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      A comparative study of 5- fluorouracil, doxorubicin, methotrexate, paclitaxel for their inhibition ability for Mpro of nCoV: Molecular docking and molecular dynamics simulations

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          Abstract

          A new corona virus (nCoV) is aetiological agent responsible for the viral pneumonia epidemic. Three is no specific therapeutic medicines available for the treatment of this condition and also effective treatment choices are few. In this work author tried to investigate some repurposing drug such as 5- fluorouracil, doxorubicin, methotrexate and paclitaxel against the main protease (Mpro) of nCoV by the computational model. Molecular docking was performed to screen out the best compound and doxorubicin was found to have minimum binding energy −121.89 kcal/mol. To further study, MD simulations were performed at 300 K and the result successfully corroborate the energy obtained by molecular docking. Temperature dependent MD simulation of the best molecule that is doxorubicin obtained from docking result was performed to check the variation in structural changes in Mpro of nCoV at 290 K, 310 K, 320 K and 325 K. It is sound that doxorubicin binds effectively with Mpro of nCoV at 290 K. Further ADME properties of the 5- fluorouracil, doxorubicin, methotrexate and paclitaxel were also evaluated to understand the bioavailability.

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

          Mark Abraham, Teemu Murtola, Roland Schulz … (2015)
          Article 0 comments Cited 4180 times – based on 0 reviews     Review now
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            SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

            Antoine Daina, Olivier Michielin, Vincent Zoete (2017)
            To be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. Drug development involves assessment of absorption, distribution, metabolism and excretion (ADME) increasingly earlier in the discovery process, at a stage when considered compounds are numerous but access to the physical samples is limited. In that context, computer models constitute valid alternatives to experiments. Here, we present the new SwissADME web tool that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP and Bioavailability Radar. Easy efficient input and interpretation are ensured thanks to a user-friendly interface through the login-free website http://www.swissadme.ch. Specialists, but also nonexpert in cheminformatics or computational chemistry can predict rapidly key parameters for a collection of molecules to support their drug discovery endeavours.
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              Structure of Mpro from COVID-19 virus and discovery of its inhibitors

              Zhenming Jin, Xiaoyu Du, Yechun Xu … (2020)
              A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the aetiological agent responsible for the 2019-2020 viral pneumonia outbreak of coronavirus disease 2019 (COVID-19)1-4. Currently, there are no targeted therapeutic agents for the treatment of this disease, and effective treatment options remain very limited. Here we describe the results of a programme that aimed to rapidly discover lead compounds for clinical use, by combining structure-assisted drug design, virtual drug screening and high-throughput screening. This programme focused on identifying drug leads that target main protease (Mpro) of SARS-CoV-2: Mpro is a key enzyme of coronaviruses and has a pivotal role in mediating viral replication and transcription, making it an attractive drug target for SARS-CoV-25,6. We identified a mechanism-based inhibitor (N3) by computer-aided drug design, and then determined the crystal structure of Mpro of SARS-CoV-2 in complex with this compound. Through a combination of structure-based virtual and high-throughput screening, we assayed more than 10,000 compounds-including approved drugs, drug candidates in clinical trials and other pharmacologically active compounds-as inhibitors of Mpro. Six of these compounds inhibited Mpro, showing half-maximal inhibitory concentration values that ranged from 0.67 to 21.4 μM. One of these compounds (ebselen) also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of our screening strategy, which can lead to the rapid discovery of drug leads with clinical potential in response to new infectious diseases for which no specific drugs or vaccines are available.
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                Author and article information

                Journal
                Title: Journal of the Indian Chemical Society
                Publisher: Indian Chemical Society. Published by Elsevier B.V.
                ISSN (Print): 0019-4522
                ISSN (Electronic): 0019-4522
                Publication date PMC-release: 3 November 2022
                Publication date (Electronic): 3 November 2022
                Electronic Location Identifier: 100790
                Affiliations
                [a ]Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
                [b ]Department of Physics & Electronics, Hansraj College, University of Delhi, Delhi, India
                [c ]Department of Chemistry, University of Delhi, Delhi, India
                [d ]Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Delhi-NCR Campus, Uttar Pradesh, India
                Author notes
                [∗ ]Corresponding author.
                [∗∗ ]Corresponding author.
                [∗∗∗ ]Corresponding author.
                Article
                Publisher Item ID: S0019-4522(22)00452-6 Publisher ID: 100790
                DOI: 10.1016/j.jics.2022.100790
                PMC ID: 9632266
                SO-VID: 3a3b0b77-7737-4bf7-be6f-bc869975bfa7
                Copyright © © 2022 Indian Chemical Society. Published by Elsevier B.V. All rights reserved.
                License:

                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
                Date received : 10 June 2022
                Date revision received : 7 October 2022
                Date accepted : 29 October 2022
                Categories
                Subject: Article

                Keywords: mpro of ncov,molecular dynamics simulations,molecular docking,adme
                Data availability:
                Keywords: mpro of ncov, molecular dynamics simulations, molecular docking, adme

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