Comprehensive Metabolomic Fingerprinting Combined with Chemometrics Identifies Species- and Variety-Specific Variation of Medicinal Herbs: An Ocimum Study

Characterization of potential bioactive molecules in Fissistigma polyanthum using UPLC-ESI-QTOF-MS-based metabolomics integrated with chemometrics approaches

Fissistigma polyanthum is a renowned medicinal plant traditionally used by over 10 ethnic groups in China to treat various ailments, including inflammation. However, research on its chemical composition and bioactivity remains limited. This study investigated the chemical profiles and biological activities across different parts of F. polyanthum, aiming to identify the bioactive molecules associated with anti-inflammatory and anti-Alzheimer's effects. To ensure accurate metabolite identification, an in-house Fissistigma compound library containing 654 chemicals was constructed and integrated with the Progenesis QI informatics platform. Using UPLC-ESI-QTOF-MS-based metabolomics, 97 compounds, including alkaloids, flavonoids and terpenoids, were identified, of which 86 were reported for the first time in this species. Heatmap analysis revealed significant content variations of these constituents across different plant parts: leaves were rich in flavonoids and terpenoids, while the root without bark was abundant in alkaloids. PCA and PLS-DA analyses confirmed significant metabolite differences among the plant parts, with 31 key differential compounds explaining the chemical variations. Comparative bioactivity assays showed that the root without bark exhibited strong anti-butyrylcholinesterase activity, with an IC50 value of 54.22 μg/mL, while the root bark and leaves demonstrated the strongest inhibition of NO production, with IC50 values of 62.64 and 71.85 μg/mL, respectively. The S-plot analysis further identified 25 potential bioactive compounds, primarily alkaloids and flavonoids, responsible for the observed bioactivities, including known anti-inflammatory and anti-Alzheimer's agents. These findings underscore the pharmaceutical potential of F. polyanthum and the effectiveness of integrating metabolomics and chemometrics to discover bioactive molecules in medicinal plants.

Gaseous exchange-dependent in vitro culture extensively alters plant growth and metabolic landscape revealed by comprehensive metabolomics

A complex interplay of environmental factors profoundly influences plant cellular metabolism, with gaseous exchange serving as a fundamental physiological process critical to growth and survival. While well-characterized in natural environments, the role of gaseous exchange in plant in-vitro culture remains underexplored. Plant in-vitro culture offers a versatile platform for studying metabolism, where metabolic networks are highly flexible and sensitive to environmental factors. Despite advancements in understanding these dynamics, there has been relatively little investigation into how gaseous exchange within tissue culture systems affects cellular metabolism. In the present study, we investigated the effects of gaseous exchange on plant growth and metabolism by comparing traditional Parafilm- and micropore-tape-based cultures designed to facilitate different levels of gaseous exchange. A comprehensive metabolomics approach using liquid chromatography-high-resolution mass spectrometry and gas chromatography-mass spectrometry was employed to delineate the metabolic changes in Arabidopsis under Parafilm- and micropore-tape-sealed culture conditions at two and three weeks of growth. Metabolic profiling identified increased levels of oxidized glutathione, arginine, ornithine, and aspartic acid, and decreased levels of TCA cycle intermediates and phenylpropanoid metabolites, indicating that restricted gas exchange alters the redox status and reprograms primary and secondary metabolism. This reprogramming affected amino acid metabolism, arginine metabolism, energy metabolism, as well as phenylpropanoid and flavonoid biosynthetic pathways. Restricted gaseous exchange in Parafilm-wrapped cultures also led to altered accumulation of several essential macro- and microelements in Arabidopsis seedlings. The present study demonstrated that restricted gaseous exchange inhibits plant growth and disrupts metabolism.

Impact of cultivar types and thermal processing methods on sweet potato metabolome, a comparative analysis via a multiplex approach of NIR and GC-MS based metabolomics coupled with chemometrics

This study comprehensively analyzes the primary metabolites of sweet potato peels and pulps from four cultivars and assesses the impact of four different processing methods on pulp metabolome using a multiplex metabolomics approach of GC-MS and NIR. A total of 69 metabolites were identified. Beauregard cv. showed the highest sugar content (387.85 mg/g), whereas Sahrawy cv. was higher in alcohols (24.63 mg/g) and organic acids (2.98 mg/g). The chemometric analysis identified key markers that distinguished each cv. represented by its pulp, peel, and processed pulp. KEGG enrichment analysis pinpointed key metabolic pathways leading to the metabolic discrepancy of the specimens. Sugars were the most altered class by processing as manifested by a 5 to 11-fold increase, notably in the air-fried pulp. Air-frying also increased alcohol and organic acid contents. NIR analysis revealed that air-frying was the preferred method of processing, preserving the majority of pulp's metabolites, including β-carotene and phenolics.

