Chemicalome and Metabolome Matching Approach to Elucidating Biological Metabolic Networks of Complex Mixtures

An integrating strategy for systematic profiling of Chinese patent drug's chemicalome and associated metabolome: Huanghou antidiarrhea dropping pills as a case study

Huanghou antidiarrhea dropping pills (HADP) is an efficient Chinese patent drug that is clinically used to treat diarrhea. However, its functional materials remain unclear due to the characteristics of traditional Chinese medicine, which is a multi-component and multi-target complex system. In this study, we investigated the intrinsic chemical components and combined with in vivo metabolism to reveal the functional material basis of HADP. Spectral behavior (accurate molecular weight and secondary fragmentation) and chromatographic behavior (retention time) were key criterions that throughout the whole research of components identification, prototypes screening, and tissue distribution. Mass defect filter (MDF), characteristic product ion filter (PIF), and neutral loss filter (NLF) were other three criterions for metabolites searching. Consequently, a total of 102 components in HADP, including alkaloids, lignans, lactones, gingerols, and alkaloid complexes were identified or tentatively characterized. About 39 metabolites that related to 37 prototypes were calculated and matched in bio-samples. Among them, 14 prototypes and 18 metabolites were detected distribution in colon, liver, heart, spleen, lung or kidney. This study provides a systematic investigation into the metabolism of HADP and offers effective analytical strategies for the characterization of compounds and metabolites in Chinese patent drugs.

Pseudotargeted metabolomics-based random forest model for tracking plant species from herbal products

BACKGROUND

The "one-to-multiple" phenomenon is prevalent in medicinal herbs. Accurate species identification is critical to ensure the safety and efficacy of herbal products but is extremely challenging due to their complex matrices and diverse compositions.

PURPOSE

This study aimed to identify the determinable chemicalome of herbs and develop a reasonable strategy to track their relevant species from herbal products.

METHODS

Take Astragali Radix-the typical "one to multiple" herb, as a case. An in-house database-driven identification of the potentially bioactive chemicalome (saponins and flavonoids) in AR was performed. Furthermore, a pseudotargeted metabolomics method was first developed and validated to obtain high-quality semi-quantitative data. Then based on the data matrix, the random forest algorithm was trained to predict Astragali Radix species from commercial products.

RESULTS

The pseudotargeted metabolomics method was first developed and validated to obtain high-quality semi-quantitative data (including 56 saponins and 49 flavonoids) from 26 batches of AR. Then the random forest algorithm was well-trained by importing the valid data matrix and showed high performance in predicting Astragalus species from ten commercial products.

CONCLUSION

This strategy could learn species-special combination features for accurate herbal species tracing and could be expected to promote the traceability of herbal materials in herbal products, contributing to manufacturing standardization.

A comprehensive perspective on the disposition, metabolism, and pharmacokinetics of representative multi-components of Dengzhan Shengmai in rats with chronic cerebral hypoperfusion after oral administration

ETHNOPHARMACOLOGICAL RELEVANCE

Dengzhan Shengmai capsule (DZSM), an evidence-based Chinese medicine comprising Erigeron breviscapus (Vaniot) Hand. -Mazz., Panax ginseng C.A.Mey., Ophiopogon japonicus (Thunb.) Ker Gawl., and Schisandra chinensis (Turcz.) Baill., exhibits an excellent efficacy in treating cardio- and cerebrovascular diseases. It contains caffeoyl compounds, flavonoids, saponins, and lignans as primary active components. However, so far, the characteristics of disposition, metabolism, and pharmacokinetics of its active components remain mostly unclear.

AIM OF STUDY

To elucidate disposition, metabolism, and pharmacokinetics of representative components of DZSM in rats with chronic cerebral hypoperfusion (CCH) by integrating ex vivo and in situ approaches.

MATERIALS AND METHODS

Exposure and distribution of absorbed prototypes and their metabolites were comprehensively investigated using sensitive LC-MS/MS and high-resolution LC-Q-TOF/MS. Pharmacokinetics of representative 16 components (12 prototypes and 4 metabolites) with different chemical categories, relatively high in vivo levels, wide tissue distribution, and reported neuroprotective activities were profiled. The ex vivo everted gut sac and in situ linked-rat models were adopted.

RESULTS

Representative 12 prototypes including 6 caffeoyl compounds (CA, 5-CQA, 3-CQA, 4-CQA, 1,3-CQA, and 3,4-CQA), 1 flavonoid (Scu), 2 saponins (Rd and Rg2), and 3 lignans (SchA, SchB, and SolA) presented characteristic absorption, disposition, and pharmacokinetics profiles in CCH rats. The caffeoyl compounds and flavonoid were well absorbed, exhibited wide distribution, and underwent extensive intestinal metabolism, such as methylation, isomerization, and sulfoconjugation. For CA, 5-CQA, Scu, and 4 related metabolites, the enterohepatic circulation was observed and resulted in bimodal or multimodal pharmacokinetic profiles. Saponins showed relatively low systemic exposure and limited distribution. The PPD-type ginsenoside Rd exhibited longer elimination half-life and systemic circulation than the PPT-type ginsenoside Rg2. No enterohepatic circulation was observed regarding saponins, suggesting that the multimodal pharmacokinetic profile of Rd could be due to its multi-site intestinal absorption. Lignans presented a low in vivo exposure and broad distribution. They were mainly transformed into hydroxylated metabolites. Corresponding to its bimodal pharmacokinetic profile, one metabolite of lignans completed the enterohepatic cycle.

