvestigationRole: SoftwareRole: Validation
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: Validation
                Role: InvestigationRole: Methodology
                Role: Formal analysisRole: Resources
                Role: InvestigationRole: SoftwareRole: Validation
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                4 March 2021
                2021
                : 16
                : 3
                : e0246319
                Affiliations
                [1 ] Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
                [2 ] Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
                [3 ] Federal University of Tocantins, Araguaína, TO, Brazil
                [4 ] Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
                [5 ] FACERES Medical School, São José do Rio Preto, Brazil
                [6 ] Faculdade de Medicina de São José do Rio Preto–FAMERP, São José do Rio Preto, Brazil
                [7 ] Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
                [8 ] Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
                [9 ] JuStruct: Jülich Centre for Structural Biology, Forchungszentrum Jülich, Jülich, Germany
                Loyola University Chicago, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0002-8763-3884
                https://orcid.org/0000-0003-1269-3783
                https://orcid.org/0000-0001-8101-6933
                Article
                PONE-D-20-32447
                10.1371/journal.pone.0246319
                7932080
                33661906
                a6d91d27-bc15-4bc2-9cdf-502b78bd915b
                © 2021 Eberle et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 15 October 2020
                : 15 January 2021
                Page count
                Figures: 8, Tables: 5, Pages: 28
                Funding
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)
                Award ID: 435913/2016-6
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award ID: 401270/2014-9
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award ID: 307338/2014-2
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001807, Fundação de Amparo à Pesquisa do Estado de São Paulo;
                Award ID: 2016/12904-0
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001807, Fundação de Amparo à Pesquisa do Estado de São Paulo;
                Award ID: 2018/12659-0
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001807, Fundação de Amparo à Pesquisa do Estado de São Paulo;
                Award ID: 2018/07572-3
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001807, Fundação de Amparo à Pesquisa do Estado de São Paulo;
                Award ID: 2019/05614-3
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100005672, Fundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia do Estado de Mato Grosso do Sul;
                Award ID: 23/200.307/2014
                Award Recipient :
                The study was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (435913/2016-6, 401270/2014-9, 307338/2014-2) received by RA. Fundação de Amparo à Pesquisa do Estado de São Paulo (2016/12904-0, 2018/12659-0, 2018/07572-3, 2019/05614-3) by RE and MC. Ciência e Tecnologia do Estado de Mato Grosso do Sul (23/200.307/2014) by MA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Togaviruses
                Alphaviruses
                Chikungunya Virus
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Viral Pathogens
                Togaviruses
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