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Item does not contain fulltext Since protease activity is highly regulated by structural and environmental influences, the abundance of a protease often does not directly correlate with its activity. Because in most of the cases it is the activity of a protease that gives rise to its biological relevance, tools to report on this activity are of great value to the research community. Activity-based probes (ABPs) are small molecule tools that allow for the monitoring and profiling of protease activities in complex biological systems. The class of fluorescent quenched ABPs (qABPs), being intrinsically "dark" and only emitting fluorescence after reaction with the target protease, are ideally suited for imaging techniques such as small animal noninvasive fluorescence imaging and live cell fluorescence microscopy. An additional powerful characteristic of qABPs is their covalent and irreversible modification of the labeled protease, enabling in-depth target characterization. Here we describe the synthesis of a pan-cysteine cathepsin qABP BMV109 and the application of this probe to live cell fluorescence imaging and fluorescent SDS-PAGE cysteine cathepsin activity profiling.

The proteasome plays essential roles in nearly all biological processes in plant defense and development, yet simple methods for displaying proteasome activities in extracts and living tissues are not available to plant science. Here, we introduce an easy and robust method to simultaneously display the activities of all three catalytic proteasome subunits in plant extracts or living plant tissues. The method is based on a membrane-permeable, small-molecule fluorescent probe that irreversibly reacts with the catalytic site of the proteasome catalytic subunits in an activity-dependent manner. Activities can be quantified from fluorescent protein gels and used to study proteasome activities in vitro and in vivo. We demonstrate that proteasome catalytic subunits can be selectively inhibited by aldehyde-based inhibitors, including the notorious caspase-3 inhibitor DEVD. Furthermore, we show that the proteasome activity, but not its abundance, is significantly increased in Arabidopsis upon treatment with benzothiadiazole (BTH). This upregulation of proteasome activity depends on NPR1, and occurs mostly in the cytoplasm. The simplicity, robustness and versatility of this method will make this method widely applicable in plant science.

Recent advances in our understanding of immunotherapeutic strategies against cancer and the development of improved analysis tools and computing power have led to a highly anticipated progression of the cancer-vaccine field. The possibilities of personalized approaches to vaccinate patients against tumor-specific antigens by the prediction of MHC-binding peptides are already in clinical studies. Currently, the field is lacking behind in antigen identification tools and optimal delivery of vaccines. The studies in this thesis are divided in two major parts which address these topics. The first part reports a novel approach for the identification of relevant MHC class I and II binding epitopes. With the combined use of exome sequencing and mass-spectrometric analysis, relevant neoantigens were characterized from MHC class I and II in murine and human models. Meanwhile, significant genomic differences were observed in the MC38 murine colorectal cancer model of different sources. The second part shows the development of a molecular approach for the tracking of ligands and peptides to improve our understanding of vaccine delivery. Therefore, bioorthogonal ‘click’ chemistry was applied for in situ ligation of fluorophores to antigen, thus providing a quantification method of processed antigens. Subsequent optimizations were explored into bioorthogonal reactions independent of copper.

The research described in this thesis aims at the development of ubiquitin-based research tools to study the enzymes of the ubiquitination pathway, the ligase enzymes and the deubiquitinating enzymes. These enzymes are responsible for the conjugation and the removal of the post-translational modifier ubiquitin. This small protein is involved in almost all cellular processes, and when conjugated onto a substrate protein it can signal for degradation and influence the localization, interaction, stability and activity of the protein. Therefore, the dysregulation of these processes can have detrimental effects of cell organization and survival which in turn has implications in numerous processes related to diseases. Hence, it is important to fully understand the ubiquitination pathway and how to interact with it. The ubiquitin-based research tools described in this thesis aim to shine light on parts of this pathway. Ranging from the selectivity and specificity of DUBs for specific Ub linkages in competition and the catalytic efficiency of these proteolytic cleavage processes to the selectivity and activity of ligases and the activity of DUBs in cells. All ubiquitin research tools are based on synthetic ubiquitin modified with unnatural amino acids, neutron-encoded amino acids, point mutations and/or fluorescent labels, in order to study the characteristics of the enzymes in vitro.

