Objective To investigate the medication rules and mechanism of national patent Traditional Chinese Medicine compounds for the treatment of bacillary dysentery. Methods Patent of Traditional Chinese Medicine compounds for the treatment of bacillary dysentery authorized in China Patent Publication Bulletin Network from the establishment of the database to January 10, 2025 were retrieved. The Microsoft Excel 2019, the Ancient and Modern Medical Records Cloud Platform (V2.3.9), and the Traditional Chinese Medicine Inheritance Computing Platform (V3.5) were adopted to analyze the frequency of use, property, flavor, meridian entry, and efficacy of the involved patent Traditional Chinese Medicine compounds, and association rule analysis and cluster analysis were employed to explore the medication and prescription rules. The core drug combinations were selected, and network pharmacology method was applied to screen effect targets of effectively active components and disease⁃related targets. A protein⁃protein interaction network and a core drug combination⁃active component⁃target network were constructed. Gene Ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed, followed by molecular docking validation. Results A total of 92 patent Traditional Chinese Medicine compounds for the treatment of bacillary dysentery were enrolled, involving 308 flavors of Traditional Chinese Medicine, with a total frequency of use of 1004 times. There were 24 flavors of high⁃frequency drugs with the frequency of use ≥10 times, with Coptidis rhizoma, Glycyrrhizae radix et rhizoma, Aucklandiae radix, Pulsatillae radix, and Portulacae herba as the core drugs. The drug properties were mainly cold, warm, and moderate. The primary flavors were bitter, acrid, and sweet. These drugs mainly belonged to the stomach, spleen, liver, and large intestine meridians. Their main efficacy of drugs were clearing heat and toxic materials, clearing heat and removing dampness, and removing heat from blood to stop bleeding. The results of association rule analysis revealed that the core prescriptions consisted of Portulacae herba, Pulsatillae radix, Aucklandiae radix, Phellodendri chinensis cortex, Coptidis rhizoma, and Fraxini cortex. Cluster analysis yielded five categories of drug combinations with different therapeutic focuses, which indicated similarities to classic famous prescriptions such as Shaoyao Decoction, Baitouweng Decoction, Yigong Powder, and Dayuan Decoction. Network pharmacology analysis demonstrated that the main active components of the core drug combination (Pulsatillae radix⁃Phellodendri chinensis cortex⁃Aucklandiae radix), namely phellamarin, cynaropicrin, berberine, kulinone, and β⁃sitosterol, acted on core targets such as TNF, GAPDH, ALB, AKT1, and TLR4, regulating the AGE/RAGE signaling pathway, chemokine signaling pathway, Toll⁃like receptor signaling pathway, and HIF⁃1 signaling pathway in the complications of diabetes mellitus. Molecular docking results interpreted good binding affinity between the main active components and the core target proteins, with kulinone exhibiting the strongest binding ability to GAPDH and ALB. Conclusion National patent Traditional Chinese Medicine compounds for the treatment of bacillary dysentery take “clearing heat and removing dampness, clearing toxic materials and stopping dysentery” as its core therapeutic principle. Its core drug combination (Pulsatillae radix⁃Phellodendri chinensis cortex⁃Aucklandiae radix) constructs comprehensive effective network of inhibiting inflammatory responses, antibiosis, and repairing intestinal mucosa through synergistic effect of multiple components, multiple targets, and multiple pathways, thereby exerting effect for treating bacillary dysentery. 

无