Exploring of Chemical Profile and Biological Activities of Three Ocimum Species From Comoros Islands: A Combination of In Vitro and In Silico Insights

Ocimum species have a great interest in different traditional medicinal systems. This study examined the chemical composition, antioxidant properties, enzyme inhibitory effects, and antibacterial and antifungal activities of the aerial parts of Ocimum gratissimum, Ocimum americanum, and Ocimum basilicum from the Comoros Islands. The extracts were analyzed using high-performance liquid chromatography-mass spectrometry (HPLC-MS) to determine their chemical composition. Antioxidant activity was assessed using 2,2-Diphenyl-1-picrylhydrazyl (DPPH), 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS), cupric reducing antioxidant capacity (CUPRAC), ferric reducing antioxidant power (FRAP), chelating ability, and phosphomolybdenum radical scavenging assays. Enzyme inhibitory activities against acetylcholinesterase (AChE), butrylcholinesterase (BChE), tyrosinase, amylase, and glucosidase were evaluated using spectrophotometric methods. Antibacterial and antifungal activities were tested using the broth microdilution method against selected pathogenic microorganisms. The selected enzymes and proteins were evaluated using in silico methods with biomolecules from these plants. In addition, 111 different metabolites were identified in the tested extracts using advanced HPLC/MS techniques. The most significant number of detected compounds were derivatives of hydroxycinnamic acids, followed by flavonoid glycosides and aglycones and derivatives of hydroxybenzoic acids. All three Ocimum species exhibited significant antioxidant activities, O. gratissimum exhibited the best-reducing abilities in CUPRAC and FRAP assays. In addition, enzyme inhibitory assays revealed that O. americanum had the most potent inhibitory effect on tyrosinase (48.01 ± 3.89 mg kojic acid equivalent [KAE]/g), and amylase (1.08 ± 0.02 mmol acarbose equivalent [ACAE]/g). Antibacterial and antifungal tests demonstrated that the extracts possess broad-spectrum activity. Molecular docking results showed that compounds exhibited remarkable binding energies with target enzymes and proteins. The molecular dynamics simulations identified chicoric acid with MurE of Staphylococcus aureus complex as the most promising drug candidate. These findings support their traditional medical and nutraceutical uses and suggest possibilities for natural functional applications.

Metabolomics-based profiling of anti-inflammatory compounds from Mentha spicata in shanghe, China

Mentha spicata is a popular herb used in foods, cosmetics, and medicines. In the present study, liquid chromatography-mass spectrometry-based metabolomics analysis and the zebrafish model were used to investigate the potential biomarkers of M. spicata growing in Shanghe County (Shandong Province, China) and their anti-inflammatory properties. Network pharmacology and molecular docking were performed to screen the main targets of the characteristic compounds to understand their mechanisms of action. Nine potential markers including sugars (1,2), polyphenolic acids (3-5), and flavonoids (6-9) were identified from the species. The inhibitory effects on leukocyte migration confirmed that compounds 1 and 3-9 played a positive role in the protective effect of Shanghe M. spicata (SM) extract against inflammation. Akt (protein kinase B), EGFR (epidermal growth factor receptor), and MMP9 (matrix metalloproteinase 9) were the core target proteins of the identified compounds in the anti-inflammatory process. The most significant Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment terms were response to abiotic stimulus (Biological Process), carbohydrate derivative binding (Molecular Function), and pathways in cancer. In docking simulations, 3-p-coumaroylquinic acid (3-PC, 4) and cirsimaritin (CN, 7) exhibited the highest potential affinity to the active sites of Akt and EGFR proteins, respectively; additionally, 5-demethylsinensetin (5-DS, 9) and luteolin (LN, 6) were considered the most suitable ligands for the MMP9 protein. The present study highlighted the use of SM resources as functional products with health benefits.

Quality markers of Polygala fallax Hemsl decoction based on qualitative and quantitative analysis combined with network pharmacology and chemometric analysis

INTRODUCTION

Polygala fallax Hemsl (PFH) is a widely used herbal medicine in Guangxi, China. At present, research on PFH mainly focuses on extraction technology and cultivation, lacking quality control standards for systematic evaluation.

OBJECTIVES

The study aimed to assess the quality of PFH from different sources and to predict markers that would help assess quality.

METHODS

Fingerprinting of 15 batches of PFH samples was performed by ultra-high performance liquid chromatography (UPLC) and similarity was assessed using hierarchical cluster analysis (HCA), principal component analysis (PCA), and orthogonal partial least squares discrimination (OPLS-DA). Differential components were screened by mathematical analysis, and a "component-target-pathway" network map was constructed in combination with network pharmacology, quality markers (Q-markers) of PFH were predicted, and quantitative analysis was performed.

RESULTS

Fifteen batches were fingerprinted for PFH, with 11 common peaks, and peak 5 was identified as 4-hydroxybenzoic acid, which was generally consistent with the results of HCA, PCA, and OPLS-DA. Network pharmacology screened 18 potential compounds, 45 core targets, and 20 key pathways, integrating fingerprinting, pattern recognition, and network pharmacology methods. One of the potential Q-markers that can identify the principle of testability, efficacy, and specificity is 4-hydroxybenzoic acid, whose content ranges from 0.0188 to 1.4517 mg/g.

CONCLUSION

The potential Q-markers of PFH were predicted by integrating fingerprinting, pattern recognition, and network pharmacological analysis, which provided a scientific basis for the overall control and evaluation of the quality of PFH and a theoretical reference for the study of the quality standard of multi-base traditional Chinese medicine.

