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NMR-Based Chromatography Readouts: Indispensable Tools to “Translate” Analytical Features into Molecular Structures. Cells 2022; 11:cells11213526. [DOI: 10.3390/cells11213526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Gaining structural information is a must to allow the unequivocal structural characterization of analytes from natural sources. In liquid state, NMR spectroscopy is almost the only possible alternative to HPLC-MS and hyphenating the effluent of an analyte separation device to the probe head of an NMR spectrometer has therefore been pursued for more than three decades. The purpose of this review article was to demonstrate that, while it is possible to use mass spectrometry and similar methods to differentiate, group, and often assign the differentiating variables to entities that can be recognized as single molecules, the structural characterization of these putative biomarkers usually requires the use of NMR spectroscopy.
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Wishart DS, Cheng LL, Copié V, Edison AS, Eghbalnia HR, Hoch JC, Gouveia GJ, Pathmasiri W, Powers R, Schock TB, Sumner LW, Uchimiya M. NMR and Metabolomics-A Roadmap for the Future. Metabolites 2022; 12:678. [PMID: 35893244 PMCID: PMC9394421 DOI: 10.3390/metabo12080678] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
Metabolomics investigates global metabolic alterations associated with chemical, biological, physiological, or pathological processes. These metabolic changes are measured with various analytical platforms including liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance spectroscopy (NMR). While LC-MS methods are becoming increasingly popular in the field of metabolomics (accounting for more than 70% of published metabolomics studies to date), there are considerable benefits and advantages to NMR-based methods for metabolomic studies. In fact, according to PubMed, more than 926 papers on NMR-based metabolomics were published in 2021-the most ever published in a given year. This suggests that NMR-based metabolomics continues to grow and has plenty to offer to the scientific community. This perspective outlines the growing applications of NMR in metabolomics, highlights several recent advances in NMR technologies for metabolomics, and provides a roadmap for future advancements.
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Affiliation(s)
- David S. Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Leo L. Cheng
- Department of Pathology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715, USA;
| | - Arthur S. Edison
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (A.S.E.); (G.J.G.); (M.U.)
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602-0001, USA
| | - Hamid R. Eghbalnia
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA; (H.R.E.); (J.C.H.)
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA; (H.R.E.); (J.C.H.)
| | - Goncalo J. Gouveia
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (A.S.E.); (G.J.G.); (M.U.)
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602-0001, USA
| | - Wimal Pathmasiri
- Nutrition Research Institute, Department of Nutrition, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Tracey B. Schock
- National Institute of Standards and Technology (NIST), Chemical Sciences Division, Charleston, SC 29412, USA;
| | - Lloyd W. Sumner
- Interdisciplinary Plant Group, MU Metabolomics Center, Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Mario Uchimiya
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (A.S.E.); (G.J.G.); (M.U.)
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3
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Alfattani A, Marcourt L, Hofstetter V, Queiroz EF, Leoni S, Allard PM, Gindro K, Stien D, Perron K, Wolfender JL. Combination of Pseudo-LC-NMR and HRMS/MS-Based Molecular Networking for the Rapid Identification of Antimicrobial Metabolites From Fusarium petroliphilum. Front Mol Biosci 2021; 8:725691. [PMID: 34746230 PMCID: PMC8569130 DOI: 10.3389/fmolb.2021.725691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/06/2021] [Indexed: 01/31/2023] Open
Abstract
An endophytic fungal strain isolated from a seagrass endemic to the Mediterranean Sea (Posidonia oceanica) was studied in order to identify its antimicrobial constituents and further characterize the composition of its metabolome. It was identified as Fusarium petroliphilum by in-depth phylogenetic analyses. The ethyl acetate extract of that strain exhibited antimicrobial activities and an ability to inhibit quorum sensing of Staphylococcus aureus. To perform this study with a few tens of mg of extract, an innovative one-step generic strategy was devised. On one side, the extract was analyzed by UHPLC-HRMS/MS molecular networking for dereplication. On the other side, semi-preparative HPLC using a similar gradient profile was used for a single-step high-resolution fractionation. All fractions were systematically profiled by 1H-NMR. The data were assembled into a 2D contour map, which we call “pseudo-LC-NMR,” and combined with those of UHPLC-HRMS/MS. This further highlighted the connection within structurally related compounds, facilitated data interpretation, and provided an unbiased quantitative profiling of the main extract constituents. This innovative strategy led to an unambiguous characterization of all major specialized metabolites of that extract and to the localization of its bioactive compounds. Altogether, this approach identified 22 compounds, 13 of them being new natural products and six being inhibitors of the quorum sensing mechanism of S. aureus and Pseudomonas aeruginosa. Minor analogues were also identified by annotation propagation through the corresponding HRMS/MS molecular network, which enabled a consistent annotation of 27 additional metabolites. This approach was designed to be generic and applicable to natural extracts of the same polarity range.
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Affiliation(s)
- Abdulelah Alfattani
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
| | - Laurence Marcourt
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
| | - Valérie Hofstetter
- Institute for Plant Production Sciences IPS, Agroscope, Nyon, Switzerland
| | - Emerson Ferreira Queiroz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
| | - Katia Gindro
- Institute for Plant Production Sciences IPS, Agroscope, Nyon, Switzerland
| | - Didier Stien
- Laboratoire de Biodiversité et Biotechnologie Microbienne, USR3579, CNRS, Sorbonne Université, Banyuls-sur-mer, France
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
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4
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Rapid Structure Determination of Bioactive 4″-Tetrahydrofurfuryl Macrozone Reaction Mixture Components by LC-SPE/Cryo NMR and MS. Molecules 2021; 26:molecules26206316. [PMID: 34684905 PMCID: PMC8537197 DOI: 10.3390/molecules26206316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
LC-SPE/cryo NMR and MS methodologies have been developed and employed for a rapid structure determination of 4″-tetrahydrofurfuryl macrozone reaction mixture components. Macrozones, novel conjugates of azithromycin, and thiosemicarbazones have shown very good in vitro antibacterial activities against susceptible and some resistant bacterial strains and are promising agents for further development. The post-column multiple trapping of the chromatographically separated reaction mixture components on the SPE cartridges increased the sensitivity and together with cryogenically cooled NMR probe made it possible to identify and structurally characterize main 4″-tetrahydrofurfuryl macrozone reaction mixture compounds including those present at very low concentration level. This approach has several advantages over a classical off-line procedure, efficiency and low solvent consumption being the two most important ones. All identified components were process-related. It has been demonstrated that two different kinds of compounds with respect to structure were identified, i.e., macrolide-related and thiosemicarbazone-related ones. This methodology can serve as a platform for reliable and effective macrolides reaction components structure profiling, serving as both isolation and identification tools.
