1
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Vilen Z, Reeves AE, Huang ML. (Glycan Binding) Activity‐Based Protein Profiling in Cells Enabled by Mass Spectrometry‐Based Proteomics. Isr J Chem 2023; 63. [PMID: 37131487 PMCID: PMC10150848 DOI: 10.1002/ijch.202200097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The presence of glycan modifications at the cell surface and other locales positions them as key regulators of cell recognition and function. However, due to the complexity of glycosylation, the annotation of which proteins bear glycan modifications, which glycan patterns are present, and which proteins are capable of binding glycans is incomplete. Inspired by activity-based protein profiling to enrich for proteins in cells based on select characteristics, these endeavors have been greatly advanced by the development of appropriate glycan-binding and glycan-based probes. Here, we provide context for these three problems and describe how the capability of molecules to interact with glycans has enabled the assignment of proteins with specific glycan modifications or of proteins that bind glycans. Furthermore, we discuss how the integration of these probes with high resolution mass spectrometry-based technologies has greatly advanced glycoscience.
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Affiliation(s)
- Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
| | - Abigail E. Reeves
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
| | - Mia L. Huang
- Skaggs Graduate School of Chemical and Biological Sciences Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
- Department of Molecular Medicine Scripps Research 10550 N. Torrey Pines Rd. La Jolla CA 92037, USA
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2
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Jain N, Tamura K, Déjean G, Van Petegem F, Brumer H. Orthogonal Active-Site Labels for Mixed-Linkage endo-β-Glucanases. ACS Chem Biol 2021; 16:1968-1984. [PMID: 33988963 DOI: 10.1021/acschembio.1c00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecule irreversible inhibitors are valuable tools for determining catalytically important active-site residues and revealing key details of the specificity, structure, and function of glycoside hydrolases (GHs). β-glucans that contain backbone β(1,3) linkages are widespread in nature, e.g., mixed-linkage β(1,3)/β(1,4)-glucans in the cell walls of higher plants and β(1,3)glucans in yeasts and algae. Commensurate with this ubiquity, a large diversity of mixed-linkage endoglucanases (MLGases, EC 3.2.1.73) and endo-β(1,3)-glucanases (laminarinases, EC 3.2.1.39 and EC 3.2.1.6) have evolved to specifically hydrolyze these polysaccharides, respectively, in environmental niches including the human gut. To facilitate biochemical and structural analysis of these GHs, with a focus on MLGases, we present here the facile chemo-enzymatic synthesis of a library of active-site-directed enzyme inhibitors based on mixed-linkage oligosaccharide scaffolds and N-bromoacetylglycosylamine or 2-fluoro-2-deoxyglycoside warheads. The effectiveness and irreversibility of these inhibitors were tested with exemplar MLGases and an endo-β(1,3)-glucanase. Notably, determination of inhibitor-bound crystal structures of a human-gut microbial MLGase from Glycoside Hydrolase Family 16 revealed the orthogonal labeling of the nucleophile and catalytic acid/base residues with homologous 2-fluoro-2-deoxyglycoside and N-bromoacetylglycosylamine inhibitors, respectively. We anticipate that the selectivity of these inhibitors will continue to enable the structural and mechanistic analyses of β-glucanases from diverse sources and protein families.
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Affiliation(s)
- Namrata Jain
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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3
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Schröder SP, Offen WA, Males A, Jin Y, de Boer C, Enotarpi J, Marino L, van der Marel GA, Florea BI, Codée JDC, Overkleeft HS, Davies GJ. Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on α-1,6 Mannanases. Chemistry 2021; 27:9519-9523. [PMID: 33878235 PMCID: PMC8362039 DOI: 10.1002/chem.202101255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 11/07/2022]
Abstract
There is a vast genomic resource for enzymes active on carbohydrates. Lagging far behind, however, are functional chemical tools for the rapid characterization of carbohydrate-active enzymes. Activity-based probes (ABPs) offer one chemical solution to these issues with ABPs based upon cyclophellitol epoxide and aziridine covalent and irreversible inhibitors representing a potent and widespread approach. Such inhibitors for enzymes active on polysaccharides are potentially limited by the requirement for several glycosidic bonds, themselves substrates for the enzyme targets. Here, it is shown that non-hydrolysable trisaccharide can be synthesized and applied even to enzymes with challenging subsite requirements. It was found that incorporation of carbasugar moieties, which was accomplished by cuprate-assisted regioselective trans-diaxial epoxide opening of carba-mannal synthesised for this purpose, yields inactivators that act as powerful activity-based inhibitors for α-1,6 endo-mannanases. 3-D structures at 1.35-1.47 Å resolutions confirm the design rationale and binding to the enzymatic nucleophile. Carbasugar oligosaccharide cyclophellitols offer a powerful new approach for the design of robust endoglycosidase inhibitors, while the synthesis procedures presented here should allow adaptation towards activity-based endoglycosidase probes as well as configurational isosteres targeting other endoglycosidase families.
