201
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Whitfield DM. DFT studies of the ionization of alpha and beta glycopyranosyl donors. Carbohydr Res 2007; 342:1726-40. [PMID: 17555731 DOI: 10.1016/j.carres.2007.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 04/26/2007] [Accepted: 05/06/2007] [Indexed: 11/28/2022]
Abstract
Current attempts at mimicking the transition states (TSs) of glycosyl processing enzymes (GPEs) that proceed through TSs with a high degree of oxacarbenium ion formation suffer from a paucity of data about the conformations of such oxacarbenium ions. Because TSs are maxima, the current models based on minimized structures may need some refinement. As part of studies directed at optimizing chemical glycosylation the ionization of 3,4,6-tri-O-acetyl-alpha/beta-D-glucopyranosyl chlorides and triflates, 2,3,4,6-tetra-O-methyl-alpha/beta-D-glucopyranosyl fluorides, chlorides and triflates, 2,3,4,6-tetra-O-methyl-alpha/beta-D-mannopyranosyl fluorides, 2,3-di-O-methyl 4,6-O-benzylidene alpha/beta-D-mannopyranosyl triflates and 2,3-di-O-methyl 4,6-O-benzylidene alpha/beta-D-glucopyranosyl triflates was studied by a prototypic density functional theory (DFT) procedure. In all cases, the alpha-anomers ionized smoothly to 4H3 half chair conformations or adjacent envelopes. By contrast, all beta-anomers exhibited an abrupt conformational change before ionization was complete. The nature of the conformations sampled depends on both the leaving group and the protecting group. The methods presented can be readily adapted to the study of any GPE or chemical glycosylation and provide a method for initial evaluation of plausible TSs, which in turn can be used in mimetic design.
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Affiliation(s)
- Dennis M Whitfield
- Institute for Biological Sciences, NRC Canada, 100 Sussex Drive, Ottawa, ON, Canada K1A 0R6.
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202
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Whitworth GE, Macauley MS, Stubbs KA, Dennis RJ, Taylor EJ, Davies GJ, Greig IR, Vocadlo DJ. Analysis of PUGNAc and NAG-thiazoline as transition state analogues for human O-GlcNAcase: mechanistic and structural insights into inhibitor selectivity and transition state poise. J Am Chem Soc 2007; 129:635-44. [PMID: 17227027 DOI: 10.1021/ja065697o] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O-GlcNAcase catalyzes the cleavage of beta-O-linked 2-acetamido-2-deoxy-beta-d-glucopyranoside (O-GlcNAc) from serine and threonine residues of post-translationally modified proteins. Two potent inhibitors of this enzyme are O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc) and 1,2-dideoxy-2'-methyl-alpha-d-glucopyranoso[2,1-d]-Delta2'-thiazoline (NAG-thiazoline). Derivatives of these inhibitors differ in their selectivity for human O-GlcNAcase over the functionally related human lysosomal beta-hexosamindases, with PUGNAc derivatives showing modest selectivities and NAG-thiazoline derivatives showing high selectivities. The molecular basis for this difference in selectivities is addressed as is how well these inhibitors mimic the O-GlcNAcase-stabilized transition state (TS). Using a series of substrates, ground state (GS) inhibitors, and transition state mimics having analogous structural variations, we describe linear free energy relationships of log(KM/kcat) versus log(KI) for PUGNAc and NAG-thiazoline. These relationships suggest that PUGNAc is a poor transition state analogue, while NAG-thiazoline is revealed as a transition state mimic. Comparative X-ray crystallographic analyses of enzyme-inhibitor complexes reveal subtle molecular differences accounting for the differences in selectivities between these two inhibitors and illustrate key molecular interactions. Computational modeling of species along the reaction coordinate, as well as PUGNAc and NAG-thiazoline, provide insight into the features of NAG-thiazoline that resemble the transition state and reveal where PUGNAc fails to capture significant binding energy. These studies also point to late transition state poise for the O-GlcNAcase catalyzed reaction with significant nucleophilic participation and little involvement of the leaving group. The potency of NAG-thiazoline, its transition state mimicry, and its lack of traditional transition state-like design features suggest that potent rationally designed glycosidase inhibitors can be developed that exploit variation in transition state poise.
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Affiliation(s)
- Garrett E Whitworth
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada
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203
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Minami A, Eguchi T. Substrate flexibility of vicenisaminyltransferase VinC involved in the biosynthesis of vicenistatin. J Am Chem Soc 2007; 129:5102-7. [PMID: 17388594 DOI: 10.1021/ja0685250] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A glycosyltransferase VinC is involved in the biosynthesis of antitumor beta-glycoside antibiotic vicenistatin. It catalyzes a glycosyl transfer reaction between dTDP-alpha-D-vicenisamine and vicenilactam. Previous identification of its broad substrate specificity toward various glycosyl acceptors enabled us to explore the potential of VinC for glycodiversification. In vitro study of the substrate specificity toward several dTDP-sugars with vicenilactam established that VinC displayed activities with alpha-anomers of several dTDP-2-deoxy-D-sugars such as mycarose, digitoxose, olivose, and 2-deoxyglucose to afford respective beta-glycosides. Notably, beta-anomers of dTDP-2-deoxy-D-sugars also appeared to be accepted by VinC to form alpha-glycosides. Furthermore, VinC is capable of catalyzing glycosyl transfer reactions from both the alpha-anomer and beta-anomer of dTDP-l-mycarose, respectively, into beta-glycoside and alpha-glycoside. These results indicate that VinC is a unique glycosyltransferase possessing broad substrate specificity. The mechanism of this axially oriented glycosidic bond formation from the equatorially oriented dTDP-sugar might be explained by conformational change of dTDP-sugar to a boat conformation during the glycosyl transfer reaction. To apply these features of VinC for glycodiversification, 22 sets of structurally diverse glycosides were constructed using unnatural glycosyl donors and acceptors.
