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      An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets

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          Highlights

          • This paper  in-silico identifies multifaceted inhibitors (Lurasidone and Lurasidone exo) for SARS-CoV-2 that can act through the “ one drug multiple targets” strategy.

          • Molecular Dynamics simulation study reveals a significantly strong binding affinity of Lurasidone and its derivative against multiple SARS-CoV-2 targets namely, main protease, papain-like protease, spike protein, RNA dependent RNA polymerase and helicase.

          • Lurasidone and Lurasidone exo possess favourable pharmacokinetic properties based on Lipinski’s rule, ADMET and target prediction studies.

          • The unique multitargeting feature of Lurasidone and Lurasidone exo warrants further  in-vitro  and  in-vivo  experiments on SARS-CoV-2 for clinical applications.

          Abstract

          The emerging paradigm shift from ‘one molecule, one target, for one disease’ towards ‘multi-targeted small molecules’ has paved an ingenious pathway in drug discovery in recent years. We extracted this idea for the investigation of drugs for COVID-19. Perceiving the importance of organosulfur compounds, seventy-six known organosulfur compounds were screened and studied for the interaction with multiple SARS-CoV-2 target proteins by molecular dynamics simulation. Lurasidone and its derivatives displayed substantial binding affinity against five proteins (Mpro, PLpro, Spro, helicase and RdRp). The pharmacokinetics, ADMET properties and target prediction studies performed in this work further potentiates the effectiveness against SARS-CoV-2.

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          Most cited references43

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

          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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            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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                Author and article information

                Journal
                Chem Phys Lett
                Chem Phys Lett
                Chemical Physics Letters
                Published by Elsevier B.V.
                0009-2614
                0009-2614
                15 November 2020
                15 November 2020
                : 138193
                Affiliations
                [a ]Discipline of Chemistry, Indian Institute of Technology Palakkad, Kerala 678 557, India
                [b ]Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Madhya Pradesh 453 552, India
                Author notes
                [* ]Corresponding authors.
                [1]

                Both authors contributed equally

                Article
                S0009-2614(20)31100-3 138193
                10.1016/j.cplett.2020.138193
                7666712
                33223560
                b60872d5-ad6d-4dcb-b641-31c6c7fa5c57
                © 2020 Published by Elsevier B.V.

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                : 2 August 2020
                : 18 October 2020
                : 11 November 2020
                Categories
                Research Paper

                Physical chemistry
                sars-cov-2,multi-targeting drugs,organosulfur compounds,molecular docking analysis,molecular dynamics simulation,mm-pbsa, main protease (mpro),papain-like protease (plpro),spike protein (spro),helicase,rna dependent rna polymerase (rdrp)

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