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5
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LC–NMR for Natural Product Analysis: A Journey from an Academic Curiosity to a Robust Analytical Tool. SCI 2021. [DOI: 10.3390/sci3010006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Liquid chromatography (LC)–nuclear magnetic resonance (NMR) combines the advantage of the outstanding separation power of liquid chromatography (LC) and the superior structural elucidating capability of nuclear magnetic resonance (NMR). NMR has proved that it is a standout detector for LC by providing maximum structural information about plant originated extracts, particularly on the isolating ability of isomeric (same molecular formula) and/or isobaric (same molecular weight) compounds as compared to other detectors. The present review provides an overview of the developmental trends and application of LC–NMR in natural product analysis. The different LC–NMR operational modes are described, and how technical improvements assist in establishing this powerful technique as an important analytical tool in the analysis of complex plant-derived compounds is also highlighted. On-flow, stop-flow and loop-storage modes, as well as the new offline mode LC–solid phase extraction (SPE)–NMR and capillary LC (capLC)–NMR configurations which avoid the ingestion of expensive deuterated solvents throughout the experiment, are mentioned. Utilization of cryogenic probe and microprobe technologies, which are the other important promising approaches for guaranteeing sensitivity, are also described. Concluding remarks and future outlooks are also discussed.
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Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020; 19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.
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Affiliation(s)
- Sandrien Desmet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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7
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LC-NMR for Natural Products Analysis: A Journey from an Academic Curiosity to a Robust Analytical Tool. SCI 2019. [DOI: 10.3390/sci1010031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
LC–NMR combines the advantage of the outstanding separation power of liquid chromatography (LC) and the superior structural elucidating capability of nuclear magnetic resonance (NMR). NMR has proved that it is a standout detector for LC by providing maximum structural information about plant originated extracts particularly in its isolating ability of isomeric (same molecular formula) and/or isobaric (same molecular weight) compounds as compared to other detectors. The present review provides an overview of the LC–NMR developmental trends and its application in natural products analysis. The different LC–NMR operational modes are described, as well as how technical improvements assist in establishing this powerful technique as an important analytical tool in the analysis of complex plant-derived compounds. On-flow, stop-flow and loop-storage modes, as well as the new offline mode LC–SPE–NMR and capLC-NMR configurations that avoid the ingestion of expensive deuterated solvents throughout the experiment are mentioned. Utilization of cryogenic probe and microprobe technologies which are the other important promising approaches for guaranteeing the sensitivity issues are also described. Concluding remarks and future outlooks are also discussed.
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8
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Sashidhara KV, Rosaiah JN. Various Dereplication Strategies Using LC-MS for Rapid Natural Product Lead Identification and Drug Discovery. Nat Prod Commun 2019. [DOI: 10.1177/1934578x0700200218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Natural products are the most consistently successful source of drug leads. The rapid identification of known compounds from natural product extracts, or ‘dereplication’, is an important step in an efficiently run drug discovery program. Modern spectroscopic methods have largely revolutionized compound identification and tremendously accelerated the pace at which isolated compounds can be identified. Dereplication strategies use analytical techniques and database searching to determine the identity of an active compound at the earliest possible stage in the discovery process. This prevents wasted effort on samples with no potential for development and allows resources to be focused on the most promising lead. In the past few years, advances in technology have allowed the development of tandem analytical techniques, such as HPLC-PDA, LC-MS, LC-MS-MS, LC-NMR, and LC-NMR-MS. This review describes the principles and performance of a number of hyphenated techniques involving LC-MS that can be used for dereplication of natural products for rapid lead identification.
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Affiliation(s)
- Koneni V Sashidhara
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Chatter Manzil Palace, Lucknow-226001, India
| | - Jammikuntla N Rosaiah
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Chatter Manzil Palace, Lucknow-226001, India
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9
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Cao H, Luo Q, Wang H, Liu Z, Li G, Liu J. Structural characterization of peptides fromLocusta migratoria manilensis(Meyen, 1835) and anti-aging effect inCaenorhabditis elegans. RSC Adv 2019; 9:9289-9300. [PMID: 35517704 PMCID: PMC9061974 DOI: 10.1039/c9ra00089e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/07/2019] [Indexed: 12/02/2022] Open
Abstract
Locusts are a kind of agricultural pest rich in protein and widely eaten by people, yet, the nutritional and antioxidant activities of locust peptide have never been explored. In the current study, the locust peptides (LPs) were isolated from the Locusta migratoria manilensis (Meyen, 1835) and the anti-aging effects on Caenorhabditis elegans (C. elegans) were evaluated. The mean lifespan of C. elegans was significantly extended using LPs with a concentration of 1.0 mg mL−1. Out of the 23 peptides, LP-1, a pentapeptide with The-Phe-Lys-His-Gly sequence, with a concentration of 2.5 mg mL−1 significantly extended the lifespan of the worms by 23.5%. Additionally, LP-1 was observed to be a strong free radical-scavenger which can improve the survival of the C. elegans under oxidative stress, thermal stress and UV radiation. Furthermore, the LP-1 can up-regulate the expression of the transcription factor DAF-16 and jnk-1, suggesting that LP-1 may promote the C. elegans lifespan and stress resistance through a JNK-1-DAF-16 pathway. This study will be significant for the development of locusts and improvement of functional insect peptide production. Locusts are a kind of agricultural pest rich in protein and widely eaten by people, yet, the nutritional and antioxidant activities of locust peptide have never been explored.![]()
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Affiliation(s)
- Hui Cao
- The Research Center of Allergy & Immunology
- Shenzhen University School of Medicine
- Shenzhen
- PR China
| | - Qiang Luo
- The Research Center of Allergy & Immunology
- Shenzhen University School of Medicine
- Shenzhen
- PR China
| | - Huailing Wang
- The Research Center of Allergy & Immunology
- Shenzhen University School of Medicine
- Shenzhen
- PR China
- Department of Allergy
| | - Zhigang Liu
- The Research Center of Allergy & Immunology
- Shenzhen University School of Medicine
- Shenzhen
- PR China
- Department of Allergy
| | - Guoqiang Li
- College of Food Science and Engineering
- Foshan University
- Foshan 528000
- PR China
| | - Jie Liu
- The Research Center of Allergy & Immunology
- Shenzhen University School of Medicine
- Shenzhen
- PR China
- Department of Allergy
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Berlinck RGS, Monteiro AF, Bertonha AF, Bernardi DI, Gubiani JR, Slivinski J, Michaliski LF, Tonon LAC, Venancio VA, Freire VF. Approaches for the isolation and identification of hydrophilic, light-sensitive, volatile and minor natural products. Nat Prod Rep 2019; 36:981-1004. [DOI: 10.1039/c9np00009g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Water-soluble, volatile, minor and photosensitive natural products are yet poorly known, and this review discusses the literature reporting the isolation strategies for some of these metabolites.