CONCLUSION

The disposition, metabolism, and pharmacokinetic profiles of representative active components of DZSM were comprehensively characterized and elucidated.

A strategy to explore the quality markers of Ziziphi Spinosae semen by combining metabolic in vivo study with network pharmacology

Ziziphi Spinosae semen (ZSS), the dried and ripe seed of Ziziphus jujube Mill. var. spinosa (Bunge) Hu ex H. F. Chou, has been used as a sedative in China and other Asian countries for over a millennium. However, its quality markers (Q-markers) are not completely clear. In this study, Q-markers selected by a metabolic in vivo study combined with network pharmacology are proposed for ZSS quality control. An UHPLC (ultra-high-performance liquid chromatography)-Q-Orbitrap-MS method was developed to identify or tentatively assign 48 components including 21 flavonoid C-glycosides, 2 flavonoid O-glycosides, 11 dammarane triterpenoid saponins, 13 alkaloids, and 1 other, using a diagnostic product ion filtering strategy in ZSS. Subsequently, 147 metabolites detected from serum, urine, bile, and feces samples of para-chlorophenylalanine-induced insomnia rats treated with ZSS aqueous extracts could be linked to their respective parent compounds, including 27 prototypes. Meanwhile, three metabolic networks of flavonoids, saponins, and alkaloids are preliminarily established and potential metabolic pathways are investigated under the insomnia condition. Finally, 12 key bioactive components against insomnia including magnoflorine, caaverine, coclaurine, norisocorydine, genkwanin, juzinrine, apigenin, jujubogenin, kaempferol-3-O-rutinoside, jujuboside A, jujuboside B, and spinosin with the highest degree values in component-target-pathways network were selected as Q-markers for the quality control of ZSS.

Adjuvant effects of Chinese medicinal tonics on gastric, liver, and colorectal cancers—OMICs-based contributions to understanding their mechanism of action

Gastric, liver, and colorectal cancers belong to gastrointestinal (GI) cancers, one of the most threatening diseases in the world. The tonics class in Chinese medicines plays a critical role in antigastrointestinal cancer as adjuvants. However, it is a challenge to study the effects and underlying mechanisms of tonics due to their multiple components and multiple targets; OMICs were introduced to facilitate the investigation of the complex mixture of tonics. In this review, the online databases PubMed, ProQuest, Web of Knowledge, China National Knowledge Infrastructure (CNKI), Chongqing VIP, and Wanfang were retrieved from 1 January 2011 to 31 May 2022, in an aim to summarize and discuss the research progress of the effects and, especially, the underlying mechanisms of tonics for antigastrointestinal cancers via OMICs. The results showed that through the combination of OMICs and other technologies, tonics have been used for gastrointestinal cancer by targeting cancer hallmarks, enhancing body resistance to carcinogenesis, enhancing therapeutic effects, and/or decreasing side effects. In conclusion, tonics may play a promising role in gastric, liver, and colorectal cancers as adjuvants and can be well investigated via the combination of OMICs and other technologies, which deserves further study.

Time-Series-Dependent Global Data Filtering Strategy for Mining and Profiling of Xenobiotic Metabolites in a Dynamic Complex Matrix: Application to Biotransformation of Flavonoids in the Extract of Ginkgo biloba by Gut Microbiota

Efficient characterization of xenobiotic metabolites and their dynamics in a changing complex matrix remains difficult. Herein, we proposed a time-series-dependent global data filtering strategy for the rapid and comprehensive characterization of xenobiotic metabolites and their dynamic variation based on metabolome data. A set of data preprocessing methods was used to screen potential xenobiotic metabolites, considering the differences between the treated and control groups and the fluctuations over time. To further identify metabolites of the target, an in-house accurate mass database was constructed by potential metabolic pathways and applied. Taking the extract of Ginkgo biloba (EGB) co-incubated with gut microbiota as an example, 107 compounds were identified as flavonoid-derived metabolites (including 67 original from EGB and 40 new) from 7468 ions. Their temporal metabolic profiles and regularities were also investigated. This study provided a systematic and feasible method to elucidate and profile xenobiotic metabolism.

Chemicalome and metabolome profiling of Chai-Gui Decoction using an integrated strategy based on UHPLC-Q-TOF-MS/MS analysis

Traditional Chinese medicine prescriptions are widely believed to exert therapeutic benefits via a multiple-component and multiple-target mode. The systemic profiling of their in vitro chemicalome and in vivo metabolome is of great importance for further understanding their clinical value. Herein, an integrated strategy using ultra-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry was proposed to profile the chemicalome and metabolome of Chai-Gui Decoction. Particularly, an approach combined mass defect filter, characteristic product ion filter, and neutral loss filter was adopted to identify metabolites in plasma, urine, bile, and feces by MetabolitePilot. Consequently, a total of 174 constituents were identified or tentatively characterized and 70 metabolites that related to 21 representative structural components were matched in rat biofluids. Among them, 19 prototypes and 7 metabolites that contributed to flavonoids, monoterpenes, and phenylpropanoids were detected distribution in brain, heart, kidney, liver, lung or spleen. This study provided a generally applicable approach to comprehensive investigation on chemicalome and metabolome of traditional Chinese medicine prescriptions, and offered reasonable guidelines for further screening of quality control indicators of Chai-Gui Decoction.

