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Akintola O, Farren-Dai M, Ren W, Bhosale S, Britton R, Świderek K, Moliner V, Bennet AJ. Glycoside Hydrolase Catalysis: Do Substrates and Mechanism-Based Covalent Inhibitors React via Matching Transition States? ACS Catal 2022. [DOI: 10.1021/acscatal.2c04027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Oluwafemi Akintola
- Department of Chemistry, Simon Fraser University, Burnaby, British ColumbiaV5A 1S6, Canada
| | - Marco Farren-Dai
- Department of Chemistry, Simon Fraser University, Burnaby, British ColumbiaV5A 1S6, Canada
| | - Weiwu Ren
- Department of Chemistry, Simon Fraser University, Burnaby, British ColumbiaV5A 1S6, Canada
| | - Sandeep Bhosale
- Department of Chemistry, Simon Fraser University, Burnaby, British ColumbiaV5A 1S6, Canada
| | - Robert Britton
- Department of Chemistry, Simon Fraser University, Burnaby, British ColumbiaV5A 1S6, Canada
| | - Katarzyna Świderek
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071Castellón, Spain
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British ColumbiaV5A 1S6, Canada
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2
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Truax NJ, Ayinde S, Liu JO, Romo D. Total Synthesis of Rameswaralide Utilizing a Pharmacophore-Directed Retrosynthetic Strategy. J Am Chem Soc 2022; 144:18575-18585. [PMID: 36166374 DOI: 10.1021/jacs.2c08245] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A pharmacophore-directed retrosynthetic strategy was applied to the first total synthesis of the cembranoid rameswaralide in order to simultaneously achieve a total synthesis while also developing a structure-activity relationship profile throughout the synthetic effort. The synthesis utilized a Diels-Alder lactonization process, including a rare kinetic resolution to demonstrate the potential of this strategy for an enantioselective synthesis providing both the 5,5,6- and, through a ring expansion, 5,5,7-tricyclic ring systems present in several Sinularia soft coral cembranoids. A pivotal synthetic intermediate, a tricyclic epoxy α-bromo cycloheptenone, displayed high cytotoxicity with interesting selectivity toward the HCT-116 colon cancer cell line. This intermediate enabled the pursuit of three unique D-ring annulation strategies including a photocatalyzed intramolecular Giese-type radical cyclization and a diastereoselective, intramolecular enamine-mediated Michael addition, with the latter annulation constructing the final D-ring to deliver rameswaralide. The serendipitous discovery of an oxidation state transposition of the tricyclic epoxy cycloheptenone proceeding through a presumed doubly vinylogous, E1-type elimination enabled the facile introduction of the required α-methylene butyrolactone. Preliminary biological tests of rameswaralide and precursors demonstrated weak cytotoxicity; however, the comparable cytotoxicity of a simple 6,7-bicyclic β-keto ester, corresponding to the CD-ring system of rameswaralide, to that of the natural product itself suggests that such bicyclic β-ketoesters may constitute an interesting pharmacophore that warrants further exploration.
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Affiliation(s)
- Nathanyal J Truax
- Department of Chemistry & Biochemistry, Baylor University, 101 Bagby Avenue, Waco, Texas 76710, United States
| | - Safiat Ayinde
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Daniel Romo
- Department of Chemistry & Biochemistry, Baylor University, 101 Bagby Avenue, Waco, Texas 76710, United States
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3
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Jain N, Tamura K, Déjean G, Van Petegem F, Brumer H. Orthogonal Active-Site Labels for Mixed-Linkage endo-β-Glucanases. ACS Chem Biol 2021; 16:1968-1984. [PMID: 33988963 DOI: 10.1021/acschembio.1c00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecule irreversible inhibitors are valuable tools for determining catalytically important active-site residues and revealing key details of the specificity, structure, and function of glycoside hydrolases (GHs). β-glucans that contain backbone β(1,3) linkages are widespread in nature, e.g., mixed-linkage β(1,3)/β(1,4)-glucans in the cell walls of higher plants and β(1,3)glucans in yeasts and algae. Commensurate with this ubiquity, a large diversity of mixed-linkage endoglucanases (MLGases, EC 3.2.1.73) and endo-β(1,3)-glucanases (laminarinases, EC 3.2.1.39 and EC 3.2.1.6) have evolved to specifically hydrolyze these polysaccharides, respectively, in environmental niches including the human gut. To facilitate biochemical and structural analysis of these GHs, with a focus on MLGases, we present here the facile chemo-enzymatic synthesis of a library of active-site-directed enzyme inhibitors based on mixed-linkage oligosaccharide scaffolds and N-bromoacetylglycosylamine or 2-fluoro-2-deoxyglycoside warheads. The effectiveness and irreversibility of these inhibitors were tested with exemplar MLGases and an endo-β(1,3)-glucanase. Notably, determination of inhibitor-bound crystal structures of a human-gut microbial MLGase from Glycoside Hydrolase Family 16 revealed the orthogonal labeling of the nucleophile and catalytic acid/base residues with homologous 2-fluoro-2-deoxyglycoside and N-bromoacetylglycosylamine inhibitors, respectively. We anticipate that the selectivity of these inhibitors will continue to enable the structural and mechanistic analyses of β-glucanases from diverse sources and protein families.
