Mechanisms of Qing-Shen-Du formula in treating diabetic kidney disease: Integrating network pharmacology, molecular docking, molecular dynamics, transcriptomics, and experimental validation

Diabetic kidney disease (DKD) represents the major contributor to end-stage renal disease globally, but no curative therapies are currently available. Qing-Shen-Du formula (QSDF), a Traditional Chinese Medicine formula, confers notable protective effects on DKD. It is yet unknown, nevertheless, how QSDF influences DKD. In this study, an analysis of the chemical compounds in QSDF was performed using UPLC-Q-TOF-MS/MS. The potential mechanism of QSDF against DKD was predicted by network pharmacology and subsequently verified by molecular docking and molecular dynamics. RNA-seq and microarray transcriptomics data from DKD patients in the GEO database were used to validate the expression of the core targets. Finally, the pharmacological effects and mechanisms of QSDF against DKD were validated both in vivo and in vitro with a high-fat diet and streptozotocin-induced rat model of DKD and a high-glucose-induced Human glomerular mesangial cell (HGMC) model, respectively. A total of 11 blood prototypical compounds in vivo absorption were identified in QSDF-containing serum. 614 putative targets related to 11 blood prototypical compounds and 5495 genes associated with DKD were obtained. Network pharmacology indicated that the therapeutic effects of QSDF against DKD are primarily mediated via the PI3K/AKT/NF-κB pathway, with PI3K, AKT, and NF-κB functioning as core proteins. The results of molecular docking and molecular dynamics simulations showed that prototypical blood compounds formed stable complexes with PI3K, AKT, and NF-κB targets. Moreover, the mRNA expression levels of PI3K, AKT, and NF-κB were upregulated in DKD patients and were negatively associated with the glomerular filtration rate. In vitro, QSDF inhibited cell proliferation and decreased apoptosis in HRMCs. In vivo, QSDF ameliorated renal injury and prevented renal histopathological damage in DKD rats. Importantly, in addition to downregulating levels of IL-1β and IL-18, QSDF also inhibited the expression of PI3K, AKT, and NF-κB p65 proteins and mRNA levels in HRMCs and the animal model. Collectively, QSDF significantly improves renal function and alleviates inflammation in DKD, mainly through regulating the PI3K/AKT/NF-κB signaling pathway, providing a scientific rationale supporting the clinical application of QSDF in DKD and laying a foundation for future studies.