Paving New Roads Towards Biodiversity-Based Drug Development in Brazil: Lessons from the Past and Future Perspectives

Although Brazil gathers two fundamental features to occupy a leading position on the development of biodiversity-based medicines, the largest flora on earth and a broad tradition on the use of medicinal plants, the number of products derived from the national genetic heritage is so far modest, either as single drugs or as herbal medicines. This article highlights some aspects that may have contributed to the low rates of success and proposes new insights for innovation. We initially approach the use of medicinal plants in Brazil, molded by its ethnic diversity, and the development of the local pharmaceutical industry. A discussion of some governmental initiatives to support plant-based drug development is then presented. Employing the economic concept of “middle-income trap,” we further propose that Brazil is stuck in a “middle-level science trap,” since the increase in the number of scientific publications that launched the country to an intermediate publishing position has not been translated into drug development. Two new approaches to escape from this trap are presented, which may result in innovative drug development. The first is based on the exploitation of the antifragility properties of herbal products aiming to investigate non-canonical pharmacodynamics mechanisms of action, aligned with the concepts of system biology. The second is the manufacture of herbal products based on the circular economy principles, including the use of byproducts for the development of new therapeutical agents. The adoption of these strategies may result in innovative phytomedicines, with global competitiveness.

An UPLC - Q - Orbitrap method for pharmacokinetics and tissue distribution of four triterpenoids in rats after oral administration of Poria cocos ethanol extracts

Poria cocos (Schw.) Wolf, is a fungus that is widely used as medicine and dietary supplement in China. But its action mechanism is still not very clear. In this paper, a rapid, specific and sensitive high performace liquid chromatography coupled with hybrid quadrupole - orbitrap mass sepctrometry (UPLC - Q - Orbitrap MS) method has been developed and validated to simultaneously determine of four triterpenoids including Dehydrotumulosic acid (DTA), Dehydropachymic acid (DPA), Pachymic acid (PA), Dehydrotrametenolic acid (DMA) from Poria cocos in rat plasma and tissues. The analyte was extracted from rat plasma and tissue homogenates by protein precipitation with acetonitrile using glibenclamide as the internal standard (IS). Chromatographic separation was carried out on ACQUITY UPLC BEH - C₁₈ column (2.1 mm × 50 mm, 1.7 μm) with a mobile phase composed of acetonitrile - water (containing 1.0 mmol/L ammonium acetate) using gradient elution at a flow rate of 0.2 mL/min. Electrospray ionization (ESI ^-) under negative ion mode was used, and its quantization was performed with multiple reaction monitoring (MRM) mode. The method was fully validated and successfully applied to pharmacokinetics and tissue distribution study in rats after oral administration of ethanol extracts of Poria cocos. Compared with that of plasma exporsure, triterpenoids could be detected in various tissues with a relatively high degree of tissue distribution. After oral administration, the concentration orders in seven different tissues were ranked as DTA > PA > DPA > DMA in intestine and stomach, wheras DTA > DMA > PA > DPA in heart, liver, spleen, lung and kidney tissues, which is speculated that DPA, PA may be converted into DMA in vivo. In conclusion, this results may provide a material basis for study of the pharmacological actions of triterpenoids in Poria cocos.

Classification-based strategies to simplify complex traditional Chinese medicine (TCM) researches through liquid chromatography-mass spectrometry in the last decade (2011-2020): Theory, technical route and difficulty

The difficulty of traditional Chinese medicine (TCM) researches lies in the complexity of components, metabolites, and bioactivities. For a long time, there has been a lack of connections among the three parts, which is not conducive to the systematic elucidation of TCM effectiveness. To overcome this problem, a classification-based methodology for simplifying TCM researches was refined from literature in the past 10 years (2011-2020). The theoretical basis of this methodology is set theory, and its core concept is classification. Its starting point is that "although TCM may contain hundreds of compounds, the vast majority of these compounds are structurally similar". The methodology is composed by research strategies for components, metabolites and bioactivities of TCM, which are the three main parts of the review. Technical route, key steps and difficulty are introduced in each part. Two perspectives are highlighted in this review: set theory is a theoretical basis for all strategies from a conceptual perspective, and liquid chromatography-mass spectrometry (LC-MS) is a common tool for all strategies from a technical perspective. The significance of these strategies is to simplify complex TCM researches, integrate isolated TCM researches, and build a bridge between traditional medicines and modern medicines. Potential research hotspots in the future, such as discovery of bioactive ingredients from TCM metabolites, are also discussed. The classification-based methodology is a summary of research experience in the past 10 years. We believe it will definitely provide support and reference for the following TCM researches.

A high-resolution MS/MS based strategy to improve xenobiotic metabolites analysis by metabolic pathway extension searching combined with parallel reaction monitoring: Flavonoid metabolism in wound site as a case

For the analysis of xenobiotic metabolism, metabolites are commonly qualified by high-resolution mass spectrometry such as orbitrap or time-of-flight mass spectrometers, and quantified by triple-quadrupole (QQQ) mass spectrometer based multiple reaction monitoring. While this workflow shows drawback in the difficulty for instrumental parameters transfer, and QQQ provides less specificity. In this work, we constructed a high-resolution MS/MS (HR-MS/MS) based strategy to improve the discovery and quantification of unknown xenobiotic metabolites by metabolic pathway extension (MPE) searching combined with parallel reaction monitoring (PRM). Taking the flavonoid metabolism in diabetes wound S9 incubates as a test case. Firstly, MPE approach was used to screen all potential metabolites. In this step, an m/z value library of all theoretic flavonoid metabolites were constructed based on predefined flavonoid structures through 21 common xenobiotic metabolic reactions, and this library was matched with all features extracted from raw data (MS1 scan) of flavonoid-S9 co-incubate, then the matched features were exported into target list for MS2 fragmentation for structure validation. Secondly, the metabolites were relatively quantified by PRM mode based on their characteristic product ions. As a result, 131 metabolites of 9 different kinds of flavonoids in the skin and muscle were identified. To our best knowledge, this is the first report on the metabolism of flavonoids in the skin or muscle tissue. The results also validated the proposed HR-MS/MS-based strategy provided high specificity throughout both discovery and quantitation process of unknown xenobiotic metabolites without need of instrumental parameter transfer.

