Solution structure of a beta-peptide ligand for hDM2

Abstract

We recently reported a beta-peptide foldamer, beta53-1, that folds into a 14-helix in aqueous solution, binds the oncoprotein hDM2 with submicromolar affinity, and potently inhibits the interaction of hDM2 with a peptide derived from the activation domain of p53 (p53AD). Here, we present the solution structure of beta53-1 in methanol. Details of the structure illustrate fundamental and novel elements of beta-peptide folding and recognition. These elements include the detailed arrangement of a complex, 14-helix-stabilizing salt bridge on one helical face, and a unique "wedge into cleft" packing interaction along a second. The structure also reveals how a subtle distortion in the beta53-1 14-helix geometry alters the presentation of its recognition epitope, rendering it particularly well suited for alpha-helix mimicry. The solution structure of beta53-1 demonstrates that well folded beta-peptide oligomers can effectively present an extended, highly variable surface that could be used as a general platform for targeting critical protein-protein interfaces.

Figure 1

(A) Chemical structure of β53–1, shown with N-terminus at left. (B) Solution structure of β53–1 in CD₃OH at 10 °C, shown as a bundle of 20 lowest-energy structures, with C-terminus at left. (C) Ribbon representation of the backbones of 20 lowest-energy structures. (D) Two subpopulations of ion pairing configurations. Superposed at left are 17 structures in which β³O1 and β³E4 are proximal; superposed at right are three structures in which β³E4 and β³O7 are proximal. (E) Conformations of β³-homovaline residues illustrating the “wedge into cleft” packing found in all 20 lowest-energy structures.

Figure 2

Overlay of the methanol solution structure of β53–1 (red ribbon and side chains) with the crystal structure of a p53AD-derived peptide (gold ribbon and side chains) bound to hDM2 (gray surface). Side chains of β53–1 not implicated in recognition have been omitted, and part of the hDM2 surface has been cut away for clarity.