1
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Ofman TP, Heming JJA, Nin-Hill A, Küllmer F, Moran E, Bennett M, Steneker R, Klein AM, Ruijgrok G, Kok K, Armstrong ZWB, Aerts JMFG, van der Marel GA, Rovira C, Davies GJ, Artola M, Codée JDC, Overkleeft HS. Conformational and Electronic Variations in 1,2- and 1,5a-Cyclophellitols and their Impact on Retaining α-Glucosidase Inhibition. Chemistry 2024; 30:e202400723. [PMID: 38623783 DOI: 10.1002/chem.202400723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
Glycoside hydrolases (glycosidases) take part in myriad biological processes and are important therapeutic targets. Competitive and mechanism-based inhibitors are useful tools to dissect their biological role and comprise a good starting point for drug discovery. The natural product, cyclophellitol, a mechanism-based, covalent and irreversible retaining β-glucosidase inhibitor has inspired the design of diverse α- and β-glycosidase inhibitor and activity-based probe scaffolds. Here, we sought to deepen our understanding of the structural and functional requirements of cyclophellitol-type compounds for effective human α-glucosidase inhibition. We synthesized a comprehensive set of α-configured 1,2- and 1,5a-cyclophellitol analogues bearing a variety of electrophilic traps. The inhibitory potency of these compounds was assessed towards both lysosomal and ER retaining α-glucosidases. These studies revealed the 1,5a-cyclophellitols to be the most potent retaining α-glucosidase inhibitors, with the nature of the electrophile determining inhibitory mode of action (covalent or non-covalent). DFT calculations support the ability of the 1,5a-cyclophellitols, but not the 1,2-congeners, to adopt conformations that mimic either the Michaelis complex or transition state of α-glucosidases.
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Affiliation(s)
- Tim P Ofman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jurriaan J A Heming
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franques 1-11, E-08028, Barcelona, Spain
| | - Florian Küllmer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Elisha Moran
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Megan Bennett
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Roy Steneker
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anne-Mei Klein
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijs Ruijgrok
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Ken Kok
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Zach W B Armstrong
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franques 1-11, E-08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020, Barcelona, Spain
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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2
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Nakayama T, Singh AK, Fukutomi T, Uchida N, Terao Y, Hamada H, Muraoka T, Muthusamy E, Kundu TK, Akagawa K. Activator of KAT3 histone acetyltransferase family ameliorates a neurodevelopmental disorder phenotype in the syntaxin 1A ablated mouse model. Cell Rep 2024; 43:114101. [PMID: 38613786 DOI: 10.1016/j.celrep.2024.114101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/15/2024] Open
Abstract
Syntaxin-1A (stx1a) repression causes a neurodevelopmental disorder phenotype, low latent inhibition (LI) behavior, by disrupting 5-hydroxytryptaminergic (5-HTergic) systems. Herein, we discovered that lysine acetyltransferase (KAT) 3B increases stx1a neuronal transcription and TTK21, a KAT3 activator, induces stx1a transcription and 5-HT release in vitro. Furthermore, glucose-derived CSP-TTK21 could restore decreased stx1a expression, 5-HTergic systems in the brain, and low LI in stx1a (+/-) mice by crossing the blood-brain barrier, whereas the KAT3 inhibitor suppresses stx1a expression, 5-HTergic systems, and LI behaviors in wild-type mice. Finally, in wild-type and stx1a (-/-) mice treated with IKK inhibitors and CSP-TTK21, respectively, we show that KAT3 activator-induced LI improvement is a direct consequence of KAT3B-stx1a pathway, not a side effect. In conclusion, KAT3B can positively regulate stx1a transcription in neurons, and increasing neuronal stx1a expression and 5-HTergic systems by a KAT3 activator consequently improves the low LI behavior in the stx1a ablation mouse model.
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Affiliation(s)
- Takahiro Nakayama
- Department of Medical Physiology, Kyorin University School of Medicine, Tokyo 181-8611, Japan.
| | - Akash K Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India; Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Toshiyuki Fukutomi
- Department of Pharmacology and Toxicology, Kyorin University School of Medicine, Tokyo 181-8611, Japan
| | - Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Yasuo Terao
- Department of Medical Physiology, Kyorin University School of Medicine, Tokyo 181-8611, Japan
| | - Hiroki Hamada
- Department of Life Science, Okayama University of Science, Okayama 700-0005, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Eswaramoorthy Muthusamy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India; Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Kimio Akagawa
- Department of Medical Physiology, Kyorin University School of Medicine, Tokyo 181-8611, Japan
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3
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Sondag D, de Kleijne FFJ, Castermans S, Chatzakis I, van Geffen M, Van't Veer C, van Heerde WL, Boltje TJ, Rutjes FPJT. Synthesis and Evaluation of Glycosyl Luciferins. Chemistry 2024; 30:e202302547. [PMID: 37849395 DOI: 10.1002/chem.202302547] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023]
Abstract
Measuring glycosidase activity is important to monitor any aberrations in carbohydrate hydrolase activity, but also for the screening of potential glycosidase inhibitors. To this end, synthetic substrates are needed which provide an enzyme-dependent read-out upon hydrolysis by the glycosidase. Herein, we present two new routes for the synthesis of caged luminescent carbohydrates, which can be used for determining glycosidase activity with a luminescent reporter molecule. The substrates were validated with glycosidase and revealed a clear linear range and enzyme-dependent signal upon the in situ generation of the luciferin moiety from the corresponding nitrile precursors. Besides, we showed that these compounds could directly be synthesized from unprotected glycosyl-α-fluorides in a two-step procedure with yields up to 75 %. The intermediate methyl imidate appeared a key intermediate which also reacted with d-cysteine to give the corresponding d-luciferin substrate rendering this a highly attractive method for synthesizing glycosyl luciferins in good yields.
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Affiliation(s)
- Daan Sondag
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Frank F J de Kleijne
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Sam Castermans
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Isa Chatzakis
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Mark van Geffen
- Enzyre BV, Novio Tech Campus, Transistorweg 5-i, 6534 AT, Nijmegen, The Netherlands
| | - Cornelis Van't Veer
- Enzyre BV, Novio Tech Campus, Transistorweg 5-i, 6534 AT, Nijmegen, The Netherlands
| | - Waander L van Heerde
- Enzyre BV, Novio Tech Campus, Transistorweg 5-i, 6534 AT, Nijmegen, The Netherlands
- Department of Haematology, Radboud University Medical Centre, Nijmegen, The Netherlands
- Haemophilia Treatment Centre, Nijmegen Eindhoven Maastricht (HTC-NEM), The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
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4
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Kim Y, Li H, Choi J, Boo J, Jo H, Hyun JY, Shin I. Glycosidase-targeting small molecules for biological and therapeutic applications. Chem Soc Rev 2023; 52:7036-7070. [PMID: 37671645 DOI: 10.1039/d3cs00032j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Glycosidases are ubiquitous enzymes that catalyze the hydrolysis of glycosidic linkages in oligosaccharides and glycoconjugates. These enzymes play a vital role in a wide variety of biological events, such as digestion of nutritional carbohydrates, lysosomal catabolism of glycoconjugates, and posttranslational modifications of glycoproteins. Abnormal glycosidase activities are associated with a variety of diseases, particularly cancer and lysosomal storage disorders. Owing to the physiological and pathological significance of glycosidases, the development of small molecules that target these enzymes is an active area in glycoscience and medicinal chemistry. Research efforts carried out thus far have led to the discovery of numerous glycosidase-targeting small molecules that have been utilized to elucidate biological processes as well as to develop effective chemotherapeutic agents. In this review, we describe the results of research studies reported since 2018, giving particular emphasis to the use of fluorescent probes for detection and imaging of glycosidases, activity-based probes for covalent labelling of these enzymes, glycosidase inhibitors, and glycosidase-activatable prodrugs.
