In Silico Identification of Potential Allosteric Inhibitors of the SARS-CoV-2 Helicase

30 June 2020, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


The 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. One of such targets is the Helicase which is an enzyme that affects all aspects of SARS-CoV-2 RNA metabolism. The aim of this study is to identify small molecules from natural products that have strong binding affinity with and inhibitory activity against an allosteric site (Pocket 26) of SARS-CoV-2 Helicase. Pyrx was used for the in silico molecular docking simulations of SARS-CoV-2 Helicase (QHD43415-12.pdb) against a library of small molecules obtained from edible African plants. Triphenylmethane which had a docking score of -7.4 kcal/mol was chosen as a reference molecule. Virtual screening for oral bioavailability was done based on the molecular descriptors of the compounds as provided by Pubchem. SwissADME, pkCSM, and Molinspiration were used for further screening for molar refractivity, saturation, promiscuity, pharmacokinetic properties, and bioactivity respectively. The Galaxy webserver which uses the GROMACS software was used for the molecular dynamic simulation and analyses. The lead compounds are Gibberellin A12, A20 and A51 obtained from Green peas and the Okra plant. Gibberellin A20 and A51 performed better than the standard. Gibberellin A51 is predicted to show the greatest inhibitory activity against SARS-CoV-2 Helicase. It is recommended that the inhibitory activities of the lead compounds be further investigated.


Molecular Dynamic Simulation


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