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Lin W, Mellinghaus K, Rodriguez-Mateos A, Globisch D. Identification of nutritional biomarkers through highly sensitive and chemoselective metabolomics. Food Chem 2023; 425:136481. [PMID: 37276670 DOI: 10.1016/j.foodchem.2023.136481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/19/2023] [Accepted: 05/26/2023] [Indexed: 06/07/2023]
Abstract
The importance of a healthy diet for humans is known for decades. The elucidation of key molecules responsible for the beneficial and adverse dietary effects is slowly developing as the tools are missing. Carbonyl-containing metabolites are a common bioproducts through conversion of diet by the microbiome. In here, we have utilized our recently developed mass spectrometric methodology based on chemoselective conjugation of carbonyl-metabolites. The method has been applied for urine sample analysis from a dietary (poly)phenol intervention study (N = 78 individuals) for the first time. We have identified a series of carbonyl-metabolites of dietary origin and the chemical structure was validated for 30 metabolites. Our sensitive analysis led to the discovery of four unknown dietary markers with high sensitivity and selectivity (AUC > 0.91). Our chemical metabolomics method has been successfully applied for large-scale analysis and provides the basis for targeted metabolomics to identify unknown nutritional and disease-related biomarkers.
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Affiliation(s)
- Weifeng Lin
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75124 Uppsala, Sweden
| | - Kiana Mellinghaus
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75124 Uppsala, Sweden
| | - Ana Rodriguez-Mateos
- Department of Nutritional Sciences, School of Life Course and Population Sciences, Faculty of Life Sciences and Medicine, King's College London, UK
| | - Daniel Globisch
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-75124 Uppsala, Sweden.
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2
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Kaur A, Lin W, Dovhalyuk V, Driutti L, Di Martino ML, Vujasinovic M, Löhr JM, Sellin ME, Globisch D. Chemoselective bicyclobutane-based mass spectrometric detection of biological thiols uncovers human and bacterial metabolites. Chem Sci 2023; 14:5291-5301. [PMID: 37234898 PMCID: PMC10207876 DOI: 10.1039/d3sc00224a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/05/2023] [Indexed: 05/28/2023] Open
Abstract
Sulfur is an essential element of life. Thiol-containing metabolites in all organisms are involved in the regulation of diverse biological processes. Especially, the microbiome produces bioactive metabolites or biological intermediates of this compound class. The analysis of thiol-containing metabolites is challenging due to the lack of specific tools, making these compounds difficult to investigate selectively. We have now developed a new methodology comprising bicyclobutane for chemoselective and irreversible capturing of this metabolite class. We utilized this new chemical biology tool immobilized onto magnetic beads for the investigation of human plasma, fecal samples, and bacterial cultures. Our mass spectrometric investigation detected a broad range of human, dietary and bacterial thiol-containing metabolites and we even captured the reactive sulfur species cysteine persulfide in both fecal and bacterial samples. The described comprehensive methodology represents a new mass spectrometric strategy for the discovery of bioactive thiol-containing metabolites in humans and the microbiome.
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Affiliation(s)
- Amanpreet Kaur
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Weifeng Lin
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Vladyslav Dovhalyuk
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Léna Driutti
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Maria Letizia Di Martino
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University 75123 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute Stockholm Sweden
| | - Mikael E Sellin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University 75123 Uppsala Sweden
| | - Daniel Globisch
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
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3
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Zhang M, Lai Z, Zhang R, Liu S, Tian H, Qiu Y, Li D, Zhou J, Li Z. Polyurea-Modified Magnetic Particles with Versatile Probes for Chemoselective Capture of Carbonyl Metabolites and Biomarker Discovery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204734. [PMID: 36354199 DOI: 10.1002/smll.202204734] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Playing a great role in human physiologies and pathologies, carbonyl metabolites are intimately associated with a variety of diseases, though the effective analysis method of them remains a challenge. A hydrazide-terminated polyurea-modified magnetic particle (HPMP) with versatile probes is developed to address this issue. The capture ability of HPMPs for carbonyl metabolite is more than 1200 µmol g-1 , which is increased by 4 orders of magnitude via the introduction of polyurea. With a broad linear range of over 4 orders of magnitude, remarkably improved sensitivity, and limit of detection at attomole quantities, HPMPs are applied in relative quantification of more than 1500 carbonyl metabolites in 113 human serum samples with high throughput and high coverage. The combined indicators of these metabolites demonstrates a great diagnostic accuracy for distinguishing between health and disease subjects as well as differentiating the patients with benign lung disease and lung cancer. Combining powerful capture ability, low-cost preparation, and convenient operation, the HPMPs demonstrate extensive application in biomarker discovery and the detailed study of the biochemical landscape.
