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Zheng C, Xue J, Jiang ZJ, Han J, Wang J, Bai JF, Chen J, Gao Z. Geometric constraints regulated regioselectivity: Pd-catalyzed α-deuteration of pyridines with secondary phosphine oxide. Chem Commun (Camb) 2024. [PMID: 39212444 DOI: 10.1039/d4cc03089c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
A Pd-catalyzed regioselective H/D exchange at the α-position of pyridines was achieved by employing secondary phosphine oxide as an internal base. The proposed five-membered structure enabled the reaction to overcome its conventional ortho-directing feature, allowing the efficient deuteration of pyridines and quinolines at adjacent sites of N-atoms.
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Affiliation(s)
- Chenxu Zheng
- NingboTech-Cuiying Joint Laboratory of Stable Isotope Technology, School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, P. R. China.
- School of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Jiben Xue
- NingboTech-Cuiying Joint Laboratory of Stable Isotope Technology, School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, P. R. China.
| | - Zhi-Jiang Jiang
- NingboTech-Cuiying Joint Laboratory of Stable Isotope Technology, School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, P. R. China.
| | - Jiawei Han
- NingboTech-Cuiying Joint Laboratory of Stable Isotope Technology, School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, P. R. China.
- School of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Jiaxin Wang
- NingboTech-Cuiying Joint Laboratory of Stable Isotope Technology, School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, P. R. China.
| | - Jian-Fei Bai
- NingboTech-Cuiying Joint Laboratory of Stable Isotope Technology, School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, P. R. China.
| | - Jia Chen
- NingboTech-Cuiying Joint Laboratory of Stable Isotope Technology, School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, P. R. China.
- Ningbo Cuiying Chemical Technology Co. Ltd., Ningbo 315100, P. R. China
| | - Zhanghua Gao
- NingboTech-Cuiying Joint Laboratory of Stable Isotope Technology, School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, P. R. China.
- Ningbo Cuiying Chemical Technology Co. Ltd., Ningbo 315100, P. R. China
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2
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Deberneh HM, Taylor ME, Borowik AK, Miyagi M, Miller BF, Sadygov RG. Numbers of Exchangeable Hydrogens from LC-MS Data of Heavy Water Metabolically Labeled Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1826-1837. [PMID: 39057601 DOI: 10.1021/jasms.4c00157] [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: 07/28/2024]
Abstract
Labeling with deuterium oxide (D2O) has emerged as one of the preferred approaches for measuring the synthesis of individual proteins in vivo. In these experiments, the synthesis rates of proteins are determined by modeling mass shifts in peptides during the labeling period. This modeling depends on a theoretical maximum enrichment determined by the number of labeling sites (NEH) of each amino acid in the peptide sequence. Currently, NEH is determined from one set of published values. However, it has been demonstrated that NEH can differ between species and potentially tissues. The goal of this work was to determine the number of NEH for each amino acid within a given experiment to capture the conditions unique to that experiment. We used four methods to compute the NEH values. To test these approaches, we used two publicly available data sets. In a de novo approach, we compute NEH values and the label enrichment from the abundances of three mass isotopomers. The other three methods use the complete isotope profiles and body water enrichment in deuterium as an input parameter. They determine the NEH values by (1) minimizing the residual sum of squares, (2) from the mole percent excess of labeling, and (3) the time course profile of the depletion of the relative isotope abundance of monoisotope. In the test samples, the method using residual sum of squares performed the best. The methods are implemented in a tool for determining the NEH for each amino acid within a given experiment to use in the determination of protein synthesis rates using D2O.
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Affiliation(s)
- Henock M Deberneh
- Department of Biochemistry and Molecular Biology The University of Texas Medical Branch 301 University of Blvd, Galveston, Texas 77555, United States
| | - Michael E Taylor
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street Oklahoma City, Oklahoma 73104, United States
| | - Agnieszka K Borowik
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street Oklahoma City, Oklahoma 73104, United States
| | - Masaru Miyagi
- Department of Pharmacology Case Western Reserve University 10900 Euclid Avenue Cleveland, Ohio 44106, United States
| | - Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street Oklahoma City, Oklahoma 73104, United States
- Oklahoma City VA, Oklahoma City, Oklahoma 73104, United States
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology The University of Texas Medical Branch 301 University of Blvd, Galveston, Texas 77555, United States
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Kasarla SS, Flocke V, Saw NMT, Fecke A, Sickmann A, Gunzer M, Flögel U, Phapale P. In-vivo tracking of deuterium metabolism in mouse organs using LC-MS/MS. J Chromatogr A 2024; 1717:464691. [PMID: 38301333 DOI: 10.1016/j.chroma.2024.464691] [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: 11/09/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Mass spectrometry-based metabolomics with stable isotope labeling (SIL) is an established tool for sensitive and precise analyses of tissue metabolism, its flux, and pathway activities in diverse models of physiology and disease. Despite the simplicity and broad applicability of deuterium (2H)-labeled precursors for tracing metabolic pathways with minimal biological perturbations, they are rarely employed in LC-MS/MS-guided metabolomics. In this study, we have developed a LC-MS/MS-guided workflow to trace deuterium metabolism in mouse organs following 2H7 -glucose infusion. The workflow includes isotopically labeled glucose infusion, mouse organ isolation and metabolite extraction, zwitterion-based hydrophilic interaction liquid chromatography (HILIC) coupled to high-resolution tandem mass spectrometry, targeted data acquisition for sensitive detection of deuterated metabolites, a spectral library of over 400 metabolite standards, and multivariate data analysis with pathway mapping. The optimized method was validated for matrix effects, normalization, and quantification to provide both tissue metabolomics and tracking the in-vivo metabolic fate of deuterated glucose through key metabolic pathways. We quantified more than 100 metabolites in five major mouse organ tissues (liver, kidney, brain, brown adipose tissue, and heart). Furthermore, we mapped isotopologues of deuterated metabolites from glycolysis, tricarboxylic acid (TCA) cycle, and amino acid pathways, which are significant for studying both health and various diseases. This study will open new avenues in LC-MS based analysis of 2H-labeled tissue metabolism research in animal models and clinical settings.
