UPLC-G2Si-HDMS untargeted metabolomics for identification of metabolic targets of Yin-Chen-Hao-Tang used as a therapeutic agent of dampness-heat jaundice syndrome

Lab-on-a-chip: an advanced technology for the modernization of traditional Chinese medicine

Benefiting from the complex system composed of various constituents, medicament portions, species, and places of origin, traditional Chinese medicine (TCM) possesses numerous customizable and adaptable efficacies in clinical practice guided by its theories. However, these unique features are also present challenges in areas such as quality control, screening active ingredients, studying cell and organ pharmacology, and characterizing the compatibility between different Chinese medicines. Drawing inspiration from the holistic concept, an integrated strategy and pattern more aligned with TCM research emerges, necessitating the integration of novel technology into TCM modernization. The microfluidic chip serves as a powerful platform for integrating technologies in chemistry, biology, and biophysics. Microfluidics has given rise to innovative patterns like lab-on-a-chip and organoids-on-a-chip, effectively challenging the conventional research paradigms of TCM. This review provides a systematic summary of the nature and advanced utilization of microfluidic chips in TCM, focusing on quality control, active ingredient screening/separation, pharmaceutical analysis, and pharmacological/toxicological assays. Drawing on these remarkable references, the challenges, opportunities, and future trends of microfluidic chips in TCM are also comprehensively discussed, providing valuable insights into the development of TCM.

Chinmedomics: a potent tool for the evaluation of traditional Chinese medicine efficacy and identification of its active components

As an important part of medical science, Traditional Chinese Medicine (TCM) attracts much public attention due to its multi-target and multi-pathway characteristics in treating diseases. However, the limitations of traditional research methods pose a dilemma for the evaluation of clinical efficacy, the discovery of active ingredients and the elucidation of the mechanism of action. Therefore, innovative approaches that are in line with the characteristics of TCM theory and clinical practice are urgently needed. Chinmendomics, a newly emerging strategy for evaluating the efficacy of TCM, is proposed. This strategy combines systems biology, serum pharmacochemistry of TCM and bioinformatics to evaluate the efficacy of TCM with a holistic view by accurately identifying syndrome biomarkers and monitoring their complex metabolic processes intervened by TCM, and finding the agents associated with the metabolic course of pharmacodynamic biomarkers by constructing a bioinformatics-based correlation network model to further reveal the interaction between agents and pharmacodynamic targets. In this article, we review the recent progress of Chinmedomics to promote its application in the modernisation and internationalisation of TCM.

Quality Markers’ Discovery and Quality Evaluation of Jigucao Capsule Using UPLC-MS/MS Method

Jigucao capsules (JGCC) have the effects of soothing the liver and gallbladder and clearing heat and detoxification. It is a good medicine for treating acute and chronic hepatitis cholecystitis with damp heat of the liver and gallbladder. However, the existing quality standard of JGCC does not have content determination items, which is not conducive to quality control. In this study, serum pharmacochemistry technology and UNIFI data processing software were used to identify the blood prototype components and metabolites under the condition of the obvious drug effects of JGCC, and the referenced literature reports and the results from in vitro analysis of JGCC in the early stage revealed a total of 43 prototype blood components and 33 metabolites in JGCC. Quality markers (Q-markers) were discovered, such as abrine, trigonelline, hypaphorine and isoschaftoside. In addition, ultra-high-performance liquid chromatography–triple quadrupole mass spectrometry (UPLC-QQQ-MS) was used to determine the active ingredients in JGCC. The components of quantitative analysis have good correlation in the linear range with R2 ≥ 0.9993. The recovery rate is 93.15%~108.92% and the relative standard deviation (RSD) is less than 9.48%. The established UPLC-MS/MS quantitative analysis method has high sensitivity and accuracy, and can be used for the quality evaluation of JGCC.

Revealing the pharmacological effect and mechanism of darutoside on gouty arthritis by liquid chromatography/mass spectrometry and metabolomics

Darutoside is a diterpenoids compound with significant anti-inflammatory activity, however the pharmacological action and mechanism are still unclear. Metabolomics strategy was used to uncovering the pharmacological action and effective mechanism of darutoside against acute gouty arthritis rats. Liquid chromatography coupled with mass spectrometry technique was performed to explore the serum metabolites and potential pathways. We found that darutoside can up-regulate the level of glutamate, alanine, chenodeoxycholic acid, 1-methyladenosine, aspartic acid, citric acid, and down-regulate the level of valine, isoleucine, glutamine, alanyl-threonine, pyruvic acid, gamma-aminobutyric acid, uric acid. Metabolic pathway analysis showed that the therapeutic effect of darutoside was involved in amino acid metabolism, sugar metabolism, fatty acid metabolism, energy metabolism, purine metabolism and butanoate metabolism. It indicated that darutoside protect against acute gouty arthritis by regulating the expression of the key protein targets. It revealed that the mechanism of darutoside on acute gouty arthritis, which may be leading to the changes of serum metabolites, metabolic pathways and key protein targets to improve immune system response, inhibit oxidative stress and inflammatory response. It provides a novel method for molecular mechanisms of natural product in the disease treatment.

