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Blériot Y, Auberger N, Désiré J. Sugar-Derived Amidines and Congeners: Structures, Glycosidase Inhibition and Applications. Curr Med Chem 2021; 29:1271-1292. [PMID: 34951354 DOI: 10.2174/0929867329666211222164545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/16/2021] [Accepted: 10/22/2021] [Indexed: 11/22/2022]
Abstract
Glycosidases, the enzymes responsible for the breakdown of glycoconjugates including di-, oligo- and polysaccharides are ubiquitous through all kingdoms of life. The extreme chemical stability of the glycosidic bond combined with the catalytic rates achieved by glycosidases makes them among the most proficient of all enzymes.
Given their multitude of roles in vivo, inhibition of these enzymes is highly attractive with potential in the treatment of a vast array of pathologies ranging from lysosomal storage and diabetes to viral infections. Therefore great efforts have been invested in the last three decades to design and synthesize inhibitors of glycosidases leading to a number of drugs currently on the market. Amongst the vast array of structures that have been disclosed, sugars incorporating an amidine moiety have been the focus of many research groups around the world because of their glycosidase transition state-like structure. In this review we report and discuss the structure, the inhibition profile and the use of these molecules including related structural congeners as transition state analogs.
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Affiliation(s)
- Yves Blériot
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "OrgaSynth", Groupe Glycochimie 4 rue Michel Brunet, 86073 Poitiers cedex 9. France
| | - Nicolas Auberger
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "OrgaSynth", Groupe Glycochimie 4 rue Michel Brunet, 86073 Poitiers cedex 9. France
| | - Jérôme Désiré
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "OrgaSynth", Groupe Glycochimie 4 rue Michel Brunet, 86073 Poitiers cedex 9. France
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2
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Deng H, Ke S, Callender R, Balakrishnan G, Spiro TG, May ER, Brooks CL. Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods. J Phys Chem B 2019; 123:7840-7851. [PMID: 31437399 PMCID: PMC6752976 DOI: 10.1021/acs.jpcb.9b06759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yersinia Protein Tyrosine Phosphatase (YopH) is the most efficient enzyme among all known PTPases and relies on its catalytic loop movements for substrate binding and catalysis. Fluorescence, NMR, and UV resonance Raman (UVRR) techniques have been used to study the thermodynamic and dynamic properties of the loop motions. In this study, a computational approach based on the pathway refinement methods nudged elastic band (NEB) and harmonic Fourier beads (HFB) has been developed to provide structural interpretations for the experimentally observed kinetic processes. In this approach, the minimum potential energy pathways for the loop open/closure conformational changes were determined by NEB using a one-dimensional global coordinate. Two dimensional data analyses of the NEB results were performed as an efficient method to qualitatively evaluate the energetics of transitions along several specific physical coordinates. The free energy barriers for these transitions were then determined more precisely using the HFB method. Kinetic parameters were estimated from the energy barriers using transition state theory and compared against experimentally determined kinetic parameters. When the calculated energy barriers are calibrated by a simple "scaling factor", as have been done in our previous vibrational frequency calculations to explain the ligand frequency shift upon its binding to protein, it is possible to make structural interpretations of several observed enzyme dynamic rates. For example, the nanosecond kinetics observed by fluorescence anisotropy may be assigned to the translational motion of the catalytic loop and microsecond kinetics observed in fluorescence T-jump can be assigned to the loop backbone dihedral angle flipping. Furthermore, we can predict that a Trp354 conformational conversion associated with the loop movements would occur on the tens of nanoseconds time scale, to be verified by future UVRR T-jump studies.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Shan Ke
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | | | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, USA 06269
| | - Charles L. Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109
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3
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Abstract
Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.
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Affiliation(s)
- Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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4
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Karnawat V, Gogia S, Balaram H, Puranik M. Differential Distortion of Purine Substrates by Human and Plasmodium falciparum Hypoxanthine-Guanine Phosphoribosyltransferase to Catalyse the Formation of Mononucleotides. Chemphyschem 2015; 16:2172-81. [PMID: 25944719 DOI: 10.1002/cphc.201500084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/10/2022]
Abstract
Plasmodium falciparum (Pf) hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a potential therapeutic target. Compared to structurally homologous human enzymes, it has expanded substrate specificity. In this study, 9-deazapurines are used as in situ probes of the active sites of human and Pf HGPRTs. Through the use of these probes it is found that non-covalent interactions stabilise the pre-transition state of the HGPRT-catalysed reaction. Vibrational spectra reveal that the bound substrates are extensively distorted, the carbonyl bond of nucleobase moiety is weakened and the substrate is destabilised along the reaction coordinate. Raman shifts of the human and Pf enzymes are used to quantify the differing degrees of hydrogen bonding in the homologues. A decreased Raman cross-section in enzyme-bound 9-deazaguanine (9DAG) shows that the phenylalanine residue (Phe186 in human and Phe197 in Pf) of HGPRT stacks with the nucleobase. Differential loss of the Raman cross-section suggests that the active site is more compact in human HGPRT as compared to the Pf enzyme, and is more so in the phosphoribosyl pyrophosphate (PRPP) complex 9DAG-PRPP-HGPRT than in 9-deazahypoxanthine (9DAH)-PRPP-HGPRT.