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Affiliation(s)
- Atsushi Minami
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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204
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Desmet T, Cantaert T, Gualfetti P, Nerinckx W, Gross L, Mitchinson C, Piens K. An investigation of the substrate specificity of the xyloglucanase Cel74A from Hypocrea jecorina. FEBS J 2007; 274:356-63. [PMID: 17229143 DOI: 10.1111/j.1742-4658.2006.05582.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The substrate specificity of the xyloglucanase Cel74A from Hypocrea jecorina (Trichoderma reesei) was examined using several polysaccharides and oligosaccharides. Our results revealed that xyloglucan chains are hydrolyzed at substituted Glc residues, in contrast to the action of all known xyloglucan endoglucanases (EC 3.2.1.151). The building block of xyloglucan, XXXG (where X is a substituted Glc residue, and G is an unsubstituted Glc residue), was rapidly degraded to XX and XG (k(cat) = 7.2 s(-1) and Km = 120 microM at 37 degrees C and pH 5), which has only been observed before with the oligoxyloglucan-reducing-end-specific cellobiohydrolase from Geotrichum (EC 3.2.1.150). However, the cellobiohydrolase can only release XG from XXXGXXXG, whereas Cel74A hydrolyzed this substrate at both chain ends, resulting in XGXX. Differences in the length of a specific loop at subsite + 2 are discussed as being the basis for the divergent specificity of these xyloglucanases.
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Affiliation(s)
- Tom Desmet
- Department of Biochemistry, Physiology and Microbiology, Faculty of Sciences, Ghent University, Belgium.
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205
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Caines MEC, Vaughan MD, Tarling CA, Hancock SM, Warren RAJ, Withers SG, Strynadka NCJ. Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms. J Biol Chem 2007; 282:14300-8. [PMID: 17329247 DOI: 10.1074/jbc.m611455200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
endo-Glycoceramidase, a membrane-associated family 5 glycosidase, deviates from the typical polysaccharide substrate specificity of other soluble members of the family, preferentially hydrolyzing glycosidic linkages between the oligosaccharide and ceramide moieties of gangliosides. Here we report the first x-ray crystal structures of an endo-glycoceramidase from Rhodococcus sp., in the apo form, in complex with the ganglioside G(M3) (Svennerholm ganglioside nomenclature (Svennerholm, L. (1964) J. Lipid Res. 5, 145-155)), and trapped as a glycosyl-enzyme intermediate. These snapshots provide the first molecular insight into enzyme recognition and association with gangliosides, revealing the structural adaptations necessary for glycosidase-catalyzed hydrolysis and detailing a novel ganglioside binding topology. Consistent with the chemical duality of the substrate, the active site of endo-glycoceramidase is split into a wide, polar cavity to bind the polyhydroxylated oligosaccharide moiety and a narrow, hydrophobic tunnel to bind the ceramide lipid chains. The specific interactions with the ceramide polar head group manifest a surprising aglycone specificity, an observation substantiated by our kinetic analyses. Collectively, the reported structural and kinetic data provide insight toward rational redesign of the synthetic glycosynthase mutant of endo-glycoceramidase to enable facile synthesis of nonnatural, therapeutically useful gangliosides.
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Affiliation(s)
- Matthew E C Caines
- Departments of Biochemistry and Molecular Biology, Chemistry, and Microbiology, University of British Columbia, Vancouver, British Columbia, Canada
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206
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Gloster TM, Meloncelli P, Stick RV, Zechel D, Vasella A, Davies GJ. Glycosidase Inhibition: An Assessment of the Binding of 18 Putative Transition-State Mimics. J Am Chem Soc 2007; 129:2345-54. [PMID: 17279749 DOI: 10.1021/ja066961g] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The inhibition of glycoside hydrolases, through transition-state mimicry, is important both as a probe of enzyme mechanism and in the continuing quest for new drugs, notably in the treatment of cancer, HIV, influenza, and diabetes. The high affinity with which these enzymes are known to bind the transition state provides a framework upon which to design potent inhibitors. Recent work [for example, Bülow, A. et al. J. Am. Chem. Soc. 2000, 122, 8567-8568; Zechel, D. L. et al. J. Am. Chem. Soc. 2003, 125, 14313-14323] has revealed quite confusing and counter-intuitive patterns of inhibition for a number of glycosidase inhibitors. Here we describe a synergistic approach for analysis of inhibitors with a single enzyme 'model system', the Thermotoga maritima family 1 beta-glucosidase, TmGH1. The pH dependence of enzyme activity and inhibition has been determined, structures of inhibitor complexes have been solved by X-ray crystallography, with data up to 1.65 A resolution, and isothermal titration calorimetry was used to establish the thermodynamic signature. This has allowed the characterization of 18 compounds, all putative transition-state mimics, in order to build an 'inhibition profile' that provides an insight into what governs binding. In contrast to our preconceptions, there is little correlation of inhibitor chemistry with the calorimetric dissection of thermodynamics. The ensemble of inhibitors shows strong enthalpy-entropy compensation, and the random distribution of similar inhibitors across the plot of DeltaH degrees a vs TDeltaS degrees a likely reflects the enormous contribution of solvation and desolvation effects on ligand binding.
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Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
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207
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Caravano A, Baillieul D, Ansiaux C, Pan W, Kovensky J, Sinaÿ P, Vincent SP. Synthesis of galactosides locked in a 1,4B boat conformation and functionalized at the anomeric position. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.12.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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208
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Behr JB, Gainvors-Claisse A, Belarbi A. Inhibition of chitin synthase by a series of 7-deoxycasuarine stereoisomers designed as constrained analogues of the potent inhibitor 6-deoxyhomoDMDP. Nat Prod Res 2007; 21:76-82. [PMID: 17365692 DOI: 10.1080/14786410601035993] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A series of polyhydroxy-pyrrolizidines were designed as constrained analogues of 6-deoxy-homoDMDP, a potent naturally occurring inhibitor of chitin synthase. Enzymatic evaluation revealed that 7-deoxycasuarine was the best inhibitor of the series (IC50 = 820 microM) displaying a noncompetitive inhibition pattern, whereas the other tested compounds had IC50 in the range 4.3-18.9 mM. This is the first report of pyrrolizidine-type iminosugars inhibiting a glycosyltransferase. In addition, the inhibitory potencies towards glycosidases of these synthetic casuarine analogues is also disclosed.