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Affiliation(s)
| | - Afif F. Monteiro
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
| | - Ariane F. Bertonha
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
| | - Darlon I. Bernardi
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
| | - Juliana R. Gubiani
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
| | - Juliano Slivinski
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
| | | | | | - Victor A. Venancio
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
| | - Vitor F. Freire
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
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Wolfender JL, Nuzillard JM, van der Hooft JJJ, Renault JH, Bertrand S. Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics. Anal Chem 2018; 91:704-742. [DOI: 10.1021/acs.analchem.8b05112] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jean-Marc Nuzillard
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | | | - Jean-Hugues Renault
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, 44035 Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, 44035 Nantes, France
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12
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Novel Natural Products for Healthy Ageing from the Mediterranean Diet and Food Plants of Other Global Sources-The MediHealth Project. Molecules 2018; 23:molecules23051097. [PMID: 29734769 PMCID: PMC6099974 DOI: 10.3390/molecules23051097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/23/2018] [Accepted: 05/01/2018] [Indexed: 01/20/2023] Open
Abstract
There is a rapid increase in the percentage of elderly people in Europe. Consequently, the prevalence of age-related diseases will also significantly increase. Therefore, the main goal of MediHealth, an international research project, is to introduce a novel approach for the discovery of active agents of food plants from the Mediterranean diet and other global sources that promote healthy ageing. To achieve this goal, a series of plants from the Mediterranean diet and food plants from other origins are carefully selected and subjected to in silico, cell-based, in vivo (fly and mouse models), and metabolism analyses. Advanced analytical techniques complement the bio-evaluation process for the efficient isolation and identification of the bioactive plant constituents. Furthermore, pharmacological profiling of bioactive natural products, as well as the identification and synthesis of their metabolites, is carried out. Finally, optimization studies are performed in order to proceed to the development of innovative nutraceuticals, dietary supplements or herbal medicinal products. The project is based on an exchange of researchers between nine universities and four companies from European and non-European countries, exploiting the existing complementary multidisciplinary expertise. Herein, the unique and novel approach of this interdisciplinary project is presented.
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13
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Gomes NG, Pereira DM, Valentão P, Andrade PB. Hybrid MS/NMR methods on the prioritization of natural products: Applications in drug discovery. J Pharm Biomed Anal 2018; 147:234-249. [DOI: 10.1016/j.jpba.2017.07.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/17/2022]
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14
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Sumner LW, Lei Z, Nikolau BJ, Saito K. Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. Nat Prod Rep 2015; 32:212-29. [PMID: 25342293 DOI: 10.1039/c4np00072b] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plant metabolomics has matured and modern plant metabolomics has accelerated gene discoveries and the elucidation of a variety of plant natural product biosynthetic pathways. This review covers the approximate period of 2000 to 2014, and highlights specific examples of the discovery and characterization of novel genes and enzymes associated with the biosynthesis of natural products such as flavonoids, glucosinolates, terpenoids, and alkaloids. Additional examples of the integration of metabolomics with genome-based functional characterizations of plant natural products that are important to modern pharmaceutical technology are also reviewed. This article also provides a substantial review of recent technical advances in mass spectrometry imaging, nuclear magnetic resonance imaging, integrated LC-MS-SPE-NMR for metabolite identifications, and X-ray crystallography of microgram quantities for structural determinations. The review closes with a discussion on the future prospects of metabolomics related to crop species and herbal medicine.
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Affiliation(s)
- Lloyd W Sumner
- The Samuel Roberts Noble Foundation, Plant Biology Division, 2510 Sam Noble Parkway, Ardmore, OK, USA.
