Comprehensive chemical profiling of Yindan Xinnaotong soft capsule and its neuroprotective activity evaluation in vitro

Two-dimensional cell membrane chromatography guided screening of myocardial protective compounds from Yindan Xinnaotong soft capsule

BACKGROUND

Cell membrane chromatography (CMC) is a biochromatography with a dual function of recognition and separation, offering a distinct advantage in screening bioactive compounds from Chinese medicines (CMs). Yindan Xinnaotong soft capsule (YD), a CM formulation, has been widely utilized in the treatment of cardiovascular disease. However, a comprehensive mapping of the myocardial protective active compounds remains elusive.

PURPOSE

To establish a stable and efficient 2D H9c2/CMC-RPLC-MS system, and to utilize it for screening the active compounds of YD that are associated with myocardial protection.

METHODS

An imidazole-modified silica gel exhibiting high modification efficiency and protein binding capacity was synthesized to enhance the longevity and efficiency of H9c2/CMC. Subsequently, the potentially bioactive compounds of YD were screened by integrating the 2D H9c2/CMC-RPLC-MS system with a high-content component knockout strategy. Additionally, an RNA-seq approach was employed to predict the targets and mechanisms of YD and the active compounds for myocardial protection.

RESULTS

The developed imidazole-modified H9c2/CMC exhibits remarkable selectivity, specificity, stability, and reproducibility. Following three rounds of screening, a total of 24 potential myocardial protective compounds were identified, comprising 8 flavonoids, 8 phenolic acids, 4 saponins, and 4 tanshinones. Bioinformatic analysis utilizing RNA-seq indicated that the FOXO signaling pathway, with FOXO3 identified as a key target, plays a significant role in the cardioprotective effects of YD. Furthermore, all 24 screened compounds exhibit strong binding affinities with FOXO3 evaluated by molecular docking.

CONCLUSION

A highly stable and efficient 2D imidazole-modified H9c2/CMC-RPLC-MS system was developed, allowing for the screening of potentially active compounds from YD. Through the integration of the bioinformatic analysis, the pharmacodynamic foundation of YD for myocardial protection has been comprehensively characterized.

Comparative profiling of the absorbed compounds and metabolites, and pharmacokinetic studies of Danshen-Chuanxiong herb pair in rat plasma and brain using liquid chromatography-tandem mass spectrometry

Danshen-Chuanxiong (DS-CX) was a classic herb pair commonly used to treat ischemic stroke. Nevertheless, the metabolic conversion and pharmacokinetic behavior of DS-CX in vivo remains unclear. This work aimed to reveal the in vivo metabolic behavior of DS-CX through establishing metabolic profiles and performing multicomponent pharmacokinetics analysis. The mass defect filtering (MDF) strategy integrated with UHPLC-QTOF-MS was firstly developed to characterize the metabolites of DS-CX in rats' plasma and brain. Moreover, a sensitive UHPLC-QQQ-MS method was utilized to perform the comparative pharmacokinetic studies of major active ingredients of DS-CX in rats' plasma. A total of 111 exogenous compounds (29 prototype compounds and 82 metabolites) were identified in rat biological samples. The major metabolic pathways were hydroxylation, methylation, deoxidation, dehydration, hydrogenation, demethylation, hydrolysis, decarboxylation and glucuronidation binding reactions. According to the results of metabolites profiling, sixteen active compounds (8 phenolic acids, 5 phthalides and 3 tanshinones) were selected as markers for further comparative pharmacokinetics study. Compared with the oral administration of DS or CX alone, the higher Cmax of salvianolic acid B, crytotanshinone and tanshinone IIA; the shorter Tmax of lithospermic acid, rosmarinic acid and tanshinone IIA; as well as the higher AUC0-∞ of ferulic acid, rosmarinic acid, salvianolic acid B, senkyunolide I and crytotanshinone, could be found after co-administration of DS-CX (P < 0.05). This study provided the overall knowledge of metabolites profiling of DS-CX in vivo, which would help to understand the effective material basis and promote the clinical application of DC-CX herb pair.

Identification and Characterization of Chemical Compounds in Compound Shougong Powder by UHPLC-Q-TOF/MSE Combined With Multiple Data Processing Techniques

Compound Shougong Powder (CSP) is a traditional Chinese medicine (TCM) preparation recognized for its efficacy in reducing swelling and relieving pain. It is primarily used clinically for the treatment of malignant tumors. However, research on the chemical compounds present in CSP remains limited. In this study, we employed ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MSE) combined with multiple data processing techniques to comprehensively characterize the chemical compounds in CSP. This included a multiple-point screening mass defect filtering (MDF), an enhanced method based on conventional MDF and boundary theory that creates a polygonal filtering zone by connecting numerous endpoints (n ≥ 5) to filter target components. Additional techniques utilized were extracted ion chromatogram (EIC), neutral loss filtering (NLF), diagnostic fragment ion filtering (DFIF), and direct identification methods considering retention time, fragmentation behavior, and reference standards. First, UHPLC-Q-TOF/MSE was applied for comprehensive profiling of CSP's chemical compounds. Then, R language combined with MZmine was used for data preprocessing, enabling the construction of an ion information list to extract valid data. Eventually, through these multiple data processing techniques, a total of 116 chemical compounds in CSP were identified, including 34 flavonoids, 38 saponins, seven stilbenes, six anthraquinones, 12 organic acids, 13 terpenoids, and six others. In summary, this study elucidates the chemical composition of CSP, contributing to the discovery of potential active ingredients for CSP. Additionally, the established strategy provided a powerful guide for the chemical characterization of TCM.

