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Metabolites
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Metabolism of Bioactives and Natural Products
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Metabolism of Bioactives and Natural Products

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

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 6567

Special Issue Editors

Dr. Kamila Misiakiewicz-Has

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Guest Editor
Department of Histology and Embryology, Pomeranian Medical University in Szczecin, 72 Powstańców Wielkopolskich Str., 70-111 Szczecin, Poland
Interests: natural products; isoflavones; saponins; inulin; diabetes; digestive system; male gonad
Prof. Dr. Barbara Wiszniewska

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Guest Editor
Department of Histology and Embryology, Faculty of Medicine and Dentistry, Pomeranian Medical University, Powst. Wlkp. 72, 70-111 Szczecin, Poland
Interests: endocrine disrupting chemicals; hormonal imbalance; male reproductive system; Isoflavones
Dr. Sylwia Rzeszotek

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Guest Editor
Department of Histology and Embryology, Pomeranian Medical University in Szczecin, 72 Powstańców Wielkopolskich Str., 70-111 Szczecin, Poland
Interests: cellular stress; autophagy; digestive system; steroid hormones imbalance; cell adhesion molecules; hemopoiesis

Special Issue Information

Dear Colleagues,

Bioactive components and natural products and their structural analogues have played an important role in pharmacotherapy, especially in the past. Now, our attention is once again turning toward potentially therapeutic/healing compounds found in nature. The sources of natural products include secondary metabolites and endogenous active compounds isolated not only from plants but also from fungi, animals, and microorganisms. Natural products provide unique characteristics compared to traditional synthetic molecules, presenting both benefits and obstacles in the drug discovery process. Natural products have a profound impact on human physiology, metabolism, and stress responses. Extensive research has demonstrated that the in vivo pharmacodynamic effects of natural products are strongly related to their metabolic profiles, depending on the bioavailability, absorption, and metabolism of bioactive compounds (in this context, the microbiota has a significant role to play). Studying bioactive metabolites in vivo and assessing their activity against various diseases is challenging due to the diversity of these chemical structures, their low and varied concentrations, and the variability in the production of specific metabolites within the population. In this Special Issue, we aim to identify and characterize compounds that affect molecular targets and their pharmacological potential, ultimately benefiting human health.

Dr. Kamila Misiakiewicz-Has
Prof. Dr. Barbara Wiszniewska
Dr. Sylwia Rzeszotek
Guest Editors

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Keywords

  • natural products
  • bioactive
  • medicinal plants
  • phytochemicals
  • isoflavones
  • triterpenes
  • coumarins
  • alkaloids
  • prebiotics
  • carotenoids
  • polyphenols
  • organosulfur compounds

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Published Papers (7 papers)

