Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers

Abstract

Unnatural oligomers that can mimic protein surfaces offer a potentially useful strategy for blocking biomedically important proteinprotein interactions. Here we evaluate an approach based on combining ␣-and ␤-amino acid residues in the context of a polypeptide sequence from the HIV protein gp41, which represents an excellent testbed because of the wealth of available structural and biological information. We show that ␣/␤-peptides can mimic structural and functional properties of a critical gp41 subunit. Physical studies in solution, crystallographic data, and results from cell-fusion and virusinfectivity assays collectively indicate that the gp41-mimetic ␣/␤-peptides effectively block HIV-cell fusion via a mechanism comparable to that of gp41-derived ␣-peptides. An optimized ␣/␤-peptide is far less susceptible to proteolytic degradation than is an analogous ␣-peptide. Our findings show how a two-stage design approach, in which sequence-based ␣3␤ replacements are followed by site-specific backbone rigidification, can lead to physical and biological mimicry of a natural biorecognition process.alpha/beta-peptides ͉ HIV ͉ protein folding ͉ protein-protein interactions I dentification of strategies for interference with specific biopolymer recognition processes constitutes a fundamental challenge. Protein-protein associations are often resistant to inhibition by small molecules because the contact surfaces on the natural partners are large (1). Current clinical approaches to inhibiting proteinprotein interactions that underlie viral infection or aberrant signaling at the cell surface are based on the use of medium-length peptides or proteins (2). It would be valuable to identify alternative sources of antagonists for this type of protein recognition event.Here we show that peptide-like oligomers with unnatural backbones can function as potent antiviral agents by blocking a key protein-protein interaction. The design strategy we employ may prove general for ␣-helix mimicry.The HIV membrane protein gp41 mediates viral envelope-host cell membrane fusion, an essential step in the viral infection cycle. During HIV cell entry, the N-terminal fusion segment of trimeric gp41 inserts into the host cell membrane (3). A profound structural rearrangement of gp41 ensues, driven by formation of an antiparallel six-helix bundle (4-6), which leads to juxtaposition of the viral and host cell membranes. The prehairpin fusion intermediate is composed of three copies of gp41 in an extended conformation. The so-called ''class I'' fusion mechanism used by HIV is common to a variety of enveloped viruses, including those responsible for influenza, Ebola, and SARS (7,8). A number of ␣-peptides based on sequences from the gp41 N-terminal heptad repeat (NHR) domain or C-heptad repeat (CHR) domain (e.g., Fig. 1B, 1 and 2) have been investigated as anti-HIV agents (9, 10). These compounds are thought to act by binding to a gp41 prehairpin intermediate, thereby preventing six-helix bundle formation and subsequent virus-cell fusion. The drug enfu...

Targeting diverse protein–protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold

“…Indeed, α/β-VEGF-1 showed substantially greater resistance to proteinase K than the 59-mer α-peptide Z-VEGF. These observations are consistent with previous findings, involving other α-vs. α/β-peptide comparisons, that have shown that α→β replacements at multiple sites can substantially enhance polypeptide resistance to protease action (6)(7)(8)(9)35). Introduction of one additional Aib residue, to convert α/β-VEGF-1 into α/β-VEGF-2, conferred additional resistance to proteinase K (half-life, 670 min; >400-fold increase relative to Z-VEGF and >3,300-fold increase relative to α-VEGF-2).…”

“…Peptidic oligomers that contain β-amino acid residues interspersed among α-residues ("α/β-peptides") can effectively mimic the recognition surface projected by an α-helix and thereby disrupt or augment protein-protein interactions in which one partner contributes a single helix to the interface (6,7). The unnatural backbone diminishes α/β-peptide susceptibility to proteolytic degradation relative to conventional peptides (α-residues only, "α-peptides").…”

An α‐Helix‐Mimicking 12,13‐Helix: Designed α/β/γ‐Foldamers as Selective Inhibitors of Protein–Protein Interactions

“…Amongst a multitude of foldamer classes where structural/ conformational determinants have been mapped,1, 2, 3, 4 β‐peptides and hybrid α/β‐peptides, in which β‐amino acids are dispersed along an α‐peptide backbone, can inhibit α‐helix‐mediated protein–protein interactions22, 23, 24, 25, 26, 27, 28, 29 and mimic the structure and the function of protein surfaces 30, 31. Nonetheless foldamers that more accurately mimic the topology and topography of the α‐helix might prove advantageous in comparison to β‐ and α/β‐peptides, which may not fully mimic the spatial presentation of α‐helix side chains.…”

Protein prosthesis: β‐peptides as reverse‐turn surrogates

“…These results encourage additional interrogations of natural structural elements with foldameric equivalents. [27][28][29][30] …”