1
|
Zhang Z, Kato K, Tamaki H, Matsuki Y. Background signal suppression by opposite polarity subtraction for targeted DNP NMR spectroscopy on mixture samples. Phys Chem Chem Phys 2024; 26:9880-9890. [PMID: 38317640 DOI: 10.1039/d3cp06280e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
A novel method for background signal suppression is introduced to improve the selectivity of dynamic nuclear polarization (DNP) NMR spectroscopy in the study of target molecules within complex mixtures. The method uses subtraction between positively and negatively enhanced DNP spectra, leading to an improved contrast factor, which is the ratio between the target and background signal intensities. The proposed approach was experimentally validated using a reverse-micelle system that confines the target molecules together with the polarizing agent, OX063 trityl. A substantial increase in the contrast factor was observed, and the contrast factor was optimized through careful selection of the DNP build-up time. A simulation study based on the experimental results provides insights into a strategy for choosing the appropriate DNP build-up time and the corresponding selectivity of the method. Further analysis revealed a broad applicability of the technique, encompassing studies from large biomolecules to surface-modified polymers, depending on the nuclear spin diffusion rate with a range of gyromagnetic ratios.
Collapse
Affiliation(s)
- Zhongliang Zhang
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Ken Kato
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Hajime Tamaki
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Yoh Matsuki
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
- Center for Quantum Information and Quantum Biology, Osaka University, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
2
|
Devi G, Gorki V, Walter NS, Sivangula S, Sobhia ME, Jachak S, Puri R, Kaur S. Exploring the efficacy of ethnomedicinal plants of Himalayan region against the malaria parasite. JOURNAL OF ETHNOPHARMACOLOGY 2024; 321:117394. [PMID: 37967777 DOI: 10.1016/j.jep.2023.117394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Plasmodium falciparum multi-drug resistant (MDR) strains are a great challenge to global health care. This predicament implies the urgent need to discover novel antimalarial drugs candidate from alternative natural sources. The Himalaya constitute a rich repository of medicinal plants which have been used traditionally in the folklore medicine since ages and having no scientific evidence for their activity. Crambe kotschyana Boiss. and Eremurus himalaicus Baker are used for their antipyretic and hepatoprotective properties in Kinnaur district of Himachal Pradesh, India. AIM OF THE STUDY This study would investigate the antiplasmodial efficacy of C. kotschyana and E. himalaicus extracts, their fractions and active components using in vitro, in vivo and in silico approaches to provide a scientific insight into their activity. METHODS The methanol extracts of C. kotschyana (CKME) and E. himalaicus (EHME) were prepared by maceration followed by fractionation using ethyl acetate. The isolation of flavonoid glycosides isorhamnetin-3, 7-di-O-glucoside from C. kotschyana and luteolin-6-C-glucoside (isoorientin) from E. himalaicus was carried out by antiplasmodial activity-guided isolation. In vitro antimalarial activity was assessed by WHO method while in vitro cytotoxicity was ascertained employing the MTT assay. Molecular docking and molecular dynamics simulation were performed using the Glide module of Schrödinger Software and Gromacs-2022 software package respectively. In vivo curative activity was assessed by Ryley and Peters method. RESULTS The methanol extracts of both the plants illustrated the best antiplasmodial activity followed by the ethyl acetate fractions. Iso-orientin (IC50 6.49 μg/ml) and Isorhamnetin-3,7-di-O-glucoside (IC50 9.22 μg/ml) illustrated considerable in vitro activity even against P. falciparum resistant strain. Extracts/fractions as well as the isolated compounds were found to be non-toxic with CC50 > 640 μg/ml. Molecular docking studies were performed with these 2 O-glucosides against four malaria targets to understand the binding pose of these molecules and the results suggested that these molecules have selectivity for lactate dehydrogenase enzyme. CKME and EHME exhibited curative activity in vivo along with increase in Mean Survival Time of mice. CONCLUSION The research delineated the scientific evidence that both the therapeutic herbs possessed antimalarial activity and notably, bioactive compounds responsible to exhibit the antimalarial activity have been isolated, identified and characterized. Further studies are underway to assess the antiplasmodial efficacy of isolated compounds alone and in combination with standard antimalarials.
Collapse
Affiliation(s)
- Geeta Devi
- Ethnobotany and Medicinal Plant Laboratory, Department of Botany, Panjab University, Chandigarh, 160014, India.
| | - Varun Gorki
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India
| | - Neha Sylvia Walter
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India
| | - Srikanth Sivangula
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S Nagar, Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S Nagar, Punjab, India
| | - Sanjay Jachak
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India
| | - Richa Puri
- Ethnobotany and Medicinal Plant Laboratory, Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Sukhbir Kaur
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014, India.
| |
Collapse
|
3
|
Steinmann SN, Wang Q, Seh ZW. How machine learning can accelerate electrocatalysis discovery and optimization. MATERIALS HORIZONS 2023; 10:393-406. [PMID: 36541226 DOI: 10.1039/d2mh01279k] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Advances in machine learning (ML) provide the means to bypass bottlenecks in the discovery of new electrocatalysts using traditional approaches. In this review, we highlight the currently achieved work in ML-accelerated discovery and optimization of electrocatalysts via a tight collaboration between computational models and experiments. First, the applicability of available methods for constructing machine-learned potentials (MLPs), which provide accurate energies and forces for atomistic simulations, are discussed. Meanwhile, the current challenges for MLPs in the context of electrocatalysis are highlighted. Then, we review the recent progress in predicting catalytic activities using surrogate models, including microkinetic simulations and more global proxies thereof. Several typical applications of using ML to rationalize thermodynamic proxies and predict the adsorption and activation energies are also discussed. Next, recent developments of ML-assisted experiments for catalyst characterization, synthesis optimization and reaction condition optimization are illustrated. In particular, the applications in ML-enhanced spectra analysis and the use of ML to interpret experimental kinetic data are highlighted. Additionally, we also show how robotics are applied to high-throughput synthesis, characterization and testing of electrocatalysts to accelerate the materials exploration process and how this equipment can be assembled into self-driven laboratories.
Collapse
Affiliation(s)
| | - Qing Wang
- Univ Lyon, ENS de Lyon, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France.
| | - Zhi Wei Seh
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis, 138634, Singapore.
| |
Collapse
|
4
|
Ortiz Restrepo SA, Adams A. Fast quantification of water content in glycols by compact 1H NMR spectroscopy. Talanta 2023; 253:123973. [PMID: 36206628 DOI: 10.1016/j.talanta.2022.123973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 12/13/2022]
Abstract
Glycols are key chemicals for many applications in different fields of activities. Being highly hydroscopic, glycols contain usually water. The presence of water, even in tiny amounts, can affect their chemical and physical properties. Therefore, the accurate determination of water content is essential for any intended applications. In this context, a novel method using low-field Nuclear Magnetic Resonance (NMR) spectroscopy is introduced. The proposed approach offers a straightforward, fast, low-cost, and versatile solution for water quantification in glycols without the need for reagents or calibration data. It is demonstrated by quantifying the water concentration up to 11 wt% in aqueous ethylene glycol (EG) and triethylene glycol (TEG) mixtures with the help of lineshape analysis of the corresponding proton spectra. The limit of detection, achieved within 1 min of measuring time, was 0.05 wt% for water in EG and 0.15 wt% in TEG. The excellent agreement between the NMR results and those from the Karl-Fischer titration indicates that the proposed NMR-based approach has a great potential to be used as an alternative to the Karl-Fischer method. In addition, it is expected that the same methodology can be applied for water quantification in more complex glycolic solutions and other mixtures.