Multi-omics joint analysis reveals that the Miao medicine Yindanxinnaotong formula attenuates non-alcoholic fatty liver disease

BACKGROUD

Non-alcoholic fatty liver disease (NAFLD) is a growing chronic liver disease worldwide, and no effective agent is approved yet for this condition. Traditional Chinese Medicine (TCM), which has been practiced for thousands of years in China and other Asian countries, is considered an important source for identifying novel medicines for various diseases. Miao medicine Yindanxinnaotong formula (YDX) is a classical TCM for the treatment of hyperlipidemia disease by reducing blood lipid content, while the role of YDX have not been clarified in NAFLD.

PURPOSE

To investigate the protective effect of YDX on NAFLD in mice induced by high fat diet (HFD) and clarify the potential mechanism.

METHODS

NAFLD mice model was constructed by receiving HFD for 10-week period with or without YDX administration. Lipid profiles, biochemical indicators, and histopathological staining were performed to evaluate the extent of hepatic lipid accumulation and hepatic steatosis. 16S rRNA sequencing was used to determine the gut microbial composition. Serum metabolomics was further used to investigate the changes in plasma biomarkers for NAFLD-associated by UPLC-Q-TOF/MS analysis. Subsequently, liver transcriptomics was employed to identify differentially expressed genes and explore regulatory pathways. Then, lipid metabolism-related proteins and inflammation factors were examined by Western blot and ELISA.

RESULTS

YDX reduced body weight gain, liver index and inflammatory cytokines levels, along with improved hepatic steatosis, serum lipid profile, sensitivity to insulin and also tolerance to glucose, and enhanced oxidative defense system in HFD-induced mice. Also, YDX remarkedly affected gut microbiota diversity and community richness and decreased the ratio of Firmicutes/Bacteroidetes. Meanwhile, YDX also reduced the production of harmful lipid metabolites in the sera of NAFLD mice, such as LPC(18:0), LPC(18:1) and carnitine. Notably, consistent with liver transcriptomics results, YDX downregulated the expression of proteins implicated in de novo lipid synthesis (Srebp-1c, Acaca, Fasn, Scd-1, and Cd36) and pro-inflammatory cytokines (IL-6 and TNF-α), and increased the expression of proteins-related fatty acid β-oxidation (Ampkα, Ppar-α, and Cpt-1) in the liver by activating Ampk pathway.

CONCLUSION

YDX is promisingly an effective therapy for preventing NAFLD by modulating the Ampk pathway, inhibiting gut microbiota disorder, and reducing the production of harmful lipid metabolites.

Integrated chemical analysis, metabolic profiling, network pharmacology, molecular docking and toxicity prediction to reveal the active ingredients and their safety of raw and prepared rhubarbs in the treatment of gastric ulcers

BACKGROUND

Rhubarb, containing raw rhubarb (RR) and two processed products (steamed rhubarb, SR; carbonized rhubarb, CR), is commonly used in high-doses for the treatment of peptic ulcer, especially gastric ulcer (GU). However, their active ingredients, therapeutic targets, and potential mechanism remain unclear. Meanwhile, the safety of these active ingredients is also worth studying.

METHODS

An offline two-dimensional low-pressure liquid chromatography/high-performance liquid chromatography coupled with high resolution mass spectrometry method was applied to identify the chemical constituents of RR, SR, and CR. Then, the plasma and urine samples of rats after oral administration of RR, SR, and CR were studied for metabolite profiling. Based on the analysis of ingredients in vivo, the key active constituents, core therapeutic targets and key signaling pathways of RR, SR, and CR against GU were screened via network pharmacology and molecular docking. Finally, the efficacy and safety of these key active ingredients were evaluated.

RESULTS

Totally, 183, 120 and 115 compounds were identified or tentatively characterized from RR, SR and CR, respectively. Meanwhile, 190, 182 and 180 components were identified after oral administration of RR, SR and CR. By network pharmacology and molecular docking, torachrysone, hydroxyemodin, 6-methylrhein, rhein and emodin anthrone might be the predominant effective constituents in RR, SR, and CR with AKT1 and EGFR being their key targets during the treatment of GU. Moreover, EGFR/PI3K/AKT signaling pathway might play a crucial role in the therapeutic mechanism of GU. In silio ADMET predictions categorized 5 compounds as drugs with good oral bioavailability, but these components may induce liver injury.

CONCLUSION

Overall, our results not only clarified the active substances and molecular mechanism for enhancing our understanding about the traditional efficacy, but also pay attention to the clinical safety issues of raw and prepared rhubarbs.

Therapeutic efficacy and pharmacological mechanism of Yindan Xinnaotong soft capsule on acute ischemic stroke: a meta-analysis and network pharmacology analysis

Yindan Xinnaotong soft capsule (YDXNT), a traditional Chinese medicine preparation, has shown a promising effect in the treatment of acute ischemic stroke (AIS). The goal of this study was to investigate the therapeutic effects and pharmacological mechanisms of YDXNT on AIS. Randomized controlled trials were searched and screened. Review Manager 5.4 was used for a meta-analysis. Active ingredients and targets of YDXNT were extracted from the Traditional Chinese Medicine Systems Pharmacology Database, Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine, and Encyclopaedia of Traditional Chinese Medicine. AIS-related targets were retrieved from GeneCards, OMIM, and DrugBank databases. We constructed PPI and ingredient-target networks, performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, and conducted molecular docking. The YDXNT group had a higher total effective rate and a higher Barthel Index score. YDXNT reduced the low-density lipoprotein cholesterol and the whole blood viscosity at high and shear rates. Our study identified 313 ingredients and 1196 common targets. The key ingredients were mainly quercetin, neocryptotanshinone II, miltionone I, neotanshinone C, and tanshiquinone B, and the key targets were mainly SRC, MAPK3, AKT1, MAPK1, and JUN. GO analysis showed that the core targets mainly involved in atherosclerosis and neural apoptosis. The core pathways were lipid and atherosclerosis, PI3K-Akt, MAPK, and other pathways. Key ingredients exhibited robust binding interactions with core targets. YDXNT could effectively improve the total effective rate, ability of daily life, blood lipids, and blood viscosity. Antiatherosclerotic and neuroprotective effects are the main pharmacological mechanisms.Registration number: CRD42023400127.

