Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation to Explore Predicted Molecular...

Intestinal inflammation can disrupt epithelial integrity, immune homeostasis, and nutrient utilization in laying hens. This entirely in silico study investigated the molecular associations between reported Fraxini Cortex constituents and intestinal inflammation by integrating network pharmacology, chicken-specific bioinformatics, molecular docking, molecular dynamics (MD) simulation, and MM/GBSA analysis. After chemical standardization and SwissADME screening, 38 candidate constituents were retained, yielding 528 nonredundant predicted human targets. Intersection with 1452 intestinal inflammation-related genes identified 170 shared human targets, which were subsequently mapped to 133 nonredundant Gallus gallus homologues. A chicken-specific protein-protein interaction network contained 117 non-isolated nodes and 683 interactions, and combined cytoHubba and MCODE analyses identified 13 core candidate targets, including BCL2, SRC, HIF1A, MMP9, ESR1, EGFR, ALB, TLR4, STAT1, PTGS2, SIRT1, JUN, and PPARG. GO and KEGG enrichment associated these targets with receptor and kinase signaling, innate immune recognition, epithelial adhesion and survival, extracellular-matrix remodeling, lipid-mediator metabolism, apoptosis, autophagy, and related processes. Molecular docking of ten candidate compounds against six prioritized targets generated 60 ligand-target combinations, with AutoDock Vina scores ranging from -7.930 to -3.412 kcal/mol. Caffeic acid-MMP9 and scopoletin-ESR1 were further evaluated using three independent 100 ns MD simulations, which showed broadly reproducible conformational behavior across replicates. MM/GBSA calculations yielded mean endpoint binding-energy estimates of -19.92 ± 0.30 kcal/mol for caffeic acid-MMP9 and -21.53 ± 0.32 kcal/mol for scopoletin-ESR1. These findings computationally prioritize caffeic acid, scopoletin, and a group of chicken homologous targets and pathways potentially associated with intestinal inflammation in laying hens and provide testable hypotheses for subsequent chicken-specific experimental validation.