Molecular mechanisms of aquaporin 1 inhibition by Bacopaside I and Bacopaside II: Insights from molecular dynamics simulations.

Aquaporin-1 (AQP1),a key water channel protein, is aberrantly overexpressed in multiple malignancies, rendering it a compelling therapeutic target. The natural products Bacopaside I and Bacopaside II have demonstrated inhibitory activity against AQP1, yet their molecular mechanisms remain elusive. To elucidate the atomic basis of this inhibition, we employed a comprehensive computational approach combining molecular docking, molecular dynamics (MD) simulations, and extensive Gaussian accelerated molecular dynamics (GaMD) simulations with molecular mechanics generalized Born surface area (MM/GBSA) analysis. Our simulations indicate that both compounds exert spatial effects by occupying pore space, physically blocking channels, and forming van der Waals interactions with hydrophobic amino acids. In addition, ligands form hydrogen bonds with amino acids near these regions, resulting in narrower channels compared to other parts of AQP1. MM/GBSA calculations indicate that Bacopaside Ⅱ (ΔGbind = -34.48 kcal/mol) has a higher binding affinity than Bacopaside I (ΔGbind = -31.76 kcal/mol). Energy decomposition analysis identifies key interacting residues Pro171, Ile174, and Ala66 that anchor the inhibitors. Although both ligands induce subtle constriction of the channel pores, Bacopaside II establishes a more persistent hydrogen bonding network, underscoring its unique energetic contribution to the inhibition profile. Overall, these findings provide a detailed mechanistic blueprint for AQP1 inhibition by Bacopasides and offer a structural framework for the rational design of next-generation AQP1-targeted anticancer therapies.