Multi-structural Molecular Docking (MOD) Combined with Molecular Dynamics Reveal the Structural Requirements of Designing Broad-spectrum Inhibitors of SARS-CoV-2 Entry to Host Cells

Overview

Journal Sci Rep

Specialty Science

Date 2023 Sep 29

PMID 37773489

Authors

Anqi Da

Meritxell Wu-Lu

Jovan Dragelj

Maria Andrea Mroginski

Kourosh H Ebrahimi

Affiliations

Soon will be listed here.

Abstract

New variants of SARS-CoV-2 that can escape immune response continue to emerge. Consequently, there is an urgent demand to design small molecule therapeutics inhibiting viral entry to host cells to reduce infectivity rate. Despite numerous in silico and in situ studies, the structural requirement of designing viral-entry inhibitors effective against multiple variants of SARS-CoV-2 has yet to be described. Here we systematically screened the binding of various natural products (NPs) to six different SARS-CoV-2 receptor-binding domain (RBD) structures. We demonstrate that Multi-structural Molecular Docking (MOD) combined with molecular dynamics calculations allowed us to predict a vulnerable site of RBD and the structural requirement of ligands binding to this vulnerable site. We expect that our findings lay the foundation for in silico screening and identification of lead molecules to guide drug discovery into designing new broad-spectrum lead molecules to counter the threat of future variants of SARS-CoV-2.

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