ABSTRACT
We investigate the binding interactions of synthesized multi-walled carbon nanotubes (MWCNTs) with SARS-CoV-2 virus. Two essential components of the SARS-CoV-2 structure i.e.6LU7 (main protease of SARS-CoV-2) and 6LZG (spike receptor-binding domain complexed with its receptor ACE2) were used for computational studies. MWCNTs of different morphologies (zigzag, armchair and chiral) were synthesized through a thermal chemical vapour deposition process as a function of pyrolysis temperature. A direct correlation between radius to volume ratio of the synthesized MWCNTs and the binding energies for all three (zigzag, armchair and chiral) conformations were observed in our computational studies. Our result suggests that MWCNTs interact with the active sites of the main protease along with the host angiotensin-converting enzyme2 (ACE2) receptors. Furthermore, it is also observed that MWCNTs have significant binding affinities towards SARS-CoV-2. However, the highest free binding energy of −87.09 kcal mol−1 with 6LZG were shown by the armchair MWCNTs with SARS-CoV-2 through the simulated molecular dynamic trajectories, which could alter the SARS-CoV-2 structure with higher accuracy. The radial distribution function also confirms the density variation as a function of distance from a reference particle of MWCNTs for the study of interparticle interactions of the MWCNT and SARS-CoV-2. Due to these interesting attributes, such MWCNTs could find potential application in personal protective equipment (PPE) and diagnostic kits. Investigation of the binding interactions of synthesized multi-walled carbon nanotubes (MWCNTs) with SARS-CoV-2 virus.
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 ΔGbinding 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.