Application of Metabolomics in the Study of Natural Products

Stemona alkaloid derivative induce ferroptosis of colorectal cancer cell by mediating carnitine palmitoyltransferase 1

Accumulation of acylcarnitines is a characteristic feature of various metabolic disorders affecting fatty acid metabolism. Despite extensive research, no specific molecules have been identified to induce ferroptosis through the regulation of acylcarnitine metabolism. In this study, acylcarnitine accumulation was identified based on cell metabolomics study after the treatment with Stemona alkaloid derivative (SA-11), which was proved to induce ferroptosis in our previous research. Furthermore, the CPT-1 level was proved to significantly increase, while the CPT-2 level indicated no significant difference, which resulted in the accumulation of acylcarnitine. Besides, the ferroptosis-inducing ability of SA-11 was significantly enhanced by the addition of exogenous acylcarnitine, presumably due to the production of additional ROS. This hypothesis was corroborated by the observation of increased ROS levels in HCT-116 cells treated with SA-11 compared to the control group. These findings suggest that targeting acylcarnitine metabolism, particularly through CPT-1, may offer a novel therapeutic strategy for cancer treatment by enhancing ferroptosis induction.

Drug or Toxic? A Brief Understanding of the Edible Corolla of Rhododendron decorum Franch. by Bai Nationality with Comparative Metabolomics Analysis

Rhododendron is a traditional ornamental and medicinal plant in China, renowned for its aesthetic appeal and therapeutic properties. Regarding Rhododendron decorum Franch., mainly distributed in Yunnan Province, its corolla is regarded as an edible food by the Bai ethnic group in Yunnan Province. However, it is still unclear why the Bai people choose to use the Rhododendron species in their seasonal diet. Here, we employed comparative metabolomics analysis to explore the variations in the metabolites and the enriched biosynthesis pathways within the different floral organs of R. decorum Franch. from Heqing and Yulong County. The metabolite analysis showed that 1340 metabolites were identified from the floral organs in the two regions. Comparing the different flower organs of the same region, 85 differential accumulated metabolites (DAMs) were found from the androecium/gynoecium and corolla in the same region, and 66 DAMs were identified from the same organ in different regions. The KEGG pathway and network analysis revealed significant disparities in both the metabolite composition and enriched pathways among the different floral organs or when comparing the same floral organs across diverse regions, with geographical variations exerting even stronger influences. From the perspective of resource utilization, it was observed that the R. decorum Franch. populations in Heqing County exhibited the greater accumulation of secondary metabolites within their flowers, rendering them more advantageous for medicinal purposes, albeit potentially more toxic. This study provides novel insights into the utilization of corollaries for potential de novo pharmacy development.

Insights into Metabolites Profiling and Pharmacological Investigation of Aconitum heterophyllum wall ex. Royle Stem through Experimental and Bioinformatics Techniques

