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Prencipe F, Barzan C, Savian C, Spalluto G, Carosati E, De Amici M, Mosconi G, Gianferrara T, Federico S, Da Ros T. Gaucher Disease: A Glance from a Medicinal Chemistry Perspective. ChemMedChem 2024; 19:e202300641. [PMID: 38329692 DOI: 10.1002/cmdc.202300641] [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: 11/17/2023] [Revised: 01/19/2024] [Accepted: 02/07/2024] [Indexed: 02/09/2024]
Abstract
Rare diseases are particular pathological conditions affecting a limited number of people and few drugs are known to be effective as therapeutic treatment. Gaucher disease, caused by a deficiency of the lysosomal enzyme glucocerebrosidase, belongs to this class of disorders, and it is considered the most common among the Lysosomal Storage Diseases. The two main therapeutic approaches are the Enzyme Replacement Therapy (ERT) and the Substrate Reduction Therapy (SRT). ERT, consisting in replacing the defective enzyme by administering a recombinant enzyme, is effective in alleviating the visceral symptoms, hallmarks of the most common subtype of the disease whereas it has no effects when symptoms involve CNS, since the recombinant protein is unable to significantly cross the Blood Brain Barrier. The SRT strategy involves inhibiting glucosylceramide synthase (GCS), the enzyme responsible for the production of the associated storage molecule. The rational design of new inhibitors of GCS has been hampered by the lack of either the crystal structure of the enzyme or an in-silico model of the active site which could provide important information regarding the interactions of potential inhibitors with the target, but, despite this, interesting results have been obtained and are herein reviewed.
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Affiliation(s)
- Filippo Prencipe
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Chiara Barzan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
- Molecular Genetics Institute, CNR Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Chiara Savian
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Emanuele Carosati
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Marco De Amici
- Department of Pharmaceutical Sciences, University of Milano Via Luigi Mangiagalli 25, 20133, Milano, Italy
| | - Giorgio Mosconi
- Fidia Farmaceutici Via Ponte della Fabbrica 3/A, 35021, Abano Terme, Italy
| | - Teresa Gianferrara
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Tatiana Da Ros
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
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2
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Cabasso O, Kuppuramalingam A, Lelieveld L, Van der Lienden M, Boot R, Aerts JM, Horowitz M. Animal Models for the Study of Gaucher Disease. Int J Mol Sci 2023; 24:16035. [PMID: 38003227 PMCID: PMC10671165 DOI: 10.3390/ijms242216035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
In Gaucher disease (GD), a relatively common sphingolipidosis, the mutant lysosomal enzyme acid β-glucocerebrosidase (GCase), encoded by the GBA1 gene, fails to properly hydrolyze the sphingolipid glucosylceramide (GlcCer) in lysosomes, particularly of tissue macrophages. As a result, GlcCer accumulates, which, to a certain extent, is converted to its deacylated form, glucosylsphingosine (GlcSph), by lysosomal acid ceramidase. The inability of mutant GCase to degrade GlcSph further promotes its accumulation. The amount of mutant GCase in lysosomes depends on the amount of mutant ER enzyme that shuttles to them. In the case of many mutant GCase forms, the enzyme is largely misfolded in the ER. Only a fraction correctly folds and is subsequently trafficked to the lysosomes, while the rest of the misfolded mutant GCase protein undergoes ER-associated degradation (ERAD). The retention of misfolded mutant GCase in the ER induces ER stress, which evokes a stress response known as the unfolded protein response (UPR). GD is remarkably heterogeneous in clinical manifestation, including the variant without CNS involvement (type 1), and acute and subacute neuronopathic variants (types 2 and 3). The present review discusses animal models developed to study the molecular and cellular mechanisms underlying GD.
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Affiliation(s)
- Or Cabasso
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel; (O.C.); (A.K.)
| | - Aparna Kuppuramalingam
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel; (O.C.); (A.K.)
| | - Lindsey Lelieveld
- Leiden Institute of Chemistry, Leiden University, 9502 Leiden, The Netherlands; (L.L.); (M.V.d.L.); (R.B.)
| | - Martijn Van der Lienden
- Leiden Institute of Chemistry, Leiden University, 9502 Leiden, The Netherlands; (L.L.); (M.V.d.L.); (R.B.)
| | - Rolf Boot
- Leiden Institute of Chemistry, Leiden University, 9502 Leiden, The Netherlands; (L.L.); (M.V.d.L.); (R.B.)
| | - Johannes M. Aerts
- Leiden Institute of Chemistry, Leiden University, 9502 Leiden, The Netherlands; (L.L.); (M.V.d.L.); (R.B.)
| | - Mia Horowitz
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel; (O.C.); (A.K.)
