Integrative Proteome-Wide Structural Analysis and High-Throughput Docking Identify Broad-Spectrum Antiviral Scaffolds Against Zika, Yellow Fever, West Nile, Saint Louis Encephalitis, and Usutu Viruses

Integrative proteome-wide virtual screening offers a powerful route to discover broad-spectrum antivirals against emerging flaviviruses, for which no approved therapeutics currently exist. Here, we address this gap by constructing homology models of all structural and nonstructural proteins from Zika, Yellow Fever, West Nile, Saint Louis Encephalitis, and Usutu viruses. We applied a standardized pipeline—combining sequence and structure based pocket prediction (Concavity), electrostatic profiling (APBS), and pharmacokinetic filtering (Lipinski’s rules, ADMET)—to generate high-confidence binding sites. A focused library of 160 natural product scaffolds and repurposed antivirals was then docked exhaustively (2,000 runs per pocket) using AutoDock4/Vina, followed by clustering and ranking by binding energy. Comparative analyses (RMSD, PCA, RMSF) confirmed conserved core folds alongside virus-specific surface signatures, guiding grid definition. Of the 45 top-ranked scaffolds, several flavonoids exhibited dual-site binding to the NS5 polymerase and E glycoprotein across ≥4 viruses, while ribavirin and sofosbuvir engaged conserved catalytic motifs in NS3/NS5, highlighting opportunities for combination strategies. Lead compounds such as myricetin (Kd ≈ 1.9 µM), temoporfin (Kd ≈ 1.2 nM), and aurintricarboxylic acid (Kd ≈ 1.9 µM) demonstrated favorable multitarget profiles. This integrative framework prioritizes robust candidates for experimental validation and optimization of panflaviviral therapeutics.