1
|
Fu Y, Tao R, Zhang L, Li S, Yang YN, Shen D, Wang Z, Meier T. Trace element detection in anhydrous minerals by micro-scale quantitative nuclear magnetic resonance spectroscopy. Nat Commun 2024; 15:7293. [PMID: 39181900 PMCID: PMC11344839 DOI: 10.1038/s41467-024-51131-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024] Open
Abstract
Nominally anhydrous minerals (NAMs) composing Earth's and planetary rocks incorporate microscopic amounts of volatiles. However, volatile distribution in NAMs and their effect on physical properties of rocks remain controversial. Thus, constraining trace volatile concentrations in NAMs is tantamount to our understanding of the evolution of rocky planets and planetesimals. Here, we present an approach of trace-element quantification using micro-scale Nuclear Magnetic Resonance (NMR) spectroscopy. This approach employs the principle of enhanced mass-sensitivity in NMR microcoils. We were able to demonstrate that this method is in excellent agreement with standard methods across their respective detection capabilities. We show that by simultaneous detection of internal reference nuclei, the quantification sensitivity can be substantially increased, leading to quantifiable trace volatile element amounts of about 50 ng/g measured in a micro-meter sized single anorthitic mineral grain, greatly enhancing detection capabilities of volatiles in geologically important systems.
Collapse
Affiliation(s)
- Yunhua Fu
- School of Earth and Space Sciences, Peking University, Beijing, China
- Center for High-Pressure Science and Technology Advance Research, Beijing, China
| | - Renbiao Tao
- Center for High-Pressure Science and Technology Advance Research, Beijing, China.
| | - Lifei Zhang
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Shijie Li
- Center for Lunar and Planetary Sciences, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Ya-Nan Yang
- State Key Laboratory of Isotope Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, China
| | - Dehan Shen
- Center for Lunar and Planetary Sciences, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Zilong Wang
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Thomas Meier
- Center for High-Pressure Science and Technology Advance Research, Beijing, China.
- Shanghai Key Laboratory MFree, Institute for Shanghai Advanced Research in Physical Sciences, Pudong, Shanghai, 201203, China.
| |
Collapse
|
2
|
Pigliapochi R, Peyear T, Ruan T, Keshari KR. Hyperpolarized Nano-NMR Platform for Quantification of Mass Limited Samples. Anal Chem 2024. [PMID: 39034921 DOI: 10.1021/acs.analchem.4c02378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Metabolic flux analysis of live cells using NMR enables the study of cancer metabolism and response to treatment. However, conventional NMR platforms require often prohibitively high numbers of cells to achieve significant resolution. In this work, we present a double 1H/13C resonance NMR probe consisting of a solenoid coil with a less than 100 nL sensitive region. In-solution robustness is demonstrated through measurement of decaying hyperpolarized signals. A suspension of live cells and hyperpolarized (HP) [1-13C]pyruvate is loaded in the coil, and dynamic changes in pyruvate and lactate concentrations by fractions of femtomoles are detected from just 2000 live cells at a time, in seconds. Through an integrated microfluidic channel, the probe is used as high-throughput platform to perform nondestructive quantitative analysis of metabolic flux of different leukemia cell lines with sensitivity to detect on target treatment response. This approach platform provides an approach to study mass-limited samples and living cells with dramatically enhanced sensitivity in real time.
Collapse
Affiliation(s)
- Roberta Pigliapochi
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, United States
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, United States
| | - Thasin Peyear
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, United States
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, United States
- Weill Cornell Medical College, Cornell University, New York City, New York 10065, United States
| | - Thomas Ruan
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, United States
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, United States
- Weill Cornell Medical College, Cornell University, New York City, New York 10065, United States
| | - Kayvan R Keshari
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, United States
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, United States
- Weill Cornell Medical College, Cornell University, New York City, New York 10065, United States
| |
Collapse
|
3
|
Sharma A, Goel A. Pathogenesis of rheumatoid arthritis and its treatment with anti-inflammatory natural products. Mol Biol Rep 2023; 50:4687-4706. [PMID: 37022525 DOI: 10.1007/s11033-023-08406-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/24/2023] [Indexed: 04/07/2023]
Abstract
Introduction Rheumatoid arthritis (RA) is a common autoimmune disease across the globe that is chronic and systemic as well. The disease is linked with autoantibodies and is inflammatory, eventually targeting several molecules along with certain modified self-epitopes. The disease majorly affects the joints of an individual. Rheumatoid arthritis is manifested clinically by polyarthritis linked with the dysfunction of the joints. This chiefly affects the synovial joint lining and is linked with progressive dysfunction, premature death, along with socioeconomic implications. The macrophage activation, along with the activation of certain defense cells, results in a response to self-epitopes that helps in providing a better understanding of the disease pathogenesis. Material and methodology For this review article, papers have been retrieved and reviewed from database including PubMed, Scopus and Web of science. Relevant papers were taken fulfilling the criteria for writing this review article. Results This has resulted in the establishment of several new therapeutic techniques that serve as potential inhibitors of such cells. Researchers have gained an interest in understanding this disease to provide strategies for treatment in the last two decades. This also includes recognition followed by the treatment of the disease at its early stages. Various allopathic treatment approaches often have chronic and toxic teratogenic effects. However, to avoid this issue of toxicity followed by side effects, certain medicinal plants have been used in treating RA. Conclusion Medicinal plants possess active phytoconstituents that entail antioxidants as well as anti-inflammatory properties, making them a helpful alternative to allopathic drugs that are often linked with highly toxic effects. This review paper entails a thorough discussion of the epidemiology, pathophysiology, diagnosis, and management of RA. The paper will also focus on the use of herbal plants in the treatment of the disease to avoid the side effects that generally occur in allopathic treatment.
Collapse
Affiliation(s)
- Ayushi Sharma
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Uttar Pradesh, 281406, Mathura, India
| | - Anjana Goel
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Uttar Pradesh, 281406, Mathura, India.
| |
Collapse
|
4
|
Wong A. A roadmap to high-resolution standard microcoil MAS NMR spectroscopy for metabolomics. NMR IN BIOMEDICINE 2023; 36:e4683. [PMID: 34970795 DOI: 10.1002/nbm.4683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/06/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Current microcoil probe technology has emerged as a significant advancement in NMR applications to biofluids research. It has continued to excel as a hyphenated tool with other prominent microdevices, opening many new possibilities in multiple omics fields. However, this does not hold for biological samples such as intact tissue or organisms, due to the considerable challenges of incorporating the microcoil in a magic-angle spinning (MAS) probe without relinquishing the high-resolution spectral data. Not until 2012 did a microcoil MAS probe show promise in profiling the metabolome in a submilligram tissue biopsy with spectral resolution on par with conventional high-resolution MAS (HR-MAS) NMR. This result subsequently triggered a great interest in the possibility of NMR analysis with microgram tissues and striving toward the probe development of "high-resolution" capable microcoil MAS NMR spectroscopy. This review gives an overview of the issues and challenges in the probe development and summarizes the advancements toward metabolomics.
