Source attribution and structure classification-assisted strategy for comprehensively profiling Chinese herbal formula: Ganmaoling granule as a case

Isolating Antipathogenic Fungal Coumarins from Coriaria nepalensis and Determining Their Primary Mechanism In Vitro

Through bioassay-guided isolation, eight undescribed coumarins (1-8), along with six reported coumarins (9-14), were obtained from Coriaria nepalensis. The new structures were determined by using IR, UV, NMR, HRESIMS, and ECD calculations. The results of the biological activity assays showed that compound 9 exhibited broad spectrum antifungal activities against all tested fungi in vitro and a significant inhibitory effect on Phytophthora nicotianae with an EC50 value of 3.00 μg/mL. Notably, compound 9 demonstrated greater curative and protective effects against tobacco balack shank than those of osthol in vivo. Thus, 9 was structurally modified to obtain new promising antifungal agents, and the novel derivatives (17b, 17j, and 17k) exhibited better effects on Sclerotinia sclerotiorum than did lead compound 9. Preliminary mechanistic exploration illustrated that 9 could enhance cell membrane permeability, destroy the morphology and ultrastructure of cells, and reduce the exopolysaccharide content of P. nicotianae mycelia. Furthermore, the cytotoxicity results revealed that compound 9 exhibited relatively low cytotoxicity against HEK293 cell lines with an inhibition rate of 33.54% at 30 μg/mL. This research is promising for the discovery of new fungicides from natural coumarins with satisfactory ecological compatibility.

Secondary metabolites related to the resistance of Psidium spp. against the nematode Meloidogyneenterolobii

The guava tree (Psidium guajava) is a tropical species native to South America and is recognized as the 11th most economically important fruit tree in Brazil. However, the presence of the nematode Meloidogyne enterolobii and the fungus Fusarium solani in the roots of guava plants leads to the development of root galls, causing significant damage. In contrast, the species P. guineense and P. cattleianum have been identified as resistant and immune to the nematode, respectively. In this study, the researchers aimed to compare the metabolomic profiles of infected and uninfected roots of P. guajava, P. cattleianum, and P. guineense using mass spectrometry coupled with liquid chromatography (LC-MS). The goal was to identify secondary metabolites that could potentially be utilized as biochemical resources for nematode control. The findings of the study demonstrated that the plant metabolism of all three species undergoes alterations in response to the phytopathogen inoculation. By employing molecular networks, the researchers identified that the secondary metabolites affected by the infection, whether produced or suppressed, are primarily of a polar chemical nature. Further analysis of the database confirmed the polar nature of the regulated substances after infection, specifically hydrolysable tannins and lignans in P. guineense and P. cattleianum. Interestingly, a group of non-polar substances belonging to the terpene class was also identified in the resistant and immune species. This suggests that these terpenes may act as inhibitors of M. enterolobii, working as repellents or as molecules that can reduce oxidative stress during the infection process, thus enhancing the guava resistance to the nematode. Overall, this study provides valuable insights into the metabolic alterations occurring in different Psidium spp. in response to M. enterolobii infection. The identification of specific secondary metabolites, particularly terpenes, opens up new possibilities for developing effective strategies to control the nematode and enhance guava resistance.

Rapid screening and characterization of 2-(2-phenylethyl)chromones in agarwood by UHPLC-Q-Exactive Orbitrap-MS

The purpose of this study is to develop an improved comprehensive data filtering strategy, which was implemented primarily through the Microsoft Office platform's Excel software for rapid screening of potential 2-(2-phenylethyl)chromone (PEC) monomers and their dimers (PEC dimers) obtained from agarwood. A total of 108 PEC monomers and 30 PEC dimers in agarwood were characterized. In conclusion, the results obtained in this work could provide useful information for the future utilization of agarwood. In particular, it is the first time to conduct an in-depth analysis of the MS/MS fragmentation behavior of a large number of PEC monomers and PEC dimers, including the identification of substituent positions of them. The proposed data filtering strategy could improve the comprehensive characterization efficiency of complex components in spices.

Targeted identification of glycosylated flavones and isomers in green tea through integrated ion-filtering strategy and mass-fragmentation characteristics based on the UPLC-Q-Orbitrap-MS/MS platform

Glycosylated flavones (GFs) are important components of green tea and have various structures and isomers. The annotation of GFs' chemical structures is challenging. Ultrahigh-performance liquid chromatography-high resolution mass spectrometry can provide informative mass ions for GF annotation. However, distinguishing the mass features of GFs from those of thousands of ions is difficult. In this study, integrated ion-filtering strategies for O- and C-glycosyl flavones were constructed, and the mass-fragmentation characteristics were summarized from GF standards. Ultimately, 29 GFs with different types of aglycones and glycosides, connection modes, and locations were annotated. According to principal component analysis and t-test results, significant differences were observed in the contents of 16 components in the two kinds of tea. Among them, the contents of 11 GFs in autumn teas were significantly higher than those in spring teas. This study provided an efficient strategy for isomer annotation in food analysis.

