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

Understanding LC/MS-Based Metabolomics: A Detailed Reference for Natural Product Analysis

Liquid chromatography, when used in conjunction with mass spectrometry (LC/MS), is a powerful tool for conducting accurate and reproducible investigations of numerous metabolites in natural products (NPs). LC/MS has gained prominence in metabolomic research due to its high throughput, the availability of multiple ionization techniques and its ability to provide comprehensive metabolite coverage. This unique method can significantly influence various scientific domains. This review offers a comprehensive overview of the current state of LC/MS-based metabolomics in the investigation of NPs. This review provides a thorough overview of the state of the art in LC/MS-based metabolomics for the investigation of NPs. It covers the principles of LC/MS, various aspects of LC/MS-based metabolomics such as sample preparation, LC modes, method development, ionization techniques and data pre-processing. Moreover, it presents the applications of LC/MS-based metabolomics in numerous fields of NPs research such as including biomarker discovery, the agricultural research, food analysis, the study of marine NPs and microbiological research. Additionally, this review discusses the challenges and limitations of LC/MS-based metabolomics, as well as emerging trends and developments in this field.

Metabolite profiling and identification of enzymes responsible for the metabolism of hirsutine, a major alkaloid from Uncaria rhynchophylla

The in vitro metabolism of hirsutine was determined using liver microsomes and human recombinant cytochrome P450 enzymes. Under the current conditions, a total of 14 phase I metabolites were tentatively identified.Ketoconazole showed significant inhibitory effect on the metabolism of hirsutine. Human recombinant cytochrome P450 enzyme analysis revealed that metabolism of hirsutine was mainly catalysed by CYP3A4.Our data revealed that hirsutine was metabolised via mono-oxygenation, di-oxygenation, N-oxygenation, dehydrogenation, demethylation and hydrolysis.In glutathione (GSH)-supplemented liver microsomes, four GSH adducts were identified. Hirsutine underwent facile P450-mediated metabolic activation, forming reactive 3-methyleneindolenine and iminoquinone intermediates.This study provided valuable information on the metabolic fates of hirsutine in liver microsomes, which would aid in understanding the hepatotoxicity caused by hirsutine or hirsutine-containing herb preparation.

Ultra-high performance liquid chromatography high-resolution mass spectrometry for metabolomic analysis of dental calculus from Duke Alessandro Farnese and Maria D'Aviz

Dental calculus is a valuable resource for the reconstruction of dietary habits and oral microbiome of past populations. In 2020 the remains of Duke Alessandro Farnese and his wife Maria D'Aviz were exhumed to get novel insights into the causes of death. This study aimed to investigate the dental calculus metabolome of the noble couple by untargeted metabolomics. The pulverized samples were decalcified in a water-formic acid mixture, extracted using methanol/acetonitrile and analyzed by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) using a reversed-phase separation followed by electrospray ionization and full scan in positive and negative ion mode. Waters Synapt-G2-Si High-Definition hybrid quadrupole time-of-flight mass spectrometer was used. Significant features were then identified using MSE acquisition mode, recording information on exact mass precursor and fragment ions within the same run. This approach, together with data pre-treatment and multivariate statistical analysis allowed for the identification of compounds able to differentiate between the investigated samples. More than 200 metabolites were identified, being fatty acids, alcohols, aldehydes, phosphatidylcholines, phosphatidylglycerols, ceramides and phosphatidylserines the most abundant classes. Metabolites deriving from food, bacteria and fungi were also determined, providing information on the habits and oral health status of the couple.