Collapse
Affiliation(s)
- Alan Wong
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, Gif-sur-Yvette, France
| |
Collapse
|
5
|
Ahmad F, Nadeem H. Mass Spectroscopy as an Analytical Tool to Harness the Production of Secondary Plant Metabolites: The Way Forward for Drug Discovery. Methods Mol Biol 2023; 2575:77-103. [PMID: 36301472 DOI: 10.1007/978-1-0716-2716-7_5] [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] [Indexed: 06/16/2023]
Abstract
The molecular map of diverse biological molecules linked with structure, function, signaling, and regulation within a cell can be elucidated using an analytically demanding omic approach. The latest trend of using "metabolomics" technologies has explained the natural phenomenon of opening a new avenue to understand and enhance bioactive compounds' production. Examination of sequenced plant genomes has revealed that a considerable portion of these encodes genes of secondary metabolism. In addition to genetic and molecular tools developed in the current era, the ever-increasing knowledge about plant metabolism's biochemistry has initiated an approach for wisely designed, more productive genetic engineering of plant secondary metabolism for improved defense systems and enhanced biosynthesis of beneficial metabolites. Secondary plant metabolites are natural products synthesized by plants that are not directly involved with their average growth and development but play a vital role in plant defense mechanisms. Plant secondary metabolites are classified into four major classes: terpenoids, phenolic compounds, alkaloids, and sulfur-containing compounds. More than 200,000 secondary metabolites are synthesized by plants having a unique and complex structure. Secondary plant metabolites are well characterized and quantified by omics approaches and therefore used by humans in different sectors such as agriculture, pharmaceuticals, chemical industries, and biofuel. The aim is to establish metabolomics as a comprehensive and dynamic model of diverse biological molecules for biomarkers and drug discovery. In this chapter, we aim to illustrate the role of metabolomic technology, precisely liquid chromatography-mass spectrometry, capillary electrophoresis mass spectrometry, gas chromatography-mass spectrometry, and nuclear magnetic resonance spectroscopy, specifically as a research tool in the production and identification of novel bioactive compounds for drug discovery and to obtain a unified insight of secondary metabolism in plants.
Collapse
Affiliation(s)
- Faheem Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | - Hera Nadeem
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Cheney DJ, Wedge CJ. Sample volume effects in optical overhauser dynamic nuclear polarization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 337:107170. [PMID: 35240365 DOI: 10.1016/j.jmr.2022.107170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
The optical dynamic nuclear polarization (DNP) method has been proposed as an alternative to microwave pumping as a hyperpolarization method for solution-state NMR studies. Using continuous laser illumination to photogenerate triplet states in the presence of a persistent radical produces chemically-induced dynamic electron polarization (CIDEP) via the radical-triplet pair mechanism (RTPM), with cross-relaxation transferring this to nuclear hyperpolarization via an Overhauser mechanism. Numerical simulations have previously indicated that reducing the sample volume while maintaining a constant optical density can significantly increase the NMR signal enhancement, due to the larger steady-state concentration of triplets obtained. Here we provide the first experimental confirmation of these effects, producing a nearly five-fold increase in the optical DNP enhancement factor just by reducing the sample volume with optimal dye and radical concentrations adjusted for each optical path length. The results are supported with an in depth analysis of volume effects in the numerical model, with which they are in good qualitative agreement. These important observations will impact on the future development of the technique, with particular significance for attempts to apply DNP methods to increase sensitivity for volume-limited biological samples.
Collapse
Affiliation(s)
- Daniel J Cheney
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, United Kingdom
| | - Christopher J Wedge
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, United Kingdom.
| |
Collapse
|
8
|
Forster LC, Clegg JK, Cheney KL, Garson MJ. Expanding the Repertoire of Spongian-16-One Derivatives in Australian Nudibranchs of the Genus Goniobranchus and Evaluation of Their Anatomical Distribution. Mar Drugs 2021; 19:680. [PMID: 34940679 PMCID: PMC8706817 DOI: 10.3390/md19120680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/21/2022] Open
Abstract
Extracts of the mantle and viscera of the Indo-Pacific nudibranchs Goniobranchus aureopurpureus and Goniobranchus sp. 1 afforded 11 new diterpenoids (1-11), all of which possess a tetracyclic spongian-16-one scaffold with extensive oxidation at C-6, C-7, C-11, C-12, C-13, and/or C-20. The structures and relative configuration were investigated by NMR experiments, while X-ray crystallography provided the absolute configuration of 1, including a 2'S configuration for the 2-methylbutanoate substituent located at C-7. Dissection of animal tissue revealed that the mantle and viscera tissues differed in their metabolite composition with diterpenes 1-11 present in the mantle tissue of the two nudibranch species.
Collapse
Affiliation(s)
- Louise C. Forster
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (L.C.F.); (J.K.C.)
| | - Jack K. Clegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (L.C.F.); (J.K.C.)
| | - Karen L. Cheney
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Mary J. Garson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (L.C.F.); (J.K.C.)
| |
Collapse
|
9
|
Lepucki P, Dioguardi AP, Karnaushenko D, Schmidt OG, Grafe HJ. The normalized limit of detection in NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 332:107077. [PMID: 34634649 DOI: 10.1016/j.jmr.2021.107077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
We derive the normalized limit of detection for frequency space (nLODf) as a parameter to measure the sensitivity of an NMR spectroscopy setup. nLODf is independent of measurement settings such as bandwidth or number of measurement points, and allows to compare performances of different setups. We demonstrate the usefulness of the new nLODf by comparing the sensitivity of NMR setups from various publications, which all use microcoils. Finally, we want to propose a standard measurement and report format for the sensitivity of new NMR setups.
Collapse
Affiliation(s)
- Piotr Lepucki
- IFW Dresden, Institut für Festkörperforschung, Helmholtzstraße 20, 01069 Dresden, Germany.
| | - Adam P Dioguardi
- IFW Dresden, Institut für Festkörperforschung, Helmholtzstraße 20, 01069 Dresden, Germany.
| | - Daniil Karnaushenko
- IFW Dresden, Institut für Integrative Nanowissenschaften, Helmholtzstraße 20, 01069 Dresden, Germany.
| | - Oliver G Schmidt
- IFW Dresden, Institut für Integrative Nanowissenschaften, Helmholtzstraße 20, 01069 Dresden, Germany; TU Dresden, Nanophysik, Häckelstraße 3, 01069 Dresden, Germany; TU Chemnitz, Material Systems for Nanoelectronics, Straße der Nationen 62, 09111 Chemnitz, Germany.
| | - Hans-Joachim Grafe
- IFW Dresden, Institut für Festkörperforschung, Helmholtzstraße 20, 01069 Dresden, Germany.
