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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Sivakrishna B, Sahoo S, Kumar A, Pal S. Development of a Divergent Synthetic Avenue towards Conduritol‐E,
allo
‐Inositol,
talo
‐Quercitol and Palitantin from D‐Ribose. ChemistrySelect 2022. [DOI: 10.1002/slct.202203346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Balija Sivakrishna
- School of Basic Sciences Indian Institute of Technology Bhubaneswar Argul Khordha, Bhubaneswar Odisha 752050
| | - Subrata Sahoo
- School of Basic Sciences Indian Institute of Technology Bhubaneswar Argul Khordha, Bhubaneswar Odisha 752050
| | - Aditya Kumar
- School of Basic Sciences Indian Institute of Technology Bhubaneswar Argul Khordha, Bhubaneswar Odisha 752050
| | - Shantanu Pal
- School of Basic Sciences Indian Institute of Technology Bhubaneswar Argul Khordha, Bhubaneswar Odisha 752050
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3
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Ofman TP, Küllmer F, van der Marel GA, Codée JDC, Overkleeft HS. An Orthogonally Protected Cyclitol for the Construction of Nigerose- and Dextran-Mimetic Cyclophellitols. Org Lett 2021; 23:9516-9519. [PMID: 34846911 PMCID: PMC8689644 DOI: 10.1021/acs.orglett.1c03723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Cyclophellitols are
potent inhibitors of exo- and endoglycosidases.
Efficient synthetic methodologies are needed to fully capitalize on
this intriguing class of mechanism-based enzyme deactivators. We report
the synthesis of an orthogonally protected cyclitol from d-glucal (19% yield over 12 steps) and its use in the synthesis of
α-(1,3)-linked di- and trisaccharide dextran mimetics. These
new glycomimetics may find use as Dextranase inhibitors, and the developed
chemistries in widening the palette of glycoprocessing enzyme-targeting
glycomimetics.
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Affiliation(s)
- Tim P Ofman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Florian Küllmer
- 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
| | - 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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4
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Su Q, Schröder SP, Lelieveld LT, Ferraz MJ, Verhoek M, Boot RG, Overkleeft HS, Aerts JMFG, Artola M, Kuo C. Xylose-Configured Cyclophellitols as Selective Inhibitors for Glucocerebrosidase. Chembiochem 2021; 22:3090-3098. [PMID: 34459538 PMCID: PMC8596838 DOI: 10.1002/cbic.202100396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/29/2021] [Indexed: 02/03/2023]
Abstract
Glucocerebrosidase (GBA), a lysosomal retaining β-d-glucosidase, has recently been shown to hydrolyze β-d-xylosides and to transxylosylate cholesterol. Genetic defects in GBA cause the lysosomal storage disorder Gaucher disease (GD), and also constitute a risk factor for developing Parkinson's disease. GBA and other retaining glycosidases can be selectively visualized by activity-based protein profiling (ABPP) using fluorescent probes composed of a cyclophellitol scaffold having a configuration tailored to the targeted glycosidase family. GBA processes β-d-xylosides in addition to β-d-glucosides, this in contrast to the other two mammalian cellular retaining β-d-glucosidases, GBA2 and GBA3. Here we show that the xylopyranose preference also holds up for covalent inhibitors: xylose-configured cyclophellitol and cyclophellitol aziridines selectively react with GBA over GBA2 and GBA3 in vitro and in vivo, and that the xylose-configured cyclophellitol is more potent and more selective for GBA than the classical GBA inhibitor, conduritol B-epoxide (CBE). Both xylose-configured cyclophellitol and cyclophellitol aziridine cause accumulation of glucosylsphingosine in zebrafish embryo, a characteristic hallmark of GD, and we conclude that these compounds are well suited for creating such chemically induced GD models.
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Affiliation(s)
- Qin Su
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Sybrin P. Schröder
- Department of Bio-organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Lindsey T. Lelieveld
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Maria J. Ferraz
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marri Verhoek
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Rolf G. Boot
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marta Artola
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Chi‐Lin Kuo
- Department of Medical BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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5
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McGregor NGS, Artola M, Nin-Hill A, Linzel D, Haon M, Reijngoud J, Ram A, Rosso MN, van der Marel GA, Codée JDC, van Wezel GP, Berrin JG, Rovira C, Overkleeft HS, Davies GJ. Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining α-l-Arabinofuranosidases. J Am Chem Soc 2020; 142:4648-4662. [PMID: 32053363 PMCID: PMC7068720 DOI: 10.1021/jacs.9b11351] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Identifying
and characterizing the enzymes responsible for an observed
activity within a complex eukaryotic catabolic system remains one
of the most significant challenges in the study of biomass-degrading
systems. The debranching of both complex hemicellulosic and pectinaceous
polysaccharides requires the production of α-l-arabinofuranosidases
among a wide variety of coexpressed carbohydrate-active enzymes. To
selectively detect and identify α-l-arabinofuranosidases
produced by fungi grown on complex biomass, potential covalent inhibitors
and probes which mimic α-l-arabinofuranosides were
sought. The conformational free energy landscapes of free α-l-arabinofuranose and several rationally designed covalent α-l-arabinofuranosidase inhibitors were analyzed. A synthetic
route to these inhibitors was subsequently developed based on a key
Wittig–Still rearrangement. Through a combination of kinetic
measurements, intact mass spectrometry, and structural experiments,
the designed inhibitors were shown to efficiently label the catalytic
nucleophiles of retaining GH51 and GH54 α-l-arabinofuranosidases.
Activity-based probes elaborated from an inhibitor with an aziridine
warhead were applied to the identification and characterization of
α-l-arabinofuranosidases within the secretome of A. niger grown on arabinan. This method was extended to
the detection and identification of α-l-arabinofuranosidases
produced by eight biomass-degrading basidiomycete fungi grown on complex
biomass. The broad applicability of the cyclophellitol-derived activity-based
probes and inhibitors presented here make them a valuable new tool
in the characterization of complex eukaryotic carbohydrate-degrading
systems and in the high-throughput discovery of α-l-arabinofuranosidases.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, U.K
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Alba Nin-Hill
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Daniël Linzel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Mireille Haon
- INRA, Aix Marseille University, Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, F-13009 Marseille, France
| | - Jos Reijngoud
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Arthur Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Marie-Noëlle Rosso
- INRA, Aix Marseille University, Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, F-13009 Marseille, France
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jean-Guy Berrin
- INRA, Aix Marseille University, Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, F-13009 Marseille, France
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica (Secció de Quı́mica Orgànica) & Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, U.K
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