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Evaluating the Molecular—Electronic Structure and the Antiviral Effect of Functionalized Heparin on Graphene Oxide Through Ab Initio Computer Simulations and Molecular Docking

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Advances in Bioinformatics and Computational Biology (BSB 2023)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13954))

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Abstract

In antiviral studies, heparin is widely used against the SARS-CoV-2 virus. In this study, computer simulations were performed to understand the role of heparin in a possible blockade of the spike protein binding with the human cell receptor. Another molecule, graphene oxide (GO), was functionalized to interact and bind with heparin to achieve an increase in binding affinity with the spike protein. In the first stage. The electronic and chemical interaction between the molecules were analyzed through ab initio simulations by using Spanish Initiative for SIESTA (Electronic Simulations with Thousands of Atoms) Software. Next, we evaluated the interaction between molecules together and separately in the spike protein target through molecular docking simulations using AutoDock Vina Software. The results were relevant because GO functionalized with heparin exhibited an increase in affinity energy to the spike protein. This affinity indicated a possible increase in antiviral activity. This increase will be verified in the future through in vitro tests. Experimental tests on the synthesis and morphology of the material preliminarily indicate a good interaction between molecules and absorption of heparin by GO. This phenomenon confirmed the results of first principles simulations.

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References

  1. Bursulaya, B.D., et al.: Comparative study of several algorithms for flexible ligand docking. J. Comput. Aided. Mol. Des. 17(11), 755–763 (2003). https://doi.org/10.1023/B:JCAM.0000017496.76572.6f

    Article  CAS  PubMed  Google Scholar 

  2. Chemcraft: Chemcraft - graphical software for visualization of quantum chemistry computationsy. https://www.chemcraftprog.com. Accessed 05 Dec 2022

  3. Clausen, T.M., et al.: SARS-CoV-2 infection depends on cellular Heparan Sulfate and ACE2. Cell 183(4), 1043-1057.e15 (2020). https://doi.org/10.1016/j.cell.2020.09.033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Dacrory, S.: Antimicrobial activity, DFT calculations, and molecular docking of Dialdehyde cellulose/graphene oxide film against Covid-19. J. Polym. Environ. 29(7), 2248–2260 (2021). https://doi.org/10.1007/s10924-020-02039-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. van Dijk, A.D.J., Bonvin, A.M.J.J.: Solvated docking: Introducing water into the modelling of biomolecular complexes. Bioinformatics 22(19), 2340–2347 (2006). https://doi.org/10.1093/bioinformatics/btl395

    Article  PubMed  Google Scholar 

  6. Fukuda, M., et al.: Lethal Interactions of SARS-CoV-2 with Graphene Oxide: Implications for COVID-19 treatment. ACS Appl. Nano Mater. 4(11), 11881–11887 (2021). https://doi.org/10.1021/acsanm.1c02446

    Article  CAS  PubMed  Google Scholar 

  7. García, A., et al.: SIESTA : recent developments and applications. J. Chem. Phys. 152(20), 204108 (2020). https://doi.org/10.1063/5.0005077

    Article  CAS  PubMed  Google Scholar 

  8. Gobeil, S.M.C., et al.: Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity. Science (1979) 373, 6555 (2021). https://doi.org/10.1126/science.abi6226

    Article  CAS  Google Scholar 

  9. Gupta, I., et al.: Antiviral properties of select carbon nanostructures and their functionalized analogs. Mater. Today. Commun. 29, 102743 (2021). https://doi.org/10.1016/j.mtcomm.2021.102743

    Article  CAS  Google Scholar 

  10. Gupta, Y., et al.: Heparin: a simplistic repurposing to prevent SARS-CoV-2 transmission in light of its in-vitro nanomolar efficacy. Int. J. Biol. Macromol. 183, 203–212 (2021). https://doi.org/10.1016/j.ijbiomac.2021.04.148

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. HOPKINS, J.: Coronavirus Resource Center. https://coronavirus.jhu.edu/map.html

  12. Hoseini-Ghahfarokhi, M., et al.: Applications of graphene and graphene oxide in smart drug/gene delivery: is the world still flat? Int. J. Nanomed. 15, 9469–9496 (2020). https://doi.org/10.2147/IJN.S265876

    Article  CAS  Google Scholar 

  13. ICMAB: Instituto de Ciência de Materiais de Barcelona. https://departments.icmab.es/leem/siesta/

  14. Martins, M.O., et al.: Docking fundamentals for simulation in nanoscience. Disciplinarum Scientia - Ciências Naturais e Tecnológicas 22(3), 67–76 (2021). https://doi.org/10.37779/nt.v22i3.4106

  15. Mycroft-West, C.J., et al.: Heparin inhibits cellular invasion by SARS-CoV-2: structural dependence of the interaction of the spike S1 receptor-binding domain with heparin. Thromb. Haemost. 120(12), 1700–1715 (2020). https://doi.org/10.1055/s-0040-1721319

    Article  PubMed  PubMed Central  Google Scholar 

  16. Oliveira, A.M.L., et al.: Graphene oxide thin films with drug delivery function. Nanomaterials 12(7), 1149 (2022). https://doi.org/10.3390/nano12071149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. PDB Protein Data Bank: SARS-CoV-2 Omicron BA.4 variant spike. https://www.rcsb.org/structure/7XNQ. https://doi.org/10.1038/s41586-022-04980-y

  18. Pedroza, L.S.: Desenvolvimento de novas aproximações para simulações ab initio. USP (2010)

    Google Scholar 

  19. Pubchem: Pubchem. https://pubchem.ncbi.nlm.nih.gov/compound/5288499. Accessed 02 Oct 2022

  20. Rhazouani, A., et al.: Can the application of graphene oxide contribute to the fight against COVID-19? Antiviral activity, diagnosis and prevention. Curr. Res. Pharmacol. Drug Discov. 2, 100062 (2021). https://doi.org/10.1016/j.crphar.2021.100062