Intestinal mucosal metabolites-guided detection of trace-level ginkgo biloba extract metabolome

The characterization of metabolome for poorly absorptive natural medicines is challenging. Previous identification strategy often relies on nontargeted scanning biological samples from animals administered with natural medicines in a data-dependent acquisition (DDA) mode by LC-MS/MS. Substances that displayed significant increases following drug administration are thus assigned as potential metabolites. The accurate m/z of precursors and the corresponding MS/MS fragment ions are used to match with herbal ingredients and to infer possible metabolic reactions. Nevertheless, the low concentration of these metabolites within complex biological matrices has often hampered the detection. Herein we developed a strategy termed intestinal mucosal metabolome-guided detection (IMMD) to tackle this challenge using ginkgo biloba (GBE) as an example. The rationale is that poorly absorptive natural products are usually concentrated and extensively metabolized by enterocytes before they enter the blood stream and distribute to other organs. Therefore, we firstly identified the metabolites from intestinal mucosa of GBE-treated rats, and then used the identified intestinal mucosal GBE metabolome as targeted repository for MRM analysis. The presences of these metabolites were subsequently examined in rat plasma, liver and brain. The resultant GBE metabolome showed significantly improved coverage with 39, 45 and 6 metabolites identified in plasma, liver and brain compared to 22, 16 and 0 metabolites from the corresponding regions via the DDA-based strategy. In addition, we integrated the previously reported nontargeted diagnostic ion network analysis to facilitate the characterization of GBE components, and a chemicalome-metabolome matching approach (CMMA) to assist the identity assignment of GBE metabolome with IMMD. Combinatorially, we establish a multi-faceted platform to streamline the workflow of metabolome characterization for herbal medicines of low bioavailability. The metabolome information is expected to shed light on the elucidation of metabolic pathways for natural products, and the underlying mechanisms of their biological efficacies.

Stepwise targeted matching strategy from in vitro to in vivo based on ultra-high performance liquid chromatography tandem mass spectrometry technology to quickly identify and screen pharmacodynamic constituents

The study of in vivo pharmacodynamic constituents (PCs) of traditional Chinese medicine (TCM) is important for providing new clues for TCM applications in clinical therapies in modern medicine. However, detecting and identifying PCs from complex biological samples remain a challenge. In this study, a practical and novel stepwise targeted matching and longitudinal analysis strategy from in vitro to in vivo was developed. This strategy combined with ultra-high performance liquid chromatography tandem mass spectrometry was applied to quickly discover PCs in TCM. This approach was developed based on a core perception that all drugs taken orally might be transformed progressively and orderly from the intestinal tract, liver, and blood to the target organ. Based on this core perception, stepwise targeted matching was orderly and efficiently accomplished by multiple screening processes that were based on a stepwise enriched in-house library. Ginseng (Panax ginseng) was set as the example of herbal medicine for validating the reliability and availability of this approach. By applying this novel strategy to the stepwise screening of metabolites, we successfully identified 113 metabolites, among which 59 compounds were defined as prototypes. Based on the in vivo metabolites, network pharmacology analysis was applied to screen the PCs of ginseng and clarified the action mechanism of ginseng for the treatment of Alzheimer's disease (AD). A total of 27 herbal constituents and 64 related targets shared commonly by compounds and AD were integrated via target network pharmacology analysis. These results demonstrated that this original approach will greatly improve high-throughput screening of metabolites and PCs on AD. It also can explicate the mechanism of action of TCM. Furthermore, this strategy is practicable to identify metabolites and screen PCs in other herbal medicines.

Targeted Screening Approach to Systematically Identify the Absorbed Effect Substances of Poria cocos in Vivo Using Ultrahigh Performance Liquid Chromatography Tandem Mass Spectrometry

Poria cocos are extensively used as nutritious food, dietary supplements, and oriental medicine in Asia. However, the effect substances are still not very clear. In this study, a targeted screening approach was developed to systematically identify absorbed constituents of Poria cocos in vivo using ultrahigh performance liquid chromatography tandem mass spectrometry combined with UNIFI software. First, incubation reactions in vitro with rat intestinal microflora and rat liver microsomes were conducted to sum up metabolic rules of main constituents. Second, the absorbed constituents in vivo were picked out and identified based on the results of metabolic study in vitro. Finally, the absorbed active constituents in the treatment of Alzheimer's disease were screened by targeted network pharmacology analysis. A total of 62 absorbed prototypes and 59 metabolites were identified and characterized in dosed plasma. Thirty potential active constituents were screened, and 86 drug-targets shared by absorbed constituents and Alzheimer's disease were discovered by targeted network pharmacology analysis. In general, this proposed targeted strategy comprehensively provides new insight for active ingredients of Poria cocos.