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Research

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21 pages, 3432 KiB  
Article
Assessment of Biochemical Composition of Fruits of Hippophae rhamnoides (Elaeagnaceae juss.), Viburnum opulus (Viburnaceae raf.) and Lonicera caerulea subsp. altaica (Caprifoliaceae juss.)
by Tatiana Vdovina, Olga Lagus, Andrei Vinokurov, Zhanar Aimenova and Aidar Sumbembayev
Metabolites 2025, 15(4), 256; https://doi.org/10.3390/metabo15040256 - 9 Apr 2025
Viewed by 306
Abstract
Background/Objectives: This study explores the biochemical diversity of Hippophae rhamnoides, Viburnum opulus, and Lonicera caerulea subsp. altaica to identify genotypes rich in bioactive compounds for breeding nutritionally valuable cultivars. Methods: Selected forms and cultivars of each species were evaluated for key [...] Read more.
Background/Objectives: This study explores the biochemical diversity of Hippophae rhamnoides, Viburnum opulus, and Lonicera caerulea subsp. altaica to identify genotypes rich in bioactive compounds for breeding nutritionally valuable cultivars. Methods: Selected forms and cultivars of each species were evaluated for key biochemical traits. Analyses included quantification of vitamins (C, B9, B12), sugars, organic acids, carotenoids, and flavonoids using HPLC and TLC. Results: In H. rhamnoides, vitamin C content ranged widely, with ‘Pamyati Baytulina Sh-9-81’ reaching 156.0 mg/%, while ‘Shetlastinka No. 7’ showed the most favorable sugar-to-vitamin C ratio. ‘Krasnoplodnaya K-14-81’ had the highest carotenoids (55.3 mg/100 g), and ‘Dolgozhdannaya No. 5’ was notable for flavonoid richness. In V. opulus, considerable variation was observed in vitamin content, sugars, and dry matter; ‘Zhemchuzhnoe Ozhele’ and ‘Shtambovaya’ were rich in rutin and robinin. In L. caerulea subsp. altaica, forms No. 5, 7, and 9 stood out for vitamin C, sugar, and flavonoid content. Hyperoside, isorhamnetin, and myricetin were common, while kaempferol and hypolaetin were form-specific. Conclusions: H. rhamnoides demonstrated the highest variability in biochemical composition, while L. caerulea subsp. altaica showed a particularly rich flavonoid profile. These species offer valuable genetic resources for developing biofortified cultivars suited to both nutritional and adaptive breeding goals. Full article
(This article belongs to the Special Issue Metabolism of Bioactives and Natural Products)
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19 pages, 2396 KiB  
Article
Valorizing Agro-Industrial By-Products for Sustainable Cultivation of Chlorella sorokiniana: Enhancing Biomass, Lipid Accumulation, Metabolites, and Antimicrobial Potential
by Elia Lio, Carlo Esposito, Jacopo Paini, Stefano Gandolfi, Francesco Secundo and Gianluca Ottolina
Metabolites 2025, 15(3), 212; https://doi.org/10.3390/metabo15030212 - 20 Mar 2025
Viewed by 381
Abstract
Background/Objectives: Mixotrophic cultivation of microalgae using agro-industrial by-products as supplements offers a sustainable strategy to enhance biomass production and bioactive compound synthesis. This study aimed to evaluate the effects of different agro-industrial by-products—orange peel extract, Cladophora glomerata macroalgal hydrolysate, and solid-state fungal fermentation [...] Read more.
Background/Objectives: Mixotrophic cultivation of microalgae using agro-industrial by-products as supplements offers a sustainable strategy to enhance biomass production and bioactive compound synthesis. This study aimed to evaluate the effects of different agro-industrial by-products—orange peel extract, Cladophora glomerata macroalgal hydrolysate, and solid-state fungal fermentation hydrolysate—on the growth and bioactivity of Chlorella sorokiniana. Methods: Microalgae were cultivated under mixotrophic conditions with different agro-industrial by-products as organic carbon sources. Biomass accumulation was monitored through dry weight measurements. Lipid extraction was carried out using dimethyl carbonate. The antimicrobial activity of the extracted compounds was assessed against Escherichia coli, Bacillus megaterium, and Bacillus subtilis by determining the minimal inhibitconcentrations. Results: Orange peel extract supplementation resulted in the highest biomass production. It increased dry weight by 13.86-fold compared to autotrophic conditions. Cladophora glomerata macroalgal hydrolysate followed with a 5.79-fold increase, and solid-state fungal fermentation hydrolysate showed a 4.14-fold increase. The lipophilic fraction extracted