In silico screening of SARS-CoV2 helicase using African natural products: Docking and molecular dynamics approaches

Hamada R Knany; Sherif A Elsabbagh; Moustafa A Shehata; Wagdy M Eldehna; Adnan A Bekhit; Tamer M Ibrahim

doi:10.1016/j.virol.2023.109863

In silico screening of SARS-CoV2 helicase using African natural products: Docking and molecular dynamics approaches

Virology. 2023 Oct:587:109863. doi: 10.1016/j.virol.2023.109863. Epub 2023 Aug 5.

Authors

Hamada R Knany¹, Sherif A Elsabbagh², Moustafa A Shehata³, Wagdy M Eldehna⁴, Adnan A Bekhit⁵, Tamer M Ibrahim⁶

Affiliations

¹ Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
² Biochemistry Department, Institute of Pharmacy, Eberhard-Karls University, Auf der Morgenstelle 8, 72076, Tuebingen, Germany.
³ Department of Zoology, Faculty of Science, Cairo University, Giza, 12613, Egypt.
⁴ Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt.
⁵ Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt; Cancer Nanotechnology Research Laboratory (CNRL), Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt; Pharmacy Program, Allied Health Department, College of Health and Sport Sciences, University of Bahrain, P.O. Box 32038, Kingdom of Bahrain.
⁶ Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt. Electronic address: Tamer_Mohamad@pharm.kfs.edu.eg.

PMID: 37586235
DOI: 10.1016/j.virol.2023.109863

Abstract

In the current medical era, there is an urgent necessity to identify new effective drugs to enrich the COVID-19's therapeutic arsenal. The SARS-COV-2 NSP13/helicase enzyme has been identified as a potential target for developing novel COVID-19 inhibitors. In this work, we aimed at endorsing effective natural products with potential inhibitory action towards the NSP13 through the virtual screening of 1012 natural products of botanical and marine origin from the South African Natural Compounds Database (SANCDB). The molecules were docked into the NTPase active site, and the best twelve compounds were chosen for further analysis. Thereafter, a combination of molecular dynamics simulations and MM-GBSA free energy calculations were carried out for a subset of best hits complexed with NSP13 helicase. We believe that the findings of this work will pave the way for additional research and experimental validation of some natural products as viable NSP13 helicase inhibitors.

Keywords: MD; MMGBSA; NSP13; SANCDB; VS.