Investigating the structure–activity relationship of marine natural polyketides as promising SARS-CoV-2 main protease inhibitors (original) (raw)
* Corresponding authors
a Chemistry Department, Organic Chemistry Division, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
E-mail: eldemerdash555@gmail.com
b Metabolic Biology & Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
c Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
E-mail: akarmalawy@horus.edu.eg
d Department of Cellular and Integrative Physiology, University of Texas Health Science Centre at San Antonio, San Antonio, Texas 78229-3900, USA
e Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
f Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
g Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
h Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
E-mail: ahmed_hassan@mans.edu.eg
Abstract
Since its first report in December 2019, the novel coronavirus virus, SARS-CoV-2, has caused an unprecedented global health crisis and economic loss imposing a tremendous burden on the worldwide finance, healthcare system, and even daily life. Even with the introduction of different preventive vaccines, there is still a dire need for effective antiviral therapeutics. Nature has been considered as the historical trove of drug discovery and development, particularly in cases of worldwide crises. Herein, a comprehensive in silico investigation of a highly focused chemical library of 34 pederin-structurally related marine compounds, belonging to four polyketides families, was initiated against the SARS-CoV-2 main protease, Mpro, being the key replicating element of the virus and main target in many drugs development programs. Two of the most potent SARS-CoV-2 Mpro co-crystallized inhibitors, O6K and N3, were added to the tested database as reference standards. Through molecular docking simulation, promising compounds including Pederin (1), Dihydro-onnamide A (11), Onnamide C (14), Pseudo-onnamide A (17), and Theopederin G (29) have been identified from different families based on their superior ligand–protein energies and relevant binding profiles with the key Mpro pocket residues. Thermodynamic behaviors of the identified compounds were investigated through 200 ns all-atom molecular dynamics simulation illustrating their significant stability and pocket accommodation. Furthermore, structural activity preferentiality was identified for the pederin-based marine compounds highlighting the importance of the terminal guanidine and cyclic hemiacetal linker, and the length of the sidechain. Our findings highlight the challenges of targeting SARS-CoV-2 Mpro as well as recommending further in vitro and in vivo studies regarding the examined marine products either alone or in combination paving the way for promising lead molecules.
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Article information
DOI
https://doi.org/10.1039/D1RA05817G
Article type
Paper
Submitted
31 Jul 2021
Accepted
16 Sep 2021
First published
22 Sep 2021
This article is Open Access
Download Citation
RSC Adv., 2021,11, 31339-31363
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Investigating the structure–activity relationship of marine natural polyketides as promising SARS-CoV-2 main protease inhibitors
A. El-Demerdash, A. A. Al-Karmalawy, T. M. Abdel-Aziz, S. S. Elhady, K. M. Darwish and A. H. E. Hassan,RSC Adv., 2021, 11, 31339DOI: 10.1039/D1RA05817G
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