Assessment of the effect of drying on Brassica greens via a multiplex approach based on LC-QTOF-MS/MS, molecular networking, and chemometrics along with their antioxidant and anticancer activities

Turnip (Brassica rapa var rapa L.) leaves are a rich source of versatile bioactive phytochemicals with great potential in the food and herbal industries. However, the effect of drying on its constituents has never been studied before. Hereto, three drying techniques were compared, namely, lyophilization (LY), vacuum oven (VO), and shade drying (SD). Chemical profiling utilizing liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (LC-QTOF-MS/MS) combined with chemometrics showed the different impacts of the drying methods on the phytochemical composition of the alcoholic leaf extracts. Unsupervised principal component analysis (PCA) and supervised partial least squares-discriminant analysis (PLS-DA) of the LC-QTOF-MS/MS data showed distinct distant clustering across the three drying techniques. Loading plots and VIP scores demonstrated that sinapic acid, isorhamnetin glycosides, and sinapoyl malate were key markers for LY samples. Meanwhile, oxygenated and polyunsaturated fatty acids were characteristic for SD samples and oxygenated polyunsaturated fatty acids and verbascoside were characteristic for VO samples. LY resulted in the highest total phenolics (TP) and total flavonoid (TF) contents followed by SD and VO. LY and SD samples had much higher antioxidant activity than VO measured by 2,2-diphenyl-1-picrylhydrazyl (DPPH), oxygen radical absorbance capacity (ORAC), and iron metal chelation assays. According to the anticancer activity, the drying methods were ranked in descending order as SD > LY ≫ VO when tested against colon, breast, liver, and lung cancer cell lines. Among the identified compounds, flavonoids and omega-3 fatty acids were key metabolites responsible for the anticancer activity as revealed by partial least squares (PLS) regression and correlation analyses. In conclusion, compared to LY, SD projected out as a cost-effective drying method without compromising the phytochemical and biological activities of Brassica greens. The current findings lay the foundation for further studies concerned with the valorization of Brassica greens.

Phytochemical Screening and GC-MS Analysis of Methanolic and Aqueous Extracts of Ocimum kilimandscharicum Leaves

Kenyans have long utilized Ocimum kilimandscharicum, an East African permanent evergreen plant, to treat measles, stomachaches, diarrhea, mosquito bites (anti-insect), congested chest, cough, and colds. Using conventional qualitative and quantitative techniques, this study was done to identify the secondary metabolites in O. kilimandscharicum leaf extracts. The chemical content of the crude extracts from the leaves of O. kilimandscharicum has also been investigated and characterized using gas chromatography-mass spectrometry (GC-MS). By using a 1:20 dilution in methanol, in cold maceration, a fine powder of O. kilimandscharicum was first extracted then filtered and concentrated after 72 h utilizing a rotary evaporator. By using also a 1:20 dilution in water at 80 °C, a fine powder of O. kilimandscharicum was extracted and then filtrated and lyophilized 1 h later. Each extract underwent further gas chromatography-mass spectrometry testing. We found that both extracts contain secondary metabolites such as alkaloids, phenolics, flavonoids, saponins, and tannins. However, the overall amount of phytochemicals in each solvent varied significantly. Total phenolics contents (TPCs) were 5.6 ± 1.20 and 10.8 ± 1.00 mg, total flavonoid contents (TFCs) were 8.2 ± 0.4 and 39.6 ± 2.2 mg, total tannin contents (TTCs) were 0 ± 0.00 and 10.5 ± 0.4 mg, the total alkaloid content (TAC) was 49.2 ± 0.40%, and the total saponin content (TSC) was 38 ± 2.00%. Additionally the gas chromatography-mass spectrometry, revealed a number of high- and low-molecular-weight bioactive molecules at various concentrations for each extract. We also found an inhibitory effect on adhP and chbR gene expression of Staphylococcus aureus and Salmonella choleraesuius, respectively. Hence, these chemicals could potentially have a biological and pharmacological significance. Therefore, the discovery of many physiologically active chemicals in the leaf extracts of O. kilimandscharicum justifies future biological and pharmaceutical research.

Unveiling Chemical Interactions Between Plants and Fungi Using Metabolomics Approaches

Metabolomics has been extensively used in clinical studies in the search for new biomarkers of human diseases. However, this approach has also been highlighted in agriculture and biological sciences, once metabolomics studies have been assisting researchers to deduce new chemical mechanisms involved in biological interactions that occur between microorganisms and plants. In this sense, the knowledge of the biological role of each metabolite (virulence factors, signaling compounds, antimicrobial metabolites, among others) and the affected biochemical pathways during the interaction contribute to a better understand of different ecological relationships established in nature. The current chapter addresses five different applications of the metabolomics approach in fungal-plant interactions research: (1) Discovery of biomarkers in pathogen-host interactions, (2) plant diseases diagnosis, (3) chemotaxonomy, (4) plant defense, and (5) plant resistance; using mass spectrometry and/or nuclear magnetic resonance spectroscopy, which are the techniques most used in metabolomics.