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Sørensen MB, Møller JK, Strube ML, Gotfredsen CH. Designing optimal experiments in metabolomics. Metabolomics 2024; 20:69. [PMID: 38941008 DOI: 10.1007/s11306-024-02122-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 04/26/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Metabolomics data is often complex due to the high number of metabolites, chemical diversity, and dependence on sample preparation. This makes it challenging to detect significant differences between factor levels and to obtain accurate and reliable data. To address these challenges, the use of Design of Experiments (DoE) techniques in the setup of metabolomic experiments is crucial. DoE techniques can be used to optimize the experimental design space, ensuring that the maximum amount of information is obtained from a limited sample space. AIM OF REVIEW This review aims at providing a baseline workflow for applying DoE when generating metabolomics data. KEY SCIENTIFIC CONCEPTS OF REVIEW The review provides insights into the theory of DoE. The review showcases the theory being put into practice by highlighting different examples DoE being applied in metabolomics throughout the literature, considering both targeted and untargeted metabolomic studies in which the data was acquired using both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry techniques. In addition, the review presents DoE concepts not currently being applied in metabolomics, highlighting these as potential future prospects.
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Affiliation(s)
- Mathies Brinks Sørensen
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800, Kongens Lyngby, Hovedstaden, Denmark
| | - Jan Kloppenborg Møller
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Asmussens Allé, 2800, Kongens Lyngby, Hovedstaden, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kongens Lyngby, Hovedstaden, Denmark
| | - Charlotte Held Gotfredsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet, 2800, Kongens Lyngby, Hovedstaden, Denmark.
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2
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Janzing NBM, Niehoff M, Sander W, Senges CHR, Schäkermann S, Bandow JE. A metabolomics perspective on clorobiocin biosynthesis: discovery of bromobiocin and novel derivatives through LC-MS E-based molecular networking. Microbiol Spectr 2024:e0042324. [PMID: 38864648 DOI: 10.1128/spectrum.00423-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
Clorobiocin is a well-known, highly effective inhibitor of DNA gyrase belonging to the aminocoumarin antibiotics. To identify potentially novel derivatives of this natural product, we conducted an untargeted investigation of clorobiocin biosynthesis in the known producer Streptomyces roseochromogenes DS 12.976 using LC-MSE, molecular networking, and analysis of fragmentation spectra. Previously undescribed clorobiocin derivatives uncovered in this study include bromobiocin, a variant halogenated with bromine instead of chlorine, hydroxylated clorobiocin, carrying an additional hydroxyl group on its 5-methyl-pyrrole 2-carboxyl moiety, and two other derivatives with modifications on their 3-dimethylallyl 4-hydroxybenzoate moieties. Furthermore, we identified several compounds not previously considered clorobiocin pathway products, which provide new insights into the clorobiocin biosynthetic pathway. By supplementing the medium with different concentrations of potassium bromide, we confirmed that the clorobiocin halogenase can utilize bromine instead of chlorine. The reaction, however, is impeded such that non-halogenated clorobiocin derivatives accumulate. Preliminary assays indicate that the antibacterial activity of bromobioin against Bacillus subtilis and efflux-impaired Escherichia coli matches that of clorobiocin. Our findings emphasize that yet unexplored compounds can be discovered from established strains and biosynthetic gene clusters by means of metabolomics analysis and highlight the utility of LC-MSE-based methods to contribute to unraveling natural product biosynthetic pathways. IMPORTANCE The aminocoumarin clorobiocin is a well-known gyrase inhibitor produced by the gram-positive bacterium Streptomyces roseochromogenes DS 12.976. To gain a deeper understanding of the biosynthetic pathway of this complex composite of three chemically distinct entities and the product spectrum, we chose a metabolite-centric approach. Employing high-resolution LC-MSE analysis, we investigated the pathway products in extracted culture supernatants of the natural producer. Novel pathway products were identified that expand our understanding of three aspects of the biosynthetic pathway, namely the modification of the noviose, transfer and methylation of the pyrrole 2-carboxyl moiety, and halogenation. For the first time, brominated products were detected. Their levels and the levels of non-halogenated products increased in medium supplemented with KBr. Based on the presented data, we propose that the enzyme promiscuity contributes to a broad product spectrum.
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Affiliation(s)
- Niklas B M Janzing
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Maurice Niehoff
- Organic Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Wolfram Sander
- Organic Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Christoph H R Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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Dawood HM, Barghouth NM, El-Mezayen NS, Ibrahim RS, Shawky E. Metabolomic insights into the therapeutic mechanisms of costus (Saussurea costus (Falc.) Lipsch.) root extract in propylthiouracil-induced hypothyroidism rat model. JOURNAL OF ETHNOPHARMACOLOGY 2024; 324:117784. [PMID: 38253277 DOI: 10.1016/j.jep.2024.117784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Saussurea costus (Falc.) Lipschitz. is one of the most reputed medicinal plants as a traditional medicine in the Arab and Middle East regions in the treatment of thyroid disorders, however, more investigations are needed to fully understand its effectiveness and mechanism of action. AIM OF THE STUDY The primary objective of the study was to assess the impact of Saussurea costus (COST) on the metabolic profiles of propylthiouracil (PTU)-induced hypothyroidism in rats. This involves a comprehensive examination of serum metabolites using UPLC/QqQ-MS analysis aiming to identify differential metabolites, elucidate underlying mechanisms, and evaluate the potential pharmacological effect of COST in restoring metabolic homeostasis. MATERIALS AND METHODS Hypothyroidism was induced in female Sprague-Dawley rats by oral administration of propylthiouracil (PTU). UPLC/QqQ MS analysis of serum samples from normal, PTU, and PTU + COST rats was utilized for annotation of intrinsic metabolites with the aid of online Human metabolome database (HMDB) and extensive literature surfing. Multivariate statistical analyses, including orthogonal partial least squares discriminant analysis (OPLS-DA), discerned variations between the different groups. Serum levels of T3, T4 and TSH in addition to arachidonic acid (ARA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) levels in thyroid gland tissues; Phospholipase A2 group IIA (PLA2G2A), and lipoprotein lipase (LPL) in liver tissues were assessed by specific ELISA kits. Gene expression for key proteins of the primary evolved pathwayswere quantified by one-step qRT-PCR technique. Histopathological evaluation of thyroid gland tissue was performed by an investigator blinded to the experimental group using light microscope. RESULTS Distinct clustering in multivariate statistical analysis models indicated significant variations in serum chemical profiles among normal, disease, and treated groups. VIP values guided the selection of differential metabolites, revealing significant changes in metabolite concentrations. Subsequent to COST treatment, 43 differential intrinsic metabolites exhibited a notable tendency to revert towards normal levels. Annotated metabolites, such as lysophosphatidylcholine (LPC), L-acetylcarnitine, gamma-glutamylserine, and others, showed differential regulation in response to PTU and subsequent S. costus treatment. Notably, 21 metabolites were associated with polyunsaturated fatty acids (PUFAs) biosynthesis, arachidonic acid (ARA) metabolism, and glycerophospholipid metabolism exhibited significant changes on conducting metabolic pathway analysis. CONCLUSIONS COST improves PTU-induced hypothyroidism by regulating biosynthesis of PUFAs signified by n-3/n-6, ARA and glycerophospholipid metabolism. The study provides us a novel mechanism to explain the improvement of hypothyroidism and associated dyslipidemia by COST, depicts a metabolic profile of hypothyroidism, and gives us another point cut for further exploring the biomarkers and pathogenesis of hypothyroidism.
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Affiliation(s)
- Hend M Dawood
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Egypt
| | - Neveen M Barghouth
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Egypt
| | - Nesrine S El-Mezayen
- Department of Pharmacology and Therapeutics, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
| | - Reham S Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Egypt
| | - Eman Shawky
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Egypt.
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Song X, Wang H, Wang Y, Zeng Q, Zheng X. Metabolomics combined with physiology and transcriptomics reveal how Nicotiana tabacum leaves respond to cold stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108464. [PMID: 38442629 DOI: 10.1016/j.plaphy.2024.108464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024]
Abstract
Low temperature-induced cold stress is a major threat to plant growth, development and distribution. Unraveling the responses of temperature-sensitive crops to cold stress and the mechanisms of cold acclimation are critical for food demand. In this study, combined physiological, transcriptomic, and metabolomic analyses were conducted on Nicotiana tabacum suffering short-term 4 °C cold stress. Our results showed that cold stress destroyed cellular membrane stability, decreased the chlorophyll (Chl) and carotenoid contents, and closed stomata, resulting in lipid peroxidation and photosynthesis restriction. Chl fluorescence measurements revealed that primary photochemistry, photoelectrochemical quenching and photosynthetic electron transport in Nicotiana tabacum leaves were seriously suppressed upon exposer to cold stress. Enzymatic and nonenzymatic antioxidants, including superoxide dismutase, catalase, peroxidase, reduced glutathione, proline, and soluble sugar, were all profoundly increased to trigger the cold acclimation defense against oxidative damage. A total of 178 metabolites and 16,204 genes were differentially expressed in cold-stressed Nicotiana tabacum leaves. MEturquoise and MEblue modules identified by WGCNA were highly correlated with physiological indices, and the corresponding hub genes were significantly enriched in pathways related to photosynthesis - antenna proteins and flavonoid biosynthesis. Untargeted metabolomic analysis identified specific metabolites, including sucrose, phenylalanine, glutamine, glutamate, and proline, that enhance plant cold acclimation. Combined transcriptomics and metabolomic analysis highlight the vital roles of carbohydrate and amino acid metabolism in enhancing the cold tolerance of Nicotiana tabacum. Our comprehensive investigation provides novel insights for efforts to alleviate low temperature-induced oxidative damage to Nicotiana tabacum plants and proposes a breeding target for cold stress-tolerant cultivars.
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Affiliation(s)
- Xiliang Song
- College of Life Sciences, Dezhou University, De'zhou, 253023, China
| | - Hui Wang
- Henan Tobacco Company, Luoyang Branch, Luoyang, 471000, China
| | - Yujie Wang
- Henan Tobacco Company, Luoyang Branch, Luoyang, 471000, China
| | - Qiangcheng Zeng
- College of Life Sciences, Dezhou University, De'zhou, 253023, China.
| | - Xuebo Zheng
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences China, Qingdao, 266101, China.
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5
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El-Hawary SS, Hassan MHA, Hudhud AO, Al-Karmalawy AA, Mustafa M, Hamed EAE, Abdelmohsen UR, Mohammed R. LC-HRMS Profiling and Cytotoxic Potential of Actinomycetes Associated with the Red Sea Soft Coral Sarcophyton glaucum: In vitro and In silico Studies. Chem Biodivers 2024; 21:e202301617. [PMID: 38193652 DOI: 10.1002/cbdv.202301617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
In the current study, the actinomycetes associated with the red sea-derived soft coral Sarcophyton glaucum were investigated in terms of biological and chemical diversity. Four different media, M1, ISP2, Marine Agar (MA), and Actinomycete isolation agar (AIA) were used for the isolation of three strains of actinomycetes that were identified as Streptomyces sp. UR 25, Micromonospora sp. UR32 and Saccharomonospora sp. UR 19. LC-HRMS analysis was used to investigate the chemical diversity of the isolated actinobacteria. The LC-HRMS data were statistically processed using MetaboAnalyst 5.0 viz to differentiate the extract groups and determine the optimal growth culturing conditions. Multivariate data statistical analysis revealed that the Micromonospora sp. extract cultured on (MA) medium is the most distinctive extract in terms of chemical composition. While, the Streptomyces sp. UR 25 extracts are differ significantly from Micromonospora sp. UR32 and Saccharomonospora sp. UR 19. Biological investigation using in vitro cytotoxic assay for actinobacteria extracts revealed the prominent potentiality of the Streptomyces sp. UR 25 cultured on oligotrophic medium against human hepatoma (HepG2), human breast adenocarcinoma (MCF-7) and human colon adenocarcinoma (CACO2) cell lines (IC50 =3.3, 4.2 and 6.8 μg/mL, respectively). SwissTarget Prediction speculated that among the identified compounds, 16-deethyl, indanomycin (8) could have reasonable affinity on HDM2 active site. In this respect, molecular docking study was performed for compound (8) to reveal a substantial affinity on HDM2 active site. In addition, molecular dynamics simulations were carried out at 200 ns for the most active compound (8) compared to the co-crystallized inhibitor DIZ giving deeper information regarding their thermodynamic and dynamic properties as well.
