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Kalník M, Gabko P, Kóňa J, Šesták S, Moncoľ J, Bella M. (5S)-5-Benzylswainsonines as potent and selective inhibitors of Golgi α-mannosidase II: synthesis, enzyme evaluation and molecular modelling. Bioorg Chem 2024; 150:107578. [PMID: 38955002 DOI: 10.1016/j.bioorg.2024.107578] [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: 06/03/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
Development of novel anti-cancer therapeutics based on Golgi α-mannosidase II (GMII) inhibition is considerably impeded by an undesired co-inhibition of lysosomal α-mannosidase leading to severe side-effects. In this contribution, we describe a fully stereoselective synthesis of (5S)-5-[4-(halo)benzyl]swainsonines as highly potent and selective inhibitors of GMII. The synthesis starts from a previously reported aldehyde readily available from l-ribose, and the key features include an intramolecular reductive amination with substrate-controlled stereoselectivity and a late-stage derivatisation of the benzyl group via ipso-substitution. These novel swainsonine analogues were found to be nanomolar inhibitors of the Golgi-type α-mannosidase AMAN-2 (Ki = 23-75 nM) with excellent selectivity (selectivity index = 205-870) over the lysosomal-type Jack bean α-mannosidase. Finally, molecular docking and pKa calculations were performed to provide more insight into the structure of the inhibitor:enzyme complexes, and a pair interaction energy analysis (FMO-PIEDA) was carried out to rationalise the observed potency and selectivity of the inhibitors.
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Affiliation(s)
- Martin Kalník
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Peter Gabko
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Juraj Kóňa
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia; Medical Vision, Civic Research Association, Záhradnícka 4837/55, SK-82108 Bratislava, Slovakia
| | - Sergej Šesták
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Ján Moncoľ
- Department of Inorganic Chemistry, Faculty of Chemical and Food Technology, Radlinského 9, SK-812 37 Bratislava, Slovakia
| | - Maroš Bella
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia.
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2
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Liu FF, Wang M, Ma GH, Kulinich A, Liu L, Voglmeir J. Characterization of Solitalea canadensis α-mannosidase with specific activity towards α1,3-Mannosidic linkages. Carbohydr Res 2024; 538:109100. [PMID: 38555657 DOI: 10.1016/j.carres.2024.109100] [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: 02/03/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
A recombinant exo-α-mannosidase from Solitalea canadensis (Sc3Man) has been characterized to exhibit strict specificity for hydrolyzing α1,3-mannosidic linkages located at the non-reducing end of glycans containing α-mannose. Enzymatic characterization revealed that Sc3Man operates optimally at a pH of 5.0 and at a temperature of 37 °C. The enzymatic activity was notably enhanced twofold in the presence of Ca2+ ions, emphasizing its potential dependency on this metal ion, while Cu2+ and Zn2+ ions notably impaired enzyme function. Sc3Man was able to efficiently cleave the terminal α1,3 mannose residue from various high-mannose N-glycan structures and from the model glycoprotein RNase B. This work not only expands the categorical scope of bacterial α-mannosidases, but also offers new insight into the glycan metabolism of S. canadensis, highlighting the enzyme's utility for glycan analysis and potential biotechnological applications.
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Affiliation(s)
- Fang-Fang Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Meng Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Guan-Hua Ma
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Anna Kulinich
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China.
