1
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Chepeleva LV, Demidov OO, Snizhko AD, Tarasenko DO, Chumak AY, Kolomoitsev OO, Kotliar VM, Gladkov ES, Kyrychenko A, Roshal AD. Binding interactions of hydrophobically-modified flavonols with β-glucosidase: fluorescence spectroscopy and molecular modelling study. RSC Adv 2023; 13:34107-34121. [PMID: 38020002 PMCID: PMC10661682 DOI: 10.1039/d3ra06276g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
Natural flavonoids are capable of inhibiting glucosidase activity, so they can be used for treating diabetes mellitus and hypertension. However, molecular-level details of their interactions with glucosidase enzymes remain poorly understood. This paper describes the synthesis and spectral characterization of a series of fluorescent flavonols and their interaction with the β-glucosidase enzyme. To tune flavonol-enzyme interaction modes and affinity, we introduced different polar halogen-containing groups or bulky aromatic/alkyl substituents in the peripheral 2-aryl ring of a flavonol moiety. Using fluorescence spectroscopy methods in combination with molecular docking and molecular dynamics simulations, we examined the binding affinity and identified probe binding patterns, which are critical for steric blockage of the key catalytic residues of the enzyme. Using a fluorescent assay, we demonstrated that the binding of flavonol 2e to β-glucosidase decreased its enzymatic activity up to 3.5 times. In addition, our molecular docking and all-atom molecular dynamics simulations suggest that the probe binding is driven by hydrophobic interactions with aromatic Trp and Tyr residues within the catalytic glycone binding pockets of β-glucosidase. Our study provides a new insight into structure-property relations for flavonol-protein interactions, which govern their enzyme binding, and outlines a framework for a rational design of new flavonol-based potent inhibitors for β-glucosidases.
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Affiliation(s)
- Liudmyla V Chepeleva
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Oleksii O Demidov
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Arsenii D Snizhko
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Dmytro O Tarasenko
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Andrii Y Chumak
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Oleksii O Kolomoitsev
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Volodymyr M Kotliar
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Eugene S Gladkov
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
- State Scientific Institution "Institute for Single Crystals", National Academy of Sciences of Ukraine 60 Nauky Ave. Kharkiv 61072 Ukraine
| | - Alexander Kyrychenko
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
- State Scientific Institution "Institute for Single Crystals", National Academy of Sciences of Ukraine 60 Nauky Ave. Kharkiv 61072 Ukraine
| | - Alexander D Roshal
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
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2
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Pengthaisong S, Piniello B, Davies GJ, Rovira C, Ketudat Cairns JR. Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation. ACS Catal 2023; 13:5850-5863. [PMID: 37180965 PMCID: PMC10167657 DOI: 10.1021/acscatal.3c00620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5-6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme-substrate complex is available for this GH family. Here, we report the structures of Thermoanaerobacterium xylanolyticum β-glucosidase (TxGH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type TxGH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed 4C1 chair at the -1 subsite. Nevertheless, the reaction can still proceed through a 4H3 half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a gauche, trans orientation with respect to the C5-O5 and C4-C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2.
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Affiliation(s)
- Salila Pengthaisong
- School
of Chemistry, Institute of Science, Suranaree
University of Technology, Nakhon
Ratchasima 30000, Thailand
- Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Beatriz Piniello
- Departament
de Quımica Inorgánica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Gideon J. Davies
- Department
of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Carme Rovira
- Departament
de Quımica Inorgánica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
| | - James R. Ketudat Cairns
- School
of Chemistry, Institute of Science, Suranaree
University of Technology, Nakhon
Ratchasima 30000, Thailand
- Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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3
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Tseng PS, Ande C, Moremen KW, Crich D. Influence of Side Chain Conformation on the Activity of Glycosidase Inhibitors. Angew Chem Int Ed Engl 2023; 62:e202217809. [PMID: 36573850 PMCID: PMC9908843 DOI: 10.1002/anie.202217809] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Indexed: 12/28/2022]
Abstract
Substrate side chain conformation impacts reactivity during glycosylation and glycoside hydrolysis and is restricted by many glycosidases and glycosyltransferases during catalysis. We show that the side chains of gluco and manno iminosugars can be restricted to predominant conformations by strategic installation of a methyl group. Glycosidase inhibition studies reveal that iminosugars with the gauche,gauche side chain conformations are 6- to 10-fold more potent than isosteric compounds with the gauche,trans conformation; a manno-configured iminosugar with the gauche,gauche conformation is a 27-fold better inhibitor than 1-deoxymannojirimycin. The results are discussed in terms of the energetic benefits of preorganization, particularly when in synergy with favorable hydrophobic interactions. The demonstration that inhibitor side chain preorganization can favorably impact glycosidase inhibition paves the way for improved inhibitor design through conformational preorganization.
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Affiliation(s)
- Po-Sen Tseng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602 (USA),Department of Chemistry, University of Georgia, Athens, GA 30602 (USA),Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 (USA)
| | - Chennaiah Ande
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602 (USA)
| | - Kelley W. Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 (USA),Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 (USA)
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602 (USA),Department of Chemistry, University of Georgia, Athens, GA 30602 (USA),Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 (USA)
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4
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Liu X, Li F, Su L, Wang M, Jia T, Xu X, Li X, Wei C, Luo C, Chen S, Chen H. Design and synthesis of novel benzimidazole-iminosugars linked a substituted phenyl group and their inhibitory activities against β-glucosidase. Bioorg Chem 2022; 127:106016. [PMID: 35841671 DOI: 10.1016/j.bioorg.2022.106016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/13/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022]
Abstract
A series of novel benzimidazole-iminosugars linked a (substuituted) phenyl group on benzene ring of benzimidazole 5(a-p) and 6(a-p) have been rationally designed and conveniently synthesized through Suzuki coupling reaction in high yields. All compounds have been evaluated for their inhibitory activities against β-glucosidase (almond). Six compounds 5d, 6d, 6e, 6i, 6n, and 6p showed more significant inhibitory activities with IC50 values in the range of 0.03-0.08 μM, almost 10-fold improved than that of the parent analogue 4, and much higher than that of the positive control castanospermine. The additional phenyl ring and the electron donating groups on it would be beneficial for the activity. Compounds 6d, 6n, and 4 had been chosen to be tested for their inhibition types against β-glucosidase. Interestingly, three compounds have different inhibition types although they had very similar structure. Their Ki values were calculated to be 0.02 ± 0.01 μM, 0.02 ± 0.01 μM, and 0.66 ± 0.14 μM, respectively. The equilibrium dissociation constant (KD) for 6d, 6n, and 4 and β-glucosidase was 0.04 μM, 0.03 μM and 0.45 μM by the ITC-based assay, respectively. Molecular docking work suggests that such benzimidazole-iminosugars derivatives might bind to the active site of β-glucosidase mainly through hydrogen bonds, the additional phenyl ring towards the solvent-exposed region played an important effect on their inhibitory activity against β-glucosidase.
