Synthesis of a nucleic acid reporter for molecular glue discovery in DNA encoded libraries

Molecular glues, small molecules that bring two proteins together, are a promising drug modality. By acting as mediators of protein-protein interactions, molecular glues give unprecedented control over protein fate, allowing disease-causing proteins to be degraded, re-localized, inactivated or even reactivated to resume normal function. Despite the widespread interest in molecular glue drug development in both academic and pharmaceutical settings, the rational design of new molecular glues has been slowed by the limited methods for their detection in high-throughput screens. To address this, we conceptualized and developed a beadfree proximity-based screening approach to record molecular glue binding events in DNA encoded libraries (DELs). We describe the synthesis of a nucleic acid reporter of molecular glue binding and demonstrate its implementation with a protein-fragment complementation-based hit selection strategy. Finally, we show that the DNA barcodes of putative molecular glues can be enriched from a pool of non-molecular glue binders by PCR. This proof-of-concept study lays the groundwork for the discovery of novel molecular glue drug candidates and delves into synthetic strategies for tuning DNA-DNA molecular recognition.