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Affiliation(s)
- Yujun Kim
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hui Li
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Joohee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Jihyeon Boo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hyemi Jo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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5
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van der Gracht D, Rowland RJ, Roig-Zamboni V, Ferraz MJ, Louwerse M, Geurink PP, Aerts JMFG, Sulzenbacher G, Davies GJ, Overkleeft HS, Artola M. Fluorescence polarisation activity-based protein profiling for the identification of deoxynojirimycin-type inhibitors selective for lysosomal retaining alpha- and beta-glucosidases. Chem Sci 2023; 14:9136-9144. [PMID: 37655021 PMCID: PMC10466331 DOI: 10.1039/d3sc01021j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/02/2023] [Indexed: 09/02/2023] Open
Abstract
Lysosomal exoglycosidases are responsible for processing endocytosed glycans from the non-reducing end to produce the corresponding monosaccharides. Genetic mutations in a particular lysosomal glycosidase may result in accumulation of its particular substrate, which may cause diverse lysosomal storage disorders. The identification of effective therapeutic modalities to treat these diseases is a major yet poorly realised objective in biomedicine. One common strategy comprises the identification of effective and selective competitive inhibitors that may serve to stabilize the proper folding of the mutated enzyme, either during maturation and trafficking to, or residence in, endo-lysosomal compartments. The discovery of such inhibitors is greatly aided by effective screening assays, the development of which is the focus of the here-presented work. We developed and applied fluorescent activity-based probes reporting on either human GH30 lysosomal glucosylceramidase (GBA1, a retaining β-glucosidase) or GH31 lysosomal retaining α-glucosidase (GAA). FluoPol-ABPP screening of our in-house 358-member iminosugar library yielded compound classes selective for either of these enzymes. In particular, we identified a class of N-alkyldeoxynojirimycins that inhibit GAA, but not GBA1, and that may form the starting point for the development of pharmacological chaperone therapeutics for the lysosomal glycogen storage disease that results from genetic deficiency in GAA: Pompe disease.
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Affiliation(s)
- Daniël van der Gracht
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Rhianna J Rowland
- York Structural Biology Laboratory, Department of Chemistry, The University of York York YO10 5DD UK
| | - Véronique Roig-Zamboni
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University Marseille France
| | - Maria J Ferraz
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Max Louwerse
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Centre 2333 ZC Leiden The Netherlands
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Gerlind Sulzenbacher
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University Marseille France
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York York YO10 5DD UK
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
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6
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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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7
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In silico modelling of the function of disease-related CAZymes. Essays Biochem 2023; 67:355-372. [PMID: 36912236 PMCID: PMC10154626 DOI: 10.1042/ebc20220218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 03/14/2023]
Abstract
In silico modelling of proteins comprises a diversity of computational tools aimed to obtain structural, electronic, and/or dynamic information about these biomolecules, capturing mechanistic details that are challenging to experimental approaches, such as elusive enzyme-substrate complexes, short-lived intermediates, and reaction transition states (TS). The present article gives the reader insight on the use of in silico modelling techniques to understand complex catalytic reaction mechanisms of carbohydrate-active enzymes (CAZymes), along with the underlying theory and concepts that are important in this field. We start by introducing the significance of carbohydrates in nature and the enzymes that process them, CAZymes, highlighting the conformational flexibility of their carbohydrate substrates. Three commonly used in silico methods (classical molecular dynamics (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and enhanced sampling techniques) are described for nonexpert readers. Finally, we provide three examples of the application of these methods to unravel the catalytic mechanisms of three disease-related CAZymes: β-galactocerebrosidase (GALC), responsible for Krabbe disease; α-mannoside β-1,6-N-acetylglucosaminyltransferase V (MGAT5), involved in cancer; and O-fucosyltransferase 1 (POFUT1), involved in several human diseases such as leukemia and the Dowling-Degos disease.
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8
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Takeoka M, Hoki Y, Yoshinaka T, Hirano K, Mitsui Y, Doi T, Takemura A, Asano T, Katoh R, Nose A, Kozaki D. Multi-Functional Separation Mode-Ion Chromatography Using L-Pyroglutamic Acid Eluent for Simultaneous Determination of Sugars, Organic Acids, and Ethanol during Multiple Parallel Fermentation of Rice Wine. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2023. [DOI: 10.1080/03610470.2022.2158437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Marino Takeoka
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi, Japan
| | | | - Taichi Yoshinaka
- Department of Brewing, Tsukasa Botan Brewing Company, Limited, Kochi, Japan
| | - Kentarou Hirano
- Department of Brewing, Tsukasa Botan Brewing Company, Limited, Kochi, Japan
| | - Yuta Mitsui
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi, Japan
| | | | - Akihiko Takemura
- Department of Brewing, Tsukasa Botan Brewing Company, Limited, Kochi, Japan
| | - Tohru Asano
- Department of Brewing, Tsukasa Botan Brewing Company, Limited, Kochi, Japan
| | | | - Akira Nose
- Department of Nutritional Science, Faculty of Human Ecology, Yasuda Women’s University, Hiroshima, Japan
| | - Daisuke Kozaki
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi, Japan
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9
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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10
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Li P, Wang X, Zhang C, Xu D. Processive binding mechanism of Cel9G from Clostridium cellulovorans: molecular dynamics and free energy landscape investigations. Phys Chem Chem Phys 2023; 25:646-657. [DOI: 10.1039/d2cp04830b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The processive binding mechanism of cellulose by Cel9G from C. cellulovorans was investigated by MD and metadynamics simulations.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Chunchun Zhang
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
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11
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Manta S, Kollatos N. Unusual seven-membered ring sugars and nucleosides: synthesis and biological properties. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:407-425. [PMID: 36451584 DOI: 10.1080/15257770.2022.2151623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Methods of the synthesis and the investigation of the properties of unnatural seven-memebered cyclic sugars and nucleosides, are of high interest. Septanoses provide conformationally more flexible sugars and due to their similarity to natural carbohydrates they have interesting and potentially useful physical, chemical, and biological properties. Additionally, nucleosides with seven-membered sugar moiety are commonly found in natural products and biologically active molecules. Modification of such nucleosides hold great promise as therapeutic agents. The present review describes the chemical synthesis and biological properties of septanoses as well as nucleosides containing septanosyl moieties.
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Affiliation(s)
- Stella Manta
- Department of Biochemistry and Biotechnology, Laboratory of Bioorganic Chemistry, University of Thessaly, Larissa, Greece
| | - Nikolaos Kollatos
- Department of Biochemistry and Biotechnology, Laboratory of Bioorganic Chemistry, University of Thessaly, Larissa, Greece
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12
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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13
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Li P, Shi M, Wang X, Xu D. QM/MM investigation of the catalytic mechanism of processive endoglucanase Cel9G from Clostridium cellulovorans. Phys Chem Chem Phys 2022; 24:11919-11930. [PMID: 35514276 DOI: 10.1039/d2cp00593j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Carbohydrate degradation catalyzed by glucoside hydrolases (GHs) is a major mechanism in biomass conversion. GH family 9 endoglucanase (Cel9G) from Clostridium cellulovorans, a typical multimodular enzyme, contains a catalytic domain closely linked to a family 3c carbohydrate-binding module (CBM3c). Unlike the conventional behavior proposed for other carbohydrate-binding modules, CBM3c has a direct impact on catalytic activity. In this work, extensive molecular dynamics (MD) simulations were employed to clarify the functional role of CBM3c. Furthermore, the detailed catalytic mechanism of Cel9G was investigated at the atomistic level using the combined quantum mechanical and molecular mechanical (QM/MM) method. Based on these simulations, owing to the rigidity of the peptide linker, CBM3c may affect the enzymatic activity via direct interactions with alpha helix 4 of GH9, especially with the K123 and H125 residues. In addition, using cellohexaose as a substrate, the QM/MM MD simulations confirmed that this enzyme can cleave the β-1,4-glycosidic linkage via an inverting mechanism. An oxocarbenium ion-like transition state was located with a barrier height of 19.6 kcal mol-1. Furthermore, the G(-1) pyranose unit preferentially adopted a distorted 1S5/4H5 conformer in the enzyme-substrate complex. For the cleavage of the glycosidic bond, we were able to identify a plausible route (1S5/4H5 → [4H5/4E]# → 4C1) from the reactant to the product at the G(-1) site.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
| | - Mingsong Shi
- State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
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14
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Efficient 2-Step Enzymatic Cascade for the Bioconversion of Oleuropein into Hydroxytyrosol. Antioxidants (Basel) 2022; 11:antiox11020260. [PMID: 35204142 PMCID: PMC8868057 DOI: 10.3390/antiox11020260] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/20/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Among the plant bioactive components, oleuropein (OLE) is the most abundant phenolic compound in all parts of olive trees (Olea europaea L.), particularly concentrated in olive leaves. It has been shown to present various remarkable biological actions, such as antimicrobial, antioxidant, anticancer and anti-inflammatory ones. On the other hand, hydroxytyrosol (HT), the main degradation product of OLE, is considered one of the most powerful antioxidant agents, with higher beneficial properties than the OLE parent compound. In this work, oleuropein was efficiently transformed into hydroxytyrosol using a 2-step biotransformation involving a thermo-halophilic β-glucosidase from Alicyclobacillus herbarius (Ahe), which gave the corresponding aglycone with complete conversion (>99%) and rapid reaction times (30 min), and an acyltransferase from Mycobacterium smegmatis (MsAcT), here employed for the first time for its hydrolytic activity. After cascade completion, hydroxytyrosol was obtained in excellent yield (>99% m.c., 96% isolated yield) in 24 h. Starting from a natural substrate and employing enzymatic approaches, the final hydroxytyrosol can be claimed and commercialized as natural too, thus increasing its market value.
