Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach

Selvakumar Murugesan; Chinnasamy Ragavendran; Amir Ali; Safir Ullah Khan; Velusamy Arumugam; Dinesh Kumar Lakshmanan; Palanikumar Palanichamy; Manigandan Venkatesan; Chinnaperumal Kamaraj; Zia-ur-Rehman Mashwani; Muhammad Younas; Juan Pedro Luna-Arias; Fabian Fernández-Luqueño

doi:10.20944/preprints202212.0008.v1

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preprints.org > biology and life sciences > virology > doi: 10.20944/preprints202212.0008.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach

Selvakumar Murugesan

Chinnasamy Ragavendran

Amir Ali

^* ,

Safir Ullah Khan

Velusamy Arumugam

Dinesh Kumar Lakshmanan

Palanikumar Palanichamy

Manigandan Venkatesan

^* ,

Chinnaperumal Kamaraj

Zia-ur-Rehman Mashwani

Muhammad Younas

Juan Pedro Luna-Arias

Fabian Fernández-Luqueño

Version 1 : Received: 1 December 2022 / Approved: 1 December 2022 / Online: 1 December 2022 (03:51:30 CET)

A peer-reviewed article of this Preprint also exists.

Murugesan, S.; Ragavendran, C.; Ali, A.; Arumugam, V.; Lakshmanan, D.K.; Palanichamy, P.; Venkatesan, M.; Kamaraj, C.; Luna-Arias, J.P.; Fabián, F.-L.; Khan, S.U.; Mashwani, Z.U.-R.; Younas, M. Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach. Int. J. Transl. Med. 2023, 3, 27-41. Murugesan, S.; Ragavendran, C.; Ali, A.; Arumugam, V.; Lakshmanan, D.K.; Palanichamy, P.; Venkatesan, M.; Kamaraj, C.; Luna-Arias, J.P.; Fabián, F.-L.; Khan, S.U.; Mashwani, Z.U.-R.; Younas, M. Screening and Druggability Analysis of Marine Active Metabolites against SARS-CoV-2: An Integrative Computational Approach. Int. J. Transl. Med. 2023, 3, 27-41.

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have triggered a recent pandemic of respiratory disease and affected almost every country all over the world. A large amount of natural bioactive compounds is under clinical investigation for various diseas-es. Especially, marine natural compounds are gaining more attention in the new drug develop-ment process. The present study has aimed to identify potential marine-derived inhibitors against the target proteins of COVID-19 using a computational approach. Currently, 16 marine clinical-level compounds were selected for computational screening against the four SARS-CoV-2 main proteases. Computational screening resulted from the best drug candidates for each target based on the binding affinity scores and amino acid interactions. Among these, five marine-derived compounds namely Chrysophaentin A (-6.6 kcal/mol), Geodisterol sulfates (-6.6 kcal/mol), Hymenidin (-6.4 kcal/mol), Plinabulin (-6.4 kcal/mol) and Tetrodotoxin (-6.3 kcal/mol) expressed the minimized binding energy and molecular interactions such as covalent and hydrophobic interactions to the SARS CoV-2 Main Protease. Using Molecular dynamic stud-ies, the Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (ROG), and Hydrogen bonds (H-Bonds) values were calculated for SARS-CoV-2 Main Protease with Hymenidin docked complex. Additionally, in silico Druglikeness and pharmaco-kinetic property assessments of the compounds demonstrated favorable druggability. These re-sults suggested that marine natural compounds are capable of fighting SARS-CoV-2. Further, in vitro and in vivo studies need to be carried out to confirm their inhibitory potential.

Keywords

COVID-19; molecular docking; ADMET; marine natural products; Chrysophaentin A; Hymenidin

Subject

Biology and Life Sciences, Virology

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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