Development of small molecule epigenetic therapeutics for prostate cancer

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Generation of constitutively active androgen-receptor (AR)-variant AR-V7, activation of glucocorticoid receptor (GR) signaling, and lineage switch from epithelial to neuroendocrine of prostate cancer (PCa) cells are three emerging mechanisms by which prostate tumor cells use to evade targeted therapy with androgen-receptor pathway inhibitors (ARPIs). There are no drugs or pipeline-agents that target these mechanisms in PCa therapeutics. Our previous and preliminary studies indicate that histone lysine demethylase KDM4B is associated with these mechanisms and may be a druggable target in castration-resistant prostate cancer (CRPC). KDM4B promotes the expression of cell cycle genes, AR-V7, and neuroendocrine markers. Genetic inactivation or pharmacological inhibition of KDM4B downregulates the expression of these genes and suppresses CRPC growth. We have generated proto-type KDM4B inhibitor B3 that effectively inhibited the growth of AR-negative and neuroendocrine-like PC3 xenograft in vivo. B3 also suppresses the growth of 22Rv1 tumor that expresses high levels of AR and AR-V7 in castrated mice and has synergistic effect with the GR antagonist CORT125134. To improve the selectivity and efficacy of B3, we performed multiple rounds of structure-based virtual screening, computational analyses, chemical synthesis, and primary cell-based screens. From >200 chemical compounds, we identified 3 more lead compounds that have improved IC50 on KDM-driven cell growth inhibition compared to that of B3. The synthesis of these chemical entities and their use in oncology have been filed for patent protection. Here we will test the efficacy of these lead compounds in various prostate xenograft models and characterize their ADME (Absorption, distribution, metabolism, and excretion) and pharmacokinetics-pharmacodynamics (PK/PD) properties with two specific aims. Aim 1. To establish the efficacy and enzymatic selectivity of candidate compound. We will test the efficacy of B3 and B3-analogs in xenografts derived from PCa models that have various degree of androgen responsiveness. We also include the non- prostate HeLa cells as a control and will perform RNA-seq to identify common and prostate cancer unique gene signature associated with the candidate compound. Selectivity of the candidate will be tested for its ability to inhibit specific KDM enzymatic activity in the demethylase assay. Aim 2. To establish the physiochemical and ADME properties of candidate compound. The drug-likeness of the candidate will be characterized including its physiochemical properties, in vitro metabolic stability, cell permeability, plasma protein binding, and PK/PD properties. The outcome of the proposal will provide us information to identify biomarker-defined subgroup(s) of PCa patients and to evaluate the effect of targeted therapy. The information will also guide us in designing and optimizing the drug-delivery route and drug formulation and performing PK/PD modeling in human in the phase II pre-IND studies. Milestone: We will prioritize the lead compounds based on their efficacy, selectivity, and ADME/PK/PD properties and take top one/two compound(s) on the list forward to phase II studies.