Multi-omics profiling of PC-3 cells reveals bufadienolides-induced lipid metabolic remodeling by regulating long-chain lipids synthesis and hydrolysis.

INTRODUCTION: Lipid metabolism participates in various biological processes such as proliferation, apoptosis, migration, invasion, and maintenance of membrane homeostasis of prostate tumor cells. Bufadienolides, the active ingredients of Chansu, show a robust anti-proliferative effect against prostate cancer cells in vitro, but whether bufadienolides could regulate the lipid metabolism in prostate cancer has not been evaluated. OBJECTIVES: Our study explored the regulatory effects of bufadienolides on lipid metabolism in human prostate carcinoma cells (PC-3). METHODS: Untargeted lipidomics and transcriptomics were combined to study the effect of different bufadienolides interventions on lipid and gene changes of PC-3 cells. The key genes related to lipid metabolism and prostate cancer development were verified by qPCR and western blotting. RESULTS: Lipidomic analysis showed that the active bufadienolides significantly downregulated the content of long-chain lipids of PC-3 cells. Based on transcriptomic and qPCR analyses, many genes related to lipid metabolism were significantly regulated by active bufadienolides, such as ELOVL6, CYP2E1, GAL3ST1, CERS1, PLA2G10, PLD1, SPTLC3, and GPX2. Bioinformatics analysis of the Cancer Genome Atlas database and literature retrieval showed that elongation of very long-chain fatty acids protein 6 (ELOVL6) and phospholipase D1 (PLD1) might be important regulatory genes. Western blot analysis revealed that active bufadienolides could downregulate PLD1 protein levels which might promote anti-prostate cancer effect. CONCLUSIONS: All these findings support that bufadienolides might induce lipid metabolic remodeling by regulating long-chain lipids synthesis and phospholipid hydrolysis to achieve an anti-prostate cancer effect, and PLD1 would probably be the key protein.

An improved strategy for identification and annotation of easily in-sourced dissociation diterpene lactones from plant natural products: Taking Andrographis paniculata (Burm. f.) as an example.

RATIONALE: Diterpene lactones (DL) in Andrographis paniculata (AP) are known as "natural antibiotics" for their excellent antibacterial activity. During mass spectrometry (MS) analysis, the hydroxyl groups in the AP DL skeleton are prone to neutral loss of H2 O, producing high in-source fragment peaks and affecting the characterization of these components. METHODS: Mass tags were applied during the MS data acquisition step, and special adduct ion form was used to guide the data processing and characterization steps. Besides, the total number of characterized AP DLs significantly increased when combining the number of neutrally lost H2 O from AP DLs, incorporating information on the diagnostic ions, and adopting molecular networks generated with the Global Natural Products Social Molecular Networking database. RESULTS: Ninety-nine DLs, comprising 6 monohydroxyl groups, 20 dihydroxyl groups, 27 trihydroxy groups, and 46 DLs with more than 3 hydroxyl groups, were characterized from AP. In addition, based on the characteristic fragments in the product ions (C3 H4 , Δm/z = 40.03 Da), it could be assumed that 90 DLs had the C19-OH structure among the identified DLs. The current study provides a new approach for collecting, processing, and characterizing MS analysis of natural DLs prone to in-source fragmentation. CONCLUSIONS: MS characterization of AP DLs was significantly improved, and many potential new compounds were identified in AP. This characterization provides new methods for the purification and identification of AP DLs.

Dissecting chemical markers for controlling "Paozhi" method of traditional Chinese medicine with untargeted metabolomics: Vinegar-baked Euphorbia kansui as a case study.

The processing of Traditional Chinese Medicine requires the appropriate parameters, while the specific chemical markers are still absent to obtain the optimized processing. In this study, we used vinegar-baked Euphorbia kansui as a case to dissect the chemical markers for the baking process using untargeted metabolomics. The robust chemical markers were selected based on the three rules, correlation, significant difference, and controllability. All the differential features were categorized based on their mass defects. After the differential analysis, 310 differential compounds were screened out and could be mainly divided into six categories: diacylglycerols and triacylglycerols demonstrated increasing trends with the baking time in the discriminant model, while ingenane-type diterpenes, jatrophane-type diterpenes, fatty acid esters, and fatty acids had decreasing trends. It was unexpected to find that the diterpenes did not correlate with the baking time. Only very few compounds meet the three rules. They were validated with a high-performance liquid chromatography method. Finally, only 13-Hydroxy-9,11-octadecadienoic acid and its isomer 9-Hydroxy-10,12-octadecadienoic acid could be used further to differentiate the commercial vinegar-baked Euphorbia kansui. It would be of interest to evaluate whether these two compounds could be utilized as markers to control more processing methods in future studies.

