Mechanistic Insight into Binding of Graphene Towards Multiple Therapeutic Target of SARS-CoV-2 by Molecular Docking and Dynamics Studies

Abstract

Background: Even after more than three years of emergence of coronavirus diseases 2019 (COVID-19), it remains incurable, despite the use of emergency-approved vaccines. The impact of the emergency-approved vaccines against it is not highly certain. The entire world may face surge of new wave of the infection, and therefore, its reoccurrence cannot be denied. Causalities and economic losses may happen in the future. In this situation, it is need of the hour to explore some suitable therapeutic agents against this highly infectious and challenging disease. Organic molecules, inactivated virus etc were largely focused to derive the vaccines, however, nanomaterials still remain untested for it. Interaction of nanomaterials like graphene against proteins of the coronavirus to inhibit its activity is yet to be tested computationally. Method: In this computational research work, graphene is tested for interaction with the viral proteins, as the dimension of the novel coronavirus also belongs to nano-scale (diameter 65-125 nm). A detailed study ondocking structures and molecular dynamics between viral proteins and graphene, is undertaken. Autodock and Discovery Studio packages were used for docking calculations and interaction analysis, respectively. Molecular dynamics simulation was performed using NAMD software and obtained results were visualized using VMD software. Results: Range of proteins of the coronavirus including spike proteins (both open and closed form), Main Protease (MPRO), Receptor-Binding Domain (RBD), RNA-dependent RNA polymerase (RdRp), and Angiotensin Converting Enzyme 2 (ACE2) have been individually evaluated for their docking and dynamics with graphene, so as to inactivate the virus. Details of interacting amino acid residues of coronavirus with graphene is found in the study. Conclusion: Computationally, it is observed that most of these proteins were found interactive through their amino acid residues with graphene. Number of interacting amino acid residues is considerable enough to collectively acquire high binding energy. It can be envisaged that cumulative perturbations of all the interactions of each protein caused by graphene can lower down or inactivate the virus.