An integrated strategy toward comprehensive characterization and quantification of multiple components from herbal medicine: An application study in Gelsemium elegans

Objective

To develop a powerful integrated strategy based on liquid chromatography coupled with mass spectrometry (LC-MS) systems for the comprehensive characterization and quantification of multiple components of herbal medicines.

Methods

Firstly, different mobile phase additives, analysis time, and MS acquisition modes were orthogonally tested with liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (LC-QTOF/MS) in order to detect as many components of Gelsemium elegans as possible with high peak intensity. Secondly, several data mining strategies, including database searching, diagnostic ion filtering and neutral loss filtering, were utilized to perform chemical profiling. Subsequently, this study focused on the quantification and validation of the performance of a liquid chromatography-triple mass spectrometry (LC-QqQ/MS) assay based on derivative multiple reaction monitoring (DeMRM).

Results

A total of 147 components from G. elegans were characterized, among them 116 nontarget components were reported for the first time. A sensitive and reproducible LC-QqQ/MS method was successfully developed and validated for the simultaneous relative quantification of 41 components of G. elegans. This LC-QqQ/MS method was then applied to compare the contents of components in the roots, stems and leaves.

Conclusion

The present integrated strategy would significantly contribute to chemical studies on herbal medicine, and its utility could be extended to other research fields, such as metabolomics, quality control, and pharmacokinetics.

Investigation of the chemical compounds in Pheretima aspergillum (E. Perrier) using a combination of mass spectral molecular networking and unsupervised substructure annotation topic modeling together with in silico fragmentation prediction

Untargeted mass spectrometry analysis is one of the most challenging and meaningful steps in the rapid structural elucidation of the highly complex and diverse constituents of traditional Chinese medicine. Specifically, it is a laborious and time-consuming way to identify unknown compounds. Herein, a workflow was proposed to expedite the annotations of the chemical structures in Pheretima aspergillum (E. Perrier) (Di-Long, DL). First, ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOFMS) was performed to obtain the untargeted mass spectral data. Then, the spectral data were uploaded to the Global Natural Products Social Molecular Networking (GNPS) platform to create a network and extract the Mass2Motifs (co-occurring fragments and neutral losses) using unsupervised substructure annotation topic modeling (MS2LDA). Finally, a structural analysis was performed using the proposed workflow of MS2LDA in combination with mass spectral molecular networking and in silico fragmentation prediction. As a result, a total of 124 compounds from DL were effectively characterized, of which 89 (7 furan sulfonic acids, 57 phospholipids and 25 carboxamides) were identified as potentially new compounds from DL. The results presented in this article significantly improve the understanding of the chemical composition of DL and provide a solid scientific basis for the future study of the quality control, underlying pharmacology and mechanism of DL. Moreover, the proposed workflow was used for the first time to accelerate the annotations of unknown molecules from TCM. Furthermore, this workflow will increase the efficiency of characterizing the 'unknown knowns' and elucidation of the 'unknown unknowns' from TCM, which are crucial steps of discovering the natural product drugs in TCM.

An ultra-robust fingerprinting method for quality assessment of traditional Chinese medicine using multiple reaction monitoring mass spectrometry

Chromatographic fingerprinting has been perceived as an essential tool for assessing quality and chemical equivalence of traditional Chinese medicine. However, this pattern-oriented approach still has some weak points in terms of chemical coverage and robustness. In this work, we proposed a multiple reaction monitoring (MRM)-based fingerprinting method in which approximately 100 constituents were simultaneously detected for quality assessment. The derivative MRM approach was employed to rapidly design MRM transitions independent of chemical standards, based on which the large-scale fingerprinting method was efficiently established. This approach was exemplified on QiShenYiQi Pill (QSYQ), a traditional Chinese medicine-derived drug product, and its robustness was systematically evaluated by four indices: clustering analysis by principal component analysis, similarity analysis by the congruence coefficient, the number of separated peaks, and the peak area proportion of separated peaks. Compared with conventional ultraviolet-based fingerprints, the MRM fingerprints provided not only better discriminatory capacity for the tested normal/abnormal QSYQ samples, but also higher robustness under different chromatographic conditions (i.e., flow rate, apparent pH, column temperature, and column). The result also showed for such large-scale fingerprints including a large number of peaks, the angle cosine measure after min-max normalization was more suitable for setting a decision criterion than the unnormalized algorithm. This proof-of-concept application gives evidence that combining MRM technique with proper similarity analysis metrices can provide a highly sensitive, robust and comprehensive analytical approach for quality assessment of traditional Chinese medicine.