Collapse
Affiliation(s)
| | - Alina Adams
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University, Templergraben 55, Aachen, 52056, Germany.
| |
Collapse
|
5
|
Borges RM, Gouveia GJ, das Chagas FO. Advances in Microbial NMR Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:123-147. [PMID: 37843808 DOI: 10.1007/978-3-031-41741-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Confidently, nuclear magnetic resonance (NMR) is the most informative technique in analytical chemistry and its use as an analytical platform in metabolomics is well proven. This chapter aims to present NMR as a viable tool for microbial metabolomics discussing its fundamental aspects and applications in metabolomics using some chosen examples.
Collapse
Affiliation(s)
- Ricardo Moreira Borges
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gonçalo Jorge Gouveia
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Fernanda Oliveira das Chagas
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
6
|
Exploring Endophytes Using “Omics”: An Approach for Sustainable Production of Bioactive Metabolites. Fungal Biol 2021. [DOI: 10.1007/978-3-030-54422-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
7
|
Enhancing Compression Level for More Efficient Compressed Sensing and Other Lessons from NMR Spectroscopy. SENSORS 2020; 20:s20051325. [PMID: 32121309 PMCID: PMC7085760 DOI: 10.3390/s20051325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/15/2022]
Abstract
Modern nuclear magnetic resonance spectroscopy (NMR) is based on two- and higher-dimensional experiments that allow the solving of molecular structures, i.e., determine the relative positions of single atoms very precisely. However, rich chemical information comes at the price of long data acquisition times (up to several days). This problem can be alleviated by compressed sensing (CS)—a method that revolutionized many fields of technology. It is known that CS performs the most efficiently when measured objects feature a high level of compressibility, which in the case of NMR signal means that its frequency domain representation (spectrum) has a low number of significant points. However, many NMR spectroscopists are not aware of the fact that various well-known signal acquisition procedures enhance compressibility and thus should be used prior to CS reconstruction. In this study, we discuss such procedures and show to what extent they are complementary to CS approaches. We believe that the survey will be useful not only for NMR spectroscopists but also to inspire the broader signal processing community.
Collapse
|
8
|
Salem MA, Perez de Souza L, Serag A, Fernie AR, Farag MA, Ezzat SM, Alseekh S. Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis. Metabolites 2020; 10:E37. [PMID: 31952212 PMCID: PMC7023240 DOI: 10.3390/metabo10010037] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/25/2019] [Accepted: 01/11/2020] [Indexed: 12/22/2022] Open
Abstract
Plant-derived natural products have long been considered a valuable source of lead compounds for drug development. Natural extracts are usually composed of hundreds to thousands of metabolites, whereby the bioactivity of natural extracts can be represented by synergism between several metabolites. However, isolating every single compound from a natural extract is not always possible due to the complex chemistry and presence of most secondary metabolites at very low levels. Metabolomics has emerged in recent years as an indispensable tool for the analysis of thousands of metabolites from crude natural extracts, leading to a paradigm shift in natural products drug research. Analytical methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) are used to comprehensively annotate the constituents of plant natural products for screening, drug discovery as well as for quality control purposes such as those required for phytomedicine. In this review, the current advancements in plant sample preparation, sample measurements, and data analysis are presented alongside a few case studies of the successful applications of these processes in plant natural product drug discovery.
Collapse
Affiliation(s)
- Mohamed A. Salem
- Department of Pharmacognosy, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shibin Elkom, Menoufia 32511, Egypt
| | - Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (L.P.d.S.); (A.R.F.)
| | - Ahmed Serag
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo 11751, Egypt;
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (L.P.d.S.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv 4000, Bulgaria
| | - Mohamed A. Farag
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt; (M.A.F.); (S.M.E.)
- Chemistry Department, School of Sciences & Engineering, The American University in Cairo, New Cairo 11835, Egypt
| | - Shahira M. Ezzat
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt; (M.A.F.); (S.M.E.)
- Department of Pharmacognosy, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 11787, Egypt
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (L.P.d.S.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv 4000, Bulgaria
| |
Collapse
|
9
|
Taarning E, Sádaba I, Jensen PR, Meier S. Discovery and Exploration of the Efficient Acyclic Dehydration of Hexoses in Dimethyl Sulfoxide/Water. CHEMSUSCHEM 2019; 12:5086-5091. [PMID: 31651090 DOI: 10.1002/cssc.201902322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/25/2019] [Indexed: 06/10/2023]
Abstract
Current gaps in the development of sustainable processes include a lack of strategies to systematically identify and optimize the formation of new products. The dehydration of hexoses to 5-hydroxymethylfurfural (HMF) is a particularly widely studied process. In an attempt to identify a new high-selectivity conversion of glucose, quantitative NMR spectroscopy is used to screen conditions that have been reported to yield high conversions of glucose but low formation of HMF. In this manner, an olefinic six-carbon byproduct is identified. By adding water, selectivity for the compound was nearly tripled relative to previous reports. The detection of high-yielding side reactions in the formation of HMF is remarkable, considering how extensively HMF formation has been studied. High selectivity for the acyclic pathway allows hitherto unobserved intermediates in this pathway to be identified by using in situ NMR spectroscopy. An additional, presumably cyclic, pathway contributes to HMF formation.