| |
Collapse
|
10
|
Abhyankar N, Szalai V. Challenges and Advances in the Application of Dynamic Nuclear Polarization to Liquid-State NMR Spectroscopy. J Phys Chem B 2021; 125:5171-5190. [PMID: 33960784 PMCID: PMC9871957 DOI: 10.1021/acs.jpcb.0c10937] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method to study the molecular structure and dynamics of materials. The inherently low sensitivity of NMR spectroscopy is a consequence of low spin polarization. Hyperpolarization of a spin ensemble is defined as a population difference between spin states that far exceeds what is expected from the Boltzmann distribution for a given temperature. Dynamic nuclear polarization (DNP) can overcome the relatively low sensitivity of NMR spectroscopy by using a paramagnetic matrix to hyperpolarize a nuclear spin ensemble. Application of DNP to NMR can result in sensitivity gains of up to four orders of magnitude compared to NMR without DNP. Although DNP NMR is now more routinely utilized for solid-state (ss) NMR spectroscopy, it has not been exploited to the same degree for liquid-state samples. This Review will consider challenges and advances in the application of DNP NMR to liquid-state samples. The Review is organized into four sections: (i) mechanisms of DNP NMR relevant to hyperpolarization of liquid samples; (ii) applications of liquid-state DNP NMR; (iii) available detection schemes for liquid-state samples; and (iv) instrumental challenges and outlook for liquid-state DNP NMR.
Collapse
Affiliation(s)
- Nandita Abhyankar
- Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD 20742, USA,National Institute of Standards and Technology, Gaithersburg, MD 20899, USA,Corresponding authors: ,
| | - Veronika Szalai
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA,Corresponding authors: ,
| |
Collapse
|
11
|
Danelius E, Halaby S, van der Donk WA, Gonen T. MicroED in natural product and small molecule research. Nat Prod Rep 2021; 38:423-431. [PMID: 32939523 PMCID: PMC7965795 DOI: 10.1039/d0np00035c] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Covering: 2013 to 2020The electron cryo-microscopy (cryo-EM) method Microcrystal Electron Diffraction (MicroED) allows the collection of high-resolution structural data from vanishingly small crystals that appear like amorphous powders or very fine needles. Since its debut in 2013, data collection and analysis schemes have been fine-tuned, and there are currently close to 100 structures determined by MicroED. Although originally developed to study proteins, MicroED is also very powerful for smaller systems, with some recent and very promising examples from the field of natural products. Herein, we review what has been achieved so far and provide examples of natural product structures, as well as demonstrate the expected future impact of MicroED to the field of natural product and small molecule research.
Collapse
Affiliation(s)
- Emma Danelius
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA.
| | | | | | | |
Collapse
|
12
|
Honrao C, Ma X, Kulkarni S, Joshi V, Malamas M, Zvonok A, Wood J, Kautz RA, Strand D, Guo JJ, Makriyannis A. Metabolic Profiling of a CB2 Agonist, AM9338, Using LC-MS and Microcoil-NMR: Identification of a Novel Dihydroxy Adamantyl Metabolite. Front Pharmacol 2020; 11:575691. [PMID: 33101030 PMCID: PMC7556269 DOI: 10.3389/fphar.2020.575691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Adamantyl groups are key structural subunit commonly used in many marketed drugs targeting diseases ranging from viral infections to neurological disorders. The metabolic disposition of adamantyl compounds has been mostly studied using LC-MS based approaches. However, metabolite quantities isolated from biological preparations are often insufficient for unambiguous structural characterization by NMR. In this work, we utilized microcoil NMR in conjunction with LC-MS to characterize liver microsomal metabolites of an adamantyl based CB2 agonist AM9338, 1-(3-(1H-1,2,3-triazol-1-yl) propyl)-N-(adamantan-1-yl)-1H-indazole-3-carboxamide, a candidate compound for potential multiple sclerosis treatment. We have identified a total of 9 oxidative metabolites of AM9338 whereas mono- or di-hydroxylation of the adamantyl moiety is the primary metabolic pathway. While it is generally believed that the tertiary adamantyl carbons are the preferred sites of CYP450 oxidation, both the mono- and di-hydroxyl metabolites of AM9338 show that the primary oxidative sites are located on the secondary adamantyl carbons. To our knowledge this di-hydroxylated metabolite is a novel adamantyl metabolite that has not been reported before. Further, the stereochemistry of both mono- and di-hydroxyl adamantyl metabolites has been determined using NOE correlations. Furthermore, docking of AM9338 into the CYP3A4 metabolic enzyme corroborates with our experimental findings, and the modelling results also provide a possible mechanism for the unusual susceptibility of adamantyl secondary carbons to metabolic oxidations. The novel dihydroxylated AM9338 metabolite identified in this study, along with the previously known adamantyl metabolites, gives a more complete picture of the metabolic disposition for adamantyl compounds.
Collapse
Affiliation(s)
- Chandrashekhar Honrao
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
| | - Xiaoyu Ma
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
| | - Shashank Kulkarni
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
| | - Vinit Joshi
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
| | - Michael Malamas
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
| | | | - JodiAnne Wood
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
| | - Roger A. Kautz
- Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, United States
| | - David Strand
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
- Protasis Corporation, Seabrook, NH, United States
| | - Jason J. Guo
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
- Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, MA, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, United States
- *Correspondence: Jason J. Guo, ; Alexandros Makriyannis,
| | - Alexandros Makriyannis
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
- MAK Scientific LLC, Burlington, MA, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, United States
- *Correspondence: Jason J. Guo, ; Alexandros Makriyannis,
| |
Collapse
|
13
|
Payne EM, Holland-Moritz DA, Sun S, Kennedy RT. High-throughput screening by droplet microfluidics: perspective into key challenges and future prospects. LAB ON A CHIP 2020; 20:2247-2262. [PMID: 32500896 DOI: 10.1039/d0lc00347f] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In two decades of development, impressive strides have been made for automating basic laboratory operations in droplet-based microfluidics, allowing the emergence of a new form of high-throughput screening and experimentation in nanoliter to femtoliter volumes. Despite advancements in droplet storage, manipulation, and analysis, the field has not yet been widely adapted for many high-throughput screening (HTS) applications. Broad adoption and commercial development of these techniques require robust implementation of strategies for the stable storage, chemical containment, generation of libraries, sample tracking, and chemical analysis of these small samples. We discuss these challenges for implementing droplet HTS and highlight key strategies that have begun to address these concerns. Recent advances in the field leave us optimistic about the future prospects of this rapidly developing technology.