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3
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Richards CM, Jabs S, Qiao W, Varanese LD, Schweizer M, Mosen PR, Riley NM, Klüssendorf M, Zengel JR, Flynn RA, Rustagi A, Widen JC, Peters CE, Ooi YS, Xie X, Shi PY, Bartenschlager R, Puschnik AS, Bogyo M, Bertozzi CR, Blish CA, Winter D, Nagamine CM, Braulke T, Carette JE. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Science 2022; 378:eabn5648. [PMID: 36074821 PMCID: PMC9547973 DOI: 10.1126/science.abn5648] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Lysosomes are key degradative compartments of the cell. Transport to lysosomes relies on GlcNAc-1-phosphotransferase-mediated tagging of soluble enzymes with mannose 6-phosphate (M6P). GlcNAc-1-phosphotransferase deficiency leads to the severe lysosomal storage disorder mucolipidosis II (MLII). Several viruses require lysosomal cathepsins to cleave structural proteins and thus depend on functional GlcNAc-1-phosphotransferase. Here, we used genome-scale CRISPR screens to identify Lysosomal Enzyme Trafficking factor (LYSET) as essential for infection by cathepsin-dependent viruses including SARS-CoV-2. LYSET deficiency resulted in global loss of M6P tagging and mislocalization of GlcNAc-1-phosphotransferase from the Golgi complex to lysosomes. Lyset knockout mice exhibited MLII-like phenotypes and human pathogenic LYSET alleles failed to restore lysosomal sorting defects. Thus, LYSET is required for correct functioning of the M6P trafficking machinery, and mutations in LYSET can explain the phenotype of the associated disorder.
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Affiliation(s)
- Christopher M Richards
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sabrina Jabs
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wenjie Qiao
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren D Varanese
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michaela Schweizer
- Department of Electron Microscopy, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter R Mosen
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | | | - Malte Klüssendorf
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - James R Zengel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.,Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Arjun Rustagi
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - John C Widen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christine E Peters
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yaw Shin Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.,Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Matthew Bogyo
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford, CA, USA
| | - Catherine A Blish
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Claude M Nagamine
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas Braulke
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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4
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Barral DC, Staiano L, Guimas Almeida C, Cutler DF, Eden ER, Futter CE, Galione A, Marques ARA, Medina DL, Napolitano G, Settembre C, Vieira OV, Aerts JMFG, Atakpa‐Adaji P, Bruno G, Capuozzo A, De Leonibus E, Di Malta C, Escrevente C, Esposito A, Grumati P, Hall MJ, Teodoro RO, Lopes SS, Luzio JP, Monfregola J, Montefusco S, Platt FM, Polishchuck R, De Risi M, Sambri I, Soldati C, Seabra MC. Current methods to analyze lysosome morphology, positioning, motility and function. Traffic 2022; 23:238-269. [PMID: 35343629 PMCID: PMC9323414 DOI: 10.1111/tra.12839] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 01/09/2023]
Abstract
Since the discovery of lysosomes more than 70 years ago, much has been learned about the functions of these organelles. Lysosomes were regarded as exclusively degradative organelles, but more recent research has shown that they play essential roles in several other cellular functions, such as nutrient sensing, intracellular signalling and metabolism. Methodological advances played a key part in generating our current knowledge about the biology of this multifaceted organelle. In this review, we cover current methods used to analyze lysosome morphology, positioning, motility and function. We highlight the principles behind these methods, the methodological strategies and their advantages and limitations. To extract accurate information and avoid misinterpretations, we discuss the best strategies to identify lysosomes and assess their characteristics and functions. With this review, we aim to stimulate an increase in the quantity and quality of research on lysosomes and further ground-breaking discoveries on an organelle that continues to surprise and excite cell biologists.