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Affiliation(s)
- Sybrin P. Schröder
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Wendy A. Offen
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Alexandra Males
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Yi Jin
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Casper de Boer
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Jacopo Enotarpi
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Laura Marino
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | | | - Bogdan I. Florea
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of ChemistryLeiden University Einsteinweg 552333CC LeidenThe Netherlands
| | - Gideon J. Davies
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
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4
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Luijkx YMCA, Jongkees S, Strijbis K, Wennekes T. Development of a 1,2-difluorofucoside activity-based probe for profiling GH29 fucosidases. Org Biomol Chem 2021; 19:2968-2977. [PMID: 33729259 DOI: 10.1039/d1ob00054c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
GH29 α-l-fucosidases catalyze hydrolysis of terminal α-l-fucosyl linkages with varying specificity and are expressed by prominent members of the human gut microbiota. Both homeostasis and dysbiosis at the human intestinal microbiota interface have been correlated with altered fucosidase activity. Herein we describe the development of a 2-deoxy-2-fluoro fucosyl fluoride derivative with an azide mini-tag as an activity-based probe (ABP) for selective in vitro labelling of GH29 α-l-fucosidases. Only catalytically active fucosidases are inactivated by this ABP, allowing their functionalization with a biotin reporter group via the CuAAC reaction and subsequent in-gel detection at nanogram levels. The ABP we present here is shown to be active against a GH29 α-l-fucosidase from Bacteroides fragilis and capable of labeling two other GH29 α-l-fucosidases with different linkage specificity, illustrating its broader utility. This novel ABP is a valuable addition to the toolbox of fucosidase probes by allowing identification and functional studies of the wide variety of GH29 fucosidases, including those in the gut microbiota.
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Affiliation(s)
- Yvette M C A Luijkx
- Department Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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5
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Wodtke R, Wodtke J, Hauser S, Laube M, Bauer D, Rothe R, Neuber C, Pietsch M, Kopka K, Pietzsch J, Löser R. Development of an 18F-Labeled Irreversible Inhibitor of Transglutaminase 2 as Radiometric Tool for Quantitative Expression Profiling in Cells and Tissues. J Med Chem 2021; 64:3462-3478. [PMID: 33705656 DOI: 10.1021/acs.jmedchem.1c00096] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The transamidase activity of transglutaminase 2 (TGase 2) is considered to be important for several pathophysiological processes including fibrotic and neoplastic tissue growth, whereas in healthy cells this enzymatic function is predominantly latent. Methods that enable the highly sensitive detection of TGase 2, such as application of radiolabeled activity-based probes, will support the exploration of the enzyme's function in various diseases. In this context, the radiosynthesis and detailed in vitro radiopharmacological evaluation of an 18F-labeled Nε-acryloyllysine piperazide are reported. Robust and facile detection of the radiotracer-TGase 2 complex by autoradiography of thin layer plates and polyacrylamide gels after chromatographic and electrophoretic separation owing to irreversible covalent bond formation was demonstrated for the isolated protein, cell lysates, and living cells. By use of this radiotracer, quantitative data on the expression profile of activatable TGase 2 in mouse organs and selected tumors were obtained for the first time by autoradiography of tissue sections.
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Affiliation(s)
- Robert Wodtke
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Johanna Wodtke
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Sandra Hauser
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Markus Laube
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - David Bauer
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.,Fakultät Chemie und Lebensmittelchemie, Technische Universität Dresden, Mommsenstraße 4, 01062 Dresden, Germany
| | - Rebecca Rothe
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.,Fakultät Chemie und Lebensmittelchemie, Technische Universität Dresden, Mommsenstraße 4, 01062 Dresden, Germany
| | - Christin Neuber
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Markus Pietsch
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Straße 24, 50931 Köln, Germany
| | - Klaus Kopka
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.,Fakultät Chemie und Lebensmittelchemie, Technische Universität Dresden, Mommsenstraße 4, 01062 Dresden, Germany
| | - Jens Pietzsch
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.,Fakultät Chemie und Lebensmittelchemie, Technische Universität Dresden, Mommsenstraße 4, 01062 Dresden, Germany
| | - Reik Löser
- Institut für Radiopharmazeutische Krebsforschung, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.,Fakultät Chemie und Lebensmittelchemie, Technische Universität Dresden, Mommsenstraße 4, 01062 Dresden, Germany
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6
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Dimakos V, Taylor MS. Recent advances in the direct O-arylation of carbohydrates. Org Biomol Chem 2021; 19:514-524. [PMID: 33331387 DOI: 10.1039/d0ob02009e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Methods for the O-arylation of hydroxyl and hemiacetal groups in carbohydrates via C(sp2)-O bond formation are discussed. Such methods provide an alternative disconnection to the traditional approach of nucleophilic substitution between a sugar-derived electrophile and a phenol or phenoxide nucleophile. They have led to new opportunities for stereoselectivity, site-selectivity and chemoselectivity in the preparation of O-aryl glycosides and carbohydrate-derived aryl ethers, compounds that are useful for a broad range of applications in medicinal chemistry, glycobiology and organic synthesis.
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Affiliation(s)
- Victoria Dimakos
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada.
| | - Mark S Taylor
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada.
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7
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Linclau B, Ardá A, Reichardt NC, Sollogoub M, Unione L, Vincent SP, Jiménez-Barbero J. Fluorinated carbohydrates as chemical probes for molecular recognition studies. Current status and perspectives. Chem Soc Rev 2021; 49:3863-3888. [PMID: 32520059 DOI: 10.1039/c9cs00099b] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review provides an extensive summary of the effects of carbohydrate fluorination with regard to changes in physical, chemical and biological properties with respect to regular saccharides. The specific structural, conformational, stability, reactivity and interaction features of fluorinated sugars are described, as well as their applications as probes and in chemical biology.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO171BJ, UK
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain.
| | | | - Matthieu Sollogoub
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Stéphane P Vincent
- Department of Chemistry, Laboratory of Bio-organic Chemistry, University of Namur (UNamur), B-5000 Namur, Belgium
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain. and Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain and Department of Organic Chemistry II, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Spain
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8
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N-Alkylated Iminosugar Based Ligands: Synthesis and Inhibition of Human Lysosomal β-Glucocerebrosidase. Molecules 2020; 25:molecules25204618. [PMID: 33050585 PMCID: PMC7594070 DOI: 10.3390/molecules25204618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/01/2023] Open
Abstract
The scope of a series of N-alkylated iminosugar based inhibitors in the d-gluco as well as d-xylo configuration towards their interaction with human lysosomal β-glucocerebrosidase has been evaluated. A versatile synthetic toolbox has been developed for the synthesis of N-alkylated iminosugar scaffolds conjugated to a variety of terminal groups via a benzoic acid ester linker. The terminal groups such as nitrile, azide, alkyne, nonafluoro-tert-butyl and amino substituents enable follow-up chemistry as well as visualisation experiments. All compounds showed promising inhibitory properties as well as selectivities for β-glucosidases, some exhibiting activities in the low nanomolar range for β-glucocerebrosidase.