Collapse
Affiliation(s)
- Esben Taarning
- Haldor Topsøe A/S, Haldor Topsøes Allé 1, 2800, KgsLyngby, Denmark
| | - Irantzu Sádaba
- Haldor Topsøe A/S, Haldor Topsøes Allé 1, 2800, KgsLyngby, Denmark
| | - Pernille Rose Jensen
- Department of Health Technology, Technical University of Denmark, Elektrovej 349, 2800, KgsLyngby, Denmark
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kemitorvet iBulding 207, 2800, KgsLyngby, Denmark
| |
Collapse
|
10
|
Elliot SG, Tosi I, Riisager A, Taarning E, Meier S. Response Factors Enable Rapid Quantitative 2D NMR Analysis in Catalytic Biomass Conversion to Renewable Chemicals. Top Catal 2019. [DOI: 10.1007/s11244-019-01131-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
11
|
Siciliano C, Bartella L, Mazzotti F, Aiello D, Napoli A, De Luca P, Temperini A. 1H NMR quantification of cannabidiol (CBD) in industrial products derived from Cannabis sativa L. (hemp) seeds. ACTA ACUST UNITED AC 2019. [DOI: 10.1088/1757-899x/572/1/012010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
12
|
Structural diversity of arthropod venom toxins. Toxicon 2018; 152:46-56. [DOI: 10.1016/j.toxicon.2018.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/29/2018] [Accepted: 07/19/2018] [Indexed: 11/19/2022]
|
13
|
1H HR-MAS NMR spectroscopy to study the metabolome of the protozoan parasite Giardia lamblia. Talanta 2018; 188:429-441. [PMID: 30029398 DOI: 10.1016/j.talanta.2018.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/29/2018] [Accepted: 06/01/2018] [Indexed: 12/30/2022]
Abstract
Knowledge of the metabolic profile and exchange processes in the protozoan parasite Giardia lamblia is of importance for a better understanding of the biochemical processes and for the development of drugs to control diseases caused by G. lamblia. In the current paper, 1H High Resolution Magic Angle Spinning (HR-MAS) NMR spectroscopy was directly applied to G. lamblia trophozoite suspensions to analyze the detectable small metabolites with a minimum of intervention. Thirty-one components were identified with main contributions from amino acids such as alanine and ornithine. The reproducibility, variability, and stability of the metabolites were investigated. Citrulline was found to be formed as an intermediate and citrulline levels depended on the stage of cell growth. Glucose-1-phosphate was found to be formed in relatively high amounts after cell harvesting if enzymes were not inactivated. In addition, the metabolic footprint of Giardia trophozoites, i.e. changes in the culture medium induced by G. lamblia, was investigated by liquid state NMR spectroscopy of culture media before and after inoculation. A quantitative comparison of the NMR spectra revealed component changes in the culture media during growth. The results suggested that not glucose but rather arginine serves as main energy supply. Biochemical functions of intracellular components and their metabolic exchange with the culture medium are discussed. The results provide an important basis for the design of HR-MAS NMR based metabolomic studies of G. lamblia in particular and any protozoan parasite samples in general.
Collapse
|
14
|
Blincoe WD, Rodriguez-Granillo A, Saurí J, Pierson NA, Joyce LA, Mangion I, Sheng H. Identification of ortho-Substituted Benzoic Acid/Ester Derivatives via the Gas-Phase Neighboring Group Participation Effect in (+)-ESI High Resolution Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:694-703. [PMID: 29488104 DOI: 10.1007/s13361-017-1884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 06/08/2023]
Abstract
Benzoic acid/ester/amide derivatives are common moieties in pharmaceutical compounds and present a challenge in positional isomer identification by traditional tandem mass spectrometric analysis. A method is presented for exploiting the gas-phase neighboring group participation (NGP) effect to differentiate ortho-substituted benzoic acid/ester derivatives with high resolution mass spectrometry (HRMS1). Significant water/alcohol loss (>30% abundance in MS1 spectra) was observed for ortho-substituted nucleophilic groups; these fragment peaks are not observable for the corresponding para and meta-substituted analogs. Experiments were also extended to the analysis of two intermediates in the synthesis of suvorexant (Belsomra) with additional analysis conducted with nuclear magnetic resonance (NMR), density functional theory (DFT), and ion mobility spectrometry-mass spectrometry (IMS-MS) studies. Significant water/alcohol loss was also observed for 1-substituted 1, 2, 3-triazoles but not for the isomeric 2-substituted 1, 2, 3-triazole analogs. IMS-MS, NMR, and DFT studies were conducted to show that the preferred orientation of the 2-substituted triazole rotamer was away from the electrophilic center of the reaction, whereas the 1-subtituted triazole was oriented in close proximity to the center. Abundance of NGP product was determined to be a product of three factors: (1) proton affinity of the nucleophilic group; (2) steric impact of the nucleophile; and (3) proximity of the nucleophile to carboxylic acid/ester functional groups. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- William D Blincoe
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA
| | | | - Josep Saurí
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA
| | - Nicholas A Pierson
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA
| | - Leo A Joyce
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA
| | - Ian Mangion
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA
| | - Huaming Sheng
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA.
| |
Collapse
|
15
|
Aspergillus flavus Secondary Metabolites: More than Just Aflatoxins. Food Saf (Tokyo) 2018; 6:7-32. [PMID: 32231944 DOI: 10.14252/foodsafetyfscj.2017024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/09/2018] [Indexed: 11/21/2022] Open
Abstract
Aspergillus flavus is best known for producing the family of potent carcinogenic secondary metabolites known as aflatoxins. However, this opportunistic plant and animal pathogen also produces numerous other secondary metabolites, many of which have also been shown to be toxic. While about forty of these secondary metabolites have been identified from A. flavus cultures, analysis of the genome has predicted the existence of at least 56 secondary metabolite gene clusters. Many of these gene clusters are not expressed during growth of the fungus on standard laboratory media. This presents researchers with a major challenge of devising novel strategies to manipulate the fungus and its genome so as to activate secondary metabolite gene expression and allow identification of associated cluster metabolites. In this review, we discuss the genetic, biochemical and bioinformatic methods that are being used to identify previously uncharacterized secondary metabolite gene clusters and their associated metabolites. It is important to identify as many of these compounds as possible to determine their bioactivity with respect to fungal development, survival, virulence and especially with respect to any potential synergistic toxic effects with aflatoxin.
Collapse
|
16
|
Liu Z, Kariya MJ, Chute CD, Pribadi AK, Leinwand SG, Tong A, Curran KP, Bose N, Schroeder FC, Srinivasan J, Chalasani SH. Predator-secreted sulfolipids induce defensive responses in C. elegans. Nat Commun 2018; 9:1128. [PMID: 29555902 PMCID: PMC5859177 DOI: 10.1038/s41467-018-03333-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 02/02/2018] [Indexed: 01/03/2023] Open
Abstract
Animals respond to predators by altering their behavior and physiological states, but the underlying signaling mechanisms are poorly understood. Using the interactions between Caenorhabditis elegans and its predator, Pristionchus pacificus, we show that neuronal perception by C. elegans of a predator-specific molecular signature induces instantaneous escape behavior and a prolonged reduction in oviposition. Chemical analysis revealed this predator-specific signature to consist of a class of sulfolipids, produced by a biochemical pathway required for developing predacious behavior and specifically induced by starvation. These sulfolipids are detected by four pairs of C. elegans amphid sensory neurons that act redundantly and recruit cyclic nucleotide-gated (CNG) or transient receptor potential (TRP) channels to drive both escape and reduced oviposition. Functional homology of the delineated signaling pathways and abolishment of predator-evoked C. elegans responses by the anti-anxiety drug sertraline suggests a likely conserved or convergent strategy for managing predator threats.