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3
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Chen WA, Chen YH, Hsieh CY, Hung PF, Chen CW, Chen CH, Lin JL, Cheng TJR, Hsu TL, Wu YT, Shen CN, Cheng WC. Harnessing natural-product-inspired combinatorial chemistry and computation-guided synthesis to develop N-glycan modulators as anticancer agents. Chem Sci 2022; 13:6233-6243. [PMID: 35733906 PMCID: PMC9159088 DOI: 10.1039/d1sc05894k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/18/2022] [Indexed: 11/25/2022] Open
Abstract
Modulation of N-glycosylation using human Golgi α-mannosidase II (α-hGMII) inhibitors is a potential anticancer approach, but the clinical utility of current α-hGMII inhibitors is limited by their co-inhibition of human lysosomal α-mannosidase (α-hLM), resulting in abnormal storage of oligomannoses. We describe the synthesis and screening of a small library of novel bicyclic iminosugar-based scaffolds, prepared via natural product-inspired combinatorial chemistry (NPICC), which resulted in the identification of a primary α-hGMII inhibitor with 13.5-fold selectivity over α-hLM. Derivatization of this primary inhibitor using computation-guided synthesis (CGS) yielded an advanced α-hGMII inhibitor with nanomolar potency and 106-fold selectivity over α-hLM. In vitro studies demonstrated its N-glycan modulation and inhibitory effect on hepatocellular carcinoma (HCC) cells. In vivo studies confirmed its encouraging anti-HCC activity, without evidence of oligomannose accumulation. An integrated strategy of Natural-Product-Inspired Combinatorial Chemistry (NPICC) and Computation-Guided Synthesis is used to develop an α-hGMII inhibitor with 106-fold selectivity over α-hLM, with inhibitory effect on hepatocellular carcinoma.![]()
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Affiliation(s)
- Wei-An Chen
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Yu-Hsin Chen
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Chiao-Yun Hsieh
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Pi-Fang Hung
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Chiao-Wen Chen
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Chien-Hung Chen
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Jung-Lee Lin
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Ting-Jen R Cheng
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Tsui-Ling Hsu
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Ying-Ta Wu
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Chia-Ning Shen
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan
| | - Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica 128, Section 2, Academia Road Taipei 11529 Taiwan .,Department of Chemistry, National Cheng-Kung University 1, University Road Tainan 701 Taiwan.,Department of Applied Chemistry, National Chiayi University 300, Xuefu Rd, East Dist. Chiayi 600 Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University 100 Shih-Chuan 1st Rd Kaohsiung 807 Taiwan
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4
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Quirke JCK, Crich D. GH47 and Other Glycoside Hydrolases Catalyze Glycosidic Bond Cleavage with the Assistance of Substrate Super-arming at the Transition State. ACS Catal 2021; 11:10308-10315. [PMID: 34777906 PMCID: PMC8579916 DOI: 10.1021/acscatal.1c02750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Super-armed glycosyl donors, whose substituents are predominantly held in pseudoaxial positions, exhibit strongly increased reactivity in glycosylation through significant stabilization of oxocarbenium-like transition states. Examination of X-ray crystal structures reveals that the GH47 family of glycoside hydrolases have evolved so as to distort their substrates away from the ground state conformation in such a manner as to present multiple C-O bonds in pseudoaxial positions and so benefit from conformational super-arming of their substrates, thereby enhancing catalysis. Through analysis of literature mutagenic studies, we show that a suitably placed aromatic residue in GHs 6 and 47 sterically enforces super-armed conformations on their substrates. GH families 45, 81, and 134 on the other hand impose conformational super-arming on their substrates, by maintaining the more active ring conformation through hydrogen bonding rather than steric interactions. The recognition of substrate super-arming by select GH families provides a further parallel with synthetic carbohydrate chemistry and nature and opens further avenues for the design of improved glycosidase inhibitors.
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Affiliation(s)
- Jonathan C K Quirke
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, GA 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, GA 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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5
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Klunda T, Hricovíni M, Šesták S, Kóňa J, Poláková M. Selective Golgi α-mannosidase II inhibitors: N-alkyl substituted pyrrolidines with a basic functional group. NEW J CHEM 2021. [DOI: 10.1039/d1nj01176f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymatic assays, molecular modeling and NMR studies of novel 1,4-dideoxy-1,4-imino-l-lyxitols provided new information on the GH38 family enzyme inhibitors and their selectivity.