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15
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Yang X, Yang J, Xu C, Huang M, Zhou Q, Lv J, Ma X, Ke C, Ye Y, Shu G, Zhao P. Antidiabetic effects of flavonoids from Sophora flavescens EtOAc extract in type 2 diabetic KK-ay mice. JOURNAL OF ETHNOPHARMACOLOGY 2015; 171:161-70. [PMID: 26051831 DOI: 10.1016/j.jep.2015.05.043] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/22/2015] [Accepted: 05/27/2015] [Indexed: 05/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Bitter and cold Chinese medicines have been long used for the treatment for diabetes mellitus (DM) for thousands of years in China. The roots of Sophora flavescens Ait., one of bitter and cold Chinese medicines commonly used to remove lung heat have been used to counteract DM and exerted good clinical effects for diabetic patients in some folk hospitals in Fujian province, PR China. However, the corresponding active principles and antidiabetic mechanism of this Traditional Chinese Medicine remain unclear. Therefore, in this study, we aim at chemical profiling of the active principles, validating the potential antidiabetic effects of the active EtOAc extract (SF-EtOAc) in vitro and in vivo, and elucidating its probable antidiabetic mechanism as well as evaluating its acute oral toxicity. MATERIALS AND METHODS An off-line semi-preparative LC-NMR and LC-UV-ESI MS protocol was developed to determine the chemical principles of the active EtOAc extract rapidly and unambiguously. The effect of SF-EtOAc on the glucose transporter type 4 (GLUT4) translocation in L6 myotubes was examined. T2DM KK-Ay mice were induced by high-fat diet. SF-EtOAc was orally administration at the dose of 30, 60 and 120 mg/kg/d, for 21 days. Metformin was used as positive control. Body weight, plasma glucose, oral glucose tolerance test, serum insulin and blood-lipid indexes were measured. Phosphorylation of the AMP-activated protein kinase (AMPK) expression in liver was measured. RESULTS We found that SF-EtOAc significantly improved oral glucose tolerance, increased serum high density lipoprotein cholesterol (HDL-C) and reduced body weight, blood glucose levels and other related blood-lipid indexes. Mechanistically, SF-EtOAc elevated phosphorylation of AMP-activated protein kinase (AMPK) and stimulated membrane translocation of GLUT4. Moreover, it was unveiled that oral median lethal dose (LD50) of SF-EtOAc was more than 7500 mg/kg, suggesting that SF-EtOAc was practically non-toxic for mice. CONCLUSIONS SF-EtOAc improves glucose tolerance, reduces hyperglycemia and resumes insulin levels, at least in part, by activating GLUT4 translocation which may be modulated by AMPK pathway. According to the results of the present study, SF-EtOAc possesses a potent antidiabetic activity and could be used as a safe remedy for the treatment of diabetes.
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MESH Headings
- Animals
- Blood Glucose/analysis
- Cell Line
- Cholesterol/blood
- Cholesterol/metabolism
- Diabetes Mellitus, Experimental/blood
- Diabetes Mellitus, Experimental/drug therapy
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 2/blood
- Diabetes Mellitus, Type 2/drug therapy
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Diet, High-Fat
- Fatty Acids, Nonesterified/blood
- Fatty Acids, Nonesterified/metabolism
- Female
- Flavonoids/pharmacology
- Flavonoids/therapeutic use
- Flavonoids/toxicity
- Glucose/metabolism
- Glucose Tolerance Test
- Hypoglycemic Agents/pharmacology
- Hypoglycemic Agents/therapeutic use
- Hypoglycemic Agents/toxicity
- Insulin/blood
- Insulin/metabolism
- Liver/drug effects
- Liver/metabolism
- Liver/pathology
- Male
- Mice
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/metabolism
- Pancreas/drug effects
- Pancreas/pathology
- Phytotherapy
- Plant Roots
- Rats
- Sophora
- Triglycerides/blood
- Triglycerides/metabolism
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Affiliation(s)
- Xinzhou Yang
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201201, PR China
| | - Jing Yang
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China
| | - Chan Xu
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China
| | - Mi Huang
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China
| | - Qi Zhou
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China
| | - Jingnan Lv
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China
| | - Xinhua Ma
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China
| | - Changqiang Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201201, PR China
| | - Yang Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201201, PR China
| | - Guangwen Shu
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China.
| | - Ping Zhao
- College of Pharmacy, South-Central University for Nationalities, 182 Min-Zu Road, Wuhan 430074, PR China.
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16
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Gaudêncio SP, Pereira F. Dereplication: racing to speed up the natural products discovery process. Nat Prod Rep 2015; 32:779-810. [PMID: 25850681 DOI: 10.1039/c4np00134f] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 1993-2014 (July)To alleviate the dereplication holdup, which is a major bottleneck in natural products discovery, scientists have been conducting their research efforts to add tools to their "bag of tricks" aiming to achieve faster, more accurate and efficient ways to accelerate the pace of the drug discovery process. Consequently dereplication has become a hot topic presenting a huge publication boom since 2012, blending multidisciplinary fields in new ways that provide important conceptual and/or methodological advances, opening up pioneering research prospects in this field.
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Affiliation(s)
- Susana P Gaudêncio
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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17
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HPLC-based activity profiling of anti-hepatocellular carcinoma constituents from the Tibetan medicine, Caragana tibetica. ACTA ACUST UNITED AC 2015; 35:450-455. [PMID: 26072088 DOI: 10.1007/s11596-015-1452-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/13/2015] [Indexed: 12/22/2022]
Abstract
During the screening of a traditional Chinese folk herb library against HepG2 and Hep3B cell lines, the EtOAc extract from the Tibetan medicine, Caragana tibetica (CT-EtOAc) exhibited potential anti-hepatocellular carcinoma (anti-HCC) activity. HPLC-based activity profiling was performed for targeted identification of anti-HCC activity from CT-EtOAc by MS-directed purification method. CT-EtOAc was separated by time-based fractionation for further anti-HCC bioassay by a semipreparative HPLC column (150 mm × 10 mm i.d., 5 μm) with a single injection of 5 mg. Bioassay-guided and ESIMS-directed large scale purification was performed with a single injection of 400 mg of CT-EtOAc by peak-based fractionation. A 1.4-mm heavy wall micro NMR tube with z-gradient was used to measure one and two dimensional NMR spectra for the minor or trace amounts of components of the extract. Two active compounds could be elucidated as naringenin chalcone (CT-1) and 3-hydroxy-8, 9-dimethoxypterocarpan (CT-2) relevant to anti-HCC effects for the EtOAc extract of C. tibetica rapidly and unambiguously by this protocol.
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18
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Wu C, Kim HK, van Wezel GP, Choi YH. Metabolomics in the natural products field--a gateway to novel antibiotics. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 13:11-17. [PMID: 26190678 DOI: 10.1016/j.ddtec.2015.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/09/2015] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Abstract
Metabolomics is a high throughput analytical technique used to globally measure low molecular weight metabolites, allowing simultaneous metabolic comparison of different biological samples and thus highlighting differentially produced compounds as potential biomarkers. Although microbes are renowned as prolific sources of antibiotics, the traditional approach for new anti-infectives discovery is time-consuming and labor-intensive. In this review, the use of NMR- or MS-based metabolomics is proposed as an efficient approach to find antimicrobials in microbial single- or co-cultures.
