Discovery of an Exquisitely Selective WDR5 Chemical Probe Accelerated by a High-Quality DEL-ML Hit

Abstract

Herein we present the rapid development of LH168, a potent and highly selective chemical probe for WDR5, streamlined by utilizing a DEL-ML (DNA Encoded Library - Machine Learning) hit as the chemical starting point. LH168 was comprehensively characterized in bioassays and demonstrated potent in-cellulo target engagement at the WIN-site pocket of WDR5, with an EC50 of approximately 10 nM, a long residence time, and exceptional proteome-wide selectivity for WDR5. In addition, we present the X-ray co-crystal structure and provide insights into the structure-activity relationships (SAR). In parallel, we developed a matched negative control compound as well as an alkyne analog (compound 16) to facilitate the development of bifunctional molecules. Taken together, we provide the scientific community with a well-characterized chemical probe to enable studies and functional manipulation of WDR5 in a cellular context, as this protein represents a therapeutically relevant target with scaffolding functions that influence multiple cellular processes.