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Affiliation(s)
- Mo Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Renjun Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Shuai Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Hongtao Tian
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yuming Qiu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Dan Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Beijing, 100871, China
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
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4
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Wang SY, Liu H, Zhu JH, Zhou SS, Xu JD, Zhou J, Mao Q, Kong M, Li SL, Zhu H. 2,4-dinitrophenylhydrazine capturing combined with mass defect filtering strategy to identify aliphatic aldehydes in biological samples. J Chromatogr A 2022; 1679:463405. [DOI: 10.1016/j.chroma.2022.463405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022]
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5
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Müller MJ, Dorst A, Paulus C, Khan I, Sieber S. Catch-enrich-release approach for amine-containing natural products. Chem Commun (Camb) 2022; 58:12560-12563. [DOI: 10.1039/d2cc04905h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemoselective approach to extract amine-containing natural products from complex matrices. The enzymatic release from the probe affords the underivatised compounds as products.
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Affiliation(s)
| | - Andrea Dorst
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Constanze Paulus
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Imran Khan
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
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6
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Lin W, Conway LP, Vujasinovic M, Löhr J, Globisch D. Chemoselective and Highly Sensitive Quantification of Gut Microbiome and Human Metabolites. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Weifeng Lin
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
| | - Louis P. Conway
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases Karolinska University Hospital Stockholm Sweden
| | - J.‐Matthias Löhr
- Department for Digestive Diseases Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science Intervention and Technology (CLINTEC) Karolinska Institute Stockholm Sweden
| | - Daniel Globisch
- Department of Chemistry—BMC Science for Life Laboratory Uppsala University, Box 599 75124 Uppsala Sweden
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7
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Progress and Challenges in Quantifying Carbonyl-Metabolomic Phenomes with LC-MS/MS. Molecules 2021; 26:molecules26206147. [PMID: 34684729 PMCID: PMC8541004 DOI: 10.3390/molecules26206147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/17/2022] Open
Abstract
Carbonyl-containing metabolites widely exist in biological samples and have important physiological functions. Thus, accurate and sensitive quantitative analysis of carbonyl-containing metabolites is crucial to provide insight into metabolic pathways as well as disease mechanisms. Although reversed phase liquid chromatography electrospray ionization mass spectrometry (RPLC-ESI-MS) is widely used due to the powerful separation capability of RPLC and high specificity and sensitivity of MS, but it is often challenging to directly analyze carbonyl-containing metabolites using RPLC-ESI-MS due to the poor ionization efficiency of neutral carbonyl groups in ESI. Modification of carbonyl-containing metabolites by a chemical derivatization strategy can overcome the obstacle of sensitivity; however, it is insufficient to achieve accurate quantification due to instrument drift and matrix effects. The emergence of stable isotope-coded derivatization (ICD) provides a good solution to the problems encountered above. Thus, LC-MS methods that utilize ICD have been applied in metabolomics including quantitative targeted analysis and untargeted profiling analysis. In addition, ICD makes multiplex or multichannel submetabolome analysis possible, which not only reduces instrument running time but also avoids the variation of MS response. In this review, representative derivatization reagents and typical applications in absolute quantification and submetabolome profiling are discussed to highlight the superiority of the ICD strategy for detection of carbonyl-containing metabolites.