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Affiliation(s)
- Changsheng Wu
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Hye Kyong Kim
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
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19
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Wolfender JL, Marti G, Thomas A, Bertrand S. Current approaches and challenges for the metabolite profiling of complex natural extracts. J Chromatogr A 2015; 1382:136-64. [DOI: 10.1016/j.chroma.2014.10.091] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 12/11/2022]
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20
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Mahrous EA, Farag MA. Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review. J Adv Res 2014; 6:3-15. [PMID: 25685540 PMCID: PMC4293671 DOI: 10.1016/j.jare.2014.10.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 01/06/2023] Open
Abstract
Today, most investigations of the plant metabolome tend to be based on either nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry (MS), with or without hyphenation with chromatography. Although less sensitive than MS, NMR provides a powerful complementary technique for the identification and quantification of metabolites in plant extracts. NMR spectroscopy, well appreciated by phytochemists as a particularly information-rich method, showed recent paradigm shift for the improving of metabolome(s) structural and functional characterization and for advancing the understanding of many biological processes. Furthermore, two dimensional NMR (2D NMR) experiments and the use of chemometric data analysis of NMR spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the development of NMR in the field of metabolomics with special focus on 2D NMR spectroscopic techniques and their applications in phytomedicines quality control analysis and drug discovery from natural sources, raising more attention at its potential to reduce the gap between the pace of natural products research and modern drug discovery demand.
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Affiliation(s)
- Engy A Mahrous
- Pharmacognosy Department, College of Pharmacy, Cairo University, Cairo, Kasr el Aini st. P.B. 11562, Egypt
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Cairo, Kasr el Aini st. P.B. 11562, Egypt
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21
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Wang L, Chen C. Emerging applications of metabolomics in studying chemopreventive phytochemicals. AAPS JOURNAL 2013; 15:941-50. [PMID: 23794098 DOI: 10.1208/s12248-013-9503-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/10/2013] [Indexed: 12/12/2022]
Abstract
Phytochemicals from diet and herbal medicines are under intensive investigation for their potential use as chemopreventive agents to block and suppress carcinogenesis. Chemical diversity of phytochemicals, together with complex metabolic interactions between phytochemicals and biological system, can overwhelm the capacity of traditional analytical platforms, and thus pose major challenges in studying chemopreventive phytochemicals. Recent progresses in metabolomics have transformed it to become a robust systems biology tool, suitable for examining both chemical and biochemical events that contribute to the cancer prevention activities of plant preparations or their bioactive components. This review aims to discuss the technical platform of metabolomics and its existing and potential applications in chemoprevention research, including identifying bioactive phytochemicals in plant extracts, monitoring phytochemical exposure in humans, elucidating biotransformation pathways of phytochemicals, and characterizing the effects of phytochemicals on endogenous metabolism and cancer metabolism.
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Affiliation(s)
- Lei Wang
- Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Avenue, 225 FScN, St. Paul, Minnesota, 55108, USA
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22
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Wolfender JL, Queiroz EF, Hostettmann K. The importance of hyphenated techniques in the discovery of new lead compounds from nature. Expert Opin Drug Discov 2013; 1:237-60. [PMID: 23495845 DOI: 10.1517/17460441.1.3.237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Nature represents an extraordinary reservoir of novel molecules and there is currently a resurgence of interest in natural products as a possible source of new lead compounds for introduction into therapeutical screening programmes. To discover new bioactive natural products, the dereplication of crude extracts performed prior to isolation work is of crucial importance for avoiding the tedious isolation of known constituents. In this respect, chemical screening strategies based on hyphenated techniques such as liquid chromatography-ultraviolet photodiode array detection, liquid chromatography-mass spectrometry, liquid chromatography tandom mass spectrometry and liquid chromatography-nuclear magnetic resonance (LC-NMR) are more and more extensively used. In the laboratory of Hostettmann's group, these analytical methods have been fully integrated into the isolation process and are used for the chemical screening of crude plant extracts, in complement with online or at-line bioassays, for rapid localisation and identification of new bioactive compounds. In this paper, possibilities and limitations of hyphenated techniques for de novo online natural product identification are discussed. As LC-NMR is playing a key role in this respect, the main part of the paper is dedicated to this technique. In particular, various ways of integrating NMR in the dereplication process are illustrated and strategies involving either direct or indirect hyphenation are presented.
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Affiliation(s)
- Jean-Luc Wolfender
- Laboratory of Pharmacognosy and Pytochemistry, School of Pharmaceutical Sciences, University of Geneva, Univerity of Lausanne, 30 quai Ernest-Ansermet, CH-1211, Geneva, Switzerland; †
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23
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Strategies in biomarker discovery. Peak annotation by MS and targeted LC-MS micro-fractionation for de novo structure identification by micro-NMR. Methods Mol Biol 2013; 1055:267-89. [PMID: 23963917 DOI: 10.1007/978-1-62703-577-4_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In metabolomic studies the identification of biomarkers is a key step but represents a serious bottleneck since the de novo identification of natural products is a lengthy process. A strategy for the dereplication and peak annotation of plant biomarkers is presented based on high resolution mass spectra acquired on a quadrupole-time-of-flight mass spectrometry coupled to ultra-high pressure liquid chromatography and chemotaxonomy information. A rational approach for the targeted LC-MS micro-isolation of biomarkers followed by de novo identification by NMR at the microgram scale is described, based on gradient transfer from the analytical scale and chromatographic modelling. The methodology is illustrated by the identification of various stress biomarkers of the plant wound response using Arabidopsis thaliana as a model.