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9
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Kytidou K, Artola M, Overkleeft HS, Aerts JMFG. Plant Glycosides and Glycosidases: A Treasure-Trove for Therapeutics. FRONTIERS IN PLANT SCIENCE 2020; 11:357. [PMID: 32318081 PMCID: PMC7154165 DOI: 10.3389/fpls.2020.00357] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/11/2020] [Indexed: 05/10/2023]
Abstract
Plants contain numerous glycoconjugates that are metabolized by specific glucosyltransferases and hydrolyzed by specific glycosidases, some also catalyzing synthetic transglycosylation reactions. The documented value of plant-derived glycoconjugates to beneficially modulate metabolism is first addressed. Next, focus is given to glycosidases, the central theme of the review. The therapeutic value of plant glycosidases is discussed as well as the present production in plant platforms of therapeutic human glycosidases used in enzyme replacement therapies. The increasing knowledge on glycosidases, including structure and catalytic mechanism, is described. The novel insights have allowed the design of functionalized highly specific suicide inhibitors of glycosidases. These so-called activity-based probes allow unprecedented visualization of glycosidases cross-species. Here, special attention is paid on the use of such probes in plant science that promote the discovery of novel enzymes and the identification of potential therapeutic inhibitors and chaperones.
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Affiliation(s)
- Kassiani Kytidou
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Marta Artola
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
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10
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Singh M, Watkinson M, Scanlan EM, Miller GJ. Illuminating glycoscience: synthetic strategies for FRET-enabled carbohydrate active enzyme probes. RSC Chem Biol 2020. [DOI: 10.1039/d0cb00134a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Carbohydrates are synthesised, refined and degraded by carbohydrate active enzymes. FRET is emerging as a powerful tool to monitor and quantify their activity as well as to test inhibitors as new drug candidates and monitor disease.
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Affiliation(s)
- Meenakshi Singh
- Lennard-Jones Laboratories
- School of Chemical and Physical Sciences
- Keele University
- Staffordshire
- UK
| | - Michael Watkinson
- Lennard-Jones Laboratories
- School of Chemical and Physical Sciences
- Keele University
- Staffordshire
- UK
| | - Eoin M. Scanlan
- School of Chemistry and Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Gavin J. Miller
- Lennard-Jones Laboratories
- School of Chemical and Physical Sciences
- Keele University
- Staffordshire
- UK
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11
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Synthesis of modified 1,5-imino-d-xylitols as ligands for lysosomal β-glucocerebrosidase. MONATSHEFTE FUR CHEMIE 2019; 150:831-842. [PMID: 31178604 PMCID: PMC6534063 DOI: 10.1007/s00706-019-02427-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022]
Abstract
Abstract Modified 1,5-dideoxy-1,5-imino-d-xylitol analogues with different substitution patterns involving position C-1 and/or the ring nitrogen were prepared, which were designed to serve as precursors for the preparation of iminoxylitol-based ligands and tools for the elucidation and modulation of human lysosomal β-glucocerebrosidase. Biological evaluation of the synthesized glycomimetics with a series of glycoside hydrolases revealed that these substitution patterns elicit excellent β-glucosidase selectivities. Graphical abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00706-019-02427-1) contains supplementary material, which is available to authorized users.
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12
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Hyun JY, Park SH, Park CW, Kim HB, Cho JW, Shin I. Trifunctional Fluorogenic Probes for Fluorescence Imaging and Isolation of Glycosidases in Cells. Org Lett 2019; 21:4439-4442. [DOI: 10.1021/acs.orglett.9b01147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Gehringer M, Laufer SA. Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology. J Med Chem 2019; 62:5673-5724. [PMID: 30565923 DOI: 10.1021/acs.jmedchem.8b01153] [Citation(s) in RCA: 370] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Targeted covalent inhibitors (TCIs) are designed to bind poorly conserved amino acids by means of reactive groups, the so-called warheads. Currently, targeting noncatalytic cysteine residues with acrylamides and other α,β-unsaturated carbonyl compounds is the predominant strategy in TCI development. The recent ascent of covalent drugs has stimulated considerable efforts to characterize alternative warheads for the covalent-reversible and irreversible engagement of noncatalytic cysteine residues as well as other amino acids. This Perspective article provides an overview of warheads-beyond α,β-unsaturated amides-recently used in the design of targeted covalent ligands. Promising reactive groups that have not yet demonstrated their utility in TCI development are also highlighted. Special emphasis is placed on the discussion of reactivity and of case studies illustrating applications in medicinal chemistry and chemical biology.
