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 −17.5 Kcal/mol in molecular docking while ΔG_binding is in the order of −28.01 ± 0.04 5 Kcal/mol for the seven-layers structure. The increase in carbon layers is associated with an increasing number of edge sp³ –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.

Communicated by Ramaswamy H. Sarma

Keywords:

• Coronavirus
• graphene
• binding affinity
• MD simulation
• Gibbs free energy

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The authors wish to thank UGC, New Delhi for the financial help towards the execution of the work. S.K.G thank the Science and Engineering Research Board (SERB), Department of Science and Technology (India) and the Russian Foundation for Basic Research (Russia) for the financial support grant numbers.: YSS/2015/001269 and INT/RUS/RFBR/IDIR/P-6/2016.