Inhibition of major-groove-binding proteins by pyrrole-imidazole polyamides with an Arg-Pro-Arg positive patch

• Published in: Chemistry & biology Vol. 5; no. 3; pp. 119 - 133
• Main Authors: Bremer, Ryan E., Baird, Eldon E., Dervan, Peter B.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 01-03-1998
• Subjects: DNA; DNA-Binding Proteins - antagonists & inhibitors; DNA-Binding Proteins - metabolism; Fungal Proteins - antagonists & inhibitors; Fungal Proteins - metabolism; hydrogen bond; Imidazoles - chemistry; Ligands; minor groove; molecular recognition; Nylons - pharmacology; Oligopeptides - chemistry; Protein Binding; Protein Kinase Inhibitors; Protein Kinases - metabolism; Pyrroles - chemistry; Saccharomyces cerevisiae Proteins; Salts; transcription factor; transcription factor; molecular recognition; minor groove; DNA; hydrogen bond
• ISSN: 1074-5521; 1879-1301
• DOI: 10.1016/S1074-5521(98)90057-6

Background: Gene-specific targeting of any protein-DNA complex by small molecules is a challenging goal at the interface of chemistry and biology. Polyamides containing
N-methylimidazole and
N-methylpyrrole amino acids are synthetic ligands that have an affinity and specificity for DNA comparable to many naturally occurring DNA-binding proteins. It has been shown that an eight-ring hairpin polyamide targeted to a specific minor-groove contact within a transcription factor binding site can inhibit protein-DNA binding and gene transcription. Polyamides and certain major-groove-binding proteins have been found to co-occupy the DNA helix, however. To expand the number of genes that can be targeted by pyrrole/imidazole polyamides, we set out to develop a class of polyamides that can selectively inhibit major-groove-binding proteins.
Results: An eight-ring hairpin polyamide conjugated to a carboxy-terminal Arg-Pro-Arg tripeptide was designed to deliver a positive residue to the DNA backbone and interfere with protein-phosphate contacts. Gel mobility shift analysis demonstrated that a polyamide hairpin-Arg-Pro-Arg binding in the minor groove selectively inhibits binding of the transcription factor GCN4 (222–281) in the adjacent major groove. Substitution within the Arg-Pro-Arg revealed that each residue was required for optimal GCN4 inhibition.
Conclusions: A pyrrole-imidazole polyamide that binds to a predetermined site in the DNA minor groove and delivers a positive patch to the DNA backbone can selectively inhibit a DNA-binding protein that recognizes the adjacent major groove. A subtle alteration of the DNA microenvironment targeted to a precise location within a specific DNA sequence could achieve both gene-specific and protein-specific targeting.