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Affiliation(s)
- Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
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14
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Ben Bdira F, Artola M, Overkleeft HS, Ubbink M, Aerts JMFG. Distinguishing the differences in β-glycosylceramidase folds, dynamics, and actions informs therapeutic uses. J Lipid Res 2018; 59:2262-2276. [PMID: 30279220 PMCID: PMC6277158 DOI: 10.1194/jlr.r086629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
Glycosyl hydrolases (GHs) are carbohydrate-active enzymes that hydrolyze a specific β-glycosidic bond in glycoconjugate substrates; β-glucosidases degrade glucosylceramide, a ubiquitous glycosphingolipid. GHs are grouped into structurally similar families that themselves can be grouped into clans. GH1, GH5, and GH30 glycosidases belong to clan A hydrolases with a catalytic (β/α)8 TIM barrel domain, whereas GH116 belongs to clan O with a catalytic (α/α)6 domain. In humans, GH abnormalities underlie metabolic diseases. The lysosomal enzyme glucocerebrosidase (family GH30), deficient in Gaucher disease and implicated in Parkinson disease etiology, and the cytosol-facing membrane-bound glucosylceramidase (family GH116) remove the terminal glucose from the ceramide lipid moiety. Here, we compare enzyme differences in fold, action, dynamics, and catalytic domain stabilization by binding site occupancy. We also explore other glycosidases with reported glycosylceramidase activity, including human cytosolic β-glucosidase, intestinal lactase-phlorizin hydrolase, and lysosomal galactosylceramidase. Last, we describe the successful translation of research to practice: recombinant glycosidases and glucosylceramide metabolism modulators are approved drug products (enzyme replacement therapies). Activity-based probes now facilitate the diagnosis of enzyme deficiency and screening for compounds that interact with the catalytic pocket of glycosidases. Future research may deepen the understanding of the functional variety of these enzymes and their therapeutic potential.
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Affiliation(s)
- Fredj Ben Bdira
- Departments of Macromolecular Biochemistry,Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Marta Artola
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Herman S Overkleeft
- Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden, The Netherlands
| | - Marcellus Ubbink
- Departments of Macromolecular Biochemistry,Leiden Institute of Chemistry, Leiden, The Netherlands
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15
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Ho LA, Winogrodzki JL, Debowski AW, Madden Z, Vocadlo DJ, Mark BL, Stubbs KA. A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to β-lactams in Pseudomonas aeruginosa. Chem Commun (Camb) 2018; 54:10630-10633. [PMID: 30178799 DOI: 10.1039/c8cc05281f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of a potent mechanism-based inactivator of NagZ, an enzyme critical to the production of inducible AmpC β-lactamase in Gram-negative bacteria, is presented. This inactivator significantly reduces MIC values for important β-lactams against a clinically relevant strain of Pseudomonas aeruginosa.
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Affiliation(s)
- Louisa A Ho
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
| | - Judith L Winogrodzki
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
| | - Aleksandra W Debowski
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia. and School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Zarina Madden
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada.
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
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16
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Click chemistry in sphingolipid research. Chem Phys Lipids 2018; 215:71-83. [DOI: 10.1016/j.chemphyslip.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/17/2023]
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17
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Schröder SP, Kallemeijn WW, Debets MF, Hansen T, Sobala LF, Hakki Z, Williams SJ, Beenakker TJM, Aerts JMFG, van der Marel GA, Codée JDC, Davies GJ, Overkleeft HS. Spiro-epoxyglycosides as Activity-Based Probes for Glycoside Hydrolase Family 99 Endomannosidase/Endomannanase. Chemistry 2018; 24:9983-9992. [PMID: 29797675 PMCID: PMC6055899 DOI: 10.1002/chem.201801902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/23/2018] [Indexed: 11/06/2022]
Abstract
N-Glycans direct protein function, stability, folding and targeting, and influence immunogenicity. While most glycosidases that process N-glycans cleave a single sugar residue at a time, enzymes from glycoside hydrolase family 99 are endo-acting enzymes that cleave within complex N-glycans. Eukaryotic Golgi endo-1,2-α-mannosidase cleaves glucose-substituted mannose within immature glucosylated high-mannose N-glycans in the secretory pathway. Certain bacteria within the human gut microbiota produce endo-1,2-α-mannanase, which cleaves related structures within fungal mannan, as part of nutrient acquisition. An unconventional mechanism of catalysis was proposed for enzymes of this family, hinted at by crystal structures of imino/azasugars complexed within the active site. Based on this mechanism, we developed the synthesis of two glycosides bearing a spiro-epoxide at C-2 as electrophilic trap, to covalently bind a mechanistically important, conserved GH99 catalytic residue. The spiro-epoxyglycosides are equipped with a fluorescent tag, and following incubation with recombinant enzyme, allow concentration, time and pH dependent visualization of the bound enzyme using gel electrophoresis.