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Affiliation(s)
- Namrata Jain
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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4
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Abstract
Glycomimetics are structural mimics of naturally occurring carbohydrates and represent important therapeutic leads in several disease treatments. However, the structural and stereochemical complexity inherent to glycomimetics often challenges medicinal chemistry efforts and is incompatible with diversity-oriented synthesis approaches. Here, we describe a one-pot proline-catalyzed aldehyde α-functionalization/aldol reaction that produces an array of stereochemically well-defined glycomimetic building blocks containing fluoro, chloro, bromo, trifluoromethylthio and azodicarboxylate functional groups. Using density functional theory calculations, we demonstrate both steric and electrostatic interactions play key diastereodiscriminating roles in the dynamic kinetic resolution. The utility of this simple process for generating large and diverse libraries of glycomimetics is demonstrated in the rapid production of iminosugars, nucleoside analogues, carbasugars and carbohydrates from common intermediates.
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5
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Fischer O, Heinrich MR. 2-Fluoro-5-nitrophenyldiazonium: A Novel Sanger-Type Reagent for the Versatile Functionalization of Alcohols. Chemistry 2021; 27:5417-5421. [PMID: 33481282 PMCID: PMC8048593 DOI: 10.1002/chem.202100187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Indexed: 12/15/2022]
Abstract
As a novel Sanger-type reagent, 2-fluoro-5-nitrophenyldiazonium tetrafluoroborate enabled the versatile functionalization of primary and secondary aliphatic alcohols. Based on a mild nucleophilic aromatic substitution of the fluorine atom under unprecedented, base-free conditions, the diazonium unit on the aromatic core of the resulting aryl-alkyl ether could be employed for such diverse transformations as radical C-H activation and cyclization, as well as palladium catalyzed cross-coupling reactions.
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Affiliation(s)
- Oliver Fischer
- Department of Chemistry and Pharmacy, Pharmaceutical ChemistryFriedrich-Alexander-Universität Erlangen-NürnbergNikolaus-Fiebiger-Str. 1091058ErlangenGermany
| | - Markus R. Heinrich
- Department of Chemistry and Pharmacy, Pharmaceutical ChemistryFriedrich-Alexander-Universität Erlangen-NürnbergNikolaus-Fiebiger-Str. 1091058ErlangenGermany
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6
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Lafond M, Tauzin AS, Bruel L, Laville E, Lombard V, Esque J, André I, Vidal N, Pompeo F, Quinson N, Perrier J, Fons M, Potocki-Veronese G, Giardina T. α-Galactosidase and Sucrose-Kinase Relationships in a Bi-functional AgaSK Enzyme Produced by the Human Gut Symbiont Ruminococcus gnavus E1. Front Microbiol 2020; 11:579521. [PMID: 33281771 PMCID: PMC7688924 DOI: 10.3389/fmicb.2020.579521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Plant α-galactosides belonging to the raffinose family oligosaccharides (RFOs) and considered as prebiotics, are commonly degraded by α-galactosidases produced by the human gut microbiome. In this environment, the Ruminococcus gnavus E1 symbiont-well-known for various benefit-is able to produce an original RgAgaSK bifunctional enzyme. This enzyme contains an hydrolytic α-galactosidase domain linked to an ATP dependent extra-domain, specifically involved in the α-galactoside hydrolysis and the phosphorylation of the glucose, respectively. However, the multi-modular relationships between both catalytic domains remained hitherto unexplored and has been, consequently, herein investigated. Biochemical characterization of heterologously expressed enzymes either in full-form or in separated domains revealed similar kinetic parameters. These results were supported by molecular modeling studies performed on the whole enzyme in complex with different RFOs. Further enzymatic analysis associated with kinetic degradation of various substrates followed by high pressure anionic exchange chromatography revealed that catalytic efficiency decreased as the number of D-galactosyl moieties branched onto the oligosaccharide increased, suggesting a preference of RgAgaSK for RFO's short chains. A wide prevalence and abundance study on a human metagenomic library showed a high prevalence of the RgAgaSK encoding gene whatever the health status of the individuals. Finally, phylogeny and synteny studies suggested a limited spread by horizontal transfer of the clusters' containing RgAgaSK to only few species of Firmicutes, highlighting the importance of these undispersed tandem activities in the human gut microbiome.