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Affiliation(s)
- Duarte C. Barral
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Institute for Genetic and Biomedical ResearchNational Research Council (CNR)MilanItaly
| | | | - Dan F. Cutler
- MRC Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | - Emily R. Eden
- University College London (UCL) Institute of OphthalmologyLondonUK
| | - Clare E. Futter
- University College London (UCL) Institute of OphthalmologyLondonUK
| | | | | | - Diego Luis Medina
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Clinical Medicine and Surgery DepartmentFederico II UniversityNaplesItaly
| | - Otília V. Vieira
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | | | | | - Gemma Bruno
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Elvira De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Institute of Biochemistry and Cell Biology, CNRRomeItaly
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | | | | | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Michael J. Hall
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Rita O. Teodoro
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Susana S. Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - J. Paul Luzio
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | | | | | | | | | - Maria De Risi
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Irene Sambri
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Chiara Soldati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Miguel C. Seabra
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
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5
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Rowland RJ, Chen Y, Breen I, Wu L, Offen WA, Beenakker TJ, Su Q, van den Nieuwendijk AMCH, Aerts JMFG, Artola M, Overkleeft HS, Davies GJ. Design, Synthesis and Structural Analysis of Glucocerebrosidase Imaging Agents. Chemistry 2021; 27:16377-16388. [PMID: 34570911 PMCID: PMC9298352 DOI: 10.1002/chem.202102359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 12/15/2022]
Abstract
Gaucher disease (GD) is a lysosomal storage disorder caused by inherited deficiencies in β‐glucocerebrosidase (GBA). Current treatments require rapid disease diagnosis and a means of monitoring therapeutic efficacy, both of which may be supported by the use of GBA‐targeting activity‐based probes (ABPs). Here, we report the synthesis and structural analysis of a range of cyclophellitol epoxide and aziridine inhibitors and ABPs for GBA. We demonstrate their covalent mechanism‐based mode of action and uncover binding of the new N‐functionalised aziridines to the ligand binding cleft. These inhibitors became scaffolds for the development of ABPs; the O6‐fluorescent tags of which bind in an allosteric site at the dimer interface. Considering GBA's preference for O6‐ and N‐functionalised reagents, a bi‐functional aziridine ABP was synthesized as a potentially more powerful imaging agent. Whilst this ABP binds to two unique active site clefts of GBA, no further benefit in potency was achieved over our first generation ABPs. Nevertheless, such ABPs should serve useful in the study of GBA in relation to GD and inform the design of future probes.
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Affiliation(s)
- Rhianna J Rowland
- Department of Chemistry, York Structural Biology Laboratory (YSBL), University of York Heslington, York, YO10 5DD, UK
| | - Yurong Chen
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinwegg 55, 2300 RA, Leiden, Netherlands
| | - Imogen Breen
- Department of Chemistry, York Structural Biology Laboratory (YSBL), University of York Heslington, York, YO10 5DD, UK
| | - Liang Wu
- Department of Chemistry, York Structural Biology Laboratory (YSBL), University of York Heslington, York, YO10 5DD, UK
| | - Wendy A Offen
- Department of Chemistry, York Structural Biology Laboratory (YSBL), University of York Heslington, York, YO10 5DD, UK
| | - Thomas J Beenakker
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinwegg 55, 2300 RA, Leiden, Netherlands
| | - Qin Su
- Department of Medicinal Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinwegg 55, 2300 RA, Leiden, Netherlands
| | | | - Johannes M F G Aerts
- Department of Medicinal Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinwegg 55, 2300 RA, Leiden, Netherlands
| | - Marta Artola
- Department of Medicinal Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinwegg 55, 2300 RA, Leiden, Netherlands
| | - Herman S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinwegg 55, 2300 RA, Leiden, Netherlands
| | - Gideon J Davies
- Department of Chemistry, York Structural Biology Laboratory (YSBL), University of York Heslington, York, YO10 5DD, UK
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6
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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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7
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Lentz CS. What you see is what you get: activity-based probes in single-cell analysis of enzymatic activities. Biol Chem 2021; 401:233-248. [PMID: 31939273 DOI: 10.1515/hsz-2019-0262] [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: 05/20/2019] [Accepted: 06/25/2019] [Indexed: 11/15/2022]
Abstract
Molecular imaging methods can provide spatio-temporal information about the distribution of biomolecules or biological processes, such as certain enzymatic activities, in single cells. Within a cell, it is possible to define the subcellular location of a target, its trafficking through the cell, colocalization with other biomolecules of interest and involvement in certain cell biological processes. On the other hand, single-cell imaging promises to distinguish cells that are phenotypically different from each other. The corresponding cellular diversity comprises the presence of functionally distinct cells in a population ('phenotypic heterogeneity'), as well as dynamic cellular responses to external stimuli ('phenotypic plasticity'), which is highly relevant, e.g. during cell differentiation, activation (of immune cells), or cell death. This review focuses on applications of a certain class of chemical probes, the so-called activity-based probes (ABPs), for visualization of enzymatic activities in the single-cell context. It discusses the structure of ABPs and other chemical probes, exemplary applications of ABPs in single-cell studies in human, mouse and bacterial systems and considerations to be made with regard to data interpretation.