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Affiliation(s)
- Seham S El-Hawary
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo, 11511, Egypt
| | - Marwa H A Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Ahmed O Hudhud
- Department of Pharmacognosy, Faculty of Pharmacy, Merit University, Sohag, 82511, Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Giza, 12566, Egypt
| | - Muhamad Mustafa
- IBMM, CNRS, ENSCM, Université de Montpellier, Montpellier, 34095, France
- Department of Medicinal Chemistry, Faculty of Pharmacy, Deraya University, Minia, 61111, Egypt
| | - Elsayed A E Hamed
- National institute of oceanography and Fisheries, Hurghada-Red Sea (NIOF), 84511, Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia, 61111, Egypt
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
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Nesterovich VM, Belykh DA, Gorokhovets NV, Kurbatov LK, Zamyatnin AA, Ikryannikova LN. Secondary metabolites of plants and their possible role in the "age of superbugs". BIOMEDITSINSKAIA KHIMIIA 2023; 69:371-382. [PMID: 38153052 DOI: 10.18097/pbmc20236906371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Bacterial infections are a serious cause of high morbidity and mortality worldwide. Over the past decades, the drug resistance of bacterial pathogens has been steadily increasing, while the rate of development of new effective antibacterial drugs remains consistently low. The plant kingdom is sometimes called a bottomless well for the search for new antimicrobial therapies. This is due to the fact that plants are easily accessible and cheap to process, while extracts and components of plant origin often demonstrate a high level of biological activity with minor side effects. The variety of compounds obtained from plant raw materials can provide a wide choice of various chemical structures for interaction with various targets inside bacterial cells, while the rapid development of modern biotechnological tools opens the way to the targeted production of bioactive components with desired properties. The objective of this review is to answer the question, whether antimicrobials of plant origin have a chance to play the role of a panacea in the fight against infectious diseases in the "post-antibiotic era".
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Affiliation(s)
| | | | | | | | - A A Zamyatnin
- Sechenov University, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
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7
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Gonçalves Vasconcelos de Alcântara B, Neto AK, Garcia DA, Casoti R, Branquinho Oliveira T, Chagas de Paula Ladvocat AC, Edrada-Ebel R, Gomes Soares M, Ferreira Dias D, Chagas de Paula DA. Anti-Inflammatory Activity of Lauraceae Plant Species and Prediction Models Based on Their Metabolomics Profiling Data. Chem Biodivers 2023; 20:e202300650. [PMID: 37540773 DOI: 10.1002/cbdv.202300650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/06/2023]
Abstract
The Lauraceae is a botanical family known for its anti-inflammatory potential. However, several species have not yet been studied. Thus, this work aimed to screen the anti-inflammatory activity of this plant family and to build statistical prediction models. The methodology was based on the statistical analysis of high-resolution liquid chromatography coupled with mass spectrometry data and the ex vivo anti-inflammatory activity of plant extracts. The ex vivo results demonstrated significant anti-inflammatory activity for several of these plants for the first time. The sample data were applied to build anti-inflammatory activity prediction models, including the partial least square acquired, artificial neural network, and stochastic gradient descent, which showed adequate fitting and predictive performance. Key anti-inflammatory markers, such as aporphine and benzylisoquinoline alkaloids were annotated with confidence level 2. Additionally, the validated prediction models proved to be useful for predicting active extracts using metabolomics data and studying their most bioactive metabolites.
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Affiliation(s)
| | - Albert Katchborian Neto
- Laboratory of Phytochemistry, Medicinal Chemistry and Metabolomics, Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, MG, Brazil
| | - Daniela Aparecida Garcia
- Laboratory of Phytochemistry, Medicinal Chemistry and Metabolomics, Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, MG, Brazil
| | - Rosana Casoti
- Antibiotics Department, Federal University of Pernambuco., 50670-901, Recife, PE, Brazil
| | | | | | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, G4 0RE, Glasgow, Scotland
| | - Marisi Gomes Soares
- Laboratory of Phytochemistry, Medicinal Chemistry and Metabolomics, Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, MG, Brazil
| | - Danielle Ferreira Dias
- Laboratory of Phytochemistry, Medicinal Chemistry and Metabolomics, Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, MG, Brazil
| | - Daniela Aparecida Chagas de Paula
- Laboratory of Phytochemistry, Medicinal Chemistry and Metabolomics, Chemistry Institute, Federal University of Alfenas, 37130-001, Alfenas, MG, Brazil
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8
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Recchia MJJ, Baumeister TUH, Liu DY, Linington RG. MultiplexMS: A Mass Spectrometry-Based Multiplexing Strategy for Ultra-High-Throughput Analysis of Complex Mixtures. Anal Chem 2023; 95:11908-11917. [PMID: 37530514 PMCID: PMC11093148 DOI: 10.1021/acs.analchem.3c00939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
High-throughput chemical analysis of natural product mixtures lags behind developments in genome sequencing technologies and laboratory automation, leading to a disconnect between library-scale chemical and biological profiling that limits new molecule discovery. Here, we report a new orthogonal sample multiplexing strategy that can increase mass spectrometry-based profiling up to 30-fold over traditional methods. Profiled pooled samples undergo subsequent computational deconvolution to reconstruct peak lists for each sample in the set. We validated this approach using in silico experiments and demonstrated a high assignment precision (>97%) for large, pooled samples (r = 30), particularly for infrequently occurring metabolites of relevance in drug discovery applications. Requiring only 5% of the previously required MS acquisition time, this approach was repeated in a recent biological activity profiling study on 925 natural product extracts, leading to the rediscovery of all previously reported bioactive metabolites. This new method is compatible with MS data from any instrument vendor and is supported by an open-source software package: https://github.com/liningtonlab/MultiplexMS.
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Affiliation(s)
| | | | - Dennis Y. Liu
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Roger G. Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
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9
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Zill NA, Du Y, Marinkovich S, Gu D, Seidel J, Zhang W. Bioactive Natural Product Discovery via Deuterium Adduct Bioactivity Screening. ACS Chem Biol 2023; 18:1192-1199. [PMID: 37125845 DOI: 10.1021/acschembio.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The discovery of bioactive natural products lies at the forefront of human medicine. The continued discovery of these molecules is imperative in the fight against infection and disease. While natural products have historically dominated the drug market, discovery in recent years has slowed significantly, partly due to limitations in current discovery methodologies. This work demonstrates a new workflow, deuterium adduct bioactivity screening (DABS), which pairs untargeted isotope labeling with whole cell binding assays for bioactive natural product discovery. DABS was validated and led to the discovery of a new isoprenyl guanidine alkaloid, zillamycin, which showed anti-cancer and anti-microbial activities. DABS thus represents a new workflow to accelerate discovery of natural products with a wide range of bioactive potentials.
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Affiliation(s)
- Nicholas A Zill
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Yongle Du
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
| | - Samantha Marinkovich
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Di Gu
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Jeremy Seidel
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 999077, China
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10
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Mannochio-Russo H, Nunes WDG, Almeida RF, Albernaz LC, Espindola LS, Bolzani VS. Old Meets New: Mass Spectrometry-Based Untargeted Metabolomics Reveals Unusual Larvicidal Nitropropanoyl Glycosides from the Leaves of Heteropterys umbellata. JOURNAL OF NATURAL PRODUCTS 2023; 86:621-632. [PMID: 36848642 DOI: 10.1021/acs.jnatprod.2c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The Aedes aegypti (Diptera: Culicidae) mosquito is the vector of several arboviruses in tropical and subtropical areas of the globe, and synthetic pesticides remain the most widely used combat strategy. This study describes the investigation of secondary metabolites with larvicidal activity from the Malpighiaceae taxon using a metabolomic and bioactivity-based approach. The workflow initially consisted of a larvicidal screening of 394 extracts from the leaves of 197 Malpighiaceae samples, which were extracted using solvents of different polarity, leading to the selection of Heteropterys umbellata for the identification of active compounds. By employing untargeted mass spectrometry-based metabolomics and multivariate analyses (PCA and PLS-DA), it was possible to determine that the metabolic profiles of different plant organs and collection sites differed significantly. A bioguided approach led to the isolation of isochlorogenic acid A (1) and the nitropropanoyl glucosides karakin (2) and 1,2,3,6-tetrakis-O-[3-nitropropanoyl]-beta-glucopyranose (3). These nitro compounds exhibited larvicidal activity, possibly potentialized by synergistic effects of their isomers in chromatographic fractions. Additionally, targeted quantification of the isolated compounds in different extracts corroborated the untargeted results from the statistical analyses. These results support a metabolomic-guided approach in combination with classical phytochemical techniques to search for natural larvicidal compounds for arboviral vector control.
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Affiliation(s)
- Helena Mannochio-Russo
- NuBBE, Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), SP, Araraquara, SP 14800-901, Brazil
| | - Wilhan D G Nunes
- Federal Institute of Education, Science and Technology of São Paulo (IFSP), Ilha Solteira, SP 15385-000, Brazil
| | - Rafael F Almeida
- Universidade Estadual de Goiás, Herbário JAR, Quirinópolis, GO 75860-000, Brazil
| | - Lorena C Albernaz
- Laboratório de Farmacognosia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF 70910-900, Brazil
| | - Laila S Espindola
- Laboratório de Farmacognosia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF 70910-900, Brazil
| | - Vanderlan S Bolzani
- NuBBE, Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), SP, Araraquara, SP 14800-901, Brazil
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11
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Zulfiqar M, Gadelha L, Steinbeck C, Sorokina M, Peters K. MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry. J Cheminform 2023; 15:32. [PMID: 36871033 PMCID: PMC9985203 DOI: 10.1186/s13321-023-00695-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid chromatography-mass spectrometry (LC-MS) to achieve a high-throughput profile of metabolites from complex biological resources, only a small fraction of these metabolites can be annotated with confidence. Many novel computational methods and tools have been developed to enable chemical structure annotation to known and unknown compounds such as in silico generated spectra and molecular networking. Here, we present an automated and reproducible Metabolome Annotation Workflow (MAW) for untargeted metabolomics data to further facilitate and automate the complex annotation by combining tandem mass spectrometry (MS2) input data pre-processing, spectral and compound database matching with computational classification, and in silico annotation. MAW takes the LC-MS2 spectra as input and generates a list of putative candidates from spectral and compound databases. The databases are integrated via the R package Spectra and the metabolite annotation tool SIRIUS as part of the R segment of the workflow (MAW-R). The final candidate selection is performed using the cheminformatics tool RDKit in the Python segment (MAW-Py). Furthermore, each feature is assigned a chemical structure and can be imported to a chemical structure similarity network. MAW is following the FAIR (Findable, Accessible, Interoperable, Reusable) principles and has been made available as the docker images, maw-r and maw-py. The source code and documentation are available on GitHub ( https://github.com/zmahnoor14/MAW ). The performance of MAW is evaluated on two case studies. MAW can improve candidate ranking by integrating spectral databases with annotation tools like SIRIUS which contributes to an efficient candidate selection procedure. The results from MAW are also reproducible and traceable, compliant with the FAIR guidelines. Taken together, MAW could greatly facilitate automated metabolite characterization in diverse fields such as clinical metabolomics and natural product discovery.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, 07743, Jena, Germany.
| | - Luiz Gadelha
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, 07743, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, 07743, Jena, Germany.
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, 07743, Jena, Germany.,Data Science and Artificial Intelligence, Research and Development, Bayer Pharmaceuticals, 13353, Berlin, Germany
| | - Kristian Peters
- iDiv - German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Leipzig, 04103, Germany. .,Geobotany and Botanical Gardens, Martin-Luther University of Halle-Wittenberg, 06108, Halle, Germany. .,Leibniz Institute of Plant Biochemistry, 06120, Halle, Germany.