    Article  PubMed  PubMed Central  Google Scholar 

  21. dos Santos, A.F., et al.: In-Silico study of antivirals and non-antivirals for the treatment of SARS-COV-2. Disciplinarum Scientia - Ciências Naturais e Tecno lógicas 23(2), 57–83 (2022). https://doi.org/10.37779/nt.v23i2.4200

  22. Schultz, J.V., et al.: Graphene oxide and flavonoids as potential inhibitors of the spike protein of SARS-CoV-2 variants and interaction between ligands: a parallel study of molecular docking and DFT. Struct. Chem. (2023). https://doi.org/10.1007/s11224-023-02135-x

    Article  PubMed  PubMed Central  Google Scholar 

  23. Seabra, A.B., et al.: Nanotoxicity of graphene and graphene oxide. Chem. Res. Toxicol. 27(2), 159–168 (2014). https://doi.org/10.1021/tx400385x

    Article  CAS  PubMed  Google Scholar 

  24. Seifi, T., Reza Kamali, A.: Antiviral performance of graphene-based materials with emphasis on COVID-19: a review. Med. Drug Discov. 11, 100099 (2021). https://doi.org/10.1016/j.medidd.2021.100099

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Shafiee, A., et al.: Graphene and graphene oxide with anticancer applications: challenges and future perspectives. MedComm. (Beijing) 3(1), e118 (2022). https://doi.org/10.1002/mco2.118

    Article  CAS  Google Scholar 

  26. Tandon, R., et al.: Effective inhibition of SARS-CoV-2 entry by heparin and enoxaparin derivatives. J. Virol. 95, 3 (2021). https://doi.org/10.1128/JVI.01987-20

    Article  Google Scholar 

  27. Trott, O., Olson, A.J.: AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. NA-NA (2009). https://doi.org/10.1002/jcc.21334

    Article  Google Scholar 

  28. Unal, M.A., et al.: Graphene oxide Nanosheets interact and interfere with SARS- CoV-2 surface proteins and cell receptors to inhibit infectivity. Small 17(25), 2101483 (2021). https://doi.org/10.1002/smll.202101483

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Valdés-Tresanco, M.S., et al.: AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4. Biol. Direct 15(1), 12 (2020). https://doi.org/10.1186/s13062-020-00267-2

    Article  PubMed  PubMed Central  Google Scholar 

  30. Wang, D., et al.: An overview of the safety, clinical application and antiviral research of the COVID-19 therapeutics. J. Infect. Public Health 13(10), 1405–1414 (2020). https://doi.org/10.1016/j.jiph.2020.07.004

    Article  PubMed  PubMed Central  Google Scholar 

  31. Wang, J., et al.: The inhibition of SARS-CoV-2 3CL Mpro by graphene and its derivatives from molecular dynamics simulations. ACS Appl. Mater. Interfaces 14(1), 191–200 (2022). https://doi.org/10.1021/acsami.1c18104

    Article  CAS  PubMed  Google Scholar 

  32. Wang, P., et al.: Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe 29(5), 747–751.e4 (2021). https://doi.org/10.1016/j.chom.2021.04.007

  33. Wang, X., et al.: Structural insights into the cofactor role of Heparin/Heparan Sulfate in binding between the SARS-CoV-2 spike protein and host Angioten sin-converting enzyme II. J. Chem. Inf. Model. 62(3), 656–667 (2022). https://doi.org/10.1021/acs.jcim.1c01484

    Article  CAS  PubMed  Google Scholar 

  34. Wang, Y., et al.: Structural basis for SARS-CoV-2 delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Nat. Commun. 13(1), 871 (2022). https://doi.org/10.1038/s41467-022-28528-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was carried out with the support of the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brazil-CAPES, Financing Code 001, TELEMEDICINA 1690389P, INCT Nanomateriais de Carbono (CNPq). Acknowledgment for computational support from CENAPAD-SP (National Center for High-Performance Processing in São Paulo).

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Authors and Affiliations

  1. Postgraduate Program in Nanosciences: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Santa Maria, RS, Brazil

    André Flores dos Santos, Mirkos Ortiz Martins, Mariana Zancan Tonel & Solange Binotto Fagan

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  1. André Flores dos Santos
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  2. Mirkos Ortiz Martins
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  3. Mariana Zancan Tonel
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  4. Solange Binotto Fagan
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Contributions

AFS, MOM, MZT developed the conception and design of the study. AFS performed computer simulations. AFS reviewed images and wrote the article under the supervision of MOM and SBF. MOM, SBF, MZT reviewed the results. All authors reviewed and commented on the manuscript. All authors approved the final manuscript.

Corresponding author

Correspondence to André Flores dos Santos .

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Editors and Affiliations

  1. Universidade Estadual de Campinas, Campinas, Brazil

    Marcelo S. Reis

  2. Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

    Raquel C. de Melo-Minardi

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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dos Santos, A.F., Martins, M.O., Tonel, M.Z., Fagan, S.B. (2023). Evaluating the Molecular—Electronic Structure and the Antiviral Effect of Functionalized Heparin on Graphene Oxide Through Ab Initio Computer Simulations and Molecular Docking. In: Reis, M.S., de Melo-Minardi, R.C. (eds) Advances in Bioinformatics and Computational Biology. BSB 2023. Lecture Notes in Computer Science(), vol 13954. Springer, Cham. https://doi.org/10.1007/978-3-031-42715-2_3

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  • DOI: https://doi.org/10.1007/978-3-031-42715-2_3

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