Targets and Effective Constituents of ZhiziBaipi Decoction for Treating Damp-Heat Jaundice Syndrome Based on Chinmedomics Coupled with UPLC-MS/MS

Background: Damp-heat jaundice syndrome (DHJS) is a diagnostic model of traditional Chinese medicine (TCM) that refers to jaundice caused by damp-heat pathogen invasion. DHJS is the most common clinical manifestation of TCM, with yellow skin, yellow eyes and anorexia. ZhiziBaipi Decoction (ZBD) is a classic TCM formula that is effective at treating DHJS and various liver diseases. However, the effective components of ZBD in the context of DHJS and the underlying mechanism are unclear.

Purpose: This study of ZBD using the DHJS rat model aimed to elucidate the pathobiology of DHJS and the metabolic targets of therapeutic ZBD, construct the network relationship between the components of ZBD and endogenous biomarkers, and clarify the underlying mechanism of ZBD in preventing and treating DHJS.

Methods: Using chinmedomics as the core strategy, an animal model was generated, and the therapeutic effect of ZBD was evaluated based on behavioral, histopathological and biochemical indicators. Metabonomics tools were used to identify biomarkers of DHJS, TCM-based serum pharmacochemistry was used to analyze the effective constituents of ZBD, and chinmedomics technology was used to identify ZBD components highly related to DHJS biomarkers.

Results: A total of 42 biomarkers were preliminarily identified, and ZBD significantly affected the levels of 29 of these biomarkers. A total of 59 compounds in ZBD were characterized in vivo. According to chinmedomics analysis, the highly correlated components found in blood were isoformononetin, 3-O-feruloylquinic acid, glycyrrhizic acid, oxyberberine, obaculactone and five metabolites.

Conclusions: Chinmedomics combined with UPLC-MS/MS was used to study the targets and effective constituents of ZBD for the treatment of DHJS.

Metabolomics Analysis Coupled With UPLC/MS on Therapeutic Effect of Jigucao Capsule Against Dampness-Heat Jaundice Syndrome

Dampness-heat Jaundice Syndrome (DHJS) is a complex Chinese medicine syndrome, while Jigucao capsule (JGCC) is an effective compound preparation of Chinese medicine for the treatment of DHJS about liver and gallbladder, but its mechanism is not clear yet. The purpose of this study is to clarify the pathogenesis of DHJS and the treatment mechanism of JGCC. We used ultra-high performance liquid chromatography/mass spectrometry (UPLC/MS) combined with pattern recognition, accompanied the advanced software and online database for the urine metabolomics of rats. The potential biomarkers disturbing metabolism were identified and the metabolic pathway was analyzed. We investigated the callback of biomarkers after treatment with JGCC. Finally, A total of 25 potential urine biomarkers were identified, including Arachidonic acid, Phenylpyruvic acid, L-Urobilin and so on, and 14 related metabolic pathways were disturbed. After treatment with JGCC, the clinical biochemical indexes and histopathological were significantly improved, and the disturbed biomarkers were also obviously adjusted. It is proved that JGCC has remarkable effect on the treatment of DHJS.

A Hypothesis From Metabolomics Analysis of Diabetic Retinopathy: Arginine-Creatine Metabolic Pathway May Be a New Treatment Strategy for Diabetic Retinopathy

Diabetic retinopathy is one of the serious complications of diabetes, which the leading causes of blindness worldwide, and its irreversibility renders the existing treatment methods unsatisfactory. Early detection and timely intervention can effectively reduce the damage caused by diabetic retinopathy. Metabolomics is a branch of systems biology and a powerful tool for studying pathophysiological processes, which can help identify the characteristic metabolic changes marking the progression of diabetic retinopathy, discover potential biomarkers to inform clinical diagnosis and treatment. This review provides an update on the known metabolomics biomarkers of diabetic retinopathy. Through comprehensive analysis of biomarkers, we found that the arginine biosynthesis is closely related to diabetic retinopathy. Meanwhile, creatine, a metabolite with arginine as a precursor, has attracted our attention due to its important correlation with diabetic retinopathy. We discuss the possibility of the arginine-creatine metabolic pathway as a therapeutic strategy for diabetic retinopathy.

