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Plant and Derived Natural Product Metabolomics Volume 2

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

Deadline for manuscript submissions: closed (15 March 2022) | Viewed by 22504

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Dr. Mario Juan Simirgiotis Aguero

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Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
Interests: stereochemistry; natural products; computational chemistry; HPLC-MS; NMR
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Ute Roessner

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Guest Editor

Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
Interests: metabolomics; analytical biochemistry; metabolism; crop improvement; biomarker discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The study and applications of metabolites, also known as metabolomics, is an interesting topic of study which has been growing in significance in the last few years. However, the systematic study of metabolites in plants and their application in natural products is still facing issues due to the high diversity of useful small metabolites in plant matrices. Metabolites in plants produce the color, taste, aroma, and scent of fruits and flowers; plant metabolites are associated with many resistance and stress responses in plants, and metabolomics analyses can be useful for various purposes, such as evaluation of pharmaceutical production, food safety assessment, chemotaxonomy, crop quality improvement, plant metabolic engineering as well as metabolites of agronomic interest. Bioactive plant metabolites are useful in a myriad of applications, mostly related to human health diseases. Moreover, the understanding of plant physiology and biology from the analysis of small molecules and physiological processes such as cellular responses to various stimuli are key aspects to consider. Therefore, in this Special Issue, I invite research and review articles for “Plant Natural Product Metabolomics.” The contribution should be clearly stated in the manuscript, mainly linked to the metabolomics of sources of bioactive natural products and related topics. The main methods used should be mass spectrometry, nuclear magnetic resonance spectroscopy, or other suitable techniques. Both untargeted and targeted analysis of bioactive metabolites is welcome. The envisaged topics include dietary and pharmacological interventions, metabolic flux analysis, genetic manipulation, in vitro/in vivo imaging, and protocol development for metabolomic experiments.

The Special Issue is open for submissions now. Certain extensions may be granted if you kindly let me know in advance. Accepted papers will be published rapidly and will be listed together on the Special Issue website.

Dr. Mario Juan Simirgiotis Aguero
Prof. Dr. Ute Roessner
Guest Editors

Manuscript Submission Information

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

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

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

HPLC MS
natural products
bioactivities
metabolomics
NMR metabolomics
agronomy

Published Papers (8 papers)

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Research

22 pages, 4841 KiB

Open AccessArticle

Rhizophora mucronata Lam. (Mangrove) Bark Extract Reduces Ethanol-Induced Liver Cell Death and Oxidative Stress in Swiss Albino Mice: In Vivo and In Silico Studies

by Chitra Jairaman, Zeyad I. Alehaideb, Syed Ali Mohamed Yacoob, Sahar S. Alghamdi, Rasha S. Suliman, Anuradha Venkataraman, Bandar Alghanem, Senthilkumar Sivanesan, Rajagopalan Vijayaraghavan, Saranya Rameshbabu, Shree Mukilan Pari and Sabine Matou-Nasri

Metabolites 2022, 12(11), 1021; https://doi.org/10.3390/metabo12111021 - 25 Oct 2022

Cited by 3 | Viewed by 1597

Abstract

The bark extract of Rhizophora mucronata (BERM) was recently reported for its prominent in vitro protective effects against liver cell line toxicity caused by various toxicants, including ethanol. Here, we aimed to verify the in vivo hepatoprotective effects of BERM against ethanol intoxication with the prediction of potential targets employing in silico studies. An oral administration of different concentrations (100, 200 and 400 mg/kg body weight) of BERM before high-dose ethanol via intraperitoneal injection was performed in mice. On day 7, liver sections were dissected for histopathological examination. The ethanol intoxication caused liver injury and large areas of necrosis. The pre-BERM administration decreased the ethanol-induced liver damage marker tumor necrosis factor-alpha (TNF-α) expression, reduced hepatotoxicity revealed by nuclear deoxyribonucleic acid (DNA) fragmentation and decreased oxidative stress indicated by malondialdehyde and glutathione contents. Our in silico studies have identified BERM-derived metabolites exhibiting the highest predicted antioxidant and free radical scavenger activities. Molecular docking studies showed that most of the metabolites were predicted to be enzyme inhibitors such as carbonic anhydrase inhibitors, which were reported to stimulate the antioxidant defense system. The metabolites predominantly presented acceptable pharmacokinetics and safety profiles, suggesting them as promising new antioxidant agents. Altogether, the BERM extract exerts antioxidative activities and shows promising hepatoprotective effects against ethanol intoxication. Identification of related bioactive compounds will be of interest for future use at physiological concentrations in ethanol-intoxicated individuals. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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16 pages, 4957 KiB