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24
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Sturm S, Seger C. Liquid chromatography-nuclear magnetic resonance coupling as alternative to liquid chromatography-mass spectrometry hyphenations: curious option or powerful and complementary routine tool? J Chromatogr A 2012; 1259:50-61. [PMID: 22658656 DOI: 10.1016/j.chroma.2012.05.032] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 05/06/2012] [Accepted: 05/08/2012] [Indexed: 01/22/2023]
Abstract
Combining the most powerful separation techniques, i.e. liquid chromatography (LC) or capillary electrophoresis (CE) with a information rich detection system - the mass spectrometer or the nuclear magnetic resonance (NMR) spectrometer - has been pursued for more than three decades. This compilation shall provide an overview of the advantages and limitations of the LC-NMR hyphenation in the light of its most valued application-the unequivocal analyte identification. Especially the post LC trapping of analytes with an in-line solid phase extraction (SPE) device prior to transferring the analyte of interest to the NMR spectrometer (LC-SPE-NMR) proved to be a robust installation allowing a significant cut-down of the amount of analyte needed for the generation of high quality heteronuclear NMR shift correlation data. Different available technical realizations will be discussed and typical application examples from natural product research and from industrial settings will be given.
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Affiliation(s)
- Sonja Sturm
- Institute of Pharmacy/Pharmacognosy, CCB - Center of Chemistry and Biomedicine, Leopold Franzens University Innsbruck, Innsbruck, Austria
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25
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Crawford AD, Liekens S, Kamuhabwa AR, Maes J, Munck S, Busson R, Rozenski J, Esguerra CV, de Witte PAM. Zebrafish bioassay-guided natural product discovery: isolation of angiogenesis inhibitors from East African medicinal plants. PLoS One 2011; 6:e14694. [PMID: 21379387 PMCID: PMC3040759 DOI: 10.1371/journal.pone.0014694] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 09/12/2010] [Indexed: 01/10/2023] Open
Abstract
Natural products represent a significant reservoir of unexplored chemical diversity for early-stage drug discovery. The identification of lead compounds of natural origin would benefit from therapeutically relevant bioassays capable of facilitating the isolation of bioactive molecules from multi-constituent extracts. Towards this end, we developed an in vivo bioassay-guided isolation approach for natural product discovery that combines bioactivity screening in zebrafish embryos with rapid fractionation by analytical thin-layer chromatography (TLC) and initial structural elucidation by high-resolution electrospray mass spectrometry (HRESIMS). Bioactivity screening of East African medicinal plant extracts using fli-1:EGFP transgenic zebrafish embryos identified Oxygonum sinuatum and Plectranthus barbatus as inhibiting vascular development. Zebrafish bioassay-guided fractionation identified the active components of these plants as emodin, an inhibitor of the protein kinase CK2, and coleon A lactone, a rare abietane diterpenoid with no previously described bioactivity. Both emodin and coleon A lactone inhibited mammalian endothelial cell proliferation, migration, and tube formation in vitro, as well as angiogenesis in the chick chorioallantoic membrane (CAM) assay. These results suggest that the combination of zebrafish bioassays with analytical chromatography methods is an effective strategy for the rapid identification of bioactive natural products.
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Affiliation(s)
| | - Sandra Liekens
- Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Appolinary R. Kamuhabwa
- Department of Pharmacognosy, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Jan Maes
- Department of Pharmaceutical Sciences, University of Leuven, Leuven, Belgium
| | - Sebastian Munck
- Department of Human Genetics, Flanders Interuniversity Institute of Biotechnology, University of Leuven, Leuven, Belgium
| | - Roger Busson
- Department of Pharmaceutical Sciences, University of Leuven, Leuven, Belgium
- Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Jef Rozenski
- Department of Pharmaceutical Sciences, University of Leuven, Leuven, Belgium
- Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Camila V. Esguerra
- Department of Pharmaceutical Sciences, University of Leuven, Leuven, Belgium
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26
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Simultaneous Screening and Chemical Characterization of Bioactive Compounds Using LC-MS-Based Technologies (Affinity Chromatography). THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2011. [DOI: 10.1007/978-3-642-18384-3_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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27
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Wolfender JL, Glauser G, Boccard J, Rudaz S. MS-based Plant Metabolomic Approaches for Biomarker Discovery. Nat Prod Commun 2009. [DOI: 10.1177/1934578x0900401019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Metabolomics, which aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples, is playing an increasingly important role in plant science. Various biological issues have been successfully studied by this holistic approach that includes global metabolite composition assessment, mutant characterization, taxonomy, developmental processes, stress response, interaction with environment, quality control assessment and mode of action of herbal medicine. This review summarizes the main mass spectrometry methods used for performing these studies and discusses the potential, but also the current limitations of the various approaches. The intention is not to cover exhaustively the field, which has considerably grown over about one decade, but to give a brief insight into the methods commonly employed and discuss some applications that reveal the potential of metabolomics in phytochemistry and systems biology.
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Affiliation(s)
- Jean-Luc Wolfender
- Laboratory of Pharmacognosy and Phytochemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 30, quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Gaetan Glauser
- Laboratory of Pharmacognosy and Phytochemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 30, quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
- Laboratory of Pharmaceutical Analytical Chemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 20, Bd d'Yvoy, CH-1211 Geneva 4, Switzerland
| | - Julien Boccard
- Laboratory of Pharmaceutical Analytical Chemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 20, Bd d'Yvoy, CH-1211 Geneva 4, Switzerland
| | - Serge Rudaz
- Laboratory of Pharmaceutical Analytical Chemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 20, Bd d'Yvoy, CH-1211 Geneva 4, Switzerland
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28
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Giera M, Heus F, Janssen L, Kool J, Lingeman H, Irth H. Microfractionation Revisited: A 1536 Well High Resolution Screening Assay. Anal Chem 2009; 81:5460-6. [DOI: 10.1021/ac900622b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Giera
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Ferry Heus
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Laura Janssen
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jeroen Kool
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Henk Lingeman
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Hubertus Irth
- Biomolecular Analysis group, Department of Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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29
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Preciado A, Williams PG. A simple microscale method for determining the relative stereochemistry of statine units. J Org Chem 2008; 73:9228-34. [PMID: 18989929 PMCID: PMC2765571 DOI: 10.1021/jo8012429] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple method to determine the relative stereochemistry of statine amino acids (gamma-amino-beta-hydroxyacids) by using (1)H NMR spectroscopy is described. Configurational assignment of statine units within complex natural products is possible without degradation or derivatization as the syn and anti diastereomers can be distinguished by using a combination of chemical shift and coupling constant information derived from the alpha-methylene ABX system. Seventy-three examples are provided, demonstrating the scope and limitations of the methodology. These examples range in complexity from simple statine units to cyclic depsipeptides, such as tamandarin B.