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Affiliation(s)
- Siva Swapna Kasarla
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany
| | - Vera Flocke
- Experimental Cardiovascular Imaging, Institute for Molecular Cardiology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Nay Min Thaw Saw
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany
| | - Antonia Fecke
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany
| | - Matthias Gunzer
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany; Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen 45122, Germany
| | - Ulrich Flögel
- Experimental Cardiovascular Imaging, Institute for Molecular Cardiology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany; Cardiovascular Research Institute Düsseldorf (CARID), Düsseldorf 40225, Germany
| | - Prasad Phapale
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany.
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Rensner JJ, Lueth P, Bellaire BH, Sahin O, Lee YJ. Rapid detection of antimicrobial resistance in methicillin-resistant Staphylococcus aureus using MALDI-TOF mass spectrometry. Front Cell Infect Microbiol 2023; 13:1281155. [PMID: 38076465 PMCID: PMC10702551 DOI: 10.3389/fcimb.2023.1281155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023] Open
Abstract
Antimicrobial resistance is a growing problem in modern healthcare. Most antimicrobial susceptibility tests (AST) require long culture times which delay diagnosis and effective treatment. Our group has previously reported a proof-of-concept demonstration of a rapid AST in Escherichia coli using deuterium labeling and MALDI mass spectrometry. Culturing bacteria in D2O containing media incorporates deuterium in newly synthesized lipids, resulting in a mass shift that can be easily detected by mass spectrometry. The extent of new growth is measured by the average mass of synthesized lipids that can be correlated with resistance in the presence of antimicrobials. In this work, we adapt this procedure to methicillin-resistant Staphylococcus aureus using the Bruker MALDI-TOF Biotyper, a low-cost instrument commonly available in diagnostic laboratories. The susceptible strain showed a significant decrease in average mass in on-target microdroplet cultures after 3 hours of incubation with 10 µg/mL methicillin, while the resistant strain showed consistent labeling regardless of methicillin concentration. This assay allows us to confidently detect methicillin resistance in S. aureus after only 3 hours of culture time and minimal sample processing, reducing the turn-around-time significantly over conventional assays. The success of this work suggests its potential as a rapid AST widely applicable in many clinical microbiology labs with minimal additional costs.
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Affiliation(s)
- Josiah J. Rensner
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Paul Lueth
- Department of Veterinary Microbiology and Preventative Medicine, Iowa State University, Ames, IA, United States
| | - Bryan H. Bellaire
- Department of Veterinary Microbiology and Preventative Medicine, Iowa State University, Ames, IA, United States
| | - Orhan Sahin
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA, United States
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5
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Deberneh HM, Abdelrahman DR, Verma SK, Linares JJ, Murton AJ, Russell WK, Kuyumcu-Martinez MN, Miller BF, Sadygov RG. A large-scale LC-MS dataset of murine liver proteome from time course of heavy water metabolic labeling. Sci Data 2023; 10:635. [PMID: 37726365 PMCID: PMC10509199 DOI: 10.1038/s41597-023-02537-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Metabolic stable isotope labeling with heavy water followed by liquid chromatography coupled with mass spectrometry (LC-MS) is a powerful tool for in vivo protein turnover studies. Several algorithms and tools have been developed to determine the turnover rates of peptides and proteins from time-course stable isotope labeling experiments. The availability of benchmark mass spectrometry data is crucial to compare and validate the effectiveness of newly developed techniques and algorithms. In this work, we report a heavy water-labeled LC-MS dataset from the murine liver for protein turnover rate analysis. The dataset contains eighteen mass spectral data with their corresponding database search results from nine different labeling durations and quantification outputs from d2ome+ software. The dataset also contains eight mass spectral data from two-dimensional fractionation experiments on unlabeled samples.