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Affiliation(s)
- Vishakha Karnawat
- Indian Institute of Science Education and Research, Pune-411008 (India)
| | - Spriha Gogia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore-560065 (India)
| | - Hemalatha Balaram
- Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore-560064 (India).
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research, Pune-411008 (India).
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5
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Deng H. Enzyme active site interactions by Raman/FTIR, NMR, and ab initio calculations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:153-82. [PMID: 24018325 PMCID: PMC5484042 DOI: 10.1016/b978-0-12-416596-0.00005-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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6
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Frohberg P, Wagner C, Meier R, Sippl W. Derivatives of arylhydrazonic acids. Part 3: Stereochemical rearrangement of Z-oxanilo-N1-dialkyl-N2-arylamidrazones. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Berti PJ, McCann JAB. Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transfer. Chem Rev 2006; 106:506-55. [PMID: 16464017 DOI: 10.1021/cr040461t] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Paul J Berti
- Department of Chemistry, McMaster University, Hamilton, Ontario, Canada.
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8
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Chiral 3-hydroxypyrrolidin-2-ones from a Baylis–Hillman adduct: convergent, stereoselective synthesis of a glycosidase inhibitor. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.08.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Desamero RZB, Cheng H, Cahill S, Girvin M, Deng H, Callender R, Rath P, Variano B, Smart JE. Physical properties of compounds promoting oral delivery of macromolecular drugs. Biopolymers 2002; 67:26-40. [PMID: 11842411 DOI: 10.1002/bip.10039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The spectroscopic and solution properties of a series of amidated acids (delivery agents), which promote the gastrointestinal absorption of USP heparin and other drugs that show poor oral bioavailability, are investigated using Raman and NMR spectroscopy. The results show evidence for self-association at low concentrations of delivery agents that increases as the concentration of the delivery agent is increased. The self-associate is characterized by ring-ring stacking interactions, and the best geometrical arrangement for the stacking is the parallel-shifted arrangement of the rings. In addition, the amide group participates in the formation of intermolecular hydrogen bonds in the self-associate. Unlike the rigid ring, the tails of these delivery agents remain relatively flexible in the self-associate. It is suggested that the limited solubility of the delivery agents at physiological pH arises from a percentage of protonated carboxyls. Their presence promotes the formation of intermolecular hydrophobic and ring stacking interactions, which are otherwise weakened by an ionized carboxyl group.
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Affiliation(s)
- Ruel Z B Desamero
- Department of Physics, City College of New York, New York, New York 10031, USA
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Lillelund VH, Jensen HH, Liang X, Bols M. Recent developments of transition-state analogue glycosidase inhibitors of non-natural product origin. Chem Rev 2002; 102:515-53. [PMID: 11841253 DOI: 10.1021/cr000433k] [Citation(s) in RCA: 614] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vinni H Lillelund
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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11
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Berti PJ, Tanaka KS. Transition State Analysis Using Multiple Kinetic Isotope Effects: Mechanisms of Enzymatic and Non-enzymatic Glycoside Hydrolysis and Transfer. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2002. [DOI: 10.1016/s0065-3160(02)37004-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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12
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Toney MD. Computational studies on nonenzymatic and enzymatic pyridoxal phosphate catalyzed decarboxylations of 2-aminoisobutyrate. Biochemistry 2001; 40:1378-84. [PMID: 11170465 DOI: 10.1021/bi0012383] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A computational study of nonenzymatic and enzymatic pyridoxal phosphate-catalyzed decarboxylation of 2-aminoisobutyrate (AIB) is presented. Four prototropic isomers of a model aldimine between AIB and 5'-deoxypyridoxal, with acetate interacting with the pyridine nitrogen, were employed in calculations of both gas phase and water model (PM3 and PM3-SM3) decarboxylation reaction paths. Calculations employing the transition state structures obtained for the four isomers allow the demonstration of stereoelectronic effects in transition state stabilization as well as a separation of the contributions of the Schiff base and pyridine ring moieties to this stabilization. The unprotonated Schiff base contribution (approximately 16 kcal/mol) is larger than that of the pyridine ring even when it is protonated (approximately 10 kcal/mol), providing an explanation of the catalytic power of pyruvoyl-dependent amino acid decarboxylases. An active site model of dialkylglycine decarboxylase was constructed and validated, and enzymatic decarboxylation reaction paths were calculated. The reaction coordinate is shown to be complex, with proton transfer from Lys272 to the coenzyme C4' likely simultaneous with C alpha--CO(2)(-) bond cleavage. The proposed concerted decarboxylation/proton-transfer mechanism provides a simple explanation for the observed specificity of this enzyme toward oxidative decarboxylation.
