Exploring Novel Kinase Targets and Novel Pharmacology for Cancer Therapeutics

Abstract

Kinases are the largest target class of clinically approved cancer therapeutics. However, these drugs only target a small fraction of the kinome—primarily receptor tyrosine kinases—and their effectiveness is limited by the rapid emergence of drug resistance. Thus, the discovery of small molecule inhibitors of novel kinase targets, to be used either alone or in combination with other drugs, as well as the development of drugs with novel modes of action, are essential to helping more cancer patients survive this distressing disease. Chapter 2 describes the development of HTH-01-091, a selective inhibitor of maternal embryonic leucine zipper kinase (MELK), which was used to examine the potential of pharmacologically inhibiting MELK for the treatment of basal-like breast cancer (BBC). Although previous genetic studies had implicated MELK as a viable target for BBC, we observed discrepant antiproliferative activities between the more selective MELK inhibitor HTH-01-091 and the clinical stage but less selective MELK inhibitor OTSSP167, which inspired us to reexamine the potential of MELK as a therapeutic target. After evaluating the consequence of perturbing MELK function in BBC lines using MELK inhibitors of various scaffolds, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genetic knockout of MELK, degradation of MELK by a novel chemical-inducible degradation system (dTAG), ribonucleic acid (RNA) interference and CRISPR interference, we concluded that MELK was not necessary for the proliferation of BBC cells. The study also revealed that off-target effects of OTSSP167 and certain MELK-targeting short hairpins might have been responsible for the previous studies that identified MELK as a viable target for treating BBC. Chapter 3 describes the evaluation of heterobifunctional degrader molecules, an emerging drug class that brings protein targets into the proximity of an E3 ligase, thereby inducing ubiquitination and subsequent degradation. This pharmacological strategy presents potential advantages over the traditional occupancy-based inhibitor paradigm, including more durable response, prevention of protein upregulation as a resistance mechanism, and the ability to abrogate scaffolding functions that would otherwise be unamenable to enzymatic inhibition. Specifically, we used an unbiased proteomic approach to analyze the degradation profile of a multi-kinase degrader derived from a promiscuous kinase inhibitor warhead. Importantly, we identified 28 kinases as readily degradable in two leukemic cell lines, which significantly expanded the number of known degradable kinases, and demonstrated that the ability to engage both the target and the E3 ligase does not guarantee targeted degradation. As proof-of-concept, we chose two targets from this list of degradable kinases, and generated potent and selective FLT3 and BTK degrader molecules with relative ease. Moreover, the selective BTK degrader exhibited a more durable antiproliferative effect in comparison with its parental BTK inhibitor in a diffuse large B-cell lymphoma cell line, underscoring its potential to improve the standard of care for BTK-dependent malignancies and possibly autoimmune diseases. Together, this thesis addressed two issues at the forefront of cancer drug discovery and provided knowledge that will make the process more efficient and effective.