Direct Targeting of the Oncogene Microphthalmia-Associated Transcription Factor (MITF) by Fragment-Based Discovery [RNA-seq]

Despite the improvement of therapeutic options for melanoma, patients with advanced metastatic disease are still in high need of durable and tolerated treatments. Analysis of clinical data from patients receiving targeted and/or immunotherapy, along with genetic and functional studies in preclinical melanoma models, show that lineage addiction to MITF is retained throughout disease progression, thus providing the rationale to pursue therapeutic inhibition of MITF. However, direct targeting of MITF or other basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors is unprecedented. Here, we report on the fragment-based discovery of high-affinity ligands for MITF. Fragment screening by NMR led to the discovery of weak binders to the kink pocket of MITF, which were optimized to sub-micromolar affinity by structure-based design enabled by crystallography and biophysics. Furthermore, NMR experiments and molecular dynamics simulations revealed a dynamic conformational exchange of the two helices in the asymmetric homodimer, which is perturbed by ligand binding. This work advances our knowledge on direct targeting of bHLH-LZ domains and sets the basis to further explore pharmacological inhibition of MITF. Overall design: RNA-seq profiling of wild-type and MITF knocked-down (KD) in naïve (parental) or resistant to the Dabrafenib and Trametinib combination MELHO cells. MITF Cut&Tag chromatin profiling in WT and MITF mutant expressed UACC-257 cells