biostudies-literatureUnknown17(1)Castelletti DDespite the improvement of therapeutic options, melanoma patients with advanced metastatic disease are still in high need of durable treatments. Analysis of clinical data from patients receiving targeted and/or immunotherapy, along with genetic and functional studies in preclinical melanoma models, demonstrates the key role of the microphthalmia-associated transcription factor (MITF) throughout disease progression, and provides a solid rationale for its therapeutic inhibition. However, direct targeting of MITF or other basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors is unprecedented. Here, we report on the discovery of ligands for the DNA binding domain of MITF, using fragment-based screening (FBS) by nuclear magnetic resonance (NMR). Initial fragments, binding the kink pocket of MITF very weakly, are optimized to sub-micromolar affinities by structure-based design enabled by X-ray crystallography and biophysics. Furthermore, NMR experiments and molecular dynamics simulations reveal a dynamic conformational exchange between helices in the asymmetric homodimer, a phenomenon that is perturbed by ligand binding. This work advances our knowledge on direct targeting of bHLH-LZ DNA binding domains and sets the basis to further explore pharmacological inhibition of MITF.Nature communications594https://www.ebi.ac.uk/biostudies/studies/S-EPMC12808237biostudies-literatureFragment-based discovery enables direct targeting of the melanoma oncogene MITF.PMC12808237Mayer PHOHenry CPlattner SMaddalo DReimer BPiperidou NCastelletti DMermet-Meillon FKurmann JKlausler SYan KAltorfer MHinrichs JJahnke WJi FPorter KADelmas CWartmann MKaufmann MFernandez CMalojcic GDesplat ABrun JSchmiedeberg NCobos-Correa ASchaeffer FVulpetti ARenatus MBaysang FPautrieux NWilcken RWirth EFuller JfalseFragment-based discovery enables direct targeting of the melanoma oncogene MITF.Despite the improvement of therapeutic options, melanoma patients with advanced metastatic disease are still in high need of durable treatments. Analysis of clinical data from patients receiving targeted and/or immunotherapy, along with genetic and functional studies in preclinical melanoma models, demonstrates the key role of the microphthalmia-associated transcription factor (MITF) throughout disease progression, and provides a solid rationale for its therapeutic inhibition. However, direct targeting of MITF or other basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors is unprecedented. Here, we report on the discovery of ligands for the DNA binding domain of MITF, using fragment-based screening (FBS) by nuclear magnetic resonance (NMR). Initial fragments, binding the kink pocket of MITF very weakly, are optimized to sub-micromolar affinities by structure-based design enabled by X-ray crystallography and biophysics. Furthermore, NMR experiments and molecular dynamics simulations reveal a dynamic conformational exchange between helices in the asymmetric homodimer, a phenomenon that is perturbed by ligand binding. This work advances our knowledge on direct targeting of bHLH-LZ DNA binding domains and sets the basis to further explore pharmacological inhibition of MITF.2025-01-01T00:00:00Z2025 Dec2026-06-10T05:23:20.932Z2026-06-10T03:07:21.684ZS-EPMC128082374136590210.1038/s41467-025-67297-0