Abstract
Zika virus (ZIKV) infection remains a global health threat with no approved antivirals or vaccines to date, creating an urgent need for therapeutics targeting ZIKV. The viral envelope (E) protein is critical for host cell entry and represents a validated target for antiviral intervention. Here, we aimed to identify natural flavonoid compounds capable of inhibiting the ZIKV E protein using a dual-phase in silico screening strategy. First, we performed density functional theory (DFT) calculations to optimize the structures of nine candidate flavonoids and obtain quantum chemical descriptors (electronic properties); we also evaluated their drug-likeness and ADMET profiles. Second, we conducted molecular docking of these optimized flavonoids to the E protein, followed by hybrid quantum mechanics/molecular mechanics (QM/MM) refinement and 100 ns molecular dynamics (MD) simulations with principal component analysis (PCA) and MM-PBSA binding free energy calculations to assess binding interactions and complex stability. Docking identified quercetin, pinocembrin, and naringenin as the top binders, with binding energies of -8.3, -8.1, and -8.0 kcal/mol, respectively. These lead flavonoids also exhibited favorable pharmacokinetic properties, including high predicted gastrointestinal absorption, efficient clearance, and minimal toxicity risk (no carcinogenic or organ-specific alerts). Notably, pinocembrin's complex demonstrated the greatest stability throughout a 100 ns MD simulation, maintaining a tightly bound conformation. In conclusion, quercetin, pinocembrin, and naringenin emerge as promising ZIKV E protein inhibitors with robust target engagement and favorable drug-like profiles. Their significant translational potential as antiviral candidates warrants further in vitro and in vivo studies to confirm efficacy and safety.