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

Júlio Cesar Mendes Lobato; Tiago da Silva Arouche; Jordan Del Nero; TarcisoAndrade Filho; Rosivaldo Dos Santos Borges; Antonio Maia de Jesus Chaves Neto

doi:10.1016/j.molstruc.2023.135604

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

J Mol Struct. 2023 Aug 15:1286:135604. doi: 10.1016/j.molstruc.2023.135604. Epub 2023 Apr 18.

Authors

Júlio Cesar Mendes Lobato^{1

2}, Tiago da Silva Arouche¹, Jordan Del Nero³, TarcisoAndrade Filho⁴, Rosivaldo Dos Santos Borges⁵, Antonio Maia de Jesus Chaves Neto^{1

3

6}

Affiliations

¹ Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil.
² Proderna, Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil.
³ Physics Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, 66075-110, Belém, PA, Brazil.
⁴ Federal University of the South and Southeast of Pará. 68507-590, Marabá - PA, Brazil.
⁵ Pharmacy Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil.
⁶ Chemistry and Biochemistry, The University of Texas at Arlington, Box 19065, 700 Planetarium Place, Room 130, Arlington, TX 76019-0065.

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 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.

Keywords: Antiviral effect; Carbon nanotube; Molecular docking, Molecular dynamics, DFT, In silico study; SARS–CoV-2.