Identification strategy of Fructus Gardeniae and its adulterant based on UHPLC/Q-orbitrap-MS and UHPLC-QTRAP-MS/MS combined with PLS regression model

Fructus Gardeniae (FG) is the desiccative and ripe fruits of Gardenia jasminoides Ellis in the Rubiaceae family, which is a commonly used in traditional Chinese medicine (TCM) for clearing away heat, detoxification, relieving restlessness, and eliminating blood stasis. At the same time, it has also been announced as the first batch of TCM with homology of medicine and food. Fructus Gardeniae Grandiflorae (FGG), the fruit of Gardenia jasminoides Ellis var. grandiflora Nakai (Rubiaceae), is a common counterfeit herbal medicine of FG, which still appears in the TCM market, and causes a certain degree of confusion. In order to effectively distinguish FG and its adulterant, the compounds in these two species were thoroughly characterized firstly by ultrahigh-performance liquid chromatography/quadrupole-orbitrap mass spectrometry (UHPLC/Q-Orbitrap MS). Furthermore, a pseudo-targeted metabonomics method with 60 targeted ion pairs was established based on UHPLC-triple quadrupole-linear ion trap mass spectrometry (UHPLC-QTRAP-MS) for discrimination. Multivariate statistical analysis showed that FG and FGG were clustered obviously, and 13 significantly differential markers were screened out by variable importance for projection (VIP) > 1 and p < 0.05 for the construction of the partial least squares (PLS) regression prediction model. The validation of the model proved that its prediction ability was quite satisfactory. Moreover, based on the absolute quantitative analysis of these 13 characteristics, the quality control standards of FG and FFG were established. In summary, an integral method of pseudo-targeted metabonomics combined with chemometrics analysis and a PLS regression model was proposed to provide an effective identification strategy for discrimination FG and FGG.

Elucidating the chemical interaction effects of herb pair Danshen-Chuanxiong and its anti-ischemic stroke activities evaluation

ETHNOPHARMACOLOGICAL RELEVANCE

Salvia miltiorrhiza Bunge (Danshen) and Ligusticum chuanxiong Hort. (Chuanxiong) is the core herb pair in traditional Chinese medicines (TCMs) formulae for treating ischemic stroke. However, the synergistic effect of Danshen-Chuanxiong against anti-ischemic stroke and its compatibility mechanism remains unclear.

AIM OF THE STUDY

This study aimed to uncover the compatibility mechanism of Danshen-Chuanxiong against ischemic stroke through chemical profiling, pharmacodynamics evaluation, network pharmacology and experimental validation.

MATERIALS AND METHODS

Ultra-high performance liquid chromatography (UHPLC) combined with quadrupole time-of-flight tandem mass spectrometry (QTOF-MS) and UHPLC connected with tandem triple quadrupole mass spectrometry (QQQ-MS) were utilized to conduct the chemical interaction analysis. Then the synergistic effects of Danshen-Chuanxiong against ischemic stroke were comprehensively evaluated by the middle cerebral artery occlusion reperfusion (MCAO/R) mice model, zebrafish ischemic stroke model and glutamic acid-induced PC12 cells injury model. Afterwards, network pharmacology and molecular docking were applied to dissect the significant active compounds and potential mechanisms. Finally, the key target proteins were experimentally validated by Western blot.

RESULTS

83 compounds were characterized in Danshen-Chuanxiong by UHPLC-QTOF-MS analysis, and 4 compounds were tentatively identified for the first time. The quantification results (24 accurately identified compounds) in 13 proportions of Danshen-Chuanxiong revealed that Danshen significantly increased the dissolution of most phthalides (from Chuanxiong), while Chuanxiong facilitated the dissolution of most phenolic acids (from Danshen) in solution. The anti-ischemic stroke effects of Danshen-Chuanxiong were significantly better than Danshen or Chuanxiong in attenuating infarct size, reducing brain edema and neurological scores in MCAO/R mice. Also, compared with single herbs, this herb pair exerted better effects of suppressing the incidence of cerebral thrombosis in zebrafish, and increasing the cell viability of glutamic acid-induced PC12 cells. In network pharmacology, 7 effective compounds (rosmarinic acid, chlorogenic acid, salvianolic acid B, (Z)-ligustilide, ferulic acid, caffeic acid, tanshinone IIA) and 5 hub targets (AKT, TNF-α, IL-1β, CASP3 and BCL2) as well as 4 key pathways were predicted. Western blot results showed that Danshen-Chuanxiong exert therapeutic effects mainly through decreasing the protein expressions of TNF-α, IL-1β and Cleaved-CASP3, elevating the levels of p-AKT and BCL2.

CONCLUSIONS

This work provided an integration strategy for uncovering the synergistic effects and compatibility mechanism of Danshen-Chuanxiong herb pair for treating ischemic stroke, and laid foundation for the further development and utilization of this herb pair.