The Aconitum genus is a leading source of a wide range of structurally diverse metabolites with significant pharmacological implications. The present study investigated metabolite profiling, pharmacological investigation, anticancer potential, and molecular docking analysis of the stem part of Aconitum heterophyllum (AHS). The metabolite profiling of the AHS extract was experimentally examined using LC-MS/MS-orbitrap in both modes (ESI+/ESI-) and GC-MS in EI mode. The in vitro MTT model was used to study the anticancer potential, while the in vivo animal model was used to study the anti-inflammatory and antinociceptive activities. The MOE software was used for the molecular docking study. A total of 118 novel and previously known metabolites, among 44 metabolites (26 in ESI+ positive mode and 18 in ESI- negative mode) in the MeOH extract, while 74 metabolites (46 in ESI+ and 28 in ESI- mode) were identified in the n-hexane extract via LCMS/MS. The identified metabolites include 24 phenolic compounds, 18 alkaloids, 10 flavonoids, 24 terpenoids, 2 coumarins, 2 lignans, and 38 other fatty acids and organic compounds. The major bioactive metabolites identified were hordenine, hernagine, formononetin, chrysin, N-methylhernagine, guineesine, shogaol, kauralexin, colneleate, zerumbone, medicarpin, boldine, miraxinthin-v, and lariciresinol-4-O-glucoside. Furthermore, the GC-MS study helped in the identification of volatile and nonvolatile chemical constituents based on the mass spectrum and retention indices. The methanol extract significantly inhibited tumor progression in H9c2 and MDCK cancer cells with IC50 values of 186.39 and 199.63 μg/mL. In comparison, the positive control aconitine exhibited potent IC50 values (132.32 and 141.58 μg/mL) against H9c2 and MDCK cell lines. The anti-inflammatory (carrageenan-induced hind paw edema) and antinociceptive (acetic acid-induced writhing) effects were significantly dose-dependent, (p < 0.001) and (p < 0.05), respectively. In addition, a molecular docking study was conducted on identified ligands against the anti-inflammatory enzyme (COX-2) (PDB ID: 5JVZ) and the cancer enzyme ADAM10 (PDB ID: 6BDZ) which confirmed the anti-inflammatory and anticancer effects in an in silico model. Among all ligands, L2, L3, and L7 exhibit the most potent potential for inhibiting COX-2 inflammation with binding energies of -7.3424, -7.0427, and -8.3562 kcal/mol. Conversely, against ADAM10 cancer protein, ligands L1, L4, L6, and L7, with binding energies of -8.0650, -7.7276, -7.0454, and -7.2080 kcal/mol, demonstrated notable effectiveness. Overall, the identified metabolites revealed in this AHS research study hold promise for discovering novel possibilities in the disciplines of chemotaxonomy and pharmacology.

Myrislignan targets extracellular signal-regulated kinase (ERK) and modulates mitochondrial function to dampen osteoclastogenesis and ovariectomy-induced osteoporosis

BACKGROUND

Activated osteoclasts cause excessive bone resorption, and disrupt bone homeostasis, leading to osteoporosis. The extracellular signal-regulated kinase (ERK) signaling is the classical pathway related to osteoclast differentiation, and mitochondrial reactive oxygen species are closely associated with the differentiation of osteoclasts. Myrislignan (MRL), a natural product derived from nutmeg, has multiple pharmacological activities; however, its therapeutic effect on osteoporosis is unclear. Here, we investigated whether MRL could inhibit osteoclastogenesis and bone mass loss in an ovariectomy mouse model by suppressing mitochondrial function and ERK signaling.

METHODS

Tartrate-resistant and phosphatase (TRAP) and bone resorption assays were performed to observe the effect of MRL on osteoclastogenesis of bone marrow macrophages. MitoSOX RED and tetramethyl rhodamine methyl ester (TMRM) staining was performed to evaluate the inhibitory effect of MRL on mitochondria. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was performed to detect whether MRL suppressed the expression of osteoclast-specific genes. The impact of MRL on the protein involved in the mitogen-activated protein kinase (MAPK) and nuclear factor-κB pathways was evaluated using western blotting. In addition, a specific ERK agonist LM22B-10, was used to revalidate the inhibitory effect of MRL on ERK. Finally, we established an ovariectomy mouse model to assess the therapeutic effect of MRL on osteoporosis in vivo.

RESULTS

MRL inhibited osteoclast differentiation and the associated bone resorption, by significantly decreasing osteoclastic gene expression. Mechanistically, MRL inhibited the phosphorylation of ERK by suppressing the mitochondrial function, thereby downregulating the nuclear factor of activated T cells 1 (NFATc1) signaling. LM22B-10 treatment further verified the targeted inhibition effect of MRL on ERK. Microscopic computed tomographic and histologic analyses of the tibial tissue sections indicated that ovariectomized mice had lower bone mass and higher expression of ERK compared with normal controls. However, MRL treatment significantly reversed these effects, indicating the anti-osteoporosis effect of MRL.