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Affiliation(s)
- Tomáš Klunda
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Michal Hricovíni
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Sergej Šesták
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Juraj Kóňa
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Monika Poláková
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
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6
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Zhang J, Zhou L, Cui L, Liu Z, Wei J, Kang W. Antioxidant and α-glucosidase inhibitiory activity of Cercis chinensis flowers. FOOD SCIENCE AND HUMAN WELLNESS 2020. [DOI: 10.1016/j.fshw.2020.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Armstrong Z, Kuo CL, Lahav D, Liu B, Johnson R, Beenakker TJM, de Boer C, Wong CS, van Rijssel ER, Debets MF, Florea BI, Hissink C, Boot RG, Geurink PP, Ovaa H, van der Stelt M, van der Marel GM, Codée JDC, Aerts JMFG, Wu L, Overkleeft HS, Davies GJ. Manno-epi-cyclophellitols Enable Activity-Based Protein Profiling of Human α-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. J Am Chem Soc 2020; 142:13021-13029. [DOI: 10.1021/jacs.0c03880] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zachary Armstrong
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Chi-Lin Kuo
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Daniël Lahav
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bing Liu
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rachel Johnson
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Thomas J. M. Beenakker
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Casper de Boer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Chung-Sing Wong
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Erwin R. van Rijssel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marjoke F. Debets
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bogdan I. Florea
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Colin Hissink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rolf G. Boot
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Paul P. Geurink
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Mario van der Stelt
- 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
| | - Johannes M. F. G. Aerts
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Liang Wu
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gideon J. Davies
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
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8
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Chen W, Sayyad A, Chen C, Chen Y, Cheng TR, Cheng W. Divergent Synthesis of Bicyclic Iminosugars: Preparation of (−)‐Swainsonine‐Based Alkaloids and Their Inhibition Study towardsα‐Human Mannosidases. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Wei‐An Chen
- Genomics Research CenterAcademia Sinica 128 Academia Road, Sec. 2 Taipei 115 Taiwan
| | - Ashik Sayyad
- Genomics Research CenterAcademia Sinica 128 Academia Road, Sec. 2 Taipei 115 Taiwan
| | - Chiao‐Wen Chen
- Genomics Research CenterAcademia Sinica 128 Academia Road, Sec. 2 Taipei 115 Taiwan
| | - Yu‐Hsin Chen
- Genomics Research CenterAcademia Sinica 128 Academia Road, Sec. 2 Taipei 115 Taiwan
| | - Ting‐Jen R. Cheng
- Genomics Research CenterAcademia Sinica 128 Academia Road, Sec. 2 Taipei 115 Taiwan
| | - Wei‐Chieh Cheng
- Genomics Research CenterAcademia Sinica 128 Academia Road, Sec. 2 Taipei 115 Taiwan
- Department of ChemistryNational Cheng-Kung University 1 University Road Tainan 701 Taiwan
- Department of Applied ChemistryNational Chiayi University 300, Xuefu Rd., East Dist. Chiayi 600 Taiwan
- Department of Medicinal and Applied ChemistryKaohsiung Medical University 100 Shih-Chuan 1st Rd. Kaohsiung 807 Taiwan
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9
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Males A, Speciale G, Williams SJ, Davies GJ. Distortion of mannoimidazole supports a B2,5 boat transition state for the family GH125 α-1,6-mannosidase from Clostridium perfringens. Org Biomol Chem 2019; 17:7863-7869. [DOI: 10.1039/c9ob01161g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Enzyme transition-state mimics can act as powerful inhibitors and allow structural studies that report on the conformation of the transition-state.
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Affiliation(s)
- Alexandra Males
- York Structural Biology Laboratory
- Department of Chemistry
- The University of York
- YO10 5DD York
- UK
| | - Gaetano Speciale
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- University of Melbourne
- Melbourne
- Australia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- University of Melbourne
- Melbourne
- Australia
| | - Gideon J. Davies
- York Structural Biology Laboratory
- Department of Chemistry
- The University of York
- YO10 5DD York
- UK
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10
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Šesták S, Bella M, Klunda T, Gurská S, Džubák P, Wöls F, Wilson IBH, Sladek V, Hajdúch M, Poláková M, Kóňa J. N-Benzyl Substitution of Polyhydroxypyrrolidines: The Way to Selective Inhibitors of Golgi α-Mannosidase II. ChemMedChem 2018; 13:373-383. [PMID: 29323461 DOI: 10.1002/cmdc.201700607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/04/2018] [Indexed: 12/24/2022]
Abstract
Inhibition of the biosynthesis of complex N-glycans in the Golgi apparatus influences progress of tumor growth and metastasis. Golgi α-mannosidase II (GMII) has become a therapeutic target for drugs with anticancer activities. One critical task for successful application of GMII drugs in medical treatments is to decrease their unwanted co-inhibition of lysosomal α-mannosidase (LMan), a weakness of all known potent GMII inhibitors. A series of novel N-substituted polyhydroxypyrrolidines was synthesized and tested with modeled GH38 α-mannosidases from Drosophila melanogaster (GMIIb and LManII). The most potent structures inhibited GMIIb (Ki =50-76 μm, as determined by enzyme assays) with a significant selectivity index of IC50 (LManII)/IC50 (GMIIb) >100. These compounds also showed inhibitory activities in in vitro assays with cancer cell lines (leukemia, IC50 =92-200 μm) and low cytotoxic activities in normal fibroblast cell lines (IC50 >200 μm). In addition, they did not show any significant inhibitory activity toward GH47 Aspergillus saitoiα1,2-mannosidase. An appropriate stereo configuration of hydroxymethyl and benzyl functional groups on the pyrrolidine ring of the inhibitor may lead to an inhibitor with the required selectivity for the active site of a target α-mannosidase.