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Affiliation(s)
- Christian S Lentz
- Department of Chemical Biology (CBIO), Helmholtz-Centre for Infection Research, Inhoffenstr. 7, D-38102 Braunschweig, Germany
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8
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The Uncovered Function of the Drosophila GBA1a-Encoded Protein. Cells 2021; 10:cells10030630. [PMID: 33809074 PMCID: PMC8000066 DOI: 10.3390/cells10030630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/25/2022] Open
Abstract
Human GBA1 encodes lysosomal acid β-glucocerebrosidase (GCase), which hydrolyzes cleavage of the beta-glucosidic linkage of glucosylceramide (GlcCer). Mutations in this gene lead to reduced GCase activity, accumulation of glucosylceramide and glucosylsphingosine, and development of Gaucher disease (GD). Drosophila melanogaster has two GBA1 orthologs. Thus far, GBA1b was documented as a bone fide GCase-encoding gene, while the role of GBA1a encoded protein remained unclear. In the present study, we characterized a mutant variant of the fly GBA1a, which underwent ERAD and mildly activated the UPR machinery. RNA-seq analyses of homozygous mutant flies revealed upregulation of inflammation-associated as well as of cell-cycle related genes and reduction in programmed cell death (PCD)-associated genes, which was confirmed by qRT-PCR. We also observed compromised cell death in the midgut of homozygous larvae and a reduction in pupation. Our results strongly indicated that GBA1a-encoded protein plays a role in midgut maturation during larvae development.
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9
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Karatas M, Dogan S, Spahiu E, Ašić A, Bešić L, Turan Y. Enzyme kinetics and inhibition parameters of human leukocyte glucosylceramidase. Heliyon 2020; 6:e05191. [PMID: 33163670 PMCID: PMC7609449 DOI: 10.1016/j.heliyon.2020.e05191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/29/2020] [Accepted: 10/05/2020] [Indexed: 11/26/2022] Open
Abstract
Glucosylceramidase (GCase) is a lysosomal enzyme that catalyzes the cleavage of β-glucosidic linkage of glucocerebroside (GC) into glucose and ceramide; thereby, plays an essential function in the degradation of complex lipids and the turnover of cellular membranes. The growing list of 460 mutations in the gene coding for it-glucosylceramidase beta acid 1 (GBA1)-is reported to abolish its catalytic activity and decrease its enzyme stability, associating it with severe health conditions such as Gaucher disease (GD), Parkinson Disease (PD) and Dementia with Lewy bodies (DLB). Although the three-dimensional structure of wild type glucosylceramidase is elucidated, little is known about its features in human cells. Moreover, alternative sources of GCase that prove to be effective in the treatment of diseases with enzyme treatment therapies, impose the need for a simple and cost-effective procedure to study the enzyme behavior. This work, for the first time, shows a well-established, yet simple, cost- and time-efficient protocol for the study of GCase enzyme in human leukocytes by the artificial substrate p-Nitrophenyl-β-D-glucopyranoside (PNPG). Characterization of the enzyme in human leukocytes for activation parameters (optimal pH, Km, and Vmax) and enzyme inhibition was done. The results indicate that the optimum pH of GCase enzyme with PNPG is 5.0. The Km and Vmax values are 12.6mM and 333 U/mg, respectively. Gluconolactone competitively inhibits GCase, with a Ki value of 0.023 mM and IC50 of 0.047 mM. Glucose inhibition is uncompetitive with a Ki of 1.94 mM and IC50 of 55.3 mM. This is the first report for the inhibitory effect of glucose, δ-gluconolactone on human leukocyte GCase activity.