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Affiliation(s)
- Sybrin P. Schröder
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Wouter W. Kallemeijn
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marjoke F. Debets
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Thomas Hansen
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Lukasz F. Sobala
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Zalihe Hakki
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Thomas J. M. Beenakker
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Gijsbert A. van der Marel
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Gideon J. Davies
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Herman S. Overkleeft
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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18
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Kytidou K, Beekwilder J, Artola M, van Meel E, Wilbers RHP, Moolenaar GF, Goosen N, Ferraz MJ, Katzy R, Voskamp P, Florea BI, Hokke CH, Overkleeft HS, Schots A, Bosch D, Pannu N, Aerts JMFG. Nicotiana benthamiana α-galactosidase A1.1 can functionally complement human α-galactosidase A deficiency associated with Fabry disease. J Biol Chem 2018; 293:10042-10058. [PMID: 29674318 PMCID: PMC6028973 DOI: 10.1074/jbc.ra118.001774] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/17/2018] [Indexed: 11/06/2022] Open
Abstract
α-Galactosidases (EC 3.2.1.22) are retaining glycosidases that cleave terminal α-linked galactose residues from glycoconjugate substrates. α-Galactosidases take part in the turnover of cell wall-associated galactomannans in plants and in the lysosomal degradation of glycosphingolipids in animals. Deficiency of human α-galactosidase A (α-Gal A) causes Fabry disease (FD), a heritable, X-linked lysosomal storage disorder, characterized by accumulation of globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3). Current management of FD involves enzyme-replacement therapy (ERT). An activity-based probe (ABP) covalently labeling the catalytic nucleophile of α-Gal A has been previously designed to study α-galactosidases for use in FD therapy. Here, we report that this ABP labels proteins in Nicotiana benthamiana leaf extracts, enabling the identification and biochemical characterization of an N. benthamiana α-galactosidase we name here A1.1 (gene accession ID GJZM-1660). The transiently overexpressed and purified enzyme was a monomer lacking N-glycans and was active toward 4-methylumbelliferyl-α-d-galactopyranoside substrate (Km = 0.17 mm) over a broad pH range. A1.1 structural analysis by X-ray crystallography revealed marked similarities with human α-Gal A, even including A1.1's ability to hydrolyze Gb3 and lyso-Gb3, which are not endogenous in plants. Of note, A1.1 uptake into FD fibroblasts reduced the elevated lyso-Gb3 levels in these cells, consistent with A1.1 delivery to lysosomes as revealed by confocal microscopy. The ease of production and the features of A1.1, such as stability over a broad pH range, combined with its capacity to degrade glycosphingolipid substrates, warrant further examination of its value as a potential therapeutic agent for ERT-based FD management.
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Affiliation(s)
| | - Jules Beekwilder
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | | | | | - Ruud H P Wilbers
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | - Geri F Moolenaar
- Cloning and Protein Purification Facility, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden
| | - Nora Goosen
- Cloning and Protein Purification Facility, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden
| | | | | | | | | | - Cornelis H Hokke
- the Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | | | - Arjen Schots
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | - Dirk Bosch
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
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19
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Wadzinski TJ, Steinauer A, Hie L, Pelletier G, Schepartz A, Miller SJ. Rapid phenolic O-glycosylation of small molecules and complex unprotected peptides in aqueous solvent. Nat Chem 2018; 10:644-652. [PMID: 29713033 PMCID: PMC5964040 DOI: 10.1038/s41557-018-0041-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 03/06/2018] [Indexed: 12/25/2022]
Abstract
Glycosylated natural products and synthetic glycopeptides represent a significant and growing source of biochemical probes and therapeutic agents. However, methods that enable the aqueous glycosylation of endogenous amino acid functionality in peptides without the use of protecting groups are scarce. Here, we report a transformation that facilitates the efficient aqueous O-glycosylation of phenolic functionality in a wide range of small molecules, unprotected tyrosine, and tyrosine residues embedded within a range of complex, fully unprotected peptides. The transformation, which uses glycosyl fluoride donors and is promoted by Ca(OH)2, proceeds rapidly at room temperature in water, with good yields and selective formation of unique anomeric products depending on the stereochemistry of the glycosyl donor. High functional group tolerance is observed, and the phenol glycosylation occurs selectively in the presence of virtually all side chains of the proteinogenic amino acids with the singular exception of Cys. This method offers a highly selective, efficient, and operationally simple approach for the protecting-group-free synthesis of O-aryl glycosides and Tyr-O-glycosylated peptides in water.
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Affiliation(s)
| | | | - Liana Hie
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | | | - Scott J Miller
- Department of Chemistry, Yale University, New Haven, CT, USA.
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20
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van Kasteren SI, Florea BI, Overkleeft HS. Activity-Based Protein Profiling: From Chemical Novelty to Biomedical Stalwart. Methods Mol Biol 2018; 1491:1-8. [PMID: 27778277 DOI: 10.1007/978-1-4939-6439-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Biological systems often respond to environmental changes by rapidly altering the activity of specific enzymes: for example through desequesterization of enzyme activities by dissociation from inhibitors, activation/deactivation through posttranslational modification, or relocation of the enzyme to different organelles. This means that expression levels of enzymes do not necessarily correlate with the activities observed for these enzymes. In this chapter we review some of the approaches used to selectively image only the active sub-populations of given enzymes, the so-called activity-based protein profiling. A focus lies on recent developments that are taking this approach from chemical novelty to biochemical stalwart.
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Affiliation(s)
- Sander I van Kasteren
- Bio-Organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| | - Bogdan I Florea
- Bio-Organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Bio-Organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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21
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Jain N, Attia MA, Offen WA, Davies GJ, Brumer H. Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor of endo-xyloglucanases. Org Biomol Chem 2018; 16:8732-8741. [DOI: 10.1039/c8ob02250j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Xyloglucan (XyG) is a complex polysaccharide that is ubiquitous and often abundant in the cell walls of terrestrial plants.
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Affiliation(s)
- Namrata Jain
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | - Mohamed A. Attia
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | | | | | - Harry Brumer
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
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22
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Xu Y, Uddin N, Wagner GK. Covalent Probes for Carbohydrate-Active Enzymes: From Glycosidases to Glycosyltransferases. Methods Enzymol 2018; 598:237-265. [DOI: 10.1016/bs.mie.2017.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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23
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Wu L, Jiang J, Jin Y, Kallemeijn WW, Kuo CL, Artola M, Dai W, van Elk C, van Eijk M, van der Marel GA, Codée JDC, Florea BI, Aerts JMFG, Overkleeft HS, Davies GJ. Activity-based probes for functional interrogation of retaining β-glucuronidases. Nat Chem Biol 2017; 13:867-873. [PMID: 28581485 DOI: 10.1038/nchembio.2395] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/10/2017] [Indexed: 02/06/2023]
Abstract
Humans express at least two distinct β-glucuronidase enzymes that are involved in disease: exo-acting β-glucuronidase (GUSB), whose deficiency gives rise to mucopolysaccharidosis type VII, and endo-acting heparanase (HPSE), whose overexpression is implicated in inflammation and cancers. The medical importance of these enzymes necessitates reliable methods to assay their activities in tissues. Herein, we present a set of β-glucuronidase-specific activity-based probes (ABPs) that allow rapid and quantitative visualization of GUSB and HPSE in biological samples, providing a powerful tool for dissecting their activities in normal and disease states. Unexpectedly, we find that the supposedly inactive HPSE proenzyme proHPSE is also labeled by our ABPs, leading to surprising insights regarding structural relationships between proHPSE, mature HPSE, and their bacterial homologs. Our results demonstrate the application of β-glucuronidase ABPs in tracking pathologically relevant enzymes and provide a case study of how ABP-driven approaches can lead to discovery of unanticipated structural and biochemical functionality.
