Structure-Based Free Energy Evaluation of Papaya Flavonoids as Dengue Virus NS5 RdRp Inhibitors via Molecular Simulations, Steered Molecular Dynamics and Umbrella Sampling

Dengue virus (DENV) NS5's RdRp domain is a conserved and functionally necessary enzyme, making it an interesting antiviral target. This study examined Carica papaya flavonoids' efficacy to inhibit DENV-RdRp's allosteric binding domain utilizing structure-based in silico methods. Eight flavonoids were evaluated for RdRp enzyme binding affinity using molecular dynamics simulations, principal component analysis, and free energy landscapes. The molecular simulation studies predicted the formation of stable protein–ligand complex structures in a biological system. Further protein-ligand structure dissociation and unbinding energetics were quantified using SMD simulations with umbrella sampling. By deriving free energy profiles, all eight RdRp-flavonoid complexes showed thermodynamic feasibility for protein-ligand binding with neohesperidin, manghaslin, and isoquercetin complexes having binding energies of –17.35, –16.52 and –16.04 kcal·mol 1 respectively. These results were aligned with the MD and post-MD MMGBSA binding free energy calculations. Thus, we successfully identified and analyzed papaya flavonoid-based natural scaffolds that target DENV-RdRp using advanced molecular simulation methods.