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Affiliation(s)
- Mickael Lafond
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Laetitia Bruel
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | | | - Jérémy Esque
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Isabelle André
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nicolas Vidal
- Yelen Analytics, Aix-Marseille Université, ICR, Marseille, France
| | | | - Nathalie Quinson
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Josette Perrier
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Michel Fons
- Aix-Marseille Université, CNRS, IMM, BIP, Marseille, France
| | | | - Thierry Giardina
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
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7
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Quirke JCK, Crich D. Glycoside Hydrolases Restrict the Side Chain Conformation of Their Substrates To Gain Additional Transition State Stabilization. J Am Chem Soc 2020; 142:16965-16973. [PMID: 32877175 PMCID: PMC7544649 DOI: 10.1021/jacs.0c05592] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carbohydrate side chain conformation confers a significant influence on reactivity during glycosylation and anomeric bond hydrolysis due to stabilization of the oxocarbenium-like transition state. By analysis of 513 pyranoside-bound glycoside hydrolase (GH) crystal structures, we determine that most glucosidases and β-mannosidases preferentially bind their substrates in the most reactive gauche,gauche (gg) conformation, thereby maximizing stabilization of the corresponding oxocarbenium ion-like transition state during hydrolysis. α-Galactoside hydrolases mostly show a preference for the second most activating gauche,trans (gt) conformation to avoid the energy penalty that would arise from imposing the gg conformation on galacto-configured ligands. These preferences stand in stark contrast to the side chain populations observed for these sugars both in free solution and bound to nonhydrolytic proteins, where for the most part a much greater diversity of side chain conformations is observed. Analysis of sequences of GH-ligand complexes reveals that side chain restriction begins with the enzyme-substrate complex and persists through the transition state until release of the hydrolysis product, despite changes in ring conformation along the reaction coordinate. This work will inform the design of new generations of glycosidase inhibitors with restricted side chains that confer higher selectivity and/or affinity.
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Affiliation(s)
- Jonathan C K Quirke
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, 140 Cedar 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
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
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8
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Ren W, Farren-Dai M, Sannikova N, Świderek K, Wang Y, Akintola O, Britton R, Moliner V, Bennet AJ. Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design. Chem Sci 2020; 11:10488-10495. [PMID: 34094307 PMCID: PMC8162432 DOI: 10.1039/d0sc04401f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Carbasugars are structural mimics of naturally occurring carbohydrates that can interact with and inhibit enzymes involved in carbohydrate processing. In particular, carbasugars have attracted attention as inhibitors of glycoside hydrolases (GHs) and as therapeutic leads in several disease areas. However, it is unclear how the carbasugars are recognized and processed by GHs. Here, we report the synthesis of three carbasugar isotopologues and provide a detailed transition state (TS) analysis for the formation of the initial GH-carbasugar covalent intermediate, as well as for hydrolysis of this intermediate, using a combination of experimentally measured kinetic isotope effects and hybrid QM/MM calculations. We find that the α-galactosidase from Thermotoga maritima effectively stabilizes TS charge development on a remote C5-allylic center acting in concert with the reacting carbasugar, and catalysis proceeds via an exploded, or loose, SN2 transition state with no discrete enzyme-bound cationic intermediate. We conclude that, in complement to what we know about the TS structures of enzyme-natural substrate complexes, knowledge of the TS structures of enzymes reacting with non-natural carbasugar substrates shows that GHs can stabilize a wider range of positively charged TS structures than previously thought. Furthermore, this enhanced understanding will enable the design of new carbasugar GH transition state analogues to be used as, for example, chemical biology tools and pharmaceutical lead compounds. Positive charge stabilized on remote C5-allylic center with catalysis occurring via a loose SN2 transition state.![]()
