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      In silico identification of potential inhibitors of vital monkeypox virus proteins from FDA approved drugs

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          Abstract

          Abstract

          The World Health Organization (WHO) recently declared the monkeypox outbreak ‘A public health emergency of international concern’. The monkeypox virus belongs to the same Orthopoxvirus genus as smallpox. Although smallpox drugs are recommended for use against monkeypox, monkeypox-specific drugs are not yet available. Drug repurposing is a viable and efficient approach in the face of such an outbreak. Therefore, we present a computational drug repurposing study to identify the existing approved drugs which can be potential inhibitors of vital monkeypox virus proteins, thymidylate kinase and D9 decapping enzyme. The target protein structures of the monkeypox virus were modelled using the corresponding protein structures in the vaccinia virus. We identified four potential inhibitors namely, Tipranavir, Cefiderocol, Doxorubicin, and Dolutegravir as candidates for repurposing against monkeypox virus from a library of US FDA approved antiviral and antibiotic drugs using molecular docking and molecular dynamics simulations. The main goal of this in silico study is to identify potential inhibitors against monkeypox virus proteins that can be further experimentally validated for the discovery of novel therapeutic agents against monkeypox disease.

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          Supplementary Information

          The online version contains supplementary material available at 10.1007/s11030-022-10550-1.

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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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            GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

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              Remdesivir for the Treatment of Covid-19 — Final Report

              Abstract Background Although several therapeutic agents have been evaluated for the treatment of coronavirus disease 2019 (Covid-19), none have yet been shown to be efficacious. Methods We conducted a double-blind, randomized, placebo-controlled trial of intravenous remdesivir in adults hospitalized with Covid-19 with evidence of lower respiratory tract involvement. Patients were randomly assigned to receive either remdesivir (200 mg loading dose on day 1, followed by 100 mg daily for up to 9 additional days) or placebo for up to 10 days. The primary outcome was the time to recovery, defined by either discharge from the hospital or hospitalization for infection-control purposes only. Results A total of 1063 patients underwent randomization. The data and safety monitoring board recommended early unblinding of the results on the basis of findings from an analysis that showed shortened time to recovery in the remdesivir group. Preliminary results from the 1059 patients (538 assigned to remdesivir and 521 to placebo) with data available after randomization indicated that those who received remdesivir had a median recovery time of 11 days (95% confidence interval [CI], 9 to 12), as compared with 15 days (95% CI, 13 to 19) in those who received placebo (rate ratio for recovery, 1.32; 95% CI, 1.12 to 1.55; P<0.001). The Kaplan-Meier estimates of mortality by 14 days were 7.1% with remdesivir and 11.9% with placebo (hazard ratio for death, 0.70; 95% CI, 0.47 to 1.04). Serious adverse events were reported for 114 of the 541 patients in the remdesivir group who underwent randomization (21.1%) and 141 of the 522 patients in the placebo group who underwent randomization (27.0%). Conclusions Remdesivir was superior to placebo in shortening the time to recovery in adults hospitalized with Covid-19 and evidence of lower respiratory tract infection. (Funded by the National Institute of Allergy and Infectious Diseases and others; ACTT-1 ClinicalTrials.gov number, NCT04280705.)
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                Author and article information

                Contributors
                asamal@imsc.res.in
                Journal
                Mol Divers
                Mol Divers
                Molecular Diversity
                Springer International Publishing (Cham )
                1381-1991
                1573-501X
                4 November 2022
                : 1-16
                Affiliations
                [1 ]GRID grid.462414.1, ISNI 0000 0004 0504 909X, The Institute of Mathematical Sciences (IMSc), ; Chennai, 600113 India
                [2 ]GRID grid.450257.1, ISNI 0000 0004 1775 9822, Homi Bhabha National Institute (HBNI), ; Mumbai, 400094 India
                Author information
                http://orcid.org/0000-0002-6796-9604
                Article
                10550
                10.1007/s11030-022-10550-1
                9638297
                36331784
                ea2cfc4d-2d6a-4120-bbdf-42a7888411b6
                © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2022, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

                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
                : 21 August 2022
                : 17 October 2022
                Categories
                Original Article

                Molecular biology
                monkeypox,virtual screening,drug repurposing,docking,molecular dynamics,antivirals
                Molecular biology
                monkeypox, virtual screening, drug repurposing, docking, molecular dynamics, antivirals

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