CONCLUSION

We report for the first time that MRL inhibits ERK signaling by suppressing mitochondrial function, thereby ameliorating ovariectomy-induced osteoporosis. Our findings can provide a basis for the development of a novel therapeutic strategy for osteoporosis.

Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

Bruceine D may affect the phenylpropanoid biosynthesis by acting on ADTs thus inhibiting Bidens pilosa L. seed germination

Bruceine D is a natural quassinoid, which was successfully isolated in our research group from the residue of Brucea javanica (L.) seeds. Our previous research showed that Bruceine D prevented Bidens pilosa L. seed germination by suppressing the activity of key enzymes and the expression levels of key genes involved in the phenylpropanoid biosynthesis pathway. In this study, integrated analyses of non-targeted metabolomic and transcriptomic were performed. A total of 356 different accumulated metabolites (DAMs) were identified, and KEGG pathway analyses revealed that most of these DAMs were involved in phenylpropanoid biosynthesis. The decreased expression of ADTs and content of L-phenylalanine implicates that Bruceine D may suppress the downstream phenylpropanoid biosynthesis pathway by disrupting primary metabolism, that is, the phenylalanine biosynthesis pathway, thus inhibiting the final products, resulting in the interruption of B. pilosa seed germination. These results suggest that Bruceine D may inhibit the B. pilosa seed germination by suppressing phenylpropanoid biosynthesis through acting on ADTs.

Therapeutic effect and mechanism of danshensu on coronary heart disease using liquid chromatography combined with mass spectrometry metabolomics

Metabolomics can discover the biomarkers and metabolic pathways, provides the possibility for insights into the pharmacological action and mechanism of natural products. The therapeutic effect and mechanism of danshensu (DSS) on total metabolic pathways has not been well investigated. The aim of this study was to explore the disturbed endogenous biomarkers and metabolic pathways reflecting the pharmacological activity of DSS, and mechanism of action of DSS using comprehensive metabolome analysis based on high-throughput metabolomics technology combined with ultra-high performance liquid chromatography (UPLC) coupled with quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS) and pattern recognition method. Through the changes of the overall metabolic profile and the related biomarkers, the intervention effect of natural product danshensu (DSS) treatment on CHD model rats was revealed. The results showed that after the model replication was established, the metabolic profile was clearly separated, and a total of 26 potential biomarkers were screened out, and involving 8 metabolic pathways. After different doses of DSS solution were given, a total of 20 biomarkers could be significantly regulated, mainly involving primary bile acid biosynthesis, glycerophospholipid metabolism, and lipid metabolism. It showed UPLC-MS-based metabolomics can be used for discovering potential biomarkers and metabolic pathways of CHD, and to further understand and dissecting pharmacological effects and mechanisms of natural products via metabolomics techniques.

An investigation of 6-Shogaol effects on MCF7 cell lines through a systems biology approach

Introduction

In the literature, to investigate hormonal mechanisms of cell growth of patients with breast cancer (BC), as the second most common cause of death in the world, the researchers frequently used MCF-7 cell lines. And, identifying the functional mechanisms of therapeutics agents as new cancer inhibitors is still unclear.

Methods

We used the NCBI-GEO dataset (GSE36973) to study the effects of 6-Shogaol on MCF-7 cell lines commonly used for more than 45 years in several studies. The pre-processing and post-processing stages were carried out for the target samples to identify the most significant differentially expressed genes between two MCF-7 with and without treated by 6-Shogaol. Furthermore, various analyses, including biological process and molecular function from the DAVID website, the protein–protein interaction (PPI) network, gene-miRNA, gene-transcription factor, gene-drugs, and gene-diseases networks, statistically significant assoications with clinical features and survival rates were conducted.