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Affiliation(s)
- Xu Liu
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Fengxin Li
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Lulu Su
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Mingchen Wang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Tongguan Jia
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Xiaoming Xu
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Xiaoliu Li
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Chao Wei
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Cheng Luo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Chen
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
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5
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Horikoshi S, Saburi W, Yu J, Matsuura H, Cairns JRK, Yao M, Mori H. Substrate specificity of glycoside hydrolase family 1 β-glucosidase AtBGlu42 from Arabidopsis thaliana and its molecular mechanism. Biosci Biotechnol Biochem 2022; 86:231-245. [PMID: 34965581 DOI: 10.1093/bbb/zbab200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/13/2021] [Indexed: 11/15/2022]
Abstract
Plants possess many glycoside hydrolase family 1 (GH1) β-glucosidases, which physiologically function in cell wall metabolism and activation of bioactive substances, but most remain uncharacterized. One GH1 isoenzyme AtBGlu42 in Arabidopsis thaliana has been identified to hydrolyze scopolin using the gene deficient plants, but no enzymatic properties were obtained. Its sequence similarity to another functionally characterized enzyme Os1BGlu4 in rice suggests that AtBGlu42 also acts on oligosaccharides. Here, we show that the recombinant AtBGlu42 possesses high kcat/Km not only on scopolin, but also on various β-glucosides, cellooligosaccharides, and laminarioligosaccharides. Of the cellooligosaccharides, cellotriose was the most preferred. The crystal structure, determined at 1.7 Å resolution, suggests that Arg342 gives unfavorable binding to cellooligosaccharides at subsite +3. The mutants R342Y and R342A showed the highest preference on cellotetraose or cellopentaose with increased affinities at subsite +3, indicating that the residues at this position have an important role for chain length specificity.
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Affiliation(s)
- Shu Horikoshi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - James R Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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6
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Zada NS, Belduz AO, Güler HI, Sahinkaya M, Khan SI, Saba M, Bektas KI, Kara Y, Kolaylı S, Badshah M, Shah AA, Khan S. Cloning, biochemical characterization and molecular docking of novel thermostable β-glucosidase BglA9 from Anoxybacillus ayderensis A9 and its application in de-glycosylation of Polydatin. Int J Biol Macromol 2021; 193:1898-1909. [PMID: 34793813 DOI: 10.1016/j.ijbiomac.2021.11.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/21/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022]
Abstract
This study reports a novel BglA9 gene of 1345 bp encoding β-glucosidase from Anoxybacillus ayderensis A9, which was amplified and expressed in E. coli BL21 (DE3): pLysS cells, purified with Ni-NTA column having molecular weight of 52.6 kDa and was used in the bioconversion of polydatin to resveratrol. The kinetic parameters values using pNPG as substrate were Km (0.28 mM), Vmax (43.8 μmol/min/mg), kcat (38.43 s-1) and kcat/Km (135.5 s-1 mM-1). The BglA9 was active in a broad pH range and had an activity half-life around 24 h at 50 °C. The de-glycosylation efficiency of BglA9 for polydatin was determined by estimating the amount of glucose released after enzymatic reaction by a dinitrosalicylic acid (DNS) assay. The kinetic parameters of BglA9 for polydatin were 5.5 mM, 20.84 μmol/min/mg, 18.28 s-1and 3.27 s-1 mM-1 for Km, Vmax, kcat, and kcat/Km values, respectively. The Ki value for glucose was determined to be 1.7 M. The residues Gln19, His120, Glu355, Glu409, Glu178, Asn222 may play a crucial role in the deglycosylation as revealed by the 3D structure of enzyme docked with polydatin.
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Affiliation(s)
- Numan Saleh Zada
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Ali Osman Belduz
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Halil Ibrahim Güler
- Department of Molecular Biology and Genetics, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Miray Sahinkaya
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Sanam Islam Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey.
