Regulation of gene expression with pyrrole-imidazole polyamides

Abstract

The natural product distamycin contains three N-methylpyrrole amino acids and binds in the minor groove of DNA at A,T tracts 4-5 base pairs (bp) in size. Distamycin inhibits DNA-dependent processes, including transcription, and has antibacterial, antimalarial, antifungal and antiviral activities, but is of limited use because of toxicity. Efforts to bring distamycin analogs to the clinic have focused on anti-infective therapeutics. These compounds have been optimized for pathogen activity and pharmacological properties, with DNA binding specificity not providing a major driving force in ligand selection. Dickerson, Rich and Wemmer revealed by X-ray and NMR structural studies that the crescent-shaped molecule could bind A,T tracts in both 1:1 and 2:1 ligand:DNA stoichiometries. Informed by these structures, we explored whether designed distamycin analogs could be tuned by chemical modification in a predictable fashion to bind to a very large number of different DNA sequences, i.e. create an artificial small molecule language to read the minor groove digitally, similar in function to nature's proteins. This might underpin a rational chemical approach to the regulation of gene expression by chemical methods. After a 20 year search, we demonstrated that synthetic analogs pf the N-methylpyrrole (Py) carboxamide ring afford a set of heterocycles that can be combined -- as unsymmetrical ring pairs -- in a modular fashion to recognize specifically a large repertoire of DNA sequences with affinities and specificities comparable to DNA-binding proteins. In this chapter we describe advances in the field of DNA-binding polyamides, cellular and nuclear uptake properties and recent biological applications.