Profiling of phenolic acids, flavonoids, terpenoids, and steroid derivatives in coconut (Cocos nucifera L.) haustorium

Coconut haustorium (CH) is formed inside coconut shell during coconut germination. This study aimed to investigate the compositions and contents of CH phytochemicals. Phytochemical compositions and contents in CH were analyzed by ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) and spectrophotometrical method. Five phenolic acids and four flavonoids were identified in CH. Ferulic acid and myricetin were the most abundant among phenolic acids and flavonoids identified in CH, respectively. Nepetariaside and 1-methylene-5α-androstan-3α-ol-17-one glucuronide were the most abundant terpenoids and steroid derivatives identified in CH, respectively. To our knowledge, this study screened several classes of phytochemicals in CH for the first. Terpenoids and steroid derivatives were likely to be more major phytochemicals than phenolic acids and flavonoids in CH. The functionality of CH itself and the compounds found in CH might be utilized in functional foods or cosmetics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01300-6.

A structural similarity networking assisted collision cross-section prediction interval filtering strategy for multi-compound identification of complex matrix by ion-mobility mass spectrometry

Ion mobility coupled with mass spectrometry (IM-MS), an emerging technology for analysis of complex matrix, has been facing challenges due to the complexities of chemical structures and original data, as well as low-efficiency and error-proneness of manual operations. In this study, we developed a structural similarity networking assisted collision cross-section prediction interval filtering (SSN-CCSPIF) strategy. We first carried out a structural similarity networking (SSN) based on Tanimoto similarities among Morgan fingerprints to classify the authentic compounds potentially existing in complex matrix. By performing automatic regressive prediction statistics on mass-to-charge ratios (m/z) and collision cross-sections (CCS) with a self-built Python software, we explored the IM-MS feature trendlines, established filtering intervals and filtered potential compounds for each SSN classification. Chemical structures of all filtered compounds were further characterized by interpreting their multidimensional IM-MS data. To evaluate the applicability of SSN-CCSPIF, we selected Ginkgo biloba extract and dripping pills. The SSN-CCSPIF subtracted more background interferences (43.24%∼43.92%) than other similar strategies with conventional ClassyFire criteria (10.71%∼12.13%) or without compound classification (35.73%∼36.63%). Totally, 229 compounds, including eight potential new compounds, were characterized. Among them, seven isomeric pairs were discriminated with the integration of IM-separation. Using SSN-CCSPIF, we can achieve high-efficient analysis of complex IM-MS data and comprehensive chemical profiling of complex matrix to reveal their material basis.

Widespread occurrence of in-source fragmentation in the analysis of natural compounds by liquid chromatography-electrospray ionization mass spectrometry

RATIONALE

The in-source fragmentation (ISF) of analyte or co-eluting substances produces unintentional fragment ions, which hampers identification and quantification by liquid chromatography-mass spectrometry (LC/MS). Natural compounds derived from plants also contain fragile moieties that may undergo ISF. However, the characteristics of ISF of natural compounds in LC/MS are still unclear.

METHODS

The ISF behavior of 214 natural compounds was assayed in LC with Q/orbitrap MS in electrospray ionization (ESI) mode and the extent of ISF was evaluated.

RESULTS

Up to 82% of tested compounds underwent ISF and half of the tested natural compounds that contain more than one fragile moiety underwent successive and severe ISF to generate serial structurally related ISF products. The major ISF-altering moieties for natural compounds were hydroxyl, lactone, glycosyl and ether, resulting in neutral loss of H₂ O or CO, deglycosylation or cleavage of ether bond, respectively. Some compounds such as terpenoids underwent severe ISF and less than 1% parent form can be observed. For natural compounds, ISF products with similar structures are more likely to cause interference in analysis because the ISF products may share identical mass-to-charge ratio and similar MS² fragmentation patterns with precursor ions of the homologs in plants. Furthermore, severe ISF may cause a false negative in the identification of the parent form.

CONCLUSIONS

In summary, ISF was a highly frequent phenomenon for analysis of natural compounds by LC/ESI-MS, and extensive and successive ISF of natural products may cause misannotation and misidentification with homologs in plants. The study should raise awareness of ISF interference during the analysis of natural compounds.

A sensitive LC-MS/MS method-based pharmacokinetic study of fifteen active ingredients of Yindan Xinnaotong soft capsule in rats and its potential mechanism in the treatment of cardiovascular diseases

Yindan Xinnaotong soft capsule (YDXNT) is a commonly used Chinese herbal preparation for the clinical treatment of coronary disease. However, there is a lack of pharmacokinetic studies on YDXNT, and its active ingredients and their mechanism in the treatment of cardiovascular diseases (CVD) are still unclear. In this study, 15 absorbed ingredients in rat plasma after oral administration of YDXNT were quickly identified based on liquid chromatography tandem quadrupole time-of-flight mass spectrometry (LC-QTOF MS), and then a sensitive and accurate quantitative method based on ultra-high performance liquid chromatography tandem triple quadrupole mass spectrometry (UHPLC-QQQ MS) was established and validated for simultaneous determination of the 15 ingredients of YDXNT in rat plasma, which was then applied to the pharmacokinetic study. Different types of compounds showed various pharmacokinetic characteristics, for instance, ginkgolides with higher maximum plasma concentration (Cmax), flavonoids presenting concentration-time curve with double peaks, phenolic acids with shorter time to reach maximum plasma concentration (Tmax), saponins with long elimination half-life (t1/2) and tanshinones showing fluctuant plasma concentration. Then the measured analytes were regarded as effective compounds and their potential targets and mechanism of action were predicted by constructing and analyzing the compound-target network of YDXNT and CVD. Those potential active compounds of YDXNT interacted with targets such as MAPK1 and MAPK8, and molecular docking showed that the binding free energies of 12 ingredients with MAPK1 were less than -5.0 kcal/mol, indicating that YDXNT intervened in the MAPK signaling pathway to display its therapeutic effect on CVD.

