High-throughput ligand diversification to discover chemical inducers of proximity
James B. Shaum, Miquel Muñoz i Ordoño, Erica Steen, Daniela V. Wenge, Hakyung Cheong, Jordan Janowski, Moritz Hunkeler, Eric M. Bilotta, Zoe Rutter, Paige Barta, Abby M. Thornhill, Natalia Milosevich, Lauren M Hargis, Timothy R. Bishop, Trever R. Carter, Bryce da Camara, Matthias Hinterndorfer, Lucas Dada, W. He, Fabian Offensperger, Hirotake Furihata, Sydney R. Schweber, Charlie Hatton, Yanhe Wen, Benjamin F. Cravatt, Keary M. Engle, Katherine A. Donovan, Bruno Melillo, Seiya Kitamura, Alessio Ciulli, Scott A. Armstrong, E. O. Fischer, Georg E. Winter, Michael A. Erb
Abstract
Abstract Chemical inducers of proximity (CIPs) stabilize biomolecular interactions, often causing an emergent rewiring of cellular biochemistry. While the discovery of heterobifunctional CIPs is expedited by rational design strategies, molecular glues have relied predominantly on serendipity. We hypothesized that preexisting ligands could be systematically decorated with chemical modifications to discover compounds that recruit proteins to a composite protein–ligand interface. Using sulfur(VI) fluoride exchange-based high-throughput chemistry (HTC) to install 3,163 structurally diverse building blocks onto ENL (eleven-nineteen leukemia) and BRD4 (bromodomain-containing protein 4) ligands, we screened each analog for degrader activity. This revealed dHTC1, an ENL degrader that recruits CRL4 CRBN complex through an extended interface of protein–protein contacts and only engages CRBN after pre-forming the ENL:dHTC1 complex. We also identified dHTC3, a molecular glue that selectively dimerizes BRD4 bromodomain 1 to SCF FBXO3 , an E3 ligase not previously accessible for chemical rewiring. Altogether, this study introduces HTC as a facile tool to discover new CIPs and new effectors for proximity pharmacology.