Identification of rotundic acid metabolites after oral administration to rats and comparison with the biotransformation by Syncephalastrum racemosum AS 3.264

The objective of this study was to identify the metabolites of rotundic acid after oral administration to rats and compare the similarities with its biotransformation by Syncephalastrum racemosum AS 3.264 using ultra-high performance liquid chromatography coupled with quadrupole time of flight mass spectrometry. A total of fourteen metabolites were determined based on the mass spectrometry and chromatographic behaviors, among which eleven (M1-M3, M7-M14) and six (M2, M4-M8) metabolites were identified in rats and S. racemosum, respectively. Three identical metabolites (M2, M7 and M8) were found in rats and S. racemosum, indicating that there were metabolic similarities. Moreover, to confirm the results of mass spectrometry, three (M2, M4 and M7) metabolites were obtained by the means of amplifying incubation and their structures were determined by various spectroscopic analyses, and M4 was proved to be a previously undescribed compound. This results showed that in vitro assisted preparation by microbial transformation is a feasible and effective method of obtaining metabolites which are in low amounts and difficult to be prepared in vivo.

Qualitatively and quantitatively investigating the regulation of intestinal microbiota on the metabolism of panax notoginseng saponins

ETHNOPHARMACOLOGICAL RELEVANCE

Intestinal microflora plays crucial roles in modulating pharmacokinetic characteristics and pharmacological actions of active ingredients in traditional Chinese medicines (TCMs). However, the exact impact of altered intestinal microflora affecting the biotransformation of TCMs remains poorly understood.

AIMS OF THE STUDY

This study aimed to reveal the specific enterobacteria which dominate the metabolism of panax notoginseng saponins (PNSs) via exploring the relationship between bacterial community structures and the metabolic profiles of PNSs.

MATERIALS AND METHODS

2, 4, 6-Trinitrobenzenesulphonic acid (TNBS)-challenged and pseudo germ-free (pseudo GF) rats, which prepared by treating TNBS and antibiotic cocktail, respectively, were employed to investigate the influence of intestinal microflora on the PNS metabolic profiles. Firstly, the bacterial community structures of the conventional, TNBS-challenged and pseudo GF rat intestinal microflora were compared via 16S rDNA amplicon sequencing technique. Then, the biotransformation of protopanaxadiol-type PNSs (ginsenoside Rb1, Rb2 and Rd), protopanaxatriol-type PNSs (ginsenoside Re, Rf, Rg1 and notoginsenoside R1) and Panax notoginseng extract (PNE) in conventional, TNBS-challenged and pseudo GF rat intestinal microbiota was systematically studied from qualitative and quantitative angles based on LC-triple-TOF/MS system. Besides, glycosidases (β-glucosidase and β-xylosidase), predominant enzymes responsible for the deglycosylation of PNSs, were measured by the glycosidases assay kits.

RESULTS

Significant differences in the bacterial community structure on phylum, class, order, family, and genera levels were observed among the conventional, TNBS-challenged and pseudo GF rats. Most of the metabolites in TNBS-challenged rat intestinal microflora were identified as the deglycosylation products, and had slightly lower exposure levels than those in the conventional rats. In the pseudo GF group, the peak area of metabolites formed by loss of glucose, xylose and rhamnose was significantly lower than that in the conventional group. Importantly, the exposure levels of the deglycosylated metabolites were found have a high correlation with the alteration of glycosidase activities and proteobacteria population. Several other metabolites, which formed by oxidation, dehydrogenation, demethylation, etc, had higher relative exposure in pseudo GF group, which implicated that the up-regulation of Bacteroidetes could enhance the activities of some redox enzymes in intestinal microbiota.

CONCLUSION

The metabolism of PNSs was greatly influenced by intestinal microflora. Proteobacteria may affect the deglycosylated metabolism of PNSs via regulating the activities of glycosidases. Besides, up-regulation of Bacteroidetes was likely to promote the redox metabolism of PNSs via improving the activities of redox metabolic enzymes in intestinal microflora.

Compound to Extract to Formulation: a knowledge-transmitting approach for metabolites identification of Gegen-Qinlian Decoction, a traditional Chinese medicine formula

Herbal medicines usually contain a large group of chemical components, which may be transformed into more complex metabolites in vivo. In this study, we proposed a knowledge-transmitting strategy for metabolites identification of compound formulas. Gegen-Qinlian Decoction (GQD) is a classical formula in traditional Chinese medicine (TCM). It is widely used to treat diarrhea and diabetes in clinical practice. However, only tens of metabolites could be detected using conventional approaches. To comprehensively identify the metabolites of GQD, a “compound to extract to formulation” strategy was established in this study. The metabolic pathways of single representative constituents in GQD were studied, and the metabolic rules were transmitted to chemically similar compounds in herbal extracts. After screening diversified metabolites from herb extracts, the knowledge was summarized to identify the metabolites of GQD. Tandem mass spectrometry (MSⁿ), fragment-based scan (NL, PRE), and selected reaction monitoring (SRM) were employed to identify, screen, and monitor the metabolites, respectively. Using this strategy, we detected 131 GQD metabolites (85 were newly generated) in rats biofluids. Among them, 112 metabolites could be detected when GQD was orally administered at a clinical dosage (12.5 g/kg). This strategy could be used for systematic metabolites identification of complex Chinese medicine formulas.

