Chemokine receptors are relevant targets for a multitude of immunological diseases, but drug attrition for these receptors is remarkably high. While many drug discovery programs have been pursued,... Show moreChemokine receptors are relevant targets for a multitude of immunological diseases, but drug attrition for these receptors is remarkably high. While many drug discovery programs have been pursued, most prospective drugs failed in the follow-up studies due to clinical inefficacy, and hence there is a clear need for alternative approaches. Allosteric modulators of receptor function represent an excellent opportunity for novel drugs, as they modulate receptor activation in a controlled manner and display increased selectivity, and their pharmacological profile can be insurmountable. Here, we discuss allosteric ligands and their pharmacological characterization for modulation of chemokine receptors. Ligands are included if (1) they show clear signs of allosteric modulation in vitro and (2) display evidence of binding in a topologically distinct manner compared to endogenous chemokines. We discuss how allosteric ligands affect binding of orthosteric (endogenous) ligands in terms of affinity as well as binding kinetics in radioligand binding assays. Moreover, their effects on signaling events in functional assays and how their binding site can be elucidated are specified. We substantiate this with examples of published allosteric ligands targeting chemokine receptors and hypothetical graphs of pharmacological behavior. This review should serve as an effective starting point for setting up assays for characterizing allosteric ligands to develop safer and more efficacious drugs for chemokine receptors and, ultimately, other G protein-coupled receptors. Show less
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
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
Bunschoten, A.; Chin, P.T.K.; Buckle, T.; Linden, M. van der; Barendregt, A.; Verheijen, M.A.; Leeuwen, F.W.B. van 2016
Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They... Show moreScientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly available through the myExperiment community and then used in other workflows. We here illustrate how scientific workflows and the Taverna workbench in particular can be used in bibliometrics. We discuss the specific capabilities of Taverna that makes this software a powerful tool in this field, such as automated data import via Web services, data extraction from XML by XPaths, and statistical analysis and visualization with R. The support of the latter is particularly relevant, as it allows integration of a number of recently developed R packages specifically for bibliometrics. Examples are used to illustrate the possibilities of Taverna in the fields of bibliometrics and scientometrics. Show less
Xin, B.T.; Bruin, G. de; Plomp, J.W.; Florea, B.I.; Marel, G.A. van der; Overkleeft, H.S. 2016
In this thesis, several orthosteric and allosteric agonists are presented for the newly discovered hydroxy-carboxylic acid (HCA) receptor 2, and their in vivo activity or in vitro structure... Show moreIn this thesis, several orthosteric and allosteric agonists are presented for the newly discovered hydroxy-carboxylic acid (HCA) receptor 2, and their in vivo activity or in vitro structure-activity relationships are described. The literature on HCA receptors was also thoroughly reviewed, providing some insight into the future of this receptor family as drug targets. The anti-cancer drug N6-(2-isopentenyl)adenosine (IPA) was shown to be a specific ligand for the adenosine A3 receptor, and its antiproliferative effect seems to be mediated by this receptor at low concentrations. A ligand discovery screen for orphan receptor GPR88 was performed, in which over 4000 compounds were tested. Show less
The first part of this thesis describes the development of inhibitors of autotaxin (ATX or ENPP2), a phosphodiesterase that is responsible for the production of the lipid lysophosphatidic acid (LPA... Show moreThe first part of this thesis describes the development of inhibitors of autotaxin (ATX or ENPP2), a phosphodiesterase that is responsible for the production of the lipid lysophosphatidic acid (LPA) in the circulation. ATX is implicated in several diseases including inflammation, fibrotic disease and cancer, making it an interesting potential drug target to study. ATX inhibitors are required in the validation process of ATX as a drug target. The second part of this thesis describes development of dual specificity phosphatases (DUSP) inhibitors that inhibit bacterial growth in human cells. These inhibitors act by inhibiting DUSP proteins in the host cell that are essential for bacterial growth. This approach can be used to control bacterial infection and could be a useful addition to the current treatment of bacterial infections that target solely the bacteria itself. Show less
