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Metabolites
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Secondary Metabolites and Their Activities: From the Identification to the...
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Secondary Metabolites and Their Activities: From the Identification to the Biological Investigation

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

Deadline for manuscript submissions: 31 August 2025 | Viewed by 5040

Special Issue Editors

Dr. Valeria Cavalloro

E-Mail Website
Guest Editor
Department of Earth and Environmental Sciences, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
Interests: pharmaceutical botany
Dr. Emanuela Martino

E-Mail Website
Guest Editor
Department of Earth and Environmental Sciences, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
Interests: pharmaceutical botany

Special Issue Information

Dear Colleagues,

Nature has always played a relevant role in the fight against different human diseases, mainly thanks to the great chemical diversity of secondary metabolites. Despite the many structures already identified, almost 80% of the chemical scaffolds produced by natural organisms have not been discovered yet. The identification of new metabolites may represent a key step in the identification of new active ingredients for use against unmet medical needs.

This Special Issue welcomes original research articles and reviews investigating the world of secondary metabolites. Contributions addressing topics such as the structural elucidation of new secondary metabolites or identification of new activities associated with already identified metabolites will be considered. Moreover, manuscripts dealing with the development of green extraction techniques will be also welcome.

Dr. Valeria Cavalloro
Dr. Emanuela Martino
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

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

  • active metabolites
  • green extraction
  • bioactivity
  • natural products
  • structural elucidation

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Published Papers (5 papers)