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15
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Blériot Y, Auberger N, Désiré J. Sugar-Derived Amidines and Congeners: Structures, Glycosidase Inhibition and Applications. Curr Med Chem 2021; 29:1271-1292. [PMID: 34951354 DOI: 10.2174/0929867329666211222164545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/16/2021] [Accepted: 10/22/2021] [Indexed: 11/22/2022]
Abstract
Glycosidases, the enzymes responsible for the breakdown of glycoconjugates including di-, oligo- and polysaccharides are ubiquitous through all kingdoms of life. The extreme chemical stability of the glycosidic bond combined with the catalytic rates achieved by glycosidases makes them among the most proficient of all enzymes.
Given their multitude of roles in vivo, inhibition of these enzymes is highly attractive with potential in the treatment of a vast array of pathologies ranging from lysosomal storage and diabetes to viral infections. Therefore great efforts have been invested in the last three decades to design and synthesize inhibitors of glycosidases leading to a number of drugs currently on the market. Amongst the vast array of structures that have been disclosed, sugars incorporating an amidine moiety have been the focus of many research groups around the world because of their glycosidase transition state-like structure. In this review we report and discuss the structure, the inhibition profile and the use of these molecules including related structural congeners as transition state analogs.
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Affiliation(s)
- Yves Blériot
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "OrgaSynth", Groupe Glycochimie 4 rue Michel Brunet, 86073 Poitiers cedex 9. France
| | - Nicolas Auberger
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "OrgaSynth", Groupe Glycochimie 4 rue Michel Brunet, 86073 Poitiers cedex 9. France
| | - Jérôme Désiré
- Université de Poitiers, IC2MP, UMR CNRS 7285, Equipe "OrgaSynth", Groupe Glycochimie 4 rue Michel Brunet, 86073 Poitiers cedex 9. France
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16
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Teze D, Zhao J, Wiemann M, Kazi ZGA, Lupo R, Zeuner B, Vuillemin M, Rønne ME, Carlström G, Duus JØ, Sanejouand YH, O'Donohue MJ, Nordberg Karlsson E, Fauré R, Stålbrand H, Svensson B. Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases. Chemistry 2021; 27:10323-10334. [PMID: 33914359 DOI: 10.1002/chem.202100110] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6-12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d/l-, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.
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Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Jiao Zhao
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Mathias Wiemann
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Zubaida G A Kazi
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Rossana Lupo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Birgitte Zeuner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Marlène Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Mette E Rønne
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Göran Carlström
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Jens Ø Duus
- Department of Chemistry, Technical University of Denmark, Kemitorvet, bulding 207, DK-2800, Kongens Lyngby, Denmark
| | - Yves-Henri Sanejouand
- UFIP, UMR 6286, Université de Nantes, CNRS, 2, chemin de la Houssiniere, Nantes, France
| | - Michael J O'Donohue
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | | | - Régis Fauré
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Henrik Stålbrand
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
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17
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Iftikhar M, Lu Y, Zhou M. An overview of therapeutic potential of N-alkylated 1-deoxynojirimycin congeners. Carbohydr Res 2021; 504:108317. [PMID: 33932806 DOI: 10.1016/j.carres.2021.108317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 01/13/2023]
Abstract
Polyhydroxylated alkaloids display a wide range of biological activities, suggesting their use in the treatment of various diseases. Their most famous representative, 1-deoxynojirimycin (DNJ), is a natural product that shows α- and β-glucosidase inhibition. This molecule has been since converted into two clinically approved drugs i.e., Zavesca® and Glyset®, targeting type I Gaucher's disease and type II diabetes mellitus, respectively. This review examines the therapeutic potential of important DNJ congeners reported in last decade and presents concise mechanism of glycosidase inhibition. A brief overview of substituents conjugation's impact on DNJ scaffold (including N-alkylated DNJ derivatives, mono-valent, di-valent and multivalent DNJ congeners, N-[5-(adamantan-1-yl-methoxy)-pentyl]-1-deoxynojirimycin (AMP-DNM) look alike DNJ based lipophilic derivatives, AMP-DNM based neoglycoconjugates, DNJ click derivatives with varying carboxylic acids and aromatic moieties, conjugates of DNJ and glucose, and N-bridged DNJ analogues) towards various enzymes such as α/β glucosidase, porcine trehalase, as F508del-CFTR correctors, α-mannosidase, human placental β-glucocerebrosidase, N370S β-GCase, α-amylase and insect trehalase as potent and selective inhibitors have been discussed with potential bioactivities, which can provide inspiration for future studies.
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Affiliation(s)
- Mehwish Iftikhar
- School of Chemical Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu, 210094, PR China
| | - Yinghong Lu
- School of Chemical Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu, 210094, PR China
| | - Min Zhou
- School of Chemical Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu, 210094, PR China.
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18
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Delgado L, Heckmann CM, Di Pisa F, Gourlay L, Paradisi F. Release of Soybean Isoflavones by Using a β-Glucosidase from Alicyclobacillus herbarius. Chembiochem 2021; 22:1223-1231. [PMID: 33237595 PMCID: PMC8048572 DOI: 10.1002/cbic.202000688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/24/2020] [Indexed: 12/17/2022]
Abstract
β-Glucosidases are used in the food industry to hydrolyse glycosidic bonds in complex sugars, with enzymes sourced from extremophiles better able to tolerate the process conditions. In this work, a novel β-glycosidase from the acidophilic organism Alicyclobacillus herbarius was cloned and heterologously expressed in Escherichia coli BL21(DE3). AheGH1 was stable over a broad range of pH values (5-11) and temperatures (4-55 °C). The enzyme exhibited excellent tolerance to fructose and good tolerance to glucose, retaining 65 % activity in the presence of 10 % (w/v) glucose. It also tolerated organic solvents, some of which appeared to have a stimulating effect, in particular ethanol with a 1.7-fold increase in activity at 10 % (v/v). The enzyme was then applied for the cleavage of isoflavone from isoflavone glucosides in an ethanolic extract of soy flour, to produce soy isoflavones, which constitute a valuable food supplement, full conversion was achieved within 15 min at 30 °C.
