1
|
Artola M, Aerts JMFG, van der Marel GA, Rovira C, Codée JDC, Davies GJ, Overkleeft HS. From Mechanism-Based Retaining Glycosidase Inhibitors to Activity-Based Glycosidase Profiling. J Am Chem Soc 2024; 146:24729-24741. [PMID: 39213505 DOI: 10.1021/jacs.4c08840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Activity-based protein profiling (ABPP) is an effective technology for the identification and functional annotation of enzymes in complex biological samples. ABP designs are normally directed to an enzyme active site nucleophile, and within the field of Carbohydrate-Active Enzymes (CAZymes), ABPP has been most successful for those enzymes that feature such a residue: retaining glycosidases (GHs). Several mechanism-based covalent and irreversible retaining GH inhibitors have emerged over the past sixty years. ABP designs based on these inhibitor chemistries appeared since the turn of the millennium, and we contributed to the field by designing a suite of retaining GH ABPs modeled on the structure and mode of action of the natural product, cyclophellitol. These ABPs enable the study of both exo- and endo-acting retaining GHs in human health and disease, for instance in genetic metabolic disorders in which retaining GHs are deficient. They are also finding increasing use in the study of GHs in gut microbiota and environmental microorganisms, both in the context of drug (de)toxification in the gut and that of biomass polysaccharide processing for future sustainable energy and chemistries. This account comprises the authors' view on the history of mechanism-based retaining GH inhibitor design and discovery, on how these inhibitors served as blueprints for retaining GH ABP design, and on some current and future developments on how cyclophellitol-based ABPs may drive the discovery of retaining GHs and their inhibitors.
Collapse
Affiliation(s)
- Marta Artola
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | | | - Carme Rovira
- Departament de Química Inorgànica I Orgànica & IQTCUB, Universitat de Barcelona, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08020, Spain
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Gideon J Davies
- Department of Chemistry, The University York, Heslington, York YO10 5DD, United Kingdom
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| |
Collapse
|
2
|
Kim Y, Li H, Choi J, Boo J, Jo H, Hyun JY, Shin I. Glycosidase-targeting small molecules for biological and therapeutic applications. Chem Soc Rev 2023; 52:7036-7070. [PMID: 37671645 DOI: 10.1039/d3cs00032j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Glycosidases are ubiquitous enzymes that catalyze the hydrolysis of glycosidic linkages in oligosaccharides and glycoconjugates. These enzymes play a vital role in a wide variety of biological events, such as digestion of nutritional carbohydrates, lysosomal catabolism of glycoconjugates, and posttranslational modifications of glycoproteins. Abnormal glycosidase activities are associated with a variety of diseases, particularly cancer and lysosomal storage disorders. Owing to the physiological and pathological significance of glycosidases, the development of small molecules that target these enzymes is an active area in glycoscience and medicinal chemistry. Research efforts carried out thus far have led to the discovery of numerous glycosidase-targeting small molecules that have been utilized to elucidate biological processes as well as to develop effective chemotherapeutic agents. In this review, we describe the results of research studies reported since 2018, giving particular emphasis to the use of fluorescent probes for detection and imaging of glycosidases, activity-based probes for covalent labelling of these enzymes, glycosidase inhibitors, and glycosidase-activatable prodrugs.
Collapse
Affiliation(s)
- Yujun Kim
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hui Li
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Joohee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Jihyeon Boo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hyemi Jo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| |
Collapse
|
3
|
Kuo CL, Su Q, van den Nieuwendijk AMCH, Beenakker TJM, Offen WA, Willems LI, Boot RG, Sarris AJ, Marques ARA, Codée JDC, van der Marel GA, Florea BI, Davies GJ, Overkleeft HS, Aerts JMFG. The development of a broad-spectrum retaining β-exo-galactosidase activity-based probe. Org Biomol Chem 2023; 21:7813-7820. [PMID: 37724332 DOI: 10.1039/d3ob01261a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Acid β-galactosidase (GLB1) and galactocerebrosidase (GALC) are retaining exo-β-galactosidases involved in lysosomal glycoconjugate metabolism. Deficiency of GLB1 may result in the lysosomal storage disorders GM1 gangliosidosis, Morquio B syndrome, and galactosialidosis, and deficiency of GALC may result in Krabbe disease. Activity-based protein profiling (ABPP) is a powerful technique to assess the activity of retaining glycosidases in relation to health and disease. This work describes the use of fluorescent and biotin-carrying activity-based probes (ABPs) to assess the activity of both GLB1 and GALC in cell lysates, culture media, and tissue extracts. The reported ABPs, which complement the growing list of retaining glycosidase ABPs based on configurational isomers of cyclophellitol, should assist in fundamental and clinical research on various β-galactosidases, whose inherited deficiencies cause debilitating lysosomal storage disorders.
