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      Potential antiviral properties of antiplatelet agents against SARS-CoV-2 infection: an in silico perspective

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          SARS-CoV-2 represents the causative agent of the current pandemic (COVID-19). The drug repurposing technique is used to search for possible drugs that can bind to SARS-CoV-2 proteins and inhibit viral replication. In this study, the FDA-approved antiplatelets are tested against the main protease and spike proteins of SARS-CoV-2 using in silico methods. Molecular docking and molecular dynamics simulation are used in the current study. The results suggest the effectiveness of vorapaxar, ticagrelor, cilostazol, cangrelor, and prasugrel in binding the main protease (M pro) of SARS-CoV-2. At the same time, vorapaxar, ticagrelor, and cilostazol are the best binders of the spike protein. Therefore, these compounds could be successful candidates against COVID-19 that need to be tested experimentally.

          Supplementary Information

          The online version contains supplementary material available at 10.1007/s11239-021-02558-5.

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          Eric F. Pettersen, Thomas Goddard, Conrad Huang … (2004)
          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            VMD: Visual molecular dynamics

            William Humphrey, Andrew Dalke, Klaus Schulten (1996)
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              AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

              Oleg Trott, Arthur Olson (2010)
              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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                Author and article information

                Contributors
                Abdo A. Elfiky:
                ORCID: http://orcid.org/0000-0003-4600-6240
                abdo@sci.cu.edu.eg , dr_abdo@cu.edu.eg
                Journal
                Journal ID (nlm-ta): J Thromb Thrombolysis
                Journal ID (iso-abbrev): J Thromb Thrombolysis
                Title: Journal of Thrombosis and Thrombolysis
                Publisher: Springer US (New York )
                ISSN (Print): 0929-5305
                ISSN (Electronic): 1573-742X
                Publication date (Electronic): 12 September 2021
                Pages: 1-9
                Affiliations
                [1 ]GRID grid.265074.2, ISNI 0000 0001 1090 2030, Cellular Genetics Laboratory, Graduate School of Science, , Tokyo Metropolitan University, ; Tokyo, Japan
                [2 ]GRID grid.412258.8, ISNI 0000 0000 9477 7793, Department of Chemistry, Biochemistry Division, Faculty of Science, , Tanta University, ; Tanta, Egypt
                [3 ]GRID grid.258269.2, ISNI 0000 0004 1762 2738, Department of Organ and Cell Physiology, , Juntendo University, ; Tokyo, Japan
                [4 ]GRID grid.7776.1, ISNI 0000 0004 0639 9286, Biophysics Department, Faculty of Sciences, , Cairo University, ; Giza, Egypt
                Author information
                http://orcid.org/0000-0003-4600-6240
                Article
                Publisher ID: 2558
                DOI: 10.1007/s11239-021-02558-5
                PMC ID: 8435103
                SO-VID: 2bb462bc-0bfb-4fa1-ae97-806c1f42b4a4
                Copyright © © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021
                License:

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                Date accepted : 26 August 2021
                Categories
                Subject: Article

                ScienceOpen disciplines: Hematology
                Keywords: sars-cov-2,covid-19,antiplatelet,drug repurposing,spike,mpro
                Data availability:
                ScienceOpen disciplines: Hematology
                Keywords: sars-cov-2, covid-19, antiplatelet, drug repurposing, spike, mpro

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