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Affiliation(s)
- Mesut Karatas
- International Burch University, Faculty of Engineering and Natural Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71000 Sarajevo, Bosnia and Herzegovina
| | - Senol Dogan
- Leipzig University, Faculty for Physics and Earth Sciences, Peter Debye Institute, Linnéstraße 5, 04103, Leipzig, Germany
| | - Emrulla Spahiu
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Adna Ašić
- International Burch University, Faculty of Engineering and Natural Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71000 Sarajevo, Bosnia and Herzegovina
| | - Larisa Bešić
- International Burch University, Faculty of Engineering and Natural Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71000 Sarajevo, Bosnia and Herzegovina
| | - Yusuf Turan
- International Burch University, Faculty of Engineering and Natural Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71000 Sarajevo, Bosnia and Herzegovina
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10
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Farfel-Becker T, Roney JC, Cheng XT, Li S, Cuddy SR, Sheng ZH. Neuronal Soma-Derived Degradative Lysosomes Are Continuously Delivered to Distal Axons to Maintain Local Degradation Capacity. Cell Rep 2020; 28:51-64.e4. [PMID: 31269450 PMCID: PMC6696943 DOI: 10.1016/j.celrep.2019.06.013] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/12/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022] Open
Abstract
Neurons face the challenge of maintaining cellular homeostasis through lysosomal degradation. While enzymatically active degradative lysosomes are enriched in the soma, their axonal trafficking and positioning and impact on axonal physiology remain elusive. Here, we characterized axon-targeted delivery of degradative lysosomes by applying fluorescent probes that selectively label active forms of lysosomal cathepsins D, B, L, and GCase. By time-lapse imaging of cortical neurons in microfluidic devices and standard dishes, we reveal that soma-derived degradative lysosomes rapidly influx into distal axons and target to autophagosomes and Parkinson disease-related α-synuclein cargos for local degradation. Impairing lysosome axonal delivery induces an aberrant accumulation of autophagosomes and α-synuclein cargos in distal axons. Our study demonstrates that the axon is an active compartment for local degradation and reveals fundamental aspects of axonal lysosomal delivery and maintenance. Our work establishes a foundation for investigations into axonal lysosome trafficking and functionality in neurodegenerative diseases.
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Affiliation(s)
- Tamar Farfel-Becker
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Room 2B-215, 35 Convent Drive, Bethesda, MD 20892-3706, USA
| | - Joseph C Roney
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Room 2B-215, 35 Convent Drive, Bethesda, MD 20892-3706, USA
| | - Xiu-Tang Cheng
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Room 2B-215, 35 Convent Drive, Bethesda, MD 20892-3706, USA
| | - Sunan Li
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Room 2B-215, 35 Convent Drive, Bethesda, MD 20892-3706, USA
| | - Sean R Cuddy
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Room 2B-215, 35 Convent Drive, Bethesda, MD 20892-3706, USA
| | - Zu-Hang Sheng
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Room 2B-215, 35 Convent Drive, Bethesda, MD 20892-3706, USA.
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11
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Kytidou K, Artola M, Overkleeft HS, Aerts JMFG. Plant Glycosides and Glycosidases: A Treasure-Trove for Therapeutics. FRONTIERS IN PLANT SCIENCE 2020; 11:357. [PMID: 32318081 PMCID: PMC7154165 DOI: 10.3389/fpls.2020.00357] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/11/2020] [Indexed: 05/10/2023]
Abstract
Plants contain numerous glycoconjugates that are metabolized by specific glucosyltransferases and hydrolyzed by specific glycosidases, some also catalyzing synthetic transglycosylation reactions. The documented value of plant-derived glycoconjugates to beneficially modulate metabolism is first addressed. Next, focus is given to glycosidases, the central theme of the review. The therapeutic value of plant glycosidases is discussed as well as the present production in plant platforms of therapeutic human glycosidases used in enzyme replacement therapies. The increasing knowledge on glycosidases, including structure and catalytic mechanism, is described. The novel insights have allowed the design of functionalized highly specific suicide inhibitors of glycosidases. These so-called activity-based probes allow unprecedented visualization of glycosidases cross-species. Here, special attention is paid on the use of such probes in plant science that promote the discovery of novel enzymes and the identification of potential therapeutic inhibitors and chaperones.