Results

The initial outcomes revealed thirty significant DEGs. Among which the approach resulted in eleven upregulated and nineteen downregulated genes. Over-expression of TRADD and CREB3L1 and low-expression of KIF4A and PALMD were substantial in the TNF signaling pathway. Moreover, hsa-mir-16-5p and hsa-mir-124-3p were inhibitors of breast cancer growth.

Conclusion

The fact that some of genes are associated with survival rates as well as various clinical features including disease stages, it can be deduced that the 6-Shogaol treatment on MCF7 cell lines at the genome level shows inhibition functionalities of the herbal medicine in breast cancer at early stages and pave the way in developing new therapeutic agents.

Antidiabetic Effect of Noodles Containing Fermented Lettuce Extracts

The aim of the current study was to examine the antidiabetic effect of noodle containing fermented lettuce extract (FLE) on diabetic mice as a pre-clinical study. The γ-aminobutyric acid (GABA) content, antioxidant capacity, and total polyphenol content of the FLE noodles were analyzed and compared with those of standard noodles. In addition, oral glucose and sucrose tolerance, and fasting blood glucose tests were performed using a high-fat diet/streptozotocin-mediated diabetic mouse model. Serum metabolite profiling of mice feed standard or FLE noodles was performed using gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS) to understand the mechanism changes induced by the FLE noodles. The GABA content, total polyphenols, and antioxidant activity were high in FLE noodles compared with those in the standard noodles. In vivo experiments also showed that mice fed FLE noodles had lower blood glucose levels and insulin resistance than those fed standard noodles. Moreover, glycolysis, purine metabolism, and amino acid metabolism were altered by FLE as determined by GC-TOF-MS-based metabolomics. These results demonstrate that FLE noodles possess significant antidiabetic activity, suggesting the applicability of fermented lettuce extract as a potential food additive for diabetic food products.

Intravenous Administration of Triptonide Attenuates CFA-Induced Pain Hypersensitivity by Inhibiting DRG AKT Signaling Pathway in Mice

Background

Currently, medical treatment of inflammatory pain is limited by a lack of safe and effective therapies. Triptonide (TPN), a major component of Tripterygium wilfordii Hook.f. with low toxicity, has been shown to have good anti-inflammatory and neuroprotective effects. The present study aims to investigate the effects of TPN on chronic inflammatory pain.

Materials and Methods

Inflammatory pain was induced by intraplantar injection of complete Freund’s adjuvant (CFA). TPN’s three different doses were intravenously administered to compare the analgesic efficacy: 0.1 mg/kg, 0.5 mg/kg, and 2.0 mg/kg. The foot swelling was quantitated by measuring paw volume. Mechanical allodynia and thermal hyperalgesia were assessed with von Frey filament testing and Hargreaves’ test, respectively. Western blots, qRT–PCR and immunofluorescence tests were used to analyze the expression of pAKT, tumor necrosis factor-α (TNF-α), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6). Two AKT inhibitors, AKT inhibitor Ⅳ and MK-2206, were used to examine AKT’s effects on pain behavior and cytokines expression.

Results

Intravenous treatment with TPN attenuated CFA-induced paw edema, mechanical allodynia, and thermal hyperalgesia. Western blotting and immunofluorescence results showed that CFA induced AKT activation in the dorsal root ganglion (DRG) neurons. However, these effects were suppressed by treatment with TPN. Furthermore, TPN treatment inhibited CFA-induced increase of pro-inflammatory cytokines, including TNF-α, IL-1β, and IL-6. Consistent with the in vivo data, TPN inhibited LPS-induced Akt phosphorylation and inflammatory mediator production in ND7/23 cells. Finally, intrathecal treatment with AKT inhibitor Ⅳ or MK-2206, attenuated CFA-induced mechanical allodynia and thermal hyperalgesia, and simultaneously decreased the mRNA expression of TNF-α, IL-1β, and IL-6 in DRG.

