Integrated Gut Microbiota–Drug Interaction Analysis and Network Pharmacology for the Investigation of Renal-Protective Effect of Polygala tenuifolia Willd

<i>Polygala tenuifolia</i> Willd., a widely used traditional Chinese medicine, has the function of coordinating heart and kidney and eliminating swelling. However, its renal-protective efficacy and possible material basis remain unknown. The aim of the study was to investigate the renal-protective effect of <i>Polygala tenuifolia</i> Willd. and identify the potential active substance and molecular mechanism. A gentamicin-induced kidney injury model was established to investigate efficacy. Secondly, potential active substances and molecular mechanisms were studied through integrated gut microbiota-drug interaction analysis and network pharmacology at a cellular level. Finally, 16S rRNA sequencing and untargeted metabolomics were used to elucidate the gut microbiota composition and metabolic profile change. <i>Polygala tenuifolia Willd.</i> extracts (PWE), with tenuifoliside A (TFSA) as the key compound, significantly reversed gentamicin-induced acute kidney injury in mice. The gut microbiota-derived carboxylesterase metabolized TFSA into four characteristic metabolites (M1-M4). Notably, both TFSA and M4 were detected in kidney and exerted protective effects via inhibiting TLR4-NF-κB pathway. Furthermore, metabolic pathways and gut microbiota composition change were identified. PWE treatment significantly increased the abundance of beneficial bacteria such as <i>Akkermansia</i> and <i>Blautia</i>, while reducing the abundance of harmful bacteria such as <i>Oscillospira</i>. Subsequently, PWE can reverse amino acid metabolic abnormalities by regulating the biosynthesis of phenylalanine, tyrosine, and tryptophan and ameliorating tryptophan metabolism disorder. This study was the first to verify the renal-protective effect of PWE and identify the effective substance basis (TFSA) and the molecular mechanism, providing a scientific foundation for the development of kidney drug treatment strategies targeting the intestinal flora.