July 1, 2018
e IKZF1 homology model was taken from17. Time-resolved fluorescence resonance energy transfer (TR-FRET) Compounds in dimerization assays were dispensed in a 384-well microplate (Corning, 4514) using D300e Digital Dispenser (HP) normalized to 2% DMSO into 200 nM biotinylated His6-avi-bromodomain (WT or mutant, see Figure legends) or 80 nM biotinylated StrepII-avi-IKZF1Î (See Figure legends), 100;e IKZF1 homology model was taken from17. Time-resolved fluorescence resonance energy transfer (TR-FRET) Compounds in dimerization assays were dispensed in a 384-well microplate (Corning, 4514) using D300e Digital Dispenser (HP) normalized to 2% DMSO into 200 nM biotinylated His6-avi-bromodomain (WT or mutant, see Figure legends) or 80 nM biotinylated StrepII-avi-IKZF1Î (See Figure legends), 100
Heterobifunctional small-molecule degraders that induce protein degradation through ligase-mediated ubiquitination have shown considerable promise as a new pharmacological modality. However, we currently lack a detailed understanding of the molecular basis for target recruitment and selectivity, which is critically required to enable rational design of degraders. Here we utilize a comprehensive characterization of the ligand-dependent CRBN-BRD4 interaction to demonstrate that binding between proteins that have not evolved to interact is plastic. Multiple X-ray crystal structures show that plasticity results in several distinct low-energy binding conformations that are selectively bound by ligands. We demonstrate that computational protein-protein docking can reveal the underlying interprotein contacts and inform the design of a BRD4 selective degrader that can discriminate between highly homologous BET bromodomains. Our findings that plastic interprotein contacts confer selectivity for ligand-induced protein dimerization provide a conceptual framework for the development of heterobifunctional ligands.
Nowak, RP; DeAngelo, SL; Buckley, D; He, Z; Donovan, KA; An, J; Safaee, N; Jedrychowski, MP; Ponthier, CM; Ishoey, M; Zhang, T; Mancias, JD; Gray, NS; Bradner, JE; Fischer, ES;
Journal: Nat. Chem. Biol. Pages: 706-714