Xiuhong Wu

Metabolomics Coupled with Proteomics Advancing Drug Discovery toward More Agile Development of Targeted Combination Therapies

To enhance the therapeutic efficacy and reduce the adverse effects of traditional Chinese medicine, practitioners often prescribe combinations of plant species and/or minerals, called formulae. Unfortunately, the working mechanisms of most of these compounds are difficult to determine and thus remain unknown. In an attempt to address the benefits of formulae based on current biomedical approaches, we analyzed the components of Yinchenhao Tang, a classical formula that has been shown to be clinically effective for treating hepatic injury syndrome. The three principal components of Yinchenhao Tang are Artemisia annua L., Gardenia jasminoids Ellis, and Rheum Palmatum L., whose major active ingredients are 6,7-dimethylesculetin (D), geniposide (G), and rhein (R), respectively. To determine the mechanisms underlying the efficacy of this formula, we conducted a systematic analysis of the therapeutic effects of the DGR compound using immunohistochemistry, biochemistry, metabolomics, and proteomics. Here, we report that the DGR combination exerts a more robust therapeutic effect than any one or two of the three individual compounds by hitting multiple targets in a rat model of hepatic injury. Thus, DGR synergistically causes intensified dynamic changes in metabolic biomarkers, regulates molecular networks through target proteins, has a synergistic/additive effect, and activates both intrinsic and extrinsic pathways.

Metabolomic analysis of key regulatory metabolites in hepatitis C virus-infected tree shrews.

Metabolomics is a powerful new technology that allows the assessment of global low-molecular-weight metabolites in a biological system and which shows great potential in biomarker discovery. Analysis of the key metabolites in body fluids has become an important part of improving the diagnosis, prognosis, and therapy of diseases. Hepatitis C virus (HCV) is a major leading cause of liver disease worldwide and a serious burden on public health. However, the lack of a small-animal model has hampered the analysis of HCV pathogenesis. We hypothesize that an animal model (Tupaia belangeri chinensis) of HCV would produce a unique characterization of metabolic phenotypes. Ultra-performance liquid-chromatography/electrospray ionization-SYNAPT-high-definition mass spectrometry (UPLC/ESI-SYNAPT-HDMS) coupled with pattern recognition methods and system analysis was carried out to obtain comprehensive metabolomics profiling and pathways of large biological data sets. Taurine, hypotaurine, ether lipid, glycerophospholipid, arachidonic acid, tryptophan, and primary bile acid metabolism pathways were acutely perturbed, and 38 differential metabolites were identified. More important, five metabolite markers were selected via the “significance analysis for microarrays” method as the most discriminant and interesting biomarkers that were effective for the diagnosis of HCV. Network construction has led to the integration of metabolites associated with the multiple perturbation pathways. Integrated network analysis of the key metabolites yields highly related signaling pathways associated with the differentially expressed proteins, which suggests that the creation of new treatment paradigms targeting and activating these networks in their entirety, rather than single proteins, might be necessary for controlling and treating HCV efficiently.

Ultra-performance LC-ESI/quadrupole-TOF MS for rapid analysis of chemical constituents of Shaoyao-Gancao decoction

Shaoyao-Gancao decoction (SGD), a traditional Chinese formulae containing Paeoniae Radix and Glycyrrhizae Radix, is commonly used to relieve abdominal pain. It has attracted increasingly much attention as one of the most popular and valuable herbal medicine in clinic. However, the systematic analysis of chemical constituents of SGD are difficult to determine and thus remain unclear. In this paper, a rapid, sensitive, and reliable ultra-performance LC-ESI/quadrupole-TOF high-definition MS (UPLC-ESI-Q-TOF-MS) with automated MetaboLynx analysis in negative ion mode were established to characterize the chemical constituents of SGD. The analysis was performed on a Waters UPLC(TM) HSS T3 (2.1 × 100 mm, 1.8 μm) using gradient elution system. MS/MS fragmentation behavior was proposed for aiding the structural identification of the components. With the optimized conditions, a total of 58 peaks were tentatively characterized by comparing the retention time and mass spectrometry data and retrieving the reference literatures. Of note, 44 ingredients were identified from Glycyrrhizae Radix, and 14 were from Paeoniae Radix. It is concluded that a rapid and robust platform based on UPLC-ESI-Q-TOF-MS was successfully developed for globally identifying multiple-constituent of traditional Chinese medicine prescriptions. This is the first report on systematic analysis of chemical constituents and in vivo metabolites of SGD.

