1
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Upadhyaya K, Osorio-Morales N, Crich D. Can Side-Chain Conformation and Glycosylation Selectivity of Hexopyranosyl Donors Be Controlled with a Dummy Ligand? J Org Chem 2023; 88:3678-3696. [PMID: 36877600 PMCID: PMC10028612 DOI: 10.1021/acs.joc.2c02889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
The use of a phenylthio group (SPh) as a dummy ligand at the 6-position to control the side-chain conformation of a series of hexopyranosyl donors is described. The SPh group limits side-chain conformation in a configuration-specific manner, which parallels that seen in the heptopyranosides, and so influences glycosylation selectivity. With both d- and l-glycero-d-galacto-configured donors, the equatorial products are highly favored as they are with an l-glycero-d-gluco donor. For the d-glycero-d-gluco donor, on the other hand, modest axial selectivity is observed. Selectivity patterns are discussed in terms of the side-chain conformation of the donors in combination with the electron-withdrawing effect of the thioacetal group. After glycosylation, removal of the thiophenyl moiety and hydrogenolytic deprotection is achieved in a single step with Raney nickel.
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Affiliation(s)
- Kapil Upadhyaya
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
| | - Nicolas Osorio-Morales
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, 302 East Campus Road, Athens, Georgia 30602, United States
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, 302 East Campus Road, Athens, Georgia 30602, United States
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
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2
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Nejatie A, Colombo C, Hakak‐Zargar B, Bennet AJ. A Mechanistic Study on the Non‐enzymatic Hydrolysis of Kdn Glycosides. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ali Nejatie
- Department of Chemistry Simon Fraser University 8888 University Drive Burnaby British Columbia V5A 1S6 Canada
| | - Cinzia Colombo
- Department of Chemistry Simon Fraser University 8888 University Drive Burnaby British Columbia V5A 1S6 Canada
| | - Benyamin Hakak‐Zargar
- Department of Chemistry Simon Fraser University 8888 University Drive Burnaby British Columbia V5A 1S6 Canada
| | - Andrew J. Bennet
- Department of Chemistry Simon Fraser University 8888 University Drive Burnaby British Columbia V5A 1S6 Canada
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3
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Upadhyaya K, Bagul RS, Crich D. Influence of Configuration at the 4- and 6-Positions on the Conformation and Anomeric Reactivity and Selectivity of 7-Deoxyheptopyranosyl Donors: Discovery of a Highly Equatorially Selective l- glycero-d- gluco-Heptopyranosyl Donor. J Org Chem 2021; 86:12199-12225. [PMID: 34343001 DOI: 10.1021/acs.joc.1c01535] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The preparation of four per-O-benzyl-d- or l-glycero-d-galacto and d- or l-glycero-d-gluco heptopyranosyl sulfoxides and the influence of their side-chain conformations on reactivity and stereoselectivity in glycosylation reactions are described. The side-chain conformation in these donors is determined by the relative configuration of its point of attachment to the pyranoside ring and the two flanking centers in agreement with a recent model. In the d- and l-glycero-d-galacto glycosyl donors, the d-glycero-d-galacto isomer with the more electron-withdrawing trans,gauche conformation of its side chain was the more equatorially selective isomer. In the d- and l-glycero-d-gluco glycosyl donors, the l-glycero-d-gluco isomer with the least disarming gauche,gauche side-chain conformation was the most equatorially selective donor. Variable temperature NMR studies, while supporting the formation of intermediate glycosyl triflates at -80 °C in all cases, were inconclusive owing to a change in the decomposition mechanism with the change in configuration. It is suggested that the equatorial selectivity of the l-glycero-d-gluco isomer arises from H-bonding between the glycosyl acceptor and O6 of the donor, which is poised to deliver the acceptor antiperiplanar to the glycosyl triflate, resulting in a high degree of SN2 character in the displacement reaction.