Conclusion

These data indicate that TPN attenuates CFA-induced pain potentially via inhibiting AKT-mediated pro-inflammatory cytokines production in DRG. TPN may be used for the treatment of chronic inflammatory pain.

Comparative investigation of phytochemicals among ten citrus herbs by ultra high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry and evaluation of their antioxidant properties

The citrus herbs have proved their important medicinal and nutritional values as medicine-food dual-purpose herbs, functional foods, or medical herbs in China. In this study, phytochemicals and antioxidant activity among ten typical citrus herbs (ethanol extracts) were investigated comprehensively. The major ingredients and their contents were analyzed by high-resolution mass spectrometry, and the differences of typical fragment ions between flavanone-7-O-rutinoside(s) and flavanone-7-O-neohesperidoside(s) were discriminated properly in negative electrospray ionization mode. Total polyphenols, total flavonoids, 1,1-diphenyl-2-picrylhydrazyl, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid), and ferric reducing antioxidant power tests were performed, which indicated their beneficial values and antioxidant effects. The medicine-food dual-purpose herbs including Chenpi, Juluo, Daidaihua, Huajuhong, Xiangyuan, and Foshou exhibited antioxidant capacities significantly by decreasing intracellular reactive oxygen species intensity (P < 0.01), enhancing superoxide dismutase, catalase, and glutathione peroxidase activities (P < 0.01) in H2 O2 -induced RIN-m5F cells. Moreover, the functional foods Zhishi, Zhiqiao, and Qingpi showed moderate antioxidant bioactivity, while the medical herb Juhe showed weak antioxidant bioactivity, which were consistent with the multivariate analysis of their major flavonoids. The study provided a new sight for the chemical differentiation and practical application of citrus herbs as medicine-food dual-purpose herbs, functional foods, or medical herbs.

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis

Plant-derived natural products have long been considered a valuable source of lead compounds for drug development. Natural extracts are usually composed of hundreds to thousands of metabolites, whereby the bioactivity of natural extracts can be represented by synergism between several metabolites. However, isolating every single compound from a natural extract is not always possible due to the complex chemistry and presence of most secondary metabolites at very low levels. Metabolomics has emerged in recent years as an indispensable tool for the analysis of thousands of metabolites from crude natural extracts, leading to a paradigm shift in natural products drug research. Analytical methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) are used to comprehensively annotate the constituents of plant natural products for screening, drug discovery as well as for quality control purposes such as those required for phytomedicine. In this review, the current advancements in plant sample preparation, sample measurements, and data analysis are presented alongside a few case studies of the successful applications of these processes in plant natural product drug discovery.

The Protective Roles of PPARα Activation in Triptolide-Induced Liver Injury

Triptolide (TP), one of the main active ingredients in Tripterygium wilfordii Hook F, is clinically used to treat immune diseases but is known to cause liver injury. The aim of this study was to investigate the biomarkers for TP-induced hepatotoxicity in mice and to determine potential mechanisms of its liver injury. LC/MS-based metabolomics was used to determine the metabolites that were changed in TP-induced liver injury. The accumulation of long-chain acylcarnitines in serum indicated that TP exposure disrupted endogenous peroxisome proliferator-activated receptor α (PPARα) signaling. Triptolide-induced liver injury could be alleviated by treatment of mice with the PPARα agonist fenofibrate, whereas the PPARα antagonist GW6471 increased hepatotoxicity. Furthermore, fenofibrate did not protect Ppara-/- mice from TP-induced liver injury, suggesting an essential role for the PPARα in the protective effect of fenofibrate. Elevated long-chain acylcarnitines may protect TP-induced liver injury through activation of the NOTCH-NRF2 pathway as revealed in primary mouse hepatocytes and in vivo. In agreement with these observations in mice, the increase in long-chain acylcarnitines was observed in the serum of patients with cholestatic liver injury compared with healthy volunteers. These data demonstrated the role of PPARα and long-chain acylcarnitines in TP-induced hepatotoxicity, and suggested that modulation of PPARα may protect against drug-induced liver injury.