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Affiliation(s)
- Lidia Delgado
- University of Nottingham, School of ChemistryDepartment of Chemical BiologyUniversity ParkNottinghamNG7 2RDUK
| | - Christian M. Heckmann
- University of Nottingham, School of ChemistryDepartment of Chemical BiologyUniversity ParkNottinghamNG7 2RDUK
| | - Flavio Di Pisa
- Dipartimento di BioscienzeUniversità di MilanoVia Celoria 2620133MilanItaly
| | - Louise Gourlay
- Dipartimento di BioscienzeUniversità di MilanoVia Celoria 2620133MilanItaly
| | - Francesca Paradisi
- University of Nottingham, School of ChemistryDepartment of Chemical BiologyUniversity ParkNottinghamNG7 2RDUK
- University of BernDepartment of Chemistry and BiochemistryFreiestrasse 33012BernSwitzerland
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19
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Jafari S, Ryde U, Irani M. QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues. J Chem Theory Comput 2021; 17:1822-1841. [PMID: 33543623 PMCID: PMC8023669 DOI: 10.1021/acs.jctc.0c01121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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Myrosinase from Sinapis alba hydrolyzes glycosidic
bonds of β-d-S-glucosides. The enzyme
shows an enhanced activity in the presence of l-ascorbic
acid. In this work, we employed combined quantum mechanical and molecular
mechanical (QM/MM) calculations and molecular dynamics simulations
to study the catalytic reaction of wild-type myrosinase and its E464A,
Q187A, and Q187E mutants. Test calculations show that a proper QM
region to study the myrosinase reaction must contain the whole substrate,
models of Gln-187, Glu-409, Gln-39, His-141, Asn-186, Tyr-330, Glu-464,
Arg-259, and a water molecule. Furthermore, to make the deglycosylation
step possible, Arg-259 must be charged, Glu-464 must be protonated
on OE2, and His-141 must be protonated on the NE2 atom. The results
indicate that assigning proper protonation states of the residues
is more important than the size of the model QM system. Our model
reproduces the anomeric retaining characteristic of myrosinase and
also reproduces the experimental fact that ascorbate increases the
rate of the reaction. A water molecule in the active site, positioned
by Gln-187, helps the aglycon moiety of the substrate to stabilize
the buildup of negative charge during the glycosylation reaction and
this in turn makes the moiety a better leaving group. The water molecule
also lowers the glycosylation barrier by ∼9 kcal/mol. The results
indicate that the Q187E and E464A mutants but not the Q187A mutant
can perform the glycosylation step. However, the energy profiles for
the deglycosylation step of the mutants are not similar to that of
the wild-type enzyme. The Glu-464 residue lowers the barriers of the
glycosylation and deglycosylation steps. The ascorbate ion can act
as a general base in the reaction of the wild-type enzyme only if
the Glu-464 and His-141 residues are properly protonated.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
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20
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Producing natural vanilla extract from green vanilla beans using a β-glucosidase from Alicyclobacillus acidiphilus. J Biotechnol 2021; 329:21-28. [PMID: 33508335 DOI: 10.1016/j.jbiotec.2021.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
Current methods for the production of natural vanilla extract are long and tedious, and the efficiency of the vanillin extraction is usually conditioned by different factors during the traditional curing process (temperatures and weather conditions). As an important fraction of vanillin is present in the form of glucovanillin in green beans, endogenous β-glucosidases contribute to its hydrolysis; however, these enzymes lose efficiency during the curing process. The use of extremophilic organisms as a source of an appropriate exogenous enzyme can offer a valid alternative when producing natural vanillin. Here, a β-glucosidase from the thermo-acidophilic organism Alicyclobacillus acidiphilus (AacGH1) was cloned, expressed in E. coli BL21, and fully characterized in respect to both function and crystal structure. Notably, AacGH1 was stable at a temperature up to 50 °C and exhibited good tolerance to glucose, fructose and organic solvents, in particular it maintained full activity in the presence of up to 20 % (v/v) ethanol. The enzyme was then successfully applied to an ethanol-water (20 % (v/v)) extract of green vanilla beans and the complete hydrolysis of glucovanillin (1.7 mM) to vanillin, and other flavour compounds commonly found in vanilla, was achieved using 0.5 mg/mL of enzyme in just 15 min at 30 °C.
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21
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Blériot Y. Contributing to the Study of Enzymatic and Chemical Glycosyl Transfer Through the Observation and Mimicry of Glycosyl Cations. SYNTHESIS-STUTTGART 2020. [DOI: 10.1055/s-0040-1706073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
AbstractThis account describes our efforts dedicated to: 1) the design of glycomimetics aimed at targeting therapeutically relevant carbohydrate processing enzymes, and 2) the observation, characterization, and exploitation of glycosyl cations as a tool for studying the glycosylation reaction. These findings have brought important data regarding this key ionic species as well as innovative strategies to access iminosugars of interest.1 Introduction2 The Glycosyl Cation, A Central Species in Glycosciences2.1 A Selection of the Strategies Developed so far to Gain Insights into Glycosyl Cations Structure2.2 When Superacids Meet Carbohydrates3 Chemical Probes to Gain Insights into the Pseudorotational Itinerary of Glycosides During Glycosidic Bond Hydrolysis3.1 Conformationally Locked Glycosides3.1.1 The Xylopyranose Case3.1.2 The Mannopyranose Case3.2 Conformationally Flexible Iminosugars3.2.1 Nojirimycin Ring Homologues3.2.2 Noeuromycin Ring Homologues3.2.3 Seven-Membered Iminosugar C-Glycosides4 N-Acetyl-d-glucosamine Mimics5 Ring Contraction: A Useful Tool to Increase Iminosugar’s Structural Diversity6 Regioselective Deprotection of Iminosugar C-Glycosides to Introduce Diversity at C2 Position7 Conclusion
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22
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Nin-Hill A, Rovira C. The Catalytic Reaction Mechanism of the β-Galactocerebrosidase Enzyme Deficient in Krabbe Disease. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alba Nin-Hill
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) & Institut de Quı́mia Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) & Institut de Quı́mia Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
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23
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Matassini C, Warren J, Wang B, Goti A, Cardona F, Morrone A, Bols M. Imino‐ and Azasugar Protonation Inside Human Acid β‐Glucosidase, the Enzyme that is Defective in Gaucher Disease. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Camilla Matassini
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 13 50019 Sesto Fiorentino (FI) Italy
| | - Julia Warren
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Bo Wang
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Andrea Goti
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 13 50019 Sesto Fiorentino (FI) Italy
| | - Francesca Cardona
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 13 50019 Sesto Fiorentino (FI) Italy
| | - Amelia Morrone
- Paediatric Neurology Unit and Laboratories, Neuroscience Department Meyer Children's Hospital, and Department of Neurosciences Pharmacology and Child Health University of Florence Viale Pieraccini 24 50139 Firenze Italy
| | - Mikael Bols
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
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24
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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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25
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Matassini C, Warren J, Wang B, Goti A, Cardona F, Morrone A, Bols M. Imino- and Azasugar Protonation Inside Human Acid β-Glucosidase, the Enzyme that is Defective in Gaucher Disease. Angew Chem Int Ed Engl 2020; 59:10466-10469. [PMID: 32191378 DOI: 10.1002/anie.202002850] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Indexed: 12/28/2022]
Abstract
Gaucher disease is caused by mutations in human acid β-glucosidase or glucocerebrosidase (GCase), the enzyme responsible for hydrolysis of glucosyl ceramide in the lysosomes. Imino- and azasugars such as 1-deoxynojirimycin and isofagomine are strong inhibitors of the enzyme and are of interest in pharmacological chaperone therapy of the disease. Despite several crystal structures of the enzyme with the imino- and azasugars bound in the active site having been resolved, the actual acid-base chemistry of the binding is not known. In this study we show, using photoinduced electron transfer (PET), that 1-deoxynojirimycin and isofagomine derivatives are protonated by human acid β-glucosidase when bound, even if they are completely unprotonated outside the enzyme. While isofagomine derivative protonation to some degree was foreshadowed by earlier crystal structures, 1-deoxynojirimycin derivatives were not believed to act as basic amines in the enzyme.
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Affiliation(s)
- Camilla Matassini
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino (FI), Italy
| | - Julia Warren
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Bo Wang
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Andrea Goti
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino (FI), Italy
| | - Francesca Cardona
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino (FI), Italy
| | - Amelia Morrone
- Paediatric Neurology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, and Department of Neurosciences, Pharmacology and Child Health, University of Florence, Viale Pieraccini 24, 50139, Firenze, Italy
| | - Mikael Bols
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
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26
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Awolade P, Cele N, Kerru N, Gummidi L, Oluwakemi E, Singh P. Therapeutic significance of β-glucuronidase activity and its inhibitors: A review. Eur J Med Chem 2020; 187:111921. [PMID: 31835168 PMCID: PMC7111419 DOI: 10.1016/j.ejmech.2019.111921] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 01/02/2023]
Abstract
The emergence of disease and dearth of effective pharmacological agents on most therapeutic fronts, constitutes a major threat to global public health and man's existence. Consequently, this has created an exigency in the search for new drugs with improved clinical utility or means of potentiating available ones. To this end, accumulating empirical evidence supports molecular target therapy as a plausible egress and, β-glucuronidase (βGLU) - a lysosomal acid hydrolase responsible for the catalytic deconjugation of β-d-glucuronides has emerged as a viable molecular target for several therapeutic applications. The enzyme's activity level in body fluids is also deemed a potential biomarker for the diagnosis of some pathological conditions. Moreover, due to its role in colon carcinogenesis and certain drug-induced dose-limiting toxicities, the development of potent inhibitors of βGLU in human intestinal microbiota has aroused increased attention over the years. Nevertheless, although our literature survey revealed both natural products and synthetic scaffolds as potential inhibitors of the enzyme, only few of these have found clinical utility, albeit with moderate to poor pharmacokinetic profile. Hence, in this review we present a compendium of exploits in the present millennium directed towards the inhibition of βGLU. The aim is to proffer a platform on which new scaffolds can be modelled for improved βGLU inhibitory potency and the development of new therapeutic agents in consequential.
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Affiliation(s)
- Paul Awolade
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Nosipho Cele
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Nagaraju Kerru
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Lalitha Gummidi
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Ebenezer Oluwakemi
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Parvesh Singh
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa.