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Research

Jump to: Review

22 pages, 2428 KiB  
Article
Assessment of Metabolic Alterations Induced by Halogenated Additives and Antifungal Activity of Extracts from the Endophytic Fungus Fusarium sp. Associated with Dizygostemon riparius (Plantaginaceae)
by Hilzimar de Jesus Freitas Sá, Anne Karoline Maiorana Santos, Adriano Souza Fonseca, Lourivaldo da Silva Santos, Josivan Regis Farias, Rosane Nassar Meireles Guerra, Edson Rodrigues-Filho, Gilmar Silverio da Silva, Cleydlenne Costa Vasconcelos, Alberto Jorge Oliveira Lopes and Antônio José Cantanhede Filho
Metabolites 2025, 15(7), 451; https://doi.org/10.3390/metabo15070451 - 4 Jul 2025
Viewed by 298
Abstract
Background/Objectives: Endophytic fungi are valuable sources of bioactive compounds with potential therapeutic applications. This study aimed to evaluate the antifungal activity of secondary metabolites produced by Fusarium sp. isolated from Dizygostemon riparius, with particular focus on the impact of culture medium [...] Read more.
Background/Objectives: Endophytic fungi are valuable sources of bioactive compounds with potential therapeutic applications. This study aimed to evaluate the antifungal activity of secondary metabolites produced by Fusarium sp. isolated from Dizygostemon riparius, with particular focus on the impact of culture medium supplementation with halogenated and metallic additives on metabolite production. Methods: The fungus was cultivated in standard Czapek medium and media supplemented with NH4Br or MnCl2. Methanolic extracts were obtained, fractionated, and chemically characterised via LC-ESI-HRMS. In vitro antifungal assays, including MIC and MFC determinations and biofilm inhibition tests, were performed against Candida albicans strains. In vivo toxicity and efficacy were assessed using Tenebrio molitor larvae. Results: Fifteen metabolites were annotated, including known antifungals such as fusaric acid and cyclosporin A. Fractions EMBr4 and EMC5 demonstrated fungicidal activity with MIC values close to fluconazole and significantly inhibited biofilm formation and maturation. In vivo, these fractions displayed low acute toxicity and improved survival in infected larvae, comparable to fluconazole treatment. Conclusions: The results indicate that culture medium modulation enhances the production of bioactive metabolites by Fusarium sp., leading to extracts with notable antifungal efficacy and safety. EMBr4 and EMC5 are promising candidates for further development as antifungal agents, particularly for targeting biofilm-associated Candida infections. These findings support the potential of endophytic fungi as sources of novel therapeutics and warrant further mechanistic and pharmacological investigations. Full article
(This article belongs to the Special Issue Secondary Metabolites and Their Activities: From the Identification to the Biological Investigation)
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15 pages, 1583 KiB  
Article
Development and Application of an In-Capillary CE-DAD Method for the Inhibitory Screening of Natural Extracts Towards Acetylcholinesterase Enzyme
by Francesca Rinaldi, Sofia Salerno, Elena Frigoli, Giulia De Soricellis, Gloria Brusotti, Stefano Negri, Matteo Radice, Francesca Merlo, Andrea Speltini, Hellas Cena and Enrica Calleri
Metabolites 2025, 15(4), 283; https://doi.org/10.3390/metabo15040283 - 18 Apr 2025
Viewed by 476
Abstract
Background: The enzymatic activity of acetylcholinesterase (AChE) has been a focal point in neurodegenerative diseases research, particularly in relation to Alzheimer’s disease. This is attributed to the significantly reduced levels of cholinergic neurons observed in Alzheimer’s patients compared to healthy individuals. The strategy [...] Read more.
Background: The enzymatic activity of acetylcholinesterase (AChE) has been a focal point in neurodegenerative diseases research, particularly in relation to Alzheimer’s disease. This is attributed to the significantly reduced levels of cholinergic neurons observed in Alzheimer’s patients compared to healthy individuals. The strategy to mitigate the onset of these diseases in patients lies in the exploration of new potential AChE inhibitors with a focus also on natural extracts. A rapid and specific capillary electrophoresis method with direct ultraviolet detection (CZE-UV/Vis) was developed to screen natural extracts by assessing their potential to inhibit AChE. Materials and Methods: To enhance the specificity when analysing complex matrixes such as natural extracts, a sequential analysis approach based on the “sandwich model” was implemented using Ellman’s reagent [5,5′-dithiobis-(2-nitrobenzoic acid)] (DTNB) as a colorimetric indicator. Results: A reference inhibitor, neostigmine, was used for system validation through IC50 and Ki values determination by subsequent injections of acetylthiocholine substrate in the presence of neostigmine at increasing concentrations, and the enzyme combined with DTNB in borate-phosphate buffer (30 mM, pH 8.0). The enzymatic product was selectively detected at 412 nm. The validated system was applied to the analysis of seven natural extracts. Conclusions: Results demonstrated promising outcomes for identifying phytotherapeutic agents with potential applications in the prevention of neurodegenerative diseases. This method provides high selectivity and automation, offering a streamlined and effective approach for screening natural matrices containing potential AChE inhibitors. Full article
(This article belongs to the Special Issue Secondary Metabolites and Their Activities: From the Identification to the Biological Investigation)
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30 pages, 6137 KiB  
Article
Comprehensive Metabolomics Profiling and Bioactivity Study of Lycium shawii (Awsaj) Extracts with Particular Emphasis on Potential Anti-Malarial Properties
by Ruba Al-Nemi, Mutaz Akkawi, Khalid Sawalha, Siska Andrina Kusumastuti, Nuralih, Susi Kusumaningrum, Tia Okselni, Vania Chlarisa Situmorang, Abdi Wira Septama, Mariusz Jaremko and Abdul-Hamid Emwas
Metabolites 2025, 15(2), 84; https://doi.org/10.3390/metabo15020084 - 1 Feb 2025
Viewed by 2001
Abstract
Background/Objectives: Although malaria is one of the oldest known human diseases, it continues to be a major global health challenge. According to UNICEF, the global malaria mortality rate exceeded 600,000 annually in 2022, which includes more than 1000 children dying each day. This [...] Read more.
Background/Objectives: Although malaria is one of the oldest known human diseases, it continues to be a major global health challenge. According to UNICEF, the global malaria mortality rate exceeded 600,000 annually in 2022, which includes more than 1000 children dying each day. This study aimed to investigate the comprehensive chemical profile and biological activities, particularly the antimalarial activity, of Lycium shawii (Awsaj), a shrub traditionally used in the Arabian Peninsula, Middle East, India, and Africa to treat a myriad of ailments. Methods: Crude extracts of L. shawii were prepared using water, ethanol, methanol, and acetone. Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) were utilized to perform untargeted metabolomics to maximize metabolite detection and tentatively identify bioactive phytochemicals. The total phenolic content (TPC) was measured for each extract, and bioassays were conducted to evaluate their antimalarial, antibacterial, and anti-inflammatory activities, particularly those of the water extract, which is the traditional method of consumption in Arabian folk medicine. Results: A total of 148 metabolites were detected, 45 of which were classified as phytochemicals. The bioassays revealed that the water extract that is traditionally used showed promising antimalarial potential by significantly inhibiting β-hematin formation in vitro at 1 mg/mL (with an absorbance of 0.140 ± 0.027). This is likely due to the rich presence of quinoline in the aqueous extract among several other bioactive phytochemicals, such as phenylpropanoids, alkaloids, flavonoids, and benzenoids. However, their anti-inflammatory and antibacterial activities were found to be weak, with only a minor inhibition of nitric oxide (NO) production in LPS-induced RAW 264.7 cells at a concentration of 500 µg/mL and weak antibacterial effects against pathogens like P. aeruginosa, MRSA, A. baumannii, and K. pneumoniae with an MIC of 500 μg/mL. The results also revealed that the methanolic extract had the highest TPC at 26.265 ± 0.005 mg GAE/g. Conclusions: The findings support the traditional medicinal use of L. shawii and highlight its potential as a source of novel therapeutic compounds, particularly for treating malaria. This study encourages further research to isolate and develop effective plant-based anti-malarial agents. Full article
(This article belongs to the Special Issue Secondary Metabolites and Their Activities: From the Identification to the Biological Investigation)
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16 pages, 3208 KiB  
Article
Essential Oils from Papaver rhoeas and Their Metabolomic Profiling
by Valeria Cavalloro, Francesco Saverio Robustelli della Cuna, Alberto Malovini, Carla Villa, Cristina Sottani, Matteo Balestra, Francesco Bracco, Emanuela Martino and Simona Collina
Metabolites 2024, 14(12), 664; https://doi.org/10.3390/metabo14120664 - 1 Dec 2024
Cited by 1 | Viewed by 885
Abstract
Background/Objectives: Essential oils (EOs) have been exploited by humans for centuries, but many sources remain poorly investigated, mainly due to the low yields associated with conventional extraction. Recently, new techniques have been developed, like solvent-free microwave extraction (SFME), able to enhance efficiency [...] Read more.
Background/Objectives: Essential oils (EOs) have been exploited by humans for centuries, but many sources remain poorly investigated, mainly due to the low yields associated with conventional extraction. Recently, new techniques have been developed, like solvent-free microwave extraction (SFME), able to enhance efficiency and sustainability. The use of Papaver rhoeas L. in traditional medicine has led researchers to investigate non-volatile fractions, but there are little data available on EOs. Methods: In the present work, we prepared EOs from the petals and leaves of P. rhoeas by SFME. GC/MS analysis of EOs revealed the presence of 106 compounds belonging to 13 different classes. Isomers of the different alkenes were identified thanks to an alkylthiolation reaction. Results: The results highlighted a predominance of saturated and unsaturated hydrocarbons, alcohols, and esters that might suggest a specific relationship with pollinators. Each population has been compared using PCA, heatmap, and barplot tools, highlighting differences in terms of composition by both comparing leaves and flowers and hill and lowland samples. Furthermore, cantharidin, a metabolite usually produced by insects, was detected in the flowers, possible present for attractiveness purposes. Conclusions: These results could contribute to ensuring a better understanding of the pollination process and of the biological activities of EOs from P. rhoeas. Full article
(This article belongs to the Special Issue Secondary Metabolites and Their Activities: From the Identification to the Biological Investigation)
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Review