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Affiliation(s)
- Sergej Šesták
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Maroš Bella
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Tomáš Klunda
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Soňa Gurská
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Puškinova 6, 775 20, Olomouc, Czech Republic
| | - Petr Džubák
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Puškinova 6, 775 20, Olomouc, Czech Republic
| | - Florian Wöls
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Iain B H Wilson
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Vladimir Sladek
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Marián Hajdúch
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Puškinova 6, 775 20, Olomouc, Czech Republic
| | - Monika Poláková
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
| | - Juraj Kóňa
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
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11
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Bobovská A, Tvaroška I, Kóňa J. Using DFT methodology for more reliable predictive models: Design of inhibitors of Golgi α-Mannosidase II. J Mol Graph Model 2016; 66:47-57. [PMID: 27035259 DOI: 10.1016/j.jmgm.2016.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/28/2022]
Abstract
Human Golgi α-mannosidase II (GMII), a zinc ion co-factor dependent glycoside hydrolase (E.C.3.2.1.114), is a pharmaceutical target for the design of inhibitors with anti-cancer activity. The discovery of an effective inhibitor is complicated by the fact that all known potent inhibitors of GMII are involved in unwanted co-inhibition with lysosomal α-mannosidase (LMan, E.C.3.2.1.24), a relative to GMII. Routine empirical QSAR models for both GMII and LMan did not work with a required accuracy. Therefore, we have developed a fast computational protocol to build predictive models combining interaction energy descriptors from an empirical docking scoring function (Glide-Schrödinger), Linear Interaction Energy (LIE) method, and quantum mechanical density functional theory (QM-DFT) calculations. The QSAR models were built and validated with a library of structurally diverse GMII and LMan inhibitors and non-active compounds. A critical role of QM-DFT descriptors for the more accurate prediction abilities of the models is demonstrated. The predictive ability of the models was significantly improved when going from the empirical docking scoring function to mixed empirical-QM-DFT QSAR models (Q(2)=0.78-0.86 when cross-validation procedures were carried out; and R(2)=0.81-0.83 for a testing set). The average error for the predicted ΔGbind decreased to 0.8-1.1kcalmol(-1). Also, 76-80% of non-active compounds were successfully filtered out from GMII and LMan inhibitors. The QSAR models with the fragmented QM-DFT descriptors may find a useful application in structure-based drug design where pure empirical and force field methods reached their limits and where quantum mechanics effects are critical for ligand-receptor interactions. The optimized models will apply in lead optimization processes for GMII drug developments.
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Affiliation(s)
- Adela Bobovská
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic; Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovak Republic.
| | - Igor Tvaroška
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic.
| | - Juraj Kóňa
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic.
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12
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Stephens K, Thaler CD, Cardullo RA. Characterization of plasma membrane associated type II α-D-mannosidase and β-N-acetylglucosaminidase of Aquarius remigis sperm. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 60:78-85. [PMID: 25801709 DOI: 10.1016/j.ibmb.2015.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/25/2015] [Accepted: 03/10/2015] [Indexed: 06/04/2023]
Abstract
For successful fertilization to occur, molecules on the surface of male and female gametes must recognize each other in a complementary manner. In some organisms, sperm possess a glycosidase on the plasma membrane overlying the head while eggs have glycoproteins that are recognized by those glycosidases resulting in sperm-egg recognition. In this study, two glycosidases, mannosidase and β-N-acetylglucosaminidase, were identified and biochemically characterized in Aquarius remigis sperm. The mannosidase had a Km of 2.36 ± 0.19 mM, a Vmax of 27.49 ± 0.88 pmol/min and a Hill coefficient of 0.94 ± 0.18 at its optimal pH of 7.0. The mannosidase was extracted most efficiently with CHAPSO but was also efficiently extracted with sodium chloride. Mannosidase activity was effectively inhibited by swainsonine, but not by kifunesine, and was significantly reduced in the presence of Mn(2+) and Mg(2+), but not Zn(2+). N-acetylglucosaminidase had a Km of 0.093 ± 0.01 mM, a Vmax of 153.80 ± 2.97 pmol/min and a Hill coefficient of 0.96 ± 0.63 at its optimal pH of 7.0. N-acetylglucosaminidase was extracted most efficiently with potassium iodide but was also efficiently extracted with Triton X-100 and Zn(2+), but not Ca(2+), Co(2+), Mn(2+) or Mg(2+), significantly inhibited its activity. Taken together, these results indicate that the A. remigis sperm surface contains at least two glycosidases that may recognize complementary glycoconjugates on the surface of water strider eggs.
