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Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays
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Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Plant Metabolism".

Deadline for manuscript submissions: 23 June 2025 | Viewed by 7401

Special Issue Editors

Dr. Chiara Toniolo

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Guest Editor
Department of Environmental Biology, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
Interests: medicinal and food plants; secondary metabolites; metabolites identification; phytochemistry; chromatography
Special Issues, Collections and Topics in MDPI journals
Dr. Luca Santi

E-Mail Website
Guest Editor
Department of Environmental Biology, “Sapienza” University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
Interests: medicinal, aromatic and food plants; secondary metabolites; antidiabetic, antihyperglycemic, antiproliferative, antioxidant and antimicrobic biological activities
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Medicinal, aromatic and food plants represent a valuable resource for both human and animal health and well-being, sustaining strong interest within the pharmaceutical industry. They are widely used in both traditional and modern medicine, as well as in the cosmetic, nutritional and supplement sectors, to treat or prevent various medical conditions and to promote or enhance overall well-being.

Each plant species is characterized by the presence of secondary metabolites, which may or may not exhibit specific biological activities. Although the term "secondary" might suggest that these compounds are of lesser importance compared to primary metabolites, secondary metabolites are, in fact, of great interest due to their unique chemical properties. Different classes of molecules can exhibit a range of biological activities that contribute to improving individual well-being. Unlike synthetic drugs, which contain a single active ingredient, plants are characterized by complex mixtures of molecules, known as the phytocomplexes. For this reason, when studying plants to analyze their biological activities, it is essential to consider not only the individual molecules but also the entire metabolic profile.

The aim of this Special Issue is to provide a platform for research on the characterization and/or quantification of secondary metabolites in medicinal, nutritional, and cosmetic plants, possibly in combination with biological analyses of plant extracts.

Dr. Chiara Toniolo
Dr. Luca Santi
Guest Editors

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • secondary metabolites
  • phytochemical analysis
  • biological activity
  • plant extracts
  • bioactive compounds
  • medicinal plants
  • food plants

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Published Papers (9 papers)