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Affiliation(s)
- M D Toney
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA.
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13
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Deng H, Callender R. Raman spectroscopic studies of the structures, energetics, and bond distortions of substrates bound to enzymes. Methods Enzymol 1999; 308:176-201. [PMID: 10507005 DOI: 10.1016/s0076-6879(99)08010-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- H Deng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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14
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Jiménez Blanco J, Ortiz Mellet C, Fuentes J, García Fernández J. Synthesis and stereoelectronic properties of sugar-shaped polyhydroxylated hexahydropyrimidine-2-thiones. Tetrahedron 1998. [DOI: 10.1016/s0040-4020(98)00872-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Abstract
All chemical transformations pass through an unstable structure called the transition state, which is poised between the chemical structures of the substrates and products. The transition states for chemical reactions are proposed to have lifetimes near 10(-13) sec, the time for a single bond vibration. No physical or spectroscopic method is available to directly observe the structure of the transition state for enzymatic reactions. Yet transition state structure is central to understanding catalysis, because enzymes function by lowering activation energy. An accepted view of enzymatic catalysis is tight binding to the unstable transition state structure. Transition state mimics bind tightly to enzymes by capturing a fraction of the binding energy for the transition state species. The identification of numerous transition state inhibitors supports the transition state stabilization hypothesis for enzymatic catalysis. Advances in methods for measuring and interpreting kinetic isotope effects and advances in computational chemistry have provided an experimental route to understand transition state structure. Systematic analysis of intrinsic kinetic isotope effects provides geometric and electronic structure for enzyme-bound transition states. This information has been used to compare transition states for chemical and enzymatic reactions; determine whether enzymatic activators alter transition state structure; design transition state inhibitors; and provide the basis for predicting the affinity of enzymatic inhibitors. Enzymatic transition states provide an understanding of catalysis and permit the design of transition state inhibitors. This article reviews transition state theory for enzymatic reactions. Selected examples of enzymatic transition states are compared to the respective transition state inhibitors.
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Affiliation(s)
- V L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.
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16
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Deng H, Callender R. Structure of Dihydrofolate When Bound to Dihydrofolate Reductase. J Am Chem Soc 1998. [DOI: 10.1021/ja9814974] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hua Deng
- Contribution from the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Robert Callender
- Contribution from the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
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17
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Berti PJ, Schramm VL. Transition State Structure of the Solvolytic Hydrolysis of NAD+. J Am Chem Soc 1997. [DOI: 10.1021/ja971316i] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paul J. Berti
- Contribution from the Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Vern L. Schramm
- Contribution from the Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
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18
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Abstract
N-ribohydrolases and transferases act on nucleosides, nucleotides and oligonucleotides to effect base removal. Advances in mechanistic and structural analysis have established that enzymes of N-riboside scission act by combinations of leaving-group and ribosyl activation. Alternative O-riboside substrates have been developed for mechanistic diagnosis. Transition-state structures have been determined, and powerful inhibitors have been designed from structural and transition-state information.
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Affiliation(s)
- V L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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19
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Huang Y, Dalton DR, Carroll PJ. The Efficient, Enantioselective Synthesis of Aza Sugars from Amino Acids. 1. The Polyhydroxylated Pyrrolidines. J Org Chem 1997; 62:372-376. [PMID: 11671412 DOI: 10.1021/jo962028s] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Beginning with (+)-serine or (-)-serine, as appropriate, convenient, high-yield, enantioselective synthesis of all eight stereoisomeric 2-hydroxymethyl-3,4-dihydroxypyrrolidines (the enantiomeric pairs of iminoribitol, -arabinitol, -xylitol, and -lyxitol) can be effected. The absolute configuration of the starting amino acid defines the set of azasugars produced.
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Affiliation(s)
- Yifang Huang
- Chemistry Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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20
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Ganem B. Inhibitors of Carbohydrate-Processing Enzymes: Design and Synthesis of Sugar-Shaped Heterocycles. Acc Chem Res 1996. [DOI: 10.1021/ar9502184] [Citation(s) in RCA: 232] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruce Ganem
- Baker Laboratory, Department of Chemistry, Cornell University, Ithaca, New York 14853-1301
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