Bridging Ethnobotanical Knowledge and Multi-Omics Approaches for Plant-Derived Natural Product Discovery
Abstract
1. Introduction
2. Plant-Derived Natural Products
2.1. Traditional Medicine Based on Plant-Derived Natural Products
Plant Name | Tissue Used | Administration | Medicinal Use/Treatment | Reference |
---|---|---|---|---|
Africa | ||||
Acacia senegal (gum arabic) | Whole plant | Oral, topical | Bleeding, bronchitis, diarrhoea, gonorrhoea, leprosy, typhoid fever, upper respiratory tract infections | [32] |
Aloe ferox (bitter aloe or Cape aloe) | Leaves | Oral | Anti-inflammatory, analgesic, calming, antiseptic, germicidal, antiviral, antiparasitic, anticancer | [33] |
Artemisia herba-alba (wormwood) | Leaves, stems | Oral | Arterial hypertension, diabetes, bronchitis, diarrhoea, hypertension, neuralgias | [34] |
Catharanthus roseus (Madagascar periwinkle) | Leaves, seeds, stems, petals | Oral | Anticancer, rheumatism, skin disorders, venereal diseases | [35] |
China | ||||
Aconitum napellus (monkshood) | Roots | Oral, topical, inhalation | Hypertension, haemorrhoids, colic, upper urinary tract cancer, kidney failure | [36] |
Trichosanthes kirilowii (Chinese cucumber) | Seeds, fruits, pericarps, roots | Oral | Tumours, reduces fevers, swelling and coughing, abscesses, amenorrhea, jaundice, polyuria | [37] |
Chrysanthemum spp. (mums) | Flowers, seeds | Oral, topical | Chest pain, high blood pressure, type 2 diabetes, fever, cold, headache, dizziness, and swelling | [38] |
Panax ginseng (ginseng) | Leaves, stems, root | Oral | Fatigue, stress, asthma, cancer, diarrhoea, anxiety, mental health | [39] |
Artemisia annua (sweet wormwood) | Leaves | Oral | Malaria, fever reduction, inflammation | [40] |
America | ||||
Allium sativum (garlic) | Cloves | Oral | Hypercholesterolemia, claudication, common cold, osteoarthritis | [41] |
Hypericum perforatum (St. John’s wort) | Leaves, flowers, seeds | Oral | Depression, menopausal symptoms, attention-deficit hyperactivity disorder (ADHD) | [42] |
Berberis vulgarisn (barberry) | Fruit, bark, root, stem | Oral | Fever, cough, liver disease, depression, hyperlipidaemia, hyperglycaemia and bleeding | [43] |
Echinacea purpurea (purple coneflower) | Leaves, flower petals | Topical, oral | Infections, wounds, urinary tract infections, cold and flu | [44] |
Taxus brevifolia (Pacific yew) | Bark | Oral | Breast and ovarian cancer | [45] |
Digitalis lanata (woolly foxglove) | Leaves | Oral | Heart failure, arrhythmia, atrial fibrillation | [46] |
India | ||||
Terminalia arjuna (Arjuna) | Stem, bark, fruits leaves | Oral | Fractures, ulcers, antibacterial, antimicrobial, antioxidant, antiallergic, antifertility, anti-HIV | [47] |
Andrographis paniculate (Kalmegh) | Whole plant | Oral | Cold, diarrhoea, fever, jaundice, as a health tonic for the liver and cardiovascular health, antioxidant | [48] |
Mucuna Pruriens (Kauch) | Fruits, seed | Oral | Parkinson disease, sexual disorders | [49] |
Acacia catechu (Khair) | Leaves, bark, wood | Oral | Mouth ulcer, anaemia, high blood pressure, dysentery, colitis, gastric problems, bronchial asthma, cough, leucorrhoea and leprosy | [50] |
Catharanthus roseus (periwinkle) | Whole plant | Oral | Cancer, diabetes, vaginal discharge, tonsillitis, chest pain, high blood pressure, sore throat, intestinal pain, inflammation, toothache | [51] |
Papaver somniferum (opium poppy) | Seeds | Oral, injection | Pain relief, cough suppressant, diarrhoea | [30] |
2.2. Chemical Characteristics of Plant-Derived Natural Products
Plant Source | Bioactive Compound | Compound Class | Effects/Bioactivity | Mechanism of Action | Reference |
---|---|---|---|---|---|