Quantitative imaging of natural products in fine brain regions using desorption electrospray ionization mass spectrometry imaging (DESI-MSI): Uncaria alkaloids as a case study

Uncaria species (Rubiaceae) are used as traditional Chinese medicines (TCMs) to treat central nervous system (CNS) diseases, and monoterpene indole alkaloids are the main bioactive constituents. Localization and quantification of CNS drugs in fine brain regions are important to provide insights into their pharmacodynamics, for which quantitative mass spectrometry imaging (MSI) has emerged as a powerful technique. A systematic study of the quantitative imaging of seven Uncaria alkaloids in rat brains using desorption electrospray ionization mass spectrometry imaging (DESI-MSI) was presented. The distribution of the alkaloids in thirteen brain regions was quantified successfully using the calibration curves generated by a modified on-tissue approach. The distribution trend of different Uncaria alkaloids in the rat brain was listed as monoterpene indole alkaloids > monoterpene oxindole alkaloids, R-configuration epimers > S-configuration epimers. Particularly, Uncaria alkaloids were detected directly in the pineal gland for the first time and their enrichment phenomenon in this region had an instructive significance in future pharmacodynamic studies.

Application of Large-Scale Molecular Prediction for Creating the Preferred Precursor Ions List to Enhance the Identification of Ginsenosides from the Flower Buds of Panax ginseng

This work was designed to evaluate the coverage of data-dependent acquisition (DDA) extensively utilized in the untargeted metabolite/component identification in the food sciences and pharmaceutical analysis. Using saponins from the flower buds of Panax ginseng (PGF) as an example, precursor ions list (PIL)-including DDA on a Q-Orbitrap mass spectrometer could enable higher coverage than the other four MS² acquisition approaches in characterizing PGF ginsenosides. A "Virtual Library of Ginsenoside" containing 13,536 ginsenoside molecules was established by C-language-programmed large-scale molecular prediction, which in combination with mass defect filtering could create a new PIL involving 1859 PGF saponin precursors. We could newly obtain the MS² spectra of at least 17 components and characterize 36 ginsenosides with unknown masses, among the 164 compounds identified from PGF. Conclusively, a molecular-prediction-oriented PIL in DDA can assist to discover more potentially novel molecules benefiting to the development of functional foods and new drugs.

Properties, Pharmacology, and Pharmacokinetics of Active Indole and Oxindole Alkaloids in Uncaria Hook

Uncaria Hook (UH) is a dry stem with hook of Ucaria plant and is contained in Traditional Japanese and Chinese medicine such as yokukansan, yokukansankachimpihange, chotosan, Gouteng-Baitouweng, and Tianma-Gouteng Yin. UH contains active indole and oxindole alkaloids and has the therapeutic effects on ailments of the cardiovascular and central nervous systems. The recent advances of analytical technology led to reports of detailed pharmacokinetics of UH alkaloids. These observations of pharmacokinetics are extremely important for understanding the treatment’s pharmacological activity, efficacy, and safety. This review describes properties, pharmacology, and the recently accumulated pharmacokinetic findings of UH alkaloids, and discusses challenges and future prospects. UH contains major indole and oxindole alkaloids such as corynoxeine, isocorynoxeine, rhynchophylline, isorhynchophylline, hirsuteine, hirsutine, and geissoschizine methyl ether (GM). These alkaloids exert neuroprotective effects against Alzheimer’s disease, Parkinson’s disease, and depression, and the mechanisms of these effects include anti-oxidant, anti-inflammatory, and neuromodulatory activities. Among the UH alkaloids, GM exhibits comparatively potent pharmacological activity (e.g., agonist activity at 5-HT_1A receptors). UH alkaloids are absorbed into the blood circulation and rapidly eliminated when orally administered. UH alkaloids are predominantly metabolized by Cytochrome P450 (CYP) and converted into various metabolites, including oxidized and demethylated forms. Regarding GM metabolism by CYPs, a gender-dependent difference is observed in rats but not in humans. Several alkaloids are detected in the brain after passing through the blood–brain barrier in rats upon orally administered. GM is uniformly distributed in the brain and binds to various channels and receptors such as the 5-HT receptor. By reviewing the pharmacokinetics of UH alkaloids, challenges were found, such as differences in pharmacokinetics between pure drug and crude drug products administration, food-influenced absorption, metabolite excretion profile, and intestinal tissue metabolism of UH alkaloids. This review will provide readers with a better understanding of the pharmacokinetics of UH alkaloids and their future challenges, and will be helpful for further research on UH alkaloids and crude drug products containing UH.