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8
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Lin W, Yang Z, Kaur A, Block A, Vujasinovic M, Löhr JM, Globisch D. Squaric acid as a new chemoselective moiety for mass spectrometry-based metabolomics analysis of amines. RSC Chem Biol 2021; 2:1479-1483. [PMID: 34704052 PMCID: PMC8496035 DOI: 10.1039/d1cb00132a] [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: 06/15/2021] [Accepted: 08/10/2021] [Indexed: 12/24/2022] Open
Abstract
The investigation of microbiome-derived metabolites is important to understand metabolic interactions with their human host. New methodologies for mass spectrometric discovery of undetected metabolites with unknown bioactivity are required. Herein, we introduce squaric acid as a new chemoselective moiety for amine metabolite analysis in human fecal samples.
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Affiliation(s)
- Weifeng Lin
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
| | - Zhen Yang
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
| | - Amanpreet Kaur
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
| | - Annika Block
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute Stockholm Sweden
| | - Daniel Globisch
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Box 599 Uppsala SE-75124 Sweden
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9
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Kijewska M, Koch T, Waliczek M, Konieczny A, Stefanowicz P, Szewczuk Z. Selective ESI-MS detection of carbonyl containing compounds by aminooxyacetic acid immobilized on a resin. Anal Chim Acta 2021; 1176:338767. [PMID: 34399903 DOI: 10.1016/j.aca.2021.338767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/28/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
There are numerous examples of bioactive compounds containing carbonyl groups including modified proteins with oxidation of side chain of amino acid residues to aldehyde/ketone groups which are frequently considered as markers of oxidative stress. The carbonyl unit can be also distinguished as a substructure in many illegal drugs including anabolic steroids as well as cations derivatives. Based on chemoselective formation of oximes by solid phase immobilized hydroxylamine derivatives we proposed the protocol for derivatization and selective detection of carbonylated compounds in human serum albumin hydrolysate as a complex peptide mixture and of testosterone in urine samples. This allowed for the removal of the matrix and the qualitative and quantitative analysis of the derivatized analyte by LC-MS/MS (or LC-MRM). Herein we report the preparation and chemical characterization of a novel, ChemMatrix - based resin functionalized with aminooxyacetic acid (AOA). The hydroxylamine moiety in this resin is combined with a peptide linker (GRG) containing an arginine residue to enhance the ionization efficiency. Application of an isotopically labeled carbonylated peptide ((H-Leu-Val-Thr(O)-Asp-Leu-Thr-Lys [13C6,15N2]-OH and testosterone-d3 allowed us to carry out quantitative analyses of detected compounds. Our method is general and may be applied for analysis of carbonylated compounds in biological samples. Our method based on application of functionalized resin allowed to quantify the level of free testosterone in small sample (0.5 mL) of urine, while the non-derivatized testosterone from urine sample was not detected during direct LC-MRM analysis.
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Affiliation(s)
- Monika Kijewska
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland.
| | - Tomasz Koch
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Andrzej Konieczny
- Department of Nephrology and Transplantation Medicine, Wrocław Medical University, Borowska 213, 50-556, Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
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10
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Lin W, Conway LP, Vujasinovic M, Löhr JM, Globisch D. Chemoselective and highly sensitive quantification of gut microbiome and human metabolites. Angew Chem Int Ed Engl 2021; 60:23232-23240. [PMID: 34339587 PMCID: PMC8597006 DOI: 10.1002/anie.202107101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/15/2021] [Indexed: 11/18/2022]
Abstract
The microbiome has a fundamental impact on the human host's physiology through the production of highly reactive compounds that can lead to disease development. One class of such compounds are carbonyl‐containing metabolites, which are involved in diverse biochemical processes. Mass spectrometry is the method of choice for analysis of metabolites but carbonyls are analytically challenging. Herein, we have developed a new chemical biology tool using chemoselective modification to overcome analytical limitations. Two isotopic probes allow for the simultaneous and semi‐quantitative analysis at the femtomole level as well as qualitative analysis at attomole quantities that allows for detection of more than 200 metabolites in human fecal, urine and plasma samples. This comprehensive mass spectrometric analysis enhances the scope of metabolomics‐driven biomarker discovery. We anticipate that our chemical biology tool will be of general use in metabolomics analysis to obtain a better understanding of microbial interactions with the human host and disease development.