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12
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Guimarães NSS, Ramos VS, Prado-Souza LFL, Lopes RM, Arini GS, Feitosa LGP, Silva RR, Nantes IL, Damasceno DC, Lopes NP, Rodrigues T. Rosemary (Rosmarinus officinalis L.) Glycolic Extract Protects Liver Mitochondria from Oxidative Damage and Prevents Acetaminophen-Induced Hepatotoxicity. Antioxidants (Basel) 2023; 12:antiox12030628. [PMID: 36978874 PMCID: PMC10045355 DOI: 10.3390/antiox12030628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Rosmarinus officinalis L. (rosemary) is an aromatic culinary herb. Native to the Mediterranean region, it is currently cultivated worldwide. In addition to its use as a condiment in food preparation and in teas, rosemary has been widely employed in folk medicine and cosmetics. Several beneficial effects have been described for rosemary, including antimicrobial and antioxidant activities. Here, we investigated the mechanisms accounting for the antioxidant activity of the glycolic extract of R. officinalis (Ro) in isolated rat liver mitochondria (RLM) under oxidative stress conditions. We also investigated its protective effect against acetaminophen-induced hepatotoxicity in vivo. A crude extract was obtained by fractionated percolation, using propylene glycol as a solvent due to its polarity and cosmeceutical compatibility. The quantification of substances with recognized antioxidant action revealed the presence of phenols and flavonoids. Dereplication studies carried out through LC-MS/MS and GC-MS, supported by The Global Natural Product Social Molecular Networking (GNPS) platform, annotated several phenolic compounds, confirming the previous observation. In accordance, Ro decreased the production of reactive oxygen species (ROS) elicited by Fe2+ or t-BOOH and inhibited the lipid peroxidation of mitochondrial membranes in a concentration-dependent manner in RLM. Such an effect was also observed in liposomes as membrane models. Ro also prevented the oxidation of mitochondrial protein thiol groups and reduced glutathione (GSH). In model systems, Ro exhibited a potent scavenger activity toward 2,2′-diphenyl-1-picrylhydrazyl (DPPH) radicals and superoxide anions. It also demonstrated an Fe2+ chelating activity. Moreover, Ro did not exhibit cytotoxicity or dissipate the mitochondrial membrane potential (∆Ψ) in rat liver fibroblasts (BRL3A cells). To evaluate whether such antioxidant protective activity observed in vitro could also be achieved in vivo, a well-established model of hepatotoxicity induced by acute exposure to acetaminophen (AAP) was used. This model depletes GSH and promotes oxidative-stress-mediated tissue damage. The treatment of rats with 0.05% Ro, administered intraperitoneally for four days, resulted in inhibition of AAP-induced lipid peroxidation of the liver and the prevention of hepatotoxicity, maintaining alanine and aspartate aminotransferase (ALT/AST) levels equal to those of the normal, non-treated rats. Together, these findings highlight the potent antioxidant activity of rosemary, which is able to protect mitochondria from oxidative damage in vitro, and effects such as the antioxidant and hepatoprotective effects observed in vivo.
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Affiliation(s)
- Natalia S. S. Guimarães
- Interdisciplinary Center of Biochemistry Investigation, University of Mogi das Cruzes (UMC), Mogi das Cruzes CEP 08780-911, SP, Brazil
| | - Vyctória S. Ramos
- Interdisciplinary Center of Biochemistry Investigation, University of Mogi das Cruzes (UMC), Mogi das Cruzes CEP 08780-911, SP, Brazil
| | - Laura F. L. Prado-Souza
- Center for Natural and Human Sciences, Federal University of ABC, Santo André CEP 09210-580, SP, Brazil
| | - Rayssa M. Lopes
- Center for Natural and Human Sciences, Federal University of ABC, Santo André CEP 09210-580, SP, Brazil
| | - Gabriel S. Arini
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-900, SP, Brazil
| | - Luís G. P. Feitosa
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-900, SP, Brazil
| | - Ricardo R. Silva
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-900, SP, Brazil
| | - Iseli L. Nantes
- Center for Natural and Human Sciences, Federal University of ABC, Santo André CEP 09210-580, SP, Brazil
| | - Debora C. Damasceno
- Laboratory of Experimental Research on Gynecology and Obstetrics, Sao Paulo State University (UNESP), Botucatu CEP 18618-687, SP, Brazil
| | - Norberto P. Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-900, SP, Brazil
| | - Tiago Rodrigues
- Interdisciplinary Center of Biochemistry Investigation, University of Mogi das Cruzes (UMC), Mogi das Cruzes CEP 08780-911, SP, Brazil
- Correspondence: ; Tel.: +55-(11)-4996-8371
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13
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da Silva FMR, Paggi GM, Brust FR, Macedo AJ, Silva DB. Metabolomic Strategies to Improve Chemical Information from OSMAC Studies of Endophytic Fungi. Metabolites 2023; 13:metabo13020236. [PMID: 36837855 PMCID: PMC9961420 DOI: 10.3390/metabo13020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/26/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Metabolomics strategies are important tools to get holistic chemical information from a system, but they are scarcely applied to endophytic fungi to understand their chemical profiles of biosynthesized metabolites. Here Penicillium sp. was cultured using One Strain Many Compounds (OSMAC) conditions as a model system to demonstrate how this strategy can help in understanding metabolic profiles and determining bioactive metabolites with the application of metabolomics and statistical analyses, as well as molecular networking. Penicillium sp. was fermented in different culture media and the crude extracts from mycelial biomass (CEm) and broth (CEb) were obtained, evaluated against bacterial strains (Staphylococcus aureus and Pseudomonas aeruginosa), and the metabolomic profiles by LC-DAD-MS were obtained and chemometrics statistical analyses were applied. The CEm and CEb extracts presented different chemical profiles and antibacterial activities; the highest activities observed were against S. aureus from CEm (MIC = 16, 64, and 128 µg/mL). The antibacterial properties from the extracts were impacted for culture media from which the strain was fermented. From the Volcano plot analysis, it was possible to determine statistically the most relevant features for the antibacterial activity, which were also confirmed from biplots of PCA as strong features for the bioactive extracts. These compounds included 75 (13-oxoverruculogen isomer), 78 (austalide P acid), 87 (austalide L or W), 88 (helvamide), 92 (viridicatumtoxin A), 96 (austalide P), 101 (dihydroaustalide K), 106 (austalide k), 110 (spirohexaline), and 112 (pre-viridicatumtoxin). Thus, these features included diketopiperazines, meroterpenoids, and polyketides, such as indole alkaloids, austalides, and viridicatumtoxin A, a rare tetracycline.
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Affiliation(s)
- Fernanda Motta Ribeiro da Silva
- Laboratory of Natural Products and Mass Spectrometry (LaPNEM), Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Gecele Matos Paggi
- Laboratory of Ecology and Evolutionary Biology (LEBio), Institute of Biosciences, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Flávia Roberta Brust
- Biofilms and Diversity Laboratory, Faculty of Pharmacy and Biotechnology Center, Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Alexandre José Macedo
- Biofilms and Diversity Laboratory, Faculty of Pharmacy and Biotechnology Center, Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Denise Brentan Silva
- Laboratory of Natural Products and Mass Spectrometry (LaPNEM), Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil
- Correspondence:
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14
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Wee SP, Loh KE, Lam KW, Ismail IS. A Study of the Interaction between Xanthine Oxidase and Its Inhibitors from Chrysanthemum morifolium Using Computational Simulation and Multispectroscopic Methods. Metabolites 2023; 13:metabo13010113. [PMID: 36677038 PMCID: PMC9864848 DOI: 10.3390/metabo13010113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/12/2023] Open
Abstract
The current therapeutic approach for gout is through the inhibition of the xanthine oxidase (XO) enzyme. Allopurinol, a clinically used XO inhibitor, causes many side effects. This study aimed to investigate the interaction between XO and inhibitors identified from Chrysanthemum morifolium by using computational simulation and multispectroscopic methods. The crude extract, petroleum ether, ethyl acetate (EtOAc), and residual fractions were subjected to an XO inhibitory assay and 1H NMR analysis. The EtOAc fraction was shown to be strongly correlated to the XO inhibitory activity by using PLS biplot regression analysis. Kaempferol, apigenin, homovanillic acid, and trans-cinnamic acid were suggested to contribute to the XO inhibitory activity. Molecular docking showed that kaempferol and apigenin bound to the active site of XO with their benzopyran moiety sandwiched between Phe914 and Phe1009, interacting with Thr1010 and Arg880 by hydrogen bonding. Kaempferol showed the lowest binding energy in molecular dynamic simulation. The residues that contributed to the binding energy were Glu802, Arg880, Phe 914, and Phe 1009. A fluorescence quenching study showed a combination of static and dynamic quenching for all four inhibitors binding to XO. Circular dichroism spectroscopy revealed that there was no major change in XO conformation after binding with each inhibitor.
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Affiliation(s)
- Sze Ping Wee
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University of Management and Technology, Jalan Genting Kelang, Setapak, Kuala Lumpur 53300, Federal Territory of Kuala Lumpur, Malaysia
| | - Khye Er Loh
- Department of Bioscience, Faculty of Applied Sciences, Tunku Abdul Rahman University of Management and Technology, Jalan Genting Kelang, Setapak, Kuala Lumpur 53300, Federal Territory of Kuala Lumpur, Malaysia
- Correspondence: ; Tel.: +60-3-41450123 (ext. 3171)
| | - Kok Wai Lam
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Federal Territory of Kuala Lumpur, Malaysia
| | - Intan Safinar Ismail
- Natural Medicine and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
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15
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Lima NM, Dos Santos GF, da Silva Lima G, Vaz BG. Advances in Mass Spectrometry-Metabolomics Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:101-122. [PMID: 37843807 DOI: 10.1007/978-3-031-41741-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass spectrometry (MS) has been successfully applied in microbial metabolomics due to its high precision, versatility, sensitivity, and wide dynamic range. The different analytical tools using MS have been employed in microbial metabolomics investigations and can contribute to the discovery or accelerate the search for bioactive substances. The coupling with chromatographic and electrophoretic separation techniques has resulted in more efficient technologies for the analysis of microbial compounds occurring in trace levels. This book chapter describes the current advances in the application of mass spectrometry-based metabolomics in the search for new biologically active agents from microbial sources; the development of new approaches for in silico annotation of natural products; the different technologies employing mass spectrometry imaging to deliver more comprehensive analysis and elucidate the metabolome involved in ecological interactions as they enable visualization of the spatial dispersion of small molecules. We also describe other ambient ionization techniques applied to the fingerprint of microbial natural products and modern techniques such as ion mobility mass spectrometry used to microbial metabolomic analyses and the dereplication of natural microbial products through MS.
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Weiss MB, Médice RV, Jacinavicius FR, Pinto E, Crnkovic CM. Metabolomics Applied to Cyanobacterial Toxins and Natural Products. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:21-49. [PMID: 37843804 DOI: 10.1007/978-3-031-41741-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The biological and chemical diversity of Cyanobacteria is remarkable. These ancient prokaryotes are widespread in nature and can be found in virtually every habitat on Earth where there is light and water. They are producers of an array of secondary metabolites with important ecological roles, toxic effects, and biotechnological applications. The investigation of cyanobacterial metabolites has benefited from advances in analytical tools and bioinformatics that are employed in metabolomic analyses. In this chapter, we review selected articles highlighting the use of targeted and untargeted metabolomics in the analyses of secondary metabolites produced by cyanobacteria. Here, cyanobacterial secondary metabolites have been didactically divided into toxins and natural products according to their relevance to toxicological studies and drug discovery, respectively. This review illustrates how metabolomics has improved the chemical analysis of cyanobacteria in terms of speed, sensitivity, selectivity, and/or coverage, allowing for broader and more complex scientific questions.
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Affiliation(s)
- Márcio Barczyszyn Weiss
- School of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, University of São Paulo, São Paulo, Brazil
| | - Rhuana Valdetário Médice
- School of Pharmaceutical Sciences, Department of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, Brazil
| | - Fernanda Rios Jacinavicius
- School of Pharmaceutical Sciences, Department of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, Brazil
| | - Ernani Pinto
- Centre for Nuclear Energy in Agriculture, Division of Tropical Ecosystem Functioning, University of São Paulo, Piracicaba, Brazil
| | - Camila Manoel Crnkovic
- School of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, University of São Paulo, São Paulo, Brazil.