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Affiliation(s)
- Kapil Upadhyaya
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
| | - Rahul S Bagul
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States.,Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States.,Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States.,Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
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4
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An X, Chen C, Wang T, Huang A, Zhang D, Han MJ, Wang J. Genetic Incorporation of Selenotyrosine Significantly Improves Enzymatic Activity of Agrobacterium radiobacter Phosphotriesterase. Chembiochem 2021; 22:2535-2539. [PMID: 32789938 DOI: 10.1002/cbic.202000460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/11/2020] [Indexed: 12/16/2022]
Abstract
Tyrosine plays important roles in many enzymes. To facilitate enzyme design, mechanistic studies and minimize structural perturbation in the active site, here we report the genetic incorporation of a novel unnatural amino acid selenotyrosine (SeHF), which has single-atom replacement in comparison to tyrosine. The arPTE-(Agrobacterium radiobacter Phosphotriesterase) Tyr309SeHF mutant exhibits a significant 12-fold increase in kcat and 3.2-fold enhancement in kcat /KM at pH 7.0. Molecular dynamics simulations show that the SeHF309 mutation results in a conformational switch which opens up the product release pocket and increases the product release rate, thereby elevating the overall enzyme activity. Significant improvement of the catalytic efficiency at neutral pH by single unnatural amino acid (UAA) mutation broadens the application of this enzyme, and provides valuable insights to the mechanism. Our method represents a new approach for designing enzymes with enhanced activity.
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Affiliation(s)
- Xiaojing An
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Chao Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,University of the Chinese Academy of Sciences (UCAS), Hefei, China
| | - Tianyuan Wang
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Ming-Jie Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Jiangyun Wang
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
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5
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Shamsi Kazem Abadi S, Deen MC, Watson JN, Shidmoossavee FS, Bennet AJ. Directed evolution of a remarkably efficient Kdnase from a bacterial neuraminidase. Glycobiology 2019; 30:325-333. [DOI: 10.1093/glycob/cwz099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 11/12/2022] Open
Abstract
AbstractN-acetylneuraminic acid (5-acetamido-3,5-dideoxy-d-glycero-d-galacto-non-2-ulosonic acid), which is the principal sialic acid family member of the non-2-ulosonic acids and their various derivatives, is often found at the terminal position on the glycan chains that adorn all vertebrate cells. This terminal position combined with subtle variations in structure and linkage to the underlying glycan chains between humans and other mammals points to the importance of this diverse group of nine-carbon sugars as indicators of the unique aspects of human evolution and is relevant to understanding an array of human conditions. Enzymes that catalyze the removal N-acetylneuraminic acid from glycoconjugates are called neuraminidases. However, despite their documented role in numerous diseases, due to the promiscuous activity of many neuraminidases, our knowledge of the functions and metabolism of many sialic acids and the effect of the attachment to cellular glycans is limited. To this end, through a concerted effort of generation of random and site-directed mutagenesis libraries, subsequent screens and positive and negative evolutionary selection protocols, we succeeded in identifying three enzyme variants of the neuraminidase from the soil bacterium Micromonospora viridifaciens with markedly altered specificity for the hydrolysis of natural Kdn (3-deoxy-d-glycero-d-galacto-non-2-ulosonic acid) glycosidic linkages compared to those of N-acetylneuraminic acid. These variants catalyze the hydrolysis of Kdn-containing disaccharides with catalytic efficiencies (second-order rate constants: kcat/Km) of greater than 105 M−1 s−1; the best variant displayed an efficiency of >106 M−1 s−1 at its optimal pH.