Collapse
Affiliation(s)
- Zheng Liu
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Maro J Kariya
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher D Chute
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01605, USA
| | - Amy K Pribadi
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sarah G Leinwand
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Ada Tong
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Kevin P Curran
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Neelanjan Bose
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jagan Srinivasan
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01605, USA
| | - Sreekanth H Chalasani
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
17
|
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]
|
18
|
Tiwari R, Ahire D, Kumar H, Sinha S, Chauthe SK, Subramanian M, Iyer R, Sarabu R, Bajpai L. Use of Hybrid Capillary Tube Apparatus on 400 MHz NMR for Quantitation of Crucial Low-Quantity Metabolites Using aSICCO Signal. Drug Metab Dispos 2017; 45:1215-1224. [PMID: 28935657 DOI: 10.1124/dmd.117.077073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/13/2017] [Indexed: 11/22/2022] Open
Abstract
Metabolites of new chemical entities can influence safety and efficacy of a molecule and often times need to be quantified in preclinical studies. However, synthetic standards of metabolites are very rarely available in early discovery. Alternate approaches such as biosynthesis need to be explored to generate these metabolites. Assessing the quantity and purity of these small amounts of metabolites with a nondestructive analytical procedure becomes crucial. Quantitative NMR becomes the method of choice for these samples. Recent advances in high-field NMR (>500 MHz) with the use of cryoprobe technology have helped to improve sensitivity for analysis of small microgram quantity of such samples. However, this type of NMR instrumentation is not routinely available in all laboratories. To analyze microgram quantities of metabolites on a routine basis with lower-resolution 400 MHz NMR instrument fitted with a broad band fluorine observe room temperature probe, a novel hybrid capillary tube setup was developed. To quantitate the metabolite in the sample, an artificial signal insertion for calculation of concentration observed (aSICCO) method that introduces an internally calibrated mathematical signal was used after acquiring the NMR spectrum. The linearity of aSICCO signal was established using ibuprofen as a model analyte. The limit of quantification of this procedure was 0.8 mM with 10 K scans that could be improved further with the increase in the number of scans. This procedure was used to quantify three metabolites-phenytoin from fosphenytoin, dextrophan from dextromethorphan, and 4-OH-diclofenac from diclofenac-and is suitable for minibiosynthesis of metabolites from in vitro systems.
Collapse
Affiliation(s)
- Ranjeet Tiwari
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Deepak Ahire
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Hemantha Kumar
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Sarmistha Sinha
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Siddheshwar Kisan Chauthe
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Murali Subramanian
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Ramaswamy Iyer
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Ramakanth Sarabu
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| | - Lakshmikant Bajpai
- Discovery Analytical Sciences (R.T., H.K., S.K.C., R.S., L.B.) and Pharmaceutical Candidate Optimization (D.A., S.S., M.S.), Bristol-Myers Squibb-Biocon Research Center, Bangalore, India; and Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey (R.I.)
| |
Collapse
|
19
|
Sreng L, Temime-Roussel B, Wortham H, Mourre C. Chemical Identification of "Maternal Signature Odors" in Rat. Chem Senses 2017; 42:211-222. [PMID: 28007788 DOI: 10.1093/chemse/bjw124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Newborn altricial mammals need just after birth to locate their mother's nipples for suckling. In this precocious behavior, including for the human baby, maternal odor via the olfactory process plays a major role. Maternal odor emitted by lactating females or by amniotic fluid (AF) attracts pups, but the chemical identity of this attractant has not yet been elucidated. Here, using behavioral tests and gas chromatography coupled with mass spectrometry (GC-MS) techniques, we show that AF extracts from rat pregnant female, nipples, ventral skin, milk, and nest extracts of mother contained 3-6 active substances. AF extracts contained 3 active compounds: ethylbenzene, benzaldehyde, and benzyl alcohol, and their mixture in similar proportions to those found in AF extracts, in a ratio, respectively, of 1:1:12 (700 ng), attracts pups as putative maternal attractant substances (MAS). These 3 AF substances have already been identified in milk, nipples, ventral wash, and nest extracts of mother, but not in feces. Moreover, anethole flavor incorporated in pregnant rat and mother's diet is also detected in AF, nipples, milk, and nest extracts and the pups are attracted to anethole odor, but not in the case of the no-anethole pups. MAS, combined with diet flavors present in the AF bath, represent olfactory signals as "maternal signature odors" (MSO) that are learned by fetus and pups. These findings open the way to improved understanding of the neurobiology of early olfactory learning and of the importance of evolutionarily conserved survival behavior in many mammal species.
Collapse
Affiliation(s)
- Leam Sreng
- Aix-Marseille Univ, CNRS, IMBE UMR 7263 (Institut Méditerranéen de la Biodiversité et d'Ecologie marine et continentale), IRD, Avignon Université, Faculté Saint Charles, 3, place Victor Hugo, Case 36 F-13331 Marseille cedex 03, France
| | - Brice Temime-Roussel
- Aix-Marseille Univ, CNRS, LCE, Laboratoire de Chimie et Environnement, UMR 7376, Case 29, Faculté Saint Charles, 3, place Victor Hugo, F-13331 Marseille cedex 03, France and
| | - Henri Wortham
- Aix-Marseille Univ, CNRS, LCE, Laboratoire de Chimie et Environnement, UMR 7376, Case 29, Faculté Saint Charles, 3, place Victor Hugo, F-13331 Marseille cedex 03, France and
| | - Christiane Mourre
- Aix-Marseille Univ, CNRS, Laboratoire de Neurosciences Cognitives, UMR 7291, Faculté Saint Charles, 3, place Victor Hugo, Case 36, F-13331 Marseille cedex 03, France
| |
Collapse
|
20
|
|
21
|
Dass R, Grudzia Ż K, Ishikawa T, Nowakowski M, Dȩbowska R, Kazimierczuk K. Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures. Front Microbiol 2017; 8:1306. [PMID: 28769889 PMCID: PMC5509914 DOI: 10.3389/fmicb.2017.01306] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/28/2017] [Indexed: 01/28/2023] Open
Abstract
The biological toolbox is full of techniques developed originally for analytical chemistry. Among them, spectroscopic experiments are very important source of atomic-level structural information. Nuclear magnetic resonance (NMR) spectroscopy, although very advanced in chemical and biophysical applications, has been used in microbiology only in a limited manner. So far, mostly one-dimensional 1H experiments have been reported in studies of bacterial metabolism monitored in situ. However, low spectral resolution and limited information on molecular topology limits the usability of these methods. These problems are particularly evident in the case of complex mixtures, where spectral peaks originating from many compounds overlap and make the interpretation of changes in a spectrum difficult or even impossible. Often a suite of two-dimensional (2D) NMR experiments is used to improve resolution and extract structural information from internuclear correlations. However, for dynamically changing sample, like bacterial culture, the time-consuming sampling of so-called indirect time dimensions in 2D experiments is inefficient. Here, we propose the technique known from analytical chemistry and structural biology of proteins, i.e., time-resolved non-uniform sampling. The method allows application of 2D (and multi-D) experiments in the case of quickly varying samples. The indirect dimension here is sparsely sampled resulting in significant reduction of experimental time. Compared to conventional approach based on a series of 1D measurements, this method provides extraordinary resolution and is a real-time approach to process monitoring. In this study, we demonstrate the usability of the method on a sample of Escherichia coli culture affected by ampicillin and on a sample of Propionibacterium acnes, an acne causing bacterium, mixed with a dose of face tonic, which is a complicated, multi-component mixture providing complex NMR spectrum. Through our experiments we determine the exact concentration and time at which the anti-bacterial agents affect the bacterial metabolism. We show, that it is worth to extend the NMR toolbox for microbiology by including techniques of 2D z-TOCSY, for total "fingerprinting" of a sample and 2D 13C-edited HSQC to monitor changes in concentration of metabolites in selected metabolic pathways.
