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Trenkler, N.E. 2023

Photocleavable activity-based acid glucosylceramidase probes

Doctoral Thesis

open access

Lysosomal acid glucosylceramidase (GBA1) is a lysosomal enzyme that degrades glucolipids with its main substrate being glucosylceramide (GlcCer). Defects in the GBA1 gene lead to... Show moreLysosomal acid glucosylceramidase (GBA1) is a lysosomal enzyme that degrades glucolipids with its main substrate being glucosylceramide (GlcCer). Defects in the GBA1 gene lead to glycosphingolipidosis Gaucher disease (GD), in which the hydrolysis of GlcCer is impaired and therefore, it accumulates in the lysosome. GD has a wide range of phenotypes that reaches from asymptomatic to neuropathologic manifestations, which are lethal within the first years of life. Although various GBA1 mutations have been identified, they cannot be systematically matched with GD phenotypes. Therefore, this thesis aims to get a better understanding of GBA1 and its role in GD by identifying GBA1’s cellular interaction partners with the aid of an enrichment assay. For this assay, photocleavable activity-based probes (ABPs) were developed, which ought to be able to isolate GBA1 from a cell lysate together with its interaction partners with the aid of streptavidin-coated beads. By photocleaving the complex off the beads, the background of the GBA1-containing samples can be lowered. So far, GBA1 could successfully be isolated from a cell lysate with the developed ABPs. Next, the assay conditions need to be optimized for isolation of GBA1 together with its interaction partners. Show less

Lit, V.A.J. 2023

Inhibitors and probes targeting mannanases

Doctoral Thesis

open access

This thesis describes the synthesis and biochemical evaluation of a variety of cyclophellitol based activity-based probes and inhibitors targeting various endo- and exo-acting retaining... Show moreThis thesis describes the synthesis and biochemical evaluation of a variety of cyclophellitol based activity-based probes and inhibitors targeting various endo- and exo-acting retaining glycosidases. In the last two decades a variety of probes and inhibitors for (hemi)cellulose degrading enzymes have been developed. However, at the onset of the work described in this thesis the focus has been mainly on cellulases, xylanases, xyloglucanases and glycanases. Chapter 2 describes the design and synthesis of a first generation of inhibitors and probes for β-mannanases. The general scaffold is composed of a β-1,4-linked mannobioside featuring either an epoxide or an aziridine warhead. All synthesized probes feature a linker attached to the nonreducing end and are condensed with either biotin or Cy5. Biochemical evaluation in an Aspergillus niger secretome revealed the utility of these compounds but also the limitations. The probes react efficiently with some endo-β-mannanases yet lack reactivity with others. Chapter 3 describes the design and synthesis of a second generation of β-mannanase probes and inhibitors designed to overcome the limitations of the first generation by changing the general scaffold. In this chapter two conceptually distinct ABP scaffolds are presented: a β-1,4-linked mannotriose and a β-1,4-linked manno-gluco configured scaffold. The second generation Cy5 probes are evaluated in Aspergillus niger secretomes and compared to the first generation. Chapter 4 describes studies towards the design and synthesis of inhibitors and ABPS for both α-N-acetylglucosaminidase and α-Nacetylgalactosaminidase. The chapter introduces an orthogonally protected ribose building block as common intermediate from which both mannoseand talose configured cyclohexenes are synthesized. Furthermore it describes a late state stereoselective C-2 inversion with an azide to install a 20 nitrogen atom at C-2. Chapter 5 presents a summary and suggestions forfuture research. Show less