Open AccessArticle

Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice

by Zhonghui Zhang, Feng Zhang, Yuan Deng, Lisong Sun, Mengdi Mao, Ridong Chen, Qi Qiang, Junjie Zhou, Tuan Long, Xuecheng Zhao, Xianqing Liu, Shouchuang Wang, Jun Yang and Jie Luo

Metabolites 2022, 12(5), 384; https://doi.org/10.3390/metabo12050384 - 22 Apr 2022

Cited by 6 | Viewed by 2768

Abstract

Rice (Oryza sativa L.) is one of the most globally important crops, nutritionally and economically. Therefore, analyzing the genetic basis of its nutritional quality is a paramount prerequisite for cultivating new varieties with increased nutritional health. To systematically compare the nutritional quality differences between landraces and cultivated rice, and to mine key genes that determine the specific nutritional traits of landraces, a seed metabolome database of 985 nutritional metabolites covering amino acids, flavonoids, anthocyanins, and vitamins by a widely targeted metabolomic approach with 114 rice varieties (35 landraces and 79 cultivars) was established. To further reveal the molecular mechanism of the metabolic differences in landrace and cultivated rice seeds, four cultivars and six landrace seeds were selected for transcriptome and metabolome analysis during germination, respectively. The integrated analysis compared the metabolic profiles and transcriptomes of different types of rice, identifying 358 differentially accumulated metabolites (DAMs) and 1982 differentially expressed genes (DEGs), establishing a metabolite–gene correlation network. A PCA revealed anthocyanins, flavonoids, and lipids as the central differential nutritional metabolites between landraces and cultivated rice. The metabolite–gene correlation network was used to screen out 20 candidate genes postulated to be involved in the structural modification of anthocyanins. Five glycosyltransferases were verified to catalyze the glycosylation of anthocyanins by in vitro enzyme activity experiments. At the same time, the different mechanisms of the anthocyanin synthesis pathway and structural diversity in landrace and cultivated rice were systematically analyzed, providing new insights for the improvement and utilization of the nutritional quality of rice landrace varieties. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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20 pages, 3854 KiB

Open AccessArticle

Phenolic Profile, Antioxidant and Enzyme Inhibition Properties of the Chilean Endemic Plant Ovidia pillopillo (Gay) Meissner (Thymelaeaceae)

by Carmen Cortés, Diego A. González-Cabrera, Ruth Barrientos, Claudio Parra, Javier Romero-Parra, Mariano Walter Pertino, Carlos Areche, Beatriz Sepúlveda, Jorge Bórquez, Alfredo Torres-Benítez and Mario J. Simirgiotis

Metabolites 2022, 12(2), 90; https://doi.org/10.3390/metabo12020090 - 18 Jan 2022

Cited by 4 | Viewed by 2532

Abstract

Ovidia pillopillo (Lloime) is an endemic species of the Valdivian Forest of Chile. Little is known on the chemistry and biological activity of this plant. In this study, the phenolic profile, antioxidant capacities and enzyme inhibition capacities (against tyrosinase and cholinesterase) of the plant were investigated for the first time. The phenolic profile of the plant was obtained by UHPLC-MS fingerprinting with high resolution, which showed the presence of several flavonoids and coumarins. The antioxidant potential was measured by FRAP and ORAC (45.56 ± 1.32; 25.33 ± 1.2 μmol Trolox equivalents/g dry plant, respectively) plus ABTS and DPPH methods (IC₅₀ = 9.95 ± 0.05 and 6.65 ± 0.5 μg/mL, respectively). Moreover, the flavonoid and phenolic contents were determined (57.33 ± 0.82 and 38.42 ± 1.32, μg of Trolox and quercetin equivalents/100 g dry weight, respectively). The ethanolic extract showed cholinesterase (IC₅₀ = 1.94 ± 0.07 and 2.73 ± 0.05 μg/mL, for AChE and BuChE, respectively) and tyrosinase (4.92 ± 0.05 μg/mL) enzyme inhibition activities. Based on these in vitro studies, in silico simulations were performed, which determined that the major compounds as ligands likely docked in the receptors of the enzymes. These results suggest that Ovidia pillopillo produce interesting special coumarins and flavonoids, which are potential candidates for the exploration and preparation of new medicines. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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13 pages, 1240 KiB

Open AccessArticle

Activity of Semi-Synthetic Mulinanes against MDR, Pre-XDR, and XDR Strains of Mycobacterium tuberculosis

by María Alejandrina Martínez-González, Luis Manuel Peña-Rodríguez, Andrés Humberto Uc-Cachón, Jorge Bórquez, Mario J. Simirgiotis, Hugo Brígido Barrios-García, Rogelio Hernández-Pando, Luis Alberto Loyola, Carlos Areche, Angel de Jesús Dzul-Beh, Jorge Alberto Barrios-Payán, Dulce Mata-Espinosa, Fabiola Escalante-Erosa, Karlina García-Sosa and Gloria María Molina-Salinas