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Zavyalov AV, Rykov SV, Lunina NA, Sushkova VI, Yarotsky SV, Berezina OV. Plant Polysaccharide Xyloglucan and Enzymes That Hydrolyze It (Review). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019070148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Wu L, Davies GJ. An Overview of the Structure, Mechanism and Specificity of Human Heparanase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1221:139-167. [PMID: 32274709 DOI: 10.1007/978-3-030-34521-1_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The retaining endo-β-D-glucuronidase Heparanase (HPSE) is the primary mammalian enzyme responsible for breakdown of the glycosaminoglycan heparan sulfate (HS). HPSE activity is essential for regulation and turnover of HS in the extracellular matrix, and its activity affects diverse processes such as inflammation, angiogenesis and cell migration. Aberrant heparanase activity is strongly linked to cancer metastasis, due to structural breakdown of extracellular HS networks and concomitant release of sequestered HS-binding growth factors. A full appreciation of HPSE activity in health and disease requires a structural understanding of the enzyme, and how it engages with its HS substrates. This chapter summarizes key findings from the recent crystal structures of human HPSE and its proenzyme. We present details regarding the 3-dimensional protein structure of HPSE and the molecular basis for its interaction with HS substrates of varying sulfation states. We also examine HPSE in a wider context against related β-D-glucuronidases from other species, highlighting the structural features that control exo/endo - glycosidase selectivity in this family of enzymes.
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Affiliation(s)
- Liang Wu
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, UK.
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, UK
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29
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Shen Y, Li Z, Huo YY, Bao L, Gao B, Xiao P, Hu X, Xu XW, Li J. Structural and Functional Insights Into CmGH1, a Novel GH39 Family β-Glucosidase From Deep-Sea Bacterium. Front Microbiol 2019; 10:2922. [PMID: 31921083 PMCID: PMC6933502 DOI: 10.3389/fmicb.2019.02922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/04/2019] [Indexed: 01/07/2023] Open
Abstract
Glucosidases play key roles in many diseases and are limiting enzymes during cellulose degradation, which is an important part of global carbon cycle. Here, we identified a novel β-glucosidase, CmGH1, isolated from marine bacterium Croceicoccus marinus E4A9T. In spite of its high sequence and structural similarity with β-xylosidase family members, CmGH1 had enzymatic activity toward p-nitrophenyl-β-D-glucopyranoside (p-NPG) and cellobiose. The Km and Kcat values of CmGH1 toward p-NPG were 0.332 ± 0.038 mM and 2.15 ± 0.081 min–1, respectively. CmGH1 was tolerant to high concentration salts, detergents, as well as many kinds of organic solvents. The crystal structure of CmGH1 was resolved with a 1.8 Å resolution, which showed that CmGH1 was composed of a canonical (α/β)8-barrel catalytic domain and an auxiliary β-sandwich domain. Although no canonical catalytic triad residues were found in CmGH1, structural comparison and mutagenesis analysis suggested that residues Gln157 and Tyr264 of CmGH1 were the active sites. Mutant Q157E significantly increased its hydrolase activity up to 15-fold, whereas Y264E totally abolished its enzymatic activity. These results might provide new insights into understanding the different catalytic mechanism during evolution for β-glucosidases and β-xylosidases.
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Affiliation(s)
- Yanfang Shen
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Luyao Bao
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Baocai Gao
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Peng Xiao
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Xiaojian Hu
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
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Panwar D, Shubhashini A, Chaudhari SR, Prashanth KVH, Kapoor M. GH36 α-galactosidase from Lactobacillus plantarum WCFS1 synthesize Gal-α-1,6 linked prebiotic α-galactooligosaccharide by transglycosylation. Int J Biol Macromol 2019; 144:334-342. [PMID: 31816385 DOI: 10.1016/j.ijbiomac.2019.12.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 02/08/2023]
Abstract
α-Galactosidases are potent industrial glycoside hydrolases which are relatively less explored for their transglycosylation potential, especially from Lactobacillus genera. A GH36 α-galactosidase from Lactobacillus plantarum WCFS1 was cloned and over expressed in Hi-control Escherichia coli BL21(DE3). Ni-NTA affinity gel chromatography resulted in purified α-galactosidase (LpαG; specific activity 3077.35 U mg-1) having a monomeric weight of ~80 kDa with 29.3% yield. Size exclusion chromatography of LpαG showed native molecular mass of ~240.5 kDa. LpαG displayed optimum activity at pH 6 and 37 °C. The Km,Vmax and kcat/Km of LpαG towards pNPαGal were found to be 0.93 mM and 714.3 μmol ml-1 min-1 and 12,075 s-1 mM-1, respectively. LpαG displayed maximum transglycosylation activity towards melibiose substrate (as both donor and acceptor) and synthesized majorly a trisaccharide with 0.26 mg ml-1 yield. Nuclear magnetic resonance (NMR) characterization revealed that trisaccharide consist of only single species of α-linked galactooligosaccharide (manninotriose; α-d-Galp-(1 → 6)-α-d-Galp-(1 → 6)-d-Glcp) with α-(1 → 6) regioselectivity. Manninotriose displayed prebiotic property by supporting the growth of probiotic L. plantarum WCFS1 and Bifidobacteria adolescentis DSM 20083.
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Affiliation(s)
- Deepesh Panwar
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India
| | - A Shubhashini
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India
| | - Sachin Rama Chaudhari
- Department of Spices and Flavour Sciences, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India
| | - K V Harish Prashanth
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India
| | - Mukesh Kapoor
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India.
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31
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Broza YY, Zhou X, Yuan M, Qu D, Zheng Y, Vishinkin R, Khatib M, Wu W, Haick H. Disease Detection with Molecular Biomarkers: From Chemistry of Body Fluids to Nature-Inspired Chemical Sensors. Chem Rev 2019; 119:11761-11817. [DOI: 10.1021/acs.chemrev.9b00437] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yoav Y. Broza
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Xi Zhou
- School of Natural and Applied Sciences, Northwestern Polytechnical University, Xi’an 710072, P.R. China
| | - Miaomiao Yuan
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518033, P.R. China
| | - Danyao Qu
- School of Advanced Materials and Nanotechnology, Interdisciplinary Research Center of Smart Sensors, Xidian University, Shaanxi 710126, P.R. China
| | - Youbing Zheng
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Rotem Vishinkin
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Muhammad Khatib
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Weiwei Wu
- School of Advanced Materials and Nanotechnology, Interdisciplinary Research Center of Smart Sensors, Xidian University, Shaanxi 710126, P.R. China
| | - Hossam Haick
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 3200003, Israel
- School of Advanced Materials and Nanotechnology, Interdisciplinary Research Center of Smart Sensors, Xidian University, Shaanxi 710126, P.R. China
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32
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Coines J, Raich L, Rovira C. Modeling catalytic reaction mechanisms in glycoside hydrolases. Curr Opin Chem Biol 2019; 53:183-191. [PMID: 31731209 DOI: 10.1016/j.cbpa.2019.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 01/21/2023]
Abstract
Modeling catalysis in carbohydrate-active enzymes is a daunting challenge because of the high flexibility and diversity of both enzymes and carbohydrates. Glycoside hydrolases (GHs) are an illustrative example, where conformational changes and subtle interactions have been shown to be critical for catalysis. GHs have pivotal roles in industry (e.g. biofuel or detergent production) and biomedicine (e.g. targets for cancer and diabetes), and thus, a huge effort is devoted to unveil their molecular mechanisms. Besides experimental techniques, computational methods have served to provide an in-depth understanding of GH mechanisms, capturing complex reaction coordinates and the conformational itineraries that substrates follow during the whole catalytic pathway, providing a framework that ultimately may assist the engineering of these enzymes and the design of new inhibitors.
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Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain
| | - Lluís Raich
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Inorgànica I Orgànica (secció de Química Orgànica) and Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona, Martí I Franquès 1 08028 Barcelona, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA) Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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33
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Montalvillo-Jiménez L, Santana AG, Corzana F, Jiménez-Osés G, Jiménez-Barbero J, Gómez AM, Asensio JL. Impact of Aromatic Stacking on Glycoside Reactivity: Balancing CH/π and Cation/π Interactions for the Stabilization of Glycosyl-Oxocarbenium Ions. J Am Chem Soc 2019; 141:13372-13384. [PMID: 31390207 DOI: 10.1021/jacs.9b03285] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Carbohydrate/aromatic stacking represents a recurring key motif for the molecular recognition of glycosides, either by protein binding domains, enzymes, or synthetic receptors. Interestingly, it has been proposed that aromatic residues might also assist in the formation/cleavage of glycosidic bonds by stabilizing positively charged oxocarbenium-like intermediates/transition states through cation/π interactions. While the significance of aromatic stacking on glycoside recognition is well stablished, its impact on the reactivity of glycosyl donors is yet to be explored. Herein, we report the first experimental study on this relevant topic. Our strategy is based on the design, synthesis, and reactivity evaluation of a large number of model systems, comprising a wide range of glycosidic donor/aromatic complexes. Different stacking geometries and dynamic features, anomeric leaving groups, sugar configurations, and reaction conditions have been explicitly considered. The obtained results underline the opposing influence exerted by van der Waals and Coulombic forces on the reactivity of the carbohydrate/aromatic complex: depending on the outcome of this balance, aromatic platforms can indeed exert a variety of effects, stretching from reaction inhibition all the way to rate enhancements. Although aromatic/glycosyl cation contacts are highly dynamic, the conclusions of our study suggest that aromatic assistance to glycosylation processes must indeed be feasible, with far reaching implications for enzyme engineering and organocatalysis.