Identification of In Vivo Metabolites of a Potential Anti-tumor Drug Candidate AMAC, in Rat Plasma, Urine and Feces Samples Using UHPLC/QTOF /MS/MS

Background:

Drugs based on natural products targeting the microtubule system remain an important component in cancer therapy. Compound 10, 4-((3-amino-4-methoxyphenyl) amino)-2Hcoumarin, derived from coumarin, showed excellent anti-proliferative activity through directly binding to the colchicine-binding site in β-tubulin, suggesting that it could be a perfect drug candidate for antitumor drug research and development. Identification and structural characterization of metabolites is a critical step of both drug discovery and development research.

Objective:

Compound 10, 4-((3-amino-4-methoxyphenyl) amino)-2H-coumarin, derived from coumarin.

Method:

In this study, an efficient and sensitive method using Ultra High-Performance Liquid Chromatography couple with Quadrupole Time of Flight tandem Mass Spectrometry (UHPLC/QTOF/ MS/MS) was successfully established and applied to identify the in vivo metabolites in plasma, urine and feces samples of rats after intravenous administration of Compound 10 with a single dose of 10 mg/kg.

Result:

A total of eight metabolites (including two phase I and six phase II metabolites) had been detected or tentatively identified in plasma, urine and feces, indicating the prominent metabolic pathways were glucuronidation, demethylation and hydroxylation. In addition, in order to understand the structure of metabolites more accurately, synthesis strategy was used to confirm the metabolite M3.

Conclusion:

The present study provides important information on the metabolism of Compound 10 in vivo for the first time, which would be helpful for understanding the potential metabolic processes of Compound 10 and paving the way for pharmacology and toxicology research.

Comparative analysis of constitutes and metabolites for traditional Chinese medicine using IDA and SWATH data acquisition modes on LC-Q-TOF MS

Identification of components and metabolites of traditional Chinese medicines (TCMs) employing liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q-TOF MS) techniques with information-dependent acquisition (IDA) approaches is increasingly frequent. A current drawback of IDA-MS is that the complexity of a sample might prevent important compounds from being triggered in IDA settings. Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) is a data-independent acquisition (DIA) method where the instrument deterministically fragments all precursor ions within the predefined m/z range in a systematic and unbiased fashion. Herein, the superiority of SWATH on the detection of TCMs’ components was firstly investigated by comparing the detection efficiency of SWATH-MS and IDA-MS data acquisition modes, and sanguisorbin extract was used as a mode TCM. After optimizing the setting parameters of SWATH, rolling collision energy (CE) and variable Q1 isolation windows were found to be more efficient for sanguisorbin identification than the fixed CE and fixed Q1 isolation window. More importantly, the qualitative efficiency of SWATH-MS on sanguisorbins was found significantly higher than that of IDA-MS data acquisition. In IDA mode, 18 kinds of sanguisorbins were detected in sanguisorbin extract. A total of 47 sanguisorbins were detected when SWATH-MS was used under rolling CE and flexible Q1 isolation window modes. Besides, 26 metabolites of sanguisorbins were identified in rat plasma, and their metabolic pathways could be deduced as decarbonylation, oxidization, reduction, methylation, and glucuronidation according to their fragmental ions acquired in SWATH-MS mode. Thus, SWATH-MS data acquisition could provide more comprehensive information for the component and metabolite identification for TCMs than IDA-MS.

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SWATH was first used to identify components and metabolites of TCMs.

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Superiority of SWATH on the detection of TCM was firstly investigated.

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The number of components detected by SWATH was greatly higher than IDA.