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Affiliation(s)
- Kassiani Kytidou
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Marta Artola
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Herman S. Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
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12
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Glucocerebrosidase: Functions in and Beyond the Lysosome. J Clin Med 2020; 9:jcm9030736. [PMID: 32182893 PMCID: PMC7141376 DOI: 10.3390/jcm9030736] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 02/07/2023] Open
Abstract
Glucocerebrosidase (GCase) is a retaining β-glucosidase with acid pH optimum metabolizing the glycosphingolipid glucosylceramide (GlcCer) to ceramide and glucose. Inherited deficiency of GCase causes the lysosomal storage disorder named Gaucher disease (GD). In GCase-deficient GD patients the accumulation of GlcCer in lysosomes of tissue macrophages is prominent. Based on the above, the key function of GCase as lysosomal hydrolase is well recognized, however it has become apparent that GCase fulfills in the human body at least one other key function beyond lysosomes. Crucially, GCase generates ceramides from GlcCer molecules in the outer part of the skin, a process essential for optimal skin barrier property and survival. This review covers the functions of GCase in and beyond lysosomes and also pays attention to the increasing insight in hitherto unexpected catalytic versatility of the enzyme.
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13
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A Route to 1-Deoxynojirimycin and 1-Deoxymannojirimycin Derivatives with Quaternary Centers Adjacent to the Ring Nitrogen from Methyl α-d
-Mannopyranoside. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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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
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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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15
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Deng H, Lei Q, Wu Y, He Y, Li W. Activity-based protein profiling: Recent advances in medicinal chemistry. Eur J Med Chem 2020; 191:112151. [PMID: 32109778 DOI: 10.1016/j.ejmech.2020.112151] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 02/05/2023]
Abstract
Activity-based protein profiling (ABPP) has become an emerging chemical proteomic approach to illustrate the interaction mechanisms between compounds and proteins. This approach has combined organic synthesis, biochemistry, cell biology, biophysics and bioinformatics to accelerate the process of drug discovery in target identification and validation, as well as in the stage of lead discovery and optimization. This review will summarize new developments and applications of ABPP in medicinal chemistry. Here, we mainly described the design principles of activity-base probes (ABPs) and general workflows of ABPP approach. Moreover, we discussed various basic and advanced ABPP strategies and their applications in medicinal chemistry, including competitive and comparative ABPP, two-step ABPP, fluorescence polarization ABPP (FluoPol-ABPP) and ABPs for visualization. In conclusion, this review will give a general overview of the applications of ABPP as a powerful and efficient technique in medicinal chemistry.
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Affiliation(s)
- Hui Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yangping Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yang He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
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16
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Komatsu T, Urano Y. Chemical toolbox for 'live' biochemistry to understand enzymatic functions in living systems. J Biochem 2020; 167:139-149. [PMID: 31553443 DOI: 10.1093/jb/mvz074] [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: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 11/12/2022] Open
Abstract
In this review, we present an overview of the recent advances in chemical toolboxes that are used to provide insights into 'live' protein functions in living systems. Protein functions are mediated by various factors inside of cells, such as protein-protein interactions, posttranslational modifications, and they are also subject to environmental factors such as pH, redox states and crowding conditions. Obtaining a true understanding of protein functions in living systems is therefore a considerably difficult task. Recent advances in research tools have allowed us to consider 'live' biochemistry as a valid approach to precisely understand how proteins function in a live cell context.
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Affiliation(s)
- Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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17
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Koenders SA, Wijaya LS, Erkelens MN, Bakker AT, van der Noord VE, van Rooden EJ, Burggraaff L, Putter PC, Botter E, Wals K, van den Elst H, den Dulk H, Florea BI, van de Water B, van Westen GJP, Mebius RE, Overkleeft HS, Le Dévédec SE, van der Stelt M. Development of a Retinal-Based Probe for the Profiling of Retinaldehyde Dehydrogenases in Cancer Cells. ACS CENTRAL SCIENCE 2019; 5:1965-1974. [PMID: 31893226 PMCID: PMC6936097 DOI: 10.1021/acscentsci.9b01022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 05/13/2023]
Abstract
Retinaldehyde dehydrogenases belong to a superfamily of enzymes that regulate cell differentiation and are responsible for detoxification of anticancer drugs. Chemical tools and methods are of great utility to visualize and quantify aldehyde dehydrogenase (ALDH) activity in health and disease. Here, we present the discovery of a first-in-class chemical probe based on retinal, the endogenous substrate of retinal ALDHs. We unveil the utility of this probe in quantitating ALDH isozyme activity in a panel of cancer cells via both fluorescence and chemical proteomic approaches. We demonstrate that our probe is superior to the widely used ALDEFLUOR assay to explain the ability of breast cancer (stem) cells to produce all-trans retinoic acid. Furthermore, our probe revealed the cellular selectivity profile of an advanced ALDH1A1 inhibitor, thereby prompting us to investigate the nature of its cytotoxicity. Our results showcase the application of substrate-based probes in interrogating pathologically relevant enzyme activities. They also highlight the general power of chemical proteomics in driving the discovery of new biological insights and its utility to guide drug discovery efforts.