A new method providing complementary explanation of the blood-enriching function and mechanism of unprocessed Angelica sinensis and its four kinds of processed products based on tissue-integrated metabolomics and confirmatory analysis

Angelica sinensis (AS) is a common Traditional Chinese Medicine used for tonifying blood in China. Unprocessed AS and its four kinds of processed products (ASs) are used to treat blood deficiency syndrome in the country. The different blood-tonifying mechanisms of ASs remain unclear. In this work, a novel method integrating metabolomics and hematological and biochemical parameters was established to provide a complementary explanation of blood supplementation mechanism of ASs. Our results revealed that different ASs exhibited various blood supplementation effect, and that AS parched with alcohol demonstrated the best blood supplementation effect. Eight metabolites from liver tissue and 12 metabolites from spleen tissue were considered to be potential biomarkers. These biomarkers were involved in four metabolic pathways. Correlation analysis results showed that l-aspartic acid and l-alanine (spleen tissue), linoleic acid, and l-cystathionine (liver tissue) exhibited a high positive or negative correlation with the aforesaid biochemical indicators. The blood-supplementation effect mechanism of ASs were related to four metabolic pathways. l-Aspartic acid and l-alanine (spleen tissue), linoleic acid, and l-cystathionine (liver tissue) were the four key metabolites associated with the blood supplementation effect of ASs. This study gives a complementary explanation of the blood supplementation effect and mechanism of action of ASs.

Andrographolide Against Lung Cancer-New Pharmacological Insights Based on High-Throughput Metabolomics Analysis Combined with Network Pharmacology

Andrographolide (Andro) has known to treat various illnesses such as colds, diarrhea, fever and infectious diseases. However, the effect mechanism of Andro is still unclear. Therefore, we used high-throughput metabolomics analysis to discover biomarkers, metabolic profiles and pathways to reveal the pharmacological action and effective mechanism of Andro against lung cancer. The metabolic effects of Andro on lung cancer animal was explored by ultra-performance liquid chromatography-triple-time of flight/mass spectrometry (UPLC-TOF/MS) analysis. Our results showed that Andro exhibited significant protective effects against lung cancer. Compared with control group, a total of 25 metabolites biomarkers was identified in urine of model animals, which 18 of them were regulated toward the normal direction after Andro treatment, and network pharmacology analysis showed that they were related with 570 proteins. Biological pathways analysis showed that the 11 metabolism pathways were regulated by Andro treatment in lung cancer mouse, and amino acid metabolism and arachidonic acid metabolism have great potential as target pathways for Andro against lung cancer. It revealed that high-throughput metabolomics combined with network pharmacology analysis provides deeply insight into the therapeutic mechanisms of natural product for promoting medicine development and disease treatment.

Functional metabolomics innovates therapeutic discovery of traditional Chinese medicine derived functional compounds

Traditional Chinese medicines (TCMs) produce chemically diverse functional compounds that are importantly chemical resource for facilitating new drug discovery and development against a diversity of diseases. However, modern exploration of TCM derived functional compounds is significantly hindered by the inefficient elucidation of pharmacological functions over past decades, because conventional research methods are incapable of efficiently elucidating therapeutic potential of TCM conferred by multiple functional compounds. Functional metabolomics has the priority-capacity to characterize systems therapeutic actions of TCM by precisely capturing molecular interactions between disease response metabolite biomarkers (DRMB) and functional compounds (secondary metabolites), which underline pharmacological efficiency and associated therapeutic mechanisms. In this critical review, we innovatively summarize systems therapeutic feature of TCM derived functional compounds from a functional-metabolism perspective, then systems metabolic targets (SMT) identified by functional metabolomics method are strategically proposed to better understanding of therapeutic discovery of TCM derived functional compounds. In addition, we propose the perspective strategy as Spatial Temporal Operative Real Metabolomics (STORM) to considerably improve analytical capacity of functional metabolomics method by selectively incorporating the cutting edge technologies of mass spectrometry imaging, isotope-metabolic fluxomics, synthetic and biosynthetic chemistry, which could considerably enhance the precision and resolution of elucidating pharmacological efficiency and associated therapeutic mechanisms of TCM derived functional compounds. Collectively, such critical review is expected to provide novel perspective-strategy that could significantly improve modern exploration and exploitation of TCM derived functional compounds that further promote new drug discovery and development against the complex diseases.

Chinmedomics, a new strategy for evaluating the therapeutic efficacy of herbal medicines

Herbal medicines have accumulated valuable clinical experience in thousands of years of applications in traditional Chinese medicine (TCM) or ethnomedicine. The unique multi-target efficacy on complex diseases made herbal medicines gained a global popularity in recent years. However, the characteristic of multi-component acting on multi-target poses a dilemma for the evaluation of therapeutic efficacy of herbal medicines. Advances in metabolomics enable efficient identification of the various changes in biological systems exposed to different treatments or conditions. The use of serum pharmacochemistry of TCM has significant implications for tackling the major issue in herbal medicines development-pharmacodynamic material basis. Chinmedomics integrates metabolomics and serum pharmacochemistry of TCM to investigate the pharmacodynamic material basis and effective mechanisms of herbal medicines on the basis of TCM syndromes and holds the promise of explaining therapeutic efficacy of herbal medicines in scientific language. In this review, the historical development of chinmedomics from concept formation to successful applications was discussed. We also took the systematic research of Yin Chen Hao Tang (YCHT) as an example to show the research strategy of chinmedomics.