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Affiliation(s)
| | - Andrés G Santana
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
| | - Francisco Corzana
- Departamento Quı́mica and Centro de Investigación en Sı́ntesis Quı́mica , Universidad de La Rioja , 26006 Logroño , Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) , 48160 Derio , Spain
| | - Jesús Jiménez-Barbero
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) , 48160 Derio , Spain.,Basque Foundation for Science, Ikerbasque , 48013 Bilbo , Spain
| | - Ana M Gómez
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
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34
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Irsheid L, Wehler T, Borek C, Kiefer W, Brenk R, Ortiz-Soto ME, Seibel J, Schirmeister T. Identification of a potential allosteric site of Golgi α-mannosidase II using computer-aided drug design. PLoS One 2019; 14:e0216132. [PMID: 31067280 PMCID: PMC6505943 DOI: 10.1371/journal.pone.0216132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/15/2019] [Indexed: 11/30/2022] Open
Abstract
Golgi α-mannosidase II (GMII) is a glycoside hydrolase playing a crucial role in the N-glycosylation pathway. In various tumour cell lines, the distribution of N-linked sugars on the cell surface is modified and correlates with the progression of tumour metastasis. GMII therefore is a possible molecular target for anticancer agents. Here, we describe the identification of a non-competitive GMII inhibitor using computer-aided drug design methods including identification of a possible allosteric binding site, pharmacophore search and virtual screening.
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Affiliation(s)
- Lina Irsheid
- Institute of Pharmacy and Biochemistry, University of Mainz, Mainz, Germany
| | - Thomas Wehler
- Institute of Pharmacy and Biochemistry, University of Mainz, Mainz, Germany
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Christoph Borek
- Institute of Pharmacy and Biochemistry, University of Mainz, Mainz, Germany
| | - Werner Kiefer
- Institute of Pharmacy and Biochemistry, University of Mainz, Mainz, Germany
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmacy and Biochemistry, University of Mainz, Mainz, Germany
- * E-mail:
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35
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Compain P. Multivalent Effect in Glycosidase Inhibition: The End of the Beginning. CHEM REC 2019; 20:10-22. [PMID: 30993894 DOI: 10.1002/tcr.201900004] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/15/2019] [Indexed: 12/21/2022]
Abstract
Glycosidases are ubiquitous enzymes involved in a diversity of key biological processes such as energy uptake or cell wall degradation. The design of specific glycosidase inhibitors has been therefore the subject of intense research efforts in academia and pharmaceutical industry. However, until recently, the study of the impact of multivalency on glycosidase inhibition was almost completely neglected. The following account will review our ten year journey on the design of multivalent glycomimetics within our research group, from the discovery of the first strong multivalent effect in glycosidase inhibition to the high-resolution crystal structures of Jack bean α-mannosidase in complex with the multimeric inhibitor displaying the largest binding enhancements reported so far.
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Affiliation(s)
- Philippe Compain
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Univ. de Strasbourg, Univ. de Haute-Alsace, CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67000, Strasbourg, France
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36
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Synthesis of N-benzyl substituted 1,4-imino-l-lyxitols with a basic functional group as selective inhibitors of Golgi α-mannosidase IIb. Bioorg Chem 2019; 83:424-431. [DOI: 10.1016/j.bioorg.2018.10.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022]
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Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning. Proc Natl Acad Sci U S A 2019; 116:5086-5095. [PMID: 30808805 DOI: 10.1073/pnas.1818411116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional GCase leads to the accumulation of its lipid substrates in lysosomes, causing Gaucher disease, an autosomal recessive disorder that displays profound genotype-phenotype nonconcordance. More than 250 disease-causing mutations in GBA1, the gene encoding GCase, have been discovered, although only one of these, N370S, causes 70% of disease. Here, we have used a knowledge-based docking protocol that considers experimental data of protein-protein binding to generate a complex between GCase and its known facilitator protein saposin C (SAPC). Multiscale molecular-dynamics simulations were used to study lipid self-assembly, membrane insertion, and the dynamics of the interactions between different components of the complex. Deep learning was applied to propose a model that explains the mechanism of GCase activation, which requires SAPC. Notably, we find that conformational changes in the loops at the entrance of the substrate-binding site are stabilized by direct interactions with SAPC and that the loss of such interactions induced by N370S and another common mutation, L444P, result in destabilization of the complex and reduced GCase activation. Our findings provide an atomistic-level explanation for GCase activation and the precise mechanism through which N370S and L444P cause Gaucher disease.
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38
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Integrating thin film microfluidics in developing a concise synthesis of DGJNAc: A potent inhibitor of α-N-acetylgalctosaminidases. Bioorg Med Chem Lett 2018; 28:3748-3751. [PMID: 30366618 DOI: 10.1016/j.bmcl.2018.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 11/23/2022]
Abstract
A simple synthesis, which utilizes a thin film microfluidic reactor for a problematic step, of a potent inhibitor of α-N-acetylhexosaminidases, DGJNAc, has been developed.
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Ando D, Fujisawa T, Katagi T. Metabolism of the Strobilurin Fungicide Mandestrobin in Wheat. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:10154-10162. [PMID: 30205687 DOI: 10.1021/acs.jafc.8b03639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The metabolic fate of a new fungicide, mandestrobin, labeled with 14C at the phenoxy or benzyl ring was examined in wheat after a single spray application at 300 g/ha. Mandestrobin penetrated into foliage over time, with both radiolabels showing similar 14C distribution in wheat, and 2.8-3.3% of the total radioactive residue remained on the surface of straw at the final harvest. In foliage, mandestrobin primarily underwent mono-oxidation at the phenoxy ring to produce 4-hydroxy or 2-/5-hydroxymethyl derivatives, followed by their subsequent formation of malonylglucose conjugates. In grain, the cleavage of its benzyl phenyl ether bond was the major metabolic reaction, releasing the corresponding alcohol derivative, while the counterpart 2,5-dimethylphenol was not detected. The constant RS enantiomeric ratio of mandestrobin showed its enantioselective metabolism to be unlikely on/in wheat.
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Affiliation(s)
- Daisuke Ando
- Environmental Health Science Laboratory , Sumitomo Chemical Co., Ltd. , 4-2-1, Takarazuka , Hyogo 665-8555 , Japan
| | - Takuo Fujisawa
- Environmental Health Science Laboratory , Sumitomo Chemical Co., Ltd. , 4-2-1, Takarazuka , Hyogo 665-8555 , Japan
| | - Toshiyuki Katagi
- Bioscience Research Laboratory , Sumitomo Chemical Co., Ltd. , 3-1-98, Kasugade-naka 3-chome, Konohana-ku , Osaka-city, Osaka 554-8558 , Japan
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40
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Wang M, Yuan Z, Xie R, Ma Y, Liu X, Yu X. Structure-function analyses reveal the mechanism of the ARH3-dependent hydrolysis of ADP-ribosylation. J Biol Chem 2018; 293:14470-14480. [PMID: 30045870 PMCID: PMC6139573 DOI: 10.1074/jbc.ra118.004284] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/20/2018] [Indexed: 01/07/2023] Open
Abstract
ADP-ribosylation of proteins plays key roles in multiple biological processes, including DNA damage repair. Recent evidence suggests that serine is an important acceptor for ADP-ribosylation, and that serine ADP-ribosylation is hydrolyzed by ADP-ribosylhydrolase 3 (ARH3 or ADPRHL2). However, the structural details in ARH3-mediated hydrolysis remain elusive. Here, we determined the structure of ARH3 in a complex with ADP-ribose (ADPR). Our analyses revealed a group of acidic residues in ARH3 that keep two Mg2+ ions at the catalytic center for hydrolysis of Ser-linked ADP-ribosyl group. In particular, dynamic conformational changes involving Glu41 were observed in the catalytic center. Our observations suggest that Mg2+ ions together with Glu41 and water351 are likely to mediate the cleavage of the glycosidic bond in the serine-ADPR substrate. Moreover, we found that ADPR is buried in a groove and forms multiple hydrogen bonds with the main chain and side chains of ARH3 residues. On the basis of these structural findings, we used site-directed mutagenesis to examine the functional roles of key residues in the catalytic pocket of ARH3 in mediating the hydrolysis of ADP-ribosyl from serine and DNA damage repair. Moreover, we noted that ADPR recognition is essential for the recruitment of ARH3 to DNA lesions. Taken together, our study provides structural and functional insights into the molecular mechanism by which ARH3 hydrolyzes the ADP-ribosyl group from serine and contributes to DNA damage repair.