from microalgal biomass showed high yields. Orange peel extract supplementation achieved the highest extraction yield (274.36 mg/g DW). Antimicrobial activity varied based on the supplement used: biomass cultivated with orange peel extract exhibited superior activity against E. coli, whereas Cladophora glomerata macroalgal hydrolysate biomass demonstrated potent activity against B. subtilis (MIC: 5.67 g/mL). Conclusions: These findings underscore the potential of agro-industrial by-products for enhancing microalgal biomass and metabolite production. The observed antimicrobial properties highlight the application of microalgal-derived compounds in sustainable bioprocesses, supporting their use in pharmaceutical and biotechnological applications. Full article
(This article belongs to the Special Issue Metabolism of Bioactives and Natural Products)
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28 pages, 10002 KiB  
Article
Silymarin as a Therapeutic Agent for Hepatocellular Carcinoma: A Multi-Approach Computational Study
by Ouided Benslama, Sabrina Lekmine, Hamza Moussa, Hichem Tahraoui, Mohammad Shamsul Ola, Jie Zhang and Abdeltif Amrane
Metabolites 2025, 15(1), 53; https://doi.org/10.3390/metabo15010053 - 15 Jan 2025
Cited by 2 | Viewed by 1144
Abstract
Background: Hepatocellular carcinoma (HCC) is a prevalent and lethal form of liver cancer with limited treatment options. Silymarin, a flavonoid complex derived from milk thistle, has shown promise in liver disease treatment due to its antioxidant, anti-inflammatory, and anticancer properties. This study aims [...] Read more.
Background: Hepatocellular carcinoma (HCC) is a prevalent and lethal form of liver cancer with limited treatment options. Silymarin, a flavonoid complex derived from milk thistle, has shown promise in liver disease treatment due to its antioxidant, anti-inflammatory, and anticancer properties. This study aims to explore the therapeutic potential of silymarin in HCC through a comprehensive in silico approach. Methods: This study employed a network pharmacology approach to identify key molecular targets of silymarin in HCC. The Genecards and Metascape databases were used for target identification and functional annotation. Molecular docking analysis was conducted on the primary silymarin components against VEGFA and SRC proteins, which are critical in HCC progression. MD simulations followed to assess the stability and interactions of the docked complexes. Results: Network pharmacology analysis identified several key molecular targets and pathways implicated in HCC. The molecular docking results revealed strong binding affinities of silymarin components to VEGFA and SRC, with Silybin A and Isosilybin B showing the highest affinities. MD simulations confirmed the stability of these interactions, indicating potential inhibitory effects on HCC progression. Conclusions: This study provides a comprehensive in silico evaluation of silymarin’s therapeutic potential in HCC. The findings suggest that silymarin, particularly its components Silybin A and Isosilybin B, may effectively target VEGFA and SRC proteins, offering a promising avenue for HCC treatment. Further experimental validation is warranted to confirm these findings and facilitate the development of silymarin-based therapeutics for HCC. Full article
(This article belongs to the Special Issue Metabolism of Bioactives and Natural Products)
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28 pages, 5142 KiB  
Article
Comparison of In Vitro Biotransformation of Olive Polyphenols Between Healthy Young and Elderly
by Stef Lauwers, Anne-Sophie Weyns, Annelies Breynaert, Tim Van Rillaer, Valerie Van Huynegem, Erik Fransen, Wout Bittremieux, Sarah Lebeer, Emmy Tuenter and Nina Hermans
Metabolites 2025, 15(1), 26; https://doi.org/10.3390/metabo15010026 - 7 Jan 2025
Viewed by 923
Abstract
Background: Olive leaves are a rich source of polyphenols, predominantly secoiridoids, flavonoids, and simple phenols, which exhibit various biological properties. Extracts prepared from olive leaves are associated with hypoglycemic, hypotensive, diuretic, and antiseptic properties. Upon ingestion, a substantial fraction of these polyphenols reaches [...] Read more.
