Ensemble Docking and Molecular Dynamics Indicate Dynamic Modulation of hnRNPA1 UP1 Interdomain Behavior by Natural Products

High Resolution Image Download MS PowerPoint Slide RNA-binding proteins exhibit substantial conformational plasticity that complicates structure-based ligand discovery and computational characterization. In this study, we applied an integrated computational approach combining high-throughput virtual screening, molecular dynamics simulations, ensemble docking, and interaction energy analysis to examine ligand binding and associated dynamic effects in the UP1 domain of hnRNPA1. Screening of 2847 phytochemicals followed by scaffold-diverse molecular dynamics evaluation identified three representative ligands─Amentoflavone, Ginkgetin, and Withanolide D─capable of associating with the interdomain surface formed between the two RNA recognition motifs. Comparative simulations revealed that all three ligands form stable complexes within this region, with Ginkgetin exhibiting the most favorable interaction energy. Extended molecular dynamics simulations focusing on Withanolide D demonstrated persistent ligand localization at the RRM1–RRM2 interface and revealed a dominant interaction hotspot centered on SER85 and ARG86. Dynamic analyses indicated that RNA binding is the primary determinant of UP1 conformational stability, whereas ligand association induces modest conformational expansion and redistribution of dynamic variance within the RNA-bound ensemble. Ensemble docking across molecular dynamics-derived conformations further indicated that RNA binding modulates ligand-binding region accessibility without substantially altering average binding energetics. Energetic analysis of the protein–RNA interface revealed a modest reduction in interaction strength upon ligand association, suggesting that ligand binding may perturb the RNA-binding surface without disrupting the overall architecture of the complex. These results provide a system-specific computational characterization of ligand association with the UP1 interdomain region and highlight the role of conformational heterogeneity in shaping ligand-binding behavior in this protein system.