Information Entropy-Based Strategy for the Quantitative Evaluation of Extensive Hyperspectral Images to Better Unveil Spatial Heterogeneity in Mass Spectrometry Imaging.

Hyperspectral images can be generated from mass spectrometry imaging (MSI) data for the intuitive data visualization purpose. However, hundreds of HSIs can be generated by different dimensionality reduction methods, which poses great challenges in selecting the high-quality images with the best intuitive visualization results of the MSI data. Here, we presented a novel approach that objectively evaluates the image quality of the hyperspectral images. The applicability of this method was demonstrated by analyzing the MSI data acquired from human prostate cancer biopsy samples and mouse brain tissue section, which harbored an intrinsic tissue heterogeneity. Our method was based on the information entropy and contrast measured from image information content and image definition, respectively. The heterogeneity of the MSI data from high-dimensional space was reduced to three-dimensional embeddings and thoroughly evaluated to achieve satisfactory visualization results. The application of information entropy and contrast can be used to choose the optimized visualization results rapidly and objectively from an extensive number of hyperspectral images and be adopted to evaluate and optimize different dimensionality reduction algorithms and their hyperparameter combinations. In conclusion, the information entropy-based strategy could be a bridge between chemometrician and biologists.

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.

Mass spectrometry imaging: new eyes on natural products for drug research and development.

Natural products (NPs) and their structural analogs represent a major source of novel drug development for disease prevention and treatment. The development of new drugs from NPs includes two crucial aspects. One is the discovery of NPs from medicinal plants/microorganisms, and the other is the evaluation of the NPs in vivo at various physiological and pathological states. The heterogeneous spatial distribution of NPs in medicinal plants/microorganisms or in vivo can provide valuable information for drug development. However, few molecular imaging technologies can detect thousands of compounds simultaneously on a label-free basis. Over the last two decades, mass spectrometry imaging (MSI) methods have progressively improved and diversified, thereby allowing for the development of various applications of NPs in plants/microorganisms and in vivo NP research. Because MSI allows for the spatial mapping of the production and distribution of numerous molecules in situ without labeling, it provides a visualization tool for NP research. Therefore, we have focused this mini-review on summarizing the applications of MSI technology in discovering NPs from medicinal plants and evaluating NPs in preclinical studies from the perspective of new drug research and development (R&D). Additionally, we briefly reviewed the factors that should be carefully considered to obtain the desired MSI results. Finally, the future development of MSI in new drug R&D is proposed.

A simple and effective method for identification of Fraxini Cortex from different sources by multi-mode fingerprint combined with chemometrics.

Fraxini Cortex has a long history of being used as a medicinal plant in traditional Chinese medicine. However, it is challenging to differentiate and make quality evaluations for Fraxini Cortex from different origins due to their similarities in morphological features, as well as general chemical composition using traditional chemical analytical methods. In this study, a simple and effective method was developed to identify Fraxini Cortex from different origins by multi-mode fingerprint combined with chemometrics. Digital images of the high-performance thin-layer chromatography profiles were converted to grayscale intensity, and the common patterns of high-performance thin-layer chromatography fingerprints were generated with ChemPattern software. Authentication and quality assessment were analyzed by similarity analysis, hierarchical cluster analysis, principal component analysis, and multivariate analysis of variance. The ultra-high-performance liquid chromatography fingerprints were analyzed by similarity analysis, principal component analysis, and orthogonal partial least square-discriminant analysis. When combined with chemometrics, high-performance thin-layer chromatography and ultra-high-performance liquid chromatography fingerprint provided a simple and effective method to evaluate the comprehensive quality of Fraxini Cortex, and to distinguish its two original medicinal materials (Fraxinus chinensis Roxb. and Fraxinus rhynchophylla Hance.) recorded in the Chinese Pharmacopeia and its three adulterants (Fraxinus mandschurica Rupr., Fraxinus pennsylvanica Marsh., and Juglans mandshurica Maxim.). A similar workflow may be applied to establish a differentiation method for other medicinal and economic plants.