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Research

11 pages, 1304 KiB  
Article
Determination of Multiple Active Components in Mume Fructus by UPLC-MS/MS
by Nannan Li, Jingyi Yue and Rui Wang
Metabolites 2025, 15(5), 312; https://doi.org/10.3390/metabo15050312 - 6 May 2025
Viewed by 227
Abstract
Background: This study presents a sensitive method for the simultaneous determination of organic acids, flavonoids, and amino acids in Mume Fructus (MF) using ultra-performance liquid chromatography coupled with triple-quadrupole linear ion-trap tandem mass spectrometry (UPLC-QTRAP-MS/MS). Methods: Analysis was performed on a UPLC system [...] Read more.
Background: This study presents a sensitive method for the simultaneous determination of organic acids, flavonoids, and amino acids in Mume Fructus (MF) using ultra-performance liquid chromatography coupled with triple-quadrupole linear ion-trap tandem mass spectrometry (UPLC-QTRAP-MS/MS). Methods: Analysis was performed on a UPLC system (Shimadzu, Kyoto, Japan) equipped with a quaternary pump solvent management system, an online degasser, a triple-quadrupole mass detector, and an autosampler. An Agilent ZORBAX SB-C18 column (3.0 mm × 100 mm, 1.8 µm) was used for chromatographic analyses. The mobile phase was distributed between 0.2% aqueous formic acid (A) and 0.2% formic acid acetonitrile (B) at a velocity of 0.2 mL/min. The gradient evolution protocol was 0–2 min at 90–70% B; 3–7 min at 70–50% B; 7–10 min at 50–20% B; 10–14.5 min at 20–90% B; and 14.5–17 min at 10% B. Results: The method was validated for matrix effects, linearity, limits of detection/quantification, precision, repeatability, stability, and recovery of target components. It effectively determined all target compounds in 12 MF batches from different drying methods. Conclusions: Principal component analysis (PCA) of 47 active components was conducted to evaluate MF quality comprehensively. The proposed method serves as a reliable approach for assessing the consistency of MF’s quality and therapeutic efficacy. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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12 pages, 1097 KiB  
Article
Quality Evaluation of the Traditional Chinese Medicine Moutan Cortex Based on UPLC Fingerprinting and Chemometrics Analysis
by Wentao Fang, Qianqian Song, Han Luo, Rui Wang and Chengwu Fang
Metabolites 2025, 15(4), 281; https://doi.org/10.3390/metabo15040281 - 18 Apr 2025
Viewed by 370
Abstract
Background: This study aims to develop a fingerprint analysis method using ultra-high performance liquid chromatography (UPLC) for Moutan Cortex sourced from different regions. The objective is to establish quality control standards validated through the integration of chemometric methods and component structure theory. Methods: [...] Read more.
Background: This study aims to develop a fingerprint analysis method using ultra-high performance liquid chromatography (UPLC) for Moutan Cortex sourced from different regions. The objective is to establish quality control standards validated through the integration of chemometric methods and component structure theory. Methods: The mobile phase for UPLC consisted of acetonitrile (A) and a 0.1% aqueous formic acid solution (B), with gradient elution set as follows: 0–1 min, 8% A → 15% A; 1–8 min, 15% A → 18% A; 8–10 min, 18% A → 30% A; 10–15 min, 30% A → 35% A; 15–20 min, 35% A → 85% A; 20–21 min, 85% A → 8% A; and 21–26 min, 8% A → 8% A. Chemical markers significantly affecting Moutan Cortex from various regions were screened, and their identification was based on comparison with reference materials and content determination. Results: A total of 15 chemical markers were identified, including gallic acid, oxypaeoniflorin, catechin, methyl gallate, paeonolide, apiopaeonoside, albiflorin, paeoniflorin, benzoic acid, 1,2,3,6-tetra-O-galloyl-D-glucose, 1,2,3,4,6-pentagalloylglucose, mudanpioside C, benzoyloxypaeoniflorin, benzoylpaeoniflorin, and paeonol. These markers align with component structure theory, allowing for an analysis of the structural characteristics of Moutan Cortex from different regions. Conclusions: The findings provide a valuable reference for the future quality evaluation of traditional Chinese medicine preparations, enhancing the understanding of the material basis components in Moutan Cortex from diverse sources. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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8 pages, 1174 KiB  
Article
Kinetics of Manganese Peroxidase Using Simple Phenolic Compounds as Substrates
by Madeline G. Gruenberg, Jonathan J. Halvorson and Michael A. Schmidt
Metabolites 2025, 15(4), 254; https://doi.org/10.3390/metabo15040254 - 9 Apr 2025
Viewed by 412
Abstract
Background/Objectives: Secondary metabolites encompass diverse groups of compounds; one such group is phenolics, which include small phenols up to larger polyphenols such as lignin and tannins. Smaller compounds such as phenolic acids can serve as substrates for soil microbes and enzymes. The specific [...] Read more.