Collapse
Affiliation(s)
- Emory M Payne
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | | | | | | |
Collapse
|
14
|
Dey P, Kundu A, Chakraborty HJ, Kar B, Choi WS, Lee BM, Bhakta T, Atanasov AG, Kim HS. Therapeutic value of steroidal alkaloids in cancer: Current trends and future perspectives. Int J Cancer 2019; 145:1731-1744. [PMID: 30387881 PMCID: PMC6767045 DOI: 10.1002/ijc.31965] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/04/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022]
Abstract
Discovery and development of new potentially selective anticancer agents are necessary to prevent a global cancer health crisis. Currently, alternative medicinal agents derived from plants have been extensively investigated to develop anticancer drugs with fewer adverse effects. Among them, steroidal alkaloids are conventional secondary metabolites that comprise an important class of natural products found in plants, marine organisms and invertebrates, and constitute a judicious choice as potential anti-cancer leads. Traditional medicine and modern science have shown that representatives from this compound group possess potential antimicrobial, analgesic, anticancer and anti-inflammatory effects. Therefore, systematic and recapitulated information about the bioactivity of these compounds, with special emphasis on the molecular or cellular mechanisms, is of high interest. In this review, we methodically discuss the in vitro and in vivo potential of the anticancer activity of natural steroidal alkaloids and their synthetic and semi-synthetic derivatives. This review focuses on cumulative and comprehensive molecular mechanisms, which will help researchers understand the molecular pathways involving steroid alkaloids to generate a selective and safe new lead compound with improved therapeutic applications for cancer prevention and therapy. In vitro and in vivo studies provide evidence about the promising therapeutic potential of steroidal alkaloids in various cancer cell lines, but advanced pharmacokinetic and clinical experiments are required to develop more selective and safe drugs for cancer treatment.
Collapse
Affiliation(s)
- Prasanta Dey
- School of PharmacySungkyunkwan UniversitySuwonRepublic of Korea
| | - Amit Kundu
- School of PharmacySungkyunkwan UniversitySuwonRepublic of Korea
| | | | - Babli Kar
- Bengal Homoeopathic Medical College and HospitalAsansolIndia
| | - Wahn Soo Choi
- School of MedicineKonkuk UniversityChungjuRepublic of Korea
| | - Byung Mu Lee
- School of PharmacySungkyunkwan UniversitySuwonRepublic of Korea
| | - Tejendra Bhakta
- Regional Institute of Pharmaceutical Science & TechnologyTripuraIndia
| | - Atanas G. Atanasov
- Institute of Genetics and Animal Breeding of the Polish Academy of SciencesJastrzebiecPoland
- Department of PharmacognosyUniversity of ViennaViennaAustria
| | - Hyung Sik Kim
- School of PharmacySungkyunkwan UniversitySuwonRepublic of Korea
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Bonam SR, Wu YS, Tunki L, Chellian R, Halmuthur MSK, Muller S, Pandy V. What Has Come out from Phytomedicines and Herbal Edibles for the Treatment of Cancer? ChemMedChem 2018; 13:1854-1872. [PMID: 29927521 DOI: 10.1002/cmdc.201800343] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/19/2018] [Indexed: 12/20/2022]
Abstract
Several modern treatment strategies have been adopted to combat cancer with the aim of minimizing toxicity. Medicinal plant-based compounds with the potential to treat cancer have been widely studied in preclinical research and have elicited many innovations in cutting-edge clinical research. In parallel, researchers have eagerly tried to decrease the toxicity of current chemotherapeutic agents either by combining them with herbals or in using herbals alone. The aim of this article is to present an update of medicinal plants and their bioactive compounds, or mere changes in the bioactive compounds, along with herbal edibles, which display efficacy against diverse cancer cells and in anticancer therapy. It describes the basic mechanism(s) of action of phytochemicals used either alone or in combination therapy with other phytochemicals or herbal edibles. This review also highlights the remarkable synergistic effects that arise between certain herbals and chemotherapeutic agents used in oncology. The anticancer phytochemicals used in clinical research are also described; furthermore, we discuss our own experience related to semisynthetic derivatives, which are developed based on phytochemicals. Overall, this compilation is intended to facilitate research and development projects on phytopharmaceuticals for successful anticancer drug discovery.
Collapse
Affiliation(s)
- Srinivasa Reddy Bonam
- UMR 7242 CNRS, Biotechnology and Cell Signaling, University of Strasbourg, Laboratory of Excellence Medalis, Illkirch, 67400, France.,Vaccine Immunology Laboratory, Natural Product Chemistry Division, CSIR - Indian Institute of Chemical Technology (IICT), Hyderabad, 500007, India.,Academy of Scientific and Innovative Research, CSIR - Indian Institute of Chemical Technology, Hyderabad, 500007, India
| | - Yuan Seng Wu
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Lakshmi Tunki
- Vaccine Immunology Laboratory, Natural Product Chemistry Division, CSIR - Indian Institute of Chemical Technology (IICT), Hyderabad, 500007, India
| | - Ranjithkumar Chellian
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mahabalarao Sampath Kumar Halmuthur
- Vaccine Immunology Laboratory, Natural Product Chemistry Division, CSIR - Indian Institute of Chemical Technology (IICT), Hyderabad, 500007, India.,Academy of Scientific and Innovative Research, CSIR - Indian Institute of Chemical Technology, Hyderabad, 500007, India
| | - Sylviane Muller
- UMR 7242 CNRS, Biotechnology and Cell Signaling, University of Strasbourg, Laboratory of Excellence Medalis, Illkirch, 67400, France.,University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, 67000, France
| | - Vijayapandi Pandy
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.,Department of Pharmacology, Chalapathi Institute of Pharmaceutical Sciences, Lam, Guntur, Andhra Pradesh, 522034, India
| |
Collapse
|
17
|
Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
Collapse
Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| |
Collapse
|
18
|
Chen Y, Mehta HS, Butler MC, Walter ED, Reardon PN, Renslow RS, Mueller KT, Washton NM. High-resolution microstrip NMR detectors for subnanoliter samples. Phys Chem Chem Phys 2018; 19:28163-28174. [PMID: 29022609 DOI: 10.1039/c7cp03933f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present the numerical optimization and experimental characterization of two microstrip-based nuclear magnetic resonance (NMR) detectors. The first detector, introduced in our previous work, was a flat wire detector with a strip resting on a substrate, and the second detector was created by adding a ground plane on top of the strip conductor, separated by a sample-carrying capillary and a thin layer of insulator. The dimensional parameters of the detectors were optimized using numerical simulations with regards to radio frequency (RF) sensitivity and homogeneity, with particular attention given to the effect of the ground plane. The influence of copper surface finish and substrate surface on the spectral resolution was investigated, and a resolution of 0.8-1.5 Hz was obtained on 1 nL deionized water depending on sample positioning. For 0.13 nmol sucrose (0.2 M in 0.63 nL H2O) encapsulated between two Fluorinert plugs, high RF homogeneity (A810°/A90° = 70-80%) and high sensitivity (expressed in the limit of detection nLODm = 0.73-1.21 nmol s1/2) were achieved, allowing for high-performance 2D NMR spectroscopy of subnanoliter samples.