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Affiliation(s)
- J-B Behr
- Laboratoire Réactions Sélectives et Applications UMR 6519, UFR Sciences, CNRS, BP 1039, 51687 Reims Cedex 2, France.
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209
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Greig IR, Williams IH. Glycosidase inhibitors as conformational transition state analogues. Chem Commun (Camb) 2007:3747-9. [PMID: 17851615 DOI: 10.1039/b705607a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A method for estimating the conformational similarity between hexopyranose rings is presented and used to probe the behaviour of various glycosyl hydrolase inhibitors as conformational transition state analogues.
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Affiliation(s)
- Ian R Greig
- Department of Chemistry, University of Bath, Bath, UK.
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210
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RCM as a tool to freeze conformation of monosaccharides: synthesis of a β-mannopyranoside mimic adopting a conformation close to the biologically relevant B2,5 boat. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.10.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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211
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Behr JB, Gainvors-Claisse A, Belarbi A. Inhibition of chitin synthase by a series of 7-deoxycasuarine stereoisomers designed as constrained analogues of the potent inhibitor 6-deoxyhomoDMDP. Nat Prod Res 2006; 20:1308-14. [PMID: 17393656 DOI: 10.1080/14786410601101928] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A series of polyhydroxy-pyrrolizidines were designed as constrained analogues of 6-deoxyhomoDMDP, a potent naturally occurring inhibitor of chitin synthase. Enzymatic evaluation revealed that 7-deoxycasuarine was the best inhibitor of the series (IC50 = 820 microM) displaying a non-competitive inhibition pattern, whereas the other tested compounds had IC50 in the range 4.3-18.9 mM. This is the first report of pyrrolizidine-type iminosugars inhibiting a glycosyltransferase. In addition, the biological evaluation towards glycosidases of these synthetic casuarine analogues is also disclosed.
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Affiliation(s)
- J B Behr
- Laboratoire Réactions Sélectives et Applications UMR 6519, UFR Sciences - CNRS, BP 1039, 51687 Reims 2, France.
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212
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Brecker L, Straganz GD, Tyl CE, Steiner W, Nidetzky B. Saturation–transfer–difference NMR to characterize substrate binding recognition and catalysis of two broadly specific glycoside hydrolases. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcatb.2006.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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213
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Mueller-Dieckmann C, Kernstock S, Lisurek M, von Kries JP, Haag F, Weiss MS, Koch-Nolte F. The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation. Proc Natl Acad Sci U S A 2006; 103:15026-31. [PMID: 17015823 PMCID: PMC1622773 DOI: 10.1073/pnas.0606762103] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Posttranslational modifications are used by cells from all kingdoms of life to control enzymatic activity and to regulate protein function. For many cellular processes, including DNA repair, spindle function, and apoptosis, reversible mono- and polyADP-ribosylation constitutes a very important regulatory mechanism. Moreover, many pathogenic bacteria secrete toxins which ADP-ribosylate human proteins, causing diseases such as whooping cough, cholera, and diphtheria. Whereas the 3D structures of numerous ADP-ribosylating toxins and related mammalian enzymes have been elucidated, virtually nothing is known about the structure of protein de-ADP-ribosylating enzymes. Here, we report the 3Dstructure of human ADP-ribosylhydrolase 3 (hARH3). The molecular architecture of hARH3 constitutes the archetype of an all-alpha-helical protein fold and provides insights into the reversibility of protein ADP-ribosylation. Two magnesium ions flanked by highly conserved amino acids pinpoint the active-site crevice. Recombinant hARH3 binds free ADP-ribose with micromolar affinity and efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins. Docking experiments indicate a possible binding mode for ADP-ribose polymers and suggest a reaction mechanism. Our results underscore the importance of endogenous ADP-ribosylation cycles and provide a basis for structure-based design of ADP-ribosylhydrolase inhibitors.
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Affiliation(s)
- Christoph Mueller-Dieckmann
- *European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Stefan Kernstock
- Institute of Immunology, University Hospital, Martinistrasse 52, D-20246 Hamburg, Germany; and
| | - Michael Lisurek
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Roessle-Strasse 10, Campus Berlin–Buch, D-13125 Berlin, Germany
| | - Jens Peter von Kries
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Roessle-Strasse 10, Campus Berlin–Buch, D-13125 Berlin, Germany
| | - Friedrich Haag
- Institute of Immunology, University Hospital, Martinistrasse 52, D-20246 Hamburg, Germany; and
| | - Manfred S. Weiss
- *European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Notkestrasse 85, D-22603 Hamburg, Germany
- To whom correspondence may be addressed. E-mail:
or
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Hospital, Martinistrasse 52, D-20246 Hamburg, Germany; and
- To whom correspondence may be addressed. E-mail:
or
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214
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215
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Suzuki KT, Somekawa L, Suzuki N. Distribution and reuse of 76Se-selenosugar in selenium-deficient rats. Toxicol Appl Pharmacol 2006; 216:303-8. [PMID: 16842833 DOI: 10.1016/j.taap.2006.05.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 05/17/2006] [Accepted: 05/18/2006] [Indexed: 10/24/2022]
Abstract
Nutritional selenium compounds are transformed to the common intermediate selenide and then utilized for selenoprotein synthesis or excreted in urine mostly as 1beta-methylseleno-N-acetyl-Dd-galactosamine (selenosugar). Since the biological significance of selenosugar formation is unknown, we investigated their role in the formation of selenoenzymes in selenium deficiency. Rats were depleted of endogenous natural abundance selenium with a single stable isotope ((82)Se) and then made Se-deficient. (76)Se-Selenosugar was administered intravenously to the rats and their urine, serum, liver, kidneys and testes were subjected to speciation analysis with HPLC inductively coupled argon plasma mass spectrometry. Most (76)Se was recovered in its intact form (approximately 80% of dose) in urine within 1 h. Speciation analysis revealed that residual endogenous natural abundance selenium estimated by (77)Se and (78)Se was negligible and distinct distributions of the labeled (76)Se were detected in the body fluids and organs without interference from the endogenous natural abundance stable isotope. Namely, intact (76)Se-selenosugar was distributed to organs after the injection, and (76)Se was used for selenoprotein synthesis. Oxidation to methylseleninic acid and/or hydrolysis of the selenoacetal group to methylselenol were proposed to the transformation of selenosugar for the reuse. Effective use of an enriched stable isotope as an absolute label in hosts depleted of natural abundance isotopes was discussed for application in tracer experiments.