Wendel, T.J. 2023

New chemical tools to illuminate N-acylphosphatidylethanolamine biosynthesis

Doctoral Thesis

some documents under embargo until 2024-09-23

This thesis describes the development and optimization of the first molecular tools to study the enzyme PLA2G4E. After remaining elusive for many years, in 2016, this enzyme was discovered to be... Show moreThis thesis describes the development and optimization of the first molecular tools to study the enzyme PLA2G4E. After remaining elusive for many years, in 2016, this enzyme was discovered to be responsible for the calcium-dependent formation of N-acylphosphatidylethanolamines (NAPEs) in cells. NAPEs are low-abundant lipid species that play roles in membrane stabilization, cell signaling and homeostasis. They are well-known as precursors to the signaling lipids of the N-acylethanolamine (NAE) class, but their own biological functions remain relatively poorly understood. To find inhibitors of PLA2G4E, a focused compound library was screened in a newly developed activity-based protein profiling (ABPP) assay. Hits were identified and optimized by building structure-activity relationships (SARs) through organic synthesis and activity assays. WEN091 was identified as potent inhibitor of PLA2G4E that was able to reduce cellular NAPE levels. Cellular target engagement was confirmed by use of a tailored activity-based probe. Using these molecular tools, the relevance of NAPEs and PLA2G4E in cellular processes and disease may be elucidated. Show less

Chen, Y. 2022

Exploring chemical space in covalent and competitive glycosidase inhibitor design

Doctoral Thesis

open access

Glycoside hydrolases (glycosidases/GHs) are widely abundant enzymes in all kingdoms of life and are important biocatalysts that catalyze the hydrolysis of glycosidic linkages in oligo... Show moreGlycoside hydrolases (glycosidases/GHs) are widely abundant enzymes in all kingdoms of life and are important biocatalysts that catalyze the hydrolysis of glycosidic linkages in oligo/polysaccharides, glycoproteins and glycolipids with tremendous efficiency. Abnormal glycosidase activity is intimately associated with a variety of human diseases. Overexpression of heparanase, for example, is implicated in almost all cancers examined, and correlates with increased tumor size, tumor angiogenesis, enhanced metastasis and poor prognosis. Specific inhibitors of glycosidases are of great value, not only because they can serve as useful biological tools to study the catalytic machinery, mechanism and itinerary of target enzymes by crystal structure analysis of (covalent) inhibitor-enzyme complexes, but also because they may act as starting points for the development of therapeutic drugs for the treatment of glycosidase-mediated diseases. Additionally, covalent mechanism-based inhibitors have been used as scaffolds for the development of activity-based probes (ABPs) which allow profiling of glycosidases in complex biological systems. The research described in this dissertation focus on the development and biochemical evaluation of covalent inhibitors and ABPs for retaining endo- and exo-glycosidases including starch-degrading enzymes and human lysosomal β-glucocerebrosidase (GBA), as well as the synthesis of a panel of uronic acid-type 1-N-iminosugars as potential competitive heparanase inhibitors. Show less

Boer, C. de 2021

Inhibitors and probes targeting endo-glycosidases

Doctoral Thesis

open access

The chemical synthesis of inhibitors and probes targeting endo-glycosidases.

Gagestein, B. 2020

Chemical tools to study lipid signaling

Doctoral Thesis

open access

Synthesis and application of chemical biology tools to study immunomodulatory signaling lipids.

Koenders, S.T.A. 2020

Visualization of vitamin A metabolism

Doctoral Thesis

open access

Vitamin A or retinol is essential in embryonic development, the visual cycle and the immune system. Vitamin A is converted to retinoic acid (RA) by aldehyde dehydrogenases (ALDHs). The family of... Show moreVitamin A or retinol is essential in embryonic development, the visual cycle and the immune system. Vitamin A is converted to retinoic acid (RA) by aldehyde dehydrogenases (ALDHs). The family of ALDHs consists of 19 members, three of which (ALDH1A1, ALDH1A2 andALDH1A3) have retinal as their preferred substrate. Due to a lack of selective and potent inhibitors for these enzymes, it is difficult to study their individual contribution to Vitamin A metabolism in biological systems.Therefore an activity-based probe based on the chemical structure of retinal has been synthesized to enable activity-based protein profiling (ABPP) of ALDHs. The probe covalently binds to the catalytic cysteine of ALDH enzymes which can then be visualized on gel or analyzed by proteomics using ligation chemistry.After biological evaluation of the probe this chemical tool has been used to study the influence of individual ALDH enzymes on the mucosal immune system and to determine the ALDH profile of several breast cancer cell lines. Thus showcasing its use to study Vitamin A metabolism in a wide variety of biological settings including but not limited to: immunology, cancer and (cancer) stem cells. Show less

