Probing the drug interactome by chemical proteomics

Abstract

Approved PDE5 inhibitors for the treatment of erectile dysfunction (ED) include sildenafil (Viagra), vardenafil (Levitra) and tadalafil (Cialis), all of which are considered very specific and ‘safe’ drugs. However, even highly selective, FDA approved drugs can have the potential to bind to other unintended targets, possibly leading to side effects. Some reported side effects observed during ED treatment include headache, flushing and transient visual problems. Understanding the molecular causes of such side effects is an important part of the drug development process and can help in the understanding of the mechanisms of drug action. In the research described in this thesis, the interactome of several, closely related, PDE5 inhibitors was characterized to obtain further insight in their ability to bind proteins other than PDE5. The pull-down affinity experiments were optimized to decrease binding of non-specific proteins. The optimized pull-down assay was then combined with high resolution quantitative proteomics to get a clear and unbiased insight into the protein interactors of PDE5 inhibitors. Several new specific interacting proteins were identified and verified and it was shown that slight modifications of the inhibitors can alter their specificity to favor these new protein targets. Throughout the work described in this thesis it has become evident that chemical proteomics can be an effective approach to describe the interactome of drugs but that it can also be used to identify potential new targets of known compounds, opening up the possibility to identify new potential therapeutic uses for known and approved drugs.