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Affiliation(s)
- Liang Wu
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - Jianbing Jiang
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Yi Jin
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - Wouter W Kallemeijn
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Chi-Lin Kuo
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Marta Artola
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Wei Dai
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Cas van Elk
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Marco van Eijk
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gijsbert A van der Marel
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Jeroen D C Codée
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bogdan I Florea
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Herman S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
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24
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Jiang J, Artola M, Beenakker TJM, Schröder SP, Petracca R, de Boer C, Aerts JMFG, van der Marel GA, Codée JDC, Overkleeft HS. The Synthesis of Cyclophellitol-Aziridine and Its Configurational and Functional Isomers. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600472] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jianbing Jiang
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marta Artola
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas J. M. Beenakker
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Sybrin P. Schröder
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Rita Petracca
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Casper de Boer
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis; Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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25
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Kwan DH, Jin Y, Jiang J, Chen HM, Kötzler MP, Overkleeft HS, Davies GJ, Withers SG. Chemoenzymatic synthesis of 6-phospho-cyclophellitol as a novel probe of 6-phospho-β-glucosidases. FEBS Lett 2016; 590:461-8. [DOI: 10.1002/1873-3468.12059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 12/19/2015] [Accepted: 12/22/2015] [Indexed: 11/10/2022]
Affiliation(s)
- David H. Kwan
- Department of Chemistry; University of British Columbia; BC Canada
| | - Yi Jin
- York Structural Biology Laboratory; Department of Chemistry; University of York; UK
| | - Jianbing Jiang
- Department of Bioorganic Synthesis; Leiden Institute of Chemistry; Leiden University; the Netherlands
| | - Hong-Ming Chen
- Department of Chemistry; University of British Columbia; BC Canada
| | | | - Herman S. Overkleeft
- Department of Bioorganic Synthesis; Leiden Institute of Chemistry; Leiden University; the Netherlands
| | - Gideon J. Davies
- York Structural Biology Laboratory; Department of Chemistry; University of York; UK
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26
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Hattie M, Cekic N, Debowski AW, Vocadlo DJ, Stubbs KA. Modifying the phenyl group of PUGNAc: reactivity tuning to deliver selective inhibitors for N-acetyl-d-glucosaminidases. Org Biomol Chem 2016; 14:3193-7. [DOI: 10.1039/c6ob00297h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of analogues of the potentN-acetylhexosamindase inhibitor PUGNAc are described and were found to vary in both potency and selectivity against a set of biologically importantN-acetyl-d-glucosaminidases.
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Affiliation(s)
- Mitchell Hattie
- School of Chemistry and Biochemistry
- The University of Western Australia
- Crawley
- Australia
| | - Nevena Cekic
- Department of Chemistry
- Simon Fraser University
- Burnaby
- Canada
| | - Aleksandra W. Debowski
- School of Chemistry and Biochemistry
- The University of Western Australia
- Crawley
- Australia
- School of Pathology and Laboratory Medicine
| | - David J. Vocadlo
- Department of Chemistry
- Simon Fraser University
- Burnaby
- Canada
- Department of Molecular Biology and Biochemistry
| | - Keith A. Stubbs
- School of Chemistry and Biochemistry
- The University of Western Australia
- Crawley
- Australia
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27
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Gamo AM, González-Vera JA, Rueda-Zubiaurre A, Alonso D, Vázquez-Villa H, Martín-Couce L, Palomares Ó, López JA, Martín-Fontecha M, Benhamú B, López-Rodríguez ML, Ortega-Gutiérrez S. Chemoproteomic Approach to Explore the Target Profile of GPCR ligands: Application to 5-HT1A
and 5-HT6
Receptors. Chemistry 2015; 22:1313-21. [DOI: 10.1002/chem.201503101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Ana M. Gamo
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Juan A. González-Vera
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Ainoa Rueda-Zubiaurre
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Dulce Alonso
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Lidia Martín-Couce
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Óscar Palomares
- Departamento de Bioquímica y Biología Molecular I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Juan A. López
- Proteomics Unit; Centro Nacional de Investigaciones Cardiovasculares, CNIC; 28029 Madrid Spain
| | - Mar Martín-Fontecha
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Bellinda Benhamú
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - María L. López-Rodríguez
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I; Facultad de Ciencias Químicas; Universidad Complutense de Madrid; 28040 Madrid Spain
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28
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Herrera Moro Chao D, Kallemeijn WW, Marques ARA, Orre M, Ottenhoff R, van Roomen C, Foppen E, Renner MC, Moeton M, van Eijk M, Boot RG, Kamphuis W, Hol EM, Aten J, Overkleeft HS, Kalsbeek A, Aerts JMFG. Visualization of Active Glucocerebrosidase in Rodent Brain with High Spatial Resolution following In Situ Labeling with Fluorescent Activity Based Probes. PLoS One 2015; 10:e0138107. [PMID: 26418157 PMCID: PMC4587854 DOI: 10.1371/journal.pone.0138107] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/26/2015] [Indexed: 11/30/2022] Open
Abstract