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MRM fingerprints are proposed for quality assessment of traditional medicine.

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MRM fingerprints show favorable robustness, coverage and discriminatory capacity.

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Similarity analysis methods for such large-scale fingerprints are proposed.

The analgesic and anti-inflammatory effects of zukamu granules, a traditional Chinese medical formulation

Context: Zukamu granule, a traditional Chinese medicine, has shown clinical treatment efficacy. However, the pharmacodynamic effects and possible anti-inflammatory mechanisms of zukamu are still unclear.Objective: To investigate the analgesic and anti-inflammatory effects and possible mechanisms of zukamu granules on acute lung injury.Materials and methods: Kunming mice and Sprague Dawley rats were gavaged with zukamu (1.35, 2.7 and 5.4 g/kg, respectively) or ganmaoling (GMLG; 2.7 g/kg) once a day for 7 d. Dexamethasone treatment (5 mg/kg) were administered only on the last day. Analgesic effects were evaluated through the hot plate test and acetic acid writhing test. The expression of cytokines and proteins was measured in serum and lung tissues to elucidate the efficacy of zukamu against lung injury.Results: Significant analgesic effects were observed at 30 min after zukamu administration at medium and high doses (p < 0.05), but the effect was not obvious at low dose until 60 min post-administration (p > 0.05). Zukamu treatment at all doses notably reduced the lung wet-to-dry (W/D) ratios compared to that of model rats (p < 0.05) and the effect was more evident at high dose compared to those at medium and low doses. The levels of cytokines and proteins in the lung tissues were inhibited by zukamu.Conclusions: Zukamu exhibited analgesic and protective effects against lung injury via regulating NF-κB signalling and inflammatory cytokines. As zukamu granules contain multiple ingredients, further exploration of the mechanisms underlying its analgesic and anti-inflammatory functions were needed.

A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines

Natural products (NPs) and traditional medicines (TMs) are used for treatment of various diseases and also to develop new drugs. However, identification of drug leads within the immense biodiversity of living organisms is a challenging task that requires considerable time, labor, and computational resources as well as the application of modern analytical instruments. LC-MS platforms are widely used for both drug discovery and quality control of TMs and food supplements. Moreover, a large dataset generated during LC-MS analysis contains valuable information that could be extracted and handled by means of various data mining and statistical tools. Novel sophisticated LC-MS based approaches are being introduced every year. Therefore, this review is prepared for the scientists specialized in pharmacognosy and analytical chemistry of NPs as well as working in related areas, in order to navigate them in the world of diverse LC-MS based techniques and strategies currently employed for NP discovery and dereplication, quality control, pattern recognition and sample comparison, and also in targeted and untargeted metabolomic studies. The suggested classification system includes the following LC-MS based procedures: elemental composition determination, isotopic fine structure analysis, mass defect filtering, de novo identification, clustering of the compounds in Molecular Networking (MN), diagnostic fragment ion (or neutral loss) filtering, manual dereplication using MS/MS data, database-assisted peak annotation, annotation of spectral trees, MS fingerprinting, feature extraction, bucketing of LC-MS data, peak profiling, predicted metabolite screening, targeted quantification of biomarkers, quantitative analysis of multi-component system, construction of chemical fingerprints, multi-targeted and untargeted metabolite profiling.

Hybrid multidimensional data acquisition and data processing strategy for comprehensive characterization of known, unknown and isomeric compounds from the compound Dan Zhi Tablet by UPLC-TWIMS-QTOFMS

