Network pharmacology, gut microbiota, and metabolomics integration reveal that Shenshuai 'an enema prescription (SSAEP) improves CRF mechanisms by reshaping the gut microbiota and correcting host–microbe cometabolism

Background Chronic renal failure (CRF) is a global health issue, and the “gut–kidney axis” plays a key role in its pathogenesis. Shenshuai 'an enema prescription (SSAEP) is a Chinese medicine compound based on the TCM theory of “regulation of bowel movement and removal of turbid qi”, which has shown good adjunctive therapeutic effects in delaying the progression of CRF in clinical practice. However, its specific mechanisms remain unclear. Purpose Herein, from the perspective of indirect pharmacology, the therapeutic effects of SSAEP on CRF rats were explored. We hypothesize that its mechanism of action may be largely indirect and occurs primarily through the gut–kidney axis. This study aimed to systematically elucidate the potential mechanism through which SSAEP improves CRF through the regulation of gut microecology using multidisciplinary approaches such as network pharmacology, 16S rRNA gene sequencing, and metabonomics. Methods A CRF rat model was established by induction with 2.5% adenine. Low and high doses of SSAEP were administered via enema, and antibiotic intervention and fecal microbiota transplantation (FMT) experiments were performed to verify the key mediating role of the gut microbiota. The chemical composition of the SSAEP and the metabolic profiles of the serum and colonic contents of the rats were analyzed using UHPLC‒MS/MS; the composition of the gut microbiota was analyzed through 16S rRNA sequencing; and the core targets and pathways were predicted using network pharmacology and molecular docking. In vitro, human renal tubular epithelial cells (HK-2) were stimulated with TGF-β1 or glycochenodeoxycholic acid (GCDCA) to verify the anti-inflammatory and antifibrotic effects of quercetin (the main active component of SSAEP) and the role of the IL-17 signaling pathway in this process. Results SSAEP treatment significantly improved renal function indicators (BUN, SCR, Cys-C, and UA) in CRF rats and alleviated pathological damage, the inflammatory response, and fibrosis in kidney tissue. Antibiotic intervention attenuated the protective effect of SSAEP, while FMT experiments confirmed that the efficacy of SSAEP could be transferred to recipient rats through the transplantation of treated fecal microbiota. SSAEP reshaped the gut microbiota, significantly increasing the abundance of Akkermansia while reducing that of Clostridium . Metabolomic analysis revealed CRF-related metabolic disturbances and identified 29 key differentially expressed metabolites regulated by SSAEP, among which glycochenodeoxycholic acid (GCDCA) was a key pathogenic metabolite. Network pharmacology predictions combined with in vitro experiments confirmed that the quercetin in SSAEP could effectively antagonize the TGF-β1- and GCDCA-induced epithelial‒mesenchymal transition and inflammatory response in HK-2 cells by inhibiting the IL-17/NF-κB signaling pathway. Conclusions This study revealed that SSAEP improves CRF through an indirect pharmacological mechanism dependent on the gut microbiota: SSAEP reshapes the balance of the gut microbiota, thereby correcting host–microbe cometabolic disorders (particularly by reducing the level of the pathogenic metabolite GCDCA) and ultimately alleviating renal inflammation and fibrosis through the inhibition of signaling pathways such as the IL-17/NF-κB pathway. This study provides new experimental evidence for the “gut–kidney axis” theory and lays the foundation for the development of CRF treatment strategies based on the regulation of the gut microbiome.