Untargeted metabolomics analysis on Cicer arietinium L.-Induced Amelioration in T2D rats by UPLC-Q-TOF-MS/MS

ETHNOPHARMACOLOGICAL RELEVANCE

Cicer arietinium L., which belongs to Cicer genus, was not only a kind of traditional Chinese medicines (TCM) recorded in Pharmacopoeia of the People's Republic of China (version 2015), but also a kind of Uighur antidiabetic medicines. It has been used as an adjuvant drug or functional food for thousand years in Xinjiang province, China. However, the mechanisms of C. arietinium treatment in T2D have not been fully understood especially on the perspective of metabolomics.

AIM OF THE STUDY

To clarify the potential mechanisms of C. arietinium treatment in T2D from the perspective of metabolomics since T2D is indeed a kind of metabolic syndromes.

MATERIALS AND METHODS

T2D rat model was built by HFD for 4 weeks, combining with STZ administration. T2D rats were administrated C. arietinium extraction or metformin (positive control) for 4 weeks. UPLC-Q-TOF-MS was applied to screen and identify differential metabolites among groups.

RESULTS

After 4 weeks of treatments, IR and inflammation were greatly ameliorated in C. arietinium group. And the therapeutic efficiency of C. arietinium treatment was comparable to metformin treatment. Differential metabolites related to C. arietinium treatment, including acylcarnitines, amino acid related metabolites and organic acids, were further used to indicate relevant pathways in T2D rats, including glyoxylate and dicarboxylate metabolism, tricarboxylic acid cycle, vitamin B6 metabolism and energy metabolism.

CONCLUSIONS

In summary, C. arietinium treatment could effectively alleviate diabetic symptoms and regulate metabolic disorders in T2D rats.

Metabolomics research on the hepatoprotective effect of cultured bear bile powder in α-naphthylisothiocyanate-induced cholestatic mice

Natural bear bile powder (NBBP) is a famous traditional medicine and has been widely used in clinic. However, access to the sources of bear bile is restricted; hence, it is essential to discover new substitutes for NBBP. Cultured bear bile powder (CBBP) is transformed from chicken bile and contains main ingredients as to NBBP. In the present study, the effect and potential mechanism of action of CBBP on cholestatic liver injury in-naphthylisothiocyanate (ANIT)-induced mouse model was explored using metabolomics. CBBP treatment ameliorated impaired hepatic dysfunction and tissue damage that induced by ANIT. Metabolomics showed there were 28 different metabolites induced by ANIT as compared with control mice, and 18 of which was reversed by CBBP. Pathway analysis revealed that those 18 metabolites are mainly involved in bile acid (BA) biosynthesis and D-glutamine and D-glutamate metabolism. Further LC-MS/MS analysis showed that CBBP and NBBP both reduced serum and liver levels of BAs, but increased their biliary levels. Additionally, CBBP and NBBP upregulated expression of BA efflux transporters, Mrp2, Mrp3, and Mrp4, and metabolic enzymes, Cyp2b10 and Ugt1a1 of liver tissue of cholestatic mice, increased the BA excretion and metabolism. Moreover, CBBP and NBBP treatment upregulated GCLc/GCLm expression, and restored glutathione metabolism. In conclusion, the protective effects of CBBP against cholestatic liver injury were similar to those of NBBP. Mechanistically, both CBBP and NBBP reversed the disruption in homeostasis of BAs and glutathione, alleviating damage to hepatocytes.

Mechanism of Huang-lian-Jie-du decoction and its effective fraction in alleviating acute ulcerative colitis in mice: Regulating arachidonic acid metabolism and glycerophospholipid metabolism

ETHNOPHARMACOLOGICAL RELEVANCE

Huang-lian-Jie-du decoction (HLJDD) is a traditional Chinese medicine prescription for clearing away heat, purging fire and detoxifying, which can be used to treat sepsis, stroke, Alzheimer's disease and gastrointestinal diseases. Our previous studies have shown that HLJDD can effectively alleviate acute ulcerative colitis (UC) in mice, and its n-butanol fraction (HLJDD-NBA) is the effective fraction. The aim of this study is to further investigate the mechanism of HLJDD and HLJDD-NBA in relieving UC in mice from a holistic perspective.

METHODS

The acute UC model of BABL/c mice was induced by 3.5% (w/v) dextran sodium sulfate drinking water. At the same time of modeling, HLJDD and HLJDD-NBA were given orally for treatment respectively. During the experiment, the clinical symptoms of mice were recorded and the physiological and biochemical indexes of mice were detected after the experiment. In addition, the plasma metabolites of mice in each group were detected and analyzed by ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry and multivariate statistical analysis method. Then, the potential target metabolic pathway of drug intervention was screened through the enrichment analysis of differential metabolites. Finally, we use molecular simulation docking technology to further explore the molecular regulatory mechanism of HLJDD and HLJDD-NBA on potential target metabolic pathways.

