Abstract Objective To evaluate the clinical efficacy and safety of Zhenzhu Qingyuan Granules through a clinical randomized controlled trial and to analyze the potential action targets and pathways of this formula using network pharmacology. Methods Patients with gastroesophageal reflux disease (GERD) of liver–stomach stagnant heat pattern who met the inclusion and exclusion criteria were randomly divided into the control group and the observation group. The control group received oral rabeprazole, whereas the observation group were given Zhenzhu Qingyuan Granules in addition to the rabeprazole. The treatment duration was 8 weeks. Clinical efficacy was observed in both groups after 8 weeks. Network pharmacology was used to analyze the action targets of Zhenzhu Qingyuan Granules and the genes related to GERD, and core targets were inferred. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were conducted to explore the potential mechanisms of this formula. Results The clinical research results showed that the total effective rate in the treatment group was 92.68%, compared with 70.00% in the control group, with a statistically significant difference (p < 0.05). After treatment, both Chinese medicine syndrome score and endoscopic score improved in both groups compared with before treatment (p < 0.05), and the treatment group showed greater improvement than the control group (p < 0.05). Network pharmacology identified effective components of Zhenzhu Qingyuan Granules for treating GERD, including quercetin, luteolin, and β-sitosterol, with potential action targets such as tumor protein 53 (TP53), protein kinase B (AKT1), and tumor necrosis factor. Conclusion Zhenzhu Qingyuan Granules can significantly improve clinical symptoms in patients with GERD of liver–stomach stagnated heat pattern, enhance clinical efficacy, and have high safety. This formula may exert therapeutic effects through multiple targets and pathways.
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