Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning
Shabbir Ahmad, Jin Xu, Jianwen A. Feng, Ashley Hutchinson, Hong Zeng, Pegah Ghiabi, Aiping Dong, Paolo A. Centrella, Matthew Clark, Marie-Aude Guié, John P. Guilinger, Anthony D. Keefe, Ying Zhang, Thomas Cerruti, John W. Cuozzo, Moritz von Rechenberg, Albina Bolotokova, Yanjun Li, P. Loppnau, Alma Seitova, Yen-Yen Li, Vijayaratnam Santhakumar, Peter J. Brown, Suzanne Ackloo, Levon Halabelian
Abstract
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 K D 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.