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Affiliation(s)
- Weiwu Ren
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Marco Farren-Dai
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Natalia Sannikova
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I 12560 Castellón Spain
| | - Yang Wang
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Oluwafemi Akintola
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Robert Britton
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I 12560 Castellón Spain
| | - Andrew J Bennet
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
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9
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Affiliation(s)
- Renat Kadyrov
- Institute of Inorganic ChemistryAcademy of Sciences of the Czech Republic 25068 Řež Czech Republic
- Evonik Resource Efficiency GmbH Rodenbacher Chaussee 4 63457 Hanau Germany
| | - Konrad Moebus
- Evonik Resource Efficiency GmbH Rodenbacher Chaussee 4 63457 Hanau Germany
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10
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Khademi Z, Nikoofar K. Applications of alkyl orthoesters as valuable substrates in organic transformations, focusing on reaction media. RSC Adv 2020; 10:30314-30397. [PMID: 35559005 PMCID: PMC9092620 DOI: 10.1039/d0ra05276k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/27/2020] [Indexed: 02/01/2023] Open
Abstract
In this review we focus on applications of alkyl orthoesters as valuable and efficient substrates to perform various classes of two-component and multi-component organic reactions. The article has classified them according to two aspects, which are: (i) a focus on the reaction medium (solvent-free conditions, aqueous media, and organic solvents); and (ii) an examination of product structures. Reaction accomplishment under solvent-free conditions is an eco-friendly process with the absence of volatile toxic solvents, which puts it in line with green chemistry goals. Water is an interesting choice in organic transformations due to its inexpensiveness and safety. The authors hope their assessment will help chemists to attain new approaches for utilizing alkyl orthoesters in various organic synthetic methods. The review covers the corresponding literature up to the beginning of 2020. In this review we focus on applications of alkyl orthoesters as valuable and efficient substrates to perform various classes of two-component and multi-component organic reactions.![]()
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Affiliation(s)
- Zahra Khademi
- Department of Chemistry, Faculty of Physics & Chemistry, Alzahra University P.O. Box 1993891176 Tehran Iran +982188041344 +982188041344
| | - Kobra Nikoofar
- Department of Chemistry, Faculty of Physics & Chemistry, Alzahra University P.O. Box 1993891176 Tehran Iran +982188041344 +982188041344
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11
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Chen SC, Wu SP, Chang YY, Hwang TS, Lee TH, Hsu CH. Crystal Structure of α-Galactosidase from Thermus thermophilus: Insight into Hexamer Assembly and Substrate Specificity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6161-6169. [PMID: 32390413 DOI: 10.1021/acs.jafc.0c00871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
α-Galactosidase catalyzes the hydrolysis of a terminal α-galactose residue in galacto-oligosaccharides and has potential in various industrial applications and food processing. We determined the crystal structures of α-galactosidase from the thermophilic microorganism Thermus thermophilus (TtGalA) and its complexes with pNPGal and stachyose. The monomer folds into an N-terminal domain, a catalytic (β/α)8 barrel domain, and a C-terminal domain. The domain organization is similar to that of the other family of 36 α-galactosidases, but TtGalA presents a cagelike hexamer. Structural analysis shows that oligomerization may be a key factor for the thermal adaption of TtGalA. The structure of TtGalA complexed with stachyose reveals only the existence of one -1 subsite and one +1 subsite in the active site. Structural comparison of the stachyose-bound complexes of TtGalA and GsAgaA, a tetrameric enzyme with four subsites, suggests evolutionary divergence of substrate specificity within the GH36 family of α-galactosidases. To the best of our knowledge, the crystal structure of TtGalA is the first report of a quaternary structure as a hexameric assembly in the α-galactosidase family.