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Affiliation(s)
- Kazuo T Suzuki
- Department of Toxicology and Environmental Health, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan.
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216
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Shanmugasundaram B, Debowski AW, Dennis RJ, Davies GJ, Vocadlo DJ, Vasella A. Inhibition of O-GlcNAcase by a gluco-configured nagstatin and a PUGNAc-imidazole hybrid inhibitor. Chem Commun (Camb) 2006:4372-4. [PMID: 17057847 DOI: 10.1039/b612154c] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of a PUGNAc-imidazole hybrid and its characterization as an inhibitor of human O-GlcNAcase through enzyme kinetics and X-ray structural analysis.
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217
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Dong C, Major LL, Srikannathasan V, Errey JC, Giraud MF, Lam JS, Graninger M, Messner P, McNeil MR, Field RA, Whitfield C, Naismith JH. RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation. J Mol Biol 2006; 365:146-59. [PMID: 17046787 PMCID: PMC1805628 DOI: 10.1016/j.jmb.2006.09.063] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 09/21/2006] [Accepted: 09/22/2006] [Indexed: 11/27/2022]
Abstract
The striking feature of carbohydrates is their constitutional, conformational and configurational diversity. Biology has harnessed this diversity and manipulates carbohydrate residues in a variety of ways, one of which is epimerization. RmlC catalyzes the epimerization of the C3' and C5' positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose. RmlC is the third enzyme of the rhamnose pathway, and represents a validated anti-bacterial drug target. Although several structures of the enzyme have been reported, the mechanism and the nature of the intermediates have remained obscure. Despite its relatively small size (22 kDa), RmlC catalyzes four stereospecific proton transfers and the substrate undergoes a major conformational change during the course of the transformation. Here we report the structure of RmlC from several organisms in complex with product and product mimics. We have probed site-directed mutants by assay and by deuterium exchange. The combination of structural and biochemical data has allowed us to assign key residues and identify the conformation of the carbohydrate during turnover. Clear knowledge of the chemical structure of RmlC reaction intermediates may offer new opportunities for rational drug design.
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Affiliation(s)
- Changjiang Dong
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
| | - Louise L. Major
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
| | | | - James C. Errey
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Joseph S. Lam
- Department of Molecular & Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Michael Graninger
- Zentrum für NanoBiotechnologie, Universität für Bodenkultur Wien, A-1180, Vienna, Austria
| | - Paul Messner
- Zentrum für NanoBiotechnologie, Universität für Bodenkultur Wien, A-1180, Vienna, Austria
| | - Michael R. McNeil
- Department of Microbiology, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert A. Field
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | - Chris Whitfield
- Department of Molecular & Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - James H. Naismith
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
- Address Correspondence to James H Naismith, Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, UK. Phone 44-1334-463792 Fax 44-1334-462595 Email
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218
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Rodríguez García E, Brimble MA, Vogel P. Synthesis of New Aza-C-disaccharides Linking 4-Deoxy-4-amino-β-L-erythro-furanose to C-2 ofD-Glucose andD-Allose. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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219
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Xu MS, Luo MF, Xing XH, Chen HZ. Characteristics of Quercetin Transglycosidation Catalysed by Penicillium Decumbens Glycosidase. FOOD AND BIOPRODUCTS PROCESSING 2006. [DOI: 10.1205/fbp.05143] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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220
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Goedl C, Griessler R, Schwarz A, Nidetzky B. Structure-function relationships for Schizophyllum commune trehalose phosphorylase and their implications for the catalytic mechanism of family GT-4 glycosyltransferases. Biochem J 2006; 397:491-500. [PMID: 16640506 PMCID: PMC1533306 DOI: 10.1042/bj20060029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The cDNA encoding trehalose phosphorylase, a family GT-4 glycosyltransferase from the fungus Schizophyllum commune, was isolated and expressed in Escherichia coli to yield functional recombinant protein in its full length of 737 amino acids. Unlike the natural phosphorylase that was previously obtained as a truncated 61 kDa monomer containing one tightly bound Mg2+, the intact enzyme produced in E. coli is a dimer and not associated with metal ions [Eis, Watkins, Prohaska and Nidetzky (2001) Biochem. J. 356, 757-767]. MS analysis of the slow spontaneous conversion of the full-length enzyme into a 61 kDa fragment that is fully active revealed that critical elements of catalysis and specificity of trehalose phosphorylase reside entirely in the C-terminal protein part. Intact and truncated phosphorylases thus show identical inhibition constants for the transition state analogue orthovanadate and alpha,alpha-trehalose (K(i) approximately 1 microM). Structure-based sequence comparison with retaining glycosyltransferases of fold family GT-B reveals a putative active centre of trehalose phosphorylase, and results of site-directed mutagenesis confirm the predicted crucial role of Asp379, His403, Arg507 and Lys512 in catalysis and also delineate a function of these residues in determining the large preference of the wild-type enzyme for the phosphorolysis compared with hydrolysis of alpha,alpha-trehalose. The pseudo-disaccharide validoxylamine A was identified as a strong inhibitor of trehalose phosphorylase (K(i)=1.7+/-0.2 microM) that displays 350-fold tighter binding to the enzyme-phosphate complex than the non-phosphorolysable substrate analogue alpha,alpha-thio-trehalose. Structural and electronic features of the inhibitor that may be responsible for high-affinity binding and their complementarity to an anticipated glucosyl oxocarbenium ion-like transition state are discussed.