The Obesity Amelioration Effect in High-Fat-Diet Fed Mice of a Homogeneous Polysaccharide from Codonopsis pilosula.

A homogeneous polysaccharide coded as CPP-1 was extracted and purified from the root of Codonopsis pilosula (Franch.) Nannf. by water extraction, ethanol precipitation, and column chromatography. Its structure was analyzed by HPGPC-ELSD, HPLC, GC-MS, FT-IR, and NMR techniques. The results indicated that CPP-1 was composed of mannose (Man), glucose (Glc), galactose (Gal), and arabinose (Ara) at a molar ratio of 5.86 : 51.69 : 34.34 : 8.08. The methylation analysis revealed that the main glycosidic linkage types of CPP-1 were (1→)-linked-Glc residue, (1→3)-linked-Glc residues, (1→4)-linked-Gal residue, (1→2,3,4)-linked-Glc residue, (1→)-linked-Man residue, (1→3,4)-linked-Glc residue, and (1→)-linked-Ara residue. In vivo efficacy trial illustrated that CPP-1 supplements could alleviate HFD-induced mice obesity significantly, as well as improve obesity-induced disorders of glucose metabolism, alleviate insulin resistance, and improve the effects of lipid metabolism. The findings indicate that this polysaccharide has the potential for the treatment of obesity.

Authentication of Shenqi Fuzheng Injection via UPLC-Coupled Ion Mobility-Mass Spectrometry and Chemometrics with Kendrick Mass Defect Filter Data Mining.

Nearly 5% of the Shenqi Fuzheng Injection's dry weight comes from the secondary metabolites of Radix codonopsis and Radix astragali. However, the chemical composition of these metabolites is still vague, which hinders the authentication of Shenqi Fuzheng Injection (SFI). Ultra-high performance liquid chromatography with a charged aerosol detector was used to achieve the profiling of these secondary metabolites in SFI in a single chromatogram. The chemical information in the chromatographic profile was characterized by ion mobility and high-resolution mass spectrometry. Polygonal mass defect filtering (PMDF) combined with Kendrick mass defect filtering (KMDF) was performed to screen potential secondary metabolites. A total of 223 secondary metabolites were characterized from the SFI fingerprints, including 58 flavonoids, 71 saponins, 50 alkaloids, 30 polyene and polycynes, and 14 other compounds. Among them, 106 components, mainly flavonoids and saponins, are contributed by Radix astragali, while 54 components, mainly alkaloids and polyene and polycynes, are contributed by Radix codonopsis, with 33 components coming from both herbs. There were 64 components characterized using the KMDF method, which increased the number of characterized components in SFI by 28.70%. This study provides a solid foundation for the authentification of SFIs and the analysis of its chemical composition.

Untargeted metabolomics coupled with chemometric analysis deducing robust markers for discrimination of processing procedures: Wine-processed Angelica sinensis as a case study.

Wine-processed Angelica Sinensis is a widely used Chinese medicinal decoction piece in China. However, there are hardly any robust markers indicating the processing procedure of wine-processed Angelica Sinensis, including the amount of rice wine and processing degree. A strategy integrating untargeted metabolomics and chemometric analysis for deducing robust markers was provided and applied to the discrimination of processing procedure. First, 86 compounds were tentatively identified in wine-processed Angelica Sinensis by ultra-high-performance liquid chromatography coupled with quadrupole-time of flight mass spectrometry. Second, 93 potential chemical markers were selected using multivariate analysis, among which nine robust chemical markers were selected by verification with commercial samples. Finally, the effects of processing temperature, time, and amount of rice wine on the three selected chemical markers were investigated through a rapid analytical method. It was demonstrated that both m/z 258.1097 and 238.1189 were positively correlated with the amount of rice wine and processing degree. In summary, this study introduced two candidate processing markers as robust markers for discriminating the processing procedures of wine-processed Angelica sinensis. It also proposed a strategy to provide the reference for the research of other decoction pieces.

Comprehensive feature-based molecular networking and metabolomics approaches to reveal the differences components in Cinnamomum cassia and Cinnamomum verum.