Artemisia glabella | Arglabin | Terpene | Antitumor | Inhibits farnesyl transferase | [75] |
Cannabis sativa | Cannabidiol | Cannabinoid | Anti-epileptic, anxiolytic, antipsychotic, and anticancer | Modulates CB1, CB2, 5HT1A receptors in the central nervous system | [76] |
Capsicum annum | Capsaicin | Alkaloid | Chronic pain syndromes such as postherpetic neuralgia and musculoskeletal pain | Activates transient receptor potential vanilloid 1 (TRPV1) in sensory nerves | [77] |
Colchicum spp. | Colchicine | Alkaloid | Gout | Scavenges reactive oxygen and nitrogen species, inhibits NF-kB, modulates activities of glutathione, catalase, and superoxide dismutase | [78] |
Genista tinctoria | Genistein | Flavonoid | Anticancer, Alzheimer’s disease | Inhibits protein-tyrosine kinase, induces apoptosis, antimetastatic and antiangiogenic activity, antioxidant | [79] |
Gossypium hirsutum | Gossypol | Terpene | Anti-infertility/male contraceptive, anticancer, antiviral, antimicrobial, antioxidant activities | Bcl-2 and sperm production inhibition, induces apoptosis, inhibits DNA polymerase and topoisomerase II | [80] |
Tabebuia avellanedae | β-Lapachone | Quinone | Variety of cancers, especially solid tumours, anti-trypanosoma, antimicrobial, and antimalarial activities | Anticancer activity through formation of ROS in NQO1-positive cells, inhibits topoisomerase, modulates the mTOR pathway | [81] |
Larrea tridentate | Masoprocol | Phenolic compound | Antineoplastic agent used in cancer chemotherapy | Inhibits 5-Lipoxygenase | [6] |
Podophyllum emodi | Podophyllotoxin | Phenolic compound | Antitumour | Suppresses formation of mitotic spindles microtubules, cycle arrest via polymerisation of tubulin | [82] |
3. Classical Approaches in NP Research
4. Computational Metabolomics in Plant-Derived NP Research
Technological Advancements in Metabolite Annotation
Tool | Website | Description/Function/Role | References |
---|---|---|---|
Data processing and analysis | |||
XCMS online | https://xcmsonline.scripps.edu | Nonlinear retention time alignment | [119] |
MZmine | https://github.com/mzmine/mzmine | Mass detection, peak deconvolution, retention time alignment | [120] |
OpenMS | https://www.openms.de/ | Peak picking, retention time alignment, baseline and noise filtering, metabolite quantification and identification | [121] |
MS-DIAL | https://systemsomicslab.github.io/compms/msdial/main.html | Spectral deconvolution, peak identification, statistical analysis | [122] |
HomologueDiscoverer | https://github.com/kevinmildau/homologueDiscoverer | Detection and omission of noise features and redundant features | [123] |
Metabolite annotation libraries | |||
METLIN | https://metlin.scripps.edu/ | Repository for searchable MS2 data (positive and negative modes) and neutral loss libraries acquired from standards | [152] |
MassBank | https://massbank.eu/MassBank/ | Spectral data repository | [153,154] |
ReSpect | https://github.com/shahab-sarmashghi/RESPECT | Spectra and taxonomy information repository | [147] |
GNPS | https://gnps.ucsd.edu/ | Repository for spectral libraries, molecular network construction | [125] |
Mass Spectral Networking, Embedding and Annotation | |||
Classical Molecular Networking (MN) | https://gnps.ucsd.edu/ | Groups metabolites based on MS/MS spectra similarity, forming molecular networks | [125] |
Feature-Based Molecular Networking (FBMN) | https://gnps.ucsd.edu/ | Enhances MN by using MS1 feature data to align nodes more precisely in molecular networks | [124] |
msFeaST | https://github.com/kevinmildau/msFeaST | Integrates MS1 and MS2 information for improved feature selection in molecular networking | [140] |
MS2LDA | https://ms2lda.org/ | Decomposition of molecular fragmentation, annotation and discovery of Mass2Motifs | [128] |