RESULTS

HLJDD and HLJDD-NBA intervention can significantly reduce the disease activity index of UC mice, inhibit colon length shortening and pathological damage, and relieve the abnormal changes of physiological and biochemical parameters of UC mice. Moreover, HLJDD and HLJDD-NBA can significantly inhibit the metabolic dysfunction of UC mice by reversing the abnormal changes of 24 metabolites in UC mice, and the arachidonic acid metabolic pathway and glycerophospholipid metabolic pathway are the target metabolic pathways regulated by them. Further literature review and molecular simulation docking analysis showed that HLJDD and HLJDD-NBA may inhibit the disorder of arachidonic acid metabolism pathway and glycerophospholipid metabolism pathway by inhibiting COX-2 protein expression and PLA2, 5-LOX activity.

CONCLUSIONS

Our experiments revealed that HLJDD and HLJDD-NBA can alleviate UC of mice by regulating arachidonic acid metabolism and glycerophospholipid metabolism, which points out the direction for further research and development of HLJDD as a new anti-ulcer drug.

HPLC-DAD-Q-TOF/MS-Based Screening and Analysis of the Multiple Absorbed Bioactive Components in Rat Serum after Oral Administration of Xiexin Tang

Background:

Xiexin Tang (XXT) is a classic Traditional Chinese Medicine (TCM) formula that has been used in herbal clinics for more than 1800 years. Recently, many studies have investigated the pharmacological effects and chemical composition of XXT. However, there is little information about systematic studies on the material basis of its efficacy. In the present study, the serum pharmacochemistry technique and HPLC-DAD-Q-TOF/MS were performed to screen and analyze the multiple absorbed bioactive components and metabolites of orally dosed XXT in rat serum.

Methods:

Bio-samples and herbal extracts were analyzed and detected by HPLC-DAD-Q-TOF/MS. Upon comparison of the chromatograms of the single-constituent decoctions with that of the XXT formulation, the peak quantity and peak intensity of the formulated decoction showed some variation from those of the single-constituent decoctions.

Results:

Twenty-one serum-adsorbed constituents were identified after intragastric administration of herbal extracts, of which 8 originated from Rhei Radix et Rhizoma (RRR), 5 from Coptidis Rhizoma (CR), and 8 from Scutellariae Radix (SR). The results showed that the main adsorbed constituents in the serum were anthraquinones, anthrones, chromones, and butyrophenones, alkaloids, and flavonoids.

Conclusion:

The results demonstrate that an effective and reliable analytical method is set up for screening the bioactive components of Chinese herbal medicine, which provided a meaningful basis for further pharmacology and active mechanism research of XXT.

Analytical strategies for the discovery and validation of quality-markers of traditional Chinese medicine

BACKGROUND

Quality control of traditional Chinese medicine (TCM) is the basis of clinical efficacy. Due to the complexity of TCM, it is difficult to unify the quality control, and hinders the further implementation of the quality standardization of TCM. As a new concept, quality-marker (Q-marker) plays a powerful role in promoting the standardization of quality control system of TCM.

HYPOTHESIS/PURPOSE

The present review aims to provide reference and scientific basis for further development of Q-marker and assist standardization of quality control of TCM.

METHODS

Extensive search of various documents and electronic databases such as Pubmed, Royal Society of Chemistry, Science Direct, Springer, Web of Science, and Wiley, etc., were used to search scientific contributions. Other online academic libraries, e.g. Google Scholars, Scopus and national pharmacology literature were also been employed to learn more relevant information about Q-marker.

RESULTS

Q-markers play vital role in promoting the standardization of quality control of TCM. The factors that affect the quality of TCM, the advantages and disadvantages of the analytical techniques commonly used in Q-marker research were reviewed, as well as the systematic research strategies, which were verified by practices.

CONCLUSION

The proposal of Q-marker not only provided a new perspective to break through the bottleneck of current quality control, but also can be used in the evaluation of pharmacological efficiency, therapeutic discovery, toxicology, etc. In addition, the Q-marker analysis strategies summarized in this paper is helpful to standardize the quality control of TCM and promote the internationalization of TCM.

Functional metabolomics using UPLC-Q/TOF-MS combined with ingenuity pathway analysis as a promising strategy for evaluating the efficacy and discovering amino acid metabolism as a potential therapeutic mechanism-related target for geniposide against alcoholic liver disease

Metabolomics has been used as a strategy to evaluate the efficacy of and potential targets for natural products.

Chemical Discrimination of Astragalus mongholicus and Astragalus membranaceus Based on Metabolomics Using UHPLC-ESI-Q-TOF-MS/MS Approach

Astragalus mongholicus (MG) and Astragalus membranaceus (MJ), both generally known as Huangqi in China, are two perennial herbals widely used in variety diseases. However, there were still some differences in the chemical ingredients between MG and MJ. In this paper, metabolomics combined with the ultra-high performance liquid chromatography coupled with electrospray ionization/quadrupole time-of-flight mass spectrometry (UHPLC-ESI-Q-TOF-MS/MS) was employed to contrastively analyze the chemical constituents between MG and MJ. As a result, principal component analysis showed that MG and MJ were separated clearly. A total of 53 chemical markers were successfully identified for the discrimination of MG and MJ. Of them, the contents of 36 components including Astragaloside I~III, Astragaloside IV, Agroastragaloside I, etc. in MJ were significantly higher than those in MG. On the contrary, the contents of 17 other components including coumaric acid, formononetin, sophoricoside, etc. in MG were obviously higher than those in MJ. The results showed that the distinctive constituents in MG and MJ were remarkable, and MJ may own stronger pharmacological activities than MG. In a word, MG and MJ may be treated as two different herbs. This paper demonstrated that metabolomics was a vitally credible technology to rapidly screen the characteristic chemical composition of traditional Chinese medicine.