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Affiliation(s)
- Christiane Goedl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Richard Griessler
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Alexandra Schwarz
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
- To whom correspondence should be addressed (email )
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221
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Substrate Distortion by a Lichenase Highlights the Different Conformational Itineraries Harnessed by Related Glycoside Hydrolases. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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222
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Money VA, Smith NL, Scaffidi A, Stick RV, Gilbert HJ, Davies GJ. Substrate Distortion by a Lichenase Highlights the Different Conformational Itineraries Harnessed by Related Glycoside Hydrolases. Angew Chem Int Ed Engl 2006; 45:5136-40. [PMID: 16823793 DOI: 10.1002/anie.200600802] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Victoria A Money
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
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223
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Kumar NS, Pinto BM. Synthesis of a sulfonium ion analogue of the glycosidase inhibitor swainsonine. J Org Chem 2006; 71:1262-4. [PMID: 16438551 DOI: 10.1021/jo052111s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of a bicyclic sulfonium ion analogue of a naturally occurring indolizidine alkaloid, swainsonine, in which the bridgehead nitrogen atom is replaced by a sulfonium ion, has been achieved by a multistep synthesis starting from (2S,3S,4R)-2,3-dibenzyloxy-4-formaldehyde-thiolane. The synthetic strategy relies on the intramolecular displacement of a leaving group on a pendant acyclic chain by a cyclic thioether. This bicyclic sulfonium salt provides a candidate with which to further probe the hypothesis that a sulfonium salt carrying a permanent positive charge would be an effective glycosidase inhibitor.
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Affiliation(s)
- Nag S Kumar
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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224
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Kumar NS, Pinto BM. Synthesis of thioswainsonine as a potential glycosidase inhibitor. Carbohydr Res 2006; 341:1685-91. [PMID: 16678808 DOI: 10.1016/j.carres.2006.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2006] [Revised: 04/10/2006] [Accepted: 04/13/2006] [Indexed: 11/25/2022]
Abstract
The synthesis of a bicyclic sulfonium-ion analogue of a naturally occurring glycosidase inhibitor, swainsonine, in which the bridgehead nitrogen atom is replaced by a sulfonium ion, has been achieved by a multi-step synthesis starting from 1,4-anhydro-2,3-di-O-benzyl-4-thio-D-lyxitol. The synthetic strategy relies on the intramolecular displacement of a leaving group on a pendant acyclic chain by a cyclic thioether. This bicyclic sulfonium salt will serve as a candidate to test the hypothesis that a sulfonium salt carrying a permanent positive charge would be an effective glycosidase inhibitor.
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Affiliation(s)
- Nag S Kumar
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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225
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Pabba J, Mohal N, Vasella A. Synthesis of Glucuronic, Mannuronic, and Galacturonic Acid-Derived Imidazoles as Inhibitors of Bovine Liverβ-Glucuronidase. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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226
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Kawatkar SP, Kuntz DA, Woods RJ, Rose DR, Boons GJ. Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions. J Am Chem Soc 2006; 128:8310-9. [PMID: 16787095 PMCID: PMC2553320 DOI: 10.1021/ja061216p] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The X-ray crystal structures of mannose trimming enzyme drosophila Golgi alpha-mannosidase II (dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E. In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements around the methionine residues in the protein. Collectively, our studies contradict the long held view that potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.
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Affiliation(s)
- Sameer P. Kawatkar
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602
| | - Douglas A Kuntz
- Ontario Cancer Institute, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602
| | - David R. Rose
- Ontario Cancer Institute, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7
- Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602
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227
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Gordon RD, Sivarajah P, Satkunarajah M, Ma D, Tarling CA, Vizitiu D, Withers SG, Rini JM. X-ray Crystal Structures of Rabbit N-acetylglucosaminyltransferase I (GnT I) in Complex with Donor Substrate Analogues. J Mol Biol 2006; 360:67-79. [PMID: 16769084 DOI: 10.1016/j.jmb.2006.04.058] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Revised: 04/24/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
Abstract
The Golgi-resident glycosyltransferase, UDP-N-acetyl-d-glucosamine:alpha-3-d-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT I), initiates the conversion of high-mannose oligosaccharides to complex and hybrid structures in the biosynthesis of N-linked glycans. Reported here are the X-ray crystal structures of GnT I in complex with UDP-CH2-GlcNAc (a non-hydrolyzable C-glycosidic phosphonate), UDP-2-deoxy-2-fluoro-glucose, UDP-glucose and UDP. Collectively, these structures provide evidence for the importance of the GlcNAc moiety and its N-acetyl group in donor substrate binding, as well as insight into the role played by the flexible 318-330 loop in substrate binding and product release. In addition, the UDP-CH2-GlcNAc complex reveals a well-defined glycerol molecule poised for nucleophilic attack on the C1 atom of the donor substrate analogue. The position and orientation of this glycerol molecule have allowed us to model the binding of the Manalpha1,3Manbeta1 moiety of the acceptor substrate and, based on the model, to suggest a rationalization for the main determinants of GnT I acceptor specificity.
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Affiliation(s)
- Roni D Gordon
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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228
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Laroche C, Behr JB, Szymoniak J, Bertus P, Schütz C, Vogel P, Plantier-Royon R. Spirocyclopropyl pyrrolidines as a new series of α-l-fucosidase inhibitors. Bioorg Med Chem 2006; 14:4047-54. [PMID: 16488612 DOI: 10.1016/j.bmc.2006.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 01/24/2006] [Accepted: 02/03/2006] [Indexed: 11/16/2022]
Abstract
Polyhydroxy 4-azaspiro[2.4]heptane derivatives (spirocyclopropyl iminosugars) were prepared in four to six steps from readily available protected aldoses. The key step of the reaction sequence involves a titanium-mediated aminocyclopropanation of glycononitriles with subsequent cyclization. Five new polyhydroxypyrrolidines so-obtained have been evaluated for their ability to inhibit 16 glycosidases. One of them exhibits selective inhibition of alpha-L-fucosidase from bovine kidney (Ki=1.6 microM, competitive).
