A novel strategy integrating gas phase fractionation with staggered mass range and LC-MS/MS molecular network for comprehensive metabolites profiling of Gui Ling Ji in rats.

Metabolite detection from complex biological samples faces challenges due to interference from endogenous substrates and the inherent limitation of multiple subsequent tandem scanning rates of instruments. Here, a new integrated approach based on gas-phase fractionation with a staggered mass range (sGPF) and a liquid chromatography-tandem mass spectrometry (LC-MS/MS) molecular network was developed to accelerate the data processing of the targeted and untargeted constituents absorbed in rats after oral administration of the traditional Chinese medicine (TCM) prescription Gui Ling Ji (GLJ). Compared with three conventional acquisition methods, sGPF at 3, 5, and 7 mass fractions could enhance MS/MS coverage with an increased MS/MS triggering rate of 29.4-206.2% over data-dependent acquisition (DDA), fast DDA and gas-phase fractionation. A mass range fraction setting of five optimized the performance. Based on the similar diagnostic fragment ions and characteristic neutral loss behaviors in the DDA-MS/MS spectrum, an initial molecular network of GLJ was created with the help of the global natural products social molecular networking (GNPS) platform. Furthermore, to remove the endogenous interference nodes, Cytoscape software was adopted to produce a clean and concise molecular network of prototype compounds and their corresponding metabolites. Using this strategy, a total of 210 compounds, including 59 prototype constituents and 151 metabolites, was unambiguously or tentatively identified in GLJ. This first systematic metabolic study of GLJ in vivo elucidated the potential pharmacodynamic basis of GLJ in clinical treatment. More importantly, this work can serve as a practical example and establish a guide for rapidly identifying TCM metabolites in biological matrices.

Combining multiple acquisition modes and computational data annotation for structural characterization in traditional Chinese medicine: Miao Nationality medicine Qijiao Shengbai Capsule as a case study.

Qijiao Shengbai Capsule (QSC) is a reputable Miao Nationality medicine used for treating leukopenia, but its chemical composition has not yet been elucidated. We herein present a strategy, by integrating multiple data acquisition, computational data annotation and processing methods to visualize and identify the complicated constituents in QSC based on ultra-high-performance liquid chromatography coupled with traveling wave ion mobility quadrupole time-of-flight mass spectrometry (UPLC-TWIMS-QTOF-MS). The multiple data acquisition modes, including data-independent mass spectrometryEnergy (MSE), data-independent high-definition mass spectrometryEnergy (HDMSE), and fast data-dependent acquisition (fast-DDA), in both positive and negative ion modes, were conducted on a Waters-SYNAPT G2-Si mass spectrometer with an ESI source. An in-house library built by the UNIFI platform could efficiently process the peak annotation of known compounds, whilst different structural types were clustered in the molecular networks for the analogous classification and structural annotation of the unknown ones. Neutral loss, diagnostic ions, feature fragmentation behaviors, and community curation of mass spectrometry data of known compounds helped exploit those similar neighboring nodes of unknown compounds. Moreover, by combination of the predicted CCS values from CCS platform with the experimental CCS values from HDMSE, as well as diagnostic fragment ions, isomer compounds were annotated. By integrating reference compound comparison, a total of 202 constituents, including 94 flavonoids, 12 saponins, 30 phthalides, 38 organic acids, 3 amino acids, 7 alkaloids and 18 others, were unambiguously characterized or tentatively identified in QSC. Among them, 5 potential new compounds were detected and 12 pairs of isomers were comprehensively distinguished. Conclusively, the established multiple acquisition modes, computational data processing and analysis strategy proved to be useful for the in-depth structural identification of QSC.

Integrated metabolomics and network pharmacology to reveal the therapeutic mechanism of Dingkun Pill on polycystic ovary syndrome.

ETHNOPHARMACOLOGICAL RELEVANCE: Dingkun Pill (DKP), a traditional Chinese medicine prescription, was modified from Bujing decoction and Xusijiangsheng pill by the imperial physician in the Qing dynasty (1700' s). It was believed to treat various gynecological diseases by nourishing qi and blood. Accumulating evidence indicates that it is effective in treating polycystic ovary syndrome (PCOS). However, the therapeutic efficacy and mechanism of action DKP against PCOS need to be further elucidated. AIM OF THE STUDY: To investigate the therapeutic effect and action mechanism of DKP against PCOS using an integrated approach of metabolomics and network pharmacology. MATERIALS AND METHODS: The rat model of PCOS was established by dehydroepiandrosterone. An integrated metabolomics and network pharmacology strategy was applied to systemically clarify the mechanism of DKP against PCOS. Theca cells were prepared to evaluate the effect of DKP and its ingredients on testosterone synthesis in vitro. RESULTS: The pharmacological experiments demonstrated that DKP could effectively convert the disordered estrous cyclicity, decrease the level of testosterone and the luteinizing hormone/follicle stimulating hormone ratio, and inhibit abnormal follicle formation in PCOS rats. By metabolomics analysis, 164 serum endogenous differential metabolites and 172 urine endogenous differential metabolites were tentatively identified. Steroid hormone biosynthesis and ovarian steroidogenesis were the most significantly impacted pathways. Based on network pharmacology and metabolomics studies, the ingredient-target-pathway network of DKP in the treatment of PCOS was constructed. Among the 10 key targets, CYP17A1, CYP19A1, STS, AR, ESR1, and MYC were closely involved in ovarian androgen synthesis. In theca cell-based assay of testosterone synthesis, DKP and its two active compounds (ligustilide and picrocrocin) showed inhibitory effects. CONCLUSION: DKP effectively improved symptoms in rats with dehydroepiandrosterone-induced PCOS. The mechanism of DKP in the treatment of PCOS is related to the CYP17A1 enzyme required for androgen synthesis.

