Graphene Quantum Dots interacting with Nipah Virus: a Docking and Dynamic Molecular analysis

Abstract

This comprehensive examination, encompassing a variation in size among the structures, aimed to elucidate the influence of size on molecular interaction dynamics through rigorous anchoring and molecular dynamics simulations. Our investigation delineated a predominant presence of hydrophobic interactions proximate to the receptor binding sites within the complexes. Notably, the affinity energy values of the ligands exhibited a direct correlation with the overall stability of the formed complexes. Concurrently, the Root Mean Square Deviation (RMSD) values of these complexes served as a reliable indicator of their stability dynamics. Consequently, our outcomes propose the potential of protein conjugation with quantum dots in enhancing the adsorption capacity for viral protein components. Moreover, our scrutiny delved deeper into the specific interactions between the Nipah virus macrostructure and quantum dots QD-K, QD-G, and QD-F, revealing robust and enduring bonds. Docking studies unveiled affinity energy scores of -13.658 kcal/mol, -13.6 kcal/mol, and − 13.9 kcal/mol, respectively, for these three ligands. Further corroborating these findings, Gibbs free energy analysis produced consistent outcomes, attributing values of 239.00 kcal/mol, 246.65 kcal/mol, and 259.52 kcal/mol to QD-F, QD-G, and QD-K, respectively. These compelling insights accentuate QD-K, QD-G, and QD-F as promising candidates for potential therapeutic interventions targeting the Nipah virus, indicative of their robust binding affinity and considerable stability within the studied complexes.