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

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

Júlio Cesar Mendes Lobato  1   2 , Tiago da Silva Arouche  1 , Jordan Del Nero  3 , TarcisoAndrade Filho  4 , Rosivaldo Dos Santos Borges  5 , Antonio Maia de Jesus Chaves Neto  1   3   6
Affiliations

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

Júlio Cesar Mendes Lobato et al. J Mol Struct. .

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.

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Conflict of interest statement

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:

Figures

Fig. 1:
Fig. 1
Molecular structure of a) M-pro, b) S-pro and c) E-pro. Source: Adapted from the PDB website.
Fig. 2:
Fig. 2
CNT 3D structures used in the in silico study: a) zig-zag, b) armchair, and c) chiral.
Fig. 3:
Fig. 3
Interaction by the MDOC process of the active site of the macrostructures with the CNT's; a), b) and c) interaction with E-pro; d), e) and f) interaction with M-pro; e), f) and g). (Source: AutoDock Vina 4.2.6.).
Fig. 4:
Fig. 4
Nanotubes- Macrostructures interactions.
Fig. 5:
Fig. 5
RMSD of the: a) E-pro, b) M-pro, and c) S-gly.
Fig. 6:
Fig. 6
RMSF of the complexes, showing the variations produced in the different subdomains and the possible allosteric effects produced in the proteins: a) E-pro, b) M-pro, and receptors c) S-gly.
Fig. 8:
Fig. 8
SASA with: a) E-Pro-b), M-pro and c) S-gly.
Fig. 9
Fig. 9
Binding energies of CNTs with the external structures of SAR-CoV-2 a) E-pro, b) M-pro and c) S-pro.
See this image and copyright information in PMC

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