Abstract:

We investigated the molecular mechanisms underlying the treatment of recurrent aphthous ulcers (RAU) using the Radix Aconiti–Cortex Phellodendri combination, based on weighted gene co-expression network analysis (WGCNA) and network pharmacology. A total of 301 active compounds were identified from the Radix Aconiti–Cortex Phellodendri combination, associated with 3,273 potential targets.

WGCNA was used to analyze RAU-related genes. The VennDiagram package in R software was employed to identify intersections between drug-related targets and WGCNA modules. Pathway and process enrichment analyses, along with hierarchical clustering, were conducted using KEGG Pathway, GO Biological Processes, and Reactome Gene Sets. These analyses highlighted involvement in apoptosis regulation and signaling, glutathione metabolism, PI3K signaling abnormalities, resistance to epidermal growth factor receptor tyrosine kinase inhibitors, cytokine signaling in the immune system, the PPAR-α pathway, and other processes related to immune regulation, metabolism, and tissue repair.

Using the MCODE plugin in Cytoscape v3.7.2, key hub genes within functional modules were identified, including ERBB2, CD44, NFKB1, and MMP2. Molecular docking showed that ERBB2 interacted with most active compounds; diterpenoid alkaloids fromAconitumand flavonoids fromPhellodendronprimarily targeted CD44; alkaloids fromPhellodendrontargeted MMP2; and both monoester and diester Aconitum alkaloids mainly targeted NFKB1. These findings suggest a complementary and synergistic effect between the two herbs in preventing RAU recurrence.

Key words: weighted gene co-expression network analysis (WGCNA), recurrent aphthous ulcers, systemic pharmacology, Radix Aconiti, Cortex Phellodendri