Cinnamon was been a widely used plant in medicinal and spices for a long time and has spread all over the world. However, the differences in the components of the bark from Cinnamomum cassia and Cinnamomum verum, the two most common types of cinnamon, have not been thoroughly investigated. In the present experiment, ultra-high-performance liquid chromatography LTQ-Orbitrap Velos Pro hybrid mass spectrometer-based metabolomics coupled with chemometrics and feature-based molecular networking were employed to dramatically distinguish and annotate Cinnamomum cassia Bark and Cinnamomum verum bark. As a consequence, principal component analysis, orthogonal projection to latent structures discriminates analysis, and heat map analysis demonstrated clear discrimination between the profiles of metabolites in cinnamon. Besides, as the known compounds, proanthocyanidins (cinnamtannin B1 and procyanidin B2) and alkaloids (norboldine, norisoboldine) with variable importance in the projection scores >6, and an unknown alkaloid (formula C24 H33 NO6 ) were selected as the best markers to discriminate cinnamon. Furthermore, large numbers of proanthocyanidins and alkaloids components were identified through feature-based molecular networking for the first time. Our investigation provides new ideas for the discovery of quality markers and identification of unknown components in natural products.

An integrated strategy for holistic quality identification of Chinese patent medicine: Liuwei Dihuang Pills as a case study.

INTRODUCTION: Liuwei Dihuang Pills (concentrated pills, simplified as LWDHP), one of the most famous classic Chinese Patent Medicine (CPM), is produced by hundreds of pharmaceutical manufacturers with billions of Chinese yuan (CNY) in annual sales. However, current quality identification of LWDHP mainly relies on a thin-layer chromatography (TLC) method that is complicated and deficient. OBJECTIVE: The goal of this study is to simplify the identification process and provide a more comprehensive quality assessment method of LWDHP by developing an integrated strategy based on liquid chromatography coupled with mass spectrometry (LC-MS) and multivariate statistical analysis. METHOD: Ultra-high-performance liquid chromatography coupled with quadrupole-time of flight mass spectrometry (UHPLC/QTOF-MS) was employed to perform qualitative analyses of a home-made LWDHP and to establish a stably characteristic compound library by analysis of batches of its component herbs. Then selective ion monitoring (SIM) of single MS was utilised to develop a rapid identification method based on the UHPLC/QTOF-MS analysis result. Multivariate statistical analysis was subsequently used for the quality assessment of different commercial samples. RESULTS: Seventy-eight characteristic compounds were characterised, and 68 of them were recorded to establish a stably characteristic compound library. Thirty-one compounds were selected from the library for the establishment of SIM identification method. Good specificity, capability, and feasibility had been respectively verified by the analysis of blank sample, negative control (NC) preparation samples, home-made LWDHP sample, and commercial sample. Multivariate statistical analysis of 20 batches of commercial LWDHP samples revealed the quality consistency of the same vendor's product and quality difference between diverse vendors' products. CONCLUSION: The SIM identification method by a single analysis could significantly simplify the identification process of LWDHP, and it was performed in a holistic mode for no less than two compounds of each component herb monitored. Moreover, it could also be combined with multivariate statistical analysis to conduct quality assessments of batches of samples. The integrated strategy used in the study of LWDHP could be applied for the identification of other CPM as well.

Structural Characterization of a Polysaccharide from Gastrodia elata and Its Bioactivity on Gut Microbiota.

A novel homogeneous polysaccharide named GEP-1 was isolated and purified from Gastrodia elata (G. elata) by hot-water extraction, ethanol precipitation, and membrane separator. GEP-1, which has a molecular weight of 20.1 kDa, contains a polysaccharide framework comprised of only glucose. Methylation and NMR analysis showed that GEP-1 contained 1,3,6-linked-α-Glcp, 1,4-linked-α-Glcp, 1,4-linked-ß-Glcp and 1,4,6-linked-α-Glcp. Interestingly, GEP-1 contained citric acid and repeating p-hydroxybenzyl alcohol as one branch. Furthermore, a bioactivity test showed that GEP-1 could significantly promote the growth of Akkermansia muciniphila (A. muciniphila) and Lacticaseibacillus paracasei (L.paracasei) strains. These results implied that GEP-1 might be useful for human by modulating gut microbiota.

