Network pharmacology integrated with molecular docking and molecular dynamics simulations to explore the mechanism of Tongxie Yaofang in the treatment of ulcerative colitis

Tongxie Yaofang (TXYF), a classical traditional Chinese medicine, is commonly used in China to treat ulcerative colitis (UC). The aim of this study was to integrate network pharmacology with molecular docking and molecular dynamics simulations to explore the mechanism of Tongxie Yaofang in the treatment of UC. The traditional Chinese medicine systems pharmacology database was used to retrieve the relevant chemical compositions of the herbs contained in TXYF. The DisGeNET, GeneCards, Online Mendelian Inheritance in Man, and Therapeutic Target Database databases were used to retrieve UC-related targets. To construct protein-protein interaction networks and screen for key targets, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the key targets of TXYF in the treatment of UC were performed using R 4.3.2 software. AutoDock Tools 1.5.7 was used for molecular docking. Molecular dynamics simulations of protein complexes and complexes of proteins with small-molecule ligands and eutectic ligands were carried out with Gromacs 2022 software. Network pharmacology analysis revealed that TXYF could act on UC through multiple targets and pathways. It may exert therapeutic effects mainly through the AGE/RAGE, TOLL, JAK/STAT, and Th17 signaling pathways. The possible targets of TXYF in the treatment of UC could be AKT1, BCL2, EGFR, HMOX1, HSP90AA1, and TGF beta 1. Molecular docking analysis revealed that AKT1 had the highest binding energy (-10.55 kcal/mol). Molecular dynamics simulations revealed that the complexes formed by the AKT1 protein and the chemical compounds MOL001910 and MOL00035 had good stability and high binding strength. AKT1 may be the most critical target of TXYF in treating UC, and the key chemical components of TXYF in treating UC may include beta-sitosterol (MOL000358) and 11alpha,12alpha-epoxy-3beta-23-dihydroxy-30-norolean-20-en-28,12beta-olide (MOL00 1910). This study revealed that TXYF may exert therapeutic effects on UC through multiple targets, multiple biological functions, and multiple signaling pathways. This study provides a new insight into the pharmacological mechanism of TXYF in treating UC.