Metabolite profiling of traditional Chinese medicine formula Dan Zhi Tablet: An integrated strategy based on UPLC-QTOF/MS combined with multivariate statistical analysis

Metabolites derived from traditional Chinese medicine (TCM) are becoming active substances of pharmacologically as well as promising sources for discovering new drugs. However, detection and identification of constituents in vivo remains a challenge for TCM, due to massive endogenous interference and low abundance of metabolites in biological matrix. Traditional Chinese medicine formula Dan Zhi Tablet (DZT), a well-established TCM formula developed based on years of clinical experiences, was widely used to treat cerebral infraction disease. In this study, an integrated strategy based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) was adopted to comprehensively identify the prototype and metabolite constituents of DZT. The potential constituents were screened by cross orthogonal partial least-squares discriminant analysis (OPLS-DA). Automatic matching analysis was performed on UNIFI platform based on the function of predicting metabolites. Using this strategy, a total of 170 compounds, including 51 prototype constituents and 119 metabolites were unambiguously or tentatively identified in rat plasma. Furthermore, 31 compounds have also been detected in rat cerebrospinal fluid. The metabolism reactions included phase I reactions (hydroxylation, hydrolysis, deglycosylation, hydrogenation, demethylation and dehydroxylation) and phase II reactions (conjugation with glutatione, cysteine, acetylcysteine, glucuronide, sulfate). It is the first systematic metabolic study of DZT in vivo and some metabolites were also reported for the first time, which could provide a scientific basis for explaining the multiple functions of DZT. More importantly, the integrated strategy also shows promising perspectives in the identification of the metabolites in TCM from a complicated biological matrix.

Quality markers based on biological activity: A new strategy for the quality control of traditional Chinese medicine

BACKGROUND

The quality and quality evaluation system of traditional Chinese medicine (TCM) are crucial in the safety and effectiveness assessment of TCM. However, they are also the major bottlenecks that restrict the quality control of TCM. Given the nature of Chinese medicine and the limitations of science and technology, the quality evaluation of TCM involves a few difficulties. Therefore, scholars have conducted considerable amount of research on this topic and obtained promising results. Biological potency and biomarkers have been used to evaluate the quality of TCM. Previous studies provided new strategies and methods to establish a system on quality evaluation.

PURPOSE

This review aims to provide a new strategy for the quality control of Chinese herbal medicine by combining biological potency and biomarkers based on biological effects.

METHODS

We reviewed the quality evaluation system of Chinese herbal medicine, focusing on quality markers (Q-markers) based on biological effects and the application of these markers in the quality evaluation of Chinese herbal medicine. We also reviewed the factors affecting quality, the difficulties related to the quality evaluation system and the attempt of researchers to improve the quality control of TCM.

RESULTS

We propose Q-biomarkers by integration of biological potency and biomarkers to evaluate the quality of TCM. The quality markers provided us significant insights in the process of definition. We further optimised the concept of Q-markers and summarised their definition and properties (including quantification, specificity and related to biological response) in accordance with the requirement of the quality evaluation of TCM.

CONCLUSION

We propose the use of Q-biomarkers in vivo related to specific diseases as a new strategy for the quality evaluation of Chinese herbal medicine. The quality evaluation system of Q-biomarkers would provide a new perspective to standardise and globalise TCM.

Post-acquisition data mining techniques for LC–MS/MS-acquired data in drug metabolite identification

Metabolite identification is a crucial part of the drug discovery process. LC–MS/MS-based metabolite identification has gained widespread use, but the data acquired by the LC–MS/MS instrument is complex, and thus the interpretation of data becomes troublesome. Fortunately, advancements in data mining techniques have simplified the process of data interpretation with improved mass accuracy and provide a potentially selective, sensitive, accurate and comprehensive way for metabolite identification. In this review, we have discussed the targeted (extracted ion chromatogram, mass defect filter, product ion filter, neutral loss filter and isotope pattern filter) and untargeted (control sample comparison, background subtraction and metabolomic approaches) post-acquisition data mining techniques, which facilitate the drug metabolite identification. We have also discussed the importance of integrated data mining strategy.