A Network-Based Approach to Explore the Mechanisms of Uncaria Alkaloids in Treating Hypertension and Alleviating Alzheimer's Disease.

Uncaria alkaloids are the major bioactive chemicals found in the Uncaria genus, which have a long history of clinical application in treating cardiovascular and mental diseases in traditional Chinese medicine (TCM). However, there are gaps in understanding the multiple targets, pathways, and biological activities of Uncaria alkaloids. By constructing the interactions among drug-targets-diseases, network pharmacology provides a systemic methodology and a novel perspective to present the intricate connections among drugs, potential targets, and related pathways. It is a valuable tool for studying TCM drugs with multiple indications, and how these multi-indication drugs are affected by complex interactions in the biological system. To better understand the mechanisms and targets of Uncaria alkaloids, we built an integrated analytical platform based on network pharmacology, including target prediction, protein-protein interaction (PPI) network, topology analysis, gene enrichment analysis, and molecular docking. Using this platform, we revealed the underlying mechanisms of Uncaria alkaloids' anti-hypertensive effects and explored the possible application of Uncaria alkaloids in preventing Alzheimer's disease. These results were further evaluated and refined using biological experiments. Our study provides a novel strategy for understanding the holistic pharmacology of TCM, as well as for exploring the multi-indication properties of TCM beyond its traditional applications.

Gastrodia elata Blume Polysaccharides: A Review of Their Acquisition, Analysis, Modification, and Pharmacological Activities.

Gastrodia elata Blume (G. elata) is a valuable Traditional Chinese Medicine (TCM) with a wide range of clinical applications. G. elata polysaccharides, as one of the main active ingredients of G. elata, have interesting extraction, purification, qualitative analysis, quantitative analysis, derivatization, and pharmacological activity aspects, yet a review of G. elata polysaccharides has not yet been published. Based on this, this article summarizes the progress of G. elata polysaccharides in terms of the above aspects to provide a basis for their further research and development.

Green Quantification Strategy Combined with Chemometric Analysis for Triglycerides in Seeds Used in Traditional Chinese Medicine.

Triglycerides are the primary constituents of some seed kernels used in traditional Chinese medicine. Quality control of seed kernels containing multiple components with an environmentally friendly method is indispensable for establishing their quality standards (called monographs) in pharmacopeia. Using coix seeds (Semen Coicis) as an example, a green quantification strategy was proposed by combining C8 core-shell particles with single standard to determine multicomponent technologies to quantify seven triglycerides simultaneously. A core-shell column, namely, Halo C8 (3.0 × 100 mm, 2.7 µm), was used. Methanol was used as the mobile phase at a flow rate of 0.3 mL/min, enabling UV detection of the elutes. Seven triglycerides were well separated in 20 min, and simultaneously quantified using triolein as a single standard. The conversion factor for each standard was set as 1.0 on ELSD, while for the conversion factors at 203 nm, the values increased with the reduction of linoleate. The recovery values were all in the range of 97 - 107% (RSD < 3.0%). The RSD values of precision, including intraday and intermediate precision, were < 3.0% when the total content of triglycerides was calculated. The linearity reached r ≥ 0.9990, and the limit of quantitation reached 40 - 70 ng. Forty-nine batches of coix seeds from four different places of origins and eight batches of adulterants were evaluated and differentiated using principal component analysis. In addition, the validated method was used successfully to quantity seven triglycerides in Semen Persicae, Semen Armeniacae Amarum, and Semen Pruni.

Design, synthesis and biological evaluation of betulinic acid derivatives as potential inhibitors of 3CL-protease of SARS-CoV-2.

During the coronavirus reproduction process, 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro) are accountable for the fragmentation of two polyprotein precursors (pp1a/pp1ab) into substructural proteins. These two proteins are vital for the replication and transcription of the viral genome. Therefore, 3CLpro is a key protein and target for the design of coronavirus inhibitors. In previous studies, we found that betulinic acid has an inhibitory effect on 3CLpro, with 51.5 % inhibition of 3CLpro at 20 µM. Then, series of betulinic acid derivatives were designed, synthesized, and evaluated for their inhibition activities. The results showed that BA02 and BA05 showed significant inhibitory activity on 3CLpro with inhibitory rates of 78.1 % and 82.5 % at 20 µM, respectively. Further evaluation of these two compounds shows that their IC50 values are 7.22 ± 0.14 µM and 6.40 ± 0.14 µM, respectively.

