LLY-507, a Cell-Active, Potent and Selective Inhibitor of Protein Lysine Methyltransferase SMYD2 [Cell Biology]

March 30th, 2015 by Nguyen, H., Allali-Hassani, A., Antonysamy, S., Chang, S., Chen, L. H., Curtis, C., Emtage, S., Fan, L., Gheyi, T., Li, F., Liu, S., Martin, J. R., Mendel, D., Olsen, J. B., Pelletier, L., Shatseva, T., Wu, S., Zhang, F. F., Arrowsmith, C. H., Brown,

SMYD2 is a lysine methyltransferase that catalyzes the mono-methylation of several protein substrates including p53. SMYD2 is over-expressed in a significant percentage of esophageal squamous primary carcinomas and that over-expression correlates with poor patient survival. However, the mechanism(s) by which SMYD2 promotes oncogenesis is not understood. A small molecule probe for SMYD2 would allow for the pharmacological dissection of this biology. In this report, we disclose LLY-507, a cell active, potent small molecule inhibitor of SMYD2. LLY-507 is >100-fold selective for SMYD2 over a broad range of methyltransferase and non-methyltransferase targets. A 1.63Å resolution crystal structure of SMYD2 in complex with LLY-507 shows the inhibitor binding in the substrate peptide binding pocket. LLY-507 is active in cells, as measured by reduction of SMYD2-induced mono-methylation of p53 K370 at sub-micromolar doses. We used LLY-507 to further test other potential roles of SMYD2. Mass spectrometry-based proteomics shows that cellular global histone methylation levels are not significantly affected by SMYD2 inhibition with LLY-507, and subcellular fractionation studies indicate that SMYD2 is primarily cytoplasmic, suggesting that SMYD2 targets a very small subset of histones at specific chromatin loci, and/or non-histone substrates. Breast and liver cancers were identified through in silico data mining as tumor types which display amplification and/or over-expression of SMYD2. LLY-507 inhibited the proliferation of several esophageal, liver and breast cancer cell lines in a dose-dependent manner. These findings suggest that LLY-507 serves as a valuable chemical probe to aid in the dissection of SMYD2 function in cancer and other biological processes.