PhD defence: Exploring Nature at the Molecular Level through Solid-State NMR and Chemical Biology

Studying whole cell walls of microorganisms such as fungi and diatoms remains a major challenge due to the number and complexity of cell wall components and their supramolecular assembly. The extracellular matrix (ECM) together with the cell wall is responsible for the regulation of important processes like assuring cellular integrity and function as well as intercellular communication and interactions of the organism with its environment. As such, ECMs are very sophisticated structures offering interesting possibilities for applications as sustainable biomaterials. It is therefore crucial to understand and control their composition and structural assembly.

In contrast to many other techniques, which are reliant on harsh chemical treatments, solid-state NMR is a non-disruptive technique that is able to provide valuable data on composition, structure and dynamics on an atomic level. It has been successfully employed in recent years to study the cell walls of microorganisms such as bacteria, plants, fungi and algae. In the present thesis solid-state NMR is used to study the cell walls of the basidiomycete Schizophyllum commune and the diatom Thalassiosira pseudonana. Both represent model organisms for their species and are interesting candidates for sustainable biomaterial applications.

Cyclophellitol derivatives have been shown to be highly potent inhibitors for glycosidases as they are able to covalently and irreversibly trap the enzyme-substrate complex. They are configurational analogues of the enzyme-bound state of the original substrates and act via transition-state mimicry. One of the most interesting druggable targets is the enzyme heparanase (HPSE), a retaining beta-D-glucuronidase that is linked to a plethora of human diseases including aggressive cancer types,  inflammation, fibrosis, diabetes and viral infections. Currently, the most promising class of heparanase inhibitors are structural analogues of the enzymes’ native substrate, heparan sulfate (HS) and have shown non-optimal physicochemical and druglike properties preventing their clinical application, such as problematic product standardization and identification due to structural heterogeneity, high molecular weight, high hydrophilicity limiting their bioavailability, and off-target effects in the coagulation pathway. The existing cyclophellitol-derived small molecule inhibitors of heparanase have proven to be highly potent and selective inhibitors, but also exhibit non-optimal druglikeness in pre-clinical studies.

During the research described in part 2 of this thesis, we aimed to synthesize glucurono-cyclophellitol derivatives carrying click-handles for the combination with an in-vitro generated cyclic peptide library and screen the resulting hybrid library against immobilized heparanase in a RaPID set-up.