Elucidating the Molecular Binding Mechanism of Banxia Xiexin Decoction Components with Acute Gastroenteritis Targets: An Integrated Approach Combining Network Pharmacology and 100-ns Molecular Dynamics Simulations

Abstract Objective: This study aimed to elucidate the molecular binding mechanism and structural stability of the active components of Banxia Xiexin Decoction (BXD) against core therapeutic targets of acute gastroenteritis (AGE) using an integrated computational framework. Methods: Active chemical constituents and AGE-related targets were retrieved from public databases (TCMSP, SwissTargetPrediction, GeneCards). Following the construction of a protein–protein interaction (PPI) network to identify core targets, molecular docking was performed to screen key active compounds. Crucially, to validate the thermodynamic stability of ligand-target interactions, 100-ns molecular dynamics (MD) simulations were conducted using GROMACS. MM-PBSA free energy calculations and Free Energy Landscape (FEL) analyses were subsequently performed to quantify binding energetics and conformational stability. Results: Network analysis identified TNF and STAT3 as core targets regulated by BXD. Molecular docking revealed that isorhamnetin and 7-methoxy-2-methyl-isoflavone exhibit strong binding affinities (-8.4 and -8.7 kcal/mol, respectively) to these targets. MD simulations confirmed that the ligand-protein complexes maintained stable conformations with minimal RMSD fluctuations. Notably, MM-PBSA decomposition demonstrated a robust binding free energy of -133.97 ± 12.83 kJ/mol for the TNF–isorhamnetin complex, driven primarily by van der Waals and electrostatic interactions. FEL analysis further verified that the complexes reside in stable low-energy basins. Conclusion: The integrated analyses provide a solid structural and thermodynamic basis for BXD’s anti-inflammatory effects in AGE. The results suggest that key BXD components can stably occupy the active sites of TNF and STAT3, potentially disrupting pathological signaling loops, which warrants future experimental exploration.