LC-MS-based metabolomics analysis of Berberine treatment in ulcerative colitis rats

Inflammatory bowel disease (IBD) is often accompanied by metabolic imbalance and Berberine can relieve the symptoms of IBD, but the mechanism is still unclear. To explore the relationship between IBD, metabolism and Berberine, dextran sulfate sodium-induced ulcerative colitis (UC) model was built and urine and feces samples were analyzed with ultra-performance liquid chromatography combined with quadrupole-time-of-flight mass spectrometry, followed by multivariate statistical analyses. Targeted metabolomics was applied to verify and supplement the result of amino acids tested by non-targeted metabolomics. The study found that Berberine could ameliorate UC and improve metabolic disorders. The level of 4 metabolites increased and 35 decreased in urine and these metabolites mainly belong to amino acid, glucide, organic acid and purine. Besides, Berberine could reduce the level of 5 metabolites and raise the level of 7 metabolites in feces, which mainly belong to amino acid and lipid. Additionally, these altered metabolites were mainly related to amino acids metabolism, purine metabolism, vitamin metabolism, lipid metabolism and citrate cycle pathways. Furthermore, microbiome metabolism may be regulated by Berberine in UC. In general, this study provides a useful approach for exploring the mechanism of Berberine in the treatment of UC from the perspective of metabolomics.

Novel applications of mass spectrometry-based metabolomics in herbal medicines and its active ingredients: Current evidence

Current evidence shows that herbal medicines could be beneficial for the treatment of various diseases. However, the complexities present in chemical compositions of herbal medicines are currently an obstacle for the progression of herbal medicines, which involve unclear bioactive compounds, mechanisms of action, undetermined targets for therapy, non-specific features for drug metabolism, etc. To overcome those issues, metabolomics can be a great to improve and understand herbal medicines from the small-molecule metabolism level. Metabolomics could solve scientific difficulties with herbal medicines from a metabolic perspective, and promote drug discovery and development. In recent years, mass spectrometry-based metabolomics was widely applied for the analysis of herbal constituents in vivo and in vitro. In this review, we highlight the value of mass spectrometry-based metabolomics and metabolism to address the complexity of herbal medicines in systems pharmacology, and to enhance their biomedical value in biomedicine, to shed light on the aid that mass spectrometry-based metabolomics can offer to the investigation of its active ingredients, especially, to link phytochemical analysis with the assessment of pharmacological effect and therapeutic potential. © 2019 Wiley Periodicals, Inc. Mass Spec Rev.

Exploration of the hepatoprotective chemical base of an orally administered herbal formulation (YCHT) in normal and CCl4-intoxicated liver injury rats. Part 1: Metabolic profiles from the liver-centric perspective

ETHNOPHARMACOLOGICAL RELEVANCE

Yin-Chen-Hao Tang (YCHT), derived from "Treatise on Febrile Diseases" in ancient China, has been a very popular hepatoprotective three-herb formula in China and Japan, although its chemical base remains unclear.

AIM OF THIS STUDY

As the first step in revealing the hepatoprotective chemical base of YCHT, we aimed to clarify the absorbed ingredients and associated metabolic pathways for orally dosed YCHT in both normal and liver injury rats from a liver-centric perspective.

MATERIALS AND METHODS

With the aid of 10 reference compounds, the absorbed ingredients and generated metabolites were systematically characterized by high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF) in the portal vein plasma (the plasma before hepatic disposition) - liver - systemic plasma (the plasma after hepatic disposition), following oral administration of YCHT in normal and CCl₄-induced liver injury rats.

RESULTS

A total of 38 compounds with six chemical structures, consisting of 10 prototypes and 28 metabolites generated through 9 biotransformations, were absolutely or tentatively identified, and 25 compounds were first reported on YCHT treatments. Among them, 8 compounds were absolutely confirmed by comparing with standard substances, and some had published hepatoprotective activities. Compared with the 35, 15, and 29 compounds identified in the portal vein plasma, liver, and systemic plasma of normal rats, respectively, the corresponding numbers of characterized compounds were 37, 13 and 29 in the liver injury rats.

CONCLUSIONS

Sulfation and glucuronidation were the predominant biotransformations, and intestinal metabolism, prior to hepatic metabolism, occurred for most compounds. CCl₄-induced liver injury caused only slight changes in the metabolic profiles of rats orally administered YCHT. These results provided the precondition for further quantitative analysis and pharmacodynamic screening of compounds in YCHT.