Background: Olive leaves are a rich source of polyphenols, predominantly secoiridoids, flavonoids, and simple phenols, which exhibit various biological properties. Extracts prepared from olive leaves are associated with hypoglycemic, hypotensive, diuretic, and antiseptic properties. Upon ingestion, a substantial fraction of these polyphenols reaches the colon where they undergo extensive metabolism by the gut microbiota. Host characteristics, like age, can influence the composition of the gut microbiome, potentially affecting the biotransformation of these compounds. Therefore, it can be hypothesised that differences in the gut microbiome between young and elderly individuals may impact the biotransformation rate and the type and amount of metabolites formed. Methods: An in vitro biotransformation model was used to mimic the conditions in the stomach, small intestine and colon of two age groups of healthy participants (20–30 years old, ≥65 years old), using oleuropein as a single compound and an olive leaf extract as test compounds. The bacterial composition and metabolite content were investigated. Results: The study revealed that, while the same metabolites were formed in both age groups, in the young age group, less metabolite formation was observed, likely due to a reduced viable cell count. Most biotransformation reactions took place within the first 24 h of colon incubation, and mainly, deglycosylation, hydrolysis, flavonoid ring cleavage, and demethylation reactions were observed. A bacterial composition analysis showed a steep drop in α-diversity after 24 h of colon incubation, likely due to favourable experimental conditions for certain bacterial species. Conclusions: Both age groups produced the same metabolites, suggesting that the potential for polyphenols to exert their health-promoting benefits persists in healthy older individuals. Full article
(This article belongs to the Special Issue Metabolism of Bioactives and Natural Products)
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24 pages, 9580 KiB  
Article
Preliminary Data on Silybum marianum Metabolites: Comprehensive Characterization, Antioxidant, Antidiabetic, Antimicrobial Activities, LC-MS/MS Profiling, and Predicted ADMET Analysis
by Sabrina Lekmine, Ouided Benslama, Mohammad Shamsul Ola, Nabil Touzout, Hamza Moussa, Hichem Tahraoui, Haroun Hafsa, Jie Zhang and Abdeltif Amrane
Metabolites 2025, 15(1), 13; https://doi.org/10.3390/metabo15010013 - 3 Jan 2025
Cited by 2 | Viewed by 1082
Abstract
Background/Objectives: Silybum marianum extract, obtained via microwave-enhanced extraction, was evaluated for its antioxidant, antidiabetic, and antimicrobial activities to explore its therapeutic potential. Methods: The extraction was performed using microwave-enhanced techniques, and LC-MS/MS was employed to profile the metabolites in the extract. Total phenolic [...] Read more.
Background/Objectives: Silybum marianum extract, obtained via microwave-enhanced extraction, was evaluated for its antioxidant, antidiabetic, and antimicrobial activities to explore its therapeutic potential. Methods: The extraction was performed using microwave-enhanced techniques, and LC-MS/MS was employed to profile the metabolites in the extract. Total phenolic and flavonoid contents were quantified using spectrophotometric methods. Antioxidant activity was assessed using DPPH, ABTS, CUPRAC, Phenanthroline, and FRAP assays. Enzyme inhibition assays were conducted to evaluate antidiabetic activity against α-glucosidase and α-amylase. Antimicrobial activity was determined using the disc diffusion method, and in silico ADMET and drug-likeness analyses were performed for key metabolites. Results: The extract contained 251.2 ± 1.2 mg GAE/g of total phenolics and 125.1 ± 1.6 mg QE/g of total flavonoids, with 33 metabolites identified, including phenolic acids, tannins, flavonoids, and flavolignans. Strong antioxidant activity was observed, with IC50 values of 19.2 ± 2.3 μg/mL (DPPH), 7.2 ± 1.7 μg/mL (ABTS), 22.2 ± 1.2 μg/mL (CUPRAC), 35.2 ± 1.8 μg/mL (Phenanthroline), and 24.1 ± 1.2 μg/mL (FRAP). Antidiabetic effects were significant, with IC50 values of 18.1 ± 1.7 μg/mL (α-glucosidase) and 26.5 ± 1.3 μg/mL (α-amylase). Antimicrobial activity demonstrated inhibition zones of 8.9 ± 1.1 mm (Bacillus subtilis), 12.6 ± 1.6 mm (Escherichia coli), 8.2 ± 1.2 mm (Fusarium oxysporum), and 9.2 ± 1.1 mm (Aspergillus niger). In silico analyses showed high absorption, favorable metabolism and excretion, and minimal toxicity, with no hERG channel inhibition or hepatotoxicity. Conclusions: The comprehensive results highlight the significant antioxidant, antidiabetic, and antimicrobial activities of S. marianum extract, suggesting its potential for therapeutic and preventive applications. Full article
(This article belongs to the Special Issue Metabolism of Bioactives and Natural Products)