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17
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Ramirez DA, Carazzone C. Small molecules putative structure elucidation in endemic Colombian fruits: CFM-ID approach. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2022. [DOI: 10.1080/10942912.2022.2147539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Daniel Arias Ramirez
- Chemistry, Department, Universidad de Los Andes, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Bogotá, Colombia
- ICP-MS Spectrometry Laboratory, Deanship of Scientific Research-Faculty of Science, Universidad de Los Andes, Bogotá, Colombia
| | - Chiara Carazzone
- Chemistry, Department, Universidad de Los Andes, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Bogotá, Colombia
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18
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Qu B, Liu Y, Shen A, Guo Z, Yu L, Liu D, Huang F, Peng T, Liang X. Combining multidimensional chromatography-mass spectrometry and feature-based molecular networking methods for the systematic characterization of compounds in the supercritical fluid extract of Tripterygium wilfordii Hook F. Analyst 2022; 148:61-73. [PMID: 36441185 DOI: 10.1039/d2an01471h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tripterygium wilfordii Hook F from the family Celastraceae is a traditional Chinese medicine (TCM) whose principal chemical constituents are terpenoids, including sesquiterpene alkaloids and diterpenoids, which have unique and diverse structures and remarkable biological activities. In order to advance pharmacological research and guide the preparation of monomer compounds derived from T. wilfordii, a systematic approach to efficiently discover new compounds or their derivatives is needed. Herein, compound separation and identification were performed by offline reversed-phase × supercritical fluid chromatography coupled mass spectrometry (RP × SFC-Q-TOF-MS/MS) and Global Natural Product Social (GNPS) molecular networking. The 2D chromatography system exhibited a high degree of orthogonality and significant peak capacity, and SFC has an advantage during the separation of sesquiterpene alkaloid isomers. Feature-based molecular networking offers the great advantage of quickly detecting and clustering unknown compounds, which greatly assists in intuitively judging the type of compound, and this networking technique has the potential to dramatically accelerate the identification and characterization of compounds from natural sources. A total of 324 compounds were identified and quantitated, including 284 alkaloids, 22 diterpenoids and 18 triterpenoids, which means that there are numerous potential new compounds with novel structures to be further explored. Overall, feature-based molecular networking provides an effective method for discovering and characterizing novel compounds and guides the separation and preparation of targeted natural products.
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Affiliation(s)
- Boquan Qu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanfang Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Aijin Shen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Zhimou Guo
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Long Yu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Dian Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Feifei Huang
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Ting Peng
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
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Jang JP, Lee B, Heo KT, Oh TH, Lee HW, Ko SK, Hwang BY, Jang JH, Hong YS. Hygrolansamycins A-D, O-Heterocyclic Macrolides from Streptomyces sp. KCB17JA11. J Microbiol Biotechnol 2022; 32:1299-1306. [PMID: 36198661 PMCID: PMC9668088 DOI: 10.4014/jmb.2206.06039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022]
Abstract
Six ansamycin derivatives were isolated from the culture broth of Streptomyces sp. KCB17JA11, including four new hygrolansamycins A-D (1-4) and known congeners divergolide O (5) and hygrocin C (6). Compounds 1-5 featured an unusual six-membered O-heterocyclic moiety. The isolation workflow was guided by a Molecular Networking-based dereplication strategy. The structures of 1-4 were elucidated using NMR and HRESIMS experiments, and the absolute configuration was established by the Mosher's method. Compound 2 exhibited mild cytotoxicity against five cancer cell lines with IC50 values ranging from 24.60 ± 3.37 μM to 49.93 ± 4.52 μM.
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Affiliation(s)
- Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Byeongsan Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea,College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Kyung Taek Heo
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea,KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Tae Hoon Oh
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Sung-Kyun Ko
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea,KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bang Yeon Hwang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea,KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea,
J.-H. Jang Phone: +82-43-240-6164 Fax: +82-43-240-6169 E-mail:
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea,KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea,Corresponding authors Y.-S. Hong Phone: +82-43-240-6144 Fax: +82-43-240-6169 E-mail:
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20
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Jian J, Yuan J, Fan Y, Wang J, Zhang T, Kool J, Jiang Z. High-Resolution Bioassay Profiling with Complemented Sensitivity and Resolution for Pancreatic Lipase Inhibitor Screening. Molecules 2022; 27:molecules27206923. [PMID: 36296516 PMCID: PMC9607159 DOI: 10.3390/molecules27206923] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
How to rapidly and accurately screen bioactive components from complex natural products remains a major challenge. In this study, a screening platform for pancreatic lipase (PL) inhibitors was established by combining magnetic beads-based ligand fishing and high-resolution bioassay profiling. This platform was well validated using a mixture of standard compounds, i.e., (-)- epigallocatechin gallate (EGCG), luteolin and schisandrin. The dose-effect relationship of high-resolution bioassay profiling was demonstrated by the standard mixture with different concentrations for each compound. The screening of PL inhibitors from green tea extract at the concentrations of 0.2, 0.5 and 1.0 mg/mL by independent high-resolution bioassay profiling was performed. After sample pre-treatment by ligand fishing, green tea extract at the concentration of 0.2 mg/mL was specifically enriched and simplified, and consequently screened through the high-resolution bioassay profiling. As a result, three PL inhibitors, i.e., EGCG, (-)-Gallocatechin gallate (GCG) and (-)-Epicatechin gallate (ECG), were rapidly identified from the complex matrix. The established platform proved to be capable of enriching affinity binders and eliminating nonbinders in sample pre-treatment by ligand fishing, which overcame the technical challenges of high-resolution bioassay profiling in the aspects of sensitivity and resolution. Meanwhile, the high-resolution bioassay profiling possesses the ability of direct bioactive assessment, parallel structural analysis and identification after separation. The established platform allowed more accurate and rapid screening of PL inhibitors, which greatly facilitated natural product-based drug screening.
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Affiliation(s)
- Jingyi Jian
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Jiaming Yuan
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Yu Fan
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Jincai Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Tingting Zhang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Zhengjin Jiang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
- Correspondence:
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21
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Chacon DS, Santos MDM, Bonilauri B, Vilasboa J, da Costa CT, da Silva IB, Torres TDM, de Araújo TF, Roque ADA, Pilon AC, Selegatto DM, Freire RT, Reginaldo FPS, Voigt EL, Zuanazzi JAS, Scortecci KC, Cavalheiro AJ, Lopes NP, Ferreira LDS, dos Santos LV, Fontes W, de Sousa MV, Carvalho PC, Fett-Neto AG, Giordani RB. Non-target molecular network and putative genes of flavonoid biosynthesis in Erythrina velutina Willd., a Brazilian semiarid native woody plant. FRONTIERS IN PLANT SCIENCE 2022; 13:947558. [PMID: 36161018 PMCID: PMC9493460 DOI: 10.3389/fpls.2022.947558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Erythrina velutina is a Brazilian native tree of the Caatinga (a unique semiarid biome). It is widely used in traditional medicine showing anti-inflammatory and central nervous system modulating activities. The species is a rich source of specialized metabolites, mostly alkaloids and flavonoids. To date, genomic information, biosynthesis, and regulation of flavonoids remain unknown in this woody plant. As part of a larger ongoing research goal to better understand specialized metabolism in plants inhabiting the harsh conditions of the Caatinga, the present study focused on this important class of bioactive phenolics. Leaves and seeds of plants growing in their natural habitat had their metabolic and proteomic profiles analyzed and integrated with transcriptome data. As a result, 96 metabolites (including 43 flavonoids) were annotated. Transcripts of the flavonoid pathway totaled 27, of which EvCHI, EvCHR, EvCHS, EvCYP75A and EvCYP75B1 were identified as putative main targets for modulating the accumulation of these metabolites. The highest correspondence of mRNA vs. protein was observed in the differentially expressed transcripts. In addition, 394 candidate transcripts encoding for transcription factors distributed among the bHLH, ERF, and MYB families were annotated. Based on interaction network analyses, several putative genes of the flavonoid pathway and transcription factors were related, particularly TFs of the MYB family. Expression patterns of transcripts involved in flavonoid biosynthesis and those involved in responses to biotic and abiotic stresses were discussed in detail. Overall, these findings provide a base for the understanding of molecular and metabolic responses in this medicinally important species. Moreover, the identification of key regulatory targets for future studies aiming at bioactive metabolite production will be facilitated.
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Affiliation(s)
- Daisy Sotero Chacon
- Department of Pharmacy, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | | | - Bernardo Bonilauri
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States
| | - Johnatan Vilasboa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cibele Tesser da Costa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Taffarel de Melo Torres
- Bioinformatics, Biostatistics and Computer Biology Nucleus, Rural Federal University of the Semiarid, Mossoró, RN, Brazil
| | | | - Alan de Araújo Roque
- Institute for Sustainable Development and Environment, Dunas Park Herbarium, Natal, RN, Brazil
| | - Alan Cesar Pilon
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | - Denise Medeiros Selegatto
- Zimmermann Group, European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Rafael Teixeira Freire
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Eduardo Luiz Voigt
- Department of Cell Biology and Genetics, Center for Biosciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Kátia Castanho Scortecci
- Department of Cell Biology and Genetics, Center for Biosciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | | | - Leandro Vieira dos Santos
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia, DF, Brazil
| | - Marcelo Valle de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia, DF, Brazil
| | - Paulo Costa Carvalho
- Computational and Structural Proteomics Laboratory, Carlos Chagas Institute, Fiocruz, PR, Brazil
| | - Arthur Germano Fett-Neto
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Raquel Brandt Giordani
- Department of Pharmacy, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
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22
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Doğan HO, Şenol O, Karadağ A, Yıldız SN. Metabolomic profiling in ankylosing spondylitis using time-of-flight mass spectrometry. Clin Nutr ESPEN 2022; 50:124-132. [PMID: 35871913 DOI: 10.1016/j.clnesp.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/19/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND & AIMS Ankylosing spondylitis (AS) is an inflammatory disease associated with destructive changes in the skeleton and joints. The exact molecular mechanism of the disease has not been fully elucidated. This study aimed to determine metabolic differences between active AS patients and healthy controls to understand the molecular mechanism of AS. PATIENTS AND METHODS The study included 38 subjects, comprising 18 patients with active AS and 20 healthy controls. Metabolic profiling of the plasma was performed using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC Q-TOF/MS). Data acquisition, classification, and identification were achieved with the METLIN (https://metlin.scripps.edu/) database and XCMS (https://xcmsonline.scripps.edu). RESULTS Significant alterations were identified in the unsaturated fatty acids (FA), linoleic acid, alpha-linolenic acid, FA degradation, and FA biosynthesis pathways. Down -regulations were observed in phosphatidylcholine (PC) (16:0/0:0), beta-d-Fructose, stearic acid, trimipramine N-Oxide and muconic acid, and up-regulation were detected in PC (18:2/0:0), 3-Methylindole, palmitic acid (PA), alpha-Tocotrienol, and beta-d-glucopyranoside in active AS patients compared to the healthy control subjects. CONCLUSION Pathway analysis revealed that dysregulation in FA metabolism is associated with AS, and therefore, modulation of diet according to PA and PC may be potential therapeutic targets.
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Affiliation(s)
- Halef Okan Doğan
- Department of Biochemistry, School of Medicine, University of Sivas Cumhuriyet, Sivas, Turkey.
| | - Onur Şenol
- Department of Analytical Chemistry, Faculty of Pharmacy, Atatürk University, Erzurum, Turkey
| | - Ahmet Karadağ
- Department of Pyhsical Medicine and Rehabilitation, School of Medicine, University of Sivas Cumhuriyet, Sivas, Turkey
| | - Seyma Nur Yıldız
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
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23
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Margaritaria nobilis L.F. (Phyllanthaceae): Ethnopharmacology and Application of Computational Tools in the Annotation of Bioactive Molecules. Metabolites 2022; 12:metabo12080681. [PMID: 35893248 PMCID: PMC9330776 DOI: 10.3390/metabo12080681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Margaritaria nobilis is a shrubby species widely distributed in Brazil from the Amazon to the Atlantic Rainforest. Its bark and fruit are used in the Peruvian Amazon for disinfecting abscesses and as a tonic in pregnancy, respectively, and its leaves are used to treat cancer symptoms. From analyses via UHPLC-MS/MS, we sought to determine the chemical profile of the ethanolic extract of M. nobilis leaves by means of putative analyses supported by computational tools and spectral libraries. Thus, it was possible to annotate 44 compounds, of which 12 are phenolic acid derivatives, 16 are O-glycosylated flavonoids and 16 hydrolysable tannins. Among the flavonoids, although they are known, except for kaempferol, which has already been isolated from this species, the other flavonoids (10, 14, 15, 21, 24–26, 28–30, 33–35, 40 and 41) are being reported for the first time in the genus. Among the hydrolysable tannins, six ellagitannins present the HHDP group (6, 19, 22, 31, 38 and 43), one presents the DHHDP group (5), and four contain oxidatively modified congeners (12, 20, 37 and 39). Through the annotation of these compounds, we hope to contribute to the improved chemosystematics knowledge of the genus. Furthermore, supported by a metric review of the literature, we observed that many of the compounds reported here are congeners of authentically bioactive compounds. Thus, we believe that this work may help in understanding future pharmacological activities.