Background/Objectives: Secondary metabolites encompass diverse groups of compounds; one such group is phenolics, which include small phenols up to larger polyphenols such as lignin and tannins. Smaller compounds such as phenolic acids can serve as substrates for soil microbes and enzymes. The specific interaction between plant secondary metabolites (PSMs) and soil enzymes determines whether the products of these reactions contribute to the formation of soil organic matter (SOM) or are degraded into small organic molecules. Methods: Here, we monitored the activity of a redox active soil enzyme, manganese peroxidase (MnP), with three small phenolic compounds. The compounds used in this study were pyrogallol, gallic acid, and benzoic acid. Results: Based on the kinetic parameters determined, pyrogallol and gallic acid are both substrates for MnP with different products and kinetics. Conclusion: Pyrogallol reacts faster and produces a more stable quinone than gallic acid. Benzoic acid is not a substrate for MnP. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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14 pages, 2223 KiB  
Article
Metal Ion Reduction, Chelation, and Cytotoxicity of Selected Bicyclic Monoterpenes and Their Binary Mixtures
by Karolina Wojtunik-Kulesza, Marcela Dubiel and Katarzyna Klimek
Metabolites 2025, 15(3), 199; https://doi.org/10.3390/metabo15030199 - 13 Mar 2025
Viewed by 484
Abstract
Background/Objectives: Bicyclic monoterpenes are one of the most common groups of secondary plant metabolites found in Nature. Their wide spectrum of biological activity can be used in the prevention and in the treatment of various diseases, including so-called ‘diseases of civilization’. Their [...] Read more.
Background/Objectives: Bicyclic monoterpenes are one of the most common groups of secondary plant metabolites found in Nature. Their wide spectrum of biological activity can be used in the prevention and in the treatment of various diseases, including so-called ‘diseases of civilization’. Their potential for synergistic interactions may influence the biological activities of more complex mixtures. Methods: This study investigated the ability of selected bicyclic monoterpenes and their binary mixtures to reduce Fe(III) and Cu(II) and chelate Fe(II) and assessed their cytotoxic activity against BJ and HepG2 cell lines. Results: The obtained results did not reveal synergistic interactions towards the biological activities, but binary mixtures proved to be safe in relation to the tested cell lines. Among the tested single monoterpenes, the most effective were 3-carene and β-pinene, with the latter exhibiting the greatest ability to decrease cell viability (CC50 for BJ and HepG2 cells was about 1.08 and 1.85 mM, respectively). Conclusions: The results revealed that both single compounds and binary mixtures demonstrate the ability to reduce selected metal ions and chelate Fe(II) ions. Synergistic interactions were not observed, but an increase in the activity of selected binary mixtures was recorded. Based on cell culture experiments, the monoterpenes and their binary mixtures can be considered safe at a concentration lower than 1 mM and close to 0.313 mM, respectively. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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41 pages, 4980 KiB  
Article
Untargeted Metabolomics and Targeted Phytohormone Profiling of Sweet Aloes (Euphorbia neriifolia) from Guyana: An Assessment of Asthma Therapy Potential in Leaf Extracts and Latex
by Malaika Persaud, Ainsely Lewis, Anna Kisiala, Ewart Smith, Zeynab Azimychetabi, Tamanna Sultana, Suresh S. Narine and R. J. Neil Emery
Metabolites 2025, 15(3), 177; https://doi.org/10.3390/metabo15030177 - 5 Mar 2025
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Abstract
Background/Objectives: Euphorbia neriifolia is a succulent plant from the therapeutically rich family of Euphorbia comprising 2000 species globally. E. neriifolia is used in Indigenous Guyanese asthma therapy. Methods: To investigate E. neriifolia’s therapeutic potential, traditionally heated leaf, simple leaf, and latex extracts [...] Read more.
Background/Objectives: Euphorbia neriifolia is a succulent plant from the therapeutically rich family of Euphorbia comprising 2000 species globally. E. neriifolia is used in Indigenous Guyanese asthma therapy. Methods: To investigate E. neriifolia’s therapeutic potential, traditionally heated leaf, simple leaf, and latex extracts were evaluated for phytohormones and therapeutic compounds. Full scan, data-dependent acquisition, and parallel reaction monitoring modes via liquid chromatography Orbitrap mass spectrometry were used for screening. Results: Pathway analysis of putative features from all extracts revealed a bias towards the phenylpropanoid, terpenoid, and flavonoid biosynthetic pathways. A total of 850 compounds were annotated using various bioinformatics tools, ranging from confidence levels 1 to 3. Lipids and lipid-like molecules (34.35%), benzenoids (10.24%), organic acids and derivatives (12%), organoheterocyclic compounds (12%), and phenylpropanoids and polyketides (10.35%) dominated the contribution of compounds among the 13 superclasses. Semi-targeted screening revealed 14 out of 16 literature-relevant therapeutic metabolites detected, with greater upregulation in traditional heated extracts. Targeted screening of 39 phytohormones resulted in 25 being detected and quantified. Simple leaf extract displayed 4.4 and 45 times greater phytohormone levels than traditional heated leaf and latex extracts, respectively. Simple leaf extracts had the greatest nucleotide and riboside cytokinin and acidic phytohormone levels. In contrast, traditional heated extracts exhibited the highest free base and glucoside cytokinin levels and uniquely contained methylthiolated and aromatic cytokinins while lacking acidic phytohormones. Latex samples had trace gibberellic acid levels, the lowest free base, riboside, and nucleotide levels, with absences of aromatic, glucoside, or methylthiolated cytokinin forms. Conclusions: In addition to metabolites with possible therapeutic value for asthma treatment, we present the first look at cytokinin phytohormones in the species and Euphorbia genus alongside metabolite screening to present a comprehensive assessment of heated leaf extract used in Indigenous Guyanese asthma therapy. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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13 pages, 1689 KiB  
Article
Studies of Piper auritum Kuntz’s Mutagenic and Antimutagenic Properties Using the Ames Test
by Luis S. Muñoz-Carrillo, Eduardo Madrigal-Bujaidar, Sandra L. Hernández-Ojeda, José A. Morales-González, Eduardo O. Madrigal-Santillán, Isela Álvarez-González and J. Javier Espinosa-Aguirre
Metabolites 2025, 15(3), 164; https://doi.org/10.3390/metabo15030164 - 1 Mar 2025
Viewed by 611
Abstract
Background: Piper auritum Kuntz is an endemic plant from Mexico and Central America, where it is called “hoja santa”, and it is widely used in both local cuisine and traditional medicine. By using the Ames test (strain TA98), we recently demonstrated that ethanol [...] Read more.
Background: Piper auritum Kuntz is an endemic plant from Mexico and Central America, where it is called “hoja santa”, and it is widely used in both local cuisine and traditional medicine. By using the Ames test (strain TA98), we recently demonstrated that ethanol extract from the plant has no mutagenic potential and that it has a significant antimutagenic effect. Objectives/Methods: In the present report, we extended this evaluation by using five strains of the Salmonella/microsome mutagenicity assay. Moreover, we evaluated the mutagenic/antimutagenic potential of the major component of the ethanol extract, safrole, with the TA98 strain and employed docking studies to examine the molecular relationship of safrole with the CYP1A1 isoform. Results: Our results confirmed the absence of mutagenicity in the ethanol plant extract, as well as a concentration-dependent inhibitory effect on the damage induced by benzo[a]pyrene (BaP). With respect to safrole, we also determined that the compound has no mutagenic potential and has a strong inhibitory effect on the damage induced by BaP. Docking and kinetic analysis confirmed the coupling of safrole with the active site of the CYP1A1 enzyme, leading to competitive inhibition. Conclusions: These results suggest that the inhibitory effect on the enzyme activity is one of the possible antimutagenic mechanisms. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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31 pages, 5603 KiB  
Article
Oregano Young Plants Cultured at Low Temperature Reveal an Enhanced Healing Effect of Their Extracts: Anatomical, Physiological and Cytotoxicity Approach
by Aikaterina L. Stefi, Maria Chalkiadaki, Katerina Dimitriou, Konstantina Mitsigiorgi, Dimitrios Gkikas, Danae Papageorgiou, Georgia C. Ntroumpogianni, Dido Vassilacopoulou, Maria Halabalaki and Nikolaos S. Christodoulakis
Metabolites 2025, 15(2), 103; https://doi.org/10.3390/metabo15020103 - 7 Feb 2025
Viewed by 1202
Abstract
Background: The germination and early development of Origanum vulgare L. subsp. hirtum (Link) Ietswaart (Greek oregano) were studied to assess the plant’s response to different temperatures. Methods: After germination, seedlings were cultivated in control (25 °C) and cold (15 °C) chambers with standard [...] Read more.
Background: The germination and early development of Origanum vulgare L. subsp. hirtum (Link) Ietswaart (Greek oregano) were studied to assess the plant’s response to different temperatures. Methods: After germination, seedlings were cultivated in control (25 °C) and cold (15 °C) chambers with standard growth parameters. Comparative analyses of plant morphology and leaf anatomy were conducted to identify structural modifications induced by different temperatures. Physiological evaluations, including photosynthetic pigment measurements, phenolic content, and antioxidant activity, were performed to assess differences between the plants grown under the two temperature conditions. Methanolic extracts from the leaves were tested for cytotoxicity on MCF-7 breast adenocarcinoma cells and SH-SY5Y neuroblastoma cells, as well as on nine microbial strains. Additionally, biomarkers from the leaves affected by temperature changes were determined using LC-HRMS/MS analysis. Results: Comparative analyses revealed distinct structural and physiological modifications under cold conditions. The methanolic extracts from plants grown at 15 °C exhibited notably higher cytotoxic activity in both cell lines but demonstrated no activity against microbial strains. The results highlight the influence of low temperature on enhancing the bioactive properties of Greek oregano. Conclusions: The findings provide valuable insights into the environmental adaptability of oregano, demonstrating the impact of low temperature on its bioactive properties. The therapeutic potential of methanolic extracts cultured at 15 °C is imprinted in cytotoxicity in SH-SY5Y and MCF-7 cells and the absence of any activity against microbial strains. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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14 pages, 2061 KiB  