Collapse
Affiliation(s)
- Ying Chen
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Carret G, Berthelot T, Berthault P. Enhancing NMR of Nonrelaxing Species Using a Controlled Flow Motion and a Miniaturized Circuit. Anal Chem 2017; 89:2995-3000. [DOI: 10.1021/acs.analchem.6b04488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guillaume Carret
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Thomas Berthelot
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Patrick Berthault
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| |
Collapse
|
20
|
Garbacz P. Chirality-sensitive effects induced by nuclear relaxation in an electric field. J Chem Phys 2016; 145:224202. [DOI: 10.1063/1.4971435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Piotr Garbacz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| |
Collapse
|
21
|
Al‐Massaedh “AA, Schmidt M, Pyell U, Reinscheid UM. Elucidation of the Enantiodiscrimination Properties of a Nonracemic Chiral Alignment Medium through Gel-based Capillary Electrochromatography: Separation of the Mefloquine Stereoisomers. ChemistryOpen 2016; 5:455-459. [PMID: 27777838 PMCID: PMC5062011 DOI: 10.1002/open.201600085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 11/07/2022] Open
Abstract
Enantiodiscrimination and enantioseparation are two highly important processes in chemistry, often performed by using NMR spectroscopy and chromatography. For a better understanding of the mechanistic details, the same system should be studied by both methods. In addition, isotropic and anisotropic NMR parameters should be obtained, the latter using alignment media so that residual dipolar couplings and chemical-shift anisotropies can be measured. Consequently, a chiral alignment medium was used for the first time in chiral gel-based capillary electrochromatography with the four stereoisomers of the antimalaria drug mefloquine as test compounds. Chromatographic data verify that enantiodiscrimination obtained with this alignment gel is caused by differences in the equilibrium constants related to associate formation. Hence, the chromatographic separation provides physicochemical data that form a basis for the understanding and optimization of alignment processes, and vice versa.
Collapse
Affiliation(s)
- “Ayat Allah” Al‐Massaedh
- Department of ChemistryUniversity of MarburgHans-Meerwein-Straße35032MarburgGermany
- Department of ChemistryFaculty of ScienceAl al-Bayt University25113MafraqJordan
| | - Manuel Schmidt
- Department of NMR-based Structural BiologyMax-Planck-Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Ute Pyell
- Department of ChemistryUniversity of MarburgHans-Meerwein-Straße35032MarburgGermany
| | - Uwe M. Reinscheid
- Department of NMR-based Structural BiologyMax-Planck-Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| |
Collapse
|
22
|
Nagato EG, Lankadurai BP, Soong R, Simpson AJ, Simpson MJ. Development of an NMR microprobe procedure for high-throughput environmental metabolomics of Daphnia magna. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:745-53. [PMID: 25891518 DOI: 10.1002/mrc.4236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 11/21/2014] [Accepted: 02/14/2015] [Indexed: 05/20/2023]
Abstract
Nuclear magnetic resonance (NMR) is the primary platform used in high-throughput environmental metabolomics studies because its non-selectivity is well suited for non-targeted approaches. However, standard NMR probes may limit the use of NMR-based metabolomics for tiny organisms because of the sample volumes required for routine metabolic profiling. Because of this, keystone ecological species, such as the water flea Daphnia magna, are not commonly studied because of the analytical challenges associated with NMR-based approaches. Here, the use of a 1.7-mm NMR microprobe in analyzing tissue extracts from D. magna is tested. Three different extraction procedures (D2O-based buffer, Bligh and Dyer, and acetonitrile : methanol : water) were compared in terms of the yields and breadth of polar metabolites. The D2O buffer extraction yielded the most metabolites and resulted in the best reproducibility. Varying amounts of D. magna dry mass were extracted to optimize metabolite isolation from D. magna tissues. A ratio of 1-1.5-mg dry mass to 40 µl of extraction solvent provided excellent signal-to-noise and spectral resolution using (1)H NMR. The metabolite profile of a single daphnid was also investigated (approximately 0.2 mg). However, the signal-to-noise of the (1)H NMR was considerably lower, and while feasible for select applications would likely not be appropriate for high-throughput NMR-based metabolomics. Two-dimensional NMR experiments on D. magna extracts were also performed using the 1.7-mm NMR probe to confirm (1)H NMR metabolite assignments. This study provides an NMR-based analytical framework for future metabolomics studies that use D. magna in ecological and ecotoxicity studies.
Collapse
Affiliation(s)
- Edward G Nagato
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Brian P Lankadurai
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
Guo W, Jin M, Miao Z, Qu K, Liu X, Zhang P, Qin H, Zhu H, Wang Y. Structure Elucidation of the Metabolites of 2', 3', 5'-Tri-O-Acetyl-N6-(3-Hydroxyphenyl) Adenosine in Rat Urine by HPLC-DAD, ESI-MS and Off-Line Microprobe NMR. PLoS One 2015; 10:e0127583. [PMID: 26029929 PMCID: PMC4451981 DOI: 10.1371/journal.pone.0127583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/16/2015] [Indexed: 11/19/2022] Open
Abstract
2', 3', 5'-Tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine (also known as WS070117) is a new adenosine analog that displays anti-hyperlipidemic activity both in vitro and in vivo experiments as shown in many preliminary studies. Due to its new structure, little is known about the metabolism of WS070117. Hence, the in vivo metabolites of WS070117 in rat urine following oral administration were investigated. Identification of the metabolites was conducted using the combination of high-performance liquid chromatography (HPLC) coupled with diode array detector (DAD), ion trap electrospray ionization-mass spectrometry (ESI-MS), and off-line microprobe nuclear magnetic resonance (NMR) measurements. Seven metabolites were obtained as pure compounds at the sub-milligram to milligram levels. Results of structure elucidation unambiguously revealed that the phase I metabolite, N6-(3-hydroxyphenyl) adenosine (M8), was a hydrolysate of WS070117 by hydrolysis on the three ester groups. N6-(3-hydr-oxyphenyl) adenine (M7), also one of the phase I metabolites, was the derivative of M8 by the loss of ribofuranose. In addition to two phase I metabolites, there were five phase II metabolites of WS070117 found in rat urine. 8-hydroxy-N6-(3-hydroxy-phenyl) adenosine (M6) was the product of M7 by hydrolysis at position 8. The other four were elucidated to be N6-(3-O-β-D-glucuronyphenyl) adenine (M2), N8-hydroxy-N6-(3-O-sulfophenyl) adenine (M3), N6-(3-O-β-D-glucuronyphenyl) adenosine (M4), and N6-(3-O- sulfophenyl) adenosine (M5). Phase II metabolic pathways were proven to consist of hydroxylation, glucuronidation and sulfation. This study provides new and valuable information on the metabolism of WS070117, and also demonstrates the HPLC/MS/off-line microprobe NMR approach as a robust means for rapid identification of metabolites.