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24
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Wang Z, Jin X, Zhang X, Xie X, Tu Z, He X. From Function to Metabolome: Metabolomic Analysis Reveals the Effect of Probiotic Fermentation on the Chemical Compositions and Biological Activities of Perilla frutescens Leaves. Front Nutr 2022; 9:933193. [PMID: 35898707 PMCID: PMC9309800 DOI: 10.3389/fnut.2022.933193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/20/2022] [Indexed: 01/22/2023] Open
Abstract
This study aimed to investigate the impact of probiotic fermentation on the active components and functions of Perilla frutescens leaves (PFL). PFL was fermented for 7 days using six probiotics (Lactobacillus Plantarum SWFU D16, Lactobacillus Plantarum ATCC 8014, Lactobacillus Rhamnosus ATCC 53013, Streptococcus Thermophilus CICC 6038, Lactobacillus Casei ATCC 334, and Lactobacillus Bulgaricus CICC 6045). The total phenol and flavonoid contents, antioxidant abilities, as well as α-glucosidase and acetylcholinesterase inhibition abilities of PFL during the fermentation process were evaluated, and its bioactive compounds were further quantified by high-performance liquid chromatography (HPLC). Finally, non-targeted ultra-HPLC-tandem mass spectroscopy was used to identify the metabolites affected by fermentation and explore the possible mechanisms of the action of fermentation. The results showed that most of the active component contents and functional activities of PFL exhibited that it first increased and then decreased, and different probiotics had clearly distinguishable effects from each other, of which fermentation with ATCC 53013 for 1 day showed the highest enhancement effect. The same trend was also confirmed by the result of the changes in the contents of 12 phenolic acids and flavonoids by HPLC analysis. Further metabolomic analysis revealed significant metabolite changes under the best fermentation condition, which involved primarily the generation of fatty acids and their conjugates, flavonoids. A total of 574 and 387 metabolites were identified in positive ion and negative ion modes, respectively. Results of Spearman's analysis indicated that some primary metabolites and secondary metabolites such as flavonoids, phenols, and fatty acids might play an important role in the functional activity of PFL. Differential metabolites were subjected to the KEGG database and 97 metabolites pathways were obtained, of which biosyntheses of unsaturated fatty acids, flavonoid, and isoflavonoid were the most enriched pathways. The above results revealed the potential reason for the differences in metabolic and functional levels of PFL after fermentation. This study could provide a scientific basis for the further study of PFL, as well as novel insights into the action mechanism of probiotic fermentation on the chemical composition and biological activity of food/drug.
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Affiliation(s)
- Zhenxing Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- College of Life Sciences, Southwest Forestry University, Kunming, China
- National R&D Center for Freshwater Fish Processing, College of Health, Jiangxi Normal University, Nanchang, China
| | - Ximeng Jin
- College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Xuechun Zhang
- College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Xing Xie
- National R&D Center for Freshwater Fish Processing, College of Health, Jiangxi Normal University, Nanchang, China
| | - Zongcai Tu
- National R&D Center for Freshwater Fish Processing, College of Health, Jiangxi Normal University, Nanchang, China
| | - Xiahong He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- College of Horticulture and Landscape, Southwest Forestry University, Kunming, China
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25
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Dong Y, Aharoni A. Image to insight: exploring natural products through mass spectrometry imaging. Nat Prod Rep 2022; 39:1510-1530. [PMID: 35735199 DOI: 10.1039/d2np00011c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2017 to 2022Mass spectrometry imaging (MSI) has become a mature molecular imaging technique that is well-matched for natural product (NP) discovery. Here we present a brief overview of MSI, followed by a thorough discussion of different MSI applications in NP research. This review will mainly focus on the recent progress of MSI in plants and microorganisms as they are the main producers of NPs. Specifically, the opportunity and potential of combining MSI with other imaging modalities and stable isotope labeling are discussed. Throughout, we focus on both the strengths and weaknesses of MSI, with an eye on future improvements that are necessary for the progression of MSI toward routine NP studies. Finally, we discuss new areas of research, future perspectives, and the overall direction that the field may take in the years to come.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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26
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Suntivich R, Songjang W, Jiraviriyakul A, Ruchirawat S, Chatwichien J. LC-MS/MS metabolomics-facilitated identification of the active compounds responsible for anti-allergic activity of the ethanol extract of Xenostegia tridentata. PLoS One 2022; 17:e0265505. [PMID: 35427369 PMCID: PMC9012362 DOI: 10.1371/journal.pone.0265505] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/02/2022] [Indexed: 12/29/2022] Open
Abstract
In vivo and in vitro anti-allergic activities of ethanol extract of Xenostegia tridentata (L.) D.F. Austin & Staples were investigated using passive cutaneous anaphylaxis reaction assay and RBL-2H3 cell degranulation assay, respectively. The crude ethanol extract exhibited promising activities when compared with the known anti-allergic agents, namely dexamethasone and ketotifen fumarate. The ethyl acetate subfraction showed the highest anti-allergic activity among various sub-partitions and showed better activity than the crude extract, consistent with the high abundance of total phenolic and flavonoid contents in this subfraction. LC-MS/MS metabolomics analysis and bioassay-guided isolation were then used to identify chemical constituents responsible for the anti-allergic activity. The results showed that major components of the ethyl acetate subfraction consist of 3,5-dicaffeoylquinic acid, quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside and luteolin-7-O-glucoside. The inhibitory activity of the isolated compounds against mast cell degranulation was validated, ensuring their important roles in the anti-allergic activity of the plant. Notably, besides showing the anti-allergic activity of X. tridentata, this work highlights the role of metabolomic analysis in identifying and selectively isolating active metabolites from plants.
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Affiliation(s)
- Rinrada Suntivich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Worawat Songjang
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, Thailand
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, Thailand
| | - Arunya Jiraviriyakul
- Department of Medical Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, Thailand
- Integrative Biomedical Research Unit (IBRU), Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, Thailand
| | - Somsak Ruchirawat
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok, Thailand
| | - Jaruwan Chatwichien
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok, Thailand
- * E-mail:
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27
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Characterization of Constituents with Potential Anti-Inflammatory Activity in Chinese Lonicera Species by UHPLC-HRMS Based Metabolite Profiling. Metabolites 2022; 12:metabo12040288. [PMID: 35448474 PMCID: PMC9027581 DOI: 10.3390/metabo12040288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/16/2022] [Accepted: 03/19/2022] [Indexed: 01/02/2023] Open
Abstract
This study centered on detecting potentially anti-inflammatory active constituents in ethanolic extracts of Chinese Lonicera species by taking an UHPLC-HRMS-based metabolite profiling approach. Extracts from eight different Lonicera species were subjected to both UHPLC-HRMS analysis and to pharmacological testing in three different cellular inflammation-related assays. Compounds exhibiting high correlations in orthogonal projections to latent structures discriminant analysis (OPLS-DA) of pharmacological and MS data served as potentially activity-related candidates. Of these candidates, 65 were tentatively or unambiguously annotated. 7-Hydroxy-5,3′,4′,5′-tetramethoxyflavone and three bioflavonoids, as well as three C32- and one C34-acetylated polyhydroxy fatty acid, were isolated from Lonicera hypoglauca leaves for the first time, and their structures were fully or partially elucidated. Of the potentially active candidate compounds, 15 were subsequently subjected to pharmacological testing. Their activities could be experimentally verified in part, emphasizing the relevance of Lonicera species as a source of anti-inflammatory active constituents. However, some compounds also impaired the cell viability. Overall, the approach was found useful to narrow down the number of potentially bioactive constituents in the complex extracts investigated. In the future, the application of more refined concepts, such as extract prefractionation combined with bio-chemometrics, may help to further enhance the reliability of candidate selection.
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28
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Machushynets NV, Elsayed SS, Du C, Siegler MA, de la Cruz M, Genilloud O, Hankemeier T, van Wezel GP. Discovery of actinomycin L, a new member of the actinomycin family of antibiotics. Sci Rep 2022; 12:2813. [PMID: 35181725 PMCID: PMC8857259 DOI: 10.1038/s41598-022-06736-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/01/2022] [Indexed: 12/25/2022] Open
Abstract
Streptomycetes are major producers of bioactive natural products, including the majority of the naturally produced antibiotics. While much of the low-hanging fruit has been discovered, it is predicted that less than 5% of the chemical space of natural products has been mined. Here, we describe the discovery of the novel actinomycins L1 and L2 produced by Streptomyces sp. MBT27, via application of metabolic analysis and molecular networking. Actinomycins L1 and L2 are diastereomers, and the structure of actinomycin L2 was resolved using NMR and single crystal X-ray crystallography. Actinomycin L is formed via spirolinkage of anthranilamide to the 4-oxoproline moiety of actinomycin X2, prior to the condensation of the actinomycin halves. Such a structural feature has not previously been identified in naturally occurring actinomycins. Adding anthranilamide to cultures of the actinomycin X2 producer Streptomyces antibioticus, which has the same biosynthetic gene cluster as Streptomyces sp. MBT27, resulted in the production of actinomycin L. This supports a biosynthetic pathway whereby actinomycin L is produced from two distinct metabolic routes, namely those for actinomycin X2 and for anthranilamide. Actinomycins L1 and L2 showed significant antimicrobial activity against Gram-positive bacteria. Our work shows how new molecules can still be identified even in the oldest of natural product families.
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Affiliation(s)
- Nataliia V Machushynets
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Chao Du
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Mercedes de la Cruz
- Fundación MEDINA, Health Sciences Technology Park, Avda Conocimiento 34, 18016, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences Technology Park, Avda Conocimiento 34, 18016, Granada, Spain
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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29
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Demarque DP, Espindola LS. Challenges, Advances and Opportunities in Exploring Natural Products to Control Arboviral Disease Vectors. Front Chem 2021; 9:779049. [PMID: 34869227 PMCID: PMC8634490 DOI: 10.3389/fchem.2021.779049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 02/02/2023] Open
Abstract
Natural products constitute an important source of molecules for product development. However, despite numerous reports of compounds and active extracts from biodiversity, poor and developing countries continue to suffer with endemic diseases caused by arboviral vectors, including dengue, Zika, chikungunya and urban yellow fever. Vector control remains the most efficient disease prevention strategy. Wide and prolonged use of insecticides has resulted in vector resistance, making the search for new chemical prototypes imperative. Considering the potential of natural products chemistry for developing natural products-based products, including insecticides, this contribution discusses the general aspects and specific characteristics involved in the development of drug leads for vector control. Throughout this work, we highlight the obstacles that need to be overcome in order for natural products compounds to be considered promising prototypes. Moreover, we analyze the bottlenecks that should be addressed, together with potential strategies, to rationalize and improve the efficiency of the drug discovery process.
