Exploring the biomarkers and therapeutic mechanism of kidney-yang deficiency syndrome treated by You-gui pill using systems pharmacology and serum metabonomics

Abstract

In this study, systems pharmacology was used to predict the molecular targets of You-gui pill (YGP) and explore the therapeutic mechanism of Kidney-Yang Deficiency Syndrome (KYDS) treated with YGP. On the basis of this, serum samples from control group, KYDS model group and YGP group rats were studied using 1 H NMR to verify the results of systems pharmacology from the level of metabonomics.Simultaneously, 1 H NMR spectra of serum samples were obtained and statistically assessed using pattern recognition analysis. Biochemical analyses of serums were performed via radioimmunoassays. Furthermore, histopathological studies were conducted on the pituitary, adrenal, and thyroid glands, and testicles of the control, KYDS and YGP rats. Using systems pharmacology to analyze the active components of YGP, 61 active compounds were finally found. These compounds were likely to have an effect on 3177 target proteins and involve 234 pathways. Using metabonomics to analyze serum from KYDS rats treated with YGP, 22 endogenous biomarkers were found. These biomarkers were mainly involved in 10 metabolic pathways. Combining systems pharmacology and metabonomics, we found that the regulation of KYDS was primarily associated with 19 active compounds of 5 Chinese herbal medicines in YGP. These active compounds mainly had an effect on 8 target proteins, including phosphoenolpyruvate carboxykinase, betaine-homocysteine s-methyltransferase 1, alcohol dehydrogenase 1C, etc. These target proteins were primarily involved in 6 overlapping pathways, namely aminoacyl-tRNA biosynthesis, glycolysis/gluconeogenesis, glycine, serine and threonine metabolism, valine, leucine and isoleucine biosynthesis, arginine and proline metabolism, and pyruvate metabolism. In addition, there were 4 non-overlapping pathways, respectively alanine, aspartate and glutamate metabolism, D-glutamine and D-glutamate metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and galactose metabolism. In summary, the therapeutic effects of YGP on KYDS were mainly associated with neuroendocrine regulation, energy metabolism, amino acid metabolism, inflammatory responses, apoptosis, oxidative stress and intestinal flora metabolism. What's more, we also found that YGP possessed the potential to protect liver and kidney function. Our study demonstrated that systems pharmacology and metabonomics methods were novel strategies for the exploration of the mechanisms of KYDS and TCM formulas.

Integrated Systems Pharmacology, Urinary Metabonomics, and Quantitative Real-Time PCR Analysis to Uncover Targets and Metabolic Pathways of the You-Gui Pill in Treating Kidney-Yang Deficiency Syndrome

“…In contrast, the You-gui pill (YGP) is a classic traditional Chinese medicine (TCM) formula for the treatment of KYDS and has been widely used to warm and recuperate KYDS clinically for hundreds of years in China [6]. It was originally described by “Jing-Yue Complete Works” in the year 1624 and consisted of ten herbs, including Radix Rehmanniae Praeparata (SDH, Shu-Di-Huang), Radix Aconiti Lateralis Prreparata (FZ, Fu-Zi), Cinnamomi cortex (RG, Rou-Gui ), Rhizoma Dioscoreae (SY, Shan-Yao), Fructus Corni (SZY, Shan-Zhu-Yu), Semen Cuscutae (TSZ, Tu-Si-Zi), Fructus Lycii (GQ, Gou-Qi), Cervi cornus colla (LJJ, Lu-Jiao-jiao), Eucommiae cortex (DZ, Du-Zhong), and Radix Angeliccae Sinensis (DG, Dang-Gui) [6,7,8]. The ratio of ten herbs in YGP was: SDH (8); SY (4); SZY (3); GQ (4); LJJ (4); TSZ (4); DZ (4); RG (2); FZ (2); DG (3).…”

“…Studies have indicated that metabonomics based on different platforms (e.g., 1 H NMR [4,5,7,10], GC/MS [2,11], LC/MS [3,12,13,14,15,16,17]) can identify some biomarkers, targets, and metabolic pathways associated with KYDS or KYDS treated by Chinese medicine. However, it is unknown whether these corresponding targets and metabolic pathways can also be found via using metabonomics based on one platform (e.g., 1 H NMR) to study different biological samples of KYDS.At the same time, relevant reports on further molecular verification (e.g., RT-qPCR analysis) of these targets related to biomarkers and metabolic pathways have not yet, to our knowledge, been seen in KYDS’s research.…”

Combined systems pharmacology and fecal metabonomics to study the biomarkers and therapeutic mechanism of type 2 diabetic nephropathy treated with Astragalus and Leech

“…52 Of the top 300 targets, Z-score $ 0.8 was considered as criteria to screen potential target proteins. 53,54…”

“…Study has shown that oxidative stress will induce TyrRS to rapidly translocate from the cytosol to the nucleus to protect against DNA damage. 54,79 Whereas TrpRS have been proved be conformational isomers of homology to TyrRS. 80 Meanwhile, Chou et al 81 have shown tryptophan catalyzed and activated by TrpRS might be regarded as a potential prognostic marker for diabetic nephropathy.…”

Global metabolomic profiling of trastuzumab resistant gastric cancer cells reveals major metabolic pathways and metabolic signatures based on UHPLC-Q exactive-MS/MS

“…16 It has been widely applied in various elds involving diagnosis of disease, identication of biomarkers and elucidation of physiological and pathophysiological processes. 17,18 Although a growing number of studies on metabolic alterations in cancers by liquid chromatographymass spectrometry (LC/MS), gas chromatography-mass spectrometry (GC/MS) and nuclear magnetic resonance (NMR) approach based on metabolomics have been reported, the mechanisms of cancer metabolism in the context of resistance have not been fully investigated. 19,20 In this study, we performed a global metabolomics based on UHPLC-Q exactive-MS/MS integrated with multivariate statistical data analysis (MVDA) to explore alterations of metabolic signatures and metabolic pathways in NCI N87/R and MKN45/R cells.…”