Rapid discovery and global characterization of chemical constituents and rats metabolites of Phellodendri amurensis cortex by ultra-performance liquid chromatography-electrospray ionization/quadrupole-time-of-flight mass spectrometry coupled with pattern recognition approach

To discover and screen the constituents or metabolites absorbed into blood after oral administration of herbal medicines tends to be more and more difficult. In this work, an integrative pattern recognition approach of principal component analysis (PCA) and orthogonal partial least squared discriminant analysis (OPLS-DA) was successfully applied for rapid discovery of natural compounds from herbal medicines. A rapid, sensitive, and reliable ultra performance liquid chromatography coupled with electrospray ionization/quadrupole-time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS) method with Masslynx™ software was established to characterize the chemical constituents and rats metabolites of Phellodendri amurensis cortex (Guan Huangbai, GHB). The analysis was performed on a Waters UPLC HSS T3 column (2.1 × 100 mm, 1.8 μm) using gradient elution system. A hyphenated electrospray ionization and quadrupole-time-of-flight analyzer was used for the determination of accurate mass of the protonated or deprotonated molecule and fragment ion in both negative and positive modes. A total of 46 peaks were obtained, 41 of which were tentatively characterized from GHB. In the S-plot of OPLS-DA, 24 interested ions (17 ions in positive mode and 6 ions in negative mode) were extracted, among them, 12 absorbed prototype components of GHB and 12 metabolites were identified in vivo. Major metabolic reactions of GHB were demethylation, methylation and glucuronidation. This is the first report on systematic analysis of chemical constituents and in vivo metabolites of GHB. It is concluded that UPLC-MS coupled with pattern recognition approach for the identification of herbal constituents in biological samples has been successfully developed. The method can also be applied to rapid discovery and global characterization of the constituents in rat serum after oral administration of other herbal medicines.

Pharmacokinetics of hesperetin and naringenin in the Zhi Zhu Wan, a traditional Chinese medicinal formulae, and its pharmacodynamics study.

Zhi Zhu Wan (ZZW), a classical Chinese medical formulae consisted of Atractylodes Rhizome and Fructus Citrus Immaturus, has been commonly used for treatment of gastrointestinal diseases. Hesperetin and naringenin are the main components of ZZW, and both can alleviate intestinal tract disorders. In this work, plasma pharmacokinetics and pharmacodynamics characteristics of ZZW after oral administration were investigated using a rapid and sensitive ultra performance liquid chromatography–tandem mass spectrometry method with an electrospray ionization source in positive ion mode. Biosamples were prepared using methanolic precipitation, and the separation of hesperetin and naringenin was achieved on a Waters ACQUITY HSS BEH (2.1 mm × 5 mm, 1.7 µm) column by linear gradient elution, and the total run time was only 3 min. Data were analyzed and estimated using WinNonlin Professional version 5.1. With pharmacokinetic analysis, the estimated pharmacokinetic parameters (i.e. Cmax, area under the concentration–time curve (AUC) and t1/2), were Cmax = 776.06 ng/mL, AUC = 9473 ng/mL·h, t1/2 = 5.26 h for hesperetin and Cmax = 2910.6 ng/mL, AUC = 40607.9 ng/mL·h, t1/2 = 4.69 h for naringenin, respectively. In the present study, we have also valuated and clarified the effect of ZZW on small intestinal movement. It was found that ZZW can accelerate intestinal motility in mice and may hold a promising treatment for intestinal diseases. Copyright

Metabolomics Coupled with Pattern Recognition and Pathway Analysis on Potential Biomarkers in Liver Injury and Hepatoprotective Effects of Yinchenhao

Metabolomics can provide an opportunity to develop the systematic analysis of the metabolites in biological samples and has been increasingly applied to discovering and identifying biomarkers and perturbed pathways. It enables us to better understand the metabolic pathways which can clarify the mechanism of traditional Chinese medicines (TCM). Yinchenhao (YCH, Artemisia annua L), a famous TCM plant, has been used clinically for more than a thousand years to relieve liver diseases in Asia, and its mechanisms are not still completely clear. Here, metabolomic techniques may provide additional insight, and our investigation was designed to assess the effects and possible mechanisms of YCH on α-naphthylisothiocyanate (ANIT)-induced liver injury. Metabolite profiling was performed by ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry (UPLC/ESI-Q-TOF/MS) combined with pathway analysis and pattern recognition approaches including independent component analysis (ICA) and partial least squares-discriminant analysis (PLS-DA). Biochemistry test was also performed for the liver tissue and plasma samples. The changes in metabolic profiling were restored to their baseline values after YCH treatment according to the ICA score plots. Of note, YCH has a potential pharmacological effect through regulating multiple perturbed pathways to normal state, correlating well to the assessment of biochemistry test. Five different potential biomarkers in the positive mode contributing to the treatment of YCH were discovered. Pathway analysis showed that these metabolites were associated with perturbations in pyrimidine metabolism, primary bile acid biosynthesis, and propanoate metabolism, which may be helpful to further understand the action mechanisms of YCH. It showed that changed biomarkers and pathways may provide evidence to insight into drug action mechanisms and drug discovery.