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Affiliation(s)
- Daniel P Demarque
- Laboratory of Pharmacognosy, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia, Brazil.,Laboratory of Pharmacognosy, Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Laila S Espindola
- Laboratory of Pharmacognosy, Department of Pharmacy, Faculty of Health Sciences, University of Brasilia, Brasilia, Brazil
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30
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A metabolomics approach to evaluate the effect of lyophilization versus oven drying on the chemical composition of plant extracts. Sci Rep 2021; 11:22679. [PMID: 34811431 PMCID: PMC8608909 DOI: 10.1038/s41598-021-02158-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/10/2021] [Indexed: 12/22/2022] Open
Abstract
Lyophilization is the “gold standard” for drying plant extracts, which is important in preserving their quality and extending their shelf-life. Compared to other methods of drying plant extracts, lyophilization is costlier due to equipment, material and operational expenses. An alternative method is post-extraction oven-drying, but the effects of this process on extract quality are unknown. In this study, crude extracts from Arthrocnemum macrostachyum shoots were compared using three post-extraction drying methods (lyophilization and oven drying at 40 and 60 °C) and two extraction solvents (water and aqueous 50% ethanol). Untargeted metabolomics coupled with chemometrics analysis revealed that post extraction oven-drying resulted in the loss of up to 27% of molecular features when compared to lyophilization in water extracts only. In contrast, only 3% of molecular features were lost in aqueous 50% ethanol extracts when subjected to oven drying. That is to say, ethanol used as a solvent has a stabilizing effect on metabolites and enhances their resistance to thermal transformation in the oven. Collectively, oven-drying of extracts was as effective as lyophilization in preserving metabolites in extracts only when 50% ethanol was used as a solvent. The results presented in this paper demonstrate the value of selecting solvent-appropriate post-extraction drying methods.
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31
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Jarmusch SA, van der Hooft JJJ, Dorrestein PC, Jarmusch AK. Advancements in capturing and mining mass spectrometry data are transforming natural products research. Nat Prod Rep 2021; 38:2066-2082. [PMID: 34612288 PMCID: PMC8667781 DOI: 10.1039/d1np00040c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: 2016 up to 2021Mass spectrometry (MS) is an essential technology in natural products research with MS fragmentation (MS/MS) approaches becoming a key tool. Recent advancements in MS yield dense metabolomics datasets which have been, conventionally, used by individual labs for individual projects; however, a shift is brewing. The movement towards open MS data (and other structural characterization data) and accessible data mining tools is emerging in natural products research. Over the past 5 years, this movement has rapidly expanded and evolved with no slowdown in sight; the capabilities of today vastly exceed those of 5 years ago. Herein, we address the analysis of individual datasets, a situation we are calling the '2021 status quo', and the emergent framework to systematically capture sample information (metadata) and perform repository-scale analyses. We evaluate public data deposition, discuss the challenges of working in the repository scale, highlight the challenges of metadata capture and provide illustrative examples of the power of utilizing repository data and the tools that enable it. We conclude that the advancements in MS data collection must be met with advancements in how we utilize data; therefore, we argue that open data and data mining is the next evolution in obtaining the maximum potential in natural products research.
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Affiliation(s)
- Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kongens Lyngby, Denmark.
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0751, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0751, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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32
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Kisiriko M, Anastasiadi M, Terry LA, Yasri A, Beale MH, Ward JL. Phenolics from Medicinal and Aromatic Plants: Characterisation and Potential as Biostimulants and Bioprotectants. Molecules 2021; 26:6343. [PMID: 34770752 PMCID: PMC8588183 DOI: 10.3390/molecules26216343] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022] Open
Abstract
Biostimulants and bioprotectants are derived from natural sources and can enhance crop growth and protect crops from pests and pathogens, respectively. They have attracted much attention in the past few decades and contribute to a more sustainable and eco-friendly agricultural system. Despite not having been explored extensively, plant extracts and their component secondary metabolites, including phenolic compounds have been shown to have biostimulant effects on plants, including enhancement of growth attributes and yield, as well as bioprotectant effects, including antimicrobial, insecticidal, herbicidal and nematicidal effects. Medicinal and aromatic plants are widely distributed all over the world and are abundant sources of phenolic compounds. This paper reviews the characterisation of phenolic compounds and extracts from medicinal and aromatic plants, including a brief overview of their extraction, phytochemical screening and methods of analysis. The second part of the review highlights the potential for use of phenolic compounds and extracts as biostimulants and bioprotectants in agriculture as well as some of the challenges related to their use.
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Affiliation(s)
- Musa Kisiriko
- Plant Science Laboratory, Cranfield University, Cranfield MK43 0AL, UK; (M.K.); (M.A.); (L.A.T.)
- AgroBioSciences Research Division, Mohammed VI Polytechnic University, Lot 660, Moulay Rachid, Ben Guerir 43150, Morocco;
- Rothamsted Research, West Common, Harpenden AL5 2JQ, UK;
| | - Maria Anastasiadi
- Plant Science Laboratory, Cranfield University, Cranfield MK43 0AL, UK; (M.K.); (M.A.); (L.A.T.)
| | - Leon Alexander Terry
- Plant Science Laboratory, Cranfield University, Cranfield MK43 0AL, UK; (M.K.); (M.A.); (L.A.T.)
| | - Abdelaziz Yasri
- AgroBioSciences Research Division, Mohammed VI Polytechnic University, Lot 660, Moulay Rachid, Ben Guerir 43150, Morocco;
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Identification of α-Glucosidase Inhibitors from Leaf Extract of Pepper ( Capsicum spp.) through Metabolomic Analysis. Metabolites 2021; 11:metabo11100649. [PMID: 34677364 PMCID: PMC8538662 DOI: 10.3390/metabo11100649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/15/2021] [Accepted: 09/18/2021] [Indexed: 12/11/2022] Open
Abstract
Metabolomics and in vitro α-glucosidase inhibitory (AGI) activities of pepper leaves were used to identify bioactive compounds and select genotypes for the management of type 2 diabetes mellitus (T2DM). Targeted metabolite analysis using UPLC-DAD-QToF-MS was employed and identified compounds that belong to flavone and hydroxycinnamic acid derivatives from extracts of pepper leaves. A total of 21 metabolites were detected from 155 samples and identified based on MS fragmentations, retention time, UV absorbance, and previous reports. Apigenin-O-(malonyl) hexoside, luteolin-O-(malonyl) hexoside, and chrysoeriol-O-(malonyl) hexoside were identified for the first time from pepper leaves. Pepper genotypes showed a huge variation in their inhibitory activity against α-glucosidase enzyme(AGE) ranging from 17% to 79%. Genotype GP38 with inhibitory activity of 79% was found to be more potent than the positive control acarbose (70.8%.). Orthogonal partial least square (OPLS) analyses were conducted for the prediction of the AGI activities of pepper leaves based on their metabolite composition. Compounds that contributed the most to the bioactivity prediction model (VIP >1.5), showed a strong inhibitory potency. Caffeoyl-putrescine was found to show a stronger inhibitory potency (IC50 = 145 µM) compared to acarbose (IC50 = 197 µM). The chemometric procedure combined with high-throughput AGI screening was effective in selecting polyphenols of pepper leaf for T2DM management.
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El‐Hawary S, Mohammed R, Bahr H, Attia E, El‐Katatny M, Abelyan N, Al‐Sanea M, Moawad A, Abdelmohsen U. Soybean-associated endophytic fungi as potential source for anti-COVID-19 metabolites supported by docking analysis. J Appl Microbiol 2021; 131:1193-1211. [PMID: 33559270 PMCID: PMC8013715 DOI: 10.1111/jam.15031] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 12/29/2022]
Abstract
AIMS To identify the metabolites produced by the endophytic fungus, Aspergillus terreus and to explore the anti-viral activity of the identified metabolites against the pandemic disease COVID-19 in-silico. METHODS AND RESULTS Herein, we reported the isolation of A. terreus, the endophytic fungus associated with soybean roots, which is then subcultured using OSMAC approach in five different culture media. Analytical analysis of media ethylacetate extracts using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) was carried out. Furthermore, the obtained LC-MS data were statistically processed with MetaboAnalyst 4.0. Molecular docking studies were performed for the dereplicated metabolites against COVID-19 main protease (Mpro ). Metabolomic profiling revealed the presence of 18 compounds belonging to different chemical classes. Quinones, polyketides and isocoumarins were the most abundant classes. Multivariate analysis revealed that potato dextrose broth and modified potato dextrose broth are the optimal media for metabolites production. Molecular docking studies declared that the metabolites, Aspergillide B1 and 3a-Hydroxy-3, 5-dihydromonacolin L showed the highest binding energy scores towards COVID-19 main protease (Mpro ) (-9·473) and (-9·386), respectively, and they interact strongly with the catalytic dyad (His41 and Cys145) amino acid residues of Mpro . CONCLUSIONS A combination of metabolomics and in-silico approaches have allowed a shorter route to search for anti-COVID-19 natural products in a shorter time. The dereplicated metabolites, aspergillide B1 and 3α-Hydroxy-3, 5-dihydromonacolin L were found to be potent anti-COVID-19 drug candidates in the molecular docking study. SIGNIFICANCE AND IMPACT OF THE STUDY This study revealed that the endophytic fungus, A. terreus can be considered as a potential source of natural bioactive products. In addition to, the possibility of developing the metabolites, aspergillide B1 and 3α-Hydroxy-3, 5-dihydromonacolin L to be used as phytopharmaceuticals for the management of COVID-19.
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Affiliation(s)
- S.S. El‐Hawary
- Department of Pharmacognosy Faculty of Pharmacy Cairo University Cairo Egypt
| | - R. Mohammed
- Department of Pharmacognosy Faculty of Pharmacy Beni‐Suef University Beni‐Suef Egypt
| | - H.S. Bahr
- Department of Pharmacognosy Faculty of Pharmacy Nahda University Beni‐Suef Egypt
| | - E.Z. Attia
- Department of Pharmacognosy Faculty of Pharmacy Minia University Minia Egypt
| | - M.H. El‐Katatny
- Department of Botany and Microbiology Faculty of Science Minia University Minia Egypt
| | - N. Abelyan
- Institute of Biomedicine and Pharmacy Russian‐Armenian University Yerevan Armenia
- Foundation for Armenian Science and Technology Yerevan Armenia
| | - M.M. Al‐Sanea
- Department of Pharmaceutical Chemistry College of Pharmacy Jouf University Sakaka Saudi Arabia
| | - A.S. Moawad
- Department of Pharmacognosy Faculty of Pharmacy Beni‐Suef University Beni‐Suef Egypt
| | - U.R. Abdelmohsen
- Department of Pharmacognosy Faculty of Pharmacy Minia University Minia Egypt
- Department of Pharmacognosy Faculty of Pharmacy Deraya University New Minia City Minia Egypt
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Collins SL, Koo I, Peters JM, Smith PB, Patterson AD. Current Challenges and Recent Developments in Mass Spectrometry-Based Metabolomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:467-487. [PMID: 34314226 DOI: 10.1146/annurev-anchem-091620-015205] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-resolution mass spectrometry (MS) has advanced the study of metabolism in living systems by allowing many metabolites to be measured in a single experiment. Although improvements in mass detector sensitivity have facilitated the detection of greater numbers of analytes, compound identification strategies, feature reduction software, and data sharing have not kept up with the influx of MS data. Here, we discuss the ongoing challenges with MS-based metabolomics, including de novo metabolite identification from mass spectra, differentiation of metabolites from environmental contamination, chromatographic separation of isomers, and incomplete MS databases. Because of their popularity and sensitive detection of small molecules, this review focuses on the challenges of liquid chromatography-mass spectrometry-based methods. We then highlight important instrumentational, experimental, and computational tools that have been created to address these challenges and how they have enabled the advancement of metabolomics research.
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Affiliation(s)
- Stephanie L Collins
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jeffrey M Peters
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Philip B Smith
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
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Organic cultivation practices enhanced antioxidant activities and secondary metabolites in giant granadilla (Passiflora quadrangularis L.). PLoS One 2021; 16:e0255059. [PMID: 34310644 PMCID: PMC8312946 DOI: 10.1371/journal.pone.0255059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/08/2021] [Indexed: 11/21/2022] Open
Abstract
Passiflora quadrangularis L. belongs to the family Passifloraceae which bears larger fruit with edible juicy mesocarp and pulp known as a good source of phytochemicals. Cultivation and plant management practices are known to influence the phytochemical compositions of agricultural produce. This study aimed to examine the influence of the cultivation practices on the antioxidant activities and secondary metabolites of the organically and conventionally grown P. quadrangularis. Findings revealed organically treated P. quadrangularis plants showed enhancement in their antioxidant properties and secondary metabolites profiles. Among the plant parts, leaves of P. quadrangularis grown organically possessed higher antioxidant activities compared to the conventional in all assays evaluated. The antioxidant activities in the edible parts of the P. quadrangularis fruit have also been enhanced through organic cultivation with significantly higher total phenolic content and DPPH in mesocarp, and the pulp showed higher total flavonoid content, DPPH and FRAP. This observation is supported by a higher level of vitamins and secondary metabolites in the samples. The secondary metabolites profile showed mesocarps were phenolic rich, the pulps were flavonoids rich while leaves showed good composition of phenolics, flavonoids and terpenoids with outstanding antioxidant activities. The common secondary metabolites for organically produced P. quadrangularis in different plant parts include 2-isopropyl-3-methoxycinnamic acid (mesocarp and pulp), myricetin isomers (pulp and leaves), and malvidin-3-O-arabinoside isomers (pulp and leaves). This study confirmed that organic cultivated P. quadrangularis possessed higher antioxidant activities contributed by its vitamins and secondary metabolites.