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Affiliation(s)
- Kimberly Stephens
- Department of Entomology, University of California, Riverside, CA 92521, USA
| | - Catherine D Thaler
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Richard A Cardullo
- Department of Entomology, University of California, Riverside, CA 92521, USA; Department of Biology, University of California, Riverside, CA 92521, USA.
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Pershagen E, Borbas KE. Multiplex Detection of Enzymatic Activity with Responsive Lanthanide-Based Luminescent Probes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408560] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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14
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Pershagen E, Borbas KE. Multiplex detection of enzymatic activity with responsive lanthanide-based luminescent probes. Angew Chem Int Ed Engl 2014; 54:1787-90. [PMID: 25504579 DOI: 10.1002/anie.201408560] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/21/2014] [Indexed: 11/06/2022]
Abstract
Multiplex analyte detection in complex dynamic systems is desirable for the investigation of cellular communication networks as well as in medical diagnostics. A family of lanthanide-based responsive luminescent probes for multiplex detection is reported. The high modularity of the probe design enabled the rapid assembly of both green and red emitters for a large variety of analytes by the simple exchange of the lanthanide or an analyte-cleavable caging group, respectively. The real-time three-color detection of up to three analytes was demonstrated, thus setting the stage for the non-invasive investigation of interconnected biological processes.
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Affiliation(s)
- Elias Pershagen
- Department of Chemistry-BMC, Uppsala University, Box 576, Uppsala, 75123 (Sweden)
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15
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Williams RJ, Iglesias-Fernández J, Stepper J, Jackson A, Thompson AJ, Lowe EC, White JM, Gilbert HJ, Rovira C, Davies GJ, Williams SJ. Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate. Angew Chem Int Ed Engl 2014; 53:1087-91. [PMID: 24339341 PMCID: PMC4138987 DOI: 10.1002/anie.201308334] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Indexed: 12/03/2022]
Abstract
Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition.
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Affiliation(s)
- Rohan J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic 3010 (Australia)
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16
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Williams RJ, Iglesias-Fernández J, Stepper J, Jackson A, Thompson AJ, Lowe EC, White JM, Gilbert HJ, Rovira C, Davies GJ, Williams SJ. Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Synthesis of a pseudo-disaccharide library and its application to the characterisation of the heparanase catalytic site. PLoS One 2013; 8:e82111. [PMID: 24260588 PMCID: PMC3832595 DOI: 10.1371/journal.pone.0082111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/19/2013] [Indexed: 12/15/2022] Open
Abstract
A novel methodology is described for the efficient and divergent synthesis of pseudodisaccharides, molecules comprising of amino carbasugar analogues linked to natural sugars. The methodology is general and enables the introduction of diversity both at the carbasugar and the natural sugar components of the pseudodisaccharides. Using this approach, a series of pseudodisaccharides are synthesised that mimic the repeating backbone unit of heparan sulfate, and are tested for inhibition of heparanase, a disease-relevant enzyme that hydrolyses heparan sulfate. A new homology model of human heparanase is described based on a family 79 β-glucuronidase. This model is used to postulate a computational rationale for the observed activity of the different pseudodisaccharides and provide valuable information that informs the design of potential inhibitors of this enzyme.