High-throughput metabolomics and ingenuity pathway approach reveals the pharmacological effect and targets of Ginsenoside Rg1 in Alzheimer's disease mice

Ginsenoside Rg1, a natural triterpenoid saponins compound isolated from the Panax species, has been found to possess neuroprotective properties in neurodegenerative diseases such as Alzheimer's disease (AD). However, its pharmacological mechanism on AD has not been studied. In this study, an ultra-performance liquid chromatography combined with quadrupole time of-flight mass spectrometry (UPLC-Q/TOF-MS) based non-targeted metabolomics strategy was performed to explore the mechanism of Ginsenoside Rg1 protecting against AD mice by characterizing metabolic biomarkers and regulation pathways changes. A total of nineteen potential metabolites in serum were discovered and identified to manifest the difference between wild-type mice and triple transgenic mice in control and model group, respectively. Fourteen potential metabolites involved in ten metabolic pathways such as linoleic acid metabolism, arachidonic acid metabolism, tryptophan metabolism and sphingolipid metabolism were affected by Rg1. From the ingenuity pathway analysis (IPA) platform, the relationship between gene, protein, metabolites alteration and protective activity of ginsenoside Rg1 in AD mice are deeply resolved, which refers to increased level of albumin, amino acid metabolism and molecular transport. In addition, quantitative analysis of key enzymes in the disturbed pathways by proteomics parallel reaction was employed to verify changed metabolic pathway under Ginsenoside Rg1. The UPLC-Q/TOF-MS based serum metabolomics method brings about new insights into the pharmacodynamic studies of Ginsenoside Rg1 on AD mice.

High-throughput metabolomics screen coupled with multivariate statistical analysis identifies therapeutic targets in alcoholic liver disease rats using liquid chromatography-mass spectrometry

Identification of metabolic alterations is useful for elucidating the pathophysiology and mass spectrometry-aided metabolomic, which provides small molecule metabolites to understand underlying mechanisms of complex diseases. In this work, we developed a novel liquid chromatography coupled with tandem mass spectrometry-based metabolomics screen coupled with multivariate statistical analysis workflow to obtaining the metabolite annotation, visualization and rapid characterization of small molecular metabolites, then revealed the altered metabolic pathway in a rat model of alcohol-induced liver damage rats as case study. The ions were detected in both positive and negative mode, and the key biomarkers were selected through multivariate statistical screening analysis. We employed the enhanced mass spectrometry coverage method to comprehensive analysis of the metabolite data. Importantly, we further find these small molecule metabolites were associated with multiple metabolic pathways. The elucidation of these altered metabolic pathways should help identify new and specific therapeutic targets. In addition, this metabolomics workflow coupled to LC-MS/MS has been successfully applied to the identification of small molecule metabolites in this complex disease. We strongly believe that metabolomics studies will benefit from incorporating liquid chromatography coupled with tandem mass spectrometry strategies.

A study of the microbial metabolomics analysis of subsurface wastewater infiltration system

Microbial action in SWIS is one of the main ways to remove contaminants. Studying the metabolic processes and pathways of microorganisms is helpful to reveal the mechanism of pollutant removal in the “black box” process of SWIS. In this study, based on metabolomics and UPLC-MS, partial least squares (PLS-DA), principal component analysis (PCA) pattern recognition and cluster analysis were used to classify the microbial samples. According to the model's variable importance factor (VIP value) being greater than 1.5, a total of 53 potential biomarkers were screened out. There was a significant correlation between the microbial metabolites and soil profile. Most microbial metabolites were concentrated in the H2 layer (subsurface layer of SWIS), while there were relatively few in the H4 and H6 layers (middle and lower layers of SWIS); organic acids and alcohol metabolites mainly existed in the anoxic environment (H4 layer); antibiotics, growth hormones and pigments and other small molecule metabolites mainly existed under anaerobic conditions (H6 layer). The results of RDA analysis indicated that environmental factors had an effect on the microbial metabolites. With the variation of different height profiles, the metabolites were significantly affected by ORP and NO₃⁻, which were negatively correlated. The above conclusions indicated that metabolomics is a reliable, accurate and effective method to quantitatively characterize the stability of SWIS.

Microbial action in SWIS is one of the main ways to remove contaminants.

Applications and potential mechanisms of herbal medicines for rheumatoid arthritis treatment: a systematic review

In this review, we systematically discuss the role of traditional Chinese medicine (TCM) in rheumatoid arthritis (RA) disease treatment. TCM classifies the subtypes of RA through its own theoretical method, which is beneficial for more accurate diagnosis and treatment with Chinese herbal medicines (CHMs) that are more suitable for different syndromes. TCM mainly uses a flexible combination of CHMs to play an important role in RA treatment. The main components of these extracts can be subdivided into alkaloids, flavonoids, triterpenes, saponins and other compounds. Using a platform of transgenic and induced arthritis models, we explore the potential mechanisms of TCM against RA with the help of omics analysis techniques and methods. These mechanisms are mainly CHM and its extracts can inhibit RA patients and experimental animal models, including synovitis, vascular proliferation and bone injury; this involves many biological signal exchange targets and pathways. In conclusion, the role of TCM in RA treatment mainly involves reducing the expression and secretion of pro-inflammatory factors, thus decreasing the degree of abnormal immune response.

