Advancements in Small Molecule Hit Discovery Technology Based on a Target Class Approach for Methyl Lysine Reader Proteins

The discovery and characterization of small molecule inhibitors that are potent andselective towards therapeutically relevant targets remains a persistent challenge. Therefore, thedevelopment of robust and effective discovery technologies, especially for target classes thathave been deemed “undruggable”, are highly desired. One such class, epigenetic reader proteins,recognizes and binds to histone marks to serve as a docking site for effector proteins to allow for avast array of possible signals known as the “histone code” to occur, thus enabling chromatinregulation. Despite playing a central role in chromatin mark recognition and subsequent systemrecruitment, this class remains relatively unexplored as the discovery of therapeutically relevantsubstances remains elusive. In response, we utilized a target-class driven strategy for the purposeof deploying multiple complementary strategies for identifying potent and selective inhibitors forreader proteins linked with methylated lysine residues (Kme readers) for chemical probedevelopment. Herein, we report the use of a target-class DNA-encoded library (DEL) platform toscreen for novel binding compounds for Kme reader targets 53BP1, KDM7B, LEDGF, CBX2,and CBX7; the discovery and development of a best-in-class, cellularly active 53BP1 antagonistusing our target-class DEL; additional efforts towards hit discovery for Kme readers 53BP1 andSETDB1; and the optimization and production of next generation, diversity-based DELs muchlarger in size to expand our screening toolbox beyond a target-class approach.