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

• Published in: Journal of molecular structure Vol. 1286; p. 135604
• Main Authors: Lobato, Júlio Cesar Mendes, Arouche, Tiago da Silva, Nero, Jordan Del, Filho, TarcisoAndrade, Borges, Rosivaldo dos Santos, Neto, Antonio Maia de Jesus Chaves
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.08.2023; Published by Elsevier B.V
• Subjects: Antiviral effect; Carbon nanotube; Molecular docking, Molecular dynamics, DFT, In silico study; SARS–CoV-2; Carbon nanotube; SARS–CoV-2; Antiviral effect; Molecular docking, Molecular dynamics, DFT, In silico study
• ISSN: 0022-2860; 1872-8014
• DOI: 10.1016/j.molstruc.2023.135604

•Thisresearch that there is a good chance of a relationship between these anchoring results and the effectiveness of Mycobacterium tuberculosis treatment.•The fourteen ligands tended to attach to the active site of the macrostructure, which suggests that this region has a greater chemical affinity.•Carbon nanotubes have shown promise as potential antiviral agents due to their ability to interact with viral proteins and inhibit their activity.•Molecular dynamics simulations have been used to study the interaction between carbon nanotubes and various viral proteins, such as the spike protein of SARSCoV-2, the virus that causes COVID-19.•Study found that single-walled carbon nanotubes can bind to the spike protein of SARS-CoV-2 and block its interaction with the human ACE2 receptor, which the virus uses to enter human cells.•Docking studies have been used to predict the binding affinity of carbon nanotubes with viral proteins, and have identified specific amino acid residues on the viral proteins that are important for this interaction. 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 zig-zag 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.