Collapse
Affiliation(s)
- Wei Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengxia Jin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhaoxia Miao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Qu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xia Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peicheng Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hailin Qin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haibo Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yinghong Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
25
|
Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
26
|
Reynolds WF, Mazzola EP. Nuclear magnetic resonance in the structural elucidation of natural products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2015; 100:223-309. [PMID: 25632562 DOI: 10.1007/978-3-319-05275-5_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
|
27
|
Zalesskiy SS, Danieli E, Blümich B, Ananikov VP. Miniaturization of NMR systems: desktop spectrometers, microcoil spectroscopy, and "NMR on a chip" for chemistry, biochemistry, and industry. Chem Rev 2014; 114:5641-94. [PMID: 24779750 DOI: 10.1021/cr400063g] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sergey S Zalesskiy
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Moscow, 119991, Russia
| | | | | | | |
Collapse
|
28
|
Seger C, Sturm S, Stuppner H. Mass spectrometry and NMR spectroscopy: modern high-end detectors for high resolution separation techniques--state of the art in natural product HPLC-MS, HPLC-NMR, and CE-MS hyphenations. Nat Prod Rep 2013; 30:970-87. [PMID: 23739842 DOI: 10.1039/c3np70015a] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Current natural product research is unthinkable without the use of high resolution separation techniques as high performance liquid chromatography or capillary electrophoresis (HPLC or CE respectively) combined with mass spectrometers (MS) or nuclear magnetic resonance (NMR) spectrometers. These hyphenated instrumental analysis platforms (CE-MS, HPLC-MS or HPLC-NMR) are valuable tools for natural product de novo identification, as well as the authentication, distribution, and quantification of constituents in biogenic raw materials, natural medicines and biological materials obtained from model organisms, animals and humans. Moreover, metabolic profiling and metabolic fingerprinting applications can be addressed as well as pharmacodynamic and pharmacokinetic issues. This review provides an overview of latest technological developments, discusses the assets and drawbacks of the available hyphenation techniques, and describes typical analytical workflows.
Collapse
Affiliation(s)
- Christoph Seger
- Institute of Pharmacy/Pharmacognosy, CCB-Centrum of Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | | | | |
Collapse
|
29
|
Singh S, Handa T, Narayanam M, Sahu A, Junwal M, Shah RP. A critical review on the use of modern sophisticated hyphenated tools in the characterization of impurities and degradation products. J Pharm Biomed Anal 2012; 69:148-73. [DOI: 10.1016/j.jpba.2012.03.044] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 03/21/2012] [Accepted: 03/22/2012] [Indexed: 11/30/2022]
|
30
|
Nadal-Desbarats L, Veau S, Blasco H, Emond P, Royere D, Andres CR, Guérif F. Is NMR metabolic profiling of spent embryo culture media useful to assist in vitro human embryo selection? MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2012; 26:193-202. [DOI: 10.1007/s10334-012-0331-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 06/11/2012] [Accepted: 07/12/2012] [Indexed: 01/12/2023]
|
31
|
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.
Collapse
Affiliation(s)
- Sonja Sturm
- Institute of Pharmacy/Pharmacognosy, CCB - Center of Chemistry and Biomedicine, Leopold Franzens University Innsbruck, Innsbruck, Austria
| | | |
Collapse
|
32
|
Dias DA, Urban S, Roessner U. A historical overview of natural products in drug discovery. Metabolites 2012; 2:303-36. [PMID: 24957513 PMCID: PMC3901206 DOI: 10.3390/metabo2020303] [Citation(s) in RCA: 877] [Impact Index Per Article: 73.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/31/2012] [Accepted: 03/31/2012] [Indexed: 12/25/2022] Open
Abstract
Historically, natural products have been used since ancient times and in folklore for the treatment of many diseases and illnesses. Classical natural product chemistry methodologies enabled a vast array of bioactive secondary metabolites from terrestrial and marine sources to be discovered. Many of these natural products have gone on to become current drug candidates. This brief review aims to highlight historically significant bioactive marine and terrestrial natural products, their use in folklore and dereplication techniques to rapidly facilitate their discovery. Furthermore a discussion of how natural product chemistry has resulted in the identification of many drug candidates; the application of advanced hyphenated spectroscopic techniques to aid in their discovery, the future of natural product chemistry and finally adopting metabolomic profiling and dereplication approaches for the comprehensive study of natural product extracts will be discussed.
Collapse
Affiliation(s)
- Daniel A Dias
- Metabolomics Australia, School of Botany, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Sylvia Urban
- School of Applied Sciences (Discipline of Applied Chemistry), Health Innovations Research Institute (HIRi) RMIT University, G.P.O. Box 2476V, Melbourne, Victoria 3001, Australia
| | - Ute Roessner
- Metabolomics Australia, School of Botany, The University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
33
|
|
34
|
From single to multiple microcoil flow probe NMR and related capillary techniques: a review. Anal Bioanal Chem 2011; 402:647-69. [PMID: 21969176 DOI: 10.1007/s00216-011-5419-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/20/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most important and powerful instrumental analytical techniques for structural elucidation of unknown small and large (complex) isolated and synthesized compounds in organic and inorganic chemistry. X-ray crystallography, neutron scattering (neutron diffraction), and NMR spectroscopy are the only suitable methods for three-dimensional structure determination at atomic resolution. Moreover, these methods are complementary. However, by means of NMR spectroscopy, reaction dynamics and interaction processes can also be investigated. Unfortunately, this technique is very insensitive in comparison with other spectrometric (e.g., mass spectrometry) and spectroscopic (e.g., infrared spectroscopy) methods. Mainly through the development of stronger magnets and more sensitive solenoidal microcoil flow probes, this drawback has been successfully counteracted. Capillary NMR spectroscopy increases the mass-based sensitivity of the NMR spectroscopic analysis up to 100-fold compared with conventional 5-mm NMR probes, and thus can be coupled online and off-line with other microseparation and detection techniques. It offers not only higher sensitivity, but in many cases provides better quality spectra than traditional methods. Owing to the immense number of compounds (e.g., of natural product extracts and compound libraries) to be examined, single microcoil flow probe NMR spectroscopy will soon be far from being sufficiently effective as a screening method. For this reason, an inevitable trend towards coupled microseparation-multiple microcoil flow probe NMR techniques, which allow simultaneous online and off-line detection of several compounds, will occur. In this review we describe the current status and possible future developments of single and multiple microcoil capillary flow probe NMR spectroscopy and its application as a high-throughput tool for the analysis of a large number of mass-limited samples. The advantages and drawbacks of different coupled microseparation-capillary NMR spectroscopy techniques, such as capillary high-performance liquid chromatography-NMR spectroscopy, capillary electrophoresis-NMR spectroscopy, and capillary gas chromatography-NMR spectroscopy, are discussed and demonstrated by specific applications. Another subject of discussion is the progress in parallel NMR detection techniques. Furthermore, the applicability and mixing capability of tiny reactor systems, termed "microreactors" or "micromixers," implemented in NMR probes is demonstrated by carbamate- and imine-forming reactions.