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Affiliation(s)
- Sheng-Chia Chen
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Szu-Pei Wu
- Department of Biotechnology and Pharmaceutical Technology, Yuanpei University of Medical Technology, Hsinchu 30015, Taiwan
| | - Yu-Yung Chang
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Tzann-Shun Hwang
- Institute of Biotechnology, Chinese Culture University, Taipei 11114, Taiwan
| | - Tzong-Huei Lee
- Institute of Fisheries Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
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12
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Galenko EE, Shakirova FM, Bodunov VA, Novikov MS, Khlebnikov AF. 1-(2H-Azirine-2-carbonyl)benzotriazoles: building blocks for the synthesis of pyrrole-containing heterocycles. Org Biomol Chem 2020; 18:2283-2296. [PMID: 32154550 DOI: 10.1039/d0ob00206b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A one-pot method was developed for the preparation of 2H-azirine-2-carbonylbenzotriazoles, formed by the reaction of benzotriazole with 2H-azirine-2-carbonyl chlorides, which were generated by the Fe(ii)-catalyzed isomerization of 5-chloroisoxazoles. The Co(ii)-catalyzed reaction of 2H-azirine-2-carbonylbenzotriazoles with 1,3-diketones provides 2-((benzotriazol-1-yl)carbonyl)pyrroles in moderate to good yields. Base-promoted annulations of 2-((benzotriazol-1-yl)carbonyl)pyrroles with aldehydes, ketones, isocyanates and isothiocyanates afford various substituted pyrrolo[1,2-c]oxazole and 1H-pyrrolo[1,2-c]imidazole derivatives in moderate to high yields. The 6-acyl group of these adducts can be removed by triflic acid, giving further new pyrrolo-fused O- and N-heterocycles, such as 6-unsubstituted pyrrolo[1,2-c]oxazol-1(3H)-one and 1H-pyrrolo[1,2-c]imidazole-1,3(2H)-dione, while the 6-acetyl substituent of 1H-pyrrolo[1,2-c]imidazole-1,3(2H)-dione, when treated with POCl3/pyridine, is transformed into the 6-ethynyl substituent.
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Affiliation(s)
- Ekaterina E Galenko
- St Petersburg State University, Institute of Chemistry, 7/9 Universitetskaya nab., St Petersburg, 199034, Russia.
| | - Firuza M Shakirova
- St Petersburg State University, Institute of Chemistry, 7/9 Universitetskaya nab., St Petersburg, 199034, Russia.
| | - Vladimir A Bodunov
- St Petersburg State University, Institute of Chemistry, 7/9 Universitetskaya nab., St Petersburg, 199034, Russia.
| | - Mikhail S Novikov
- St Petersburg State University, Institute of Chemistry, 7/9 Universitetskaya nab., St Petersburg, 199034, Russia.
| | - Alexander F Khlebnikov
- St Petersburg State University, Institute of Chemistry, 7/9 Universitetskaya nab., St Petersburg, 199034, Russia.
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13
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An overview of activity-based probes for glycosidases. Curr Opin Chem Biol 2019; 53:25-36. [DOI: 10.1016/j.cbpa.2019.05.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 11/22/2022]
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14
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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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15
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Osorio MI, Cabrera MA, González-Nilo F, Pérez-Donoso JM. Odd Loop Regions of XenA and XenB Enzymes Modulate Their Interaction with Nitro-explosives Compounds and Provide Structural Support for Their Regioselectivity. J Chem Inf Model 2019; 59:3860-3870. [PMID: 31454238 DOI: 10.1021/acs.jcim.9b00357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nitro-explosive compounds 2,4,6-trinitrotoluene, 2,4,6-trinitrophenol, and 1,2,3-trinitroglycerol are persistent environmental contaminants. The presence of different functional groups in these molecules represents a great challenge to enzymatic catalysis. The chemical variety of these three substrates is such that they do not bind and interact with catalytic residues within an enzyme with the same affinity. In this context, two Xenobiotic Reductase enzymes produced by the bacteria Pseudomonas putida can catalyze the reduction of these compounds with different affinities and regioselectivity. The structural bases that support this substrate promiscuity and catalytic preferences are unknown. Therefore, through molecular dynamics simulations and free energy calculations, we explored the structural properties driving the specific interactions of these enzymes with their substrates and cofactor. Models of Xenobiotic Reductase A and B enzymes in complex with 2,4,6-trinitrotoluene, 2,4,6-trinitrophenol, or 1,2,3-trinitroglycerol were built, and the ligand enzyme interaction was simulated by molecular dynamics. The structural analysis of the molecular dynamics simulations shows that loops 3, 5, 7, 9, 11, and 13 of Xenobiotic Reductase B, and loops 4, 5, 7, 11, 13, and 15 Xenobiotic Reductase A, are in contact with the ligands during the first stages of the molecular recognition. These loops are the most flexible regions for both enzymes; however, Xenobiotic Reductase B presents a greater range of movement and a higher number of residues interacting with the ligands. Finally, the distance between the cofactor and the different reactive groups in the substrate reflects the regioselectivity of the enzymes, and the free energy calculations are consistent with the substrate specificity of both enzymes studied. The simulation shows a stable interaction between the aromatic ring of the substrates and Xenobiotic Reductase B. In contrast, a less stable interaction with the different nitro groups of the aromatic ligands was observed. In the case of 1,2,3-trinitroglycerol, Xenobiotic Reductase B interacts more closely with the nitro groups of carbon 1 or 3, while Xenobiotic Reductase A is more selective by nitro groups of carbon 2. The obtained results suggest that the flexibility of the loops in Xenobiotic Reductase B and the presence of polar and aromatic residues present in loops 5 and 7 are fundamental to determine the affinity of the enzyme with the different substrates, and they also contribute to the proper orientation of the ligands that directs the catalytic reaction.
