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African Journal of Infectious Diseases ; 16(2):80-96, 2022.
Article in English | CAB Abstracts | ID: covidwho-2056737


Background: The 2'-O-methyltransferase is responsible for the capping of SARS-CoV-2 mRNA and consequently the evasion of the host's immune system. This study aims at identifying prospective natural inhibitors of the active site of SARS-CoV-2 2'O-methyltransferase (2'-OMT) through an in silico approach. Materials and Method: The target was docked against a library of natural compounds obtained from edible African plants using PyRx - virtual screening software. The antiviral agent, Dolutegravir which has a binding affinity score of -8.5 kcal mol-1 with the SARS-CoV-2 2'-OMT was used as a standard. Compounds were screened for bioavailability through the SWISSADME web server using their molecular descriptors. Screenings for pharmacokinetic properties and bioactivity were performed with PKCSM and Molinspiration web servers respectively. The PLIP and Fpocket webservers were used for the binding site analyses. The Galaxy webserver was used for simulating the time-resolved motions of the apo and holo forms of the target while the MDWeb web server was used for the analyses of the trajectory data.

Tropical Journal of Natural Product Research ; 5(1):165-177, 2021.
Article in English | Scopus | ID: covidwho-1090087


The Coronavirus Disease 2019 (COVID-19) pandemic ravages the globe causing unprecedented health and economic challenges. As the world prospects for a cure, scientists are looking critically at strategic protein targets within the SARS-CoV-2 that have therapeutic significance. The Helicase is one of such targets and it is an enzyme that affects all facets of the SARS-CoV-2 RNA metabolism. This study is aimed at identifying small molecules from natural products that have strong binding affinity with and exhibit inhibitory activity against an allosteric site (Pocket 26) on the SARS-CoV-2 Helicase. The molecular docking simulations of SARS-CoV-2 Helicase (QHD43415-12.pdb) against a library of small molecules obtained from edible African plants was executed using PyRx. Triphenylmethane, which had a docking score of-7.4 kcal/mol on SARS CoV-2 Helicase was chosen as a reference compound. Based on the molecular descriptors of the compounds as provided by PubChem, a virtual screening for oral bioavailability was performed. Further screening for molar refractivity, pharmacokinetic properties, and bioactivity were performed using SwissADME, pkCSM, and Molinspiration webservers respectively. Molecular dynamic simulation and analyses were performed using the Galaxy webserver which uses the GROMACS software. The lead compounds are Gibberellin A12, A20, and A51 obtained from Green peas and the Okra plant. Gibberellin A20 and A51 were predicted to perform better than the standard and Gibberellin A51 showed the greatest inhibitory activity against SARS-CoV-2 Helicase. © 2021 Rowaiye et al and the authors.