Kuo, C.L. 2019

Applications for activity-based probes in biomedical research on glycosidases

Doctoral Thesis

open access

Lysosomal glycosidases are acid hydrolases that fragment glycoconjugates in lysosomes. Their inherited deficiency in human is the cause of a number of lysosomal storage disorders (LSDs),... Show moreLysosomal glycosidases are acid hydrolases that fragment glycoconjugates in lysosomes. Their inherited deficiency in human is the cause of a number of lysosomal storage disorders (LSDs), showing characteristic lysosomal accumulation of undegraded glycoconjugates. In the past, activity-based probes (ABPs) based on cyclophellitol or cyclophellitol aziridine scaffold have emerged as powerful tools enabling sensitive quantification of a number of lysosomal glycosidases in extracts of cells and tissue, as well as in intact cells. This thesis describes the characterization of several novel ABP classes targeting α-glucosidase, β-glucuronidase, α-L-iduronidase, α-mannosidase, β-mannosidase, and β-galactosidase, as well as a broad scale of applications for ABPs in LSD research. Novel glucocerebrosidase inhibitors based on the cyclophellitol scaffold are also described, which are brain-permeable, selective, and potently inactivate the enzyme in adult zebrafish. Additionally, a protocol for gel-based and microscopy-based detection of glucocerebrosidase is described. Show less

Esbroeck, A.C.M. van 2019

Activity-based protein profiling in drug-discovery

Doctoral Thesis

open access

In the last decades, activity-based protein profiling (ABPP) has emerged as a powerful chemical tool that may aid the ever-challenging drug discovery process. In this thesis ABPP is explored as a... Show moreIn the last decades, activity-based protein profiling (ABPP) has emerged as a powerful chemical tool that may aid the ever-challenging drug discovery process. In this thesis ABPP is explored as a versatile tool in drug discovery and cell biology.ABPP enabled rapid assessment of clinical samples from patients suffering from cardiac ischemia, thereby giving insight into the serine hydrolase activity profile of these patients. The identification of molecular role players may lead to the discovery of novel therapeutic targets or biomarkers. In addition, ABPP can provide insight in a drug’s interaction landscape, by enabling target engagement studies and inhibitor selectivity profiling. This was demonstrated by the identification of multiple off targets of the experimental drug BIA 10-2474 that caused severe neurological symptoms in a phase I clinical trial. In zebrafish larvae, the ABPP methodology enabled in vivo selectivity profiling and in addition served as a powerful tool to map the kinase and serine hydrolase landscape throughout embryonic development. Lastly, combining ABPP with other biochemical techniques including CRISPR/Cas9 technology and lipidomics, can provide new insights in cellular biology, which was showcased by the identification of ABHD6 as a diacylglycerol-lipase in a cellular model of neuronal differentiation. Show less