Gaucher disease is characterized by lysosomal accumulation of glucosylceramide due to deficient activity of lysosomal glucocerebrosidase (GBA). In cells, glucosylceramide is also degraded outside lysosomes by the enzyme glucosylceramidase 2 (GBA2) of which inherited deficiency is associated with ataxias. The interest in GBA and glucosylceramide metabolism in the brain has grown following the notion that mutations in the GBA gene impose a risk factor for motor disorders such as α-synucleinopathies. We earlier developed a β-glucopyranosyl-configured cyclophellitol-epoxide type activity based probe (ABP) allowing in vivo and in vitro visualization of active molecules of GBA with high spatial resolution. Labeling occurs through covalent linkage of the ABP to the catalytic nucleophile residue in the enzyme pocket. Here, we describe a method to visualize active GBA molecules in rat brain slices using in vivo labeling. Brain areas related to motor control, like the basal ganglia and motor related structures in the brainstem, show a high content of active GBA. We also developed a β-glucopyranosyl cyclophellitol-aziridine ABP allowing in situ labeling of GBA2. Labeled GBA2 in brain areas can be identified and quantified upon gel electrophoresis. The distribution of active GBA2 markedly differs from that of GBA, being highest in the cerebellar cortex. The histological findings with ABP labeling were confirmed by biochemical analysis of isolated brain areas. In conclusion, ABPs offer sensitive tools to visualize active GBA and to study the distribution of GBA2 in the brain and thus may find application to establish the role of these enzymes in neurodegenerative disease conditions such as α-synucleinopathies and cerebellar ataxia.
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Affiliation(s)
- Daniela Herrera Moro Chao
- Department of Medical Biochemistry, Academic Medical Center, Amsterdam, The Netherlands
- Department of Endocrinology and Metabolism, Academic Medical Center, Amsterdam, The Netherlands
| | - Wouter W. Kallemeijn
- Department of Medical Biochemistry, Academic Medical Center, Amsterdam, The Netherlands
- Department of Biochemistry, Leiden Insitute of Chemistry, Leiden, The Netherlands
| | - Andre R. A. Marques
- Department of Medical Biochemistry, Academic Medical Center, Amsterdam, The Netherlands
| | - Marie Orre
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Roelof Ottenhoff
- Department of Medical Biochemistry, Academic Medical Center, Amsterdam, The Netherlands
| | - Cindy van Roomen
- Department of Medical Biochemistry, Academic Medical Center, Amsterdam, The Netherlands
| | - Ewout Foppen
- Department of Endocrinology and Metabolism, Academic Medical Center, Amsterdam, The Netherlands
| | - Maria C. Renner
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Martina Moeton
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Marco van Eijk
- Department of Biochemistry, Leiden Insitute of Chemistry, Leiden, The Netherlands
| | - Rolf G. Boot
- Department of Biochemistry, Leiden Insitute of Chemistry, Leiden, The Netherlands
| | - Willem Kamphuis
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Elly M. Hol
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Aten
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic Synthesis, Leiden institute of Chemistry, Leiden, The Netherlands
| | - Andries Kalsbeek
- Department of Endocrinology and Metabolism, Academic Medical Center, Amsterdam, The Netherlands
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
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Jiang J, Beenakker TJM, Kallemeijn WW, van der Marel GA, van den Elst H, Codée JDC, Aerts JMFG, Overkleeft HS. Comparing CyclophellitolN-Alkyl andN-Acyl Cyclophellitol Aziridines as Activity-Based Glycosidase Probes. Chemistry 2015; 21:10861-9. [DOI: 10.1002/chem.201501313] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Indexed: 11/12/2022]
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Burke HM, Gunnlaugsson T, Scanlan EM. Recent advances in the development of synthetic chemical probes for glycosidase enzymes. Chem Commun (Camb) 2015; 51:10576-88. [PMID: 26051717 DOI: 10.1039/c5cc02793d] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The emergence of synthetic glycoconjugates as chemical probes for the detection of glycosidase enzymes has resulted in the development of a range of useful chemical tools with applications in glycobiology, biotechnology, medical and industrial research. Critical to the function of these probes is the preparation of substrates containing a glycosidic linkage that when activated by a specific enzyme or group of enzymes, irreversibly releases a reporter molecule that can be detected. Starting from the earliest examples of colourimetric probes, increasingly sensitive and sophisticated substrates have been reported. In this review we present an overview of the recent advances in this field, covering an array of strategies including chromogenic and fluorogenic substrates, lanthanide complexes, gels and nanoparticles. The applications of these substrates for the detection of various glycosidases and the scope and limitations for each approach are discussed.
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Affiliation(s)
- Helen M Burke
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College, Pearse St, Dublin 2, Ireland.
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31
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Jiang J, Kallemeijn WW, Wright DW, van den Nieuwendijk AMCH, Rohde VC, Folch EC, van den Elst H, Florea BI, Scheij S, Donker-Koopman WE, Verhoek M, Li N, Schürmann M, Mink D, Boot RG, Codée JDC, van der Marel GA, Davies GJ, Aerts JMFG, Overkleeft HS. In vitro and in vivo comparative and competitive activity-based protein profiling of GH29 α-l-fucosidases. Chem Sci 2015; 6:2782-false. [PMID: 29142681 PMCID: PMC5654414 DOI: 10.1039/c4sc03739a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/09/2015] [Indexed: 01/07/2023] Open
Abstract
GH29 α-l-fucosidases catalyze the hydrolysis of α-l-fucosidic linkages. Deficiency in human lysosomal α-l-fucosidase (FUCA1) leads to the recessively inherited disorder, fucosidosis. Herein we describe the development of fucopyranose-configured cyclophellitol aziridines as activity-based probes (ABPs) for selective in vitro and in vivo labeling of GH29 α-l-fucosidases from bacteria, mice and man. Crystallographic analysis on bacterial α-l-fucosidase confirms that the ABPs act by covalent modification of the active site nucleophile. Competitive activity-based protein profiling identified l-fuconojirimycin as the single GH29 α-l-fucosidase inhibitor from eight configurational isomers.
