Discovery of a Potent and Selective Fragment-like Inhibitor of Methyllysine Reader Protein Spindlin 1 (SPIN1)

By
screening an epigenetic compound library, we identified that
UNC0638, a highly potent inhibitor of the histone methyltransferases
G9a and GLP, was a weak inhibitor of SPIN1 (spindlin 1), a methyllysine
reader protein. Our optimization of this weak hit resulted in the
discovery of a potent, selective, and cell-active SPIN1 inhibitor,
compound 3 (MS31). Compound 3 potently inhibited
binding of trimethyllysine-containing peptides to SPIN1, displayed
high binding affinity, was highly selective for SPIN1 over other epigenetic
readers and writers, directly engaged SPIN1 in cells, and was not
toxic to nontumorigenic cells. The crystal structure of the SPIN1–compound 3 complex indicated that it selectively binds tudor domain
II of SPIN1. We also designed a structurally similar but inactive
compound 4 (MS31N) as a negative control. Our results
have demonstrated for the first time that potent, selective, and cell-active
fragment-like inhibitors can be generated by targeting a single tudor
domain.