Janssen, A.P.A. 2019

Inhibitor selectivity: profiling and prediction

Doctoral Thesis

open access

Less than 1 in 10 drug candidates that enter phase 1 clinical trials actually gets approved for human use. The high failure rate is in part due to unforeseen side effects or toxicity. A better... Show moreLess than 1 in 10 drug candidates that enter phase 1 clinical trials actually gets approved for human use. The high failure rate is in part due to unforeseen side effects or toxicity. A better understanding of the role of selectivity and a better insight in the off-target activities of drug candidates could greatly aid in preventing candidates to fail for these reasons. This thesis has tried to address some aspects in this challenging part of drug discovery. The use of activity-based protein profiling as presented in Chapters 2 and 3 in drug discovery and hit-to-lead optimization, and in Chapter 5 and 6 for the interaction profiling of a drug candidate, highlights the versatility and importance of this chemical biology technique. Combined with knowledge derived from biochemical assays, such as that developed in Chapter 4, ABPP can greatly aid the medicinal chemist. The recent surge in popularity of machine learning algorithms, backed by exponential growth of the amount of biological data available, holds great promise for drug discovery. Chapters 7 and 8 showed the applicability of one such algorithm, which was able to quite reliably predict interaction profiles. The challenges in finding, determining and predicting selectivity are far from solved, but, by incrementally expanding our understanding of the binding of small molecules to their (off-)targets, truly selective inhibitors might at some point become a reality or their necessity might be mitigated. Show less

Rooden, E.J. van 2018

Activity-based proteomics of the endocannabinoid system

Doctoral Thesis

open access

This thesis describes the use of an activity-based proteomics method to study the endocannabinoid system. A protocol for label-free chemical proteomics to measure serine hydrolase activity in mouse... Show moreThis thesis describes the use of an activity-based proteomics method to study the endocannabinoid system. A protocol for label-free chemical proteomics to measure serine hydrolase activity in mouse tissue is described. This method is used to compare a Niemann-Pick Type C mouse model to healthy mice. Additionally, several novel activity-based probes for the enzymes diacylglycerol lipase alpha and a/b-hydrolase domain containing protein 6 are described. Show less

Schröder, S.P. 2018

Cyclophellitol analogues for profiling of exo- and endo-glycosidases

Doctoral Thesis

open access

To this day, all cyclophellitol-based inhibitors and ABPs have been close analogues of their natural substrate counterparts. As a result, these probes showed high selectivity towards their... Show moreTo this day, all cyclophellitol-based inhibitors and ABPs have been close analogues of their natural substrate counterparts. As a result, these probes showed high selectivity towards their target glycosidases. While such probes are of high value for studying these specific enzyme classes, they impede the simultaneous profiling of glycosidases that process different substrate configurations with a single probe. This Thesis focusses on structural derivatization of cyclophellitol-based probes with the aim of enabling inter-class labelling of glycosidases. The synthesis of cyclophellitol-based inhibitors and probes is described, which either lack the hydroxymethylene functionality at C2, C4 and C5, or are furanose-based cyclitol aziridines. Their labelling is biochemically evaluated on complex biological samples. The synthesis of a novel reversible inhibitor, gluco-1H-imidazole, is described in Chapter 5. In the last Chapters of this Thesis, synthetic methodologies for the construction of endo-glycosidase probes are described. Chapter 6 reports on the introduction of a spiro-epoxide warhead onto a disaccharide moiety for the purpose of constructing probes for GH99 endo-α-mannosidases, while the construction of xylobiose-cyclophellitol probes from xylo-cyclophellitol acceptors via direct glycosylation is described in Chapter 7. Finally, Chapter 8 provides a summary of this Thesis, followed by future prospects. Show less

Beenakker, T.J.M. 2017

Design and development of conformational inhibitors and activity-based probes for retaining glycosidases

