1
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Chettri D, Verma AK. Biological significance of carbohydrate active enzymes and searching their inhibitors for therapeutic applications. Carbohydr Res 2023; 529:108853. [PMID: 37235954 DOI: 10.1016/j.carres.2023.108853] [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: 11/23/2022] [Revised: 05/01/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Glycans are the most abundant and diverse group of biomolecules with a crucial role in all the biological processes. Their structural and functional diversity is not genetically encoded, but depends on Carbohydrate Active Enzymes (CAZymes) which carry out all catalytic activities in terms of synthesis, modification, and degradation. CAZymes comprise large families of enzymes with specific functions and are widely used for various commercial applications ranging from biofuel production to textile and food industries with impact on biorefineries. To understand the structure and functional mechanism of these CAZymes for their modification for industrial use, together with knowledge of therapeutic aspects of their dysfunction associated with various diseases, CAZyme inhibitors can be used as a valuable tool. In search for new inhibitors, the screening of various secondary metabolites using high-throughput techniques and rational design techniques have been explored. The inhibitors can thus help tune CAZymes and are emerging as a potential research interest.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok, 737102, Sikkim, India.
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2
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Lee J, Chai M, Bleiholder C. Differentiation of Isomeric, Nonseparable Carbohydrates Using Tandem-Trapped Ion Mobility Spectrometry-Mass Spectrometry. Anal Chem 2023; 95:747-757. [PMID: 36547374 PMCID: PMC10126951 DOI: 10.1021/acs.analchem.2c02844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates play important roles in biological processes, but their identification remains a significant analytical problem. While mass spectrometry has increasingly enabled the elucidation of carbohydrates, current approaches are limited in their abilities to differentiate isomeric carbohydrates when these are not separated prior to tandem-mass spectrometry analysis. This analytical challenge takes on increased relevance because of the pervasive presence of isomeric carbohydrates in biological systems. Here, we demonstrate that TIMS2-MS2 workflows enabled by tandem-trapped ion mobility spectrometry-mass spectrometry (tTIMS/MS) provide a general approach to differentiate isomeric, nonseparated carbohydrates. Our analysis shows that (1) cross sections measured by TIMS are sufficiently precise and robust for ion identification; (2) fragment ion cross sections from TIMS2 analysis can be analytically exploited to identify carbohydrate precursors even if the precursor ions are not separated by TIMS; (3) low-abundant fragment ions can be exploited to identify carbohydrate precursors even if the precursor ions are not separated by IMS. (4) MS2 analysis of fragment ions produced by TIMS2 can be used to validate and/or further characterize carbohydrate structures. Taken together, our analysis underlines the opportunities that tandem-ion mobility spectrometry/MS methods offer for the characterization of mixtures of isomeric carbohydrates.
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Affiliation(s)
- Jusung Lee
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Mengqi Chai
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, USA
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3
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Stereoselective synthesis of a 4-⍺-glucoside of valienamine and its X-ray structure in complex with Streptomyces coelicolor GlgE1-V279S. Sci Rep 2021; 11:13413. [PMID: 34183716 PMCID: PMC8238978 DOI: 10.1038/s41598-021-92554-9] [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: 03/12/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Glycoside hydrolases (GH) are a large family of hydrolytic enzymes found in all domains of life. As such, they control a plethora of normal and pathogenic biological functions. Thus, understanding selective inhibition of GH enzymes at the atomic level can lead to the identification of new classes of therapeutics. In these studies, we identified a 4-⍺-glucoside of valienamine (8) as an inhibitor of Streptomyces coelicolor (Sco) GlgE1-V279S which belongs to the GH13 Carbohydrate Active EnZyme family. The results obtained from the dose-response experiments show that 8 at a concentration of 1000 µM reduced the enzyme activity of Sco GlgE1-V279S by 65%. The synthetic route to 8 and a closely related 4-⍺-glucoside of validamine (7) was achieved starting from readily available D-maltose. A key step in the synthesis was a chelation-controlled addition of vinylmagnesium bromide to a maltose-derived enone intermediate. X-ray structures of both 7 and 8 in complex with Sco GlgE1-V279S were solved to resolutions of 1.75 and 1.83 Å, respectively. Structural analysis revealed the valienamine derivative 8 binds the enzyme in an E2 conformation for the cyclohexene fragment. Also, the cyclohexene fragment shows a new hydrogen-bonding contact from the pseudo-diaxial C(3)-OH to the catalytic nucleophile Asp 394 at the enzyme active site. Asp 394, in fact, forms a bidentate interaction with both the C(3)-OH and C(7)-OH of the inhibitor. In contrast, compound 7 disrupts the catalytic sidechain interaction network of Sco GlgE1-V279S via steric interactions resulting in a conformation change in Asp 394. These findings will have implications for the design other aminocarbasugar-based GH13-inhibitors and will be useful for identifying more potent and selective inhibitors.