Article
Exploring the Antineoplastic Properties of the Lebanese Jania rubens Against Colorectal Cancer
by Mariam Rifi, Zeina Radwan, Nouha Sari-Chmayssem, Rayan Kassir, Ziad Fajloun, Abir Abdel Rahman, Marwan El-Sabban, Corinne Prévostel, Zeina Dassouki and Hiba Mawlawi
Metabolites 2025, 15(2), 90; https://doi.org/10.3390/metabo15020090 - 2 Feb 2025
Viewed by 1169
Abstract
Background/Objective: Colon cancer poses a significant health burden, with current treatments often associated with severe side effects and limited effectiveness for some patients. Natural products are gaining interest as adjuvant therapies, potentially reducing side effects and improving responses to conventional treatments. We previously [...] Read more.
Background/Objective: Colon cancer poses a significant health burden, with current treatments often associated with severe side effects and limited effectiveness for some patients. Natural products are gaining interest as adjuvant therapies, potentially reducing side effects and improving responses to conventional treatments. We previously highlighted the potent antineoplastic effects of organic extracts derived from the Lebanese red algae Jania rubens. This study, investigated the anticancer activities of polysaccharide, protein, and lipid extracts from J. rubens, which may serve as adjuvant therapies to enhance conventional treatments. Methods: we employed colorimetric assays, wound healing assays, and cell cycle analysis to evaluate the anticancer activities of the extracts. The polysaccharide extract was characterized for sulfate content and structure using barium chloride-gelatin and FT-IR methods. Results: All J. rubens extracts exhibited significant anticancer effects, with the polysaccharide extract showing particularly strong cytotoxicity, apoptosis induction, and antiproliferative and anti-migratory activities. Conclusion: These findings confirm that J. rubens is a source of bioactive compounds with anticancer potential. Further investigations are needed to elucidate the molecular pathways targeted by J. rubens extracts in cancer cells. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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15 pages, 3566 KiB  
Article
Advanced Amperometric Microsensors for the Electrochemical Quantification of Quercetin in Ginkgo biloba Essential Oil from Regenerative Farming Practices
by Elena Oancea, Ioana Adina Tula, Gabriela Stanciu, Raluca-Ioana Ștefan-van Staden, Jacobus (Koos) Frederick van Staden and Magdalena Mititelu
Metabolites 2025, 15(1), 6; https://doi.org/10.3390/metabo15010006 - 31 Dec 2024
Viewed by 917
Abstract
In this study, we present a novel approach using amperometric microsensors to detect quercetin in cosmetic formulations and track its metabolic behavior after topical application. This method offers a sensitive, real-time alternative to conventional techniques, enabling the detection of quercetin’s bioavailability, its transformation [...] Read more.
In this study, we present a novel approach using amperometric microsensors to detect quercetin in cosmetic formulations and track its metabolic behavior after topical application. This method offers a sensitive, real-time alternative to conventional techniques, enabling the detection of quercetin’s bioavailability, its transformation into active metabolites, and its potential therapeutic effects when applied to the skin. Quercetin (Q) is a bioactive flavonoid known for its potent antioxidant properties, naturally present in numerous plants, particularly those with applications in cosmetic formulations. In response to the growing interest in developing novel plant-based dermo-cosmetic solutions, this study investigates the electrochemical detection of quercetin, a ketone-type flavonoid, extracted from Gingko biloba essential oil. Three newly designed amperometric microsensors were developed to assess their efficacy in detecting quercetin in botanical samples. The sensor configurations utilized two forms of carbon material as a foundation: graphite (G) and carbon nanoparticles (CNs). These base materials were modified with paraffin oil, chitosan (CHIT), and cobalt(II) tetraphenylporphyrin (Co(II)TPP) to enhance sensitivity. Differential pulse voltammetry (DPV) served as the analytical method for this investigation. Among the sensors, the CHIT/G–CN microsensor exhibited the highest sensitivity, with a detection limit of 1.22 × 10−7 mol L−1, followed by the G–CN (5.64 × 10−8 mol L−1) and Co(II)TPP/G–CN (9.80 × 10−8 mol L−1) microsensors. The minimum detectable concentration was observed with the G–CN and CoP/G–CN microsensors, achieving a threshold as low as 0.0001 μmol L−1. Recovery rates and relative standard deviation (RSD) values averaged 97.4% ± 0.43, underscoring the sensors’ reliability for quercetin detection in botanical matrices. Full article
(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)
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