Synthesis of exfoliated multilayer graphene and its putative interactions with SARS-CoV-2 virus investigated through computational studies

Abstract

Our work investigates the interaction of synthesized graphene with the SARS-CoV-2 virus using molecular docking and molecular dynamics (MD) simulation method. The layer dependent inhibitory effect of graphene nanosheets on spike receptor-binding domain of 6LZG, complexed with host receptor i.e. angiotensin-converting enzyme 2 (ACE2) of SARS-CoV-2 was investigated through computational study. Graphene sample was synthesized using mechanical exfoliation with shear stress and its mechanism of inhibition towards the SARS-CoV-2 virus was explored by molecular docking and molecular dynamics (MD) simulation method. The thermodynamics study for the free binding energy of graphene towards the SARS-CoV-2 virus was analyzed. The binding energy of graphene towards the virus increased with an increasing number of layers. It shows the highest affinity of À17.5 Kcal/mol in molecular docking while DG binding is in the order of À28.01 ± 0.04 5 Kcal/mol for the seven-layers structure. The increase in carbon layers is associated with an increasing number of edge sp 3-type carbon, providing greater curvature, further increase the surface reactivity responsible for high binding efficiency. The MD simulation data reveals the high inhibition efficiency of the synthesized graphene towards SARS-CoV-2 virus which would help to design future in-vitro studies. The graphene system could find potential applications in personal protective equipment and diagnostic kits.

Effect of the Graphene Nanosheet on Functions of the Spike Protein in Open and Closed States: Comparison between SARS-CoV-2 Wild Type and the Omicron Variant

“…Previous studies have shown that it is suitable to dock the GN (with a small size) to the proteins using AutoDock Vina. 45,53,54 AutoDock Vina can provide the docking score and the root-mean-square deviation (RMSD). The docking score indicates the affinity between the receptor and the ligand, and the RMSD represents the difference in the position of the ligand from the best model.…”

Review on benefits, toxicity, challenges, and future of graphene-based face masks in the prevention of COVID-19 pandemic

“…Graphene, a material with antimicrobial and antiviral properties, has increased the interest of the scientific community in investigating its use in preventive measures, detection, and diagnosis of COVID-19 (Damiati et al, 2021;Mojsoska et al, 2021;Payandehpeyman et al, 2021;Pinals et al, 2021;Raval et al, 2020;Torrente-Rodríguez et al, 2020). Graphene-based face masks are newly developed biocompatible medicinal weapons that seem worthy of facing the COVID-19 pandemic.…”

Potential of graphene based photocatalyst for antiviral activity with emphasis on COVID-19: A review

“…This electronic movement destroyed the lipid membrane, generated highly reactive species, and reduction in metabolism, which finally degrade the glutathione and virus. For instance, a computational study demonstrated an efficient binding mechanism between mechanically exfoliated multilayered graphene and the S-protein receptor binding site of SARS-CoV-2 [68] . Herein, the binding mechanism between virus and graphene flakes increased (ΔG= 28.01 Kcal/mol) as the number of layers in graphene sheets increased with edged sp 2 carbon atoms, improving catalytic surface reactivity.…”