Collapse
|
35
|
Jones CJ, Larive CK. Could smaller really be better? Current and future trends in high-resolution microcoil NMR spectroscopy. Anal Bioanal Chem 2011; 402:61-8. [DOI: 10.1007/s00216-011-5330-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/02/2011] [Accepted: 08/06/2011] [Indexed: 11/28/2022]
|
36
|
Brkljača R, Urban S. RECENT ADVANCEMENTS IN HPLC-NMR AND APPLICATIONS FOR NATURAL PRODUCT PROFILING AND IDENTIFICATION. J LIQ CHROMATOGR R T 2011. [DOI: 10.1080/10826076.2011.587748] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Robert Brkljača
- a School of Applied Sciences, Health Innovations Research Institute (HIRi) RMIT University , Melbourne, Victoria, Australia
| | - Sylvia Urban
- a School of Applied Sciences, Health Innovations Research Institute (HIRi) RMIT University , Melbourne, Victoria, Australia
| |
Collapse
|
37
|
Grimes JH, O'Connell TM. The application of micro-coil NMR probe technology to metabolomics of urine and serum. JOURNAL OF BIOMOLECULAR NMR 2011; 49:297-305. [PMID: 21380855 DOI: 10.1007/s10858-011-9488-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 11/26/2010] [Indexed: 05/30/2023]
Abstract
Increasing the sensitivity and throughput of NMR-based metabolomics is critical for the continued growth of this field. In this paper the application of micro-coil NMR probe technology was evaluated for this purpose. The most commonly used biofluids in metabolomics are urine and serum. In this study we examine different sample limited conditions and compare the detection sensitivity of the micro-coil with a standard 5 mm NMR probe. Sample concentration is evaluated as a means to leverage the greatly improved mass sensitivity of the micro-coil probes. With very small sample volumes, the sensitivity of the micro-coil probe does indeed provide a significant advantage over the standard probe. Concentrating the samples does improve the signal detection, but the benefits do not follow the expected linear increase and are both matrix and metabolite specific. Absolute quantitation will be affected by concentration, but an analysis of relative concentrations is still possible. The choice of the micro-coil probe over a standard tube based probe will depend upon a number of factors including number of samples and initial volume but this study demonstrates the feasibility of high-throughput metabolomics with the micro-probe platform.
Collapse
Affiliation(s)
- John H Grimes
- Hamner-UNC Institute for Drug Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, NC, USA
| | | |
Collapse
|
38
|
Nanogram-scale preparation and NMR analysis for mass-limited small volatile compounds. PLoS One 2011; 6:e18178. [PMID: 21464906 PMCID: PMC3065492 DOI: 10.1371/journal.pone.0018178] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Accepted: 02/22/2011] [Indexed: 11/19/2022] Open
Abstract
Semiochemicals are often produced in infinitesimally small quantities, so their isolation requires large amounts of starting material, not only requiring significant effort in sample preparation, but also resulting in a complex mixture of compounds from which the bioactive compound needs to be purified and identified. Often, compounds cannot be unambiguously identified by their mass spectra alone, and NMR analysis is required for absolute chemical identification, further exacerbating the situation because NMR is relatively insensitive and requires large amounts of pure analyte, generally more than several micrograms. We developed an integrated approach for purification and NMR analysis of <1 µg of material. Collections from high performance preparative gas-chromatography are directly eluted with minimal NMR solvent into capillary NMR tubes. With this technique, 1H-NMR spectra were obtained on 50 ng of geranyl acetate, which served as a model compound, and reasonable H-H COSY NMR spectra were obtained from 250 ng of geranyl acetate. This simple off-line integration of preparative GC and NMR will facilitate the purification and chemical identification of novel volatile compounds, such as insect pheromones and other semiochemicals, which occur in minute (sub-nanogram), and often limited, quantities.
Collapse
|
39
|
Kingston DGI. Modern natural products drug discovery and its relevance to biodiversity conservation. JOURNAL OF NATURAL PRODUCTS 2011; 74:496-511. [PMID: 21138324 PMCID: PMC3061248 DOI: 10.1021/np100550t] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Natural products continue to provide a diverse and unique source of bioactive lead compounds for drug discovery, but maintaining their continued eminence as source compounds is challenging in the face of the changing face of the pharmaceutical industry and the changing nature of biodiversity prospecting brought about by the Convention on Biological Diversity. This review provides an overview of some of these challenges and suggests ways in which they can be addressed so that natural products research can remain a viable and productive route to drug discovery. Results from International Cooperative Biodiversity Groups (ICBGs) working in Madagascar, Panama, and Suriname are used as examples of what can be achieved when biodiversity conservation is linked to drug discovery.
Collapse
Affiliation(s)
- David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States.
| |
Collapse
|
40
|
van Bentum PJM, van der Heijden GHA, Villanueva-Garibay JA, Kentgens APM. Quantitative analysis of high field liquid state dynamic nuclear polarization. Phys Chem Chem Phys 2011; 13:17831-40. [DOI: 10.1039/c1cp22002k] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
41
|
Fratila RM, Velders AH. Small-volume nuclear magnetic resonance spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:227-249. [PMID: 21391818 DOI: 10.1146/annurev-anchem-061010-114024] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most information-rich analytical techniques available. However, it is also inherently insensitive, and this drawback precludes the application of NMR spectroscopy to mass- and volume-limited samples. We review a particular approach to increase the sensitivity of NMR experiments, namely the use of miniaturized coils. When the size of the coil is reduced, the sample volume can be brought down to the nanoliter range. We compare the main coil geometries (solenoidal, planar, and microslot/stripline) and discuss their applications to the analysis of mass-limited samples. We also provide an overview of the hyphenation of microcoil NMR spectroscopy to separation techniques and of the integration with lab-on-a-chip devices and microreactors.
Collapse
Affiliation(s)
- Raluca M Fratila
- MIRA Institute for Biomedical Engineering and Technical Medicine, Faculty of Science and Technology, University of Twente, 7500 AE Enschede, The Netherlands.
| | | |
Collapse
|
42
|
Jones CJ, Beni S, Limtiaco JFK, Langeslay DJ, Larive CK. Heparin characterization: challenges and solutions. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:439-465. [PMID: 21469955 DOI: 10.1146/annurev-anchem-061010-113911] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Although heparin is an important and widely prescribed pharmaceutical anticoagulant, its high degree of sequence microheterogeneity and size polydispersity make molecular-level characterization challenging. Unlike nucleic acids and proteins that are biosynthesized through template-driven assembly processes, heparin and the related glycosaminoglycan heparan sulfate are actively remodeled during biosynthesis through a series of enzymatic reactions that lead to variable levels of O- and N-sulfonation and uronic acid epimers. As summarized in this review, heparin sequence information is determined through a bottom-up approach that relies on depolymerization reactions, size- and charge-based separations, and sensitive mass spectrometric and nuclear magnetic resonance experiments to determine the structural identity of component oligosaccharides. The structure-elucidation process, along with its challenges and opportunities for future analytical improvements, is reviewed and illustrated for a heparin-derived hexasaccharide.