Comprehensive chemical profiling and quantitative analysis of ethnicYi medicine Miao-Fu-Zhi-Tong granules using UHPLC-MS/MS

Developing analytical methods for the chemical components of natural medicines remains a challenge due to its diversity and complexity. Miao-Fu-Zhi-Tong (MFZT) granules, an ethnic Yi herbal prescription, comprises 10 herbs and has been clinically applied for gouty arthritis (GA) therapy. Herein, a series of chemical profiling strategies including in-house library matching, molecular networking and MS/MS fragmentation behavior validation based on ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) were developed for qualitative analysis of MFZT granules. A total of 207 compounds were identified or characterized in which several rare guanidines were discovered and profiled into alkyl substituted or cyclic subtypes. Moreover, network pharmacology analysis indicated that MFZT's anti-gout mechanism was mostly associated with the nuclear factor kappa-B (NF-κB) signaling, nucleotide oligomerization domain (NOD)-like signaling and rheumatoid arthritis pathways, along with the synergistic effect of 84 potential active compounds. In addition, a quantitative analytical method was developed to simultaneously determine the 29 potential effective components. Among them, berberine, pellodendrine, 3-feruloylquinic acid, neoastilbin, isoacteoside and chlorogenic acid derivatives at higher concentrations were considered as the chemical markers for quality control. These findings provide a holistic chemical basis for MFZT granules and will support the development of effective analytical methods for the herbal formulas of natural medicines.

Multicomponent Characterization of the Flower Bud of Panax notoginseng and Its Metabolites in Rat Plasma by Ultra-High Performance Liquid Chromatography/Ion Mobility Quadrupole Time-of-Flight Mass Spectrometry

The flower bud of Panax notoginseng (PNF) consumed as a tonic shows potential in the prevention and treatment of cardiovascular diseases. To identify the contained multi-components and, in particular, to clarify which components can be absorbed and what metabolites are transformed, unveiling the effective substances of PNF is of vital significance. A unique ultrahigh-performance liquid chromatography/ion mobility quadrupole time-of-flight mass spectrometry (UHPLC/IM-QTOF-MS) profiling approach and efficient data processing by the UNIFI^TM bioinformatics platform were employed to comprehensively identify the multi-components of PNF and the related metabolites in the plasma of rats after oral administration (at a dose of 3.6 g/kg). Two MS² data acquisition modes operating in the negative electrospray ionization mode, involving high-definition MS^E (HDMS^E) and data-dependent acquisition (DDA), were utilized aimed to extend the coverage and simultaneously ensure the quality of the MS² spectra. As a result, 219 components from PNF were identified or tentatively characterized, and 40 thereof could be absorbed. Moreover, 11 metabolites were characterized from the rat plasma. The metabolic pathways mainly included the phase I (deglycosylation and oxidation). To the best of our knowledge, this is the first report that systematically studies the in vivo metabolites of PNF, which can assist in better understanding its tonifying effects and benefit its further development.

Integrative Analysis of Transcriptomic and Metabolomic Data for Identification of Pathways Related to Matrine-Induced Hepatotoxicity

Matrine (MT) is a major bioactive compound extracted from Sophorae tonkinensis. However, the clinical application of MT is relatively restricted due to its potentially toxic effects, especially hepatotoxicity. Although MT-induced liver injury has been reported, little is known about the underlying molecular mechanisms. In this study, transcriptomics and metabolomics were applied to investigate the hepatotoxicity of MT in mice. The results indicated that liver injury occurred when the administration of MT (30 or 60 mg/kg, i.g) lasted for 2 weeks, including dramatically increased alanine aminotransferase (ALT), aspartate aminotransferase (AST), etc. The metabolomic results revealed that steroid biosynthesis, purine metabolism, glutathione metabolism, and pyruvate metabolism were involved in the occurrence and development of MT-induced hepatotoxicity. Further, the transcriptomic data indicated that the downregulation of NSDHL with CYP51, FDFT1, and DHCR7, involved in steroid biosynthesis, resulted in a lower level of cholic acid. Besides, Gstps and Nat8f1 were related to the disorder of glutathione metabolism, and HMGCS1 could be treated as the marker gene of the development of MT-induced hepatotoxicity. In addition, other metabolites, such as taurine, flavin mononucleotide (FMN), and inosine monophosphate (IMP), also made a contribution to the boosting of MT-induced hepatotoxicity. In this work, our results provide clues for the mechanism investigation of MT-induced hepatotoxicity, and several biomarkers (metabolites and genes) closely related to the liver injury caused by MT are also provided. Meanwhile, new insights into the understanding of the development of MT-induced hepatotoxicity or other monomer-induced hepatotoxicity were also provided.

Targeted discovery and characterization of secoiridoid glycosides from Jasminum pentaneurum Hand.-Mazz by ultra-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry based on diagnostic ion and neutral loss filtering strategy

In this study, we proposed an integrated analytical strategy for the rapid and comprehensive discovery of a specific class of secoiridoid glycosides from a Yao medicine, Jasminum pentaneurum Hand.-Mazz. The strategy fully took advantage of the accuracy of ultra-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry, and the efficiency of diagnostic ion filtering and neutral loss filtering. 24 secoiridoid glycosides, including 3 known ones and 21 unreported ones, were rapidly discovered and characterized based on the detail analysis of their MS data. Particularly, 10-syringicoyl-ligustroside (18) was isolated under the guidance of MS analysis. Its chemical structure was elucidated on the base of extensive spectroscopic data analysis, and absolute configuration was further elucidated by comparison of its experimental and electronic circular dichroism spectra. Furthermore, the MS data of 18 was analyzed and the corresponding results indicated that its fragment pathway was fully consistent with the applied diagnostic ion filtering and neutral loss filtering rules and thus the precision and efficiency of the integrated strategy were validated. The result demonstrated that the proposed integrated strategy could serve as a rapid, accurate, and comprehensive targeted components discovery method to effectively screen out those ingredients of interest from the complex herbal medicines. This article is protected by copyright. All rights reserved.