In vivo and in vitro metabolism study of traditional Chinese medicine formula Dingkun Dan in rats by using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry.

Dingkun Dan (DKD), a reputable traditional Chinese medicine formula, has been used to treat gynecological diseases and showed significant clinical effects since ancient times. However, the application and development of DKD are seriously hampered by the unclear active substances. Structural characterization of compounds absorbed in vivo and their corresponding metabolites is significant for clarifying the pharmacodynamic material basis. In this study, an integrated strategy using ultra-performance liquid chromatography, coupled with quadrupole time-of-flight mass spectrometry and UNIFI™ software, was used to identify prototypes and metabolites after oral administration of DKD in rats. As a result, a total of 261 compounds, including 140 prototypes and 121 metabolites, were tentatively characterized in rat plasma, urine, and feces. The metabolic pathways of prototypes have been studied to clarify their possible transformation process in vivo. Moreover, an in vitro metabolism study was applied for verifying the metabolites under simulating the metabolic environment in vivo. This first systematic metabolic study of DKD is important for elucidating the metabolites and metabolic pathways and could provide a scientific basis for explaining the integrative mechanism in further pharmacology study.

A sensitive ultra-fast liquid chromatography with tandem mass spectrometry method for simultaneous determination of ten constituents of Deng-Zhan-Xi-Xin injection in rat plasma and its application to a comparative pharmacokinetic study in sham and middle cerebral artery occlusion rats.

Deng-Zhan-Xi-Xin injection is widely used to treat cerebrovascular and cardiovascular diseases in clinical practice. A rapid and selective method based on ultra-fast liquid chromatography with tandem mass spectrometry was established and validated to simultaneously quantify chlorogenic acid, 1,3-O-dicaffeoylquinic acid, isochlorogenic acid A, neochlorogenic acid, erigeside I, cryptochlorogenic acid, apigenin-7-O-glucuronide, scutellarin, isochlorogenic acid B, and isochlorogenic acid C of Deng-Zhan-Xi-Xin injection in both sham and middle cerebral artery occlusion rats. This was the first quantitative analysis of these ten constituents in both sham and middle cerebral artery occlusion rats. Chromatographic separation of these ten constituents was accomplished on an Acquity HSS T3 column with the mobile phase consisting of acetonitrile and 0.1% formic acid in water. Mass analysis was performed in negative ion mode with an electrospray ionization source using multiple reaction monitoring technology. The pharmacokinetic study of the ten constituents in sham and middle cerebral artery occlusion rats after intravenous administration of Deng-Zhan-Xi-Xin injection was successfully accomplished by using this validated method. Based on the results of pharmacokinetic parameters, significant differences were observed between the two groups, which might be due to the pathological factors of middle cerebral artery occlusion and pharmacological effects of Deng-Zhan-Xi-Xin injection.

Systematic characterization of the chemical constituents in vitro and prototypes in vivo of Dingkun Dan using ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry combined with the UNIFI™ software.

Dingkun Dan (DKD), a famous traditional Chinese medicine, has been widely used in the treatment of irregular menstruation, leucorrhea abnormality, and postpartum gynecological diseases since Qing dynasty (1739). It comprises 30 flavors of Chinese medicinal materials, which results in its complex chemical composition. In this study, an integrative method was developed to rapidly characterize the chemical components of DKD using ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry combined with the UNIFI™ software. A total of 234 compounds, including 47 triterpenoid saponins, 55 flavonoids, and 38 alkaloids, were identified. Of them, 170 compounds were characterized initially and 61 compounds were identified unambiguously using reference standards. Under the same analysis conditions, 43 prototypical components, which were tentatively assigned as triterpenoid saponins, flavonoids, alkaloids, terpenoids, phenylpropanoids, and others, were absorbed in rat by serum pharmacochemistry analysis. DKD exhibited diverse pharmacological activities through the combined effect of these components. This study was the first systematic study of chemical components in vitro originating from 30 medicinal materials and prototypes in vivo of DKD, which could provide scientific evidence for explaining its therapeutic effect.