Review

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25 pages, 1447 KiB  
Review
Trimethylamine-N-Oxide (TMAO) as a Rising-Star Metabolite: Implications for Human Health
by Eugenio Caradonna, Federico Abate, Elisabetta Schiano, Francesca Paparella, Fulvio Ferrara, Emilio Vanoli, Rossana Difruscolo, Vito Maria Goffredo, Bruno Amato, Carlo Setacci, Francesco Setacci and Ettore Novellino
Metabolites 2025, 15(4), 220; https://doi.org/10.3390/metabo15040220 - 24 Mar 2025
Viewed by 1320
Abstract
The intestinal microbiota, hosting trillions of microorganisms that inhabit the gastrointestinal tract, functions as a symbiotic organism that plays a crucial role in regulating health by producing biologically active molecules that can enter systemic circulation. Among them, trimethylamine-N-oxide (TMAO), an organic compound derived [...] Read more.
The intestinal microbiota, hosting trillions of microorganisms that inhabit the gastrointestinal tract, functions as a symbiotic organism that plays a crucial role in regulating health by producing biologically active molecules that can enter systemic circulation. Among them, trimethylamine-N-oxide (TMAO), an organic compound derived from dietary sources and microbial metabolism, has emerged as a critical biomarker linking diet, the gut microbiota, and the host metabolism to various pathological conditions. This comprehensive review highlights TMAO’s biosynthesis, physiological functions, and clinical significance, focusing on its mechanistic contributions to cardiovascular and neurodegenerative diseases. Notably, TMAO-mediated pathways include endothelial dysfunction, inflammation via NLRP3 inflammasome activation, and cholesterol metabolism disruption, which collectively accelerate atherosclerosis and disease progression. Nonetheless, this work underscores the innovative potential of targeting TMAO through dietary, nutraceutical, and microbiota-modulating strategies to mitigate its pathological effects, marking a transformative approach in the prevention and management of TMAO-related disorders. Full article
(This article belongs to the Special Issue Metabolism of Bioactives and Natural Products)
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30 pages, 4051 KiB  
Review
Diverse Physiological Roles of Kynurenine Pathway Metabolites: Updated Implications for Health and Disease
by Yuechang Wang, Yonggang Zhang, Wei Wang, Yanmin Zhang, Xueqian Dong and Yang Liu
Metabolites 2025, 15(3), 210; https://doi.org/10.3390/metabo15030210 - 20 Mar 2025
Viewed by 605
Abstract
Tryptophan is an essential amino acid critical for human health. It plays a pivotal role in numerous physiological and biochemical processes through its metabolism. The kynurenine (KYN) pathway serves as the principal metabolic route for tryptophan, producing bioactive metabolites, including KYN, quinolinic acid, [...] Read more.
Tryptophan is an essential amino acid critical for human health. It plays a pivotal role in numerous physiological and biochemical processes through its metabolism. The kynurenine (KYN) pathway serves as the principal metabolic route for tryptophan, producing bioactive metabolites, including KYN, quinolinic acid, and 3-hydroxykynurenine. Numerous studies are actively investigating the relationship between tryptophan metabolism and physiological functions. These studies are highlighting the interactions among metabolites that may exert synergistic or antagonistic effects, such as neuroprotective or neurotoxic, and pro-oxidative or antioxidant activities. Minor disruptions in the homeostasis of these metabolites can result in immune dysregulation, contributing to a spectrum of diseases. These diseases include neurological disorders, mental illnesses, cardiovascular conditions, autoimmune diseases, and chronic kidney disease. Therefore, understanding the physiological roles of the KYN pathway metabolites is essential for elucidating the contribution of tryptophan metabolism to health regulation. The present review emphasizes the physiological roles of KYN pathway metabolites and their mechanisms in disease development, aiming to establish a theoretical basis for leveraging dietary nutrients to enhance human health. Full article
(This article belongs to the Special Issue Metabolism of Bioactives and Natural Products)
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