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

Nanocarriers allow the connection between biomolecules and other structures to enhance the treatment efficacy, through the biomolecule's properties to an existing drug, or to allow a better and specific delivery. Apigenin and orientin are biomolecules with excellent therapeutic properties that are proposed in the fight against COVID-19. Besides that, graphene oxide is a nanomaterial that exhibits antiviral activity and is used as a nanocarrier of several drugs. We evaluated in this work, through molecular docking, the binding affinity between these structures to the receptor-binding domain of spike protein of two coronavirus variants, Delta and Omicron. The results indicate that all the structures exhibit affinity with the two protein targets, with binding affinity values of -11.88 to -6.65 kcal/mol for the Delta variant and values of -9.58 to -13.20 kcal/mol for the Omicron variant, which is a successful value as found in the literature as a potential inhibitor of SARS-CoV-2 infection. Also, through first-principles calculations based on Density Functional Theory, the interaction of graphene oxide with the biomolecules apigenin and orientin occurred. The results exhibit weak binding energy, which indicates that physical adsorption occurs, with better results when the biomolecule is set in parallel to the nanomaterial due to attractive pi-pi staking. These results are conducive to the development of a nanocarrier.

Automated summary

Nanocarriers are utilized to enhance treatment by connecting biomolecules with other structures, allowing for better drug delivery or utilizing the properties of biomolecules to improve efficacy. This study evaluated the binding affinity between apigenin and orientin, two biomolecules with therapeutic properties, and the receptor-binding domain of spike protein from the Delta and Omicron variants of COVID-19. The results showed that all structures exhibited affinity with the protein targets, indicating their potential as inhibitors of SARS-CoV-2 infection. Additionally, graphene oxide was found to have weak binding energy with apigenin and orientin, suggesting physical adsorption and the potential for nanocarrier development.