Metabolites 2021, 11(12), 876; https://doi.org/10.3390/metabo11120876 - 16 Dec 2021

Cited by 1 | Viewed by 2304

Abstract

Tuberculosis causes more than 1.2 million deaths each year. Worldwide, it is the first cause of death by a single infectious agent. The emergence of drug-resistant strains has limited pharmacological treatment of the disease and today, new drugs are urgently needed. Semi-synthetic mulinanes have previously shown important activity against multidrug-resistant (MDR) Mycobacterium tuberculosis. In this investigation, a new set of semi-synthetic mulinanes were synthetized, characterized, and evaluated for their in vitro activity against three drug-resistant clinical isolates of M. tuberculosis: MDR, pre-extensively Drug-Resistant (pre-XDR), and extensively Drug-Resistant (XDR), and against the drug-susceptible laboratory reference strain H37Rv. Derivative 1a showed the best anti-TB activity (minimum inhibitory concentration [MIC] = 5.4 µM) against the susceptible strain and was twice as potent (MIC = 2.7 µM) on the MDR, pre-XDR, and XDR strains and also possessed a bactericidal effect. Derivative 1a was also tested for its anti-TB activity in mice infected with the MDR strain. In this case, 1a produced a significant reduction of pulmonary bacilli loads, six times lower than the control, when tested at 0.2536 mg/Kg. In addition, 1a demonstrated an adjuvant effect by shortening second-line chemotherapy. Finally, the selectivity index of >15.64 shown by 1a when tested on Vero cells makes this derivative an important candidate for future studies in the development of novel antitubercular agents. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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11 pages, 1775 KiB

Open AccessArticle

Direct Infusion Metabolomics of the Photosystem and Chlorophyll Related Metabolites within a Drought Tolerant Plant Introduction of Glycine max

by Kevin J. Zemaitis, Heng Ye, Henry T. Nguyen and Troy D. Wood

Metabolites 2021, 11(12), 843; https://doi.org/10.3390/metabo11120843 - 06 Dec 2021

Viewed by 2371

Abstract

Drought is the most prolific form of abiotic stress that legumes and cereal plants alike can endure, and the planting of an improper cultivar at the beginning of a season can cause unexpected losses up to fifty percent under water deficient conditions. Herein, a plant introduction (PI) of an exotic cultivar of soybean (Glycine max), PI 567731, which demonstrates a slow wilting (SW) canopy phenotype in maturity group III, was profiled under drought conditions in field trials in Missouri against a drought susceptible check cultivar, Pana. Metabolomic profiling was carried out on samples of leaves from each of these cultivars at V5 and R2 growth stages both while irrigated and while under drought stress for three weeks. PI 567731 was observed to have differential phytochemical content, and enhanced levels of chlorophyll (Chl) a/b and pheophytin (Pheo) were profiled by direct infusion electrospray Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Indicating drought induced changes of the photosystem and photosynthetic capabilities alongside water preservation strategies are important within the SW phenotype drought response. Subsequent multivariate analysis was able to form predictive models, encompassing the variance of growth and drought stress of the cultivar. Moreover, the existence of unique Chl-related metabolites (CRM) (m/z > 900) were confirmed through tandem mass spectrometry. The resultant coordination of fatty acids to the core of the porphyrin ring was observed and played an unknown role in the proliferation of the photosynthesis. However, the relative ratio of the most abundant CRM is undisturbed by drought stress in PI 567731, in contrast to the drought susceptible cultivar. These results provide key insights into drought related metabolic mechanisms. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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16 pages, 1992 KiB

Open AccessArticle

Tessaria absinthioides (Hook. & Arn.) DC. (Asteraceae) Decoction Improves the Hypercholesterolemia and Alters the Expression of LXRs in Rat Liver and Hypothalamus

by Mariana Rey, María S. Kruse, Rocío N. Magrini-Huamán, Jessica Gómez, Mario J. Simirgiotis, Alejandro Tapia, Gabriela E. Feresin and Héctor Coirini

Metabolites 2021, 11(9), 579; https://doi.org/10.3390/metabo11090579 - 27 Aug 2021

