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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.

Original publication

DOI

10.1021/acs.jmedchem.9b00522

Type

Journal article

Journal

J med chem

Publication Date

24/10/2019

Volume

62

Pages

8996 - 9007

Keywords

Cell Cycle Proteins, Chromatography, High Pressure Liquid, Crystallography, X-Ray, Drug Discovery, HEK293 Cells, Humans, Microtubule-Associated Proteins, Molecular Structure, Phosphoproteins, Proton Magnetic Resonance Spectroscopy, Quinazolines