| | - Marium Saba
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Kadriye Inan Bektas
- Department of Molecular Biology and Genetics, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Yakup Kara
- Department of Chemistry, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Sevgi Kolaylı
- Department of Chemistry, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Malik Badshah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Samiullah Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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7
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Lolok N, Sumiwi SA, Muhtadi A, Susilawati Y, Hendriani R, Ramadhan DSF, Levita J, Sahidin I. Molecular docking and molecular dynamics studies of bioactive compounds contained in noni fruit ( Morinda citrifolia L.) against human pancreatic α-amylase. J Biomol Struct Dyn 2021; 40:7091-7098. [PMID: 33682637 DOI: 10.1080/07391102.2021.1894981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human pancreatic α-amylase inhibition is currently a promising therapeutic target against type 2 diabetes (DMT2) because it can reduce aggressive digestion of carbohydrates into absorbable monosaccharides. In Indonesia, medicinal plants, e.g. Morinda citrifolia fruit, have been empirically utilized as a blood-sugar reducer, however, the inhibitory activity of compounds in this plant against human pancreatic α-amylase is still limited or none. Therefore, this study aimed to test the interaction of 7 compounds (americanin, asperulosidic acid, damnacanthal, quercetin, rutin, scopoletin, and ursolic acid) contained in noni fruit against human pancreatic α-amylase by molecular docking and molecular dynamics and compared their binding modes with that of acarbose. Results of the molecular docking simulation indicated that the ursolic acid compound possesses the best binding energy (-8.58 kcal/mol) and comparable to that of acarbose (-8.59 kcal/mol). The molecular dynamics study at 100 ns simulation, the values of RMSD, RMSF, the radius of gyration (Rg), the solvent-accessible surface area (SASA), principal component analysis (PCA), and MM-PBSA binding free energy were stable and identical to those of acarbose. It could be concluded that ursolic acid might be potential in inhibiting human pancreatic α-amylase, thus, potential to be developed as an anti-DMT2 drug candidate. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nikeherpianti Lolok
- Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia.,Department of Pharmacy, Universitas Mandala Waluya Kendari, Kendari, Indonesia
| | - Sri Adi Sumiwi
- Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ahmad Muhtadi
- Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | | | - Rini Hendriani
- Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | | | - Jutti Levita
- Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Idin Sahidin
- Faculty of Pharmacy, Halu Oleo University, Kendari, Indonesia
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8
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Febbraio F, Ionata E, Marcolongo L. Forty years of study on the thermostable β-glycosidase from S. solfataricus: Production, biochemical characterization and biotechnological applications. Biotechnol Appl Biochem 2020; 67:602-618. [PMID: 32621790 DOI: 10.1002/bab.1982] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aim of this paper is to make the point on the fortieth years study on the β-glycosidase from Sulfolobus solfataricus. This enzyme represents one of the thermophilic biocatalysts, which is more extensively studied as witnessed by the numerous literature reports available since 1980. Comprehensive biochemical studies highlighted its broad substrate specificity for β-d-galacto-, gluco-, and fuco-sides and also showed its remarkable exo-glucosidase and transglycosidase activities. The enzyme demonstrated to be active and stable over a wide range of temperature and pHs, withstanding to several drastic conditions comprising solvents and detergents. Over the years, a great deal of studies were focused on its homotetrameric tridimensional structure, elucidating several structural features involved in the enzyme stability, such as ion pairs and post-translational modifications. Several β-glycosidase mutants were produced in the years in order to understand its peculiar behavior in extreme conditions and/or to improve its functional properties. The β-glycosidase overproduction was also afforded reporting numerous studies dealing with its production in the mesophilic host Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, and Lactococcus lactis. Relevant applications in food, beverages, bioenergy, pharmaceuticals, and nutraceutical fields of this enzyme, both in free and immobilized forms, highlighted its biotechnological relevance.
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Affiliation(s)
- Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, Italy
| | - Elena Ionata
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
| | - Loredana Marcolongo
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
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9
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Nutho B, Pengthaisong S, Tankrathok A, Lee VS, Ketudat Cairns JR, Rungrotmongkol T, Hannongbua S. Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7. Biomolecules 2020; 10:biom10060907. [PMID: 32549280 PMCID: PMC7356692 DOI: 10.3390/biom10060907] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/07/2023] Open
Abstract
β-Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B2,5 transition state (TS) conformation preferred for mannosides and glucosides via their preferred 4H3/4E TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the -1 subsite in a 4H3/4E conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the B2,5 conformation rapidly relaxed to a E3/4H3 conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the B2,5 conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant β-glycosidases.
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Affiliation(s)
- Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Salila Pengthaisong
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Anupong Tankrathok
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - James R. Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
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10
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Alonso-Gil S. Mimicking the transition state of reactions of glycoside hydrolases: Updating the conformational space of the oxocarbenium cation. J Carbohydr Chem 2020. [DOI: 10.1080/07328303.2020.1766481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague 8, Czech Republic
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11
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Strazzulli A, Perugino G, Mazzone M, Rossi M, Withers SG, Moracci M. Probing the role of an invariant active site His in family GH1 β-glycosidases. J Enzyme Inhib Med Chem 2019; 34:973-980. [PMID: 31072150 PMCID: PMC6522968 DOI: 10.1080/14756366.2019.1608198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The reaction mechanism of glycoside hydrolases belonging to family 1 (GH1) of carbohydrate-active enzymes classification, hydrolysing β-O-glycosidic bonds, is well characterised. This family includes several thousands of enzymes with more than 20 different EC numbers depending on the sugar glycone recognised as substrate. Most GH1 β-glycosidases bind their substrates with similar specificity through invariant amino acid residues. Despite extensive studies, the clear identification of the roles played by each of these residues in the recognition of different glycones is not always possible. We demonstrated here that a histidine residue, completely conserved in the active site of the enzymes of this family, interacts with the C2-OH of the substrate in addition to the C3-OH as previously shown by 3 D-structure determination.
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Affiliation(s)
- Andrea Strazzulli
- a Department of Biology , University of Naples "Federico II", Complesso Universitario di Monte S. Angelo , Napoli , Italy.,b Task Force on Microbiome Studies, University of Naples Federico II , Naples , Italy
| | - Giuseppe Perugino
- c Institute of Biosciences and BioResources - National Research Council of Italy , Naples , Italy
| | - Marialuisa Mazzone
- c Institute of Biosciences and BioResources - National Research Council of Italy , Naples , Italy
| | - Mosè Rossi
- c Institute of Biosciences and BioResources - National Research Council of Italy , Naples , Italy
| | - Stephen G Withers
- d Department of Chemistry , University of British Columbia , Vancouver , Canada
| | - Marco Moracci
- a Department of Biology , University of Naples "Federico II", Complesso Universitario di Monte S. Angelo , Napoli , Italy.,b Task Force on Microbiome Studies, University of Naples Federico II , Naples , Italy.,c Institute of Biosciences and BioResources - National Research Council of Italy , Naples , Italy
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12
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Effects of Random Mutagenesis and In Vivo Selection on the Specificity and Stability of a Thermozyme. Catalysts 2019. [DOI: 10.3390/catal9050440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Factors that give enzymes stability, activity, and substrate recognition result from the combination of few weak molecular interactions, which can be difficult to study through rational protein engineering approaches. We used irrational random mutagenesis and in vivo selection to test if a β-glycosidase from the thermoacidophile Saccharolobus solfataricus (Ssβ-gly) could complement an Escherichia coli strain unable to grow on lactose. The triple mutant of Ssβ-gly (S26L, P171L, and A235V) was more active than the wild type at 85 °C, inactivated at this temperature almost 300-fold quicker, and showed a 2-fold higher kcat on galactosides. The three mutations, which were far from the active site, were analyzed to test their effect at the structural level. Improved activity on galactosides was induced by the mutations. The S26L and P171L mutations destabilized the enzyme through the removal of a hydrogen bond and increased flexibility of the peptide backbone, respectively. However, the flexibility added by S26L mutation improved the activity at T > 60 °C. This study shows that random mutagenesis and biological selection allowed the identification of residues that are critical in determining thermal activity, stability, and substrate recognition.