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18
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Characterisation of class I and II α-mannosidases from Drosophila melanogaster. Glycoconj J 2013; 30:899-909. [DOI: 10.1007/s10719-013-9495-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/02/2013] [Accepted: 08/07/2013] [Indexed: 12/31/2022]
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19
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Cheng TR, Chan T, Tsou E, Chang S, Yun W, Yang P, Wu Y, Cheng W. From Natural Product‐Inspired Pyrrolidine Scaffolds to the Development of New Human Golgi α‐Mannosidase II Inhibitors. Chem Asian J 2013; 8:2600-4. [DOI: 10.1002/asia.201300680] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Ting‐Jen R. Cheng
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Ting‐Hao Chan
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - En‐Lun Tsou
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Shang‐Yu Chang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Wen‐Yi Yun
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Pei‐Jung Yang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Ying‐Ta Wu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
| | - Wei‐Chieh Cheng
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115 (Taiwan)
- Department of Chemistry, National Cheng‐Kung University, 1, University Road, Tainan (Taiwan), Fax: (+886) 2 27899931
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20
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Concia AL, Gómez L, Bujons J, Parella T, Vilaplana C, Cardona PJ, Joglar J, Clapés P. Chemo-enzymatic synthesis and glycosidase inhibitory properties of DAB and LAB derivatives. Org Biomol Chem 2013; 11:2005-21. [PMID: 23381224 DOI: 10.1039/c3ob27343a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A chemo-enzymatic strategy for the preparation of 2-aminomethyl derivatives of (2R,3R,4R)-2-(hydroxymethyl)pyrrolidine-3,4-diol (also called 1,4-dideoxy-1,4-imino-D-arabinitol, DAB) and its enantiomer LAB is presented. The synthesis is based on the enzymatic preparation of DAB and LAB followed by the chemical modification of their hydroxymethyl functionality to afford diverse 2-aminomethyl derivatives. This strategy leads to novel aromatic, aminoalcohol and 2-oxopiperazine DAB and LAB derivatives. The compounds were preliminarily explored as inhibitors of a panel of commercial glycosidases, rat intestinal disaccharidases and against Mycobacterium tuberculosis, the causative agent of tuberculosis. It was found that the inhibitory profile of the new products differed considerably from the parent DAB and LAB. Furthermore, some of them were active inhibiting the growth of M. tuberculosis.
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Affiliation(s)
- Alda Lisa Concia
- Dept Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
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21
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Lahiri R, Ansari AA, Vankar YD. Recent developments in design and synthesis of bicyclic azasugars, carbasugars and related molecules as glycosidase inhibitors. Chem Soc Rev 2013; 42:5102-18. [DOI: 10.1039/c3cs35525j] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Development of inhibitors as research tools for carbohydrate-processing enzymes. Biochem Soc Trans 2012; 40:913-28. [DOI: 10.1042/bst20120201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates, which are present in all domains of life, play important roles in a host of cellular processes. These ubiquitous biomolecules form highly diverse and often complex glycan structures without the aid of a template. The carbohydrate structures are regulated solely by the location and specificity of the enzymes responsible for their synthesis and degradation. These enzymes, glycosyltransferases and glycoside hydrolases, need to be functionally well characterized in order to investigate the structure and function of glycans. The use of enzyme inhibitors, which target a particular enzyme, can significantly aid this understanding, and may also provide insights into therapeutic applications. The present article describes some of the approaches used to design and develop enzyme inhibitors as tools for investigating carbohydrate-processing enzymes.
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23
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Sánchez‐Fernández EM, Rísquez‐Cuadro R, Ortiz Mellet C, García Fernández JM, Nieto PM, Angulo J. sp
2
‐Iminosugar
O
‐,
S
‐, and
N
‐Glycosides as Conformational Mimics of α‐Linked Disaccharides; Implications for Glycosidase Inhibition. Chemistry 2012; 18:8527-39. [DOI: 10.1002/chem.201200279] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 02/28/2012] [Indexed: 12/29/2022]
Affiliation(s)
- Elena M. Sánchez‐Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Rocío Rísquez‐Cuadro
- Departmento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Prof. García González 1, 41012, Sevilla (Spain), Fax: (+34) 954624960
| | - Carmen Ortiz Mellet
- Departmento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Prof. García González 1, 41012, Sevilla (Spain), Fax: (+34) 954624960
| | - José M. García Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Pedro M. Nieto
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Jesús Angulo
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
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24
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Poláková M, Šesták S, Lattová E, Petruš L, Mucha J, Tvaroška I, Kóňa J. α-d-Mannose derivatives as models designed for selective inhibition of Golgi α-mannosidase II. Eur J Med Chem 2011; 46:944-52. [DOI: 10.1016/j.ejmech.2011.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 12/21/2010] [Accepted: 01/08/2011] [Indexed: 10/18/2022]
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25
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Stütz AE, Wrodnigg TM. Imino sugars and glycosyl hydrolases: historical context, current aspects, emerging trends. Adv Carbohydr Chem Biochem 2011; 66:187-298. [PMID: 22123190 DOI: 10.1016/b978-0-12-385518-3.00004-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forty years of discoveries and research on imino sugars, which are carbohydrate analogues having a basic nitrogen atom instead of oxygen in the sugar ring and, acting as potent glycosidase inhibitors, have made considerable impact on our contemporary understanding of glycosidases. Imino sugars have helped to elucidate the catalytic machinery of glycosidases and have refined our methods and concepts of utilizing them. A number of new aspects have emerged for employing imino sugars as pharmaceutical compounds, based on their profound effects on metabolic activities in which glycosidases are involved. From the digestion of starch to the fight against viral infections, from research into malignant diseases to potential improvements in hereditary storage disorders, glycosidase action and inhibition are essential issues. This account aims at combining general developments with a focus on some niches where imino sugars have become useful tools for glycochemistry and glycobiology.