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Affiliation(s)
- Weifeng Lin
- Uppsala University: Uppsala Universitet, Dept. Chemistry - BMC, Uppsala, SWEDEN
| | - Louis P Conway
- Uppsala University: Uppsala Universitet, Dept. Chem. - BMC, 75421, Uppsala, SWEDEN
| | - Miroslav Vujasinovic
- Karolinska University Hospital: Karolinska Universitetssjukhuset, Dept. for Digestive Diseases, Stockholm, SWEDEN
| | - J-Matthias Löhr
- Karolinska Institute: Karolinska Institutet, Dept. Clinical Science, Intervention and Technology, Stockholm, SWEDEN
| | - Daniel Globisch
- Uppsala University, Department of Medicinal Chemistry, Husaragatan 3, Biomedical Center, Box 574, 75123, Uppsala, SWEDEN
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11
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Endo S, Matsunaga T, Nishinaka T. The Role of AKR1B10 in Physiology and Pathophysiology. Metabolites 2021; 11:332. [PMID: 34063865 PMCID: PMC8224097 DOI: 10.3390/metabo11060332] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
AKR1B10 is a human nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductase belonging to the aldo-keto reductase (AKR) 1B subfamily. It catalyzes the reduction of aldehydes, some ketones and quinones, and interacts with acetyl-CoA carboxylase and heat shock protein 90α. The enzyme is highly expressed in epithelial cells of the stomach and intestine, but down-regulated in gastrointestinal cancers and inflammatory bowel diseases. In contrast, AKR1B10 expression is low in other tissues, where the enzyme is upregulated in cancers, as well as in non-alcoholic fatty liver disease and several skin diseases. In addition, the enzyme's expression is elevated in cancer cells resistant to clinical anti-cancer drugs. Thus, growing evidence supports AKR1B10 as a potential target for diagnosing and treating these diseases. Herein, we reviewed the literature on the roles of AKR1B10 in a healthy gastrointestinal tract, the development and progression of cancers and acquired chemoresistance, in addition to its gene regulation, functions, and inhibitors.
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Affiliation(s)
- Satoshi Endo
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Gifu 501-1196, Japan
| | - Toshiyuki Matsunaga
- Education Center of Green Pharmaceutical Sciences, Gifu Pharmaceutical University, Gifu 502-8585, Japan;
| | - Toru Nishinaka
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi 584-8540, Osaka, Japan;
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12
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Beard HA, Korovesis D, Chen S, Verhelst SHL. Cleavable linkers and their application in MS-based target identification. Mol Omics 2021; 17:197-209. [PMID: 33507200 DOI: 10.1039/d0mo00181c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covalent chemical probes are important tools in chemical biology. They range from post-translational modification (PTM)-derived metabolic probes, to activity-based probes and photoaffinity labels. Identification of the probe targets is often performed by tandem mass spectrometry-based proteomics methods. In the past fifteen years, cleavable linker technologies have been implemented in these workflows in order to identify probe targets with lower background and higher confidence. In addition, the linkers have enabled identification of modification sites. Overall, this has led to an increased knowledge of PTMs, enzyme function and drug action. This review gives an overview of the different types of cleavable linkers, and their benefits and limitations. Their applicability in target identification is also illustrated by several specific examples.
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Affiliation(s)
- Hester A Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 box 802, 3000 Leuven, Belgium.
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13
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Li H, Li T, Shi X, Xu G. Recent development of nanoparticle-assisted metabolites analysis with mass spectrometry. J Chromatogr A 2020; 1636:461785. [PMID: 33340742 DOI: 10.1016/j.chroma.2020.461785] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023]
Abstract
Metabolomics systematically studies the changes of metabolites in biological systems in the temporal or spatial dimensions. It is a challenging task for comprehensive analysis of metabolomics because of diverse physicochemical properties and wide concentration distribution of metabolites. Used as enrichment sorbents, chemoselective probes, chromatographic stationary phases, MS ionization matrix, nanomaterials play excellent roles in improving the selectivity, separation performance, detection sensitivity and identification efficiency of metabolites when mass spectrometry is employed as the detection technique. This review summarized the recent development of nanoparticle-assisted metabolites analysis in terms of assisting the pretreatment of biological samples, improving the separation performance and enhancing the MALDI-MS detection.