High-Resolution Liquid Chromatography-Mass Spectrometry-Based Metabolomic Discrimination of Citrus-Type Crude Drugs and Comparison with Nuclear Magnetic Resonance Spectroscopy-Based Metabolomics

Five Citrus-type crude drugs (40 samples) were classified using liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. The following six flavonoid derivatives were identified as contributors from the loading plots of multivariate analysis: naringin (1), neohesperidin (2), neoeriocitrin (3), narirutin (9), hesperidin (10), and 3,5,6,7,8,3',4'-heptamethoxyflavone (12). Three coumarin derivatives, namely, meranzin (6), meranzin hydrate (7), and meranzin glucoside (8), were also identified as contributors. Furthermore, compared with our previous studies on proton (¹H) and ¹³C NMR spectroscopy-based metabolomics, the present study revealed that the Citrus-type crude drugs were distinguished with the same pattern; however, the contributors differed between the ¹H and ¹³C NMR spectroscopy-based metabolomics. The high dynamic range of NMR spectroscopy provided broad coverage of the metabolomes including the primary and secondary metabolites. However, LC-MS appeared to be superior in detecting secondary metabolites with high sensitivity, some of which occurred in quantities that were undetectable using NMR spectroscopy.

Role of Metabolic Activation in Elemicin-Induced Cellular Toxicity

Elemicin, an alkenylbenzene constituent of natural oils of several plant species, is widely distributed in food, dietary supplements, and medicinal plants. 1'-Hydroxylation is known to cause metabolic activation of alkenylbenzenes leading to their potential toxicity. The aim of this study was to explore the relationship between elemicin metabolism and its toxicity through comparing the metabolic maps between elemicin and 1'-hydroxyelemicin. Elemicin was transformed into a reactive metabolite of 1'-hydroxyelemicin, which was subsequently conjugated with cysteine (Cys) and N-acetylcysteine (NAC). Administration of NAC could significantly ameliorate the elemicin- and 1'-hydroxyelemicin-induced cytotoxicity of HepG2 cells, while depletion of Cys with diethyl maleate (DEM) increased cytotoxicity. Recombinant human CYP screening and CYP inhibition experiments revealed that multiple CYPs, notably CYP1A1, CYP1A2, and CYP3A4, were responsible for the metabolic activation of elemicin. This study revealed that metabolic activation plays a critical role in elemicin cytotoxicity.

Metabolic profiling analysis of corilagin in vivo and in vitro using high-performance liquid chromatography quadrupole time-of-flight mass spectrometry

Corilagin is an Ellagitannin with favorable pharmacological activities. But there was no report regarding the metabolism of corilagin in vitro or in vivo. In this study, the metabolic profile of corilagin in rats as well as in rat intestinal bacteria and liver microsomes incubation system in vitro were investigated comprehensively for the first time. Consequently, with the aid of sensitive HPLC-Q-TOF-MS/MS, corilagin and its twenty-four metabolites (fourteen phase II conjugate metabolites of corilagin, three hydrolyzed metabolites EA, GA, M3 and their seven derived metabolites) were absolutely or tentatively identified in rat biological samples (urine, feces, plasma and tissues) after oral administration of corilagin. In vitro, the three hydrolyzed metabolites were identified in rat intestinal microflora and liver microsomes. These results demonstrated that corilagin itself not only could underwent extensive phase II metabolism in rats, but also could underwent hydrolysis reaction in rats as well as in rat intestinal bacteria and liver microsomes in vitro. This study is first report to identify phase II conjugate metabolites (except mono-methylate conjugated metabolites) of pure Ellagitannin and distribution of these metabolites in vivo. In addition, clear, detailed metabolic pathways of corilagin were shown to involve hydrolysis, methylation, glycosylation, reduction, glucuronidation and sulfation.