Collapse
Affiliation(s)
- Rupashree Dass
- Centre of New Technologies, University of WarsawWarsaw, Poland
| | - Katarzyna Grudzia Ż
- Faculty of Chemistry, Biological and Chemical Research Centre, University of WarsawWarsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Faculty of Biology, Institute of Biochemistry, University of WarsawWarsaw, Poland
| | | | - Renata Dȩbowska
- Dr Irena Eris Cosmetic Laboratories, Centre for Science and ResearchWarsaw, Poland
| | | |
Collapse
|
22
|
Pantoja CF, Bolaños JA, Bernal A, Wist J. Mutual Diffusion Driven NMR: a new approach for the analysis of mixtures by spatially resolved NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:519-524. [PMID: 27930830 DOI: 10.1002/mrc.4561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
We introduce a new approach for resolving the NMR spectra of mixtures that relies on the mutual diffusion of dissolved species when a concentration gradient is established within the NMR tube. This is achieved by cooling down a biphasic mixture of triethylamine and deuterated water below its mixing temperature, where a single phase is expected. Until equilibrium is reached, a gradient of concentration, from 'pure' triethylamine to 'pure' water, establishes within the tube. The amount of time required to reach this equilibrium is controlled by the mutual diffusion coefficient of both species. Moreover, a gradient of concentration exists for each additional compound dissolved in this system, related to the partition coefficient for that compound in the original biphasic state. Using slice selective experiments, it was possible to measure these concentration gradients and use them to separate signals from all the present species. We show the results acquired for a mixture composed of n-octanol, methanol, acetonitrile and benzene and compare them with those obtained by pulse field gradient NMR. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Christian F Pantoja
- Chemistry Department, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Jose A Bolaños
- Chemistry Department, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Andrés Bernal
- Chemistry Department, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| | - Julien Wist
- Chemistry Department, Universidad del Valle, Calle 13 # 100-00, Cali, Colombia
| |
Collapse
|
23
|
Cleary JL, Condren AR, Zink KE, Sanchez LM. Calling all hosts: Bacterial communication in situ. Chem 2017; 2:334-358. [PMID: 28948238 DOI: 10.1016/j.chempr.2017.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteria are cosmopolitan organisms that in recent years have demonstrated many roles in maintaining host equilibrium. In this review, we discuss three roles bacteria can occupy in a host: pathogenic, symbiotic, and transient, with a specific focus on how bacterial small molecules contribute to homeostasis or dysbiosis. First, we will dissect how small molecules produced by pathogenic bacteria can be used as a source for communication during colonization and as protection against host immune responses. The ability to achieve a higher level of organization through small molecule communication gives pathogenic bacteria an opportunity for increased virulence and fitness. Conversely, in symbiotic relationships with hosts, small molecules are used in the initial acquisition, colonization, and maintenance of this beneficial population. Chemical signals can come from both the host and symbiont, and it is often observed that these interKingdom symbioses result in coevolution of both species involved. Furthermore, the transition from transient to commensal or opportunistic likely relies on molecular mechanisms. The small molecules utilized and produced by transient bacteria are desirable for both the immune and nutritional benefits they provide to the host. Finally, the advantages and disadvantages of modern analytical techniques that are available to researchers in order to study small molecules in situ is an important aspect of this review. It is our opinion that small molecules produced by bacteria are central to many biological processes and a larger focus on uncovering the function and identity of these small molecules is required to gain a deeper understanding of host-microbe associations.
Collapse
Affiliation(s)
- Jessica L Cleary
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Alanna R Condren
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Katherine E Zink
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Laura M Sanchez
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| |
Collapse
|
24
|
Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
25
|
Covington BC, McLean JA, Bachmann BO. Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites. Nat Prod Rep 2017; 34:6-24. [PMID: 27604382 PMCID: PMC5214543 DOI: 10.1039/c6np00048g] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.
Collapse
Affiliation(s)
- Brett C Covington
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
| | - John A McLean
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA. and Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
| |
Collapse
|
26
|
Batista Silva W, Daloso DM, Fernie AR, Nunes-Nesi A, Araújo WL. Can stable isotope mass spectrometry replace radiolabelled approaches in metabolic studies? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 249:59-69. [PMID: 27297990 DOI: 10.1016/j.plantsci.2016.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 04/21/2016] [Accepted: 05/13/2016] [Indexed: 05/03/2023]
Abstract
Metabolic pathways and the key regulatory points thereof can be deduced using isotopically labelled substrates. One prerequisite is the accurate measurement of the labeling pattern of targeted metabolites. The subsequent estimation of metabolic fluxes following incubation in radiolabelled substrates has been extensively used. Radiolabelling is a sensitive approach and allows determination of total label uptake since the total radiolabel content is easy to detect. However, the incubation of cells, tissues or the whole plant in a stable isotope enriched environment and the use of either mass spectrometry or nuclear magnetic resonance techniques to determine label incorporation within specific metabolites offers the possibility to readily obtain metabolic information with higher resolution. It additionally also offers an important complement to other post-genomic strategies such as metabolite profiling providing insights into the regulation of the metabolic network and thus allowing a more thorough description of plant cellular function. Thus, although safety concerns mean that stable isotope feeding is generally preferred, the techniques are in truth highly complementary and application of both approaches in tandem currently probably provides the best route towards a comprehensive understanding of plant cellular metabolism.
Collapse
Affiliation(s)
- Willian Batista Silva
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
| | - Danilo M Daloso
- Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1, 14476,Golm Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1, 14476,Golm Potsdam, Germany.
| | - Adriano Nunes-Nesi
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
| | - Wagner L Araújo
- Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa-MG, Brazil.
| |
Collapse
|
27
|
Bell NGA, Graham MC, Uhrín D. Isotope-filtered nD NMR spectroscopy of complex mixtures to unravel the molecular structures of phenolic compounds in tagged soil organic matter. Analyst 2016; 141:4614-24. [PMID: 27277943 DOI: 10.1039/c6an00999a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Unravelling structures of molecules contained in complex, chromatographically inseparable mixtures is a challenging task. Due to the number of overlapping resonances in NMR spectra of these mixtures, unambiguous chemical shift correlations attributable to individual molecules cannot be achieved and thus their structure determination is elusive by this technique. Placing a tag carrying an NMR active nucleus onto a subset of molecules enables (i) to eliminate signals from the non-tagged molecules, and (ii) to obtain a set of correlated chemical shifts and coupling constants belonging to a single molecular type. This approach provides an opportunity for structure determination without the need for compound separation. Focusing on the most abundant functional groups of natural organic matter molecules, the carboxyl and hydroxyl groups were converted into esters and ethers, respectively by introducing (13)CH3O groups. A set of (13)C-filtered nD NMR experiments was designed yielding structures/structural motives of tagged molecules. The relative sensitivity of these experiments was compared and a step-by-step guide how to use these experiments to analyse the structures of methylated phenolics is provided. The methods are illustrated using an operational fraction of soil organic matter, fulvic acid isolated from a Scottish peat bog. Analysis of 33 structures identified in this sample revealed a correlation between the position of the methoxy cross-peaks in the (1)H, (13)C HSQC spectra and the compound type. This information enables profiling of phenolic compounds in natural organic matter without the need to acquire a full set of experiments described here or access to high field cryoprobe NMR spectrometers.