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Affiliation(s)
- Sebastiaan
T. A. Koenders
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
- Oncode Institute, Utrecht 3521 AL, The Netherlands
| | - Lukas S. Wijaya
- Cancer
Therapeutics and Drug Safety, Division of Drug Discovery and Safety,
Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Martje N. Erkelens
- Department
of Molecular Cell Biology and Immunology, Amsterdam University Medical Centra, Amsterdam 1081 HV, The Netherlands
| | - Alexander T. Bakker
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Vera E. van der Noord
- Cancer
Therapeutics and Drug Safety, Division of Drug Discovery and Safety,
Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Eva J. van Rooden
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Lindsey Burggraaff
- Computational
Drug Discovery, Division of Drug Discovery and Safety, Leiden Academic
Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Pasquale C. Putter
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Else Botter
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Kim Wals
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
- Oncode Institute, Utrecht 3521 AL, The Netherlands
| | - Hans van den Elst
- Department
of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Hans den Dulk
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Bogdan I. Florea
- Department
of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Bob van de Water
- Cancer
Therapeutics and Drug Safety, Division of Drug Discovery and Safety,
Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Gerard J. P. van Westen
- Computational
Drug Discovery, Division of Drug Discovery and Safety, Leiden Academic
Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Reina E. Mebius
- Department
of Molecular Cell Biology and Immunology, Amsterdam University Medical Centra, Amsterdam 1081 HV, The Netherlands
| | - Herman S. Overkleeft
- Department
of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Sylvia E. Le Dévédec
- Cancer
Therapeutics and Drug Safety, Division of Drug Discovery and Safety,
Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Mario van der Stelt
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
- Oncode Institute, Utrecht 3521 AL, The Netherlands
- E-mail:
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18
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Artola M, Kuo CL, Lelieveld LT, Rowland RJ, van der Marel GA, Codée JDC, Boot RG, Davies GJ, Aerts JMFG, Overkleeft HS. Functionalized Cyclophellitols Are Selective Glucocerebrosidase Inhibitors and Induce a Bona Fide Neuropathic Gaucher Model in Zebrafish. J Am Chem Soc 2019; 141:4214-4218. [PMID: 30811188 PMCID: PMC6418866 DOI: 10.1021/jacs.9b00056] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Gaucher disease is caused by inherited deficiency in glucocerebrosidase (GBA, a retaining β-glucosidase), and deficiency in GBA constitutes the largest known genetic risk factor for Parkinson's disease. In the past, animal models of Gaucher disease have been generated by treatment with the mechanism-based GBA inhibitors, conduritol B epoxide (CBE), and cyclophellitol. Both compounds, however, also target other retaining glycosidases, rendering generation and interpretation of such chemical knockout models complicated. Here we demonstrate that cyclophellitol derivatives carrying a bulky hydrophobic substituent at C8 are potent and selective GBA inhibitors and that an unambiguous Gaucher animal model can be readily generated by treatment of zebrafish with these.
