Small-molecule switches for zinc finger transcription factors

We have developed a general approach to generate selective small-molecule switches for zinc finger transcription factors based on the notion of structural complementation. A small molecule, 2-(4′-quinoline)benzimidazole (7), was identified by screening of a heterocycle library, which functionally rescues a structurally compromised transcription factor C7-F116A/H125G-VP16. Compound 7 induces the activity of the mutant zinc finger in a luciferase-based transactivation assay by about 18-fold at 100 μM concentration. Surface plasmon resonance measurements revealed that compound 7 enhances the affinity between the mutant C7 and its cognate DNA sequence by 16-fold while a structurally analogous compound, 2-(2-naphthyl)benzimidazole (8), showed no affinity enhancement, indicating there is a specific interaction between compound 7 and the mutant zinc finger. Taken together, these results suggest that the partial affinity recovery of the mutant transcription factor may be the mechanism for the functional rescue of the zinc finger transcription factor by compound 7.