Collapse
Affiliation(s)
- N G A Bell
- EastCHEM School of Chemistry, University of Edinburgh, King's Buildings, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | | | | |
Collapse
|
28
|
Baccile JA, Spraker JE, Le HH, Brandenburger E, Gomez C, Bok JW, Macheleidt J, Brakhage AA, Hoffmeister D, Keller NP, Schroeder FC. Plant-like biosynthesis of isoquinoline alkaloids in Aspergillus fumigatus. Nat Chem Biol 2016; 12:419-24. [PMID: 27065235 PMCID: PMC5049701 DOI: 10.1038/nchembio.2061] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/22/2016] [Indexed: 01/09/2023]
Abstract
Natural product discovery efforts have focused primarily on microbial biosynthetic gene clusters (BGCs) containing large multi-modular PKSs and NRPSs; however, sequencing of fungal genomes has revealed a vast number of BGCs containing smaller NRPS-like genes of unknown biosynthetic function. Using comparative metabolomics, we show that a BGC in the human pathogen Aspergillus fumigatus named fsq, which contains an NRPS-like gene lacking a condensation domain, produces several novel isoquinoline alkaloids, the fumisoquins. These compounds derive from carbon-carbon bond formation between two amino acid-derived moieties followed by a sequence that is directly analogous to isoquinoline alkaloid biosynthesis in plants. Fumisoquin biosynthesis requires the N-methyltransferase FsqC and the FAD-dependent oxidase FsqB, which represent functional analogs of coclaurine N-methyltransferase and berberine bridge enzyme in plants. Our results show that BGCs containing incomplete NRPS modules may reveal new biosynthetic paradigms and suggest that plant-like isoquinoline biosynthesis occurs in diverse fungi.
Collapse
Affiliation(s)
- Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Joseph E Spraker
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Eileen Brandenburger
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Christian Gomez
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Jin Woo Bok
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - Juliane Macheleidt
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany.,Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Axel A Brakhage
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany.,Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| |
Collapse
|
29
|
MALDI-TOF mass spectrometry and reversed-phase HPLC-ELSD chromatography for structural and quantitative studies of major steroid saponins in commercial extracts of Yucca schidigera Roezl. J Pharm Biomed Anal 2016; 120:270-82. [DOI: 10.1016/j.jpba.2015.12.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 11/23/2022]
|
30
|
Abstract
Chemical ecology elucidates the nature and role of natural products as mediators of organismal interactions. The emerging techniques that can be summarized under the concept of metabolomics provide new opportunities to study such environmentally relevant signaling molecules. Especially comparative tools in metabolomics enable the identification of compounds that are regulated during interaction situations and that might play a role as e.g. pheromones, allelochemicals or in induced and activated defenses. This approach helps overcoming limitations of traditional bioassay-guided structure elucidation approaches. But the power of metabolomics is not limited to the comparison of metabolic profiles of interacting partners. Especially the link to other -omics techniques helps to unravel not only the compounds in question but the entire biosynthetic and genetic re-wiring, required for an ecological response. This review comprehensively highlights successful applications of metabolomics in chemical ecology and discusses existing limitations of these novel techniques. It focuses on recent developments in comparative metabolomics and discusses the use of metabolomics in the systems biology of organismal interactions. It also outlines the potential of large metabolomics initiatives for model organisms in the field of chemical ecology.
Collapse
Affiliation(s)
- Constanze Kuhlisch
- Friedrich Schiller University, Institute of Inorganic and Analytical Chemistry, Lessingstr. 8, D-07743 Jena, Germany.
| | | |
Collapse
|
31
|
Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes. Proc Natl Acad Sci U S A 2015; 112:12175-80. [PMID: 26324907 DOI: 10.1073/pnas.1500873112] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed "genome mining" as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N(5)-hydroxyarginine; valinophos, an N-acetyl l-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products.
Collapse
|
32
|
Schimming O, Challinor VL, Tobias NJ, Adihou H, Grün P, Pöschel L, Richter C, Schwalbe H, Bode HB. Structure, Biosynthesis, and Occurrence of Bacterial Pyrrolizidine Alkaloids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504877] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
33
|
Schimming O, Challinor VL, Tobias NJ, Adihou H, Grün P, Pöschel L, Richter C, Schwalbe H, Bode HB. Structure, Biosynthesis, and Occurrence of Bacterial Pyrrolizidine Alkaloids. Angew Chem Int Ed Engl 2015; 54:12702-5. [PMID: 26465655 DOI: 10.1002/anie.201504877] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Indexed: 12/24/2022]
Abstract
Pyrrolizidine alkaloids (PAs) are widespread plant natural products with potent toxicity and bioactivity. Herein, the identification of bacterial PAs from entomopathogenic bacteria using differential analysis by 2D NMR spectroscopy (DANS) and mass spectrometry is described. Their biosynthesis was elucidated to involve a non-ribosomal peptide synthetase. The occurrence of these biosynthesis gene clusters in Gram-negative and Gram-positive bacteria indicates an important biological function in bacteria.
Collapse
Affiliation(s)
- Olivia Schimming
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Victoria L Challinor
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Nicholas J Tobias
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Hélène Adihou
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Peter Grün
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Laura Pöschel
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Christian Richter
- Institut für Organische und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Harald Schwalbe
- Institut für Organische und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101. .,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany).
| |
Collapse
|
34
|
Yew JY, Chung H. Insect pheromones: An overview of function, form, and discovery. Prog Lipid Res 2015; 59:88-105. [DOI: 10.1016/j.plipres.2015.06.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 05/01/2015] [Accepted: 06/12/2015] [Indexed: 12/17/2022]
|
35
|
Yim JJ, Bose N, Meyer JM, Sommer RJ, Schroeder FC. Nematode signaling molecules derived from multimodular assembly of primary metabolic building blocks. Org Lett 2015; 17:1648-51. [PMID: 25782998 PMCID: PMC4878434 DOI: 10.1021/acs.orglett.5b00329] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the nematode model organisms Caenorhabditis elegans and Pristionchus pacificus, a new class of natural products based on modular assembly of primary-metabolism-derived building blocks control organismal development and behavior. We report identification and biological activities of the first pentamodular metabolite, pasa#9, and the 8-oxoadenine-containing npar#3 from P. pacificus. These structures suggest co-option of nucleoside and tryptophan metabolic pathways for the biosynthesis of endogenous metabolite libraries that transcend the dichotomy between "primary" and "secondary" metabolism.