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4
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Ren W, Farren-Dai M, Sannikova N, Świderek K, Wang Y, Akintola O, Britton R, Moliner V, Bennet AJ. Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design. Chem Sci 2020; 11:10488-10495. [PMID: 34094307 PMCID: PMC8162432 DOI: 10.1039/d0sc04401f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Carbasugars are structural mimics of naturally occurring carbohydrates that can interact with and inhibit enzymes involved in carbohydrate processing. In particular, carbasugars have attracted attention as inhibitors of glycoside hydrolases (GHs) and as therapeutic leads in several disease areas. However, it is unclear how the carbasugars are recognized and processed by GHs. Here, we report the synthesis of three carbasugar isotopologues and provide a detailed transition state (TS) analysis for the formation of the initial GH-carbasugar covalent intermediate, as well as for hydrolysis of this intermediate, using a combination of experimentally measured kinetic isotope effects and hybrid QM/MM calculations. We find that the α-galactosidase from Thermotoga maritima effectively stabilizes TS charge development on a remote C5-allylic center acting in concert with the reacting carbasugar, and catalysis proceeds via an exploded, or loose, SN2 transition state with no discrete enzyme-bound cationic intermediate. We conclude that, in complement to what we know about the TS structures of enzyme-natural substrate complexes, knowledge of the TS structures of enzymes reacting with non-natural carbasugar substrates shows that GHs can stabilize a wider range of positively charged TS structures than previously thought. Furthermore, this enhanced understanding will enable the design of new carbasugar GH transition state analogues to be used as, for example, chemical biology tools and pharmaceutical lead compounds. Positive charge stabilized on remote C5-allylic center with catalysis occurring via a loose SN2 transition state.![]()
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Affiliation(s)
- Weiwu Ren
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Marco Farren-Dai
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Natalia Sannikova
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I 12560 Castellón Spain
| | - Yang Wang
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Oluwafemi Akintola
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Robert Britton
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I 12560 Castellón Spain
| | - Andrew J Bennet
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
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5
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Li W, McArthur JB, Chen X. Strategies for chemoenzymatic synthesis of carbohydrates. Carbohydr Res 2018; 472:86-97. [PMID: 30529493 DOI: 10.1016/j.carres.2018.11.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/30/2022]
Abstract
Carbohydrates are structurally complex but functionally important biomolecules. Therefore, they have been challenging but attractive synthetic targets. While substantial progress has been made on advancing chemical glycosylation methods, incorporating enzymes into carbohydrate synthetic schemes has become increasingly practical as more carbohydrate biosynthetic and metabolic enzymes as well as their mutants with synthetic application are identified and expressed for preparative and large-scale synthesis. Chemoenzymatic strategies that integrate the flexibility of chemical derivatization with enzyme-catalyzed reactions have been extremely powerful. Briefly summarized here are our experiences on developing one-pot multienzyme (OPME) systems and representative chemoenzymatic strategies from others using glycosyltransferase-catalyzed reactions for synthesizing diverse structures of oligosaccharides, polysaccharides, and glycoconjugates. These strategies allow the synthesis of complex carbohydrates including those containing naturally occurring carbohydrate postglycosylational modifications (PGMs) and non-natural functional groups. By combining these srategies with facile purification schemes, synthetic access to the diverse space of carbohydrate structures can be automated and will not be limited to specialists.