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Affiliation(s)
- Hua Li
- SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Ting Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian, 116024, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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14
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Dicarbonyl derived post-translational modifications: chemistry bridging biology and aging-related disease. Essays Biochem 2020; 64:97-110. [PMID: 31939602 DOI: 10.1042/ebc20190057] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/17/2023]
Abstract
In living systems, nucleophilic amino acid residues are prone to non-enzymatic post-translational modification by electrophiles. α-Dicarbonyl compounds are a special type of electrophiles that can react irreversibly with lysine, arginine, and cysteine residues via complex mechanisms to form post-translational modifications known as advanced glycation end-products (AGEs). Glyoxal, methylglyoxal, and 3-deoxyglucosone are the major endogenous dicarbonyls, with methylglyoxal being the most well-studied. There are several routes that lead to the formation of dicarbonyl compounds, most originating from glucose and glucose metabolism, such as the non-enzymatic decomposition of glycolytic intermediates and fructosyl amines. Although dicarbonyls are removed continuously mainly via the glyoxalase system, several conditions lead to an increase in dicarbonyl concentration and thereby AGE formation. AGEs have been implicated in diabetes and aging-related diseases, and for this reason the elucidation of their structure as well as protein targets is of great interest. Though the dicarbonyls and reactive protein side chains are of relatively simple nature, the structures of the adducts as well as their mechanism of formation are not that trivial. Furthermore, detection of sites of modification can be demanding and current best practices rely on either direct mass spectrometry or various methods of enrichment based on antibodies or click chemistry followed by mass spectrometry. Future research into the structure of these adducts and protein targets of dicarbonyl compounds may improve the understanding of how the mechanisms of diabetes and aging-related physiological damage occur.
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15
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Correia MSP, Lin W, Aria AJ, Jain A, Globisch D. Rapid Preparation of a Large Sulfated Metabolite Library for Structure Validation in Human Samples. Metabolites 2020; 10:metabo10100415. [PMID: 33081284 PMCID: PMC7603051 DOI: 10.3390/metabo10100415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/04/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Metabolomics analysis of biological samples is widely applied in medical and natural sciences. Assigning the correct chemical structure in the metabolite identification process is required to draw the correct biological conclusions and still remains a major challenge in this research field. Several metabolite tandem mass spectrometry (MS/MS) fragmentation spectra libraries have been developed that are either based on computational methods or authentic libraries. These libraries are limited due to the high number of structurally diverse metabolites, low commercial availability of these compounds, and the increasing number of newly discovered metabolites. Phase II modification of xenobiotics is a compound class that is underrepresented in these databases despite their importance in diet, drug, or microbiome metabolism. The O-sulfated metabolites have been described as a signature for the co-metabolism of bacteria and their human host. Herein, we have developed a straightforward chemical synthesis method for rapid preparation of sulfated metabolite standards to obtain mass spectrometric fragmentation pattern and retention time information. We report the preparation of 38 O-sulfated alcohols and phenols for the determination of their MS/MS fragmentation pattern and chromatographic properties. Many of these metabolites are regioisomers that cannot be distinguished solely by their fragmentation pattern. We demonstrate that the versatility of this method is comparable to standard chemical synthesis. This comprehensive metabolite library can be applied for co-injection experiments to validate metabolites in different human sample types to explore microbiota-host co-metabolism, xenobiotic, and diet metabolism.
