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

doi:10.1016/j.molstruc.2023.135604

. 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 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.

PMID: 37089815
PMCID: PMC10111146
DOI: 10.1016/j.molstruc.2023.135604

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. 2023.

. 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.

PMID: 37089815
PMCID: PMC10111146
DOI: 10.1016/j.molstruc.2023.135604

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**
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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References

1. Abraham M.J., Murtola T., Schulz R., Páll S., Smith J.C., Hess B., Lindah E. Gromacs: high-performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1-2:19–25. doi: 10.1016/j.softx.2015.06.001. - DOI
1. Alrasheid A.A., Babiker M.Y., &Awad T.A. Evaluation of certain medicinal plants compounds as new potential inhibitors of novel corona virus (COVID-19) using molecular docking analysis. In Silico Pharmacol. 2021;9(10):1–7. doi: 10.1007/s40203-020-00073-8. - DOI - PMC - PubMed
1. Andersson M.P., Uvdal P. New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-ζ basis Set 6-311+G(d,p) J. Phys. Chem. A. 2005;109:2937–2941. doi: 10.1021/jp045733a. - DOI - PubMed
1. Arouche T.da S., Reis A.F., Martins A.Y., Costa J.F.S., Carvalho Junior R.N., Neto J.C., A M. Interactions between remdesivir, ribavirin, favipiravir, galidesivir, hydroxychloroquine and chloroquine with fragment molecular of the COVID-19 main protease with inhibitor N3 complex (PDB ID:6LU7) using molecular docking. J. Nanosci. Nanotechnol. 2020;20(12):7311–7323. doi: 10.1166/jnn.2020.18955. - DOI - PubMed
1. Baranovich T., Wong S.-.S., Armstrong J., Marjuki H., Webby R.J., Webster R.G., &Govorkova E.A. T-705 (Favipiravir) induces lethal mutagenesis in influenza A H1N1 viruses in vitro. J. Virol. 2013;87(7):3741–3751. doi: 10.1128/jvi.02346-12. - DOI - PMC - PubMed

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[1] Abraham M.J., Murtola T., Schulz R., Páll S., Smith J.C., Hess B., Lindah E. Gromacs: high-performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1-2:19–25. doi: 10.1016/j.softx.2015.06.001. - DOI

[2] Abraham M.J., Murtola T., Schulz R., Páll S., Smith J.C., Hess B., Lindah E. Gromacs: high-performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1-2:19–25. doi: 10.1016/j.softx.2015.06.001. - DOI

[3] Alrasheid A.A., Babiker M.Y., &Awad T.A. Evaluation of certain medicinal plants compounds as new potential inhibitors of novel corona virus (COVID-19) using molecular docking analysis. In Silico Pharmacol. 2021;9(10):1–7. doi: 10.1007/s40203-020-00073-8. - DOI - PMC - PubMed

[4] Alrasheid A.A., Babiker M.Y., &Awad T.A. Evaluation of certain medicinal plants compounds as new potential inhibitors of novel corona virus (COVID-19) using molecular docking analysis. In Silico Pharmacol. 2021;9(10):1–7. doi: 10.1007/s40203-020-00073-8. - DOI - PMC - PubMed

[5] Andersson M.P., Uvdal P. New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-ζ basis Set 6-311+G(d,p) J. Phys. Chem. A. 2005;109:2937–2941. doi: 10.1021/jp045733a. - DOI - PubMed

[6] Andersson M.P., Uvdal P. New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-ζ basis Set 6-311+G(d,p) J. Phys. Chem. A. 2005;109:2937–2941. doi: 10.1021/jp045733a. - DOI - PubMed

[7] Arouche T.da S., Reis A.F., Martins A.Y., Costa J.F.S., Carvalho Junior R.N., Neto J.C., A M. Interactions between remdesivir, ribavirin, favipiravir, galidesivir, hydroxychloroquine and chloroquine with fragment molecular of the COVID-19 main protease with inhibitor N3 complex (PDB ID:6LU7) using molecular docking. J. Nanosci. Nanotechnol. 2020;20(12):7311–7323. doi: 10.1166/jnn.2020.18955. - DOI - PubMed

[8] Arouche T.da S., Reis A.F., Martins A.Y., Costa J.F.S., Carvalho Junior R.N., Neto J.C., A M. Interactions between remdesivir, ribavirin, favipiravir, galidesivir, hydroxychloroquine and chloroquine with fragment molecular of the COVID-19 main protease with inhibitor N3 complex (PDB ID:6LU7) using molecular docking. J. Nanosci. Nanotechnol. 2020;20(12):7311–7323. doi: 10.1166/jnn.2020.18955. - DOI - PubMed

[9] Baranovich T., Wong S.-.S., Armstrong J., Marjuki H., Webby R.J., Webster R.G., &Govorkova E.A. T-705 (Favipiravir) induces lethal mutagenesis in influenza A H1N1 viruses in vitro. J. Virol. 2013;87(7):3741–3751. doi: 10.1128/jvi.02346-12. - DOI - PMC - PubMed

[10] Baranovich T., Wong S.-.S., Armstrong J., Marjuki H., Webby R.J., Webster R.G., &Govorkova E.A. T-705 (Favipiravir) induces lethal mutagenesis in influenza A H1N1 viruses in vitro. J. Virol. 2013;87(7):3741–3751. doi: 10.1128/jvi.02346-12. - DOI - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

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References

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Abstract

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