Contains fulltext : 286405.pdf (Publisher’s version ) (Open Access) Radboud University, 26 januari 2023 Promotor : Figdor, C.G. Co-promotores : Verdoes, M., Weiden, J. 248 p.

Contains fulltext : 292276.pdf (Publisher’s version ) (Open Access) Radboud University, 16 mei 2023 Promotor : Figdor, C.G. Co-promotor : Verdoes, M. 241 p.

Contains fulltext : 249029.pdf (Publisher’s version ) (Open Access) Radboud University, 17 mei 2022 Promotor : Figdor, C.G. Co-promotor : Verdoes, M. 261 p.

Cancer vaccines are aimed at raising an immune responses aganist defined tumor antigens. The formulation of a vaccine has a direct impact on the potency of the immune response generated. Cancer vaccines require particular effort in their formulation, as the immune system has to overcome immune suppression exerted by the tumor. In this thesis, different formulations to enhance cancer vaccine efficacy were explored. In the first part it is shown how chemical conjugation of antigen and adjuvant in form synthetic Toll-like receptor ligands represent a strategy to enahnce vaccine potency. Next, it is presented how the loading of peptide antigens onto dextran nanogel contributes to increase the breadth of the immune response induced. Lastly, a new DNA vaccine containing multiple tumor neoantigens was explored as a platform for personalized cancer vaccines. Together, these studies display how the formulation of cancer vaccines can be modified and optimized to achieve stronger therapeutic efficacy in the clinic.

Contains fulltext : 228860.pdf (Publisher’s version ) (Open Access) Radboud University, 25 januari 2021 Promotor : Figdor, C.G. Co-promotores : Verdoes, M., Scheeren, F.A. 195 p.

Contains fulltext : 235389.pdf (Publisher’s version ) (Open Access) Radboud University, 25 augustus 2021 Promotor : Figdor, C.G. Co-promotores : Verdoes, M., Scheeren, F.A. 143 p.

This thesis describes the development of a variety of mannosylated conjugates. Antigen presenting cells bear mannoside recognizing receptors that actively transport antigen into the cell. This thesis exploits this feature for the development of improved vaccines.

Contains fulltext : 226631.pdf (Publisher’s version ) (Open Access) Radboud University, 07 december 2020 Promotor : Figdor, C.G. Co-promotores : Verdoes, M., Hammink, R.

Contains fulltext : 213928.pdf (Publisher’s version ) (Open Access) Radboud University, 31 januari 2020 Promotor : Figdor, C.G. Co-promotores : Verdoes, M., Tel, J.

Chapter 2 describes a post-synthetic methodology to introduce a fluorescent label in highly lipophilic, Pam3Cys based conjugates. The fluorescent labels were appended to the peptide part of the conjugate with the aid of a strain promoted [3+2] azide-alkyne cycloaddition. In Chapter 3 a synthesis is discussed of a structurally simple human specific TLR-2 ligand with diminished lipophilicity, as compared to Pam3Cys. Conjugation of such moiety to peptide is studied and optimized to produce human specific analogues of the conjugates described in Chapter 2 with higher solubility and an equal propensity to activate TLR-2. The synthesis of a newly designed TLR-7 agonist is demonstrated in Chapter 4 as well as the synthesis of a selection of self-adjuvanting immunogenic peptides that contain a model MHC-I epitope (SIINFEKL). A biocompatible methodology to reduce an azide in a side chains of peptides is described in Chapter 5 with a particular focus on side reaction occurring during the reduction. A selection of phosphines is evaluated under biocompatible aqueous conditions. 6 describes the development of a convergent synthesis of the naturally occurring conjugate between the 5’- terminal fragment of genomic RNA from Coxsackie virus and the full-length viral genome-linked protein (VPg).