Computational Investigation of Natural Substances as SARS-CoV-2 Main Protease Inhibitors: A Virtual Screening Method

Abstract

Introduction: The coronavirus disease 2019 (COVID-19) pandemic, caused the by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had a profound impact on public health, overburdening healthcare systems, and disrupting global economies. Moreover, the absence of specific antiviral drugs remains a major challenge in COVID-19 treatment. The SARS-CoV-2 main protease (Mpro) is a crucial therapeutic target due to its essential role in viral replication. The objective of this study was to identify natural compounds with potential inhibitory activity against SARS-CoV-2 Mpro, which could be used alone or in combination with repositioned drugs for the treatment of COVID-19.

Methods: A total of 224,205 natural compounds from the ZINC database were virtually screened against SARS-CoV-2 Mpro using a sequential molecular docking protocol with increasing levels of exhaustiveness. The top 88 compounds were further evaluated using MM-GBSA calculations to determine their binding free energies. Molecular dynamics (MD) simulations (100 ns) were conducted for the top four compounds to assess complex stability and ligand interactions. Structural stability and protein-ligand interactions were assessed using various statistical parameters. Post-MD binding free energy calculations were also performed.

Results: Four compounds, ZINC000085626103, ZINC000085625768, ZINC000085488571, and ZINC000085569275, were identified based on their docking scores (ranging from -11.876 to -12.682 kcal/mol) and MM-GBSA binding energies (ranging from -50.11 to -64.8 kcal/mol). All these compounds formed stable complexes with Mpro during MD simulations, with ZINC000085488571 exhibiting the lowest protein RMSD (0.15 ± 0.02 nm) and RMSF (0.10 ± 0.04 nm). These compounds interacted with key active site residues and maintained stable hydrogen bonding and compact structures throughout the simulation. Post-simulation binding free energy values ranged from -38.29 to -18.07 kcal/mol, further indicating strong and stable binding affinities.

Discussion: The in silico screening results confirmed the strong binding affinity and structural stability of the selected natural compounds at the SARS-CoV-2 Mpro active site. The MD simulation results further highlighted consistent engagement with catalytically relevant residues, indicating their potential for inhibitory activity.

Conclusion: This study identifies four natural compounds with strong binding affinity and structural stability against SARS-CoV-2 Mpro, supporting their candidacy for further investigation as potential antiviral agents for COVID-19 treatment.

Keywords: COVID-19; MD Simulations; MMGBSA.; Molecular Docking; Mpro inhibitor; ZINC database.