Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens

Significance The emergence of powerful new chemical library-screening approaches and the generation of new types of chemical structures makes novel methods available to link candidate chemicals to potential target genes, e.g., as in the interaction with and effects on chromatin-bound targets. Here we report a method that can provide the genome-wide location of a candidate drug. One such synthetic chemical, SD70—first identified in a screen for inhibitors of tumor translocation events—was resynthesized with a tag permitting a ChIP-sequencing–like analysis, referred to as “Chemical affinity capture and massively parallel DNA sequencing (Chem-seq).” As a consequence of finding its recruitment on androgen receptor-bound functional enhancers, we were able to demonstrate that SD70 could inhibit the prostate cancer cell transcriptional program, in part by inhibition of the demethylase KDM4C. Understanding the mechanisms by which compounds discovered using cell-based phenotypic screening strategies might exert their effects would be highly augmented by new approaches exploring their potential interactions with the genome. For example, altered androgen receptor (AR) transcriptional programs, including castration resistance and subsequent chromosomal translocations, play key roles in prostate cancer pathological progression, making the quest for identification of new therapeutic agents and an understanding of their actions a continued priority. Here we report an approach that has permitted us to uncover the sites and mechanisms of action of a drug, referred to as “SD70,” initially identified by phenotypic screening for inhibitors of ligand and genotoxic stress-induced translocations in prostate cancer cells. Based on synthesis of a derivatized form of SD70 that permits its application for a ChIP-sequencing–like approach, referred to as “Chem-seq,” we were next able to efficiently map the genome-wide binding locations of this small molecule, revealing that it largely colocalized with AR on regulatory enhancers. Based on these observations, we performed the appropriate global analyses to ascertain that SD70 inhibits the androgen-dependent AR program, and prostate cancer cell growth, acting, at least in part, by functionally inhibiting the Jumonji domain-containing demethylase, KDM4C. Global location of candidate drugs represents a powerful strategy for new drug development by mapping genome-wide location of small molecules, a powerful adjunct to contemporary drug development strategies.