MS2Query | https://github.com/iomega/ms2query | Integrates Spec2Vec and MS2Deepscore, ranks potential analogues and exact matches | [155] |
Spec2Vec | https://github.com/iomega/spec2vec | Assess and rank spectral similarities | [133] |
MS2Deepscore | https://github.com/matchms/ms2deepscore | Predicts structural similarity between MS/MS spectra | [134] |
NAP | https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp | Improves in silico fragmentation candidate structure ranking | [135] |
DEREPLICATOR | https://gnps.ucsd.edu/ | In silico identification of both peptidic and non-peptidic natural products | [136] |
SIRIUS+CSI:FingerID | https://github.com/computational-metabolomics/sirius-csifingerid-galaxy | Analysis of isotope patterns, compound class prediction. | [156,157] |
ClassyFire | https://bio.tools/ClassyFire | Large-scale automated chemical/metabolite classification | [138] |
MolNetEnhancer | https://gnps.ucsd.edu/ | Enhances molecular networks by integrating chemical classification data to assign chemical ontologies to metabolites. Helps identify molecular families and structural variations | [132] |
Bioactivity-Based Molecular Networking (BBMN) | https://gnps.ucsd.edu | Links molecular networks to bioactivity data to discover bioactive compounds | [139] |
FERMO | https://fermo.bioinformatics.nl | Links bioactivity information to metabolite features in natural product discovery | [141] |
Cytoscape | https://cytoscape.org/ | Network data integration, analysis, and visualisation | [127] |
Metabologenomics | |||
antiSMASH | https://github.com/antismash/antismash | Identify, annotate, and compare gene clusters that encode the biosynthesis of NPs | [142] |
Paired Omics Data Platform (PoDP) | https://pairedomicsdata.bioinformatics.nl | Standardise links between genomic and metabolomics data in a computer readable format to further the field of natural products discovery | [146] |
plantiSMASH | http://plantismash.secondarymetabolites.org/ | A specialised version of antiSMASH designed for the identification, annotation, and analysis of BGCs in plant genomes | [144] |
NPLinker | https://github.com/nplinker/nplinker | Links BGCs with metabolomics data to facilitate the discovery of natural products by integrating and analysing paired omics datasets | [158] |
5. Integration of Omics Technologies for NP Discovery
5.1. Genomics: Uncovering Biosynthetic Potential
5.2. Transcriptomics: Understanding Gene Expression Dynamics
5.3. Proteomics: Linking Genotype to Phenotype
5.4. Applications of Integrated Omics in NP Discovery
6. Conclusions and Future Perspectives
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Chele, K.H.; Piater, L.A.; van der Hooft, J.J.J.; Tugizimana, F. Bridging Ethnobotanical Knowledge and Multi-Omics Approaches for Plant-Derived Natural Product Discovery. Metabolites 2025, 15, 362. https://doi.org/10.3390/metabo15060362
Chele KH, Piater LA, van der Hooft JJJ, Tugizimana F. Bridging Ethnobotanical Knowledge and Multi-Omics Approaches for Plant-Derived Natural Product Discovery. Metabolites. 2025; 15(6):362. https://doi.org/10.3390/metabo15060362
Chicago/Turabian StyleChele, Kekeletso H., Lizelle A. Piater, Justin J. J. van der Hooft, and Fidele Tugizimana. 2025. "Bridging Ethnobotanical Knowledge and Multi-Omics Approaches for Plant-Derived Natural Product Discovery" Metabolites 15, no. 6: 362. https://doi.org/10.3390/metabo15060362
APA StyleChele, K. H., Piater, L. A., van der Hooft, J. J. J., & Tugizimana, F. (2025). Bridging Ethnobotanical Knowledge and Multi-Omics Approaches for Plant-Derived Natural Product Discovery. Metabolites, 15(6), 362. https://doi.org/10.3390/metabo15060362