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Evaluation interaction of graphene oxide with heparin for antiviral blockade: a study of ab initio simulations, molecular docking, and experimental analysis

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Abstract

Context

Heparin, one of the drugs reused in studies with antiviral activity, was chosen to investigate a possible blockade of the SARS-CoV-2 spike protein for viral entry through computational simulations and experimental analysis. Heparin was associated to graphene oxide to increase in the binding affinity in biological system. First, the electronic and chemical interaction between the molecules was analyzed through ab initio simulations. Later, we evaluate the biological compatibility of the nanosystems, in the target of the spike protein, through molecular docking. The results show that graphene oxide interacts with the heparin with an increase in the affinity energy with the spike protein, indicating a possible increment in the antiviral activity. Experimental analysis of synthesis and morphology of the nanostructures were carried out, indicating heparin absorption by graphene oxide, confirming the results of the first principle simulations. Experimental tests were conducted on the structure and surface of the nanomaterial, confirming the heparin aggregation on the synthesis with a size between the GO layers of 7.44 Å, indicating a C–O type bond, and exhibiting a hydrophilic surface characteristic (36.2°).

Methods

Computational simulations of the ab initio with SIESTA code, LDA approximations, and an energy shift of 0.05 eV. Molecular docking simulations were performed in the AutoDock Vina software integrated with the AMDock Tools Software using the AMBER force field. GO, GO@2.5Heparin, and GO@5Heparin were synthesized by Hummers and impregnation methods, respectively, and characterized by X-ray diffraction and surface contact angle.

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Acknowledgements

Acknowledgment for computational support from CENAPAD-SP (National Center for High-Performance Processing in São Paulo).

Funding

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).

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AFS, MOM, DMD, JSL, CBD, and MZT developed the conception and design of the study. AKM, CBD, and DVL developed the methodology and are conducting safety and efficacy tests with cells. DMD, SRM, and MSF developed the methodology and performed compound characterization tests. AFS, MOM, MZT, JSL, and JOA performed computer simulations. AFS, MZT, JOA, CBD, AKM, and DVS reviewed the images and wrote the article under the supervision of IZS, SF, and SRM. AFS, JOA, JSL, and DMD reviewed the results. All authors reviewed and commented on the manuscript. All authors approved the final manuscript.

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Correspondence to André Flores dos Santos.

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Supplementary Material

Video 1 of version 01 of the ab initio simulation results. (MPG 1339 kb)

Video 2 of version 02 of the ab initio simulation results. (MPG 3968 kb)

Video 3 of version 03 of the ab initio simulation results. (MPG 870 kb)

Video 4 of version 04 of the ab initio simulation results. (MPG 4700 kb)

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dos Santos, A.F., Martins, M.O., Lameira, J. et al. Evaluation interaction of graphene oxide with heparin for antiviral blockade: a study of ab initio simulations, molecular docking, and experimental analysis. J Mol Model 29, 235 (2023). https://doi.org/10.1007/s00894-023-05645-x

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