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Cibichakravarthy B, Jose PA. Biosynthetic Potential of Streptomyces Rationalizes Genome-Based Bioprospecting. Antibiotics (Basel) 2021; 10:antibiotics10070873. [PMID: 34356794 PMCID: PMC8300671 DOI: 10.3390/antibiotics10070873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/04/2022] Open
Abstract
Streptomyces are the most prolific source of structurally diverse microbial natural products. Advancing genome-based analysis reveals the previously unseen potential of Streptomyces to produce numerous novel secondary metabolites, which allows us to take natural product discovery to the next phase. However, at present there is a huge disproportion between the rate of genome reports and discovery of new compounds. From this perspective of harnessing the enduring importance of Streptomyces, we discuss the recent genome-directed advancements inspired by hidden biosynthetic wealth that provide hope for future antibiotics.
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Affiliation(s)
- Balasubramanian Cibichakravarthy
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761000, Israel;
| | - Polapass Arul Jose
- Department of Entomology and Plant Pathology & Microbiology, The Hebrew University of Jerusalem, POB 12, Rehovot 761000, Israel
- Correspondence:
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Ding L, Bar-Shalom R, Aharonovich D, Kurisawa N, Patial G, Li S, He S, Yan X, Iwasaki A, Suenaga K, Zhu C, Luo H, Tian F, Fares F, Naman CB, Luzzatto-Knaan T. Metabolomic Characterization of a cf. Neolyngbya Cyanobacterium from the South China Sea Reveals Wenchangamide A, a Lipopeptide with In Vitro Apoptotic Potential in Colon Cancer Cells. Mar Drugs 2021; 19:md19070397. [PMID: 34356822 PMCID: PMC8307421 DOI: 10.3390/md19070397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolomics can be used to study complex mixtures of natural products, or secondary metabolites, for many different purposes. One productive application of metabolomics that has emerged in recent years is the guiding direction for isolating molecules with structural novelty through analysis of untargeted LC-MS/MS data. The metabolomics-driven investigation and bioassay-guided fractionation of a biomass assemblage from the South China Sea dominated by a marine filamentous cyanobacteria, cf. Neolyngbya sp., has led to the discovery of a natural product in this study, wenchangamide A (1). Wenchangamide A was found to concentration-dependently cause fast-onset apoptosis in HCT116 human colon cancer cells in vitro (24 h IC50 = 38 μM). Untargeted metabolomics, by way of MS/MS molecular networking, was used further to generate a structural proposal for a new natural product analogue of 1, here coined wenchangamide B, which was present in the organic extract and bioactive sub-fractions of the biomass examined. The wenchangamides are of interest for anticancer drug discovery, and the characterization of these molecules will facilitate the future discovery of related natural products and development of synthetic analogues.
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Affiliation(s)
- Lijian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
| | - Rinat Bar-Shalom
- Department of Human Biology, Faculty of Life Sciences, University of Haifa, Haifa 31905, Israel; (R.B.-S.); (F.F.)
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
| | - Naoaki Kurisawa
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
| | - Gaurav Patial
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Shuang Li
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Xiaojun Yan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Arihiro Iwasaki
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Kiyotake Suenaga
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Chengcong Zhu
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Haixi Luo
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Fuli Tian
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Fuad Fares
- Department of Human Biology, Faculty of Life Sciences, University of Haifa, Haifa 31905, Israel; (R.B.-S.); (F.F.)
| | - C. Benjamin Naman
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
- Correspondence: (C.B.N.); (T.L.-K.)
| | - Tal Luzzatto-Knaan
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
- Correspondence: (C.B.N.); (T.L.-K.)
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Zhang XY, Liu YH, Liu DZ, Xu JY, Zhang Q. Insulin-Mimic Components in Acer truncatum Leaves: Bio-Guided Isolation, Annual Variance Profiling and Regulating Pathway Investigated by Omics. Pharmaceuticals (Basel) 2021; 14:ph14070662. [PMID: 34358088 PMCID: PMC8308865 DOI: 10.3390/ph14070662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 01/17/2023] Open
Abstract
Insulin mimic can promote transporting glucose to muscle tissue and accelerate glucose consumption. It is commonly occurring in many functional foods or traditional medicines. Anti-diabetes molecules from food sources are highly safe and suitable for long-term use to prevent early diabetes. The leaves of Acer truncatum was found glucose uptake promotion in our phenotypic screening. However, its bioactive components and mechanism are still unclear. We collected leaves from trees of different ages (2, 3, 4, 7 and 11 years old) and profiled the ingredients by LC-MS/MS. The essential active component (myricitrin) was acquired following bio-guide on a whole organism Zebrafish (Danio rerio). Its content in the leaves was not affected by tree ages. Therefore, myricitrin can serve as a quality mark for functional foods derived from A. truncatum leaves. The transcriptomic and metabolomic analysis in Zebrafish explored the differentially expressed genes and metabolites. Based on joint-pathway enrichment and qRT-PCR verification, the critical bioactive component myricitrin was found to affect toll-like receptors signaling pathways to regulate glucose uptake. Our findings disclosed a bioactive marker (myricitrin) in A. truncatum leaves and explored its regulation mechanism, which rationalized the anti-diabetes function of the herbal food.
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40
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Tinte MM, Chele KH, van der Hooft JJJ, Tugizimana F. Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview. Metabolites 2021; 11:445. [PMID: 34357339 PMCID: PMC8305945 DOI: 10.3390/metabo11070445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 12/27/2022] Open
Abstract
Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These are limiting their development and productivity and are subsequently threatening our food security, especially when considering the pressure of the increasing global population. Thus, there is an urgent need for the next generation of crops with high productivity and resilience to climate change. The dawn of a new era characterized by the emergence of fourth industrial revolution (4IR) technologies has redefined the ideological boundaries of research and applications in plant sciences. Recent technological advances and machine learning (ML)-based computational tools and omics data analysis approaches are allowing scientists to derive comprehensive metabolic descriptions and models for the target plant species under specific conditions. Such accurate metabolic descriptions are imperatively essential for devising a roadmap for the next generation of crops that are resilient to environmental deterioration. By synthesizing the recent literature and collating data on metabolomics studies on plant responses to abiotic stresses, in the context of the 4IR era, we point out the opportunities and challenges offered by omics science, analytical intelligence, computational tools and big data analytics. Specifically, we highlight technological advancements in (plant) metabolomics workflows and the use of machine learning and computational tools to decipher the dynamics in the chemical space that define plant responses to abiotic stress conditions.
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Affiliation(s)
- Morena M. Tinte
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.T.); (K.H.C.)
| | - Kekeletso H. Chele
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.T.); (K.H.C.)
| | | | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.T.); (K.H.C.)
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa
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Wang A, Pi Z, Liu S, Zheng Z, Liu Z, Song F. Mass spectrometry-based urinary metabolomics for exploring the treatment effects of Radix ginseng-Schisandra chinensis herb pair on Alzheimer's disease in rats. J Sep Sci 2021; 44:3158-3166. [PMID: 34110709 DOI: 10.1002/jssc.202100061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 11/06/2022]
Abstract
Herb pairs are the unique combinations of two relatively fixed herbs, intrinsically convey the basic idea of traditional Chinese medicine prescriptions. The compatibility of Radix ginseng and Schisandra chinensis has been used in traditional Chinese medicine for treating Alzheimer's disease for many years. However, there are few studies on Radix ginseng-Schisandra chinensis herb pair, and the underlying action mechanism is still unclear. In this study, the mechanism of Radix ginseng-Schisandra chinensis herb pair on Alzheimer's disease was investigated by using the mass spectrometry-based urinary metabolomics method. Sixteen urinary endogenous metabolites were identified as potential biomarkers. Meanwhile, 10 biomarkers were quantified with tandem mass spectrometry. The study result showed that the brain pathologic symptoms of model rats were improved and the potential biomarkers were adjusted backward significantly after the herb pair administration. The metabolic pathways linked to the herb pair-regulated endogenous biomarkers included phenylalanine and tyrosine metabolism, tryptophan metabolism, purine metabolism, and so on. The above metabolic pathways reflected that Radix ginseng-Schisandra chinensis herb pair mainly regulates abnormal energy metabolism, reduces inflammation, and regulates gut microbiota and neurotransmitters in the treatment of Alzheimer's disease.
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Affiliation(s)
- Aimin Wang
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, P. R. China
| | - Zifeng Pi
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Shu Liu
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Zhong Zheng
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Zhiqiang Liu
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, P. R. China
| | - Fengrui Song
- State Key Laboratory of Electroanalytical Chemistry, National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, P. R. China
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Hu XL, Lu H, Hassan MM, Zhang J, Yuan G, Abraham PE, Shrestha HK, Villalobos Solis MI, Chen JG, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Cheng ZMM, Yang X. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. HORTICULTURE RESEARCH 2021; 8:130. [PMID: 34059650 PMCID: PMC8167165 DOI: 10.1038/s41438-021-00570-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 05/02/2023]
Abstract
Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zong-Ming Max Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Nguyen NH, Ha TKQ, Yang JL, Pham HTT, Oh WK. Triterpenoids from the genus Gynostemma: Chemistry and pharmacological activities. JOURNAL OF ETHNOPHARMACOLOGY 2021; 268:113574. [PMID: 33186700 DOI: 10.1016/j.jep.2020.113574] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/20/2020] [Accepted: 11/05/2020] [Indexed: 05/28/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE G. pentaphyllum, also known as Jiao-Gu-Lan, has been used traditionally as folk remedies for many diseases, including diabetes mellitus, metabolic syndrome, aging, and neurodegenerative diseases in China and some countries in East and Southeast Asia. It is considered as an "immortality herb" in Guizhou Province, because it was consumed regularly by the elderly native inhabitants. Other species of the same genus Gynostemma such as G. longipes and G. laxum have been used as alternatives to G. pentaphyllum in ethno-medicine in Vietnam and other Asian countries. AIM OF THE REVIEW The review aims to summarize up-to-date study results on Gynostemma species, including traditional usage, phytochemical profile, pharmacological activities, and toxicological studies, in order to suggest future research orientation and therapeutic applications on acute and chronic diseases. MATERIALS AND METHODS The relevant literature on the genus Gynostemma was gathered from secondary databases (Web of Science and PubMed), books, and official websites. The latest literature cited in this review was published in February 2020. RESULTS The genus Gynostemma has been widely used in traditional medicine, mainly for treatment of diabetes, hypertension, obesity, and hepatosteatosis. To date, 328 dammarane-type saponins were isolated and structurally elucidated from Gynostemma species. Crude extracts, saponin-rich fractions (gypenosides), and pure compounds were reported to show a wide range of pharmacological activities in both in vitro and in vivo experiments. The most notable pharmacological effects were anti-cancer, cardioprotective, hepatoprotective, neuroprotective, anti-diabetic, anti-obesity, and anti-inflammatory activities. Toxicological studies were conducted only on G. pentaphyllum, showing that the plant extracts were relatively safe in both acute and long-term toxicity experiments at the given dosage while no toxicological studies were reported for the other species. CONCLUSIONS The review summarizes current studies on traditional uses, phytochemistry, biological properties, and toxicology of medicinal Gynostemma species. Till now, the majority of publications still focused only on G. pentaphyllum. However, the promising preliminary data of other Gynostemma species indicated the research potential of this genus, both in phytochemical and pharmacological aspects. Furthermore, clinical data are required to evaluate the efficacy and undesired effects of crude extracts, standard saponin fractions, and pure compounds prepared from Gynostemma medicinal plants.