Doctoral Thesis

open access

Glycosidases are essential in fundamental biological processes and are responsible for the degradation of most (oligo)saccharides, glycolipids and glycoproteins. Malfunctioning of glycosidases... Show moreGlycosidases are essential in fundamental biological processes and are responsible for the degradation of most (oligo)saccharides, glycolipids and glycoproteins. Malfunctioning of glycosidases causes various complex pathologies in man, for example, lysosomal storage disorders such as Fabry disease and Krabbe disease. Activity-Based Protein Profiling (ABPP) is a powerful technique to selectively analyze functional proteins in their physiological surroundings. Potent and selective activity-based glycosidase probes (ABPs) could help to understand the pathological processes connected with these enzymes. The first part of this Thesis describes the design, synthesis and application of a set of ABPs for retaining α-galactosidases, β-galactosidases, α-mannosidases and β-mannosidases.Several reversible, competitive glycosidase inhibitors have been developed in the past and are employed for therapeutic applications. The second part of this Thesis focuses on the design of functionalized bicycle [4.1.0] heptanes, carba-cyclophellitols, as new potential competitive inhibitors of glycosidases (α-galactosidases, β-galactosidases, α-glucosidases and β-glucosidases) and glycosyltransferases (both galactosyltransferases and glucosyltransferases). Herein a specific substituted carba-cyclophellitol turned out to be highly potent towards Thermotoga maritima TmGH1 β-glucosidase and therefore conformational strain induced through a cyclopropyl unit may be added to the armory of tight-binding inhibitor designs. Show less

Baggelaar, M.P. 2017

Activity-based protein profiling of diacylglycerol lipases

Doctoral Thesis

open access

Diacylglycerol lipase (DAGL)-α and -β are enzymes responsible for the biosynthesis of the endocannabinoid 2-arachidonoylglycerol. Selective and reversible inhibitors are required to study the... Show moreDiacylglycerol lipase (DAGL)-α and -β are enzymes responsible for the biosynthesis of the endocannabinoid 2-arachidonoylglycerol. Selective and reversible inhibitors are required to study the function of DAGLs in neuronal cells in an acute and temporal fashion. The work described in this thesis has led to the identification of an activity-based probe (ABP) for DAGL-α. This ABP was instrumental for the identification of a new class of highly selective DAGL inhibitors.

These novel inhibitors can be used to investigate the role of the diacylglycerol lipases in metabolic syndrome and neurodegenerative diseases such a Parkinson’s disease, Alzheimer’s disease and Multiple Sclerosis.

Show less

Liu, N. 2016

Development of kinase inhibitors and activity-based probes

Doctoral Thesis

open access

Kinases play a role in many diseases including cancer, diabetes and infection diseases. Therefore, kinases are interesting drug targets. Inhibitors for some kinases are already in use as... Show moreKinases play a role in many diseases including cancer, diabetes and infection diseases. Therefore, kinases are interesting drug targets. Inhibitors for some kinases are already in use as clinical drugs, however due to resistance and side effects, but also to target kinases related to diseases for which there is currently no treatment, research on the discovery of new classes of kinase inhibitors is imperative. To achieve this, not only new inhibitor classes need to be designed and synthesized, but also tools to profile kinases in physiological context and to determine the selectivity of inhibitors are required. The research in this thesis has focused on the development of more potent AKT1 and FLT3 kinase inhibitors and on the synthesis and application of new chemical tools for the profiling of kinases involved in various types of cancers and other diseases.In this thesis, new powerful tools and assays have been developed that unite the fields of synthetic chemistry, protein biochemistry and cell biology for the global analysis of kinase expression and function. The value of chemical profiling as a method for functional proteome analysis has been further highlighted by its application as a screen to evaluate the potency and selectivity of kinase inhibitors. Show less

Jiang, J. 2016

Activity-based protein profiling of glucosidases, fucosidases and glucuronidases

Doctoral Thesis

open access

Glycoside hydrolases (GHs), enzymes that catalyze the hydrolytic cleavage of glycosidic bonds, receive continuing interest both in fundamental and applied biology and biomedicine. Lysosomal... Show more Glycoside hydrolases (GHs), enzymes that catalyze the hydrolytic cleavage of glycosidic bonds, receive continuing interest both in fundamental and applied biology and biomedicine. Lysosomal storage disorders (LSDs) are caused by inborn metabolic errors due to deficiency in specific lysosomal enzymes, most commonly GHs. Diagnosis and treatment of LSDs require regular quantification of the active lysosomal enzymes in patient tissues. Activity-based protein profiling (ABPP) has emerged in the past decades as a powerful technique to study enzyme families in cell extracts and living tissues. Originally developed for serine hydrolases and cysteine proteases, various enzyme classes can be studied by means of ABPP today, including retaining GHs. The research described in this thesis focused on expanding the field of activity-based glycosidase profiling through the development of functional and configurational analogues of cyclophellitol aziridine as activity-based probes (ABPs) for various retaining glycoside hydrolases (GHs), namely α-L-fucosidases, β-glucosidases, α-glucosidases and β-glucuronidases. Attention is focused on the design and synthesis of the cyclophellitol aziridine derivatives and their application in chemical biology studies of various retaining GHs. Show less