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Affiliation(s)
- Saeideh Shamsi Kazem Abadi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Matthew C Deen
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jacqueline N Watson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Fahimeh S Shidmoossavee
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J Bennet
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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6
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Colombo C, Bennet AJ. The physical organic chemistry of glycopyranosyl transfer reactions in solution and enzyme-catalyzed. Curr Opin Chem Biol 2019; 53:145-157. [PMID: 31689605 DOI: 10.1016/j.cbpa.2019.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
Our understanding of the mechanisms of glycopyranosyl transfer that occur in solution, both for the chemical synthesis of complex structures and that for the cleavage of glycosidic bonds has allowed us to design biologically active molecules. Recent efforts on the reactivity of glycopyranosides, which are critical entities in all biological systems, coupled with the advent of modern spectroscopic instrumentation have allowed physical organic chemists to broaden our knowledge of glycosyl transfer reaction transition states, both in solution and for enzyme-catalyzed processes, and of critical high energy intermediates. This review details recent physical organic, kinetic and structural studies that have led to elucidation of several different mechanism for the transfer of glycopyranosyl moieties from various substrates to acceptors, such as water or a sugar hydroxyl group.
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7
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Colombo C, Podlipnik Č, Lo Presti L, Niikura M, Bennet AJ, Bernardi A. Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. PLoS One 2018; 13:e0193623. [PMID: 29489903 PMCID: PMC5831633 DOI: 10.1371/journal.pone.0193623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/14/2018] [Indexed: 11/19/2022] Open
Abstract
The rise of drug-resistant influenza A virus strains motivates the development of new antiviral drugs, with different structural motifs and substitution. Recently, we explored the use of a bicyclic (bicyclo[3.1.0]hexane) analogue of sialic acid that was designed to mimic the conformation adopted during enzymatic cleavage within the neuraminidase (NA; sialidase) active site. Given that our first series of compounds were at least four orders of magnitude less active than available drugs, we hypothesized that the new carbon skeleton did not elicit the same interactions as the cyclohexene frameworks used previously. Herein, we tried to address this critical point with the aid of molecular modeling and we proposed new structures with different functionalization, such as the introduction of free ammonium and guanidinium groups and ether side chains other than the 3-pentyl side chain, the characteristic side chain in Oseltamivir. A highly simplified synthetic route was developed, starting from the cyclopropanation of cyclopentenone and followed by an aziridination and further functionalization of the five-member ring. This allowed the efficient preparation of a small library of new bicyclic ligands that were characterized by enzyme inhibition assays against influenza A neuraminidases N1, its H274Y mutant, and N2. The results show that none of the new structural variants synthesized, including those containing guanidinium groups rather than free ammonium ions, displayed activity against influenza A neuraminidases at concentrations less than 2 mM. We conclude that the choice and positioning of functional groups on the bicyclo[3.1.0]hexyl system still need to be properly tuned for producing complementary interactions within the catalytic site.
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Affiliation(s)
- Cinzia Colombo
- Università degli Studi di Milano, Dipartimento di Chimica, Milano, Italy
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
| | - Črtomir Podlipnik
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia
| | - Leonardo Lo Presti
- Università degli Studi di Milano, Dipartimento di Chimica, Milano, Italy
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anna Bernardi
- Università degli Studi di Milano, Dipartimento di Chimica, Milano, Italy
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8
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Zhou X, Wang P, Zhang L, Chen P, Ma M, Song N, Ren S, Li M. Transition-Metal-Free Synthesis of C-Glycosylated Phenanthridines via K 2S 2O 8-Mediated Oxidative Radical Decarboxylation of Uronic Acids. J Org Chem 2018; 83:588-603. [PMID: 29261315 DOI: 10.1021/acs.joc.7b02346] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have developed an efficient protocol for the synthesis of C-glycosylated phenanthridines. Tetrafuranos-4-yl and pentapyranos-5-yl radicals, generated from K2S2O8-mediated oxidative decarboxylation of furan- and pyranuronic acids, undergo attack to 2-isocyanodiphenyls and ensuing homolytic aromatic substitution to provide diverse C-glycosylated phenanthridines in satisfactory yields without resort to transition metals. This reaction tolerates various functional groups, and enables ready synthesis of complex oligosaccharide-based phenanthridines. The C-glycosylated phenanthridine derived from β-cyclodextrin has been prepared, which might be potential in medicinal and biological chemistry due to its flexible conformation.