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Affiliation(s)
- Henock M Deberneh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
| | - Doaa R Abdelrahman
- Department of Surgery, The University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center of Aging, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Sunil K Verma
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Neuroscience, Cell Biology and Anatomy, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Molecular Physiology and Biological Physics, The University of Virginia, Charlottesville, Virginia, USA
| | - Jennifer J Linares
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew J Murton
- Department of Surgery, The University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center of Aging, The University of Texas Medical Branch, Galveston, Texas, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Neuroscience, Cell Biology and Anatomy, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Molecular Physiology and Biological Physics, The University of Virginia, Charlottesville, Virginia, USA
| | - Benjamin F Miller
- Aging and Metabolism Research Foundation, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Oklahoma City VA, Oklahoma City, Oklahoma, USA
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
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Brender JR, Assmann JC, Farthing DE, Saito K, Kishimoto S, Warrick KA, Maglakelidze N, Larus TL, Merkle H, Gress RE, Krishna MC, Buxbaum NP. In vivo deuterium magnetic resonance imaging of xenografted tumors following systemic administration of deuterated water. Sci Rep 2023; 13:14699. [PMID: 37679461 PMCID: PMC10485001 DOI: 10.1038/s41598-023-41163-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023] Open
Abstract
In vivo deuterated water (2H2O) labeling leads to deuterium (2H) incorporation into biomolecules of proliferating cells and provides the basis for its use in cell kinetics research. We hypothesized that rapidly proliferating cancer cells would become preferentially labeled with 2H and, therefore, could be visualized by deuterium magnetic resonance imaging (dMRI) following a brief period of in vivo systemic 2H2O administration. We initiated systemic 2H2O administration in two xenograft mouse models harboring either human colorectal, HT-29, or pancreatic, MiaPaCa-2, tumors and 2H2O level of ~ 8% in total body water (TBW). Three schemas of 2H2O administration were tested: (1) starting at tumor seeding and continuing for 7 days of in vivo growth with imaging on day 7, (2) starting at tumor seeding and continuing for 14 days of in vivo growth with imaging on day 14, and (3) initiation of labeling following a week of in vivo tumor growth and continuing until imaging was performed on day 14. Deuterium chemical shift imaging of the tumor bearing limb and contralateral control was performed on either day 7 of 14 after tumor seeding, as described. After 14 days of in vivo tumor growth and 7 days of systemic labeling with 2H2O, a clear deuterium contrast was demonstrated between the xenografts and normal tissue. Labeling in the second week after tumor implantation afforded the highest contrast between neoplastic and healthy tissue in both models. Systemic labeling with 2H2O can be used to create imaging contrast between tumor and healthy issue, providing a non-radioactive method for in vivo cancer imaging.
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Affiliation(s)
- Jeffrey R Brender
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julian C Assmann
- Experimental Transplantation and Immunotherapy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Don E Farthing
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keita Saito
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shun Kishimoto
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kathrynne A Warrick
- Experimental Transplantation and Immunotherapy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Natella Maglakelidze
- Experimental Transplantation and Immunotherapy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Terri L Larus
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hellmut Merkle
- Laboratory for Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ronald E Gress
- Experimental Transplantation and Immunotherapy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Murali C Krishna
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nataliya P Buxbaum
- Experimental Transplantation and Immunotherapy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- Pediatric Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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Junghans P, Zuz G, Faust H. Measurement of plasma protein and whole body protein metabolism using [ 15N]glycine in a young adult man - a pilot study. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2023; 59:511-528. [PMID: 37724354 DOI: 10.1080/10256016.2023.2252572] [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: 07/01/2023] [Accepted: 07/24/2023] [Indexed: 09/20/2023]
Abstract
A novel simplified method is presented for the estimation of the metabolism of plasma proteins (albumin, fibrinogen, α, β and γ-globulin, glycoprotein) with regard to the whole body protein metabolism in a young male volunteer (22 years, 81 kg body mass). This method is based on multiple oral administration of [15N]glycine followed by measurement of 15N in plasma proteins, total free amino acids, urea and excreted urinary N. The fractional synthesis rate of albumin was estimated to 6.8 % d-1 based on amino acids and 3.3 % d-1 based on urea, respectively. The fractional synthesis rate of the other plasma proteins ranged from 4.3 % d-1 (γ-globulin) to 26.4 % d-1 (α-globulin, fibrinogen). We conclude that the simplified approach using [15N]glycine provides results which are similar to results based on the simultaneously applied 131I-human serum albumin technique as 'gold standard' and to those reported in literature. The compartmental analysis considering comprehensive tracer kinetic data ensures reliable data treatment and enables statistical evaluation. The analytical effort is minimal because the 15N enrichment of plasma protein after chemical digestion may be directly used. Therefore, the novel stable isotope 15N method is suitable for studies in clinical and nutritional research and practice.
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Affiliation(s)
- Peter Junghans
- Research Institute for Farm Animal Biology (FBN), Institute of Nutritional Physiology 'Oskar Kellner', Dummerstorf, Germany
| | - Gerhard Zuz
- Stünz-Mölkauer Weg 48, Leipzig 04318, Germany
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