The profiling of the metabolites of hirsutine in rat by ultra-high performance liquid chromatography coupled with linear ion trap Orbitrap mass spectrometry: An improved strategy for the systematic screening and identification of metabolites in multi-samples in vivo

Drug metabolites identification and construction of metabolic profile are meaningful work for the drug discovery and development. The great challenge during this process is the work of the structural clarification of possible metabolites in the complicated biological matrix, which often resulting in a huge amount data sets, especially in multi-samples in vivo. Analyzing these complex data manually is time-consuming and laborious. The object of this study was to develop a practical strategy for screening and identifying of metabolites from multiple biological samples efficiently. Using hirsutine (HTI), an active components of Uncaria rhynchophylla (Gouteng in Chinese) as a model and its plasma, urine, bile, feces and various tissues were analyzed with data processing software (Metwork), data mining tool (Progenesis QI), and HR-MSⁿ data by ultra-high performance liquid chromatography/linear ion trap-Orbitrap mass spectrometry (U-HPLC/LTQ-Orbitrap-MS). A total of 67 metabolites of HTI in rat biological samples were tentatively identified with established library, and to our knowledge most of which were reported for the first time. The possible metabolic pathways were subsequently proposed, hydroxylation, dehydrogenation, oxidation, N-oxidation, hydrolysis, reduction and glucuronide conjugation were mainly involved according to metabolic profile. The result proved application of this improved strategy was efficient, rapid, and reliable for metabolic profiling of components in multiple biological samples and could significantly expand our understanding of metabolic situation of TCM in vivo.

Target and non-target identification of chemical components in Lamiophlomis rotata by liquid chromatography/quadrupole time-of-flight mass spectrometry using a three-step protocol

RATIONALE

As a herbal plant used in traditional Chinese medicine, Lamiophlomis rotata (Benth.) Kudo mainly displays its pharmacological effect by promoting blood circulation and hemostasis, dispelling wind, and acting as an analgesic. To identify the components contained in L. rotata, global detection and structural elucidation of both target and non-target components in the medicinal material was performed.

METHODS

L. rotata was ultrasonically extracted with methanol. Separation and analysis were achieved using liquid chromatography/quadrupole time-of-flight mass spectrometry (LC/QTOF-MS). A three-step protocol which included (1) potential components screening, (2) collection of qualitative information, and (3) database searching and structural elucidation was used for target and non-target identification.

RESULTS

A total of 42 components were tentatively identified, which included 12 iridoids (2 aglycones and 10 glucosides), 11 flavonoids (4 aglycones and 7 glucosides), and 13 phenylethanoid glycosides. Moreover, components of L. rotata extract belonging to the three main structural categories could be well separated in a 3D point plot according to their retention times, mass defects and degrees of unsaturation, facilitating the structural classification and identification in the subsequent studies.

CONCLUSIONS

The results provide a reasonable picture of the components contained in L. rotata extract and promote the further pharmacodynamic and/or pharmacokinetic characterization of this medical material, meanwhile demonstrating the utility of a universal methodology for the systematical study of herbal medicines. Copyright © 2016 John Wiley & Sons, Ltd.

Metabolic profile of Guge Fengtong tablet in rat urine and bile after oral administration, using high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry

In the present study, we developed and validated a rapid analytical method using high performance liquid chromatography coupled with quadrupole time of flight mass spectrometry (HPLC-Q-TOF/MS) to investigate the metabolic profile of Guge Fengtong tablet (GGFTT), a traditional Chinese medicine. The urine and bile samples were collected with 24 h after oral administration of GGFTT. A total of 34 compounds, including 11 parent compounds and 23 metabolites were unambiguously or tentatively identified. Our results indicated that glucuronidation, oxidation and methylation were the major metabolic pathways of the constituents in GGFTT. In addition, the results of this work also demonstrated the feasibility of HPLC-ESI-Q-TOF/MS for reliable characterization of the in vivo metabolites from herbal preparations.

A rapid integrated bioactivity evaluation system based on near-infrared spectroscopy for quality control of Flos Chrysanthemi

For quality control of herbal medicines or functional foods, integral activity evaluation has become more popular in recent studies. The majority of researchers focus on the relationship between chromatography/mass spectroscopy and bioactivity, but the connection with spectrum-activity is easily ignored. In this paper, the near infrared reflection spectra (NIRS) of Flos Chrysanthemi samples were collected as a representative spectrum technology, and corresponding anti-inflammation activities were utilized to illustrate the spectrum-activity study. HPLC/Q-TOF-MS identification and heat map clustering were used to select the quality markers (Q-marker) from five cultivars of Flos Chrysanthemi. Using boxplot analysis and the interval limits of detection (LODs) theory, six crucial markers, namely, chlorogenic acid, 3,5-dicaffeoylquinic acid, 1,5-dicaffeoylquinic acid, luteoloside, apigenin-7-O-β-d-glucoside, and luteolin-7-O-6-malonylglucoside were screened out. Then partial least squares regression (PLSR) calibration models combined with synergy interval partial least squares (siPLS) and 12 different spectral pretreatment methods were developed for the parameters optimization of these Q-markers in Flos Chrysanthemi powder. After comparing the relationship between Q-marker contents and anti-inflammation activity via three machine learning approaches and PLSR, back-propagation neural network (BP-ANN) displayed a more excellent non-linear fitting effect, as its R for new batches reached 0.89. These results indicated that the integrated NIRS and bioactive strategy was suitable for fast quality management in Flos Chrysanthemi, and also applied to other botanical food quality control.