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Affiliation(s)
- Christophe Laroche
- Laboratoire Réactions Sélectives et Applications, Université de Reims Champagne-Ardenne, UMR URCA/CNRS 6519, UFR Sciences, BP 1039, F-51687 Reims Cedex 2, France
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229
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Mildvan A, Xia Z, Azurmendi H, Legler P, Balfour M, Lairson L, Withers S, Gabelli S, Bianchet M, Amzel L. Hydrogen bonding in the mechanism of GDP-mannose mannosyl hydrolase. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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230
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Gloster TM, Madsen R, Davies GJ. Dissection of Conformationally Restricted Inhibitors Binding to a β-Glucosidase. Chembiochem 2006; 7:738-42. [PMID: 16628756 DOI: 10.1002/cbic.200600005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tracey M Gloster
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK
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231
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Buser S, Vasella A. Norbornane Mimics of Distortedβ-D-Glucopyranosides – Inhibitors ofβ-D-Glucopyranosidases? Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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232
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Yip VLY, Withers SG. Breakdown of oligosaccharides by the process of elimination. Curr Opin Chem Biol 2006; 10:147-55. [PMID: 16495121 DOI: 10.1016/j.cbpa.2006.02.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Accepted: 02/09/2006] [Indexed: 12/22/2022]
Abstract
Several new mechanisms for enzyme-catalyzed breakdown of oligosaccharides have been uncovered in recent years. A common feature is the recruitment of elimination steps rather than direct displacements. Bond cleavage can proceed via E1 mechanisms with cationic transition states or E1(cb) mechanisms with anionic transition states, and can even involve NAD(+)-mediated redox steps. A common feature emerging from studies on disparate syn-eliminating enzymes is the use of a single catalytic residue, often tyrosine, as both general acid and base.
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Affiliation(s)
- Vivian L Y Yip
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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233
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Pabba J, Rempel B, Withers S, Vasella A. Synthesis of Glycaro-1,5-lactams and Tetrahydrotetrazolopyridine-5-carboxylates: Inhibitors ofβ-D-Glucuronidase andα-L-Iduronidase. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690066] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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234
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Buser S, Vasella A. Synthesis of 2-Azabicyclo[3.2.2]nonane-Derived Monosaccharide Mimics and Their Evaluation as Glycosidase Inhibitors. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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235
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González-Bello C, Castedo L, Cañada FJ. Synthesis of Spiro Carba-Sugars by Ring-Closing Metathesis. European J Org Chem 2006. [DOI: 10.1002/ejoc.200500655] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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236
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Dubost E, Le Nouën D, Streith J, Tarnus C, Tschamber T. Synthesis of Substituted Imidazolo[1,2-a]piperidinoses and Their Evaluation as Glycosidase Inhibitors. European J Org Chem 2006. [DOI: 10.1002/ejoc.200500414] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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237
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Crennell SJ, Cook D, Minns A, Svergun D, Andersen RL, Nordberg Karlsson E. Dimerisation and an Increase in Active Site Aromatic Groups as Adaptations to High Temperatures: X-ray Solution Scattering and Substrate-bound Crystal Structures of Rhodothermus marinus Endoglucanase Cel12A. J Mol Biol 2006; 356:57-71. [PMID: 16343530 DOI: 10.1016/j.jmb.2005.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 10/25/2005] [Accepted: 11/02/2005] [Indexed: 10/25/2022]
Abstract
Cellulose, a polysaccharide consisting of beta-1,4-linked glucose, is the major component of plant cell walls and consequently one of the most abundant biopolymers on earth. Carbohydrate polymers such as cellulose are molecules with vast diversity in structure and function, and a multiplicity of hydrolases operating in concert are required for depolymerisation. The bacterium Rhodothermus marinus, isolated from shallow water marine hot springs, produces a number of carbohydrate-degrading enzymes including a family 12 cellulase Cel12A. The structure of R.marinus Cel12A in the ligand-free form (at 1.54 angstroms) and structures of RmCel12A after crystals were soaked in cellopentaose for two different lengths of time, have been determined. The shorter soaked complex revealed the conformation of unhydrolysed cellotetraose, while cellopentaose had been degraded more completely during the longer soak. Comparison of these structures with those of mesophilic family 12 cellulases in complex with inhibitors and substrate revealed that RmCel12A has a more extensive aromatic network in the active site cleft which ejects products after hydrolysis. The substrate structure confirms that during hydrolysis by family 12 cellulases glucose does not pass through a (2,5)B conformation. Small-angle X-ray scattering analysis of RmCel12A showed that the enzyme forms a loosely associated antiparallel dimer in solution, which may target the enzyme to the antiparallel polymer strands in cellulose.
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Affiliation(s)
- Susan J Crennell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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238
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Cicchi S, Marradi M, Vogel P, Goti A. One-Pot Synthesis of Cyclic Nitrones and Their Conversion to Pyrrolizidines: 7a-epi-Crotanecine Inhibits α-Mannosidases. J Org Chem 2006; 71:1614-9. [PMID: 16468814 DOI: 10.1021/jo0523518] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] A new straightforward and inexpensive one-pot procedure is described for the preparation of enantiopure five-membered cyclic nitrones starting from the corresponding lactols. Its efficiency relies on the condensation of unprotected hydroxylamine with readily available lactols and on the chemoselectivity of the subsequent esterification with methanesulfonyl chloride. The targeted enantiomerically pure pyrroline N-oxides are versatile synthetic intermediates: one of the nitrones so-obtained has been converted into new polyhydroxypyrrolizidines, analogues of the alkaloids rosmarinecine and crotanecine, which were assayed for their inhibitory activities toward 22 commercially available glycosidase enzymes. One of them ((-)-7a-epi-crotanecine) is a potent and selective inhibitor of alpha-mannosidases from jack beans and almonds.