Collapse
Affiliation(s)
- Joshua J. Yim
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tubingen 72076, Germany
| | - Neelanjan Bose
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jan M. Meyer
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tubingen 72076, Germany
| | - Ralf J. Sommer
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tubingen 72076, Germany
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
36
|
Miao Z, Jin M, Liu X, Guo W, Jin X, Liu H, Wang Y. The application of HPLC and microprobe NMR spectroscopy in the identification of metabolites in complex biological matrices. Anal Bioanal Chem 2015; 407:3405-16. [PMID: 25814271 PMCID: PMC4392169 DOI: 10.1007/s00216-015-8556-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 02/08/2015] [Accepted: 02/10/2015] [Indexed: 12/28/2022]
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics can be used directly to identify a variety of metabolites in biological fluids and tissues. Metabolite analysis is an important part of life science and metabolomics research. However, the identification of some metabolites using NMR spectroscopy remains a big challenge owing to low abundance or signal overlap. It is important to develop a method to measure these compounds accurately. Two-dimensional NMR spectroscopy, metabolite prediction software packages, and spike-in experiments with authentic standards are often used to solve these problems, but they are costly and time-consuming. In this study, methods were developed to identify metabolites in complex biological mixtures using both high-performance liquid chromatography (HPLC) and off-line microprobe NMR spectroscopy. With use of these methods, 83 and 73 metabolites were identified in Sprague Dawley rat urine and feces, respectively. Among them, 40 and 45 metabolites, respectively, could not be identified with traditional NMR methods. Our research revealed that the combination of HPLC and NMR techniques could significantly improve the accuracy of trace and overlapped metabolite identification, while offering an effective and convenient approach to identify potential biomarkers in complex biological systems.
Collapse
Affiliation(s)
- Zhaoxia Miao
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | | | | | | | | | | | | |
Collapse
|
37
|
Scognamiglio M, D'Abrosca B, Esposito A, Fiorentino A. Chemical Composition and Seasonality of Aromatic Mediterranean Plant Species by NMR-Based Metabolomics. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:258570. [PMID: 25785229 PMCID: PMC4345260 DOI: 10.1155/2015/258570] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 05/31/2023]
Abstract
An NMR-based metabolomic approach has been applied to analyse seven aromatic Mediterranean plant species used in traditional cuisine. Based on the ethnobotanical use of these plants, the approach has been employed in order to study the metabolic changes during different seasons. Primary and secondary metabolites have been detected and quantified. Flavonoids (apigenin, quercetin, and kaempferol derivatives) and phenylpropanoid derivatives (e.g., chlorogenic and rosmarinic acid) are the main identified polyphenols. The richness in these metabolites could explain the biological properties ascribed to these plant species.
Collapse
Affiliation(s)
- Monica Scognamiglio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Brigida D'Abrosca
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Assunta Esposito
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Antonio Fiorentino
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| |
Collapse
|
38
|
Yamada H, Hasegawa Y, Imai H, Takayama Y, Sugihara F, Matsuda T, Tochio H, Shirakawa M, Sando S, Kimura Y, Toshimitsu A, Aoyama Y, Kondo T. Magnetic Resonance Imaging of Tumor with a Self-Traceable Phosphorylcholine Polymer. J Am Chem Soc 2015; 137:799-806. [DOI: 10.1021/ja510479v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hisatsugu Yamada
- Advanced
Biomedical Engineering Research Unit, Center for the Promotion of
Interdisciplinary Education and Research, Kyoto University, Katsura, Nishikyo-ku,
Kyoto 615-8510, Japan
| | - Yoshinori Hasegawa
- Department
of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hirohiko Imai
- Department
of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Takayama
- Department
of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fuminori Sugihara
- Department
of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tetsuya Matsuda
- Department
of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hidehito Tochio
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masahiro Shirakawa
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shinsuke Sando
- Department of Chemistry & Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yu Kimura
- Research
and Educational Unit of Leaders for Integrated Medical System, Center
for the Promotion of Interdisciplinary Education and Research, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Akio Toshimitsu
- Department
of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Division
of Multidisciplinary Chemistry, Institute for Chemical Research, Kyoto University, Gokanosho, Uji, Kyoto 611-0011, Japan
| | - Yasuhiro Aoyama
- Kyoto University, Katsura, Nishikyo-ku,
Kyoto 615-8510, Japan
| | - Teruyuki Kondo
- Advanced
Biomedical Engineering Research Unit, Center for the Promotion of
Interdisciplinary Education and Research, Kyoto University, Katsura, Nishikyo-ku,
Kyoto 615-8510, Japan
- Department
of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| |
Collapse
|
39
|
Larive CK, Barding GA, Dinges MM. NMR spectroscopy for metabolomics and metabolic profiling. Anal Chem 2014; 87:133-46. [PMID: 25375201 DOI: 10.1021/ac504075g] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Cynthia K Larive
- Department of Chemistry, University of California-Riverside , Riverside, California 92521, United States
| | | | | |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Alzweiri M, Al-Shudeifat M, Al-Khaldi K, Al-Hiari Y, Afifi FU. Acetylated Ferulenol-Oxy-Ferulenol as a Proposed Marker for Fresh Ferula Toxicity: A Metabolomic Approach. J LIQ CHROMATOGR R T 2014. [DOI: 10.1080/10826076.2014.908781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- M. Alzweiri
- a Faculty of Pharmacy , The University of Jordan , Amman , Jordan
| | | | | | - Y. Al-Hiari
- a Faculty of Pharmacy , The University of Jordan , Amman , Jordan
| | - F. U. Afifi
- a Faculty of Pharmacy , The University of Jordan , Amman , Jordan
| |
Collapse
|
42
|
Recent advances in genome-based polyketide discovery. Curr Opin Biotechnol 2014; 29:107-15. [DOI: 10.1016/j.copbio.2014.03.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/11/2014] [Accepted: 03/14/2014] [Indexed: 11/27/2022]
|
43
|
Yadav VG. Biosynthonics: Charting the Future Role of Biocatalysis and Metabolic Engineering in Drug Discovery. Ind Eng Chem Res 2014. [DOI: 10.1021/ie500329d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Vikramaditya G. Yadav
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts United States
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts United States
- Department of Chemical & Biological Engineering, The University of British Columbia, Vancouver, British Columbia Canada
| |
Collapse
|
44
|
Bouslimani A, Sanchez LM, Garg N, Dorrestein PC. Mass spectrometry of natural products: current, emerging and future technologies. Nat Prod Rep 2014; 31:718-29. [PMID: 24801551 PMCID: PMC4161218 DOI: 10.1039/c4np00044g] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although mass spectrometry is a century old technology, we are entering into an exciting time for the analysis of molecular information directly from complex biological systems. In this Highlight, we feature emerging mass spectrometric methods and tools used by the natural product community and give a perspective of future directions where the mass spectrometry field is migrating towards over the next decade.
