Discovery of molecular glues that bind FKBP12 and structurally distinct targets using DNA-encoded libraries

Molecular glues are small molecules that engage their target and presenter proteins cooperatively. FKBP12 molecular glues (FK506 and rapamycin) were discovered several decades ago and have been used clinically, but our understanding of the breadth of FKBP12 molecular glues and targets has yet to be fully revealed. To expand the target classes of FKBP12 molecular glues, we construct and screen a multi-million-member non-macrocyclic FKBP12-ligand DNA-encoded library using 25 structurally distinct proteins. Synthesis and validation of select hits in biophysical and cell-based assays confirm FKBP12-dependent molecular-glue recruitment to bromodomain-containing protein 9 (BRD9) and quinoid dihydropteridine reductase (QDPR). One glue shows no measurable binding to QDPR alone but has appreciable binding in the presence of FKBP12 using either purified proteins or intact cells. The sites of recruitment are characterized with mutational analysis, competition-based methods and X-ray crystallography. The results of this study confirm that FKBP12-binding DELs can yield molecular glues generating highly selective FKBP12-target protein interactions. In this study, authors screen a 3.2 million member FKBP scaffold-directed DNA-encoded library and identify FKBP12-binding molecular glues for both bromodomain-containing protein 9 (BRD9) and quinoid dihydropteridine reductase (QDPR).