In Silico Analysis of Structural Compatibility Between Histo-Blood Group Antigen-Associated Glycans and VP1 P Domains of Human and Animal Noroviruses

Noroviruses are leading causes of acute gastroenteritis worldwide, with host susceptibility and viral attachment influenced by interactions between the VP1 protruding (P) domain and histo-blood group antigens (HBGAs). Although HBGA recognition has been extensively investigated in human noroviruses, the structural capacity of animal-associated genotypes to accommodate HBGA-related glycans remains comparatively underexplored. In this study, we performed a comparative in silico analysis of the structural compatibility of VP1 P domains with six HBGA-related glycans: lacto-N-biose (LNB), H type 1, antigen A, antigen B, Lewis A, and Lewis Y. Human and animal-associated norovirus genotypes were evaluated using structural modeling, CB-Dock2/AutoDock Vina docking, Vina score-derived ligand efficiency, residue-contact mapping, and three independent 100 ns molecular dynamics simulations of the GII.4 P-domain–H type 1 complex. Site-informed selection of CB-Dock2 cavity-based poses yielded heavy-atom RMSD values of 0.327–1.895 Å for four crystallographic complexes, although only two selected poses were top-ranked among cavity-based outputs. Complementary carbohydrate-aware redocking with Vina–Carb recovered a crystallographically similar pose (<2 Å) among the top ten solutions for two of the four complexes, indicating complex-dependent pose-recovery performance. Score-derived ligand-efficiency distributions broadly overlapped between the analyzed human and animal-associated datasets. Analysis of selected docking configurations, guided by the literature, identified geometrically plausible glycan arrangements and recurrent polar and aromatic contact environments, with genotype-dependent variation in pocket organization. However, the automatically top-ranked blind-docking solutions were spatially separated from targeted P2 configurations in the four representative H type 1 complexes, indicating that P2-associated accommodation was dependent on site-directed sampling rather than independently identified by blind docking. In the replicated molecular dynamics simulations, the P-domain remained globally stable, whereas H type 1 displayed substantial positional mobility, intermittent increases in protein–ligand distance, and variable hydrogen-bond formation, indicating that the initial docking pose was not continuously maintained. Overall, the findings support a hypothesis-generating framework of structural compatibility and genotype-dependent topological variability under sampling conditions that are guided by the literature, without establishing biological glycan binding or quantitative binding affinity.