Cited by 4 | Viewed by 2663

Abstract

Chronic high-fat diet consumption induces hypercholesterolemia. The effect of Tessaria absinthioides (Hook. & Arn.) DC. (Asteraceae) was studied on the levels of total cholesterol (TC), high-density lipoprotein cholesterol (HDL-c), and triglycerides, and on the expression of liver X receptors (LXRs) in a hypercholesterolemic model. Adult male rats received a normal diet (ND) or a high-fat diet (HFD; normal diet + bovine fat + cholesterol). After 14 days, rats received water (W) or a decoction of the aerial parts of T. absinthioides (Ta; 10% w/v) for 2, 4, or 6 weeks. Four and six weeks of Ta improved the levels of TC and HDL-c in HFD. After 6 weeks of Ta, the expression of LXRs in HFD was the same as that in ND in both tissues. The Ta chemical profile was studied with an ultrahigh resolution liquid chromatography Orbitrap MS analysis (UHPLC–PDA–OT-MS/MS). Fifty-one compounds were identified, of which twelve are reported for the first time. Among these compounds, caffeoylquinic acid and its derivatives could modify the lipid profile and the expression of LXRs. This is the first in vivo report of T. absinthioides, which may be a potential candidate against hypercholesterolemia. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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16 pages, 14952 KiB

Open AccessArticle

An Oenothera biennis Cell Cultures Extract Endowed with Skin Anti-Ageing Activity Improves Cell Mechanical Properties

by Sara Ceccacci, Adriana De Lucia, Annalisa Tito, Assunta Tortora, Danila Falanga, Stefania Arciello, Giovanni Ausanio, Chiara Di Cicco, Maria Chiara Monti and Fabio Apone

Metabolites 2021, 11(8), 527; https://doi.org/10.3390/metabo11080527 - 09 Aug 2021

Cited by 3 | Viewed by 3318

Abstract

Skin aging is a very well-known process setting a gradual worsening of skin mechanical features due to a decline in the production of the extra-cellular matrix machinery and to a concurrent change in the contraction process. To slow this progression, it is crucial to induce the expression of several proteins able to promote elastic fibers formation and tissue repair. Here, the Oenothera biennis cell culture aqueous extract has been investigated from a chemical point of view and then it was tested in vitro, in cell, and in ex vivo experiments as adjuvant in counteracting skin aging. Accordingly, it has been shown that the Oenothera biennis extract was able, by increasing MYLK gene expression, to promote matrix collagen contraction, actin polymerization, and the production of essential ECM proteins. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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22 pages, 3226 KiB

Open AccessArticle

UHPLC-MS Chemical Fingerprinting and Antioxidant, Antiproliferative, and Enzyme Inhibition Potential of Gaultheria pumila Berries

by Carlos Fernández-Galleguillos, Luisa Quesada-Romero, Adrián Puerta, José M. Padrón, Ernane Souza, Javier Romero-Parra and Mario J. Simirgiotis

Metabolites 2021, 11(8), 523; https://doi.org/10.3390/metabo11080523 - 07 Aug 2021

Cited by 7 | Viewed by 2989

Abstract

Gaultheria pumila (Ericaceae) (known as Chaura or Mutilla) is a Chilean native small shrub that produces berry fruits consumed by local Mapuche people. In this study, the chemical fingerprinting and antioxidant, enzyme inhibition, and antiproliferative activities of the berries were investigated for the first time. Thirty-six metabolites were identified in the fruits by ultra-high performance liquid chromatography-photodiode array detection, hyphenated with Orbitrap mass spectrometry analysis (UHPLC-DAD-Orbitrap-MS). Metabolites, included anthocyanins, phenolic acids, flavonoids, iridoids, diterpenes, and fatty acids. Moderate inhibitory activities against acetylcholinesterase (7.7 ± 0.3 µg/mL), butyrylcholinesterase (34.5 ± 0.5 µg/mL), and tyrosinase (3.3 ± 0.2 µg/mL) enzymes were found. Moreover, selected major compounds were subjected to docking assays in light of their experimental inhibition. Results indicated that hydrogen bonding, π–π interaction, and a salt bridge interaction contributed significantly. Gaultheria pumila berries showed a total phenolic content of 189.2 ± 0.2 mg of gallic acid equivalents/g, total flavonoid content of 51.8 ± 0.1 mg quercetin equivalents/g, and total anthocyanin content of 47.3 ± 0.2 mg of cianydin-3-glucoside equivalents/g. Antioxidant activity was assessed using DPPH (92.8 ± 0.1 µg/mL), FRAP (134.1 ± 0.1 μmol Trolox equivalents/g), and ORAC (4251.6 ± 16.9 μmol Trolox equivalents/g) assays. Conversely, Gaultheria pumila showed a scarce antiproliferative potential against several solid human cancer cells. Our findings suggest that Gaultheria pumila berries have several bioactive metabolites with inhibitory effects against acetylcholinesterase, butyrylcholinesterase, and tyrosinase, and have the potential for use in food supplements. Full article

(This article belongs to the Special Issue Plant and Derived Natural Product Metabolomics Volume 2)

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