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13
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Schröder SP, Wu L, Artola M, Hansen T, Offen WA, Ferraz MJ, Li KY, Aerts JMFG, van der Marel GA, Codée JDC, Davies GJ, Overkleeft HS. Gluco-1 H-imidazole: A New Class of Azole-Type β-Glucosidase Inhibitor. J Am Chem Soc 2018; 140:5045-5048. [PMID: 29601200 PMCID: PMC5942873 DOI: 10.1021/jacs.8b02399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Gluco-azoles competitively inhibit glucosidases by transition-state mimicry and their ability to interact with catalytic acid residues in glucosidase active sites. We noted that no azole-type inhibitors described, to date, possess a protic nitrogen characteristic for 1 H-imidazoles. Here, we present gluco-1 H-imidazole, a gluco-azole bearing a 1 H-imidazole fused to a glucopyranose-configured cyclitol core, and three close analogues as new glucosidase inhibitors. All compounds inhibit human retaining β-glucosidase, GBA1, with the most potent ones inhibiting this enzyme (deficient in Gaucher disease) on a par with glucoimidazole. None inhibit glucosylceramide synthase, cytosolic β-glucosidase GBA2 or α-glucosidase GAA. Structural, physical and computational studies provide first insights into the binding mode of this conceptually new class of retaining β-glucosidase inhibitors.
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Affiliation(s)
| | - Liang Wu
- Department of Chemistry, York Structural Biology Laboratory , University of York , Heslington, York YO10 5DD , United Kingdom
| | | | | | - Wendy A Offen
- Department of Chemistry, York Structural Biology Laboratory , University of York , Heslington, York YO10 5DD , United Kingdom
| | | | | | | | | | | | - Gideon J Davies
- Department of Chemistry, York Structural Biology Laboratory , University of York , Heslington, York YO10 5DD , United Kingdom
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14
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Shin KC, Choi HY, Seo MJ, Oh DK. Improved conversion of ginsenoside Rb 1 to compound K by semi-rational design of Sulfolobus solfataricus β-glycosidase. AMB Express 2017; 7:186. [PMID: 28980170 PMCID: PMC5628084 DOI: 10.1186/s13568-017-0487-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/28/2017] [Indexed: 01/10/2023] Open
Abstract
Ginsenoside compound K has been used as a key nutritional and cosmetic component because of its anti-fatigue and skin anti-aging effects. β-Glycosidase from Sulfolobus solfataricus (SS-BGL) is known as the most efficient enzyme for compound K production. The hydrolytic pathway from ginsenoside Rb1 to compound K via Rd and F2 is the most important because Rb1 is the most abundant component in ginseng extract. However, the enzymatic conversion of ginsenoside Rd to F2 is a limiting step in the hydrolytic pathway because of the relatively low activity for Rd. A V209 residue obtained from error-prone PCR was related to Rd-hydrolyzing activity, and a docking pose showing an interaction with Val209 was selected from numerous docking poses. W361F was obtained by rational design using the docking pose that exhibited 4.2-fold higher activity, 3.7-fold higher catalytic efficiency, and 3.1-fold lower binding energy for Rd than the wild-type enzyme, indicating that W361F compensated for the limiting step. W361F completely converted Rb1 to compound K with a productivity of 843 mg l−1 h−1 in 80 min, and showed also 7.4-fold higher activity for the flavanone, hesperidin, than the wild-type enzyme. Therefore, the W361F variant SS-BGL can be useful for hydrolysis of other glycosides as well as compound K production from Rb1, and semi-rational design is a useful tool for enhancing hydrolytic activity of β-glycosidase.
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15
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Li Y, Arakawa G, Tokuda G, Watanabe H, Arioka M. Heterologous expression in Pichia pastoris and characterization of a β-glucosidase from the xylophagous cockroach Panesthia angustipennis spadica displaying high specific activity for cellobiose. Enzyme Microb Technol 2017; 97:104-113. [DOI: 10.1016/j.enzmictec.2016.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/18/2016] [Accepted: 11/14/2016] [Indexed: 01/14/2023]
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16
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Tankrathok A, Iglesias-Fernández J, Williams RJ, Pengthaisong S, Baiya S, Hakki Z, Robinson RC, Hrmova M, Rovira C, Williams SJ, Ketudat Cairns JR. A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01547] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Anupong Tankrathok
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Department of Biotechnology, Faculty of Agro-Industrial
Technology, Rajamangala University of Technology, Isan, Kalasin Campus, Kalasin 46000, Thailand
| | - Javier Iglesias-Fernández
- Departament de Quı́mica
Orgànica/Institut de Quı́mica Teòrica i
Computacional (IQTCUB), Universitat de Barcelona, Martı́ i Franquès
1, 08028 Barcelona, Spain
| | - Rohan J. Williams
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Salila Pengthaisong
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Supaporn Baiya
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Zalihe Hakki
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robert C. Robinson
- Institute of Molecular
and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
- Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597
| | - Maria Hrmova
- School of Agriculture, Food and Wine, Australian
Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glenn
Osmond, Australia
| | - Carme Rovira
- Departament de Quı́mica
Orgànica/Institut de Quı́mica Teòrica i
Computacional (IQTCUB), Universitat de Barcelona, Martı́ i Franquès
1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluı́s Companys, 23, 08018 Barcelona, Spain
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James R. Ketudat Cairns
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
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17
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Development of inhibitors as research tools for carbohydrate-processing enzymes. Biochem Soc Trans 2012; 40:913-28. [DOI: 10.1042/bst20120201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates, which are present in all domains of life, play important roles in a host of cellular processes. These ubiquitous biomolecules form highly diverse and often complex glycan structures without the aid of a template. The carbohydrate structures are regulated solely by the location and specificity of the enzymes responsible for their synthesis and degradation. These enzymes, glycosyltransferases and glycoside hydrolases, need to be functionally well characterized in order to investigate the structure and function of glycans. The use of enzyme inhibitors, which target a particular enzyme, can significantly aid this understanding, and may also provide insights into therapeutic applications. The present article describes some of the approaches used to design and develop enzyme inhibitors as tools for investigating carbohydrate-processing enzymes.