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16
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Hoki JS, Le HH, Mellott KE, Zhang YK, Fox BW, Rodrigues PR, Yu Y, Helf MJ, Baccile JA, Schroeder FC. Deep Interrogation of Metabolism Using a Pathway-Targeted Click-Chemistry Approach. J Am Chem Soc 2020; 142:18449-18459. [PMID: 33053303 DOI: 10.1021/jacs.0c06877] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Untargeted metabolomics indicates that the number of unidentified small-molecule metabolites may exceed the number of protein-coding genes for many organisms, including humans, by orders of magnitude. Uncovering the underlying metabolic networks is essential for elucidating the physiological and ecological significance of these biogenic small molecules. Here we develop a click-chemistry-based enrichment strategy, DIMEN (deep interrogation of metabolism via enrichment), that we apply to investigate metabolism of the ascarosides, a family of signaling molecules in the model organism C. elegans. Using a single alkyne-modified metabolite and a solid-phase azide resin that installs a diagnostic moiety for MS/MS-based identification, DIMEN uncovered several hundred novel compounds originating from diverse biosynthetic transformations that reveal unexpected intersection with amino acid, carbohydrate, and energy metabolism. Many of the newly discovered transformations could not be identified or detected by conventional LC-MS analyses without enrichment, demonstrating the utility of DIMEN for deeply probing biochemical networks that generate extensive yet uncharacterized structure space.
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Affiliation(s)
- Jason S Hoki
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Karlie E Mellott
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Pedro R Rodrigues
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yan Yu
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Maximilian J Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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17
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Qiao Y, Hayashi H, Chong Teo S. Chemical Toolbox to Decode the Microbiota Lexicon. Chem Asian J 2020; 15:2117-2128. [PMID: 32558250 DOI: 10.1002/asia.202000541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/14/2020] [Indexed: 12/15/2022]
Abstract
The human microbiota deploys a diverse range of molecules and metabolites to engage in chemical communications with the host, mediating fundamental aspects of host health. Studies of the structures and activities of bioactive molecules produced by the microbiota are imperative to address their implications in microbiota associated diseases in human. By drawing experiences from different research fields, chemists and chemical biologists, who are experts in dealing with chemical molecules, are uniquely positioned to contribute to the emerging knowledge of human microbiota. In this minireview, we discuss the current chemical tools and methods that are pertinent to the discovery of microbiota molecules and metabolites, characterizations of their protein targets, as well as evaluations of their biodistributions in hosts. These are key aspects in understanding the chemical underpinnings of the microbiota-host interactions that would enable future development of diagnostics and therapeutics targeting the human microbiota.
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Affiliation(s)
- Yuan Qiao
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
| | - Hirohito Hayashi
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
| | - Seng Chong Teo
- School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), 21 Nanyang Link, CBC 04-22, Singapore, 637371, Singapore
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18
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Lin W, Conway LP, Block A, Sommi G, Vujasinovic M, Löhr JM, Globisch D. Sensitive mass spectrometric analysis of carbonyl metabolites in human urine and fecal samples using chemoselective modification. Analyst 2020; 145:3822-3831. [PMID: 32393929 DOI: 10.1039/d0an00150c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Metabolites with ketone or aldehyde functionalities comprise a large proportion of the human metabolome, most notably in the form of sugars. However, these reactive molecules are also generated through oxidative stress or gut microbiota metabolism and have been linked to disease development. The discovery and structural validation of this class of metabolites over the large concentration range found in human samples is crucial to identify their links to pathogenesis. Herein, we have utilized an advanced chemoselective probe methodology alongside bioinformatic analysis to identify carbonyl-metabolites in urine and fecal samples. In total, 99 metabolites were identified in urine samples and the chemical structure for 40 metabolites were unambiguously validated using a co-injection procedure. We also describe the preparation of a metabolite-conjugate library of 94 compounds utilized to efficiently validate these ketones and aldehydes. This method was used to validate 33 metabolites in a pooled fecal sample extract to demonstrate the potential for rapid and efficient metabolite detection over a wide metabolite concentration range. This analysis revealed the presence of six metabolites that have not previously been detected in either sample type. The constructed library can be utilized for straightforward, large-scale, and expeditious analysis of carbonyls in any sample type.
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Affiliation(s)
- Weifeng Lin
- Department of Medicinal Chemistry, Science for Life Laboratory, Uppsala University, Box 574, SE-75123 Uppsala, Sweden.
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19
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Chen J, Tian Y, Zhang YX, Xu FG. Chemoselective Probes Serving as Promising Derivatization Tools in Targeted Metabolomics Research. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00125-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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