Discovery of Potent Selective Inhibitors of the Histone Methyltransferase SUV39H1 for the Treatment of Cancer

PROJECT SUMMARY Cancer treatment has been transformed by a class of drugs, that includes Keytruda and Opdivo, that enables the immune system to recognize and selectively kill cancer cells. Unfortunately, many cancers are refractory to such immuno-oncology (IO) drugs, and so developing novel approaches to augment their efficacy is a high priority, as these would undoubtedly lead to a significant reduction in disease mortality. One potentially promising way to achieve this is to promote the transcriptional reactivation of ancient endogenous retroviruses (ERVs) and retrotransposons in cancer cells beyond a threshold level of tolerance such that they elicit an immune response, an approach termed “viral mimicry”. Cancer cells with reactivated ERVs/retrotransposons phenotypically resemble virus-infected cells and are subsequently recognized and killed by cytotoxic T and natural killer (NK) cells. We discovered that histone methyltransferase SUV39H1 is a key component of an enzymatic complex that is essential for the transcriptional silencing of ERVs/retrotransposons in cancer cells. SUV39H1 targeting reactivated ERVs/retrotransposons in cancer cells, leading to stimulation of intracellular antiviral pathways and interferon (IFN) signaling. In preclinical studies, SUV39H1 inhibition stimulated the intra-tumoral infiltration of cytotoxic T/NK cells (i.e., converted “cold” tumors to “hot”), and sensitized refractory tumors to immune checkpoint therapy. SUV39H1 targeting also exhibited stand-alone antitumor activity by inducing replication stress and double-strand-breaks (DSB) in cancer cells, presumably by promoting transcription-replication fork conflicts at reactivated ERVs/retrotransposons. Importantly, SUV39H1 inhibition had no effect on ERV/retrotransposon silencing in normal cells, indicating a therapeutic window for cancer treatment. The overall objective of this project is to discover potent and selective SUV39H1 inhibitors with properties suitable to definitively test our hypothesis that such compounds would be powerful stand-alone antitumor drugs and immunomodulators. In preliminary studies, we profiled the properties of known SUV39H1/H2 inhibitors (chemical probes) and provide data from a 1536-well TR-FRET assay that demonstrates robustness and readiness for a high throughput screen (HTS). Our research plan to advance these preliminary studies has four aims: Aim 1 will identify selective SUV39H1 hit scaffolds from a 320,000 compound HTS campaign. Aim 2 will utilize a structure- based design approach to convert a clinical grade SUV39H2 inhibitor into potent SUV39H1-selective compounds. Aim 3 will use biochemical and ADME assays and iterative cycles of medicinal chemistry to identify lead compounds with potent cellular activity. Aim 4 will further optimize these leads to compounds with drug-like properties and explore their stand-alone antitumor and immunomodulatory effects using in vivo cancer models. The resulting drug leads developed from this study are anticipated to have broad utility to test our therapeutic hypothesis and represent a critical step in our overall objective to develop SUV39H1 inhibitors as therapeutics for cancer patients, and specifically those with tumors refractory to IO regimes.