Collapse
Affiliation(s)
- Christopher J Jones
- Department of Chemistry, University of California, Riverside, California 92521, USA.
| | | | | | | | | |
Collapse
|
43
|
Tang JA, Jerschow A. Practical aspects of liquid-state NMR with inductively coupled solenoid coils. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:763-770. [PMID: 20665467 DOI: 10.1002/mrc.2651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Sensitivity enhancement by the use of inductively coupled milli- and microcoils has been demonstrated in solid-state as well as liquid-state NMR. In this work, we discuss the practical aspects of using inductively coupled solenoid coils of different sizes in a liquid-state NMR spectrometer. The sensitivity and resolution enhancements from these resonant coils, with sizes ranging between 3.0 and 0.75 mm i.d., are measured for (23)Na single-pulse and multidimensional imaging experiments and compared to the results obtained with the conventional liquids NMR 5.0-mm saddle coil. Enhancements in voxel-based sensitivity (SNR per √scans) were measured in multidimensional MR images and were found to be as large as 20.4 with the 0.75-mm coil.
Collapse
Affiliation(s)
- Joel A Tang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | | |
Collapse
|
44
|
Molinski TF. Microscale methodology for structure elucidation of natural products. Curr Opin Biotechnol 2010; 21:819-26. [PMID: 20880694 DOI: 10.1016/j.copbio.2010.09.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Revised: 09/01/2010] [Accepted: 09/02/2010] [Indexed: 11/15/2022]
Abstract
Advances in microscale spectroscopic techniques, particularly microcryoprobe NMR, allow discovery and structure elucidation of new molecules down to only a few nanomole. Newer methods for utilizing circular dichroism (CD) have pushed the limits of detection to picomole levels. NMR and CD methods are complementary to the task of elucidation of complete stereostructures of complex natural products. Together, integrated microprobe NMR spectroscopy, microscale degradation and synthesis, are synergistic tools for the discovery of bioactive natural products and have opened new realms for discovery among extreme sources including compounds from uncultured microbes, rare invertebrates and environmental samples.
Collapse
Affiliation(s)
- Tadeusz F Molinski
- Department of Chemistry and Biochemistry and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive MC0358, CA 92093, USA.
| |
Collapse
|
45
|
Dalisay DS, Molinski TF. Structure elucidation at the nanomole scale. 3. Phorbasides G-I from Phorbas sp. JOURNAL OF NATURAL PRODUCTS 2010; 73:679-82. [PMID: 20184337 PMCID: PMC2859111 DOI: 10.1021/np1000297] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Three new phorbasides (G-I), chlorocyclopropyl ene-yne macrolide glycosides, were isolated from the sponge Phorbas sp. in yields of 7-9.5 mug and fully characterized by MS, CD, and microcryoprobe NMR. The structures of the new compounds differ only in the nature of the sugar residues. The absolute configurations of the new compounds were correlated by ROESY and CD with the parent compounds phorbasides A and B.
Collapse
Affiliation(s)
| | - Tadeusz F. Molinski
- To whom correspondence should be addressed: Tel: +1 (858) 534-7115. Fax: +1 (858) 822-0386.
| |
Collapse
|
46
|
Kreutz JE, Shukhaev A, Du W, Druskin S, Daugulis O, Ismagilov RF. Evolution of catalysts directed by genetic algorithms in a plug-based microfluidic device tested with oxidation of methane by oxygen. J Am Chem Soc 2010; 132:3128-32. [PMID: 20148558 PMCID: PMC2861856 DOI: 10.1021/ja909853x] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This paper uses microfluidics to implement genetic algorithms (GA) to discover new homogeneous catalysts using the oxidation of methane by molecular oxygen as a model system. The parameters of the GA were the catalyst, a cocatalyst capable of using molecular oxygen as the terminal oxidant, and ligands that could tune the catalytic system. The GA required running hundreds of reactions to discover and optimize catalyst systems of high fitness, and microfluidics enabled these numerous reactions to be run in parallel. The small scale and volumes of microfluidics offer significant safety benefits. The microfluidic system included methods to form diverse arrays of plugs containing catalysts, introduce gaseous reagents at high pressure, run reactions in parallel, and detect catalyst activity using an in situ indicator system. Platinum(II) was identified as an active catalyst, and iron(II) and the polyoxometalate H(5)PMo(10)V(2)O(40) (POM-V2) were identified as active cocatalysts. The Pt/Fe system was further optimized and characterized using NMR experiments. After optimization, turnover numbers of approximately 50 were achieved with approximately equal production of methanol and formic acid. The Pt/Fe system demonstrated the compatibility of iron with the entire catalytic cycle. This approach of GA-guided evolution has the potential to accelerate discovery in catalysis and other areas where exploration of chemical space is essential, including optimization of materials for hydrogen storage and CO(2) capture and modifications.
Collapse
Affiliation(s)
- Jason E. Kreutz
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Anton Shukhaev
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Wenbin Du
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Sasha Druskin
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| | - Olafs Daugulis
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003
| | - Rustem F. Ismagilov
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637
| |
Collapse
|
47
|
Abstract
Metabolomics approaches provide an analysis of changing metabolite levels in biological samples. In the past decade, technical advances have spurred the application of metabolomics in a variety of diverse research areas spanning basic, biomedical, and clinical sciences. In particular, improvements in instrumentation, data analysis software, and the development of metabolite databases have accelerated the measurement and identification of metabolites. Metabolomics approaches have been applied to a number of important problems, which include the discovery of biomarkers as well as mechanistic studies aimed at discovering metabolites or metabolic pathways that regulate cellular and physiological processes. By providing access to a portion of biomolecular space not covered by other profiling approaches (e.g., proteomics and genomics), metabolomics offers unique insights into small molecule regulation and signaling in biology. In the following review, we look at the integration of metabolomics approaches in different areas of basic and biomedical research, and try to point out the areas in which these approaches have enriched our understanding of cellular and physiological biology, especially within the context of pathways linked to disease.
Collapse
Affiliation(s)
| | - Edwin A. Homan
- Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138
| | - Alan Saghatelian
- Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138
| |
Collapse
|
48
|
|
49
|
Sukumaran DK, Garcia E, Hua J, Tabaczynski W, Odunsi K, Andrews C, Szyperski T. Standard operating procedure for metabonomics studies of blood serum and plasma samples using a 1H-NMR micro-flow probe. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47 Suppl 1:S81-S85. [PMID: 19688872 DOI: 10.1002/mrc.2469] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A standard operating procedure (SOP) is presented for high-throughput metabonomics studies using a 600 MHz NMR spectrometer equipped with a micro-flow probe that is connected to an auto-sampler. The procedure is designed to minimize random and systematic variation of NMR data collection. In addition, a protocol is described to assess the quality of the data acquired by a given NMR spectroscopist to ensure that (i) all researchers involved in the NMR data acquisition of a metabonomics research program perform equally and (ii) operator-associated variation of NMR data collection is statistically not relevant for the interpretation of results obtained from multivariate data analyses.
Collapse
Affiliation(s)
- Dinesh K Sukumaran
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, NY, USA
| | | | | | | | | | | | | |
Collapse
|
50
|
Pelczer I. NMR-based mixture analysis--metabolomics and beyond.. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47 Suppl 1:S1. [PMID: 19899104 DOI: 10.1002/mrc.2547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
|