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Affiliation(s)
- Alejandro Preciado
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822
| | - Philip G. Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822
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30
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Nuclear magnetic resonance and liquid chromatography-mass spectrometry combined with an incompleted separation strategy for identifying the natural products in crude extract. Anal Chim Acta 2008; 632:221-8. [PMID: 19110097 DOI: 10.1016/j.aca.2008.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 10/29/2008] [Accepted: 11/02/2008] [Indexed: 11/23/2022]
Abstract
NMR and LC-MS combined with an incompleted separation strategy were proposed to the simultaneous structure identification of natural products in crude extracts, and a novel method termed as NMR/LC-MS parallel dynamic spectroscopy (NMR/LC-MS PDS) was developed to discover the intrinsic correlation between retention time (Rt), mass/charge (m/z) and chemical shift (delta) data of the same constituent from mixture spectra by the co-analysis of parallelly visualized multispectroscopic datasets from LC-MS and (1)H NMR. The extracted ion chromatogram (XIC) and (1)H NMR signals deriving from the same individual constituent were correlated through fraction ranges and intensity changing profiles in NMR/LC-MS PDS spectrum due to the signal amplitude co-variation resulted from the concentration variation of constituents in a series of incompletely separated fractions. NMR/LC-MS PDS was applied to identify 12 constituents in an active herbal extract including flavonol glycosides, which was separated into a series of fractions by flash column chromatography. The complementary spectral information of the same individual constituent in the crude extract was discovered simultaneously from mixture spectra. Especially, two groups of co-eluted isomers were identified successfully. The results demonstrated that NMR/LC-MS PDS combined with the incompleted separation strategy achieved the similar function of on-line LC-NMR-MS analysis in off-line mode and had the potential for simplifying and accelerating the analytical routes for structure identification of constituents in herbs or their active extracts.
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31
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Graça G, Duarte IF, J Goodfellow B, Carreira IM, Couceiro AB, Domingues MDR, Spraul M, Tseng LH, Gil AM. Metabolite profiling of human amniotic fluid by hyphenated nuclear magnetic resonance spectroscopy. Anal Chem 2008; 80:6085-92. [PMID: 18564856 DOI: 10.1021/ac800907f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The metabolic profiling of human amniotic fluid (HAF) is of potential interest for the diagnosis of disorders in the mother or the fetus. In order to build a comprehensive metabolite database for HAF, hyphenated NMR has been used, for the first time, for systematic HAF profiling. Experiments were carried out using reverse-phase (RP) and ion-exchange liquid chromatography (LC), in order to detect less and more polar compounds, respectively. RP-LC conditions achieved good separation of amino acids, some sugars, and xanthines. Subsequent NMR and MS analysis enabled the rapid identification of 30 compounds, including 3-methyl-2-oxovalerate and 4-aminohippurate identified in HAF for the first time, to our knowledge. Under ion-exchange LC conditions, a different set of 30 compounds was detected, including sugars, organic acids, several derivatives of organic acids, and amino acids. In this experiment, five compounds were identified for the first time in HAF: D-xylitol, amino acid derivatives (N-acetylalanine, N-acetylglycine, 2-oxoleucine), and isovalerate. The nonendogenous nature of some metabolites (caffeine, paraxanthine, D-xylitol, sorbitol) is discussed. Hyphenated NMR has allowed the rapid detection of approximately 60 metabolites in HAF, some of which are not detectable by standard NMR due to low abundance (microM) and signal overlap thus enabling an extended metabolite database to be built for HAF.
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Affiliation(s)
- Gonçalo Graça
- CICECO-Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
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32
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Thiocone A, Farmer EE, Wolfender JL. Screening for wound-induced oxylipins in Arabidopsis thaliana by differential HPLC-APCI/MS profiling of crude leaf extracts and subsequent characterisation by capillary-scale NMR. PHYTOCHEMICAL ANALYSIS : PCA 2008; 19:198-205. [PMID: 18197596 DOI: 10.1002/pca.1051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A simple non-targeted differential HPLC-APCI/MS approach has been developed in order to survey metabolome modifications that occur in the leaves of Arabidopsis thaliana following wound-induced stress. The wound-induced accumulation of metabolites, particularly oxylipins, was evaluated by HPLC-MS analysis of crude leaf extracts. A generic, rapid and reproducible pressure liquid extraction procedure was developed for the analysis of restricted leaf samples without the need for specific sample preparation. The presence of various oxylipins was determined by head-to-head comparison of the HPLC-MS data, filtered with a component detection algorithm, and automatically compared with the aid of software searching for small differences in similar HPLC-MS profiles. Repeatability was verified in several specimens belonging to different series. Wound-inducible jasmonates were efficiently highlighted by this non-targeted approach without the need for complex sample preparation as is the case for the 'oxylipin signature' procedure based on GC-MS. Furthermore this HPLC-MS screening technique allowed the isolation of induced compounds for further characterisation by capillary-scale NMR (CapNMR) after HPLC scale-up. In this paper, the screening method is described and applied to illustrate its potential for monitoring polar and non-polar stress-induced constituents as well as its use in combination with CapNMR for the structural assignment of wound-induced compounds of interest.
