Combining Computational Chemistry, Synthesis and Enzymology for the Design of Covalent Inhibitors Applied to Prolyl Oligopeptidase Inhibition

Book excerpt: "Medicinal chemistry and structure-based drug design are largely focused on non-covalent interactions. Shape complementarity and optimization of hydrogen-bonds and hydrophobic interactions have been the gold standard of most drug design and development projects. In the recent years, light has been shed on the prevalence of covalent linkage between natural or synthetic ligands and their associated biological targets. Indeed, with the advance of analytical techniques, it has been found that widely used drugs such as aspirin act by covalently modifying their targets. Despite this established past and present prevalence, there is still reluctance to incorporate covalent inhibitors in drug discovery programs. In this thesis, we started by looking at what it would take to successfully incorporate covalent interactions into the design of potential drugs. Specific considerations have been reviewed at different stages of a classical drug discovery project, from target selection to lead optimization. From this perspective, we applied this knowledge to the discovery and development of prolyl oligopeptidase (POP) covalent inhibitors. POP is a post-proline cleaving serine protease involved in various conditions such as neurodegenerative disorders (e.g. Alzheimer's disease) and cancer. Different strategies were employed, going from virtual screening to computer-aided rational design to guide the discovery of covalent POP inhibitors. The syntheses of those designed inhibitors were conceived with effectiveness and diversity in mind. In order to fully understand the reaction pathway a mechanistic study on the acylation/intramolecular Diels-Alder step was carried out. This led to the discovery of diverse POP inhibitors in the low nanomolar affinity range (Ki = 1-50 nM). We have also looked at the effect of different reactive functional groups and fluorine atoms activating these groups on the inhibition of POP. In order to gain further information on covalent inhibition, we decided to investigate the binding kinetics of our inhibitors. Methods have been developed to provide experimental measurement of binding kinetics and a preliminary structure kinetics relationship has been established. Lastly, we turned our efforts towards exploration of dual inhibition of POP and fibroblast activation protein-[alpha] (FAP) which is a proline peptidase involved in the development of various cancers. A chiral scaffold has been designed and synthesized in order to probe the geometrical requirement associated to the inhibition of those two enzymes. This work led to the discovery of potent POP inhibitors (Ki = 15-20 nM) and provided additional insights in the requirements for FAP inhibition." --