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18
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Deckert K, Budiardjo SJ, Brunner LC, Lovell S, Karanicolas J. Designing allosteric control into enzymes by chemical rescue of structure. J Am Chem Soc 2012; 134:10055-60. [PMID: 22655749 DOI: 10.1021/ja301409g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligand-dependent activity has been engineered into enzymes for purposes ranging from controlling cell morphology to reprogramming cellular signaling pathways. Where these successes have typically fused a naturally allosteric domain to the enzyme of interest, here we instead demonstrate an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. We present two examples, W33G in a β-glycosidase enzyme (β-gly) and W492G in a β-glucuronidase enzyme (β-gluc), in which we engineer indole-dependent activity into enzymes by removing a buried tryptophan side chain that serves as a buttress for the active site architecture. In both cases, we observe a loss of function, and in both cases we find that the subsequent addition of indole can be used to restore activity. Through a detailed analysis of β-gly W33G kinetics, we demonstrate that this rescued enzyme is fully functionally equivalent to the corresponding wild-type enzyme. We then present the apo and indole-bound crystal structures of β-gly W33G, which together establish the structural basis for enzyme inactivation and rescue. Finally, we use this designed switch to modulate β-glycosidase activity in living cells using indole. Disruption and recovery of protein structure may represent a general technique for introducing allosteric control into enzymes, and thus may serve as a starting point for building a variety of bioswitches and sensors.
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Affiliation(s)
- Katelyn Deckert
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045-7534, USA
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19
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Liu L, Zeng Z, Zeng G, Chen M, Zhang Y, Zhang J, Fang X, Jiang M, Lu L. Study on binding modes between cellobiose and β-glucosidases from glycoside hydrolase family 1. Bioorg Med Chem Lett 2012; 22:837-43. [DOI: 10.1016/j.bmcl.2011.12.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/07/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
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20
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Li T, Guo L, Zhang Y, Wang J, Zhang Z, Li J, Zhang W, Lin J, Zhao W, Wang PG. Structure–activity relationships in a series of C2-substituted gluco-configured tetrahydroimidazopyridines as β-glucosidase inhibitors. Bioorg Med Chem 2011; 19:2136-44. [DOI: 10.1016/j.bmc.2011.02.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 02/22/2011] [Accepted: 02/23/2011] [Indexed: 12/26/2022]
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21
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Trapero A, Alfonso I, Butters TD, Llebaria A. Polyhydroxylated Bicyclic Isoureas and Guanidines Are Potent Glucocerebrosidase Inhibitors and Nanomolar Enzyme Activity Enhancers in Gaucher Cells. J Am Chem Soc 2011; 133:5474-84. [DOI: 10.1021/ja111480z] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ana Trapero
- Research Unit on Bioactive Molecules (RUBAM), Departament de Química Biomèdica, Institut de Química Avançada de Catalunya (IQAC−CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ignacio Alfonso
- Departament de Química Biològica y Modelització Molecular, IQAC−CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Terry D. Butters
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Amadeu Llebaria
- Research Unit on Bioactive Molecules (RUBAM), Departament de Química Biomèdica, Institut de Química Avançada de Catalunya (IQAC−CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
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22
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Khan S, Pozzo T, Megyeri M, Lindahl S, Sundin A, Turner C, Karlsson EN. Aglycone specificity of Thermotoga neapolitana β-glucosidase 1A modified by mutagenesis, leading to increased catalytic efficiency in quercetin-3-glucoside hydrolysis. BMC BIOCHEMISTRY 2011; 12:11. [PMID: 21345211 PMCID: PMC3056771 DOI: 10.1186/1471-2091-12-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 02/23/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND The thermostable β-glucosidase (TnBgl1A) from Thermotoga neapolitana is a promising biocatalyst for hydrolysis of glucosylated flavonoids and can be coupled to extraction methods using pressurized hot water. Hydrolysis has however been shown to be dependent on the position of the glucosylation on the flavonoid, and e.g. quercetin-3-glucoside (Q3) was hydrolysed slowly. A set of mutants of TnBgl1A were thus created to analyse the influence on the kinetic parameters using the model substrate para-nitrophenyl-β-D-glucopyranoside (pNPGlc), and screened for hydrolysis of Q3. RESULTS Structural analysis pinpointed an area in the active site pocket with non-conserved residues between specificity groups in glycoside hydrolase family 1 (GH1). Three residues in this area located on β-strand 5 (F219, N221, and G222) close to sugar binding sub-site +2 were selected for mutagenesis and amplified in a protocol that introduced a few spontaneous mutations. Eight mutants (four triple: F219L/P165L/M278I, N221S/P165L/M278I, G222Q/P165L/M278I, G222Q/V203M/K214R, two double: F219L/K214R, N221S/P342L and two single: G222M and N221S) were produced in E. coli, and purified to apparent homogeneity. Thermostability, measured as Tm by differential scanning calorimetry (101.9°C for wt), was kept in the mutated variants and significant decrease (ΔT of 5-10°C) was only observed for the triple mutants. The exchanged residue(s) in the respective mutant resulted in variations in KM and turnover. The KM-value was only changed in variants mutated at position 221 (N221S) and was in all cases monitored as a 2-3 × increase for pNPGlc, while the KM decreased a corresponding extent for Q3.Turnover was only significantly changed using pNPGlc, and was decreased 2-3 × in variants mutated at position 222, while the single, double and triple mutated variants carrying a mutation at position 221 (N221S) increased turnover up to 3.5 × compared to the wild type. Modelling showed that the mutation at position 221, may alter the position of N291 resulting in increased hydrogen bonding of Q3 (at a position corresponding to the +1 subsite) which may explain the decrease in KM for this substrate. CONCLUSION These results show that residues at the +2 subsite are interesting targets for mutagenesis and mutations at these positions can directly or indirectly affect both KM and turnover. An affinity change, leading to a decreased KM, can be explained by an altered position of N291, while the changes in turnover are more difficult to explain and may be the result of smaller conformational changes in the active site.
