Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning

WD40 repeat-containing protein 91
(WDR91) regulates early-to-late
endosome conversion and plays vital roles in endosome fusion, recycling,
and transport. WDR91 was recently identified as a potential host factor
for viral infection. We employed DNA-encoded chemical library (DEL)
selection against the WDR domain of WDR91, followed by machine learning
to predict ligands from the synthetically accessible Enamine REAL
database. Screening of predicted compounds identified a WDR91 selective
compound 1, with a KD of
6 ± 2 μM by surface plasmon resonance. The co-crystal structure
confirmed the binding of 1 to the WDR91 side pocket,
in proximity to cysteine 487, which led to the discovery of covalent
analogues 18 and 19. The covalent adduct
formation for 18 and 19 was confirmed by
intact mass liquid chromatography–mass spectrometry. The discovery
of 1, 18, and 19, accompanying
structure–activity relationship, and the co-crystal structures
provide valuable insights for designing potent and selective chemical
tools against WDR91 to evaluate its therapeutic potential.