The compound Dan Zhi Tablet (DZT), a reputable traditional Chinese medicine prescription, is widely used for the treatment of ischemic stroke in clinic. However, its systematic chemical constituents have rarely been elucidated, which hampers its quality evaluation, the study of bioactive constituents and the mechanism of action interpretation. In this study, we developed a combination of multidimensional data acquisition and data processing strategy with the aim to globally and comprehensively identify the chemical constituents in DZT based on UPLC-TWIMS-QTOFMS. First, multidimensional acquisition modes (MSE, Fast DDA and HDMSE) were performed on UPLC-TWIMS-QTOFMS. Second, targeted characterizations of the known compounds and their analogues present in DZT were carried out on the basis of the corresponding commercial standards or Mass2Motifs. Third, untargeted identification of unknown compounds in DZT was performed by extracting shared Mass2Motifs from the raw fragmentation spectra. Finally, the coeluting isomers were characterized using a precursor and/or product ion mobility. Consequently, 202 compounds were detected from DZT: 29 of them were unambiguously identified by comparison with reference compounds, 29 unknown compounds were discovered in specific medicinal materials, and ten pairs of coeluting isomers, which could not be distinguished using conventional MSE or Fast-DDA, were resolved using HDMSE only. This strategy was successfully used for the rapid and global identification of complex compounds including known, unknown and coeluting isomeric compounds in DZT and provided helpful chemical information for further quality control, pharmacology and active mechanism research on DZT.

Simultaneously targeted and untargeted multicomponent characterization of Erzhi Pill by offline two-dimensional liquid chromatography/quadrupole-Orbitrap mass spectrometry

Large-scale targeted and untargeted metabolites characterization can be achieved by feat of different liquid chromatography/mass spectrometry (LC-MS) platforms by multiple MS experiments or using data-independent acquisition followed by precursor-product ions matching based on certain algorithms. The resulting insufficiency in efficiency and availability greatly restricts the applicability of these strategies in large-scale profiling and identification of various metabolites. A strategy simultaneously enabling both the targeted and untargeted metabolites characterization is established on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer, by integrating precursor ions list-triggered data-dependent MS² acquisition (PIL/dd-MS²) of the targeted components and using the "If idle-pick others" (IIPO) function to induce untargeted metabolites fragmentation. A compounds-specific mass defect filter (MDF) algorithm is proposed as a method to generate the PIL. As a proof of concept, this strategy coupled with offline two-dimensional liquid chromatography (2D-LC) was applied to identify the multicomponents of a traditional Chinese medicine formula Erzhi Pill (EZP). A rigid MDF vehicle was elaborated by orthogonal screening of the integer mass and integer mass-dependent dynamic mass defects considering a variation of 20 ppm. The Full MS/dd-MS² method enabling PIL and IIPO exhibited better performance than Full MS/dd-MS² and Targeted SIM/dd-MS² (selected ion monitoring) in respect of the sensitivity in identifying the targeted components and the ability to characterize more untargeted ones. As a consequence, 270 components were separated from EZP, and 146 thereof were selectively characterized. In conclusion, it is a practical, multifaced strategy facilitating the in-depth metabolites profiling and characterization of complex herbal and biological samples.

A hybrid method for the determination of tubeimoside I in rat plasma after oral administration by LC-IT-TOF and UPLC-MS/MS

Tubeimoside I (Tub) is a triterpenoid saponin isolated from Bolbostemma paniculatum[Maxim]Franquet. A sensitive and validated method was developed to determine Tub in rat plasma. This method combined the qualitative and quantitative advantages from liquid chromatography coupled with hybrid ion trap-time of flight mass spectrometer (HPLC-DAD-IT-TOF-MS) and a triple quadrupole-linear ion trap mass spectrometer 5500 (Qtrap 5500), owing to the narrow molecular range of Qtrap 5500 relative to the molecular weight of Tub. Initially, ion detection was achieved using negative ionization mode along with full scan on IT-TOF-MS. The detected precursor and product ions of Tub with the optimal mass parameters were determined on Qtrap 5500 by an online stepped optimization strategy and operated in negative multiple reaction monitoring mode. A simple methanol precipitation was employed with saikosaponin A as internal standard. The method was validated over the range from 20 to 2000 ng/mL with a lower limit of quantification of 20 ng/mL for Tub in plasma. The developed method was successfully applied to the pharmacokinetic study of Tub in rats following oral administration. Moreover, this method has some directive significance for the determination of other drugs whose parent ions exceeding the upper detection limit in Qtrap 5500.