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Affiliation(s)
- Samiullah Khan
- Biotechnology, Dept of Chemistry, Lund University, P,O, Box 124, SE-221 00 Lund, Sweden
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23
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Stütz AE, Wrodnigg TM. Imino sugars and glycosyl hydrolases: historical context, current aspects, emerging trends. Adv Carbohydr Chem Biochem 2011; 66:187-298. [PMID: 22123190 DOI: 10.1016/b978-0-12-385518-3.00004-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forty years of discoveries and research on imino sugars, which are carbohydrate analogues having a basic nitrogen atom instead of oxygen in the sugar ring and, acting as potent glycosidase inhibitors, have made considerable impact on our contemporary understanding of glycosidases. Imino sugars have helped to elucidate the catalytic machinery of glycosidases and have refined our methods and concepts of utilizing them. A number of new aspects have emerged for employing imino sugars as pharmaceutical compounds, based on their profound effects on metabolic activities in which glycosidases are involved. From the digestion of starch to the fight against viral infections, from research into malignant diseases to potential improvements in hereditary storage disorders, glycosidase action and inhibition are essential issues. This account aims at combining general developments with a focus on some niches where imino sugars have become useful tools for glycochemistry and glycobiology.
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Affiliation(s)
- Arnold E Stütz
- Institut für Organische Chemie, Technische Universität Graz, Austria
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24
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Ketudat Cairns JR, Esen A. β-Glucosidases. Cell Mol Life Sci 2010; 67:3389-405. [PMID: 20490603 PMCID: PMC11115901 DOI: 10.1007/s00018-010-0399-2] [Citation(s) in RCA: 365] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 04/13/2010] [Accepted: 04/30/2010] [Indexed: 10/19/2022]
Abstract
β-Glucosidases (3.2.1.21) are found in all domains of living organisms, where they play essential roles in the removal of nonreducing terminal glucosyl residues from saccharides and glycosides. β-Glucosidases function in glycolipid and exogenous glycoside metabolism in animals, defense, cell wall lignification, cell wall β-glucan turnover, phytohormone activation, and release of aromatic compounds in plants, and biomass conversion in microorganisms. These functions lead to many agricultural and industrial applications. β-Glucosidases have been classified into glycoside hydrolase (GH) families GH1, GH3, GH5, GH9, and GH30, based on their amino acid sequences, while other β-glucosidases remain to be classified. The GH1, GH5, and GH30 β-glucosidases fall in GH Clan A, which consists of proteins with (β/α)(8)-barrel structures. In contrast, the active site of GH3 enzymes comprises two domains, while GH9 enzymes have (α/α)(6) barrel structures. The mechanism by which GH1 enzymes recognize and hydrolyze substrates with different specificities remains an area of intense study.
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Affiliation(s)
- James R Ketudat Cairns
- Schools of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, Thailand.
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25
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Abdula AM, Khalaf RA, Mubarak MS, Taha MO. Discovery of new β-D-galactosidase inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening. J Comput Chem 2010; 32:463-82. [PMID: 20730780 DOI: 10.1002/jcc.21635] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 05/14/2010] [Accepted: 06/23/2010] [Indexed: 11/11/2022]
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26
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Discovery of new β-d-glucosidase inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening. J Mol Model 2010; 17:443-64. [PMID: 20490878 DOI: 10.1007/s00894-010-0737-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 04/28/2010] [Indexed: 10/19/2022]
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27
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Anand K, Mathur D, Anant A, Garg LC. Structural studies of phosphoglucose isomerase from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:490-7. [PMID: 20445242 DOI: 10.1107/s1744309110011656] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 03/27/2010] [Indexed: 01/17/2023]
Abstract
Phosphoglucose isomerase (PGI) plays a key role in both glycolysis and gluconeogenesis inside the cell, whereas outside the cell it exhibits cytokine properties. PGI is also known to act as an autocrine motility factor, a neuroleukin agent and a differentiation and maturation mediator. Here, the first crystal structure of PGI from Mycobacterium tuberculosis H37Rv (Mtb) is reported. The structure was refined at 2.25 A resolution and revealed the presence of one molecule in the asymmetric unit with two globular domains. As known previously, the active site of Mtb PGI contains conserved residues including Glu356, Glu216 and His387 (where His387 is from the neighbouring molecule). The crystal structure of Mtb PGI was observed to be rather more similar to human PGI than other nonbacterial PGIs, with only a few differences being detected in the loops, arm and hook regions of the human and Mtb PGIs, suggesting that the M. tuberculosis enzyme uses the same enzyme mechanism.
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Affiliation(s)
- Kanchan Anand
- European Molecular Biology Laboratory Heidelberg, Structural and Computational Biology Unit, Meyerhof Strasse 1, D-69117 Heidelberg, Germany. ,
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28
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Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases. Appl Microbiol Biotechnol 2010; 87:9-19. [DOI: 10.1007/s00253-010-2567-6] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/09/2010] [Accepted: 03/15/2010] [Indexed: 10/19/2022]
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29
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Gloster TM, Davies GJ. Glycosidase inhibition: assessing mimicry of the transition state. Org Biomol Chem 2010; 8:305-20. [PMID: 20066263 PMCID: PMC2822703 DOI: 10.1039/b915870g] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 09/30/2009] [Indexed: 12/15/2022]
Abstract
Glycoside hydrolases, the enzymes responsible for hydrolysis of the glycosidic bond in di-, oligo- and polysaccharides, and glycoconjugates, are ubiquitous in Nature and fundamental to existence. The extreme stability of the glycosidic bond has meant these enzymes have evolved into highly proficient catalysts, with an estimated 10(17) fold rate enhancement over the uncatalysed reaction. Such rate enhancements mean that enzymes bind the substrate at the transition state with extraordinary affinity; the dissociation constant for the transition state is predicted to be 10(-22) M. Inhibition of glycoside hydrolases has widespread application in the treatment of viral infections, such as influenza and HIV, lysosomal storage disorders, cancer and diabetes. If inhibitors are designed to mimic the transition state, it should be possible to harness some of the transition state affinity, resulting in highly potent and specific drugs. Here we examine a number of glycosidase inhibitors which have been developed over the past half century, either by Nature or synthetically by man. A number of criteria have been proposed to ascertain which of these inhibitors are true transition state mimics, but these features have only be critically investigated in a very few cases.
