Designer Frankenproteins That Halt the Proliferation of Myc-Driven Cancer Cells

Overexpression of the proto-oncogene MYC occurs in >70% of cancers and is especially prevalent in breast cancer. Myc partners with transcription factor Max to bind to the E-box DNA response element. By patterning our frankenproteins on the basic region/helix-loop-helix/leucine zipper motif of Max, we designed MEF and MEF/C93 to bind to the E-box. In bacterial one-hybrid assays and quantitative electrophoretic mobility shift assay, both proteins bound specifically to the E-box with high sequence-specificity and affinity (<i>K</i>_d = 8 nM) rivaling native transcription factors. Quantitative PCR revealed that MEF and MEF/C93 selectively downregulated Myc target genes in Myc-dependent MDA-MB-231 breast cancer cells, but not in Myc-independent MCF-7 cells. Fluorescence colocalization demonstrated transport into cell nuclei. Our proteins displayed IC₅₀ values of 1-2 μM in cell viability assays in MDA-MB-231, compared with ∼25 μM in MCF-7. These results demonstrate the specificity of targeting Myc-dependent cancer cells and mark significant progress toward protein-based therapies aimed at Myc-driven cancers.