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A Versatile Fluorescent Molecular Probe for the Assay of Histone Methyltransferases
Daniel A. Bochar1,2, Levi L. Blazer1, Margaret L. Collins1, Gregory S. Keyes1, Rana S. Sidhu1,Anna E. Simon1, Fang Sun1, Raymond C. Trievel2, Stephen D. Barrett1, Gregory W. Endres1, and Jeffrey K. Johnson1.
1Cayman Chemical Company Inc., Ann Arbor, MI.
2Department of Biological Chemistry, University of Michigan; Ann Arbor, MI.

Sponsored by Cayman Chemical
Histone methyltransferases (HMTs) play a major role in the epigenetic regulation of gene expression by catalyzing the methylation of a diverse set of histone and non-histone substrates. The observation that aberrant HMT activity plays a role in the progression of certain human malignances validates HMTs as an important new class of drug targets. Therefore, efficient methods to identify small molecule modulators of HMT activity via high-throughput screening are desirable. To this end, we have developed a novel fluorescent small molecule probe that binds with nanomolar affinity to the S-adenosylmethionine (SAM) cofactor binding site on HMTs. We have characterized the binding of this probe against a panel of methyltransferases using a robust 384-well assay format (Z’=0.7). To validate this assay for HTS, we performed a pilotscale high-throughput screen of 14,400 compounds against the histone methyltransferases SET7/9 and GLP. Active compounds from the primary screen were confirmed in secondary concentration response assays. These compounds represent novel chemotypes for inhibitors targeting the SAM binding site. We have also used this assay to profile SET7/9 and GLP against Cayman’s exclusive small molecule epigenetics screening library. This assay provides an HTS-amenable non-kinetic assay to identify SAM binding site inhibitors of HMTs.

Posttranslational modification of chromatin provides a complex and important cellular mechanism for the regulation of gene transcription. One major form of histone posttranslational modification is the methylation of lysine or arginine residues. Histone methylation can activate or repress gene transcription based upon the residue that is modified and upon the degree to which the residue is methylated. Proper control of histone methylation is required for physiological processes ranging from fetal development to cellular senescence. It is also becoming increasingly evident that dysregulation of histone methylation patterns is a common occurrence in a variety of human malignancies. Because of the importance of this mark in the regulation of gene activity, there exists a complex regulatory system for histone methylation that is founded upon histone methyltransferases and histone demethylases.

Histone methyltransferases transfer a methyl group from the cofactor S-adenosylmethionine to an amine on lysine or arginine residues of histones. All histone lysine methyltransferases with the exception of DOT1L contain a SET domain that catalyzes this methyl transfer reaction. This domain contains an S-adenosylmethionine (SAM) binding site located on the opposite side of the protein from the histone substrate binding channel, providing a distinct SAM binding site. Due to the heterogeneity of the SAM binding site across the methyltransferase family, it may be possible to develop substantial selectivity by targeting this binding site. With this objective, we sought to develop a unique small-molecule fluorescent probe that binds to the SAM-binding site of SET domain methyltransferases. Ideally, this probe would provide the foundation for a high-throughput assay to identify small molecule ligands of the SAM-binding site of several methyltransferases.
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