In this review, we systematically discuss the role of traditional Chinese medicine (TCM) in rheumatoid arthritis (RA) disease treatment.

High-throughput metabolomics for discovering metabolic biomarkers from intestinal tumorigenesis in APC min/+ mice based on liquid chromatography/mass spectrometry

As a major public health concern, colon cancer is one of the most common cancer types, which is also the second cause of cancer death in developed countries and the third most common cancer in other parts of the world. It was reported that patients diagnosed at early stage have a chance to obtain 5-year survival rates at least compared to patients with late stage. Facing the multistep process in intestinal tumorigenesis, there is an urgent need to develop more effective early detection strategies for ameliorating the patient clinical outcome. Metabolomics open up a novel avenue of seeking valuable potential biomarkers for assessing disease severity and prognosticating course by dynamic snapshot of small molecule metabolites. The study aims to provide deeper insights into the discovery, identification and functional pathways analysis of differentially expressed metabolites in intestinal tumorigenesis in APC ^min/+ mice used by the serum metabolomics, and bring about useful information for further effective prevention and treatment of the disease. 17 marker metabolites and related metabolism pathway were identified using non-targeted metabolomics based on liquid chromatography/mass spectrometry (LC/MS) associated with multivariate statistical analysis. The ingenuity pathway analysis platform involved multiple-pathways was applied to metabolic network analysis for further understanding the relationship between functional metabolic pathways and disease.

Functional metabolomics discover pentose and glucuronate interconversion pathways as promising targets for Yang Huang syndrome treatment with Yinchenhao Tang

Yinchenhao Tang (YCHT), a classic traditional Chinese medicine (TCM) formulae, plays an important role in the treatment of Yang Huang syndrome (YHS). With the emergence of new biomarkers of YHS uncovered via metabonomics, the underlying functional mechanisms are still not clear. Functional metabolomics aims at converting biomarkers derived from metabonomics into disease mechanisms. Here, an integrated non-target metabolomics and IPA strategy were used to investigate the YCHT intervention on YHS. Our metabolomics study has shown that the potential protective effect of YCHT on YHS mice leads to significant changes in the metabolic profile by modulating the biomarkers and regulating the metabolic disorders. Twenty two differential metabolite biomarkers and fifteen involved metabolic pathways were correlated with the regulation of YCHT treatment on YHS. Functional metabolomics identified a core biomarker, d-glucuronic acid in pentose and glucuronate interconversion pathways, which was directly related to the target prediction of UDP-glucuronosyltransferase 1A1 and eventually leaded to a series of disturbances. In conclusion, this study shows that functional metabolomics can discover metabolic pathways as promising targets.

Yinchenhao Tang (YCHT), a classic traditional Chinese medicine (TCM) formulae, plays an important role in the treatment of Yang Huang syndrome (YHS).

High-throughput metabolomics used to identify potential therapeutic targets of Guizhi Fuling Wan against endometriosis of cold coagulation and blood stasis

Metabolomics is an emerging and robust discipline and involves the comprehensive evaluation of small molecule endogenous metabolites and enables the exploration of the pathogenesis of diseases. For example, endometriosis – a common disease which mostly occurs in women of childbearing age. A cure for endometriosis of cold coagulation and blood stasis (ECB) is highly sought after. This study was conducted to discover the potential biomarkers of ECB and the effective mechanism undertaken by Guizhi Fuling Wan (GFW) in treating ECB in rats. Urinary metabolomics were performed by using UPLC-Q-TOF-MS with pattern recognition methods to evaluate the changes in metabolic profiles and to identify biomarkers for elucidating the mechanism of the treatment of ECB with GFW. The results showed that urinary metabolism in the two groups were distinctly separated on the 28^th day, and a total of 20 differential biomarkers (16 in the positive mode, 4 in the negative mode) were confirmed involving several key metabolic pathways which included phenylalanine, tyrosine and tryptophan biosynthesis, valine, leucine and isoleucine biosynthesis, glyoxylate and dicarboxylate metabolism, tyrosine metabolism and the citrate cycle. Following the oral administration of GFW, certain pathways were affected; these included the following: phenylalanine, tyrosine and tryptophan biosynthesis, valine, leucine and isoleucine biosynthesis, glyoxylate and dicarboxylate metabolism, tyrosine metabolism, citrate cycle, steroid hormone biosynthesis, tryptophan metabolism, phenylalanine metabolism, primary bile acid biosynthesis, and aminoacyl-tRNA biosynthesis. This study also demonstrated that the administration of GFW affected the levels of urine endogenous metabolites, thereby laying a foundation for further study of the pharmacodynamical mechanism of GFW.

Metabolomics is an emerging and robust discipline and involves the comprehensive evaluation of small molecule endogenous metabolites and enables the exploration of the pathogenesis of diseases.