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

• Published in: Journal of molecular modeling 2023-08, Vol.29 (8), p.235-235, Article 235
• Main Authors: dos Santos, André Flores, Martins, Mirkos Ortiz, Lameira, Jerônimo, de Oliveira Araújo, Jéssica, Frizzo, Marcela Sagrilo, Davidson, Carolina Bordin, de Souza, Diulie Valente, Machado, Alencar Kolinski, Mortari, Sérgio Roberto, Druzian, Daniel Moro, Tonel, Mariana Zancan, da Silva, Ivana Zanella, Fagan, Solange Binotto
• Format: Article
• Language: English
• Subjects: absorption; Affinity; Antiviral Agents - pharmacology; antiviral properties; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; computer software; Contact angle; COVID-19; energy; First principles; Graphene; graphene oxide; Heparin; Heparin - metabolism; Humans; hydrophilicity; IX Symposium on Electronic Structure and Molecular Dynamics – IX SeedMol; Molecular docking; Molecular Docking Simulation; Molecular Medicine; Nanomaterials; Original Paper; Proteins; SARS-CoV-2 - metabolism; Severe acute respiratory syndrome coronavirus 2; Simulation; Software; Spike Glycoprotein, Coronavirus - metabolism; Surface properties; Synthesis; Theoretical and Computational Chemistry; X-ray diffraction
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-023-05645-x

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.