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Affiliation(s)
- Mengxi Wang
- From the College of Life Sciences, Hebei University, Baoding, 071000 Hebei, China
| | - Zenglin Yuan
- the State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, Shandong, China, and
| | - Rong Xie
- From the College of Life Sciences, Hebei University, Baoding, 071000 Hebei, China, ,the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010
| | - Yinliang Ma
- From the College of Life Sciences, Hebei University, Baoding, 071000 Hebei, China, ,the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010
| | - Xiuhua Liu
- From the College of Life Sciences, Hebei University, Baoding, 071000 Hebei, China, , To whom correspondence may be addressed. E-mail:
| | - Xiaochun Yu
- From the College of Life Sciences, Hebei University, Baoding, 071000 Hebei, China, ,the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, To whom correspondence may be addressed. E-mail:
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41
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Pourfarjam Y, Ventura J, Kurinov I, Cho A, Moss J, Kim IK. Structure of human ADP-ribosyl-acceptor hydrolase 3 bound to ADP-ribose reveals a conformational switch that enables specific substrate recognition. J Biol Chem 2018; 293:12350-12359. [PMID: 29907568 PMCID: PMC6093245 DOI: 10.1074/jbc.ra118.003586] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/30/2018] [Indexed: 01/07/2023] Open
Abstract
ADP-ribosyl-acceptor hydrolase 3 (ARH3) plays important roles in regulation of poly(ADP-ribosyl)ation, a reversible post-translational modification, and in maintenance of genomic integrity. ARH3 degrades poly(ADP-ribose) to protect cells from poly(ADP-ribose)-dependent cell death, reverses serine mono(ADP-ribosyl)ation, and hydrolyzes O-acetyl-ADP-ribose, a product of Sirtuin-catalyzed histone deacetylation. ARH3 preferentially hydrolyzes O-linkages attached to the anomeric C1″ of ADP-ribose; however, how ARH3 specifically recognizes and cleaves structurally diverse substrates remains unknown. Here, structures of full-length human ARH3 bound to ADP-ribose and Mg2+, coupled with computational modeling, reveal a dramatic conformational switch from closed to open states that enables specific substrate recognition. The glutamate flap, which blocks substrate entrance to Mg2+ in the unliganded closed state, is ejected from the active site when substrate is bound. This closed-to-open transition significantly widens the substrate-binding channel and precisely positions the scissile 1″-O-linkage for cleavage while securing tightly 2″- and 3″-hydroxyls of ADP-ribose. Our collective data uncover an unprecedented structural plasticity of ARH3 that supports its specificity for the 1″-O-linkage in substrates and Mg2+-dependent catalysis.
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Affiliation(s)
- Yasin Pourfarjam
- From the Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221
| | - Jessica Ventura
- From the Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221
| | - Igor Kurinov
- Cornell University, Department of Chemistry and Chemical Biology, Northeastern Collaborative Access Team Advanced Photon Source (NE-CAT APS), Argonne, Illinois 60439, and
| | - Ahra Cho
- From the Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221
| | - Joel Moss
- Pulmonary Branch, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - In-Kwon Kim
- From the Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, , Supported by the University of Cincinnati startup fund. To whom correspondence should be addressed:
Dept. of Chemistry, University of Cincinnati, 301 Clifton Ct., Cincinnati, OH 45221. Tel.:
513-556-1909; Fax:
513-556-9239; E-mail:
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42
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Li Z, Zhang X, Wang Q, Li C, Zhang N, Zhang X, Xu B, Ma B, Schrader TE, Coates L, Kovalevsky A, Huang Y, Wan Q. Understanding the pH-Dependent Reaction Mechanism of a Glycoside Hydrolase Using High-Resolution X-ray and Neutron Crystallography. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01472] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhihong Li
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Xiaoshuai Zhang
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Qingqing Wang
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Chunran Li
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Nianying Zhang
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Xinkai Zhang
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Birui Xu
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Baoliang Ma
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Tobias E. Schrader
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Garching 85747, Germany
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen 361021, People’s Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
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43
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Selective glycosidase inhibitors: A patent review (2012–present). Int J Biol Macromol 2018; 111:82-91. [DOI: 10.1016/j.ijbiomac.2017.12.148] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/24/2017] [Accepted: 12/28/2017] [Indexed: 01/01/2023]
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Suzuki R, Fujimoto Z, Kaneko S, Hasegawa T, Kuno A. Enhanced Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant. J Appl Glycosci (1999) 2018; 65:1-8. [PMID: 34354506 PMCID: PMC8056907 DOI: 10.5458/jag.jag.jag-2017_011] [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] [Received: 07/19/2017] [Accepted: 11/27/2017] [Indexed: 11/04/2022] Open
Abstract
Glycoside hydrolases require carboxyl groups as catalysts for their activity. A retaining xylanase from Streptomyces olivaceoviridis E-86 belonging to glycoside hydrolase family 10 possesses Glu128 and Glu236 that respectively function as acid/base and nucleophile. We previously developed a unique mutant of the retaining xylanase, N127S/E128H, whose deglycosylation is triggered by azide. A crystallographic study reported that the transient formation of a Ser–His catalytic dyad in the reaction cycle possibly reduced the azidolysis reaction. In the present study, we engineered a catalytic dyad with enhanced stability by site-directed mutagenesis and crystallographic study of N127S/E128H. Comparison of the Michaelis complexes of N127S/E128H with pNP-X2 and with xylopentaose showed that Ser127 could form an alternative hydrogen bond with Thr82, which disrupts the formation of the Ser–His catalytic dyad. The introduction of T82A mutation in N127S/E128H produces an enhanced first-order rate constant (6 times that of N127S/E128H). We confirmed the presence of a stable Ser–His hydrogen bond in the Michaelis complex of the triple mutant, which forms the productive tautomer of His128 that acts as an acid catalyst. Because the glycosyl azide is applicable in the bioconjugation of glycans by using click chemistry, the enzyme-assisted production of the glycosyl azide may contribute to the field of glycobiology.
