Molecular design, synthesis and evaluation of chemical biology tools

Chapter 1 provides a perspective of synthetic organic chemistry as a discipline involved in the design, synthesis and evaluation of complex molecules. The reader is introduced with a brief history of synthetic organic chemistry, all the while dealing with different aspects of synthetic organic chemistry. These aspects include design, synthesis and evaluation of complex molecules, which are described with representative examples. For instance, chapter 1 described different strategies to design antibiotics like penicillin. Furthermore, efforts at the interface of chemistry and biology has led to the emerging of a new subdisciplines such as chemical biology. Although this discipline is relatively new, the scientific community has witnessed many breakthrough discoveries and some of these discoveries are highlighted in this chapter. After the general introduction presented in chapter 1, the following chapters of this thesis focus on the design, synthesis and evaluation of small molecular probes towards the study of proteins and glycans in plant and mammalian cells. Most of these probes are complex glycomimetic small molecules that in many instances are prepared with a nitrone-olefin [3+2] cycloaddition as a key step. In chapter 2, a novel nitrone is presented for the nitrone-olefin [3+2] cycloaddition reaction. This reaction is a powerful tool in synthetic organic chemistry for the synthesis of a wide range of complex molecules. The versatile nature of the reaction is illustrated by the synthesis of several classes of natural product such as vitamins and alkaloids – all complex molecules containing multiple neighboring chiral centers – through the nitrone-olefin [3+2] cycloaddition. However, most nitrones that show good regio- and stereoselectivity are limited in their synthetic versatility, as subsequent synthetic modification of the cycloaddition products are limited. The nitrone described in chapter 2 is a novel masked aldehyde-containing nitrone. This nitrone is prepared by a simple and scalable procedure and can be combined with a diverse set of olefins and other dipolarophiles to afford a broad range of cycloadducts. These cycloadducts can be considered as a masked form of amino-aldehydes, which makes them interesting from a synthetic point of view as illustrated by several postcycloaddition modifications. The nitrone-olefin [3+2] cycloaddition is also utilized in chapter 3 for the synthesis of glycomimetic building blocks. Glycomimetics such as iminosugars and pipecolic acids are found in nature and possess a variety of biological activities. The potential of glycomimetics have led to the development of drugs for the treatment of diseases such as type 2 diabetes, Gaucher disease and HIV. Chapter 3 describes how glycomimetic building blocks can be obtained through a nitrone-olefin [3+2] cycloaddition, providing different bicyclic isoxazolidines. These cycloadducts are synthetically versatile, as we report a set of reactions that allow selective modification at each functional position. Accordingly, these versatile bicyclic isoxazolidines enable the synthesis of different glycomimetic building blocks. For example, we were able to make a library of pipecolic acid derivatives – a popular drug-motif – via a one-pot Staudinger/aza-Wittig/Ugi three-component reaction. The bicyclic isoxazolidines, discussed in chapter 3, are also reported in chapter 4. This chapter describes the development of a synthetic route towards an activity-based probe (ABP) to study the enzymatic activity of neuraminidases. Neuraminidases are a class of enzymes found in a range of organisms including mammals. The importance of neuraminidases is illustrated by the existence of a neuraminidase-related genetic disease, sialidosis. With no cure for this fatal disease being very limited, there is keen interest in the discovery of novel mechanisms to restore neuraminidase activity. The poor enzyme-activity of a different enzyme-related disease, Gaucher disease, could be improved through the identification of a small molecule that stabilizes and/or promotes the folding of the active enzyme. The validation of this small molecule was aided greatly by the development of a sensitive ABP targeting this disease specific enzyme. Accordingly, the development of a neuramidase-ABP would provide a diagnostic tool to study the activity of neuramidases and ultimately help identify small molecules that could increase the activity of mutant-neuraminidase molecules by stabilizing and/or promoting the folding of this enzyme. The synthesis of a carbocyclic neuraminidase ABP was the goal of chapter 4 and was approached by starting with the nitrone-olefin [3+2] cycloaddition as the key-step. This reaction provided a bicyclic cycloadduct that was used for the development of a synthetic route, which led to a high yielding and practical synthesis of an advance intermediate possessing the majority of the stereochemistry of the required carbocyclic neuraminidase ABP. Chapter 5 describes the synthesis and evaluation of chemical tools to study phoshatidyl ethanolamine-binding proteins (PEBPs). This family of proteins is found in a variety of organisms including mammals and plants. This family includes FLOWERING LOCUS T (FT), a signaling protein that acts as a vital flowering hormone in plants. No small molecule inhibitors for FT are known, but an inhibitor called locostatin has been reported to bind in the highly conserved ligand binding site of a structurally related protein. Based on this conservation and overall structurally similarity with FT it was hypothesized that locostatin or derivatives thereof could covalently bind in the ligand binding pocket of FT and hence affect flowering. Chapter 5 reports on the synthesis of novel locostatin-based chemical PEBP probes, followed by evaluation for their ability and selectivity towards FT and a mammalian PEBP. Chemical tools were also used to study plants in chapter 6, although different aspects of plants were investigated. This chapter describes the direct molecular imaging of carbohydrates (glycans) in Arabidopsis thaliana. Glycans play a crucial but not fully understood role in plant health and development. The formation of glycans is not genetically encoded, which makes it impossible to image them in vivo using genetically encoded fluorescent tags and related molecular biology approaches. A solution to this problem is the use of tailor-made glycans that are metabolically incorporated in plants via the roots, which may then be visualized with copper-catalyzed click labeling. However, this labelling-technique is toxic to plants and future applications would benefit from bio-orthoganol copper-free labeling techniques. Chapter 6 shows, for the first time in metabolic labeling and imaging of plant glycans, the potential of two copper-free click chemistry methods. These methods are bio-orthogonal and lead to more uniform labeling. Furthermore, this chapter also describes the metabolic incorporation of five novel monosaccharide probes in Arabidopsis thaliana roots and their imaging after (copper-free) fluorescent labeling. Finally, chapter 7 contains a general discussion, critically summarizing the body of this thesis along with additional ideas and recommendations for further research.