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Affiliation(s)
- Tracey M. Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK. ; ; Fax: +44 1904 328266; Tel: +44 1904 328260
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK. ; ; Fax: +44 1904 328266; Tel: +44 1904 328260
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Wu H, Ho C, Ko T, Popat S, Lin C, Wang A. Structural Basis of α‐Fucosidase Inhibition by Iminocyclitols with
K
i
Values in the Micro‐ to Picomolar Range. Angew Chem Int Ed Engl 2010; 49:337-40. [DOI: 10.1002/anie.200905597] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hsing‐Ju Wu
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Ching‐Wen Ho
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
- Department of Chemistry, National Tsing‐Hua University, Taipei (Taiwan)
| | - Tzu‐Ping Ko
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Shinde D. Popat
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Chun‐Hung Lin
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Andrew H.‐J. Wang
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
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Wu H, Ho C, Ko T, Popat S, Lin C, Wang A. Structural Basis of α‐Fucosidase Inhibition by Iminocyclitols withKiValues in the Micro‐ to Picomolar Range. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200905597] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hsing‐Ju Wu
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Ching‐Wen Ho
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
- Department of Chemistry, National Tsing‐Hua University, Taipei (Taiwan)
| | - Tzu‐Ping Ko
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Shinde D. Popat
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Chun‐Hung Lin
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Andrew H.‐J. Wang
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
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Balcewich MD, Stubbs KA, He Y, James TW, Davies GJ, Vocadlo DJ, Mark BL. Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ. Protein Sci 2009; 18:1541-51. [PMID: 19499593 DOI: 10.1002/pro.137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
NagZ is an exo-N-acetyl-beta-glucosaminidase, found within Gram-negative bacteria, that acts in the peptidoglycan recycling pathway to cleave N-acetylglucosamine residues off peptidoglycan fragments. This activity is required for resistance to cephalosporins mediated by inducible AmpC beta-lactamase. NagZ uses a catalytic mechanism involving a covalent glycosyl enzyme intermediate, unlike that of the human exo-N-acetyl-beta-glucosaminidases: O-GlcNAcase and the beta-hexosaminidase isoenzymes. These latter enzymes, which remove GlcNAc from glycoconjugates, use a neighboring-group catalytic mechanism that proceeds through an oxazoline intermediate. Exploiting these mechanistic differences we previously developed 2-N-acyl derivatives of O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), which selectively inhibits NagZ over the functionally related human enzymes and attenuate antibiotic resistance in Gram-negatives that harbor inducible AmpC. To understand the structural basis for the selectivity of these inhibitors for NagZ, we have determined its crystallographic structure in complex with N-valeryl-PUGNAc, the most selective known inhibitor of NagZ over both the human beta-hexosaminidases and O-GlcNAcase. The selectivity stems from the five-carbon acyl chain of N-valeryl-PUGNAc, which we found ordered within the enzyme active site. In contrast, a structure determination of a human O-GlcNAcase homologue bound to a related inhibitor N-butyryl-PUGNAc, which bears a four-carbon chain and is selective for both NagZ and O-GlcNAcase over the human beta-hexosamnidases, reveals that this inhibitor induces several conformational changes in the active site of this O-GlcNAcase homologue. A comparison of these complexes, and with the human beta-hexosaminidases, reveals how selectivity for NagZ can be engineered by altering the 2-N-acyl substituent of PUGNAc to develop inhibitors that repress AmpC mediated beta-lactam resistance.
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Affiliation(s)
- Misty D Balcewich
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Bikadi Z, Hazai E. Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. J Cheminform 2009; 1:15. [PMID: 20150996 PMCID: PMC2820493 DOI: 10.1186/1758-2946-1-15] [Citation(s) in RCA: 346] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 09/11/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Molecular docking methods are commonly used for predicting binding modes and energies of ligands to proteins. For accurate complex geometry and binding energy estimation, an appropriate method for calculating partial charges is essential. AutoDockTools software, the interface for preparing input files for one of the most widely used docking programs AutoDock 4, utilizes the Gasteiger partial charge calculation method for both protein and ligand charge calculation. However, it has already been shown that more accurate partial charge calculation - and as a consequence, more accurate docking- can be achieved by using quantum chemical methods. For docking calculations quantum chemical partial charge calculation as a routine was only used for ligands so far. The newly developed Mozyme function of MOPAC2009 allows fast partial charge calculation of proteins by quantum mechanical semi-empirical methods. Thus, in the current study, the effect of semi-empirical quantum-mechanical partial charge calculation on docking accuracy could be investigated. RESULTS The docking accuracy of AutoDock 4 using the original AutoDock scoring function was investigated on a set of 53 protein ligand complexes using Gasteiger and PM6 partial charge calculation methods. This has enabled us to compare the effect of the partial charge calculation method on docking accuracy utilizing AutoDock 4 software. Our results showed that the docking accuracy in regard to complex geometry (docking result defined as accurate when the RMSD of the first rank docking result complex is within 2 A of the experimentally determined X-ray structure) significantly increased when partial charges of the ligands and proteins were calculated with the semi-empirical PM6 method. Out of the 53 complexes analyzed in the course of our study, the geometry of 42 complexes were accurately calculated using PM6 partial charges, while the use of Gasteiger charges resulted in only 28 accurate geometries. The binding affinity estimation was not influenced by the partial charge calculation method - for more accurate binding affinity prediction development of a new scoring function for AutoDock is needed. CONCLUSION Our results demonstrate that the accuracy of determination of complex geometry using AutoDock 4 for docking calculation greatly increases with the use of quantum chemical partial charge calculation on both the ligands and proteins.
