Discovery of a potent stapled helix peptide that binds to the 70N domain of replication protein A.

Frank AO, Vangamudi B, Feldkamp MD, Souza-Fagundes EM, Luzwick JW, Cortez D, Olejniczak ET, Waterson AG, Rossanese OW, Chazin WJ, Fesik SW
J Med Chem. 2014 57 (6): 2455-61

PMID: 24491171 · PMCID: PMC3969094 · DOI:10.1021/jm401730y

Stapled helix peptides can serve as useful tools for inhibiting protein-protein interactions but can be difficult to optimize for affinity. Here we describe the discovery and optimization of a stapled helix peptide that binds to the N-terminal domain of the 70 kDa subunit of replication protein A (RPA70N). In addition to applying traditional optimization strategies, we employed a novel approach for efficiently designing peptides containing unnatural amino acids. We discovered hot spots in the target protein using a fragment-based screen, identified the amino acid that binds to the hot spot, and selected an unnatural amino acid to incorporate, based on the structure-activity relationships of small molecules that bind to this site. The resulting stapled helix peptide potently and selectively binds to RPA70N, does not disrupt ssDNA binding, and penetrates cells. This peptide may serve as a probe to explore the therapeutic potential of RPA70N inhibition in cancer.

MeSH Terms (19)

Alanine Amino Acid Sequence Cell Line Crystallization Crystallography, X-Ray DNA, Single-Stranded Drug Discovery Electrophoretic Mobility Shift Assay Fluorescence Polarization Magnetic Resonance Spectroscopy Microscopy, Fluorescence Models, Molecular Molecular Sequence Data Penetrance Peptides Protein Conformation Replication Protein A Structure-Activity Relationship Tumor Suppressor Protein p53

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