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Affiliation(s)
- Manuel I Osorio
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andres Bello , Av. República 330 , Santiago 8370146 , Chile
| | - Ma Angeles Cabrera
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andres Bello , Av. República 330 , Santiago 8370146 , Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andres Bello , Av. República 330 , Santiago 8370146 , Chile
| | - José M Pérez-Donoso
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida , Universidad Andres Bello , Av. República 330 , Santiago 8370146 , Chile
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16
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Ray S, Murkin AS. New Electrophiles and Strategies for Mechanism-Based and Targeted Covalent Inhibitor Design. Biochemistry 2019; 58:5234-5244. [PMID: 30990686 DOI: 10.1021/acs.biochem.9b00293] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Covalent inhibitors are experiencing a growing resurgence in drug design and are an increasingly useful tool in molecular biology. The ability to attach inhibitors to their targets by a covalent linkage offers pharmacodynamic and pharmacokinetic advantages, but this can also be a liability if undesired off-target reactions are not mitigated. The discovery of new electrophilic groups that react selectively with specific amino acid residues is therefore highly desirable in the design of targeted covalent inhibitors (TCIs). Additionally, the ability to control the reactivity through exploitation of the target enzyme's machinery, as in mechanism-based inhibitors (MBIs), greatly benefits from the discovery of new strategies. This Perspective showcases recent advances in electrophile development and their application in TCIs and MBIs, exhibiting high selectivity for their targets.
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Affiliation(s)
- Sneha Ray
- Department of Chemistry , University at Buffalo, The State University of New York , Buffalo , New York 14260-3000 , United States
| | - Andrew S Murkin
- Department of Chemistry , University at Buffalo, The State University of New York , Buffalo , New York 14260-3000 , United States
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17
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Evans GB, Schramm VL, Tyler PC. The transition to magic bullets - transition state analogue drug design. MEDCHEMCOMM 2018; 9:1983-1993. [PMID: 30627387 PMCID: PMC6295874 DOI: 10.1039/c8md00372f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/24/2018] [Indexed: 12/17/2022]
Abstract
In the absence of industry partnerships, most academic groups lack the infrastructure to rationally design and build drugs via methods used in industry. Instead, academia needs to work smarter using mechanism-based design. Working smarter can mean the development of new drug discovery paradigms and then demonstrating their utility and reproducibility to industry. The collaboration between Vern Schramm's group at the Albert Einstein College of Medicine, USA and Peter Tyler at the Ferrier Research Institute at The Victoria University of Wellington, NZ has refined a drug discovery process called transition state analogue design. This process has been applied to several biomedically relevant nucleoside processing enzymes. In 2017, Mundesine®, conceived using transition state analogue design, received market approval for the treatment of peripheral T-cell lymphoma in Japan. This short review looks at a brief history of transition state analogue design, the fundamentals behind the development of this process, and the success of enzyme inhibitors produced using this drug design methodology.
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Affiliation(s)
- Gary B Evans
- The Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Rd , Lower Hutt , 5010 , New Zealand . ; Tel: +64 4 463 0048
- The Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Auckland , New Zealand
| | - Vern L Schramm
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , NY 10461 , USA
| | - Peter C Tyler
- The Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Rd , Lower Hutt , 5010 , New Zealand . ; Tel: +64 4 463 0048
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18
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Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level. Nat Commun 2018; 9:3243. [PMID: 30104598 PMCID: PMC6089974 DOI: 10.1038/s41467-018-05702-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/17/2018] [Indexed: 01/14/2023] Open
Abstract
Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate’s structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based α-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an α-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair (2H3) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (2H3) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties. Mechanism-based inhibitors of glycoside hydrolases are useful probes for basic research and represent potential drug candidates. Here, the authors present a series of mechanism-based covalent α-galactosidase inhibitors and elucidate the kinetic and structural basis of their inhibitory activity.