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Affiliation(s)
- Ngoc-Hieu Nguyen
- Faculty of Pharmacy, PHENIKAA University, Hanoi, 12116, Viet Nam; PHENIKAA Research and Technology Institute (PRATI), A&A Green Phoenix Group JSC, No. 167 Hoang Ngan, Trung Hoa, Cau Giay, Hanoi, 11313, Viet Nam
| | - Thi Kim Quy Ha
- College of Natural Sciences, Cantho University, Campus II, Cantho City, Viet Nam
| | - Jun-Li Yang
- Key Laboratory of Chemistry of Northwestern Plant Resources of CAS and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, PR China
| | - Ha Thanh Tung Pham
- Department of Botany, Hanoi University of Pharmacy, Hanoi, 100000, Viet Nam
| | - Won Keun Oh
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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A Molecular Networking Strategy: High-Throughput Screening and Chemical Analysis of Brazilian Cerrado Plant Extracts against Cancer Cells. Cells 2021; 10:cells10030691. [PMID: 33804755 PMCID: PMC8004027 DOI: 10.3390/cells10030691] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/22/2022] Open
Abstract
Plants have historically been a rich source of successful anticancer drugs and chemotherapeutic agents, with research indicating that this trend will continue. In this contribution, we performed high-throughput cytotoxicity screening of 702 extracts from 95 plant species, representing 40 families of the Brazilian Cerrado biome. Activity was investigated against the following cancer cell lines: colon (Colo205 and Km12), renal (A498 and U031), liver (HEP3B and SKHEP), and osteosarcoma (MG63 and MG63.3). Dose-response tests were conducted with 44 of the most active extracts, with 22 demonstrating IC50 values ranging from <1.3 to 20 µg/mL. A molecular networking strategy was formulated using the Global Natural Product Social Molecular Networking (GNPS) platform to visualize, analyze, and annotate the compounds present in 17 extracts active against NCI-60 cell lines. Significant cytotoxic activity was found for Salacia crassifolia, Salacia elliptica, Simarouba versicolor, Diospyros hispida, Schinus terebinthifolia, Casearia sylvestris var. lingua, Magonia pubescens, and Rapanea guianensis. Molecular networking resulted in the annotation of 27 compounds. This strategy provided an initial overview of a complex and diverse natural product data set, yielded a large amount of chemical information, identified patterns and known compounds, and assisted in defining priorities for further studies.
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Stavropoulou MI, Termentzi A, Kasiotis KM, Cheilari A, Stathopoulou K, Machera K, Aligiannis N. Untargeted Ultrahigh-Performance Liquid Chromatography-Hybrid Quadrupole-Orbitrap Mass Spectrometry (UHPLC-HRMS) Metabolomics Reveals Propolis Markers of Greek and Chinese Origin. Molecules 2021; 26:molecules26020456. [PMID: 33467182 PMCID: PMC7830967 DOI: 10.3390/molecules26020456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Chemical composition of propolis depends on the plant source and thus on the geographic and climatic characteristics of the site of collection. The aim of this study was to investigate the chemical profile of Greek and Chinese propolis extracts from different regions and suggest similarities and differences between them. Untargeted ultrahigh-performance liquid chromatography coupled to hybrid quadrupole-Orbitrap mass spectrometry (UHPLC-HRMS) method was developed and 22 and 23 propolis samples from Greece and China, respectively, were analyzed. The experimental data led to the observation that there is considerable variability in terms of quality of the distinctive propolis samples. Partial least squares - discriminant analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) models were constructed and allowed the identification of significant features for sample discrimination, adding relevant information for the identification of class-determining metabolites. Chinese samples overexpressed compounds that are characteristic of the poplar type propolis, whereas Greek samples overexpress the latter and the diterpenes characteristic of the Mediterranean propolis type.
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Affiliation(s)
- Maria-Ioanna Stavropoulou
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 11527 Athens, Greece; (M.-I.S.); (A.C.); (K.S.)
| | - Aikaterini Termentzi
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (A.T.); (K.M.K.); (K.M.)
| | - Konstantinos M. Kasiotis
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (A.T.); (K.M.K.); (K.M.)
| | - Antigoni Cheilari
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 11527 Athens, Greece; (M.-I.S.); (A.C.); (K.S.)
| | - Konstantina Stathopoulou
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 11527 Athens, Greece; (M.-I.S.); (A.C.); (K.S.)
| | - Kyriaki Machera
- Laboratory of Pesticides’ Toxicology, Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, Kifissia, 14561 Athens, Greece; (A.T.); (K.M.K.); (K.M.)
| | - Nektarios Aligiannis
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 11527 Athens, Greece; (M.-I.S.); (A.C.); (K.S.)
- Correspondence: ; Tel.: +30-210-727-4524
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Liu R, Kool J, Jian J, Wang J, Zhao X, Jiang Z, Zhang T. Rapid Screening α-Glucosidase Inhibitors from Natural Products by At-Line Nanofractionation with Parallel Mass Spectrometry and Bioactivity Assessment. J Chromatogr A 2020; 1635:461740. [PMID: 33271429 DOI: 10.1016/j.chroma.2020.461740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/09/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022]
Abstract
In this study, a novel at-line nanofractionation screening platform was successfully developed for the rapid screening and identification of α-glucosidase inhibitors from natural products. A time-course bioassay based on high density well-plates was performed in parallel with high resolution mass spectrometry (MS), providing a straightforward and rapid procedure to simultaneously obtain chemical and biological information of active compounds. Through multiple nanofractionations into the same well-plate and comparisons of the orthogonal separation results of hydrophilic interaction liquid chromatography (HILIC) and reversed-phase liquid chromatography (RPLC), the α-glucosidase inhibitors can be accurately identified from co-eluates. The screening platform was comprehensively evaluated and validated, and was applied to the screenings of green tea polyphenols and Ginkgo folium flavonoids. After accurate peak shape and retention time matching between the bioactivity chromatograms and MS chromatograms, ten α-glucosidase inhibitors were successfully screened out and identified. The proposed screening method is rapid, effective and can avoid ignoring low abundant/active inhibitors.
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Affiliation(s)
- Ruijie Liu
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, 510632, China; Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drug Research, Jinan University, Guangzhou 510632, China
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Jingyi Jian
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, 510632, China; Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drug Research, Jinan University, Guangzhou 510632, China
| | - Jincai Wang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, 510632, China; Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drug Research, Jinan University, Guangzhou 510632, China
| | | | - Zhengjin Jiang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, 510632, China; Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drug Research, Jinan University, Guangzhou 510632, China.
| | - Tingting Zhang
- Institute of Pharmaceutical Analysis, College of Pharmacy, Jinan University, Guangzhou, 510632, China; Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drug Research, Jinan University, Guangzhou 510632, China.
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Morais LS, Dusi RG, Demarque DP, Silva RL, Albernaz LC, Báo SN, Merten C, Antinarelli LMR, Coimbra ES, Espindola LS. Antileishmanial compounds from Connarus suberosus: Metabolomics, isolation and mechanism of action. PLoS One 2020; 15:e0241855. [PMID: 33156835 PMCID: PMC7647111 DOI: 10.1371/journal.pone.0241855] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/21/2020] [Indexed: 11/27/2022] Open
Abstract
Leishmaniasis is a disease impacting public health worldwide due to its high incidence, morbidity and mortality. Available treatments are costly, lengthy and toxic, not to mention the problem of parasite resistance. The development of alternative treatments is warranted and natural products demonstrate promising activity. This study investigated the activity of Connarus suberosus extracts and compounds against Leishmania species. Several C. suberosus extracts were tested against L. amazonensis promastigotes. Active and inactive extracts were analyzed by UHPLC-MS and data evaluated using a metabolomics platform, revealing an unknown neoflavonoid (connarin, 3), isolated together with the pterocarpans: hemileiocarpin (1) and leiocarpin (2). The aforementioned compounds (1-3), together with the benzoquinones: rapanone (4), embelin (5) and suberonone (6) previously isolated by our group from the same species, were tested against: (i) L. amazonensis and L. infantum promastigotes, and (ii) L. amazonensis intracellular amastigotes, with the most active compound (3) also tested against L. infantum amastigotes. Cytotoxicity against murine peritoneal macrophages was also investigated. Compounds 2 and 3 presented an IC50 33.8 μM and 11.4 μM for L. amazonensis promastigotes; and 44.3 μM and 13.3 μM for L. infantum promastigotes, respectively. For L. amazonensis amastigotes, the IC50 of 2 was 20.4 μM with a selectivity index (SI) of 5.7, while the IC50 of 3 was 2.9 μM with an SI of 6.3. For L. infantum amastigotes, the IC50 of 3 was 7.7 μM. Compounds 2 and 3 presented activity comparable with the miltefosine positive control, with compound 3 found to be 2-4 times more active than the positive control, depending on the Leishmania species and form. The extracts and isolated compounds showed moderate toxicity against macrophages. Compounds 2 and 3 altered the mitochondrial membrane potential (ΔΨm) and neutral lipid body accumulation, while 2 also impacted plasma membrane permeabilization, culminating in cellular disorder and parasite death. Transmission electron microscopy of L. amazonensis promastigotes treated with compound 3 confirmed the presence of lipid bodies. Leiocarpin (2) and connarin (3) demonstrated antileishmanial activity. This study provides knowledge of natural products with antileishmanial activity, paving the way for prototype development to fight this neglected tropical disease.
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Affiliation(s)
- Lais S. Morais
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
| | - Renata G. Dusi
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
| | - Daniel P. Demarque
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
- Fakultät für Chemie und Biochemie, Organische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Raquel L. Silva
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
| | - Lorena C. Albernaz
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
| | - Sônia N. Báo
- Laboratório de Microscopia e Microanálise, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
| | - Christian Merten
- Fakultät für Chemie und Biochemie, Organische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Luciana M. R. Antinarelli
- Departamento de Parasitologia, Microbiologia e Imunologia, I.C.B., Universidade Federal de Juiz de Fora, Campus Universitário Juiz de Fora, Minas Gerais, Brazil
| | - Elaine S. Coimbra
- Departamento de Parasitologia, Microbiologia e Imunologia, I.C.B., Universidade Federal de Juiz de Fora, Campus Universitário Juiz de Fora, Minas Gerais, Brazil
| | - Laila S. Espindola
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, DF, Brazil
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Gorlenko CL, Kiselev HY, Budanova EV, Zamyatnin AA, Ikryannikova LN. Plant Secondary Metabolites in the Battle of Drugs and Drug-Resistant Bacteria: New Heroes or Worse Clones of Antibiotics? Antibiotics (Basel) 2020; 9:antibiotics9040170. [PMID: 32290036 PMCID: PMC7235868 DOI: 10.3390/antibiotics9040170] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Infectious diseases that are caused by bacteria are an important cause of mortality and morbidity in all regions of the world. Bacterial drug resistance has grown in the last decades, but the rate of discovery of new antibiotics has steadily decreased. Therefore, the search for new effective antibacterial agents has become a top priority. The plant kingdom seems to be a deep well for searching for novel antimicrobial agents. This is due to the many attractive features of plants: they are readily available and cheap, extracts or compounds from plant sources often demonstrate high-level activity against pathogens, and they rarely have severe side effects. The huge variety of plant-derived compounds provides very diverse chemical structures that may supply both the novel mechanisms of antimicrobial action and provide us with new targets within the bacterial cell. In addition, the rapid development of modern biotechnologies opens up the way for obtaining bioactive compounds in environmentally friendly and low-toxic conditions. In this short review, we ask the question: do antibacterial agents derived from plants have a chance to become a panacea against infectious diseases in the "post-antibiotics era".
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Affiliation(s)
- Cyrill L. Gorlenko
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (C.L.G.); (H.Y.K.); (E.V.B.)
| | - Herman Yu. Kiselev
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (C.L.G.); (H.Y.K.); (E.V.B.)
| | - Elena V. Budanova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (C.L.G.); (H.Y.K.); (E.V.B.)
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (C.L.G.); (H.Y.K.); (E.V.B.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (A.A.Z.J.); (L.N.I.); Tel.: +7-495-622-98-43 (A.A.Z.J.); +7-910-472-01-49 (L.N.I.)
| | - Larisa N. Ikryannikova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (C.L.G.); (H.Y.K.); (E.V.B.)
- Correspondence: (A.A.Z.J.); (L.N.I.); Tel.: +7-495-622-98-43 (A.A.Z.J.); +7-910-472-01-49 (L.N.I.)
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