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30 pages, 2043 KiB  
Review
Berberine as a Bioactive Alkaloid: Multi-Omics Perspectives on Its Role in Obesity Management
by Bartłomiej Zieniuk and Magdalena Pawełkowicz
Metabolites 2025, 15(7), 467; https://doi.org/10.3390/metabo15070467 - 9 Jul 2025
Viewed by 492
Abstract
Berberine, a bioactive isoquinoline alkaloid derived from medicinal plants such as Berberis and Coptis species, shows significant promise for managing obesity and associated metabolic disorders. This review synthesizes evidence on its modulation of AMP-activated protein kinase (AMPK) signaling, gut microbiota composition, lipid metabolism, [...] Read more.
Berberine, a bioactive isoquinoline alkaloid derived from medicinal plants such as Berberis and Coptis species, shows significant promise for managing obesity and associated metabolic disorders. This review synthesizes evidence on its modulation of AMP-activated protein kinase (AMPK) signaling, gut microbiota composition, lipid metabolism, and adipokine networks, elucidating how these actions converge to suppress adipogenesis and improve insulin sensitivity. Metabolomic profiling reveals critical shifts in bile acid metabolism, short-chain fatty acid production, and mitochondrial function. Recent studies also highlight berberine’s anti-inflammatory effects and regulatory influence on glucose homeostasis. Despite its promise, challenges in oral bioavailability and drug interactions necessitate the development of advanced delivery strategies. We further discuss nanoformulations and multi-omics approaches, which integrate data from genomics, transcriptomics, proteomics, and metabolomics, provide new insights into berberine’s mechanisms, and may guide personalized therapeutic applications. While promising, further studies are needed to validate these findings in humans and translate them into effective clinical strategies. Full article
(This article belongs to the Special Issue Secondary Metabolites and Their Activities: From the Identification to the Biological Investigation)
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