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Affiliation(s)
- S Cicchi
- Dipartimento di Chimica Organica Ugo Schiff, Università di Firenze, ICCOM C.N.R., via della Lastruccia 13, I-50019 Sesto Fiorentino (FI), Italy
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239
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Gallienne E, Gefflaut T, Bolte J, Lemaire M. Synthesis of New Nitrogen Analogues of Salacinol and Deoxynojirimycin and Their Evaluation as Glycosidase Inhibitors. J Org Chem 2006; 71:894-902. [PMID: 16438498 DOI: 10.1021/jo0517388] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of two enantiomerically pure iminosugars, analogues of 1-L-deoxynojirimycin (l-DNJ) and 1-D-deoxymannojirimycin (DMJ), was achieved using cyclic sulfate substituted isoxazoline derivatives. The piperidine ring was formed via the reduction of an isoxazoline into an amine which underwent a spontaneous intramolecular cyclization by reaction with the cyclic sulfate moiety. The nucleophilic attack of these two trisubstituted piperidines and morpholine on L- and D-erythritol-1,3-cyclic sulfates gave six new nitrogen analogues of salacinol. The inhibitory properties of the synthesized salacinol analogues were evaluated on several commercial glycosidases.
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Affiliation(s)
- Estelle Gallienne
- Laboratoire SEESIB, UMR 6504 CNRS, Université Blaise Pascal, 24 avenue des Landais, 63177 Aubière Cedex, France
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240
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Smith DM, Woerpel KA. Electrostatic interactions in cations and their importance in biology and chemistry. Org Biomol Chem 2006; 4:1195-201. [PMID: 16557303 DOI: 10.1039/b600056h] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrostatic effects exert strongly stabilizing influences on cations, in many cases controlling the conformational preferences of these cations. The lowest energy conformers are ones where the positive charge is brought closest to substituents bearing partial negative charges. These conformational biases, along with stereoelectronic effects, can control the stereoselectivity of reactions involving carbocationic intermediates.
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Affiliation(s)
- Deborah M Smith
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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241
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Li H, Schütz C, Favre S, Zhang Y, Vogel P, Sinaÿ P, Blériot Y. Nucleophilic opening of epoxyazepanes: expanding the family of polyhydroxyazepane-based glycosidase inhibitors. Org Biomol Chem 2006; 4:1653-62. [PMID: 16633556 DOI: 10.1039/b518117h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A range of new tetra- and pentahydroxylated seven-membered iminoalditols has been efficiently synthesized from epoxyazepane precursors via nucleophilic opening with hydride or oxygenated species and subsequent hydrogenolysis. One tetrahydroxylated azepane, a ring homologue of deoxymannojirimycin, displays a selective and fairly good inhibition of alpha-L-fucosidase.
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Affiliation(s)
- Hongqing Li
- Ecole Normale Supérieure, Département de Chimie, UMR 8642 associée au CNRS, Paris, France
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242
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Mechanisms for nucleophilic aliphatic substitution at glycosides. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0065-3160(06)41005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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243
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Major LL, Wolucka BA, Naismith JH. Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site. J Am Chem Soc 2005; 127:18309-20. [PMID: 16366586 PMCID: PMC3315049 DOI: 10.1021/ja056490i] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GDP-mannose-3',5'-epimerase (GME) from Arabidopsis thaliana catalyzes the epimerization of both the 3' and 5' positions of GDP-alpha-D-mannose to yield GDP-beta-L-galactose. Production of the C5' epimer of GDP-alpha-D-mannose, GDP-beta-L-gulose, has also been reported. The reaction occurs as part of vitamin C biosynthesis in plants. We have determined structures of complexes of GME with GDP-alpha-D-mannose, GDP-beta-L-galactose, and a mixture of GDP-beta-L-gulose with GDP-beta-L-4-keto-gulose to resolutions varying from 2.0 to 1.4 A. The enzyme has the classical extended short-chain dehydratase/reductase (SDR) fold. We have confirmed that GME establishes an equilibrium between two products, GDP-beta-L-galactose and GDP-beta-L-gulose. The reaction proceeds by C4' oxidation of GDP-alpha-D-mannose followed by epimerization of the C5' position to give GDP-beta-L-4-keto-gulose. This intermediate is either reduced to give GDP-beta-L-gulose or the C3' position is epimerized to give GDP-beta-L-4-keto-galactose, then C4' is reduced to GDP-beta-L-galactose. The combination of oxidation, epimerization, and reduction in a single active site is unusual. Structural analysis coupled to site-directed mutagenesis suggests C145 and K217 as the acid/base pair responsible for both epimerizations. On the basis of the structure of the GDP-beta-L-gulose/GDP-beta-L-4-keto-gulose co-complex, we predict that a ring flip occurs during the first epimerization and that a boat intermediate is likely for the second epimerization. Comparison of GME with other SDR enzymes known to abstract a protein alpha to the keto function of a carbohydrate identifies key common features.
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Affiliation(s)
- Louise L Major
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife, Scotland KY16 9ST, United Kingdom
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244
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Blériot Y, Gretzke D, Krülle TM, Butters TD, Dwek RA, Nash RJ, Asano N, Fleet GWJ. Looking glass inhibitors: efficient synthesis and biological evaluation of d-deoxyfuconojirimycin. Carbohydr Res 2005; 340:2713-8. [PMID: 16274755 DOI: 10.1016/j.carres.2005.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 10/03/2005] [Accepted: 10/11/2005] [Indexed: 11/24/2022]
Abstract
1,6-Dideoxygalactostatin, the mirror image of 1-deoxy-L-fuconojirimycin, was efficiently prepared from 2,3-O-isopropylidene-L-lyxonolactone in four steps and evaluated as a glycosidase inhibitor.
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Affiliation(s)
- Yves Blériot
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.