Global profiling and rapid matching of natural products using diagnostic product ion network and in silico analogue database: Gastrodia elata as a case study

Rapid discovery of novel compounds of a traditional herbal medicine is of vital significance for pharmaceutical industry and plant metabolic pathway analysis. However, discovery of unknown or trace natural products is an ongoing challenge. This study presents a universal targeted data-independent acquisition and mining strategy to globally profile and effectively match novel natural product analogues from an herbal extract. The famous medical plant Gastrodia elata was selected as an example. This strategy consists of three steps: (i) acquisition of accurate parent and adduct ions (PAIs) and the product ions data of all eluting compounds by untargeted full-scan MS(E) mode; (ii) rapid compound screening using diagnostic product ions (DPIs) network and in silico analogue database with SUMPRODUCT function to find novel candidates; and (iii) identification and isomerism discrimination of multiple types of compounds using ClogP and ions fragment behavior analyses. Using above data mining methods, a total of 152 compounds were characterized, and 70 were discovered for the first time, including series of phospholipids and novel gastroxyl derivatives. Furthermore, a number of gastronucleosides and phase II metabolites of gastrodin and parishins were discovered, including glutathionylated, cysteinylglycinated and cysteinated compounds, and phosphatidylserine analogues. This study extended the application of classical DPIs filter strategy and developed a structure-based screening approach with the potential for significant increase of efficiency for discovery and identification of trace novel natural products.

An Integrated Approach for Studying Exposure, Metabolism, and Disposition of Multiple Component Herbal Medicines Using High-Resolution Mass Spectrometry and Multiple Data Processing Tools

A typical prescription of traditional Chinese medicine (TCM) contains up to a few hundred prototype components. Studying their absorption, metabolism, distribution, and elimination (ADME) presents great challenges. The objective of this study was to develop a practical approach for investigating ADME of individual prototypes in TCM. An active fraction of Xiao-Xu-Ming decoction (AF-XXMD) as a model TCM prescription was orally administered to rats. AF-XXMD-related components in plasma, urine, bile, and feces were detected using high-resolution mass spectrometry and background subtraction, an untargeted data-mining tool. Components were then structurally characterized on the basis of MS(n) spectral data. Connection of detected AF-XXMD metabolites to their precursor species, either prototypes or upstream metabolites, were determined on the basis of mass spectral similarity and the matching of biotransformation reactions. As a result, 247 AF-XXMD-related components were detected and structurally characterized in rats, 134 of which were metabolites. Among 198 AF-XXMD prototypes dosed, 65 were fully or partially absorbed and 13 prototypes and 34 metabolites were found in the circulation. Glucuronidation, isomerization, and deglycosylation followed by biliary and urinary excretions and direct elimination of prototypes via kidney and liver were the major clearance pathways of AF-XXMD prototypes. As an example, the ADME profile of H56, the single major AF-XXMD component in rat plasma, was elucidated on the basis of profiles of H56-related components in plasma and excreta. The results demonstrate that the new analytical approach is a useful tool for rapid and comprehensive detection and characterization of TCM components in biologic matrix in a TCM ADME study.

Development of a multiple reaction monitoring (MRM) method based on high performance liquid chromatography/tandem mass spectrometry to analyze in vivo exposure profiles of complex herbal components independent of standards

Exposure profiles of herbal componentsin vivoplay pivotal roles in pharmacodynamic and pharmacokinetic evaluation. The proposed MRM method has enabled profile exposure components, time and relative levels accurately.

Pharmacokinetics of a multicomponent herbal preparation in healthy Chinese and African volunteers

K-601 is an herbal formulation for influenza consisting of Lonicera japonica, Isatis indigotica, Rheum palmatum, Phellodendron chinense, and Scutellaria baicalensis. In this work, we characterized the chemical constituents in K-601, identified the absorbed compounds and determined their pharmacokinetics in 6 Chinese and African volunteers by liquid chromatography with time-of-flight mass spectrometry. Similarity evaluation for chromatographic fingerprint of nine different batches showed values above 0.983. Totally, 50 components were identified in K-601. Then, 15 major prototype compounds and 17 metabolites were identified in human plasma. Major metabolic pathways included glucuronidation, sulfation, methylation, demethylation, and reduction. The pharmacokinetics of the most abundant prototype compounds, berberine, jatrorrhizine, palmatine and magnoflorine were determined. Significant pharmacokinetic differences were observed between the African and Chinese subjects. The AUCs of the African is about 4–10 fold higher than that of the Chinese for the three benzylisoquinoline alkaloids. Magnoflorine, an aporphine alkaloid, was absorbed better in the Chinese than in the African. The biotransformation of K-601 by human intestinal microflora was also investigated. The major reactions included hydroxylation, methylation, demethylation, acetylation and reduction. Glucuronidation and sulfation were not observed with fecal flora. These results may be important and useful in linking data from pharmacological assays and clinical effects.

A strategy for the identification of combinatorial bioactive compounds contributing to the holistic effect of herbal medicines

It has been well claimed that herbal medicines (HMs) elicit effects via a multi-compounds and multi-targets synergistic mode. However, it lacks appropriate strategies to uncover the combinatory compounds that take effect together and contribute to a certain pharmacological effect of an herb as a whole, which represents a major bottleneck in providing sound evidence in supporting the clinic benefits of HMs. Here, we proposed a strategy to the identification of combinatory compounds contributing to the anti-inflammatory activity of Cardiotonic Pill (CP). The strategy proposed herein contains four core steps, including the identification of bioequivalent combinatorial compounds, chemical family classification-based combinatorial screen, interactive mode evaluation, and activity contribution index assay. Using this strategy, we have successfully identified six compounds in combination responsible for the anti-inflammatory effect of CP, whose anti-inflammatory activities were found comparable to that of the whole CP. Additionally, these six compounds take effect via an additive mode but little synergism. This study, together with our recent work in the identification of bioactive equivalent compounds combination, provides a widely applicable strategy to the identification of combinatory compounds responsible for a certain pharmacological activity of HMs.

