Biocatalytic- and Chemoproteomic-Guided Discovery of a PHGDH Inhibitor from Chemoenzymatic-Promoted DNA-Encoded Libraries Selection Platform

DNA-encoded libraries
(DELs) have emerged as an effective
and efficient
selection strategy for lead compound discovery in academia and industry
over the past few decades. Despite recent advancements in this field,
DEL remains limited by sensitive DNA-based constructs, particularly
with low selection success rates resulting from the random selection
of targets. Here, we describe a chemoenzymatic on-DNA reaction for
DEL syntheses and develop a chemoproteomic-guided DEL selection platform.
This platform, termed FF tags-biocatDEL, integrates DEL technology,
chemoenzymatic synthesis, and fully functionalized (FF) chemical tags
to match DELs with selection targets, even with limited information
about ligandable hotspots. Using two diazirine-based FF indole probes,
we comprehensively surveyed binding partners in cells and identified
phosphoglycerate dehydrogenase (PHGDH) as a potential target for DEL
selection. DEL01 and DEL02 were designed, synthesized, and selected
against PHGDH, leading to the identification of a novel enzyme-active
compound with an IC50 value of 2.5 μM. Our strategy,
utilizing FF tags-biocatDEL, establishes a generalizable workflow
for rapid target hunting and ligand discovery. It provides an effective
method for precisely matching DELs with potential targets, demonstrating
its significant potential as a complementary approach to drug discovery
based on DELs.