Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Molecular Docking and Dynamics Identifies Potential Repurposed Drug Candidates for COVID-19 Studies

Mohammed Muzaffar-Ur-Rehman
,
Chougule Suryakant
,
Ala Chandu
,
Banoth Kumar
ORCID logo ,
Renuka Joshi
,
Snehal Jadhav
,
Sankaranarayanan Murugesan
* ORCID logo ,
Seshadri Vasan
* ORCID logo
Version 1 : Received: 3 January 2023 / Approved: 4 January 2023 / Online: 4 January 2023 (09:38:47 CET)

A peer-reviewed article of this Preprint also exists.

Muzaffar-Ur-Rehman, M., Suryakant, C. K., Chandu, A., Kumar, B. K., Joshi, R. P., Jadav, S. R., ... & Vasan, S. S. (2023). Molecular Docking and Dynamics Identify Potential Drugs to be Repurposed as SARS-CoV-2 Inhibitors. Journal of Computational Biophysics and Chemistry, 1-23. Muzaffar-Ur-Rehman, M., Suryakant, C. K., Chandu, A., Kumar, B. K., Joshi, R. P., Jadav, S. R., ... & Vasan, S. S. (2023). Molecular Docking and Dynamics Identify Potential Drugs to be Repurposed as SARS-CoV-2 Inhibitors. Journal of Computational Biophysics and Chemistry, 1-23.

Abstract

The novel coronavirus disease 19 (COVID-19) has resulted in an estimated 20 million excess deaths and the recent resurgence of COVID-19 in China is predicted to result in up to 1 million deaths over the next few months. With vaccines unable to halt transmission it is important to continue our quest for safe, effective, affordable drugs that will be available to all countries. Drug repurposing is one of the strategies being explored in this context. Recently, out of 7,817 approved drugs, 214 candidates were systematically down-selected using a combination of 11 filters including approval status, assay data against SARS-CoV-2, pharmacokinetic, pharmacodynamic and toxicity profiles. These drugs were subjected in this study to virtual screening against various targets of SARS-CoV-2 followed by molecular dynamic studies of the best scoring ligands against each target. The chosen molecular targets were Spike receptor binding domain, Nucleocapsid protein RNA binding domain, and key non-structural proteins 3, 5, 12, 13 and 14. Four drugs approved for other indications — alendronate, cromolyn, natamycin and treprostinil — look sufficiently promising from our in silicostudies to warrant further in vitro and in vivo investigations as appropriate to ascertain their extent of anti-viral activities.

Keywords

COVID-19; drug repurposing; long COVID; molecular docking; molecular dynamics; SARS-CoV-2

Subject

Chemistry and Materials Science, Medicinal Chemistry

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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