The food metabolome: a window over dietary exposure

The food metabolome is defined as the part of the human metabolome directly derived from the digestion and biotransformation of foods and their constituents. With >25,000 compounds known in various foods, the food metabolome is extremely complex, with a composition varying widely according to the diet. By its very nature it represents a considerable and still largely unexploited source of novel dietary biomarkers that could be used to measure dietary exposures with a high level of detail and precision. Most dietary biomarkers currently have been identified on the basis of our knowledge of food compositions by using hypothesis-driven approaches. However, the rapid development of metabolomics resulting from the development of highly sensitive modern analytic instruments, the availability of metabolite databases, and progress in (bio)informatics has made agnostic approaches more attractive as shown by the recent identification of novel biomarkers of intakes for fruit, vegetables, beverages, meats, or complex diets. Moreover, examples also show how the scrutiny of the food metabolome can lead to the discovery of bioactive molecules and dietary factors associated with diseases. However, researchers still face hurdles, which slow progress and need to be resolved to bring this emerging field of research to maturity. These limits were discussed during the First International Workshop on the Food Metabolome held in Glasgow. Key recommendations made during the workshop included more coordination of efforts; development of new databases, software tools, and chemical libraries for the food metabolome; and shared repositories of metabolomic data. Once achieved, major progress can be expected toward a better understanding of the complex interactions between diet and human health.

Identification of nuclear factor-κB inhibitors and β2 adrenergic receptor agonists in Chinese medicinal preparation Fuzilizhong pills using UPLC with quadrupole time-of-flight MS

INTRODUCTION

Fuzilizhong Pills (FZLZ), a modified form of a famous traditional Chinese medicine (TCM) Lizhong Wan in Treatise on Febrile Diseases and consisting of Panax ginseng C.A.Mey. (Ren Shen), Aconitum carmichaelii Debx. (Fu Zi, Zhi), Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat. or Glycyrrhiza glabra L. (Gan Cao), Atractylodes macrocephala Koidz. (Bai Zhu) and Zingiber offcinale Rosc. (Gan Jiang), show strong clinical therapeutic effects for dyspnea and pulmonary oedema. However, the bioactive compounds are still unclear. In this study, FZLZ was analysed using a rapid detection method to identify its anti-inflammatory and spasmolytic constituents.

OBJECTIVE

To develop a simple screening method to detect the anti-inflammatory and spasmolytic constituents of FZLZ.

METHODS

Ultra-performance liquid chromatography with quadrupole time-of-flight mass spectrometry combined with dual-bioactive (NF-κB and β2 -adrenergic receptor) luciferase reporter assay systems was employed.

RESULTS

Two β2 -adrenergic receptor agonists (salsolinol and higeramine) and three terpenoidal analogues of NF-κB inhibitors such as ginsenosides derivatives, triperpenoids derivatives and diester-diterpenoid aconitum alkaloid derivatives were characterised. Mesaconitine, flaconitine, ginsenosides Rb2, Rf, Rg2, F1 and Ro were considered to be new NF-κB inhibitors. Furthermore, IL-8 detection by enzyme linked immunosorbent assay confirmed the anti-inflammatory effects of the potential NF-κB inhibitors.

CONCLUSION

Compared with conventional fingerprints, activity-integrated fingerprints that contain both chemical and bioactive details offer a more comprehensive understanding of the chemical composition of plant materials. This strategy clearly demonstrated that dual bioactivity-integrated fingerprinting is a powerful tool for the improved screening and identification of potential dual-target lead compounds in complex herbal medicines.

Study on the plasma protein binding rate of Schisandra lignans based on the LC-IT-TOF/MS technique with relative quantitative analysis

The main objective of the current study was to develop a universal method for a protein binding assay of complicated herbal components, and to investigate the possible relationship between compound polarity and protein binding using Schisadra lignans as an example. Firstly, the rat, dog and human plasma were spiked with three different concentrations of Schisandra chinensis extract (SLE), and ultramicrofiltration was used to obtain the unbound ingredients. Secondly, thirty-one Schisandra lignans in total plasma and ultrafiltered fluid were measured by LC-IT-TOFMS. Lastly, a relative exposure approach, which entailed calculating the relative concentrations of each Schisandra lignan from the corresponding calibration equation created from the calibration samples spiked with the stock solution of SLE, was applied in order to overcome the absence of authentic standards. The results showed that Schisandra lignans exhibited a high capability to bind with plasma protein, furthermore, the protein binding ratio of the lignan components increased proportionally with their individual chromatographic retention time, which indicated that the ratio of protein binding of lignans might increase accordingly with decreasing polarity. This study suggested that the compound polarity might be an important factor affecting the plasma protein binding of herbal components.

Characterization of the herb-derived components in rats following oral administration of Carthamus tinctorius extract by extracting diagnostic fragment ions (DFIs) in the MSn chromatograms

An E(DFI)MSⁿCs-based strategy was proposed to rapidly detect and identify the in vivo components derived from the extract of Carthamus tinctorius using LC-IT-TOF-MSⁿ.