beta-Peptides as inhibitors of protein-protein interactions

Abstract

We became interested several years ago in exploring whether 14-helical beta-peptide foldamers could bind protein surfaces and inhibit protein-protein interactions, and if so, whether their affinities and specificities would compare favorably with those of natural or miniature proteins. This exploration was complicated initially by the absence of a suitable beta-peptide scaffold, one that possessed a well-defined 14-helical structure in water and tolerated the diverse sequence variation required to generate high-affinity protein surface ligands. In this perspective, we describe our approach to the design of adaptable beta-peptide scaffolds with high levels of 14-helix structure in water, track the subsequent development of 14-helical beta-peptide protein-protein interaction inhibitors, and examine the potential of this strategy for targeting other therapeutically important proteins.

Figure 1

(A) Comparison of secondary structures formed by α- and β-amino acid oligomers. Carbon atoms are shown in black, nitrogen atoms in blue, oxygen atoms in red, and amide hydrogen atoms in white. Other hydrogen atoms are omitted for clarity. (B) β-Amino acid monomers that promote the formation of unique helices.

Figure 2

Helical net diagrams (A) and circular dichroism (CD) spectra (B) of β³-peptides with significant 14-helix stability in water. Residues are abbreviated β³X, where X denotes the common single-letter abbreviation of the analogous α-amino acid. CD spectra are plotted in units of mean residue ellipticity, and were obtained at 25°C from samples containing 100μM β-peptide in 1mM sodium phosphate/citrate/borate buffer (pH7.0). Note the relative intensities of minima near 214nm; while circular dichroism spectra of β-peptides must be interpreted with care, these values are commonly used to estimate relative 14-helix content in a series of analogous peptides.,–

Figure 3

NMR solution structure of β53-1 in CD₃OH at 20°C, viewed from the side and down the helical axis. Models shown represent the mean of 20 lowest-energy structures. Backbone carbons are shown in gray, nitrogens in blue, oxygens in red, and side chain carbons in green. Hydrogen atoms have been omitted for clarity.

Figure 4

(A) Helical net illustration of the sequence of β53-1. (B) Plots illustrating the fraction of fluorescein-labeled p53AD– (p53AD^Flu, blue circles), β53-1 labeled on its N-terminus (^Fluβ53-1, pink squares), or β53-1 labeled on its C-terminus (β53-1^Flu, pink diamonds) bound as a function of hDM2 concentration as measured by fluorescence polarization. Labeled peptides were incubated at a concentration of 25nM with various concentrations of hDM2_1-188 at room temperature until equilibrium was reached.

Figure 5

NMR solution structure of β53-1 in CD₃OH as viewed down the helix axis (left) or from the side (right). Models shown are overlays of the 20 lowest-energy conformations. Carbon atoms are shown in black, nitrogens in blue, and oxygens in red.