Ensemble-Based Reconstruction and Prioritization of Binding Sites in Influenza A Nucleoprotein

Influenza A nucleoprotein (NP) is essential for viral RNA binding, ribonucleoprotein assembly, and NP oligomerization, making it an attractive antiviral target; however, static structures incompletely capture the conformational variability governing pocket formation and accessibility. Here, 17,178 pockets detected across 753 monomeric NP conformations from three independent molecular dynamics simulations were grouped by pocket-lining residue composition to reconstruct recurrent binding-site regions. Six potentially druggable sites were retained and characterized according to their recurrence, residue-level organization, conformational plasticity, and assembly context, revealing three compact, residue-stable sites, two adaptive RNA-proximal regions, and an extended E339-centered interdomain groove. Four sites corresponded to experimentally characterized or structurally supported ligand-binding environments, while assembly mapping revealed context-dependent exposure near RNA- and NP-NP interaction surfaces, thereby identifying dynamic NP binding-site regions prioritized for ligand-specific investigation and distinguishing stable pockets from plastic regions whose organization and accessibility depend on conformational and assembly context.