A database-guided integrated strategy for comprehensive chemical profiling of traditional Chinese medicine

A comprehensive chemical profiling of traditional Chinese medicine is the basic issue for further pharmacological research and quality assessment. To facilitate chemical identification and potential components discovery, the present study proposed an integrated identification strategy guided by a self-built component database constructed from literatures to carry out the global profiling of complex matrixes. Lanqin Oral Liquid was applied as example to validate the feasibility of this strategy. Based on LQL Component Database containing 710 compounds, modified MDF windows was established to extract the interested analogues, isoquinoline alkaloids, flavonoids and iridoid glycosides, according to their regular integral masses and mass defect. For compounds with characteristic substructures, such as quinic acids, crocins and some glycoside derivatives, the associated neutral losses and diagnostic fragment ions were collected to assist in profiling. Directly matching the m/z or formulas in database was proposed to components with limited regularity of accurate masses and substructures, like indole alkaloids, sesquiterpenes and some nucleosides. Eventually, 170 ions of 1038 precursor ions were identified or temporarily deduced, including 59 alkaloids, 36 flavonoids, 48 terpenoids, 24 organic acids and their derivatives, 2 oligosaccharides, and 1 lignans. Among them, 52 putative compounds were confirmed by chemical standards. The results indicated that the database-oriented identification strategy could locate potential components quickly and eliminate interfering ions, which have the potential for in-depth analysis of compounds.

Spectrum-Effect Relationship Analysis of Bioactive Compounds in Zanthoxylum nitidum (Roxb.) DC. by Ultra-High Performance Liquid Chromatography Mass Spectrometry Coupled With Comprehensive Filtering Approaches

Zanthoxylum nitidum (Roxb.) DC. (ZN), with strong effects of anti-inflammation and antioxidant activities is treated as a core herb in traditional Chinese medicine (TCM) preparation for treating stomachache, toothache, and rheumatoid arthritis. However, the active ingredients of ZN are not fully clarified due to its chemical complexity. In the present study, a double spectrum–effect analysis strategy was developed and applied to explore the bioactive components in herbs, and ZN was used as an example. Here, the chemical components in ZN were rapidly and comprehensively profiled based on the mass defect filtering-based structure classification (MDFSC) and diagnostic fragment-ion-based extension approaches. Furthermore, the fingerprints of 20 batches of ZN samples were analyzed by high-performance liquid chromatography, and the anti-inflammatory and antioxidant activities of the 20 batches of ZN samples were studied. Finally, the partial least squares regression (PLSR), gray relational analysis models, and Spearman’s rank correlation coefficient (SRCC) were applied to discover the bioactive compounds in ZN. As a result, a total of 48 compounds were identified or tentatively characterized in ZN, including 35 alkaloids, seven coumarins, three phenolic acids, two flavonoids, and one lignan. The results achieved by three prediction models indicated that peaks 4, 12, and 17 were the potential anti-inflammatory compounds in ZN, whereas peaks 3, 5, 7, 12, and 13 were involved in the antioxidant activity. Among them, peaks 4, 5, 7, and 12 were identified as nitidine, chelerythrine, hesperidin, and oxynitidine by comparison with the standards and other references. The data in the current study achieved by double spectrum–effect analysis strategy had great importance to improve the quality standardization of ZN, and the method might be an efficiency tool for the discovery of active components in a complex system, such as TCMs.

An image-based fingerprint-efficacy screening strategy for uncovering active compounds with interactive effects in Yindan Xinnaotong soft capsule

BACKGROUND

Yindan Xinnaotong soft capsule (YDXNT) is a clinically effective herbal prescription used for the treatment of cardiovascular and cerebrovascular diseases. Since Chinese medicines (CMs) exert their effects via a "multiple-components and multiple-targets" mode, discovery of the active compounds with interactive effects may contribute to reveal their mechanisms of action.

PURPOSE

This study aimed to establish an image-based fingerprint-efficacy screening strategy to identify active compounds with interaction effects from CM prescription, using YDXNT to inhibit microglia-mediated neuroinflammation as an instance.

METHODS

A multi-component random content-oriented chemical library of YDXNT was constructed by uniform design, and their chemical fingerprint was profiled by liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) methods. Then the neuroinflammation activities of chemical library members of YDXNT were determined by image-based dual phenotypic quantification. Subsequently, fingerprint-efficacy correlation and random forest analysis were applied to predict the potentially active compounds with interactive effects. Finally, the interactive effects among the active compounds were confirmed by quantitative polymerase chain reaction (qPCR) and apoptosis analysis, and network pharmacology was applied to explore the possible mechanisms.

RESULTS

Image-based fingerprint-efficacy correlation analysis revealed that six tanshinones (TNs) and four flavonoids (FAs) were potential anti-neuroinflammatory compounds. The inter-family of TNs and FAs possessed obvious interactive effects (combination index ≤ 0.825). Moreover, the combination of scutellarein and tanshinone I (2:1, w/w) was discovered as the possible interactive combinatorial components, which, comparing with individual scutellarein or tanshinone I, shown more powerful effects on anti-inflammatory and anti-apoptotic effects in lipopolysaccharide (LPS)-induced BV2 cells. Network pharmacology showed that the active compounds might suppress microglia-mediated neuroinflammation via multiple targets in the T cell receptor, Jak-STAT, and Toll-like receptor signaling pathways.