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19
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Sakharov PA, Novikov MS, Khlebnikov AF. 2-Diazoacetyl-2 H-azirines: Source of a Variety of 2 H-Azirine Building Blocks with Orthogonal and Domino Reactivity. J Org Chem 2018; 83:8304-8314. [PMID: 29963871 DOI: 10.1021/acs.joc.8b01004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A synthesis of 2-diazoacetyl-2 H-azirines was developed starting from 2 H-azirine-2-carbonyl chlorides, generated by Fe(II)-catalyzed isomerization of 5-chloroisoxazoles. 2-Diazoacetyl-2 H-azirines easily undergo reactions characteristic of α-diazo ketones with preservation of the azirine ring. Reactions with hydrohalogenic, carboxylic, and p-toluenesulfonic acids provide novel 1-(3-aryl-2 H-azirin-2-yl)-2-halo- and 2-(R-oxy)ethan-1-ones in good yields. The synthesized 2 H-azirines can offer many possibilities for chemical manipulation in heterocyclic synthesis, due to the presence of highly reactive azirine and the exocyclic C(O)-CHN2 or C(O)-CH2X functionalities, which can show orthogonal or domino reactivity. The synthetic usefulness of the developed building blocks was demonstrated by the preparation of new types of heterocyclic dyads (azirine-oxazole, azirine-pyrazoline, azirine-thiazole, azirine-oxirane, pyrrole-oxazole) as well as an azirine chalcone analogue, 2-azidoacetyl-2 H-azirine, and 2-diazoacetylaziridine derivatives.
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Affiliation(s)
- Pavel A Sakharov
- Institute of Chemistry , Saint Petersburg State University , 7/9 Universitetskaya nab. , St. Petersburg 199034 , Russia
| | - Mikhail S Novikov
- Institute of Chemistry , Saint Petersburg State University , 7/9 Universitetskaya nab. , St. Petersburg 199034 , Russia
| | - Alexander F Khlebnikov
- Institute of Chemistry , Saint Petersburg State University , 7/9 Universitetskaya nab. , St. Petersburg 199034 , Russia
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20
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Saunders J, Adamson C, Ganga-Sah Y, Lewis AR, Bennet AJ. Rearrangement and nucleophilic trapping of bicyclo[4.1.0]hept-2-yl derived nonclassical bicyclobutenium ions. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Here we describe the synthesis of two specifically labelled 13C isotopologues of cis-2-(4-nitrophenoxy)bicyclo[4.1.0]heptane and their solvolysis reactions in trifluoroethanol. By using one- and two-dimensional 1H- and 13C-NMR spectroscopy, we characterized the pathways for the rearrangement of these isotopologues to give 13C-labelled 4-(2,2,2-trifluoroethoxy)cycloheptene. We show that the initially formed cationic intermediate undergoes a degenerate rearrangement, which does not reach equilibrium before nucleophilic capture of the cation. Moreover, we show that the nonclassical carbocation, cyclohept-3-ene(3,1,4-deloc)ylium, gives an approximate 6:1 ratio of the cis- to trans-diastereomeric 2-(2,2,2-trifluoroethoxy)bicyclo[4.1.0]heptane as reaction intermediates that subsequently solvolyze to the 4-(2,2,2-trifluoroethoxy)cycloheptene product.
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Affiliation(s)
- James Saunders
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Chris Adamson
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Yumeela Ganga-Sah
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Andrew R. Lewis
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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21
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Jain N, Attia MA, Offen WA, Davies GJ, Brumer H. Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor of endo-xyloglucanases. Org Biomol Chem 2018; 16:8732-8741. [DOI: 10.1039/c8ob02250j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Xyloglucan (XyG) is a complex polysaccharide that is ubiquitous and often abundant in the cell walls of terrestrial plants.
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Affiliation(s)
- Namrata Jain
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | - Mohamed A. Attia
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | | | | | - Harry Brumer
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
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22
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Shamsi Kazem Abadi S, Tran M, Yadav AK, Adabala PJP, Chakladar S, Bennet AJ. New Class of Glycoside Hydrolase Mechanism-Based Covalent Inhibitors: Glycosylation Transition State Conformations. J Am Chem Soc 2017; 139:10625-10628. [PMID: 28723089 DOI: 10.1021/jacs.7b05065] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The design of covalent inhibitors in glycoscience research is important for the development of chemical biology probes. Here we report the synthesis of a new carbocyclic mechanism-based covalent inhibitor of an α-glucosidase. The enzyme efficiently catalyzes its alkylation via either an allylic cation or a cationic transition state. We show this allylic covalent inhibitor has different catalytic proficiencies for pseudoglycosylation and deglycosylation. Such inhibitors have the potential to be useful chemical biology tools.