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Affiliation(s)
- Xin Zhou
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , 5 Yushan Road, Qingdao 266003, People's Republic of China
| | - Peng Wang
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , 5 Yushan Road, Qingdao 266003, People's Republic of China
| | - Li Zhang
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , 5 Yushan Road, Qingdao 266003, People's Republic of China
| | - Pengwei Chen
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , 5 Yushan Road, Qingdao 266003, People's Republic of China
| | - Mingxu Ma
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , 5 Yushan Road, Qingdao 266003, People's Republic of China
| | - Ni Song
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , 5 Yushan Road, Qingdao 266003, People's Republic of China
| | - Sumei Ren
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , 5 Yushan Road, Qingdao 266003, People's Republic of China
| | - Ming Li
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , 5 Yushan Road, Qingdao 266003, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237, People's Republic of China
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9
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Measurement of Kinetic Isotope Effects by Continuously Monitoring Isotopologue Ratios Using NMR Spectroscopy. Methods Enzymol 2017. [DOI: 10.1016/bs.mie.2017.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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10
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Colombo C, Pinto BM, Bernardi A, Bennet AJ. Synthesis and evaluation of influenza A viral neuraminidase candidate inhibitors based on a bicyclo[3.1.0]hexane scaffold. Org Biomol Chem 2016; 14:6539-53. [DOI: 10.1039/c6ob00999a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the synthesis of constrained oseltamivir analogues designed to mimic the proposed boat conformation of the enzymatic transition state.
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Affiliation(s)
- Cinzia Colombo
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
| | - B. Mario Pinto
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
| | - Anna Bernardi
- Università degli Studi di Milano
- Dipartimento di Chimica
- I-20133 Milano
- Italy
| | - Andrew J. Bennet
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
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11
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Zhu Y, Laval S, Tang Y, Lian G, Yu B. A Polystyrene-Bound Triphenylphosphine Gold(I) Catalyst for the Glycosylation of Glycosylortho-Hexynylbenzoates. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201500276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yugen Zhu
- State Key Laboratory of Bio-organic and Natural Products Chemistry; ?Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Stéphane Laval
- State Key Laboratory of Bio-organic and Natural Products Chemistry; ?Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Yu Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry; ?Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Gaoyan Lian
- State Key Laboratory of Bio-organic and Natural Products Chemistry; ?Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Biao Yu
- State Key Laboratory of Bio-organic and Natural Products Chemistry; ?Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
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12
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Thiery E, Reniers J, Wouters J, Vincent SP. Stereoselective Synthesis of Boat-Locked Glycosides Designed as Glycosyl Hydrolase Conformational Probes. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Speciale G, Thompson AJ, Davies GJ, Williams SJ. Dissecting conformational contributions to glycosidase catalysis and inhibition. Curr Opin Struct Biol 2014; 28:1-13. [PMID: 25016573 PMCID: PMC4220041 DOI: 10.1016/j.sbi.2014.06.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/02/2014] [Accepted: 06/10/2014] [Indexed: 01/15/2023]
Abstract
The conformational itinerary describes the changes in sugar shape during catalysis. Stereoelectronic requirements for glycoside hydrolysis are discussed. Major and emerging approaches to define conformational itineraries are reviewed. New assignments of glycosidase conformational itineraries are summarized.
Glycoside hydrolases (GHs) are classified into >100 sequence-based families. These enzymes process a wide variety of complex carbohydrates with varying stereochemistry at the anomeric and other ring positions. The shapes that these sugars adopt upon binding to their cognate GHs, and the conformational changes that occur along the catalysis reaction coordinate is termed the conformational itinerary. Efforts to define the conformational itineraries of GHs have focussed upon the critical points of the reaction: substrate-bound (Michaelis), transition state, intermediate (if relevant) and product-bound. Recent approaches to defining conformational itineraries that marry X-ray crystallography of enzymes bound to ligands that mimic the critical points, along with advanced computational methods and kinetic isotope effects are discussed.
