Solution-phase synthesis of pyrrole-imidazole polyamides

Pyrrole-Imidazole polyamides are DNA-binding molecules that are programmable for a large repertoire of DNA sequences. Typical syntheses of this class of heterocyclic oligomers rely on solid-phase methods. Solid-phase methodologies offer rapid assembly on a micromole scale sufficient for biophysical characterizations and cell culture studies. In order to produce gram-scale quantities necessary for efficacy studies In animals, polyamides must be readily synthesized In solution. An 8-ring hairpin polyamide 1, which targets the DNA sequence 5′-WGWWCW-3′, was chosen for our synthesis studies as this oligomer exhibits androgen receptor antagonism In cell culture models of prostate cancer. A convergent solution-phase synthesis of 1 from a small set of commercially available building blocks Is presented which highlights principles for preparing gram quantities of pyrrole-Imidazole oligomers with minimal chromatography.