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Affiliation(s)
- Saeideh Shamsi Kazem Abadi
- Departments of Biochemistry and Molecular Biology, and ‡Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Michael Tran
- Departments of Biochemistry and Molecular Biology, and ‡Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Anuj K Yadav
- Departments of Biochemistry and Molecular Biology, and ‡Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Pal John Pal Adabala
- Departments of Biochemistry and Molecular Biology, and ‡Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Saswati Chakladar
- Departments of Biochemistry and Molecular Biology, and ‡Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J Bennet
- Departments of Biochemistry and Molecular Biology, and ‡Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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23
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Sato M, Liebschner D, Yamada Y, Matsugaki N, Arakawa T, Wills SS, Hattie M, Stubbs KA, Ito T, Senda T, Ashida H, Fushinobu S. The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors. J Biol Chem 2017; 292:12126-12138. [PMID: 28546425 DOI: 10.1074/jbc.m117.777391] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/22/2017] [Indexed: 11/06/2022] Open
Abstract
The α-N-acetylgalactosaminidase from the probiotic bacterium Bifidobacterium bifidum (NagBb) belongs to the glycoside hydrolase family 129 and hydrolyzes the glycosidic bond of Tn-antigen (GalNAcα1-Ser/Thr). NagBb is involved in assimilation of O-glycans on mucin glycoproteins by B. bifidum in the human gastrointestinal tract, but its catalytic mechanism has remained elusive because of a lack of sequence homology around putative catalytic residues and of other structural information. Here we report the X-ray crystal structure of NagBb, representing the first GH129 family structure, solved by the single-wavelength anomalous dispersion method based on sulfur atoms of the native protein. We determined ligand-free, GalNAc, and inhibitor complex forms of NagBb and found that Asp-435 and Glu-478 are located in the catalytic domain at appropriate positions for direct nucleophilic attack at the anomeric carbon and proton donation for the glycosidic bond oxygen, respectively. A highly conserved Asp-330 forms a hydrogen bond with the O4 hydroxyl of GalNAc in the -1 subsite, and Trp-398 provides a stacking platform for the GalNAc pyranose ring. Interestingly, a metal ion, presumably Ca2+, is involved in the recognition of the GalNAc N-acetyl group. Mutations at Asp-435, Glu-478, Asp-330, and Trp-398 and residues involved in metal coordination (including an all-Ala quadruple mutant) significantly reduced the activity, indicating that these residues and the metal ion play important roles in substrate recognition and catalysis. Interestingly, NagBb exhibited some structural similarities to the GH101 endo-α-N-acetylgalactosaminidases, but several critical differences in substrate recognition and reaction mechanism account for the different activities of these two enzymes.
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Affiliation(s)
- Mayo Sato
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Dorothee Liebschner
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Yusuke Yamada
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Siobhán S Wills
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Mitchell Hattie
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Tasuku Ito
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Hisashi Ashida
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa-shi, Wakayama 649-6493, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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24
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Guo J, Li W, Xue W, Ye XS. Transition State-Based Sialyltransferase Inhibitors: Mimicking Oxocarbenium Ion by Simple Amide. J Med Chem 2017; 60:2135-2141. [PMID: 28165727 DOI: 10.1021/acs.jmedchem.6b01644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the new transition-state based sialyltransferase inhibitors, an amide group was placed at the corresponding C-2 position of CMP-sialic acid to mimic the geometry and charge distribution in the transition state, and simple aromatic or aliphatic rings were used instead of the sialic acid moiety. All synthetic compounds exhibited excellent α(2-6)-sialyltransferase inhibition, resulting in up to a 2600-fold higher affinity for the enzyme than CMP-Neu5Ac, suggesting that amide is a key element for simulating transition-state features.
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Affiliation(s)
- Jian Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Xue Yuan Road no. 38, Beijing 100191, China
| | - Wenming Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Xue Yuan Road no. 38, Beijing 100191, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University , Daxuecheng South Road no. 55, Chongqing 401331, China
| | - Xin-Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Xue Yuan Road no. 38, Beijing 100191, China
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25
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Colombo C, Bennet AJ. Probing Transition State Analogy in Glycoside Hydrolase Catalysis. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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