title: The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-myc.
abstract: Intrinsically disordered proteins are attractive therapeutic targets owing to their prevalence in several diseases. Yet their lack of well-defined structure renders ligand discovery a challenging task. An intriguing example is provided by the oncoprotein c-Myc, a transcription factor that is over expressed in a broad range of cancers. Transcriptional activity of c-Myc is dependent on heterodimerization with partner protein Max. This protein-protein interaction is disrupted by the small molecule 10058-F4 (1), that binds to monomeric and disordered c-Myc. To rationalize the mechanism of inhibition, structural ensembles for the segment of the c-Myc domain that binds to 1 were computed in the absence and presence of the ligand using classical force fields and explicit solvent metadynamics molecular simulations. The accuracy of the computed structural ensembles was assessed by comparison of predicted and measured NMR chemical shifts. The small molecule 1 was found to perturb the composition of the apo equilibrium ensemble and to bind weakly to multiple distinct c-Myc conformations. Comparison of the apo and holo equilibrium ensembles reveals that the c-Myc conformations binding 1 are already partially formed in the apo ensemble, suggesting that 1 binds to c-Myc through an extended conformational selection mechanism. The present results have important implications for rational ligand design efforts targeting intrinsically disordered proteins.
authors: EastCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom. mail@julienmichel.net
authors: Julien
authors: J
authors: Michel
authors: Rémi
authors: R
authors: Cuchillo
mesh_terms: D005786:Gene Expression Regulation; D006801:Humans; D020128:Inhibitory Concentration 50; D007700:Kinetics; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008954:Models, Biological; D008956:Models, Chemical; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods; D017433:Protein Structure, Secondary; D016271:Proto-Oncogene Proteins c-myc / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D013844:Thiazoles / Q000494:pharmacology; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: C524814:5-(4-ethylbenzylidene)-2-thioxothiazolidin-4-one; D008024:Ligands; D016271:Proto-Oncogene Proteins c-myc; D013844:Thiazoles; D014157:Transcription Factors