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Affiliation(s)
- Wanqing Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - John B McArthur
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
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6
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Bevan JGM, Lourenço EC, Chaves-Ferreira M, Rodrigues JA, Rita Ventura M. Immobilization of UDP-Galactose on an Amphiphilic Resin. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jessica G. M. Bevan
- Biology of Parasitism Laboratory; Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
- Bioorganic Chemistry Laboratory; Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Apartado 127 2780-901 Oeiras Portugal
| | - Eva C. Lourenço
- Bioorganic Chemistry Laboratory; Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Apartado 127 2780-901 Oeiras Portugal
| | - Miguel Chaves-Ferreira
- Biology of Parasitism Laboratory; Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - João A. Rodrigues
- Biology of Parasitism Laboratory; Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - M. Rita Ventura
- Bioorganic Chemistry Laboratory; Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Apartado 127 2780-901 Oeiras Portugal
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7
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Manabe Y, Kasahara S, Takakura Y, Yang X, Takamatsu S, Kamada Y, Miyoshi E, Yoshidome D, Fukase K. Development of α1,6-fucosyltransferase inhibitors through the diversity-oriented syntheses of GDP-fucose mimics using the coupling between alkyne and sulfonyl azide. Bioorg Med Chem 2017; 25:2844-2850. [PMID: 28284868 DOI: 10.1016/j.bmc.2017.02.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 12/18/2022]
Abstract
We developed α1,6-fucosyltransferase (FUT8) inhibitors through a diversity-oriented synthesis. The coupling reaction between the fucose unit containing alkyne and the guanine unit containing sulfonyl azide under various conditions afforded a series of Guanosine 5'-diphospho-β-l-fucose (GDP-fucose) analogs. The synthesized compounds displayed FUT8 inhibition activity. A docking study revealed that the binding mode of the inhibitor synthesized with FUT8 was similar to that of GDP-fucose.
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Affiliation(s)
- Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Satomi Kasahara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yohei Takakura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Xiaoxiao Yang
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinji Takamatsu
- Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Kamada
- Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiji Miyoshi
- Division of Health Sciences, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Daisuke Yoshidome
- Schrödinger K.K., 17F Marunouchi Trust Tower North, 1-8-1 Marunouchi, Chiyoda-ku, Tokyo 100-0005, Japan
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
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8
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Balachandran N, To F, Berti PJ. Linear Free Energy Relationship Analysis of Transition State Mimicry by 3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) Oxime, a DAHP Synthase Inhibitor and Phosphate Mimic. Biochemistry 2017; 56:592-601. [PMID: 28045507 DOI: 10.1021/acs.biochem.6b01211] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Naresh Balachandran
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Frederick To
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul J. Berti
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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9
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Merino P, Delso I, Tejero T, Ghirardello M, Juste-Navarro V. Nucleoside Diphosphate Sugar Analogues that Target Glycosyltransferases. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Pedro Merino
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Ignacio Delso
- NMR Service, Center of Chemistry and Materials of Aragon (CEQMA); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Tomás Tejero
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Mattia Ghirardello
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Verónica Juste-Navarro
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
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10
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Song YY, Kinami K, Kato A, Jia YM, Li YX, Fleet GWJ, Yu CY. First total synthesis of (+)-broussonetine W: glycosidase inhibition of natural product & analogs. Org Biomol Chem 2016; 14:5157-74. [DOI: 10.1039/c6ob00720a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Broussonetine W and its 11 analogues have been first synthesized from cyclic nitrones and assayed as potential gycosidase inhibitors.
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Affiliation(s)
- Ying-Ying Song
- Beijing National Laboratory for Molecular Science (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Kyoko Kinami
- Department of Hospital Pharmacy
- University of Toyama
- Toyama 930-0194
- Japan
| | - Atsushi Kato
- Department of Hospital Pharmacy
- University of Toyama
- Toyama 930-0194
- Japan
| | - Yue-Mei Jia
- Beijing National Laboratory for Molecular Science (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Yi-Xian Li
- Beijing National Laboratory for Molecular Science (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - George W. J. Fleet
- Chemistry Research Laboratory
- Department of Chemistry
- University of Oxford
- Oxford
- UK
| | - Chu-Yi Yu
- Beijing National Laboratory for Molecular Science (BNLMS)
- CAS Key Laboratory of Molecular Recognition and Function
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
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11
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Boisson J, Thomasset A, Racine E, Cividino P, Banchelin Sainte-Luce T, Poisson JF, Behr JB, Py S. Hydroxymethyl-Branched Polyhydroxylated Indolizidines: Novel Selective α-Glucosidase Inhibitors. Org Lett 2015; 17:3662-5. [DOI: 10.1021/acs.orglett.5b01505] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Julien Boisson
- Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France
- CNRS, DCM, F-38000 Grenoble, France
| | - Amélia Thomasset
- Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France
- CNRS, DCM, F-38000 Grenoble, France
| | - Emilie Racine
- Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France
- CNRS, DCM, F-38000 Grenoble, France
| | - Pascale Cividino
- Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France
- CNRS, DCM, F-38000 Grenoble, France
| | | | - Jean-François Poisson
- Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France
- CNRS, DCM, F-38000 Grenoble, France
| | - Jean-Bernard Behr
- Université de Reims Champagne-Ardenne, Institut de
Chimie Moléculaire de Reims (ICMR), CNRS UMR 7312, UFR Sciences
Exactes et Naturelles, BP
1039, 51687 Reims Cedex 2, France
| | - Sandrine Py
- Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France
- CNRS, DCM, F-38000 Grenoble, France
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12
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Abstract
There is a long research history of studying the function of glycosylation in relation to the development and progression of different types of cancer. The technological advances of the "omic" have in the last decade have afforded many new opportunities and approaches for studying the cancer glycome. A collection of research articles has been assembled that collectively summarize the progress in this area for each type of major O-linked and N-linked glycan species and other classes of glycans, as well as what is known about specific glycans associated with individual types of cancer (brain, breast, colon, liver, lung, ovarian, pancreatic, prostate). These chapters also include descriptions of the latest cutting-edge technologies that have been developed recently for cancer glycomic studies. An introduction to these topics and highlights of emerging areas of research opportunity for cancer glycomics are presented. This includes the development of new glycomics-based cancer biomarkers and therapeutic targets, as well as different integrated cancer "omics" strategies.
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Affiliation(s)
- Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA.
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13
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Synthesis of a pseudo-disaccharide library and its application to the characterisation of the heparanase catalytic site. PLoS One 2013; 8:e82111. [PMID: 24260588 PMCID: PMC3832595 DOI: 10.1371/journal.pone.0082111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/19/2013] [Indexed: 12/15/2022] Open
Abstract
A novel methodology is described for the efficient and divergent synthesis of pseudodisaccharides, molecules comprising of amino carbasugar analogues linked to natural sugars. The methodology is general and enables the introduction of diversity both at the carbasugar and the natural sugar components of the pseudodisaccharides. Using this approach, a series of pseudodisaccharides are synthesised that mimic the repeating backbone unit of heparan sulfate, and are tested for inhibition of heparanase, a disease-relevant enzyme that hydrolyses heparan sulfate. A new homology model of human heparanase is described based on a family 79 β-glucuronidase. This model is used to postulate a computational rationale for the observed activity of the different pseudodisaccharides and provide valuable information that informs the design of potential inhibitors of this enzyme.
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14
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Gkizis P, Argyropoulos NG, Coutouli-Argyropoulou E. A sort synthesis of polyhydroxylated pyrrolizidines via sequential 1,3-dipolar cycloaddition and reductive amination. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.07.098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Zmudka MW, Thoden JB, Holden HM. The structure of DesR from Streptomyces venezuelae, a β-glucosidase involved in macrolide activation. Protein Sci 2013; 22:883-92. [PMID: 23225731 DOI: 10.1002/pro.2204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 11/26/2012] [Indexed: 11/11/2022]
Abstract
Antibiotics have, indeed, altered the course of human history as is evidenced by the increase in human life expectancy since the 1940s. Many of these natural compounds are produced by bacteria that, by necessity, must have efficient self-resistance mechanisms. The methymycin/pikromycin producing species Streptomyces venezuelae, for example, utilizes β-glucosylation of its macrolide products to neutralize their effects within the confines of the cell. Once released into the environment, these compounds are activated by the removal of the glucose moiety. In S. venezuelae, the enzyme responsible for removal of the sugar from the parent compound is encoded by the desR gene and referred to as DesR. It is a secreted enzyme containing 828 amino acid residues, and it is known to be a retaining glycosidase. Here, we describe the structure of the DesR/D-glucose complex determined to 1.4-Å resolution. The overall architecture of the enzyme can be envisioned in terms of three regions: a catalytic core and two auxiliary domains. The catalytic core harbors the binding platform for the glucose ligand. The first auxiliary domain adopts a "PA14 fold," whereas the second auxiliary domain contains an immunoglobulin-like fold. Asp 273 and Glu 578 are in the proper orientation to function as the catalytic base and proton donor, respectively, required for catalysis. The overall fold of the core region places DesR into the GH3 glycoside hydrolase family of enzymes. Comparison of the DesR structure with the β-glucosidase from Kluyveromyces marxianus shows that their PA14 domains assume remarkably different orientations.
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Affiliation(s)
- Matthew W Zmudka
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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