Hierarchical small molecule inhibition of MYST acetyltransferases

Abstract

Abstract MYST lysine acetyltransferases (KATs) are a class of epigenetic enzymes critical for cellular function that constitute an emerging therapeutic target in cancer. Recently, several drug-like MYST inhibitors have been reported that show promise in preclinical models as well as in clinical trials of breast cancer. Understanding the specificity of these molecules is critical for their effective use as chemical probes. Here we apply an integrated profiling strategy to systematically define the potency and selectivity of drug-like MYST KAT inhibitors. First, we use optimized chemoproteomic profiling and histone acetylation biormarkers to study the industry-developed KAT inhibitor PF-9363. This reveals dose-dependent engagement of native KAT complexes, with hierarchical inhibition following the order KAT6A/B > KAT7 » KAT8 > KAT5. This pattern of target engagement is shared by the clinical candidate PF-8144. Next, we demonstrate how PF-9363’s ability to disrupt capture of MYST complex members in chemoproteomic experiments can be leveraged to identify uncharacterized candidate members of these complexes, including the transcription factor FOXK2. Applying insights from these studies to WM-8014, WM-1119 and WM-3835, which have been extensively applied in the literature as MYST probes, highlights unexpected cross-inhibition and suggests a framework for how these small molecules and biomarkers may be applied to differentiate KAT6A/B and KAT7-dependent phenotypes. Finally, we benchmark the activity of PF-9363 in the NCI-60 cell line screen, providing evidence that its ability to engage KAT8 at elevated concentrations can drive acute growth inhibition. Collectively, our studies indicate the potential for MYST KAT inhibitors, including clinical candidates, to exhibit dose-dependent target engagement reminiscent of kinase inhibitors. The assays and biomarkers described here should find broad utility in assessing selective target engagement by this inhibitor class.