In many diseases we find proteins that are too active, such as bone-degrading proteins in osteoporosis or growth receptors in certain types of cancer. These diseases can be treated with drugs that bind to the protein and thus block protein function (inhibit activity). The inhibitory effect often diminishes quickly as the drug eventually releases the protein, requiring the patient to take multiple doses of the drug throughout the day. Over the past two decades, we’ve seen a rise in drugs that can permanently inhibit protein function through formation of an unbreakable, covalent interaction with the protein. The chemical building blocks used for this purpose are carefully selected: they must not be too reactive, because that could lead to permanent inhibition of other proteins (with serious consequences), but if they are not reactive enough, the drug will not be effective.
This thesis describes the research into the possibilities of using 'nonactivated alkynes' as a novel chemical building block in covalent inhibitors. Alkynes are known to rarely spontaneously form unbreakable (covalent) bonds with proteins, but in this work we show that the alkyne can be applied to permanently inhibit bone-degrading cysteine protease CatK. Furthermore, using fluorescently labeled probes, we demonstrate that there is much more flexibility in chemical structure than was previously assumed. This unique combination of a reactive but also highly selective chemical group thus has the potential to make irreversible drugs safer.