Structural characterization of ZIKV M protein as a candidate viroporin: insights from molecular dynamics, evolutionary coupling and DFT

Viroporins are small viral membrane proteins that facilitate ion transport and play critical role in viral pathogenicity. In this study, we investigate the Zika virus M protein viroporin to elucidate its proposed pore forming architecture using a combined computational framework of molecular dynamics (MD) simulations and density functional theory (DFT) calculations. Sequence analysis shows 75 amino acid long Zika M protein is highly conserved across the continents and a significant variation is observed within different flaviviruses. The ab-initio model determined by AlphaFold is characterized by two hydrophobic C-terminal alpha helices and a N-terminal compact ectodomain. MD simulations in DPPC bilayers indicate that a pentameric pore-like assembly was the most structurally persistent model tested, featuring a single pore with a mixed distribution of polar and nonpolar residues. Leu12, Ile30, Trp35, Phe42, Ile49, Tyr63, Ile67, and Tyr74 provide structural rigidity and pore geometry, thereby stabilizing oligomeric packing. DFT analyses provide atomistic insights into electronic interactions and energetics that underpin conformational switching. Ca2+ displays well-defined multidentate coordination and strong structural organization, whereas Na+, K+, H+, and Cl− engage more weakly, governed mainly by long-range electrostatics and solvation effects. Virtual screening of >170 marketed ion channel modulators identified Lumacaftor and Gliquidone as the highest-scoring compounds for the Zika M oligomer pore-binding pocket, generating hypotheses for future experimental validation. Our study provides a structural and computational framework for the ZIKV M protein as a candidate viroporin, offering testable hypotheses regarding oligomeric stoichiometry, pore-lining architecture, and ion coordination that motivate future experimental validation.