Integrated strategy for identifying minor components in complex samples combining mass defect, diagnostic ions and neutral loss information based on ultra-performance liquid chromatography-high resolution mass spectrometry platform: Folium Artemisiae Argyi as a case study

Ultra-performance liquid chromatography coupled to high-resolution mass spectrometry (UPLC-HRMS) has been used as a powerful tool to profile chemicals in traditional Chinese medicines. However, identification of potentially bioactive compounds is still a challenging work because of the large amount of information contained in the raw UPLC-HRMS data. Especially the ubiquitous matrix interference makes it more difficult to characterize the minor components. Therefore, rapid recognition and efficient extraction of the corresponding parent ions is critically important for identifying the attractive compounds in complex samples. Herein, we propose an integrated filtering strategy to remove un-related or interference MS¹ ions from the raw UPLC-HRMS data, which helps to retain the MS features of the target components and expose the compounds of interest as effective as possible. The proposed strategy is based on the use of a combination of different filtering methods, including nitrogen rule, mass defect, and neutral loss/diagnostic fragment ions filtering. The strategy was validated by rapid screening and identification of 16 methoxylated flavonoids and 55 chlorogenic acids analogues from the raw UPLC-HRMS dataset of Folium Artemisiae Argyi. Particularly, successful detection of several minor components indicated that the integrated strategy has obvious advantages over individual filtering methods, and it can be used as a promising method for screening and identifying compounds from complex samples, such as herbal medicines.

Rapid characterization of chemical constituents and metabolites of Qi-Jing-Sheng-Bai granule by using UHPLC-Q-TOF-MS

Qi-Jing-Sheng-Bai granule is an effective traditional Chinese medicine formula that has been widely used for the treatment of leukopenia post radiotherapy or chemotherapy. However, its chemical constituents were still unclear, which hindered interpreting bioactive constituents and studying integrative mechanisms. In this study, we developed a three-step strategy to characterize the chemical constituents and metabolites of Qi-Jing-Sheng-Bai by using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. As a result, a total of 143 compounds, including 56 flavonoids, 51 saponins, and 36 other compounds, of which contained six pairs of isomers, were tentatively identified and characterized via reference standards and by comparing mass spectrometry data with literature. After oral administration of 15 g/kg Qi-Jing-Sheng-Bai, a number of 42 compounds including 24 prototype compounds and 18 metabolites have been detected in the serum of rats. This work serves as the first reference for Qi-Jing-Sheng-Bai chemical components and metabolites. Moreover, it provided a rapid and valid analytical strategy for characterization of the chemical compounds and metabolites of traditional Chinese medicine formula.

An enhanced targeted identification strategy for the selective identification of flavonoid O-glycosides from Carthamus tinctorius by integrating offline two-dimensional liquid chromatography/linear ion-trap-Orbitrap mass spectrometry, high-resolution diagnostic product ions/neutral loss filtering and liquid chromatography-solid phase extraction-nuclear magnetic resonance

Targeted identification of potentially bioactive molecules from herbal medicines is often stymied by the insufficient chromatographic separation, ubiquitous matrix interference, and pervasive isomerism. An enhanced targeted identification strategy is presented and validated by the selective identification of flavonoid O-glycosides (FOGs) from Carthamus tinctorius. It consists of four steps: (i) enhanced separation and detection by offline two-dimensional liquid chromatography/LTQ-Orbitrap MS (offline 2D-LC/LTQ-Orbitrap MS) using collision-induced dissociation (CID) and high-energy C-trap dissociation (HCD); (ii) improved identification of the major aglycones by acid hydrolysis and LC-SPE-NMR; (iii) simplified spectral elucidation by high-resolution diagnostic product ions/neutral loss filtering; and (iv) more convincing structural identification by matching an in-house library. An offline 2D-LC system configuring an Acchrom XAmide column and a BEH Shield RP-18 UPLC^® column enabled much better separation of the easily co-eluting components. Combined use of CID and HCD could produce complementary fragmentation information. The intensity ratios of the aglycone ion species ([Y₀-H]^-/Y₀^- and [Y₀-2H]^-/Y₀^-) in the HCD-MS² spectra were found diagnostic for discriminating the aglycone subtypes and characterizing the glycosylation patterns. Five aglycone structures (kaempferol, 6-hydroxykaempferol, 6-methoxykaempferol, carthamidin, and isocarthamidin) were identified based on the ¹H-NMR data recorded by LC-SPE-NMR. Of the 107 characterized flavonoids, 80 FOGs were first reported from C. tinctorius. Unknown aglycones, pentose, and novel acyl substituents were discovered. A new compound thereof was isolated and fully identified, which could partially validate the MS-oriented identification. This integral strategy can improve the potency, efficiency, and accuracy in the detection of new compounds from medicinal herbs and other natural sources.

MRM-based strategy for the homolog-focused detection of minor ginsenosides from notoginseng total saponins by ultra-performance liquid chromatography coupled with hybrid triple quadrupole-linear ion trap mass spectrometry

A validated MRM-based strategy was established for targeted detection of minor ginsenosides from NGTS by using a LC-Q-Trap/MS.