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Affiliation(s)
- Aly Thiocone
- Laboratory of Pharmacognosy and Phytochemistry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 30, quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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Optimized liquid chromatography-mass spectrometry approach for the isolation of minor stress biomarkers in plant extracts and their identification by capillary nuclear magnetic resonance. J Chromatogr A 2007; 1180:90-8. [PMID: 18177881 DOI: 10.1016/j.chroma.2007.12.021] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 12/04/2007] [Accepted: 12/07/2007] [Indexed: 11/20/2022]
Abstract
A LC-MS approach is presented for the isolation of minor key plant biomarkers, in view of their characterization by NMR at the microgram scale. Due to the complexity of plant extracts, the purification of metabolites present in low concentrations is critical. The strategy used relies on the optimization of the chromatographic analysis using ultra-performance liquid chromatography-time-of-flight mass spectrometry (UPLC-TOF-MS), thanks to modelling software. The optimized method is then transferred to semi-preparative LC conditions with MS detection. The approach is illustrated by the isolation of wound-induced jasmonate derivatives revealed by a metabolomic study in Arabidopsis thaliana leaves and their subsequent characterization by capillary NMR (CapNMR).
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Harvey AL. Natural products as a screening resource. Curr Opin Chem Biol 2007; 11:480-4. [PMID: 17884696 DOI: 10.1016/j.cbpa.2007.08.012] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 08/02/2007] [Accepted: 08/07/2007] [Indexed: 11/30/2022]
Abstract
Natural products have been the most productive source of leads for new drugs, but they are currently out of fashion with the pharmaceutical industry. New approaches to sourcing novel compounds from untapped areas of biodiversity coupled with the technical advances in analytical techniques (such as microcoil NMR and linked LC-MS-NMR) have removed many of the difficulties in using natural products in screening campaigns. As the 'chemical space' occupied by natural products is both more varied and more drug-like than that of combinatorial chemical collections, synthetic and biosynthetic methods are being developed to produce screening libraries of natural product-like compounds. A renaissance of drug discovery inspired by natural products can be predicted.
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Affiliation(s)
- Alan L Harvey
- Strathclyde Institute for Drug Research, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, UK.
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Sumner LW, Huhman DV, Urbanczyk-Wochniak E, Lei Z. Methods, applications and concepts of metabolite profiling: secondary metabolism. EXS 2007; 97:195-212. [PMID: 17432269 DOI: 10.1007/978-3-7643-7439-6_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Plants manufacture a vast array of secondary metabolites/natural products for protection against biotic or abiotic environmental challenges. These compounds provide increased fitness due to their antimicrobial, anti-herbivory, and/or alleopathic activities. Secondary metabolites also serve fundamental roles as key signaling compounds in mutualistic interactions and plant development. Metabolic profiling and integrated functional genomics are advancing the understanding of these intriguing biosynthetic pathways and the response of these pathways to environmental challenges. This chapter provides an overview of the basic methods, select applications, and future directions of metabolic profiling of secondary metabolism. The emphasis of the application section includes the combination of primary and secondary metabolic profiling. The future directions section describes the need for increased chromatographic and mass resolution, as well as the inevitable need and benefit of spatially and temporally resolved metabolic profiling.
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Affiliation(s)
- Lloyd W Sumner
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
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Djukovic D, Liu S, Henry I, Tobias B, Raftery D. Signal enhancement in HPLC/microcoil NMR using automated column trapping. Anal Chem 2006; 78:7154-60. [PMID: 17037915 PMCID: PMC2577147 DOI: 10.1021/ac0605748] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A new HPLC NMR system is described that performs analytical separation, preconcentration, and NMR spectroscopy in rapid succession. The central component of our method is the online preconcentration sequence that improves the match between postcolumn analyte peak volume and microcoil NMR detection volume. Separated samples are collected on to a C18 guard column with a mobile phase composed of 90% D2O/10% acetonitrile-D3 and back-flushed to the NMR microcoil probe with 90% acetonitrile-D3/10% D2O. To assess the performance of our unit, we separated a standard mixture of 1 mM ibuprofen, naproxen, and phenylbutazone using a commercially available C18 analytical column. The S/N measurements from the NMR acquisitions indicated that we achieved signal enhancement factors up to 10.4 (+/-1.2)-fold. Furthermore, we observed that preconcentration factors increased as the injected amount of analyte decreased. The highest concentration enrichment of 14.7 (+/-2.2)-fold was attained injecting 100 microL of solution of 0.2 mM (approximately 4 microg) ibuprofen.
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Affiliation(s)
- Danijel Djukovic
- Department of Chemistry, Purdue University 560 Oval Drive, West Lafayette, IN 47907
| | - Shuhui Liu
- Department of Chemistry, Purdue University 560 Oval Drive, West Lafayette, IN 47907
| | - Ian Henry
- Department of Chemistry, Purdue University 560 Oval Drive, West Lafayette, IN 47907
| | | | - Daniel Raftery
- Department of Chemistry, Purdue University 560 Oval Drive, West Lafayette, IN 47907
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Betz M, Saxena K, Schwalbe H. Biomolecular NMR: a chaperone to drug discovery. Curr Opin Chem Biol 2006; 10:219-25. [PMID: 16679046 PMCID: PMC7185745 DOI: 10.1016/j.cbpa.2006.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 04/24/2006] [Indexed: 11/16/2022]
Abstract
Biomolecular NMR now contributes routinely to every step in the development of new chemical entities ahead of clinical trials. The versatility of NMR--from detection of ligand binding over a wide range of affinities and a wide range of drug targets with its wealth of molecular information, to metabolomic profiling, both ex vivo and in vivo--has paved the way for broadly distributed applications in academia and the pharmaceutical industry. Proteomics and initial target selection both benefit from NMR: screenings by NMR identify lead compounds capable of inhibiting protein-protein interactions, still one of the most difficult development tasks in drug discovery. NMR hardware improvements have given access to the microgram domain of phytochemistry, which should lead to the discovery of novel bioactive natural compounds. Steering medicinal chemists through the lead optimisation process by providing detailed information about protein-ligand interactions has led to impressive success in the development of novel drugs. The study of biofluid composition--metabonomics--provides information about pharmacokinetics and helps toxicological safety assessment in animal model systems. In vivo, magnetic resonance spectroscopy interrogates metabolite distributions in living cells and tissues with increasing precision, which significantly impacts the development of anticancer or neurological disorder therapeutics. An overview of different steps in recent drug discovery is presented to illuminate the links with the most recent advances in NMR methodology.
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