Collapse
Affiliation(s)
- Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | | | | | | |
Collapse
|
45
|
Wyatt T. Introduction to Chemical Signaling in Vertebrates and Invertebrates. Front Neurosci 2014. [DOI: 10.1201/b16511-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
46
|
Mahanti P, Bose N, Bethke A, Judkins JC, Wollam J, Dumas KJ, Zimmerman AM, Campbell SL, Hu PJ, Antebi A, Schroeder FC. Comparative metabolomics reveals endogenous ligands of DAF-12, a nuclear hormone receptor, regulating C. elegans development and lifespan. Cell Metab 2014; 19:73-83. [PMID: 24411940 PMCID: PMC3924769 DOI: 10.1016/j.cmet.2013.11.024] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/25/2013] [Accepted: 11/22/2013] [Indexed: 01/02/2023]
Abstract
Small-molecule ligands of nuclear hormone receptors (NHRs) govern the transcriptional regulation of metazoan development, cell differentiation, and metabolism. However, the physiological ligands of many NHRs remain poorly characterized, primarily due to lack of robust analytical techniques. Using comparative metabolomics, we identified endogenous steroids that act as ligands of the C. elegans NHR, DAF-12, a vitamin D and liver X receptor homolog regulating larval development, fat metabolism, and lifespan. The identified molecules feature unexpected chemical modifications and include only one of two DAF-12 ligands reported earlier, necessitating a revision of previously proposed ligand biosynthetic pathways. We further show that ligand profiles are regulated by a complex enzymatic network, including the Rieske oxygenase DAF-36, the short-chain dehydrogenase DHS-16, and the hydroxysteroid dehydrogenase HSD-1. Our results demonstrate the advantages of comparative metabolomics over traditional candidate-based approaches and provide a blueprint for the identification of ligands for other C. elegans and mammalian NHRs.
Collapse
Affiliation(s)
- Parag Mahanti
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Neelanjan Bose
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Axel Bethke
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Joshua C Judkins
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Joshua Wollam
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany
| | - Kathleen J Dumas
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna M Zimmerman
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sydney L Campbell
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Patrick J Hu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Departments of Internal Medicine and Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany; Huffington Center on Aging, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
47
|
Schofield MM, Sherman DH. Meta-omic characterization of prokaryotic gene clusters for natural product biosynthesis. Curr Opin Biotechnol 2013; 24:1151-8. [PMID: 23731715 PMCID: PMC3797859 DOI: 10.1016/j.copbio.2013.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/14/2013] [Accepted: 05/07/2013] [Indexed: 01/04/2023]
Abstract
Microorganisms produce a remarkable selection of bioactive small molecules. The study and exploitation of these secondary metabolites have traditionally been restricted to the cultivable minority of bacteria. Rapid advances in meta-omics challenge this paradigm. Breakthroughs in metagenomic library methodologies, direct sequencing, single cell genomics, and natural product-specific bioinformatic tools now facilitate the retrieval of previously inaccessible biosynthetic gene clusters. Similarly, metaproteomic developments enable the direct study of biosynthetic enzymes from complex microbial communities. Additional methods within and beyond meta-omics are also in development. This review discusses recent reports in these arenas and how they can be utilized to characterize natural product biosynthetic gene clusters and pathways.
Collapse
Affiliation(s)
- Michael M. Schofield
- Life Sciences Institute and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - David H. Sherman
- Life Sciences Institute and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Departments of Medicinal Chemistry, and Chemistry, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
| |
Collapse
|
48
|
Bingol K, Brüschweiler R. Multidimensional approaches to NMR-based metabolomics. Anal Chem 2013; 86:47-57. [PMID: 24195689 DOI: 10.1021/ac403520j] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kerem Bingol
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210
| | | |
Collapse
|
49
|
Balayssac S, Retailleau E, Bertrand G, Escot MP, Martino R, Malet-Martino M, Gilard V. Characterization of heroin samples by 1H NMR and 2D DOSY 1H NMR. Forensic Sci Int 2013; 234:29-38. [PMID: 24378299 DOI: 10.1016/j.forsciint.2013.10.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/17/2013] [Accepted: 10/20/2013] [Indexed: 01/06/2023]
Abstract
Twenty-four samples of heroin from different illicit drug seizures were analyzed using proton Nuclear Magnetic Resonance ((1)H NMR) and two-dimensional diffusion-ordered spectroscopy (2D DOSY) (1)H NMR. A careful assignment and quantification of (1)H signals enabled a comprehensive characterization of the substances present in the samples investigated: heroin, its main related impurities (6-acetylmorphine, acetylcodeine, morphine, noscapine and papaverine) and cutting agents (caffeine and acetaminophen in nearly all samples as well as lactose, lidocaine, mannitol, piracetam in one sample only), and hence to establish their spectral signatures. The good agreement between the amounts of heroin, noscapine, caffeine and acetaminophen determined by (1)H NMR and gas chromatography, the reference method in forensic laboratories, demonstrates the validity of the (1)H NMR technique. In this paper, 2D DOSY (1)H NMR offers a new approach for a whole characterization of the various components of these complex mixtures.
Collapse
Affiliation(s)
- Stéphane Balayssac
- Groupe de RMN Biomédicale, Laboratoire SPCMIB (UMR CNRS 5068), Université Paul Sabatier, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex, France
| | - Emmanuel Retailleau
- Groupe de RMN Biomédicale, Laboratoire SPCMIB (UMR CNRS 5068), Université Paul Sabatier, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex, France
| | - Geneviève Bertrand
- Institut National de Police Scientifique/Laboratoire de Police Scientifique de Toulouse, 23 boulevard de l'Embouchure, BP 92162, 31021 Toulouse cedex 02, France
| | - Marie-Pierre Escot
- Institut National de Police Scientifique/Laboratoire de Police Scientifique de Toulouse, 23 boulevard de l'Embouchure, BP 92162, 31021 Toulouse cedex 02, France
| | - Robert Martino
- Groupe de RMN Biomédicale, Laboratoire SPCMIB (UMR CNRS 5068), Université Paul Sabatier, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex, France
| | - Myriam Malet-Martino
- Groupe de RMN Biomédicale, Laboratoire SPCMIB (UMR CNRS 5068), Université Paul Sabatier, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex, France
| | - Véronique Gilard
- Groupe de RMN Biomédicale, Laboratoire SPCMIB (UMR CNRS 5068), Université Paul Sabatier, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse cedex, France.
| |
Collapse
|
50
|
Brunetti C, George RM, Tattini M, Field K, Davey MP. Metabolomics in plant environmental physiology. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4011-20. [PMID: 23922358 DOI: 10.1093/jxb/ert244] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Changes in plant metabolism are at the heart of plant developmental processes, underpinning many of the ways in which plants respond to the environment. As such, the comprehensive study of plant metabolism, or metabolomics, is highly valuable in identifying phenotypic effects of abiotic and biotic stresses on plants. When study is in reference to analysing samples that are relevant to environmental or ecologically based hypotheses, it is termed 'environmental metabolomics'. The emergence of environmental metabolomics as one of the latest of the omics technologies has been one of the most critically important recent developments in plant physiology. Its applications broach the entire landscape of plant ecology, from the understanding of plant plasticity and adaptation through to community composition and even genetic modification in crops. The multitude of novel studies published utilizing metabolomics methods employ a variety of techniques, from the initial stages of tissue sampling, through to sample preservation, transportation, and analysis. This review introduces the concept and applications of plant environmental metabolomics as an ecologically important investigative tool. It examines the main techniques used in situ within field sites, with particular reference to sampling and processing, and those more appropriate for use in laboratory-based settings with emphasis on secondary metabolite analysis.
Collapse
Affiliation(s)
- Cecilia Brunetti
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell' Ambiente (DISPAA), Sez. Coltivazioni Arboree, Università di Firenze, Viale delle Idee 30, I-50019 Sesto Fiorentino, Firenze, Italy
| | | | | | | | | |
Collapse
|