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Affiliation(s)
- Ryuichiro Suzuki
- 1 Department of Biological Production, Akita Prefectural University.,2 Department of Material and Biological Chemistry, Faculty of Science, Yamagata University
| | - Zui Fujimoto
- 3 Advanced Analysis Center, National Agriculture and Food Research Organization (NARO)
| | - Satoshi Kaneko
- 4 Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus
| | - Tsunemi Hasegawa
- 2 Department of Material and Biological Chemistry, Faculty of Science, Yamagata University
| | - Atsushi Kuno
- 5 Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST)
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45
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Bhuma N, Burade SS, Louat T, Herman J, Kawade S, Doshi PJ, Dhavale DD. Fluorinated piperidine iminosugars and their N -alkylated derivatives: Synthesis, conformational analysis, immunosuppressive and glycosidase inhibitory activity studies. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.12.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Nierengarten JF, Schneider JP, Trinh TMN, Joosten A, Holler M, Lepage ML, Bodlenner A, García-Moreno MI, Ortiz Mellet C, Compain P. Giant Glycosidase Inhibitors: First- and Second-Generation Fullerodendrimers with a Dense Iminosugar Shell. Chemistry 2018; 24:2483-2492. [DOI: 10.1002/chem.201705600] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Jean-François Nierengarten
- Laboratoire de Chimie des Matériaux Moléculaires; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Jérémy P. Schneider
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Thi Minh Nguyet Trinh
- Laboratoire de Chimie des Matériaux Moléculaires; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Antoine Joosten
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Michel Holler
- Laboratoire de Chimie des Matériaux Moléculaires; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Mathieu L. Lepage
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Anne Bodlenner
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - M. Isabel García-Moreno
- Departamento de Química Orgánica; Facultad de Química; Universidad de Sevilla; Profesor García González 1 41012 Sevilla Spain
| | - Carmen Ortiz Mellet
- Departamento de Química Orgánica; Facultad de Química; Universidad de Sevilla; Profesor García González 1 41012 Sevilla Spain
| | - Philippe Compain
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
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47
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Kuo CL, van Meel E, Kytidou K, Kallemeijn WW, Witte M, Overkleeft HS, Artola ME, Aerts JM. Activity-Based Probes for Glycosidases: Profiling and Other Applications. Methods Enzymol 2017; 598:217-235. [PMID: 29306436 DOI: 10.1016/bs.mie.2017.06.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycosidases mediate the fragmentation of glycoconjugates in the body, including the vital recycling of endogenous molecules. Several inherited diseases in man concern deficiencies in lysosomal glycosidases degrading glycosphingolipids. Prominent is Gaucher disease caused by an impaired lysosomal β-glucosidase (glucocerebrosidase, GBA) and resulting in pathological lysosomal storage of glucosylceramide (glucocerebroside) in tissue macrophages. GBA is a retaining glucosidase with a characteristic glycosyl-enzyme intermediate formed during catalysis. Using the natural suicide inhibitor cyclophellitol as a lead, we developed mechanism-based irreversible inhibitors of GBA equipped with a fluorescent reporter. These reagents covalently link to the catalytic nucleophile residue of GBA and permit specific and sensitive visualization of active enzyme molecules. The amphiphilic activity-based probes (ABPs) allow in situ detection of active GBA in cells and organisms. Furthermore, they may be used to biochemically confirm the diagnosis of Gaucher disease and they might assist in screening for small compounds interacting with the catalytic pocket. While the focus of this chapter is ABPs for β-glucosidases and Gaucher disease, the described concept has meanwhile been extended to other retaining glycosidases and related disease conditions as well.
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Affiliation(s)
- Chi-Lin Kuo
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Eline van Meel
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Kassiani Kytidou
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Martin Witte
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Marta Elena Artola
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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48
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Meleiro LP, Salgado JCS, Maldonado RF, Carli S, Moraes LAB, Ward RJ, Jorge JA, Furriel RPM. Engineering the GH1 β-glucosidase from Humicola insolens: Insights on the stimulation of activity by glucose and xylose. PLoS One 2017; 12:e0188254. [PMID: 29145480 PMCID: PMC5690678 DOI: 10.1371/journal.pone.0188254] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/05/2017] [Indexed: 12/31/2022] Open
Abstract
The activity of the GH1 β-glucosidase from Humicola insolens (Bglhi) against p-nitrophenyl-β-D-glucopyranoside (pNP-Glc) and cellobiose is enhanced 2-fold by glucose and/or xylose. Kinetic and transglycosylation data showed that hydrolysis is preferred in the absence of monosaccharides. Stimulation involves allosteric interactions, increased transglycosylation and competition of the substrate and monosaccharides for the -1 glycone and the +1/+2 aglycone binding sites. Protein directed evolution has been used to generate 6 mutants of Bglhi with altered stimulation patterns. All mutants contain one of three substitutions (N235S, D237V or H307Y) clustered around the +1/+2 aglycone binding sites. Two mutants with the H307Y substitution preferentially followed the transglycosylation route in the absence of xylose or glucose. The strong stimulation of their pNP-glucosidase and cellobiase activities was accompanied by increased transglycosylation and higher monosaccharide tolerance. The D237V mutation favoured hydrolysis over transglycosylation and the pNP-glucosidase activity, but not the cellobiase activity, was stimulated by xylose. The substitution N235S abolished the preference for hydrolysis or transglycosylation; the cellobiase, but not the pNP-glucosidase activity of the mutants was strongly inhibited by xylose. Both the D237V and N235S mutations lowered tolerance to the monosaccharides. These results provide evidence that the fine modulation of the activity of Bglhi and mutants by glucose and/or xylose is regulated by the relative affinities of the glycone and aglycone binding sites for the substrate and the free monosaccharides.
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Affiliation(s)
- Luana Parras Meleiro
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
- * E-mail:
| | - José Carlos Santos Salgado
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Raquel Fonseca Maldonado
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, São José dos Campos, São Paulo, Brasil
| | - Sibeli Carli
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Luiz Alberto Beraldo Moraes
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Richard John Ward
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - João Atílio Jorge
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Rosa Prazeres Melo Furriel
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
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49
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Artola M, Wu L, Ferraz MJ, Kuo CL, Raich L, Breen IZ, Offen WA, Codée JDC, van der Marel GA, Rovira C, Aerts JMF, Davies GJ, Overkleeft HS. 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor. ACS CENTRAL SCIENCE 2017; 3:784-793. [PMID: 28776021 PMCID: PMC5532717 DOI: 10.1021/acscentsci.7b00214] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 05/28/2023]
Abstract
The essential biological roles played by glycosidases, coupled to the diverse therapeutic benefits of pharmacologically targeting these enzymes, provide considerable motivation for the development of new inhibitor classes. Cyclophellitol epoxides and aziridines are recently established covalent glycosidase inactivators. Inspired by the application of cyclic sulfates as electrophilic equivalents of epoxides in organic synthesis, we sought to test whether cyclophellitol cyclosulfates would similarly act as irreversible glycosidase inhibitors. Here we present the synthesis, conformational analysis, and application of novel 1,6-cyclophellitol cyclosulfates. We show that 1,6-epi-cyclophellitol cyclosulfate (α-cyclosulfate) is a rapidly reacting α-glucosidase inhibitor whose 4C1 chair conformation matches that adopted by α-glucosidase Michaelis complexes. The 1,6-cyclophellitol cyclosulfate (β-cyclosulfate) reacts more slowly, likely reflecting its conformational restrictions. Selective glycosidase inhibitors are invaluable as mechanistic probes and therapeutic agents, and we propose cyclophellitol cyclosulfates as a valuable new class of carbohydrate mimetics for application in these directions.
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Affiliation(s)
- Marta Artola
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Liang Wu
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Maria J. Ferraz
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Chi-Lin Kuo
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Imogen Z. Breen
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Wendy A. Offen
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Jeroen D. C. Codée
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gijsbert A. van der Marel
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Fundació
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Johannes M. F.
G. Aerts
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Gideon J. Davies
- Department
of Chemistry, University of York, Heslington, York, YO10
5DD, U.K.
| | - Herman S. Overkleeft
- Department
of Bio-organic Synthesis and Department of Medical Biochemistry,
Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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50
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Abdul Manas NH, Md Illias R, Mahadi NM. Strategy in manipulating transglycosylation activity of glycosyl hydrolase for oligosaccharide production. Crit Rev Biotechnol 2017; 38:272-293. [PMID: 28683572 DOI: 10.1080/07388551.2017.1339664] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The increasing market demand for oligosaccharides has intensified the need for efficient biocatalysts. Glycosyl hydrolases (GHs) are still gaining popularity as biocatalyst for oligosaccharides synthesis owing to its simple reaction and high selectivity. PURPOSE Over the years, research has advanced mainly directing to one goal; to reduce hydrolysis activity of GHs for increased transglycosylation activity in achieving high production of oligosaccharides. DESIGN AND METHODS This review concisely presents the strategies to increase transglycosylation activity of GHs for oligosaccharides synthesis, focusing on controlling the reaction equilibrium, and protein engineering. Various modifications of the subsites of GHs have been demonstrated to significantly modulate the hydrolysis and transglycosylation activity of the enzymes. The clear insight of the roles of each amino acid in these sites provides a platform for designing an enzyme that could synthesize a specific oligosaccharide product. CONCLUSIONS The key strategies presented here are important for future improvement of GHs as a biocatalyst for oligosaccharide synthesis.
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Affiliation(s)
- Nor Hasmaliana Abdul Manas
- a Department of Chemical Engineering and Energy Sustainability, Faculty of Engineering , Universiti Malaysia Sarawak , Kota Samarahan , Malaysia.,b BioMolecular and Microbial Process Research Group , Health and Wellness Research Alliance, Universiti Teknologi Malaysia , Johor , Malaysia
| | - Rosli Md Illias
- b BioMolecular and Microbial Process Research Group , Health and Wellness Research Alliance, Universiti Teknologi Malaysia , Johor , Malaysia.,c Department of Bioprocess Engineering, Faculty of Chemical and Energy Engineering , Universiti Teknologi Malaysia , Skudai , Malaysia
| | - Nor Muhammad Mahadi
- d Comparative Genomics and Genetics Research Centre , Malaysia Genome Institute , Kajang , Malaysia
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