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Affiliation(s)
| | | | | | - Rhianna J Rowland
- Department of Chemistry, York Structural Biology Laboratory , University of York , Heslington, York YO10 5DD , United Kingdom
| | | | | | | | - Gideon J Davies
- Department of Chemistry, York Structural Biology Laboratory , University of York , Heslington, York YO10 5DD , United Kingdom
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19
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Woeste MA, Stern S, Raju DN, Grahn E, Dittmann D, Gutbrod K, Dörmann P, Hansen JN, Schonauer S, Marx CE, Hamzeh H, Körschen HG, Aerts JMFG, Bönigk W, Endepols H, Sandhoff R, Geyer M, Berger TK, Bradke F, Wachten D. Species-specific differences in nonlysosomal glucosylceramidase GBA2 function underlie locomotor dysfunction arising from loss-of-function mutations. J Biol Chem 2019; 294:3853-3871. [PMID: 30662006 DOI: 10.1074/jbc.ra118.006311] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/16/2019] [Indexed: 11/06/2022] Open
Abstract
The nonlysosomal glucosylceramidase β2 (GBA2) catalyzes the hydrolysis of glucosylceramide to glucose and ceramide. Mutations in the human GBA2 gene have been associated with hereditary spastic paraplegia (HSP), autosomal-recessive cerebellar ataxia (ARCA), and the Marinesco-Sjögren-like syndrome. However, the underlying molecular mechanisms are ill-defined. Here, using biochemistry, immunohistochemistry, structural modeling, and mouse genetics, we demonstrate that all but one of the spastic gait locus #46 (SPG46)-connected mutations cause a loss of GBA2 activity. We demonstrate that GBA2 proteins form oligomeric complexes and that protein-protein interactions are perturbed by some of these mutations. To study the pathogenesis of GBA2-related HSP and ARCA in vivo, we investigated GBA2-KO mice as a mammalian model system. However, these mice exhibited a high phenotypic variance and did not fully resemble the human phenotype, suggesting that mouse and human GBA2 differ in function. Whereas some GBA2-KO mice displayed a strong locomotor defect, others displayed only mild alterations of the gait pattern and no signs of cerebellar defects. On a cellular level, inhibition of GBA2 activity in isolated cerebellar neurons dramatically affected F-actin dynamics and reduced neurite outgrowth, which has been associated with the development of neurological disorders. Our results shed light on the molecular mechanism underlying the pathogenesis of GBA2-related HSP and ARCA and reveal species-specific differences in GBA2 function in vivo.
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Affiliation(s)
- Marina A Woeste
- From the Institute of Innate Immunity, University Hospital, University of Bonn, 53127 Bonn, Germany
| | - Sina Stern
- the German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Diana N Raju
- From the Institute of Innate Immunity, University Hospital, University of Bonn, 53127 Bonn, Germany
| | - Elena Grahn
- the Center of Advanced European Studies and Research (Caesar), 53175 Bonn, Germany
| | - Dominik Dittmann
- From the Institute of Innate Immunity, University Hospital, University of Bonn, 53127 Bonn, Germany
| | - Katharina Gutbrod
- the Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53115 Bonn, Germany
| | - Peter Dörmann
- the Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, 53115 Bonn, Germany
| | - Jan N Hansen
- From the Institute of Innate Immunity, University Hospital, University of Bonn, 53127 Bonn, Germany
| | - Sophie Schonauer
- the Center of Advanced European Studies and Research (Caesar), 53175 Bonn, Germany
| | - Carina E Marx
- the Center of Advanced European Studies and Research (Caesar), 53175 Bonn, Germany
| | - Hussein Hamzeh
- the Center of Advanced European Studies and Research (Caesar), 53175 Bonn, Germany
| | - Heinz G Körschen
- the Center of Advanced European Studies and Research (Caesar), 53175 Bonn, Germany
| | - Johannes M F G Aerts
- the Leiden Institute of Chemistry, Leiden University, 2333 CD Leiden, The Netherlands
| | - Wolfgang Bönigk
- the Center of Advanced European Studies and Research (Caesar), 53175 Bonn, Germany
| | - Heike Endepols
- the Institute of Radiochemistry and Experimental Molecular Imaging (IREMB) and Department of Nuclear Medicine, University Hospital of Cologne, 50937 Cologne, Germany
| | - Roger Sandhoff
- the Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany.,the Lipid Pathobiochemistry Group, German Cancer Research Center, 69120 Heidelberg, Germany, and
| | - Matthias Geyer
- the Institute of Structural Biology, University Hospital, University of Bonn, 53127 Bonn, Germany
| | - Thomas K Berger
- the Center of Advanced European Studies and Research (Caesar), 53175 Bonn, Germany
| | - Frank Bradke
- the German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Dagmar Wachten
- From the Institute of Innate Immunity, University Hospital, University of Bonn, 53127 Bonn, Germany, .,the Center of Advanced European Studies and Research (Caesar), 53175 Bonn, Germany
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