Systematic assessment of druggable cavities in a histone deacetylase complex

Although drug discovery efforts have drastically evolved over the past decades, the budget to bring a lead compound to successful FDA-approval has enormously increased and the number of new drugs continued to stagnate. One of the reasons is that most efforts have largely focused on well-known drug binding sites from five functional target families: enzymes, GPCRs, ion channels, nuclear receptors and transporters1. Most members of these families play key roles in normal and dysfunctional biological processes but their corresponding binding pockets are highly similar, making selective inhibition more challenging2. However, a wealth of other cavities exists on protein surfaces and could be exploited to selectively perturb key functionalities of a target while leaving the others intact3.

To identify chemicals capable of binding different cavities in a multi-subunit histone deacetylase (HDAC) complex, we have implemented an unbiased phenotypic screening approach and dissected the targeted machinery into its fundamental parts. After screening ~55,000 drugs from 9 diverse libraries, we have isolated 59 primary hits for which the impact on the HDAC complex was compared to that of subunit deletions. Interestingly, except for a handful of compounds, the inhibition profiles were very different than that for deletions, suggesting divergent mechanisms of action. Among the fraction of divergent candidates, we identified 4 compounds that were capable of inhibiting specific binary protein-protein interactions (PPIs) between known subunits of the complex. These compounds were also validated in orthogonal PPI assays and did not perturb HDAC enzyme activity, suggesting they might be true functional inhibitors of binary PPIs.

Our findings support the use of unbiased phenotypic approaches to identify functional inhibitors capable of binding under-explored cavities, such as those involved in PPIs, that will potentially lead to the development of new drugs and more targeted therapies.