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Affiliation(s)
- Arnold E Stütz
- Institut für Organische Chemie, Technische Universität Graz, Austria
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26
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Synthesis and inhibitory activities of novel C-3 substituted azafagomines: A new type of selective inhibitors of α-l-fucosidases. Bioorg Med Chem 2010; 18:4648-60. [DOI: 10.1016/j.bmc.2010.05.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 05/05/2010] [Accepted: 05/06/2010] [Indexed: 11/20/2022]
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27
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Petersen L, Ardèvol A, Rovira C, Reilly PJ. Molecular Mechanism of the Glycosylation Step Catalyzed by Golgi α-Mannosidase II: A QM/MM Metadynamics Investigation. J Am Chem Soc 2010; 132:8291-300. [DOI: 10.1021/ja909249u] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luis Petersen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Albert Ardèvol
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Carme Rovira
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Peter J. Reilly
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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28
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Bello C, Cea M, Dal Bello G, Garuti A, Rocco I, Cirmena G, Moran E, Nahimana A, Duchosal MA, Fruscione F, Pronzato P, Grossi F, Patrone F, Ballestrero A, Dupuis M, Sordat B, Nencioni A, Vogel P. Novel 2-[(benzylamino)methyl]pyrrolidine-3,4-diol derivatives as α-mannosidase inhibitors and with antitumor activities against hematological and solid malignancies. Bioorg Med Chem 2010; 18:3320-34. [PMID: 20346684 DOI: 10.1016/j.bmc.2010.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 03/01/2010] [Accepted: 03/04/2010] [Indexed: 11/28/2022]
Affiliation(s)
- Claudia Bello
- Laboratory of Glycochemistry and Asymmetric Synthesis (LGSA), Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochime, CH-1015 Lausanne, Switzerland.
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29
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Kuntz DA, Nakayama S, Shea K, Hori H, Uto Y, Nagasawa H, Rose DR. Structural Investigation of the Binding of 5-Substituted Swainsonine Analogues to Golgi α-Mannosidase II. Chembiochem 2010; 11:673-80. [DOI: 10.1002/cbic.200900750] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Suits MDL, Zhu Y, Taylor EJ, Walton J, Zechel DL, Gilbert HJ, Davies GJ. Structure and kinetic investigation of Streptococcus pyogenes family GH38 alpha-mannosidase. PLoS One 2010; 5:e9006. [PMID: 20140249 PMCID: PMC2815779 DOI: 10.1371/journal.pone.0009006] [Citation(s) in RCA: 36] [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: 11/12/2009] [Accepted: 01/13/2010] [Indexed: 01/13/2023] Open
Abstract
Background The enzymatic hydrolysis of α−mannosides is catalyzed by glycoside hydrolases (GH), termed α−mannosidases. These enzymes are found in different GH sequence–based families. Considerable research has probed the role of higher eukaryotic “GH38” α−mannosides that play a key role in the modification and diversification of hybrid N-glycans; processes with strong cellular links to cancer and autoimmune disease. The most extensively studied of these enzymes is the Drosophila GH38 α−mannosidase II, which has been shown to be a retaining α−mannosidase that targets both α−1,3 and α−1,6 mannosyl linkages, an activity that enables the enzyme to process GlcNAc(Man)5(GlcNAc)2 hybrid N-glycans to GlcNAc(Man)3(GlcNAc)2. Far less well understood is the observation that many bacterial species, predominantly but not exclusively pathogens and symbionts, also possess putative GH38 α−mannosidases whose activity and specificity is unknown. Methodology/Principal Findings Here we show that the Streptococcus pyogenes (M1 GAS SF370) GH38 enzyme (Spy1604; hereafter SpGH38) is an α−mannosidase with specificity for α−1,3 mannosidic linkages. The 3D X-ray structure of SpGH38, obtained in native form at 1.9 Å resolution and in complex with the inhibitor swainsonine (Ki 18 µM) at 2.6 Å, reveals a canonical GH38 five-domain structure in which the catalytic “–1” subsite shows high similarity with the Drosophila enzyme, including the catalytic Zn2+ ion. In contrast, the “leaving group” subsites of SpGH38 display considerable differences to the higher eukaryotic GH38s; features that contribute to their apparent specificity. Conclusions/Significance Although the in vivo function of this streptococcal GH38 α−mannosidase remains unknown, it is shown to be an α−mannosidase active on N-glycans. SpGH38 lies on an operon that also contains the GH84 hexosaminidase (Spy1600) and an additional putative glycosidase. The activity of SpGH38, together with its genomic context, strongly hints at a function in the degradation of host N- or possibly O-glycans. The absence of any classical signal peptide further suggests that SpGH38 may be intracellular, perhaps functioning in the subsequent degradation of extracellular host glycans following their initial digestion by secreted glycosidases.