Preliminary identification of the absorbed bioactive components and metabolites in rat plasma after oral administration of Shaoyao-Gancao decoction by ultra-performance liquid chromatography with electrospray ionization tandem mass spectrometry

Background: Shaoyao-Gancao decoction (SGD), a traditional Chinese medicine formula, has been used for the treatment of abdominal pain and dysmenorrhea disease in Asia over long period of time. Its effectiveness has been confirmed in clinic, but its active constituents remain unclear. Materials and methods: In this paper, a rapid, sensitive and reliable ultra-performance liquid chromatography-electrospray ionization/quadrupole-time-of-flight high-definition mass spectrometry (UPLC-ESI-Q-TOF-MS) in positive and negative ion mode were established to characterize the active constituents of SGD in vitro. The analysis was performed on a Waters UPLCTM HSS T3 (2.1 × 100 mm, 1.8 µm) using gradient elution system. Automated MetaboLynxTM technique was employed to screen for the potentially bioactive components in rat plasma after oral administration of SGD. MS/MS fragmentation behavior was proposed for aiding the structural identification of the components. Results: Based on the developed method of fingerprint analysis, an injection run of the plasma sample was finished in 15.0 min. A total of 12 compounds including 9 prototype components such as gallicacid, albiflorin, liquiritin, pallidiflorin, liquiritigenin, isoLiquiritigenin, formononetin, isolicoflavonol, licoricone, C9H10O3 and 2 metabolites such as liquiritigenin-4’-O-glucuronide, formononetin glucuronide were identified or tentatively characterized. Of note, 3 ingredients were identified from Radix Paeoniae Alba, and 9 were from Radix Glycyrrhizae. Conclusion: The compounds found in dosed plasma could be the effective substances of SGT for treating dysmenorrheal, and may provide important experimental data for further pharmacological and clinical research of SGD. Furthermore, this work has demonstrated that the feasibility of the UPLC-ESI-Q-TOF-MS for rapid and reliable characterization of identification and structural elucidation of the chemical constituents and their metabolites from herbal medicines.

Chemical discrimination of cortex Phellodendri amurensis and cortex Phellodendri chinensis by multivariate analysis approach

Background: As herbal medicines have an important position in health care systems worldwide, their current assessment, and quality control are a major bottleneck. Cortex Phellodendri chinensis (CPC) and Cortex Phellodendri amurensis (CPA) are widely used in China, however, how to identify species of CPA and CPC has become urgent. Materials and Methods: In this study, multivariate analysis approach was performed to the investigation of chemical discrimination of CPA and CPC. Results: Principal component analysis showed that two herbs could be separated clearly. The chemical markers such as berberine, palmatine, phellodendrine, magnoflorine, obacunone, and obaculactone were identified through the orthogonal partial least squared discriminant analysis, and were identified tentatively by the accurate mass of quadruple-time-of-flight mass spectrometry. A total of 29 components can be used as the chemical markers for discrimination of CPA and CPC. Of them, phellodenrine is significantly higher in CPC than that of CPA, whereas obacunone and obaculactone are significantly higher in CPA than that of CPC. Conclusion: The present study proves that multivariate analysis approach based chemical analysis greatly contributes to the investigation of CPA and CPC, and showed that the identified chemical markers as a whole should be used to discriminate the two herbal medicines, and simultaneously the results also provided chemical information for their quality assessment.

Metabolomic analysis of diet-induced type 2 diabetes using UPLC/MS integrated with pattern recognition approach.

Metabolomics represents an emerging discipline concerned with comprehensive assessment of small molecule endogenous metabolites in biological systems and provides a powerful approach insight into the mechanisms of diseases. Type 2 diabetes (T2D), called the burden of the 21st century, is growing with an epidemic rate. However, its precise molecular mechanism has not been comprehensively explored. In this study, we applied urinary metabolomics based on the UPLC/MS integrated with pattern recognition approaches to discover differentiating metabolites, to characterize and explore metabolic pathway disruption in an experimental model for high-fat-diet induced T2D. Six differentiating urinary metabolites were found in the negative mode, and two (2-(4-hydroxy-3-methoxy-phenyl) acetaldehyde sulfate, 2-phenylethanol glucuronide) of which were identified involving the key metabolic pathways linked to pentose and glucuronate interconversions, starch, sucrose metabolism and tyrosine metabolism. Our study provides new insight into pathophysiologic mechanisms and may enhance the understanding of T2D pathogenesis.

Metabolomics study of type 2 diabetes and therapeutic effects of Tianqijiangtang-capsule using ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry

Tianqijiangtang-capsule (TQC) is a famous Chinese prescription which has displayed bright prospects in the prevention and therapy of type 2 diabetes (T2D). However, its precise molecular mechanism has not been comprehensively explored. Metabolomics is the comprehensive assessment of low-molecular-weight endogenous metabolites in a biological system and may provide valuable insights into the mechanisms of diseases. In this study, urinary metabolomics based on ultra-performance liquid chromatography-electrospray ionization quadruple time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS) was used to evaluate the efficacy and mechanism of TQC. UPLC-ESI-Q-TOF-MS combined with pattern recognition approaches including principal components analysis and partial least squares-discriminant analysis were integrated to discover differentiating metabolites. Results indicate 12 ions in the negative mode as differentiating metabolites. Of note, TQC has potential pharmacological effect through regulating multiple perturbed pathways to the normal state. The changes in urine metabolites suggest that the disorders of starch and sucrose metabolism, pentose and glucuronate interconversions are related to T2D and the potential effect of TQC on all of these metabolic pathways. This work will provide better understanding of the mechanism of TQC in clinical use. It also demonstrated that the metabolomics method is a potentially powerful tool to study the essence of T2D and therapeutic effect mechanism of TQC.