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Metabolomics of Medicinal Plants

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 December 2025 | Viewed by 927

Special Issue Editors


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Guest Editor
Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Ciudad de Mexico 11340, Mexico
Interests: natural products; plant and food metabolomics; NMR-based metabolomics; asymmetric synthesis
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Guest Editor
Centro de Nanociencias y Micro y Nanotecnologías del Instituto Politécnico Nacional, Mexico City, Mexico
Interests: NMR-based metabolomics; plant and food metabolomics; natural products

Special Issue Information

Dear Colleagues,

Metabolomics is the qualitative and/or quantitative study of a set of small molecules (typically less than 1,500 Da) produced through the metabolism of a biological system. The metabolome reflects the functional phenotype of cells, tissues, or organisms and is derived from gene expression, protein activity, and environmental interactions. In particular, the study of the metabolomics of medicinal plants offers a comprehensive approach to discovering their therapeutic potential, contributing to drug discovery, quality control, and the regulation of their consumption. The rapid growth of this field of research is linked to technological advances in the various analytical platforms commonly used for metabolomic studies, such as nuclear magnetic resonance (NMR), mass spectrometry (MS) and its variants, infrared spectroscopy, and high-performance liquid chromatography/gas chromatography (HPLC/GC). Additionally, the bioinformatic resources currently available facilitate the transformation of raw metabolomic data into biological knowledge, which can provide multiple benefits in biomedical and biotechnological research. In this context, we are pleased to announce a Special Issue of International Journal of Molecular Sciences entitled “Metabolomics of Medicinal Plants”. This Special Issue will present original research papers that take a metabolomic approach to improving our understanding of the complex biochemical networks that regulate the production of bioactive compounds in medicinal plants. This knowledge will be useful in harnessing the therapeutic potential of these compounds and establishing traditional medicine as an effective and safe treatment option for the wide range of conditions that society is currently facing.

Therefore, we invite submissions of original research articles and reviews on the following topics, developed in a metabolomic context:

  • The discovery of novel metabolites;
  • The validation of traditional medicine;
  • Quality control and chemotyping in herbal products;
  • Integrative omics in medicinal plants;
  • Decoding metabolic pathways;
  • Dereplication strategies in natural products;
  • Network pharmacology;
  • AI and machine learning;
  • Bioinformatic-assisted procedures;
  • Cutting-edge metabolomic tools.

Dr. L. Gerardo Zepeda Vallejo
Dr. Elvia Becerra-Martínez
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 250 words) can be sent to the Editorial Office for assessment.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • metabolomics
  • medicinal plants
  • nuclear magnetic resonance
  • mass spectrometry
  • bioinformatic
  • phenotyping
  • metabolic pathways
  • bioactive metabolites

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Published Papers (2 papers)

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Research

18 pages, 2780 KB  
Article
Integrated Transcriptomic and Metabolomic Analysis Reveals Biochar-Induced Enhancement of Growth and Secondary Metabolism in the Medicinal Plant Echinacea purpurea
by Liru Tan, Ling Liu, Jun Liu, Yawen Fu, Ying Zhang, Caixia Sun and Yulan Zhang
Int. J. Mol. Sci. 2025, 26(23), 11249; https://doi.org/10.3390/ijms262311249 - 21 Nov 2025
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Abstract
Echinacea purpurea (L.) Moench is a medicinally valuable plant with well-documented pharmacological properties; however, its physiological and molecular responses to biochar amendment remain largely unexplored. This study applied integrated transcriptomic and metabolomic approaches to investigate the underlying mechanisms of biochar-induced effects in E. [...] Read more.
Echinacea purpurea (L.) Moench is a medicinally valuable plant with well-documented pharmacological properties; however, its physiological and molecular responses to biochar amendment remain largely unexplored. This study applied integrated transcriptomic and metabolomic approaches to investigate the underlying mechanisms of biochar-induced effects in E. purpurea. Biochar amendment significantly promoted plant growth and improved nutrient status. Concurrent transcriptomic analysis revealed the molecular basis for these changes, identifying 4733 differentially expressed genes (DEGs). Further analysis showed significant enrichment in plant hormone signal transduction pathways, particularly those of auxin and jasmonic acid (JA). The activation of the JA pathway was specifically validated by the concurrent upregulation of its biosynthetic and metabolic genes, together with the marked accumulation of JA, jasmonoyl-isoleucine, and 12-hydroxy-jasmonoyl-isoleucine. Metabolomic profiling further revealed a pronounced upregulation of phenylpropanoid pathway metabolites, including 3-hydroxy-4-methoxycinnamic acid, chlorogenic acid methyl ester, ferulic acid O-hexoside, and coumarin derivatives such as 7-methoxy-4-methylcoumarin. Correlation analysis of transcriptomic and metabolomic data confirmed the concurrent up-regulation of phenylpropanoid biosynthetic genes. These integrated results reveal the mechanistic basis through which biochar application simultaneously promotes growth and enhances the secondary metabolism of E. purpurea by coordinately activating phytohormone signaling and phenylpropanoid biosynthesis. These results establish the potential of biochar in enhancing E. purpurea cultivation, with future work needed to determine optimal application rates. Full article
(This article belongs to the Special Issue Metabolomics of Medicinal Plants)
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13 pages, 1971 KB  
Article
Metabolomics Provides Insight into the Chemical Characteristics Underlying Bioactivity Differences Among Various Parts of Atractylodes Chinensis (DC.) Koidz.
by Yehui Hu, Xiangui Mei, Yingying Cui, Zhenying Wang, Chuanzhi Kang and Shengci Fan
Int. J. Mol. Sci. 2025, 26(22), 11034; https://doi.org/10.3390/ijms262211034 - 14 Nov 2025
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Abstract
Atractylodes chinensis (DC.) Koidz. (AK) is a kind of medicinal plant in the Asteraceae family, and its dried rhizomes have the functions of drying dampness, strengthening the spleen, dispelling wind and cold, and brightening the eyes. However, there remains insufficient development and utilization [...] Read more.
Atractylodes chinensis (DC.) Koidz. (AK) is a kind of medicinal plant in the Asteraceae family, and its dried rhizomes have the functions of drying dampness, strengthening the spleen, dispelling wind and cold, and brightening the eyes. However, there remains insufficient development and utilization of other portions of the plant. To reveal the chemical characteristics and bioactivity potential of different AK parts, this study adopted UPLC-QE-MS/MS-based widely targeted metabolomics to analyze the metabolic components in ethanol extracts of AK rhizomes, fibrous roots, stems and leaves, flowers, and seeds. We then compared the antioxidant activities of these AK parts. The results showed that the highest ethanol extraction rate was from the rhizomes, while the flowers showed the strongest antioxidant activity. A total of 165 metabolites were categorized into seven major categories that included organic acids, flavonoids, and coumarins. Among these, organic acids were found with higher content in stems and leaves, fibrous roots, and seeds, while flavonoids were higher in flowers. This study explored the chemical composition and preliminary bioactivities of different AK parts based on widely targeted metabolomics. The results confirmed that the non-medicinal AK parts have high utilization values, and provided a scientific basis for the further development and utilization of this promising medicinal plant. Full article
(This article belongs to the Special Issue Metabolomics of Medicinal Plants)
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