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Affiliation(s)
- Michael D. L. Suits
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Yanping Zhu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Edward J. Taylor
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Julia Walton
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - David L. Zechel
- Departments of Chemistry, Queen's University, Kingston, Canada
| | - Harry J. Gilbert
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
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31
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Wu H, Ho C, Ko T, Popat S, Lin C, Wang A. Structural Basis of α‐Fucosidase Inhibition by Iminocyclitols with
K
i
Values in the Micro‐ to Picomolar Range. Angew Chem Int Ed Engl 2010; 49:337-40. [DOI: 10.1002/anie.200905597] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hsing‐Ju Wu
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Ching‐Wen Ho
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
- Department of Chemistry, National Tsing‐Hua University, Taipei (Taiwan)
| | - Tzu‐Ping Ko
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Shinde D. Popat
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Chun‐Hung Lin
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Andrew H.‐J. Wang
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
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32
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Wu H, Ho C, Ko T, Popat S, Lin C, Wang A. Structural Basis of α‐Fucosidase Inhibition by Iminocyclitols withKiValues in the Micro‐ to Picomolar Range. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200905597] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hsing‐Ju Wu
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Ching‐Wen Ho
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
- Department of Chemistry, National Tsing‐Hua University, Taipei (Taiwan)
| | - Tzu‐Ping Ko
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Shinde D. Popat
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Chun‐Hung Lin
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
| | - Andrew H.‐J. Wang
- Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529 (Taiwan), Fax: (+886) 2‐2788‐9759
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33
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Calveras J, Egido-Gabás M, Gómez L, Casas J, Parella T, Joglar J, Bujons J, Clapés P. Dihydroxyacetone Phosphate Aldolase Catalyzed Synthesis of Structurally Diverse Polyhydroxylated Pyrrolidine Derivatives and Evaluation of their Glycosidase Inhibitory Properties. Chemistry 2009; 15:7310-28. [DOI: 10.1002/chem.200900838] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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34
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Ramstadius C, Hekmat O, Eriksson L, Stålbrand H, Cumpstey I. β-Mannosidase and β-hexosaminidase inhibitors: synthesis of 1,2-bis-epi-valienamine and 1-epi-2-acetamido-2-deoxy-valienamine from d-mannose. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kuntz DA, Zhong W, Guo J, Rose DR, Boons GJ. The molecular basis of inhibition of Golgi alpha-mannosidase II by mannostatin A. Chembiochem 2009; 10:268-77. [PMID: 19101978 PMCID: PMC3956299 DOI: 10.1002/cbic.200800538] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Indexed: 11/10/2022]
Abstract
Mannostatin A is a potent inhibitor of the mannose-trimming enzyme, Golgi alpha-mannosidase II (GMII), which acts late in the N-glycan processing pathway. Inhibition of this enzyme provides a route to blocking the transformation-associated changes in cancer cell surface oligosaccharide structures. Here, we report on the synthesis of new Mannostatin derivatives and analyze their binding in the active site of Drosophila GMII by X-ray crystallography. The results indicate that the interaction with the backbone carbonyl of Arg876 is crucial to the high potency of the inhibitor-an effect enhanced by the hydrophobic interaction between the thiomethyl group and an aromatic pocket vicinal to the cleavage site. The various structures indicate that differences in the hydration of protein-ligand complexes are also important determinants of plasticity as well as selectivity of inhibitor binding.
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Affiliation(s)
- Douglas A. Kuntz
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7. Fax: 416-581-7562
| | - Wei Zhong
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602. Fax: 706-542-4412
| | - Jun Guo
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602. Fax: 706-542-4412
| | - David R. Rose
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7. Fax: 416-581-7562
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602. Fax: 706-542-4412
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