CONCLUSION

The image-based fingerprint-efficacy strategy simplifies the screening process of efficacious component combinations in CMs for complex diseases, which also offers a promising approach to explore the integrative therapeutic mechanisms of CMs.

Characterization of multiple chemical components of GuiLingJi by UHPLC-MS and 1H NMR analysis

GuiLingJi (GLJ), a classic traditional Chinese medicine (TCM) formula, is composed of over 20 herbs, according to the Pharmacopeia of the People's Republic of China. Owing to its various activities, GLJ has been used in clinical settings for more than 400 years in China. However, the ambiguous chemical material basis limits the development of studies on the quality control and pharmacological mechanisms of GLJ. Therefore, comprehensive characterization of the multiple chemical components of GLJ is of great significance for the modernization of this formula. Given the great variety of herbs in GLJ, both UHPLC-MS and ¹H NMR techniques were employed in this study. In addition, solvent extraction with different polarities was used to eliminate signal interference and the concentration of trace components. A variety of MS analytic methods were also used, including implementation of a self-built compound database, diagnostic ion filtering, mass defect filtering, and Compound Discoverer 3.0 analysis software. Based on the above strategies, a total of 150 compounds were identified, including 5 amino acids, 13 phenolic acids and glycosides, 11 coumarins, 72 flavones, 20 triterpenoid and triterpenoid saponins, 23 fatty acids, and 6 other compounds. Moreover, 13 compounds were identified by ¹H NMR spectroscopy. The UHPLC-MS and ¹H NMR results supported and complemented each other. This strategy provides a rapid approach to analyzing and identifying the chemical composition of Chinese herbal prescriptions. The current study provides basis for further research on the quality control and pharmacological mechanism of GLJ.

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The integrated approach of UHPLC-MS and ¹H NMR techniques coupled with polarity partition strategy has been used for comprehensively characterizing the multiple chemical components of GLJ.

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A variety of HRMS analytic methods used included self-built compounds database, diagnostic ions filtering, mass defect filtering, and software analysis for rapid identification the chemical components of GLJ.

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The 163 compounds including flavones, phenolic acids and glycosides, triterpenoid and triterpenoid saponins, coumarin, fatty acids, amino acids, organic acids, organic bases and sugars were rapidly identified, and to clarify the chemical material basis of GLJ.

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Established an analysis strategy which could be applied to other TCM formula for comprehensive characterization and identification of chemical components.

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.

Insight into chemical basis of traditional Chinese medicine based on the state-of-the-art techniques of liquid chromatography-mass spectrometry

Traditional Chinese medicine (TCM) has been an indispensable source of drugs for curing various human diseases. However, the inherent chemical diversity and complexity of TCM restricted the safety and efficacy of its usage. Over the past few decades, the combination of liquid chromatography with mass spectrometry has contributed greatly to the TCM qualitative analysis. And novel approaches have been continuously introduced to improve the analytical performance, including both the data acquisition methods to generate a large and informative dataset, and the data post-processing tools to extract the structure-related MS information. Furthermore, the fast-developing computer techniques and big data analytics have markedly enriched the data processing tools, bringing benefits of high efficiency and accuracy. To provide an up-to-date review of the latest techniques on the TCM qualitative analysis, multiple data-independent acquisition methods and data-dependent acquisition methods (precursor ion list, dynamic exclusion, mass tag, precursor ion scan, neutral loss scan, and multiple reaction monitoring) and post-processing techniques (mass defect filtering, diagnostic ion filtering, neutral loss filtering, mass spectral trees similarity filter, molecular networking, statistical analysis, database matching, etc.) were summarized and categorized. Applications of each technique and integrated analytical strategies were highlighted, discussion and future perspectives were proposed as well.

Explore the effects of Shidan granules on chronic atrophic gastritis using LC-MS based plasma metabolomics study

Shidan granule (SDG), a traditional Chinese medicine in-hospital preparation, has been demonstrated to exert good effects on chronic atrophic gastritis (CAG) in clinics. However, the underlying mechanism of SDG against CAG is still unclear. This study utilized an untargeted plasma metabolomics approach to explore the potential mechanism of SDG in CAG rats using LC-MS and pattern recognition analysis. The results indicated that SDG could effectively improve the biochemical indexes and pathology features of CAG rats. Nineteen potential biomarkers (variable importance in projection > 1 and P < 0.05) contributing to CAG progress were identified. After SDG intervention, 17 biomarkers were obviously restored to normal levels. Further metabolic pathway analysis showed that aspartate and glutamate metabolism, arachidonic acid metabolism, arginine and proline metabolism, and TCA cycle were the most related pathways for SDG treatment. Based on these findings, the main mechanisms of SDG against CAG might be attributed to the regulatory effects of energy balance, inflammatory suppression, and improvement in disturbed amino acid and lipid metabolism. This study provided information for the mechanism research of SDG against CAG and would promote its clinical application.

