Abstract 1143: Targeting the transcriptional kinases CDK12 and CDK13 in breast and ovarian cancer
Authors: Michael Bradley, Jason Marineau, Yoon Choi, Kristin Hamman, Goran Malojcic, David Orlando, Yixuan Ren, Nan Ke, Shanhu Hu, Eric Olson, Christian Fritz, Christopher Roberts
Journal: Cancer Research (2017)

Abstract CDK12 and CDK13 regulate expression of large transcripts requiring substantial processing to produce mature mRNA. This transcriptional regulation includes coordinated phosphorylation of specific repeats within the C-terminal domain of RNA polymerase II and association with RNA processing factors (Chila, 2016). RNAi knockdown of CDK12 in cell culture decreases expression of DNA damage response genes, including BRCA1 and ATR, while enhancing sensitivity to DNA damaging agents (Blazek, 2011; Liang, 2015). Recently THZ531, a selective covalent inhibitor of CDK12 and CDK13, was shown to decrease expression of DNA damage response genes in cell culture (Zhang, 2016). Here we present further studies with THZ531 to guide our discovery program toward molecules suitable for clinical development and to explore mechanistic rationales for combining a CDK12/13 inhibitor with PARP inhibitors or DNA damaging agents for difficult-to-treat cancers such as high-grade serous ovarian cancer and triple-negative breast cancer. Using THZ531 as a benchmark, we developed assays capable of discriminating sub-nM inhibitors, including quantifying time-dependent covalent inhibition and cell-based CDK occupancy. Since CDK7, like CDK12 and CDK13, contains a cysteine residue proximal to the kinase active site, these approaches are critical to understand covalent inhibitor selectivity. Furthermore, we performed kinome paneling studies to better understand selectivity of this scaffold in support of our ongoing efforts to optimize CDK12/13 potency and selectivity. To pharmacologically investigate the previously reported effects of CDK12 RNAi, growth inhibition of a panel of ovarian and breast cancer cell lines was assessed following treatment with THZ531 (OVA EC50 = 50-200 nM (n=6); BRCA EC50 &amp;lt;50 nM (n=4)). Expression profiling revealed that THZ531 treatment resulted in different sets of genes being affected than was observed following treatment with inhibitors targeting CDK7, CDK9 or BET-bromodomain proteins. Additionally, CDK12/13, CDK7 and CDK9 inhibitors were profiled in a broad cell line panel (n&amp;gt;400) to reveal relationships between inhibitor sensitivity, mutation status, gene expression, and potential oncology indications that may be addressed by these different mechanisms. Finally THZ531 was synergistic with both PARP inhibitors and DNA damaging agents in ovarian and breast cancer cell lines. These data highlight cancer indications and combinations that may be particularly amenable to treatment with CDK12/13 inhibitors. While the pharmacokinetic properties of THZ531 preclude adequate target engagement in tumor tissue at tolerated doses in mouse model systems, our ongoing medicinal chemistry program is progressing to identify and optimize CDK12/13 inhibitors suitable for clinical evaluation. Citation Format: Michael Bradley, Jason Marineau, Yoon Choi, Kristin Hamman, Goran Malojcic, David Orlando, Yixuan Ren, Nan Ke, Shanhu Hu, Eric Olson, Christian Fritz, Christopher Roberts. Targeting the transcriptional kinases CDK12 and CDK13 in breast and ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1143. doi:10.1158/1538-7445.AM2017-1143