Direct Inhibition of Tumor Hypoxia Response with Synthetic Transcriptional Repressors

Many oncogenic transcription factors (TFs) are considered to be undruggable due to their reliance on large protein-protein and protein-DNA interfaces. TFs like hypoxia-inducible factors (HIFs) and X-box binding protein 1 (XBP1) are induced by hypoxia and other stressors in solid tumors and bind to UPRE/HRE motifs to control oncogenic gene programs. Here, we report a strategy to create synthetic transcriptional repressors (STRs) that mimic the bZIP domain of XBP1 and recognize the UPRE/HRE motif. A lead molecule, STR22, binds UPRE/HRE DNA sequences with high fidelity and competes with both TFs in cells. Under hypoxia, STR22 globally suppresses HIF1a binding to HRE-containing promoters/enhancers, inhibits hypoxia-induced gene expression and blocks pro-tumorigenic phenotypes in TNBC cells. In vivo, intratumoral and systemic STR22 treatment inhibited hypoxia-dependent gene expression, primary tumor growth and metastasis of TNBC tumors. These data validate a novel strategy to target the tumor hypoxia response through coordinated inhibition of TF-DNA binding.