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Affiliation(s)
- Zsolt Bikadi
- Virtua Drug Ltd, Csalogany Street 4C Budapest, Hungary
| | - Eszter Hazai
- Virtua Drug Ltd, Csalogany Street 4C Budapest, Hungary
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Vocadlo DJ, Davies GJ. Mechanistic insights into glycosidase chemistry. Curr Opin Chem Biol 2009; 12:539-55. [PMID: 18558099 DOI: 10.1016/j.cbpa.2008.05.010] [Citation(s) in RCA: 300] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/16/2022]
Abstract
The enzymatic hydrolysis of the glycosidic bond continues to gain importance, reflecting the critically important roles complex glycans play in health and disease as well as the rekindled interest in enzymatic biomass conversion. Recent advances include the broadening of our understanding of enzyme reaction coordinates, through both computational and structural studies, improved understanding of enzyme inhibition through transition state mimicry and fascinating insights into mechanism yielded by physical organic chemistry approaches.
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Affiliation(s)
- David J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, Canada.
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35
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Aguilar M, Gloster TM, García-Moreno MI, Ortiz Mellet C, Davies GJ, Llebaria A, Casas J, Egido-Gabás M, García Fernandez JM. Molecular Basis for β-Glucosidase Inhibition by Ring-Modified Calystegine Analogues. Chembiochem 2008; 9:2612-8. [DOI: 10.1002/cbic.200800451] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Hill AD, Reilly PJ. Computational analysis of glycoside hydrolase family 1 specificities. Biopolymers 2008; 89:1021-31. [DOI: 10.1002/bip.21052] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Kuntz DA, Tarling CA, Withers SG, Rose DR. Structural Analysis of Golgi α-Mannosidase II Inhibitors Identified from a Focused Glycosidase Inhibitor Screen. Biochemistry 2008; 47:10058-68. [DOI: 10.1021/bi8010785] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Douglas A. Kuntz
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada, and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chris A. Tarling
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada, and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G. Withers
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada, and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - David R. Rose
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada, and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
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Tailford LE, Offen WA, Smith NL, Dumon C, Morland C, Gratien J, Heck MP, Stick RV, Blériot Y, Vasella A, Gilbert HJ, Davies GJ. Structural and biochemical evidence for a boat-like transition state in β-mannosidases. Nat Chem Biol 2008; 4:306-12. [PMID: 18408714 DOI: 10.1038/nchembio.81] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 02/15/2008] [Indexed: 11/09/2022]
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Dorfmueller HC, Borodkin VS, Schimpl M, Shepherd SM, Shpiro NA, van Aalten DMF. GlcNAcstatin: a picomolar, selective O-GlcNAcase inhibitor that modulates intracellular O-glcNAcylation levels. J Am Chem Soc 2007; 128:16484-5. [PMID: 17177381 PMCID: PMC7116141 DOI: 10.1021/ja066743n] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many phosphorylation signal transduction pathways in the eukaryotic cell are modulated by posttranslational modification of specific serines/threonines with N-acetylglucosamine (O-GlcNAc). Levels of O-GlcNAc on key proteins regulate biological processes as diverse as the cell cycle, insulin signaling, and protein degradation. The two enzymes involved in this dynamic and abundant modification are the O-GlcNAc transferase and O-GlcNAcase. Structural data have recently revealed that the O-GlcNAcase possesses an active site with significant structural similarity to that of the human lysosomal hexosaminidases HexA/HexB. PUGNAc, an O-GlcNAcase inhibitor widely used to raise levels of O-GlcNAc in human cell lines, also inhibits these hexosaminidases. Here, we have exploited recent structural information of an O-GlcNAcase-PUGNAc complex to design and synthesize a glucoimidazole-based inhibitor, GlcNAcstatin, which is a 5 pM competitive inhibitor of enzymes of the O-GlcNAcase family, shows 100000-fold selectivity over HexA/B, and binds to the O-GlcNAcase active site by mimicking the transition state as revealed by X-ray crystallography. This compound is able to raise O-GlcNAc levels in human HEK 293 and SH-SY5Y neuroblastoma cell lines and thus provides a novel, potent tool for the study of the role of O-GlcNAc in intracellular signal transduction pathways.
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Gloster TM, Meloncelli P, Stick RV, Zechel D, Vasella A, Davies GJ. Glycosidase Inhibition: An Assessment of the Binding of 18 Putative Transition-State Mimics. J Am Chem Soc 2007; 129:2345-54. [PMID: 17279749 DOI: 10.1021/ja066961g] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The inhibition of glycoside hydrolases, through transition-state mimicry, is important both as a probe of enzyme mechanism and in the continuing quest for new drugs, notably in the treatment of cancer, HIV, influenza, and diabetes. The high affinity with which these enzymes are known to bind the transition state provides a framework upon which to design potent inhibitors. Recent work [for example, Bülow, A. et al. J. Am. Chem. Soc. 2000, 122, 8567-8568; Zechel, D. L. et al. J. Am. Chem. Soc. 2003, 125, 14313-14323] has revealed quite confusing and counter-intuitive patterns of inhibition for a number of glycosidase inhibitors. Here we describe a synergistic approach for analysis of inhibitors with a single enzyme 'model system', the Thermotoga maritima family 1 beta-glucosidase, TmGH1. The pH dependence of enzyme activity and inhibition has been determined, structures of inhibitor complexes have been solved by X-ray crystallography, with data up to 1.65 A resolution, and isothermal titration calorimetry was used to establish the thermodynamic signature. This has allowed the characterization of 18 compounds, all putative transition-state mimics, in order to build an 'inhibition profile' that provides an insight into what governs binding. In contrast to our preconceptions, there is little correlation of inhibitor chemistry with the calorimetric dissection of thermodynamics. The ensemble of inhibitors shows strong enthalpy-entropy compensation, and the random distribution of similar inhibitors across the plot of DeltaH degrees a vs TDeltaS degrees a likely reflects the enormous contribution of solvation and desolvation effects on ligand binding.
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Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
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