Structure-based Virtual Screening and Molecular Dynamic Simulation Studies of the Natural Inhibitors of SARS-CoV-2 Main Protease

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ID: 106283
2020
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Abstract
In the month of December 2019, the outbreak of COVID-19 disease in China marked the beginning of a global health challenge and the urgent need to discover and design appropriate therapeutic agents. The causative agent, SARS-CoV-2 has a high rate of infectivity and its Main protease enzyme plays a major role in the replication mechanism of the virus.  This study is aimed at prospecting for natural compounds that have strong binding affinity and the ability to inhibit the SARS-CoV-2 Main Protease. A library of 1,048 natural compounds (with zero violations for Lipinski and Veber rules) obtained from edible African plants were used for this study. These compounds were molecularly docked against the SARS-CoV-2 Main Protease and the results were screened with the docking score obtained from N3 (-7.8 kcal/mol), which is a co-crystallized ligand of the target protein. Further screening for molar refractivity, pharmacokinetic properties and bioactivity was done with SWISSADME, pKCSM, and Molinspiration webservers respectively. The binding site analyses were done using the PLIP and Fpocket webservers. Molecular dynamic studies and analyses of Apo and Holo structures of target protein were done with the Galaxy webserver. The lead compounds, Rhamnetin and Ellagic acid show better therapeutic prediction than the standard. Whilst Rhamnetin binds at the active site, Ellagic acid binds at another cavity with a probable allosteric effect as suggested by the molecular dynamic studies. Further tests are required to evaluate the SARS-CoV-2 Main protease inhibition properties of the lead compounds.
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Rowaiye2020JournalStructure-based Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Adekunle Babajide Rowaiye;Adekunle Babajide Rowaiye;Olukemi Adejoke Onuh;Olukemi Adejoke Onuh;Rita Maneju Sunday;Rita Maneju Sunday;Zainab Dauda Abdulmalik;Zainab Dauda Abdulmalik;Doofan Bur;Doofan Bur;Nkoli Winifred Emeter;Nkoli Winifred Emeter;Oluwaseun Adeola Obideyi;Oluwaseun Adeola Obideyi;Charles Diweni Pelletri;Charles Diweni Pelletri;Inikpi Rabi Ujah-Samuel;Inikpi Rabi Ujah-Samuel;Chiamaka Rosemary Iwuozor;Chiamaka Rosemary Iwuozor;Priscilla Yahemba Aondona;Priscilla Yahemba Aondona;Victoria Onyayi. Etalong;Victoria Onyayi. Etalong;Nuratu Yussuff;Nuratu Yussuff;Jude Nnamdi Akpa;Jude Nnamdi Akpa;
Journal journal of ongoing chemical research
Year 2020
DOI
DOI not found
URL
https://scimatic.org/show_manuscript/213
Keywords
covid-19 ellagic acid sars-cov-2 main protease molecular dynamic studies rhamnetin

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