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Affiliation(s)
- Jianbing Jiang
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
| | - Wouter W Kallemeijn
- Department of Medical Biochemistry , Academic Medical Center , Meibergdreef 15 , 1105 AZ Amsterdam , The Netherlands
| | - Daniel W Wright
- Department of Chemistry , University of York , Heslington , York , YO10 5DD , UK
| | | | - Veronica Coco Rohde
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
| | - Elisa Colomina Folch
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
| | - Hans van den Elst
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
| | - Bogdan I Florea
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
| | - Saskia Scheij
- Department of Medical Biochemistry , Academic Medical Center , Meibergdreef 15 , 1105 AZ Amsterdam , The Netherlands
| | - Wilma E Donker-Koopman
- Department of Medical Biochemistry , Academic Medical Center , Meibergdreef 15 , 1105 AZ Amsterdam , The Netherlands
| | - Marri Verhoek
- Department of Medical Biochemistry , Academic Medical Center , Meibergdreef 15 , 1105 AZ Amsterdam , The Netherlands
| | - Nan Li
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
| | - Martin Schürmann
- DSM Innovative Synthesis , Urmonderbaan 22 , NL-6167 RD Geleen , The Netherlands
| | - Daniel Mink
- DSM Innovative Synthesis , Urmonderbaan 22 , NL-6167 RD Geleen , The Netherlands
| | - Rolf G Boot
- Department of Medical Biochemistry , Academic Medical Center , Meibergdreef 15 , 1105 AZ Amsterdam , The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
| | - Gideon J Davies
- Department of Chemistry , University of York , Heslington , York , YO10 5DD , UK
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ; .,Department of Medical Biochemistry , Academic Medical Center , Meibergdreef 15 , 1105 AZ Amsterdam , The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry , Leiden University , P. O. Box 9502 , 2300 RA Leiden , The Netherlands . ;
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33
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Alcaide A, Trapero A, Pérez Y, Llebaria A. Galacto configured N-aminoaziridines: a new type of irreversible inhibitor of β-galactosidases. Org Biomol Chem 2015; 13:5690-7. [DOI: 10.1039/c5ob00532a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Aminoaziridines are potent irreversible inhibitors of galactosidases.
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Affiliation(s)
- Anna Alcaide
- Medicinal Chemistry Laboratory (MedChemLab)
- Departament de Química Biomèdica
- Institut de Química Avançada de Catalunya (IQAC–CSIC)
- Barcelona
- Spain
| | - Ana Trapero
- Medicinal Chemistry Laboratory (MedChemLab)
- Departament de Química Biomèdica
- Institut de Química Avançada de Catalunya (IQAC–CSIC)
- Barcelona
- Spain
| | - Yolanda Pérez
- NMR Unit
- Institut de Química Avançada de Catalunya (IQAC–CSIC)
- Barcelona
- Spain
| | - Amadeu Llebaria
- Medicinal Chemistry Laboratory (MedChemLab)
- Departament de Química Biomèdica
- Institut de Química Avançada de Catalunya (IQAC–CSIC)
- Barcelona
- Spain
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34
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Kennedy EJ. EMBO conference series: Chemical Biology 2014. Chembiochem 2014; 15:2783-7. [PMID: 25318996 DOI: 10.1002/cbic.201402527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 11/07/2022]
Abstract
Around 300 people from 18 countries took part in the fourth biennial Chemical Biology conference at The European Molecular Biology Laboratory (EMBL) in Heidelberg, from August 20 to 23, 2014. Many advances in the field of chemical biology were presented in talks and poster sessions. Picture: Petra Riedinger (EMBL).
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Affiliation(s)
- Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green Street, Athens, GA 30602 (USA).
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35
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Li KY, Jiang J, Witte MD, Kallemeijn WW, Donker-Koopman WE, Boot RG, Aerts JMFG, Codée JDC, van der Marel GA, Overkleeft HS. Exploring functional cyclophellitol analogues as human retaining beta-glucosidase inhibitors. Org Biomol Chem 2014; 12:7786-91. [DOI: 10.1039/c4ob01611d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Of six cyclophellitol analogues, the N-pentylaziridine is the most effective retaining human beta-glucosidase inhibitor considering potency and compound stability.
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Affiliation(s)
- Kah-Yee Li
- Leiden Institute of Chemistry
- Leiden University
- 2300 RA Leiden, the Netherlands
| | - Jianbing Jiang
- Leiden Institute of Chemistry
- Leiden University
- 2300 RA Leiden, the Netherlands
| | - Martin D. Witte
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen, the Netherlands
| | - Wouter W. Kallemeijn
- Department of Medical Biochemistry
- Academic Medical Center
- Amsterdam, the Netherlands
| | | | - Rolf G. Boot
- Department of Medical Biochemistry
- Academic Medical Center
- Amsterdam, the Netherlands
| | - Johannes M. F. G. Aerts
- Leiden Institute of Chemistry
- Leiden University
- 2300 RA Leiden, the Netherlands
- Department of Medical Biochemistry
- Academic Medical Center
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry
- Leiden University
- 2300 RA Leiden, the Netherlands
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