Collapse
Affiliation(s)
- Chi-Lin Kuo
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - Qin Su
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | | | - Thomas J M Beenakker
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - Wendy A Offen
- Department of Chemistry, University of York, Heslington, York, YO10 5DD York, UK
| | - Lianne I Willems
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
- Department of Chemistry, University of York, Heslington, York, YO10 5DD York, UK
| | - Rolf G Boot
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - Alexi J Sarris
- Bioorganic Synthesis group, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - André R A Marques
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - Jeroen D C Codée
- Bioorganic Synthesis group, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - Gijsbert A van der Marel
- Bioorganic Synthesis group, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - Bogdan I Florea
- Bioorganic Synthesis group, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York, YO10 5DD York, UK
| | - Herman S Overkleeft
- Bioorganic Synthesis group, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands.
| |
Collapse
|
4
|
Hansen T, Nin-Hill A, Codée JDC, Hamlin TA, Rovira C. Rational Tuning of the Reactivity of Three-Membered Heterocycle Ring Openings via S N 2 Reactions. Chemistry 2022; 28:e202201649. [PMID: 35896443 DOI: 10.1002/chem.202201649] [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: 05/27/2022] [Indexed: 01/07/2023]
Abstract
The development of small-molecule covalent inhibitors and probes continuously pushes the rapidly evolving field of chemical biology forward. A key element in these molecular tool compounds is the "electrophilic trap" that allows a covalent linkage with the target enzyme. The reactivity of this entity needs to be well balanced to effectively trap the desired enzyme, while not being attacked by off-target nucleophiles. Here we investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with a nitrogen (aziridine), phosphorus (phosphirane), oxygen (epoxide) or sulfur atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring opening of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C6 H10 Y with Y=NH, PH, O, S). It was revealed that the activation energy of the ring opening does not necessarily follow the trend that is expected from C-Y leaving-group bond strength, but steeply decreases from Y=NH, to PH, to O, to S. We illustrate that the HOMONu -LUMOSubstrate interaction is an all-important factor for the observed reactivity. In addition, we show that the activation energy of aziridines and phosphiranes can be tuned far below that of the corresponding epoxides and thiiranes by the addition of proper electron-withdrawing ring substituents. Our results provide mechanistic insights to rationally tune the reactivity of this class of popular electrophilic traps and can guide the experimental design of covalent inhibitors and probes for enzymatic activity.
Collapse
Affiliation(s)
- Thomas Hansen
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (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, 08028, Barcelona, Spain
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020, Barcelona, Spain
| |
Collapse
|
5
|
Witte MD, Minnaard AJ. Site-Selective Modification of (Oligo)Saccharides. ACS Catal 2022; 12:12195-12205. [PMID: 36249871 PMCID: PMC9552177 DOI: 10.1021/acscatal.2c03876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/14/2022] [Indexed: 11/29/2022]
Abstract
Oligosaccharides, either as such or as part of glycolipids, glycopeptides, or glycoproteins, are ubiquitous in nature and fulfill important roles in the living cell. Also in medicine and to some extent in materials, oligosaccharides play an important role. In order to study their function, modifying naturally occurring oligosaccharides, and building in reactive groups and reporter groups in oligosaccharides, are key strategies. The development of oligosaccharides as drugs, or vaccines, requires the introduction of subtle modifications in the structure of oligosaccharides to optimize efficacy and, in the case of antibiotics, circumvent bacterial resistance. Provided the natural oligosaccharide is available, site-selective modification is an attractive approach as total synthesis of the target is often very laborious. Researchers in catalysis areas, such as transition-metal catalysis, enzyme catalysis, organocatalysis, and photoredox catalysis, have made considerable progress in the development of site-selective and late-stage modification methods for mono- and oligosaccharides. It is foreseen that the fields of enzymatic modification of glycans and the chemical modification of (oligo)saccharides will approach and potentially meet each other, but there is a lot to learn and discover before this will be the case.
Collapse
Affiliation(s)
- Martin D. Witte
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Adriaan J. Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| |
Collapse
|