A strategy for intelligent chemical profiling-guided precise quantitation of multi-components in traditional Chinese medicine formulae-QiangHuoShengShi decoction

Due to the tremendous clinical value, more and more Traditional Chinese Medicines (TCMs) and their formulae are attracted by world's attention. QiangHuoShengShi (QHSS) decoction is one of classic TCM formulae, which is clinically used for treating various rheumatic diseases. However, the phytochemical constituents of QHSS have rarely been reported. A simple, intelligent, and comprehensive strategy was developed to characterize the phytochemical-fingerprint and quantify the chemical-markers for precise quality evaluation of QHSS. Firstly, a new deep-learning assisted mass defect filter (MDF) method was built for rapid and accurate classification of mass spectrum (MS) ions acquired by ultra-high performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UHPLC-Q-TOF/MS). Subsequently, herb species-specific chemical-category and characteristic identification were used for further characterization of multi-components. As the result, seven major types of compounds in QHSS were intelligently differentiated and 183 phytochemical compounds were tentatively identified. Finally, a sensitive scheduled multiple reaction monitoring (sMRM) detection method was applied to precisely quantify 37 target analytes in QHSS decoction. This integrated strategy would provide an alternative method for chemical-material basis study of more herbal medicine or natural products.

Diagnostic ion filtering targeted screening and isolation of anti-inflammatory iridoid glycosides from Hedyotis diffusa

Efficient and targeted screening and isolation of bioactive compounds from complex natural products is still a challenging work. Herein, diagnostic ion filtering based high-performance liquid chromatography-quadrupole time-of-flight-tandem mass spectrometry was firstly developed to screen six main iridoid glycosides from Hedyotis diffusa. Then, online extraction-high-speed counter current chromatography was proposed for targeted enrichment and preparative isolation using ethyl acetate/n-butanol/water (4.5:0.5:5, v/v/v) as solvent system. After that, Sephadex LH-20 column chromatography using methanol as solvent system was selected for further purification of six iridoid glycosides with purities over 98%. They were finally identified as monotropein, desacetylasperuloside acid, asperuloside, 6-O-(Z)-p-coumaroyl scandoside methyl ester, 6-O-(Z)-feruloyl scandoside methyl ester, and 6-O-(E)-p-coumaroyl scandoside methyl ester. And their anti-inflammatory activities were evaluated and confirmed by lipopolysaccharide activated RAW 264.7 macrophages. Obviously, the results provide a scientific basis for the potential applications of H. diffusa, and the developed methodology is efficient and reliable for targeted screening and isolation of bioactive compounds from natural products.

Deciphering bioactive compounds of complex natural products by tandem mass spectral molecular networking combined with an aggregation-induced emission based probe

Natural products are great treasure troves for the discovery of bioactive components. Current bioassay guided fractionation for identification of bioactive components is time- and workload-consuming. In this study, we proposed a robust and convenient strategy for deciphering the bioactive profile of natural products by mass spectral molecular networking combined with rapid bioassay. As a proof-of-concept, the strategy was applied to identify angiotensin converting enzyme (ACE) inhibitors of Fangjihuangqi decoction (FJHQD), a traditional medicine clinically used for the treatment of heart failure. The chemical profile of FJHQD was comprehensively revealed with the assistance of tandem mass spectral molecular networking, and a total of 165 compounds were identified. With characterized constituents, potential clinical applications of FJHQD were predicted by Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine, and a range of cardiovascular related diseases were significantly enriched. ACE inhibitory activities of FJHQD and its constituents were then investigated with an aggregation-induced emission based fluorescent probe. FJHQD exhibited excellent ACE inhibitory effects, and a bioactive molecular network was established to elucidate the ACE inhibitory profile of constituents in FJHQD. This bioactive molecular network provided a panoramic view of FJHQD's ACE inhibitory activities, which demonstrated that flavones from Astragali Radix and Glycyrrhizae Radix et Rhizoma, saponins from Astragali Radix, and sesquiterpenoids from Atractylodis Macrocephalae Rhizoma were principal components responsible for this effect of FJHQD. Among them, four novel ACE inhibitors were the first to be reported. Our study indicated that the proposed strategy offers a useful approach to uncover the bioactive profile of traditional medicines and provides a pragmatic workflow for exploring bioactive components.

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A novel strategy for deciphering the bioactive profile of traditional medicines was proposed.

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The chemical profile of FJHQD was revealed with assist of tandem mass spectral molecular networking.

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Four new angiotensin converting enzyme inhibitors were discovered.

Comparatively Evaluating the Role of Herb Pairs Containing Angelicae Sinensis Radix in Xin-Sheng-Hua Granule by Withdrawal Analysis

The present study aims to investigate the roles of herb pairs containing Angelicae Sinensis Radix (Danggui) in Xin-Sheng-Hua Granule (XSHG) on hemolytic and aplastic anemia (HAA) mice. HAA model mice were induced by acetyl phenylhydrazine and cyclophosphamide; then the samples of XSHG and its decomposed recipes (DY, DC, DT, DH, DJ, and DZ) were orally administrated to these mice. Indicators of peripheral blood routine, organ index, and ATPase activities were tested. Moreover, the main effective components in these samples were also analyzed by UHPLC-TQ-MS/MS. Clear separation between the control and model groups from score plot of principal component analysis (PCA) was easily seen, indicating that HAA model was successfully conducted. Afterwards, relative distance calculation method between dose groups and control group from PCA score plot was adopted to evaluate the integrated effects of hematinic function of different samples. And the orders of hematinic effects were as follows: XHSG > DJ > DT > DZ > DH > DC > DY. Further analysis of these samples by UHPLC-TQ-MS/MS revealed that XSHG underwent complicated changes when herb pairs containing Danggui were excluded from XSHG, respectively. Compared with XSHG, the vast majority of active compounds in sample DY (formula minus herb pair Danggui-Yimucao) decreased significantly, which could partly explain why herb pair Danggui-Yimucao made great contribution to XSHG. These findings showed that withdrawal analysis method is a valuable tool to analyze the impacts of herb pairs containing Danggui on XSHG, which could lay foundation to reveal the compatibility rules of this formula.

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.