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Affiliation(s)
- Gaetano Speciale
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew J Thompson
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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14
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Yeung JHF, Telford JC, Shidmoossavee FS, Bennet AJ, Taylor GL, Moore MM. Kinetic and Structural Evaluation of Selected Active Site Mutants of the Aspergillus fumigatus KDNase (Sialidase). Biochemistry 2013; 52:9177-86. [DOI: 10.1021/bi401166f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | | | | | | | - Garry L. Taylor
- BSRC, University of St Andrews, St Andrews, Fife KY16 9ST, U.K
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15
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Kinetic isotope effects for studying post-translational modifying enzymes. Curr Opin Chem Biol 2012; 16:472-8. [PMID: 23146439 DOI: 10.1016/j.cbpa.2012.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 11/20/2022]
Abstract
The ongoing development of new experimental approaches for the measurement of isotope effects is improving our understanding of the physical and chemical changes that occur during biological catalysis. Biological catalysis involves numerous steps that include binding, conformational changes, chemical catalysis and product release. The critical points on the free energy surface for biologically catalyzed reactions include all bound intermediates and the intervening transition states. Isotope effects can be used to investigate both intermediate (equilibrium isotope effects) and transition state (kinetic isotope effects) structures along the reaction coordinate. This review details new techniques for measuring isotope effects and provides several examples of their use in solving transition state structures for post-translational modifying enzymes.
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16
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Díaz A, Díaz-Lobo M, Grados E, Guinovart JJ, Fita I, Ferrer JC. Lyase activity of glycogen synthase: Is an elimination/addition mechanism a possible reaction pathway for retaining glycosyltransferases? IUBMB Life 2012; 64:649-58. [PMID: 22648728 DOI: 10.1002/iub.1048] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 04/05/2012] [Indexed: 11/10/2022]
Abstract
Despite the biological relevance of glycosyltrasferases (GTs) and the many efforts devoted to this subject, the catalytic mechanism through which a subclass of this large family of enzymes, namely those that operate with net retention of the anomeric configuration, has not been fully established. Here, we show that in the absence of an acceptor, an archetypal retaining GT such as Pyrococcus abyssi glycogen synthase (PaGS) reacts with its glucosyl donor substrate, uridine 5'-diphosphoglucose (UDP-Glc), to produce the scission of the covalent bond between the terminal phosphate oxygen of UDP and the sugar ring. X-ray diffraction analysis of the PaGS/UDP-Glc complex shows no electronic density attributable to the UDP moiety, but establishes the presence in the active site of the enzyme of a glucose-like derivative that lacks the exocyclic oxygen attached to the anomeric carbon. Chemical derivatization followed by gas chromatography/mass spectrometry of the isolated glucose-like species allowed us to identify the molecule found in the catalytic site of PaGS as 1,5-anhydro-D-arabino-hex-1-enitol (AA) or its tautomeric form, 1,5-anhydro-D-fructose. These findings are consistent with a stepwise S(N) i-like mechanism as the modus operandi of retaining GTs, a mechanism that involves the discrete existence of an oxocarbenium intermediate. Even in the absence of a glucosyl acceptor, glycogen synthase (GS) promotes the formation of the cationic intermediate, which, by eliminating the proton of the adjacent C2 carbon atom, yields AA. Alternatively, these observations could be interpreted assuming that AA is a true intermediate in the reaction pathway of GS and that this enzyme operates through an elimination/addition mechanism.
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Affiliation(s)
- Adelaida Díaz
- Institute for Research in Biomedicine, IRB Barcelona
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17
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Kanai M, Saito K. SYNTHESIS OF A NEW OSELTAMIVIR DERIVATIVE THROUGH LATE-STAGE CATALYTIC C–H FUNCTIONALIZATION. HETEROCYCLES 2012. [DOI: 10.3987/com-12-s(n)94] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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