Mechanisms Underlying the Therapeutic Effects of GeXiaZhuYu Decoction Treating Colorectal Cancer based on Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulations

INTRODUCTION: GeXiaZhuYu Decoction (GXZYD) has long been used in the context of Colorectal Cancer (CRC), yet its active constituents and associated molecular features remain incompletely characterized at the systems level. METHODS: An integrative computational strategy combining network pharmacology, molecular docking, Molecular Dynamics (MD) simulations, and MM-GBSA binding free-energy analysis was applied to characterize the potential pharmacological landscape of GXZYD in CRC. Active compounds and predicted targets were collected from multiple databases, and CRC-related genes were integrated from GeneCards, OMIM, TTD and DrugBank. Overlapping targets were analyzed by PPI networks and GO/KEGG enrichment analyses. MD simulations and MMGBSA calculations were performed to evaluate the dynamic and energetic characteristics of representative ligand-protein associations. Single-cell RNA-seq data (GSE144735) were analyzed to determine cell-type-specific expression of key targets. RESULTS: Quercetin, luteolin, and kaempferol were identified as representative flavonoid constituents of GXZYD, while HSP90AA1, AKT1, and TP53 were highlighted as network-prioritized targets. Molecular docking suggested favorable binding tendencies between these flavonoids and the selected targets. MD simulations revealed target-dependent dynamic behaviors, with HSP90AA1-associated complexes showing comparatively smaller structural fluctuations, AKT1- associated complexes exhibiting moderate stability, and TP53-associated complexes displaying larger conformational variability consistent with its intrinsic flexibility. MM-GBSA analysis supported relatively favorable binding free-energy trends for flavonoids interacting with HSP90AA1 among the examined targets. Single-cell analysis indicated that HSP90AA1 shows relatively higher expression in epithelial cell populations compared with AKT1 and TP53. DISCUSSION: These computational findings provide a systems-level and structure-informed perspective on the potential molecular associations of GXZYD constituents with CRC-related targets, while not implying direct pharmacological effects or causal mechanisms. CONCLUSION: This study delineates representative active constituents, network-prioritized targets, and pathway-level associations related to GXZYD in colorectal cancer, offering testable hypotheses and a theoretical framework for future experimental validation.