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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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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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