Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics

Abstract

Molecular modeling techniques are used to describe the process of interaction between nanotubes and the main structures of the Covid-19 virus: the envelope protein, the main protease, and the Spike glycoprotein. Molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics simulations provide information on the mean squared deviation of atomic positions ​​between 0.5 and 3.0 Å. The Gibbs free energy model and solvent accessible surface area approaches are used. Through the results obtained through molecular dynamics simulations, it is noted that the zigzag nanotube prefers to interact with E-pro, M-pro, and S-gly, respectively. Molecular couplings and free energy showed that the S-gly active site residues strongly interact with zigzag, chiral, and armchair nanotubes, in this order. The interactions demonstrated in this manuscript may predict some promising candidates for virus antagonists, which may be confirmed through experimental approaches.

COVID‐19: Prevention, Detection, and Treatment by Using Carbon Nanotubes‐Based Materials

“…[179] The advantages of using CNTs over nanoparticles to inhibit the HIV-1 virus seen here correspond to their geometric complementarity and strong van der Waals force interactions with the protease active site. [180] Likewise, molecular docking studies by Lobato et al [181] revealed that the zigzag-like shape of CNTs favorably interacted with the M PRO , E PRO , and S-gly proteins. Their findings were important in selecting the best type of CNTs for COVID-19 antiviral treatment.…”