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245
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Stam MR, Blanc E, Coutinho PM, Henrissat B. Evolutionary and mechanistic relationships between glycosidases acting on α- and β-bonds. Carbohydr Res 2005; 340:2728-34. [PMID: 16226731 DOI: 10.1016/j.carres.2005.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 09/15/2005] [Indexed: 10/25/2022]
Abstract
Because of the fast accumulation of sequences derived from genome sequencing efforts, the sampling of the sequence space in glycosidase and related enzyme families is such that sensitive sequence similarity detection methods like PSI-BLAST are now able to reveal distant, but clear, structural and evolutionary relations between glycosidases acting on alpha- and beta-bonds. We have observed this trend within groups of glycosidases with completely different folds. We postulate that the evolutionary interconversion between alpha- and beta-acting glycosidases was greatly facilitated by the fact that both types share a similar axial orientation of the glycosidic bond in the reactive bound substrate. Glycosides in the beta anomeric configuration, require a sugar ring distortion, resulting in an axial orientation of the glycosidic bond, equivalent to that of an alpha glycosidic bond, prior to displacement by nucleophilic substitution.
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Affiliation(s)
- Mark R Stam
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, Centre National de la Recherche Scientifique, Universités d'Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
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246
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Buser S, Vasella A. 7-Oxanorbornane and Norbornane Mimics of a Distortedβ-D-Mannopyranoside: Synthesis and Evaluation asβ-Mannosidase Inhibitors. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590255] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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247
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Davies GJ, Gloster TM, Henrissat B. Recent structural insights into the expanding world of carbohydrate-active enzymes. Curr Opin Struct Biol 2005; 15:637-45. [PMID: 16263268 DOI: 10.1016/j.sbi.2005.10.008] [Citation(s) in RCA: 199] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 09/21/2005] [Accepted: 10/20/2005] [Indexed: 11/16/2022]
Abstract
Enzymes that catalyse the synthesis and breakdown of glycosidic bonds account for 1-3% of the proteins encoded by the genomes of most organisms. At the current rate, over 12 000 glycosyltransferase and glycoside hydrolase open reading frames will appear during 2006. Recent advances in the study of the structure and mechanism of these carbohydrate-active enzymes reveal that glycoside hydrolases continue to display a wide variety of scaffolds, whereas nucleotide-sugar-dependent glycosyltransferases tend to be grafted onto just two protein folds. The past two years have seen significant advances, including the discovery of a novel NAD+-dependent glycosidase mechanism, the dissection of the reaction coordinate of sialidases and a better understanding of the expanding roles of auxiliary carbohydrate-binding domains.
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Affiliation(s)
- Gideon J Davies
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK.
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248
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Patel C, Koh D, Jacobson M, Oliveira M. Identification of three critical acidic residues of poly(ADP-ribose) glycohydrolase involved in catalysis: determining the PARG catalytic domain. Biochem J 2005; 388:493-500. [PMID: 15658938 PMCID: PMC1138956 DOI: 10.1042/bj20040942] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
PARG [poly(ADP-ribose) glycohydrolase] catalyses the hydrolysis of alpha(1''-->2') or alpha(1'''-->2'') O-glycosidic linkages of ADP-ribose polymers to produce free ADP-ribose. We investigated possible mechanistic similarities between PARG and glycosidases, which also cleave O-glycosidic linkages. Glycosidases typically utilize two acidic residues for catalysis, thus we targeted acidic residues within a conserved region of bovine PARG that has been shown to contain an inhibitor-binding site. The targeted glutamate and aspartate residues were changed to asparagine in order to minimize structural alterations. Mutants were purified and assayed for catalytic activity, as well as binding, to an immobilized PARG inhibitor to determine ability to recognize substrate. Our investigation revealed residues essential for PARG catalytic activity. Two adjacent glutamic acid residues are found in the conserved sequence Gln755-Glu-Glu757, and a third residue found in the conserved sequence Val737-Asp-Phe-Ala-Asn741. Our functional characterization of PARG residues, along with recent identification of an inhibitor-binding residue Tyr796 and a glycine-rich region Gly745-Gly-Gly747 important for PARG function, allowed us to define a PARG 'signature sequence' [vDFA-X3-GGg-X6-8-vQEEIRF-X3-PE-X14-E-X12-YTGYa], which we used to identify putative PARG sequences across a range of organisms. Sequence alignments, along with our mapping of PARG functional residues, suggest the presence of a conserved catalytic domain of approx. 185 residues which spans residues 610-795 in bovine PARG.
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Affiliation(s)
- Chandra N. Patel
- *Department of Pharmaceutical Sciences, College of Pharmacy, Markey Cancer Center and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, U.S.A
| | - David W. Koh
- *Department of Pharmaceutical Sciences, College of Pharmacy, Markey Cancer Center and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, U.S.A
| | - Myron K. Jacobson
- †Department of Pharmacology and Toxicology, College of Pharmacy and Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, U.S.A
| | - Marcos A. Oliveira
- *Department of Pharmaceutical Sciences, College of Pharmacy, Markey Cancer Center and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, U.S.A
- To whom correspondence should be addressed (email )
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249
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Kumar NS, Pinto BM. Synthesis and Conformational Analysis of Bicyclic Sulfonium Salts. Structures Related to the Glycosidase Inhibitor Australine. J Org Chem 2005; 71:2935-43. [PMID: 16599585 DOI: 10.1021/jo051560p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The syntheses of eight sulfonium compounds with structures related to the naturally occurring pyrrolizidine alkaloid, australine, in which the bridgehead nitrogen atom is replaced by a sulfonium ion, are described. The synthetic strategy relies on the intramolecular attack of a cyclic thioether across a terminal double bond in the presence of a suitable electrophile. We postulate that these compounds, having a permanent positive charge on the sulfur atom, will mimic the highly unstable oxacarbenium ion transition state in a glycosidase-catalyzed hydrolysis reaction. The conformational preferences of these compounds, based on analysis of 1H-1H vicinal coupling constants and 1D-NOESY data, are attributed to both steric and electrostatic interactions. These compounds will be used in the study of structure-activity relationships with glycosidase enzymes.
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Affiliation(s)
- Nag S Kumar
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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250
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Łysek R, Schütz C, Vogel P. (1S,2S,3R,6R)-6-Aminocyclohex-4-ene-1,2,3-triol (= (−)-Conduramine B-1) Is a Selective Inhibitor ofα-Mannosidases. Its Inhibitory Activity Is Enhanced byN-Benzylation. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590220] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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