Hoogendoorn, S. 2014

A chemical biology approach for targeting of ligand-drug conjugates

Doctoral Thesis

open access

Cells express a large array of membrane receptors on their surface that function as a communication channel between the extra- and intracellular environment of the cell. Ligands for these receptors... Show moreCells express a large array of membrane receptors on their surface that function as a communication channel between the extra- and intracellular environment of the cell. Ligands for these receptors span a wide range of biomolecules, from proteins to carbohydrates to small molecules. Some receptors are continuously recycling between the membrane and the inside of a cell, whereas others are in a steady-state at the membrane and need ligand binding for their activation and subsequent internalization. Synthetic molecules that bind to these membrane receptors can be used to either modulate their function, or to target a reporter group (i.e. a fluorescent dye) and/or a bio-active compound (drug, protein) to cells that express this receptor, ensuring delivery to a specific cell-type. The research described in this Thesis combines synthetic and biochemical methodologies to create ligands that interact selectively with membrane receptors of the GPCR and lectin-binding families. Attachment of synthetic probes, proteins or cytostatic molecules to these ligands by a variety of chemical and enzymatic methods ensured their uptake exclusively into cells that expressed the receptor of interest. Visualization of this process was enabled by the incorporation of a fluorescent dye into the final constructs. Show less

Walvoort, M.T.C. 2012

On the reactivity and selectivity of donor glycosides in glycochemistry and glycobiology

Doctoral Thesis

open access

The processes of glycosidic bond formation and destruction are a central theme in glycochemistry and glycobiology, and form the basis of the research described in this Thesis. In the first part,... Show moreThe processes of glycosidic bond formation and destruction are a central theme in glycochemistry and glycobiology, and form the basis of the research described in this Thesis. In the first part, studies towards the stereoselective construction of two complex bacterial oligosaccharide fragments are described. These fragments contain mannuronic acid residues connected through a beta-linkage, which is amongst the most challenging linkages to construct synthetically. In the second part, the use of mannuronic acid building blocks in the automated synthesis of alginates using solid-phase chemistry is presented. Using a second-generation carbohydrate synthesizer, alginate fragments up to 12 residues were assembled with high stereoselectivity. Using the same automated set-up, fragments of hyaluronic acid of up to 15 residues were synthesized. In the third part, 2-deoxy-2-fluoroglucosides are investigated as activity-based probes for glucocerebrosidase, a retaining beta-glucosidase enzyme. Show less

Geurink, P.P. 2010

Synthetic tools to illuminate matrix metalloproteinase and proteasome activities

Doctoral Thesis

open access

This thesis describes the design, synthesis and application of chemical tools for the activity-based protein profiling of proteases, with the main focus on matrix metalloproteinases (MMPs) and the... Show moreThis thesis describes the design, synthesis and application of chemical tools for the activity-based protein profiling of proteases, with the main focus on matrix metalloproteinases (MMPs) and the proteasome. The use of photoaffinity labeling is described and the thesis starts with an extensive outline of the three most often used photoreactive groups and their application in (recently published) protein profiling studies. Targeting MMPs is performed by application of photoaffinity probes, while the proteasome is commonly targeted by so-called suicide inhibitors. The last experimental chapter deals with the creation of a novel chemoselective cleavable linker and its use in the pull-down of active proteasome subunits. Show less

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