Energy preservation for skeletal muscles: Shenqi Fuzheng injection prevents tissue wasting and restores bioenergetic profiles in a mouse model of chemotherapy-induced cachexia.

BACKGROUND: Energy deficiency is the characteristic of chemotherapy-induced cachexia (CIC) which is manifested by muscle wasting. glycolysis, tricarboxylic acid (TCA) cycle, and lipid metabolism are central to muscle bioenergy production, which is vulnerable to chemotherapy during cancer treatment. Recent investigations have spotlighted the potential of Shenqi Fuzheng injection (SQ), a Chinese proprietary medicine comprising Radix Codonopsis and Radix Astragali, in alleviating CIC. However, the specific effects of SQ on muscle energy metabolism remains less explored. PURPOSE AND METHODS: Here, we integrated transcriptomics, spatial metabolomics, gas chromatography-mass spectrometry targeted quantitative analysis, and transmission electron microscopy techniques, combined with Seahorse live-cell metabolic analysis to reveal the changes in genes and pathways related to energy metabolism in the CIC model and SQ's protective effects at molecular and functional levels. RESULTS: Our data showed that chemotherapeutic agents caused glycolysis imbalance, which further leads to metabolic derangements of TCA cycle intermediates. SQ maintained glycolysis balance by facilitating pyruvate fluxing to mitochondria for more efficient bioenergy production, which involved a dual effect on promoting functions of mitochondrial pyruvate dehydrogenase complexes and inhibiting lactate dehydrogenase for lactate production. As a result of the sustained pyruvate level achieved by SQ administration, glycolysis balance was maintained, which further led to the preservation of mitochondrial integrity and function of electron transport chain, thereby, ensuring the normal operation of the TCA cycle and the proper synthesis of adenosine triphosphate (ATP). The above results were further validated using the Seahorse live-cell assay. CONCLUSION: In conclusion, our study highlights SQ as a promising strategy for CIC management, emphasizing its ability to harmonize the homeostasis of the muscle bioenergetic profile. Beyond its therapeutic implications, this study also offers a novel perspective for the development of innovative treatments in the realm of herbal medicine.

Shenqi Fuzheng injection alleviates chemotherapy-induced cachexia by restoring glucocorticoid signaling in hypothalamus.

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Determination of the intermediates in glycolysis and tricarboxylic acid cycle with an improved derivatization strategy using gas chromatography-mass spectrometry in complex samples.

Traditional Chinese medicine (TCM) is recognized as a complex matrix, and improved analytical methods are crucial to extract the key indicators and depict the interaction and alteration of the complex matrix. Shenqi Fuzheng Injection (SQ), a water extract of Radix Codonopsis and Radix Astragali, has demonstrated preventative effects on myotube atrophy induced by chemotherapeutic agents. To achieve the improved analytical capability of complex biological samples, we established a highly reproducible, sensitive, specific, and robust gas chromatography-tandem mass spectrometry (GC-MS) method to detect glycolysis and tricarboxylic acid (TCA) cycle intermediates with optimized factors in the extraction and derivatization process. Our method detected fifteen metabolites and covered most intermediate metabolites in glycolysis and TCA cycles, including glucose, glucose-6-phosphate, fructose-6-phosphate, dihydroxyacetone phosphate, 3-diphosphoglycerate, phosphoenolpyruvate, pyruvate, lactate, citrate, cis-aconitate, isocitrate, α-ketoglutarate, succinate, fumarate, and malate. Through methodological verification of the method, it was found that the linear correlation coefficients of each compound in the method were greater than 0.98, all of which had lower limits of quantification, the recovery rate was 84.94-104.45%, and the accuracy was 77.72-104.92%. The intraday precision was 3.72-15.37%, the interday precision was 5.00-18.02%, and the stability was 7.85-15.51%. Therefore, the method has good linearity, accuracy, precision, and stability. The method was further applied to study the attenuating effects of the SQ in a chemotherapeutic agents-induced C2C12 myotube atrophy model to evaluate the changes in the tricarboxylic acid cycle and glycolytic products under the action by the complex systems of TCM and disease model. Our study provided an improved method to explore TCM's pharmacodynamic constituents and action mechanisms.