ConspectusThe functions carried out by proteins and nucleic acids provide the foundation for life, and chemists have begun to ask whether it is possible to design synthetic oligomers that approach the structural and functional complexity of these biopolymers. The study of foldamers, non-natural oligomers with discrete folding propensities, has demonstrated that a variety of synthetic backbones can show biopolymer-like conformational behavior. Early work in this area focused on oligomers comprised of a single type of monomer subunit, but recent efforts have highlighted the potential of mixed or "heterogeneous" backbones to expand the structural and functional repertoire of foldamers. In this Account, we illustrate the promise of heterogeneous backbone foldamers by focusing on examples containing both α-and β-amino acid residues.The use of heterogeneous backbone foldamers offers advantages over homogeneous backbone counterparts, including access to many new molecular shapes, based on variations in the stoichiometries and patterns of subunit combination, and improved prospects for side chain diversification. Recent efforts to develop α/β-peptide foldamers can be divided into two conceptually distinct classes. The first includes entities prepared by a "block" strategy, in which α-peptide segments and β-peptide segments are combined to form a hybrid oligomer. The second class encompasses designs in which α-and β-amino acid monomers are interspersed in a regular pattern throughout an oligomer sequence. A variety of secondary structures has been generated from α/β-peptides via these approaches. Helical secondary structures available to α/β-peptides have recently been parlayed into higher order structure, specifically, helix bundle quaternary structure.Desirable biological functions have been elicited from α/β-peptide foldamers. Efforts to mimic naturally occurring host-defense α-peptides have yielded new antimicrobial agents and led to a reexamination of the long-held views regarding structure-activity relationships among α-peptides and other amphiphilic oligomers. Foldamers offer new platforms for mimicry of molecular surfaces involved in specific protein-protein recognition events; recent achievements with α/β-peptide inhibitors of protein-protein interactions involved in apoptotic signaling have revealed benefits of heterogeneous backbones relative to homogeneous backbones for foldamer-based designs. These initial successes in the development of α/β-peptides with specific biological activities highlight the E-mail: gellman@chem.wisc.edu. NIH Public Access IntroductionFoldamers are unnatural oligomers that display conformational propensities akin to those of proteins and nucleic acids, the oligomers that play starring roles in living systems. 1 The relationship between folding and function among proteins has long been a source of fascination to the molecularly inclined scientist. The interplay between α-amino acid residue sequence and the three-dimensional arrangement of these subunits that results from adoption of ...

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...

In this paper, we present 1,2,3-triazole epsilon2-amino acids incorporated as a dipeptide surrogate at three positions in the sequence of a known alpha-helical coiled coil. Biophysical characterization indicates that the modified peptides retain much of the helical structure of the parent sequence, and that the thermodynamic stability of the coiled coil depends on the position of the incorporation of the epsilon-residue. Crystal structures obtained for each peptide give insight into the chemical behavior and conformational preferences of the non-natural amino acid and show that the triazole ring can participate in the backbone hydrogen bonding of the alpha-helix as well as template an interhelical crossing between chains in the bundle.

The conformational preferences of polyglutamine (polyQ) sequences are of major interest because of their central importance in the expanded CAG repeat diseases that include Huntington’s disease (HD). Here we explore the response of various biophysical parameters to the introduction of β-hairpin motifs within polyQ sequences. These motifs (trpzip, disulfide, D-Pro-Gly, Coulombic attraction, L-Pro-Gly) enhance formation rates and stabilities of amyloid fibrils with degrees of effectiveness well-correlated with their known abilities to enhance β-hairpin formation in other peptides. These changes led to decreases in the critical nucleus for amyloid formation from a value of n* = 4 for a simple, unbroken Q23 sequence to approximate unitary n* values for similar length polyQs containing β-hairpin motifs. At the same time, the morphologies, secondary structures, and bioactivities of the resulting fibrils were essentially unchanged from simple polyQ aggregates. In particular, the signature pattern of SSNMR 13C Gln resonances that appears to be unique to polyQ amyloid is replicated exactly in fibrils from a β-hairpin polyQ. Importantly, while β-hairpin motifs do produce enhancements in the equilibrium constant for nucleation in aggregation reactions, these Kn* values remain quite low (~ 10−10) and there is no evidence for significant embellishment of β-structure within the monomer ensemble. The results indicate an important role for β-turns in the nucleation mechanism and structure of polyQ amyloid and have implications for the nature of the toxic species in expanded CAG repeat diseases.

Peptidic oligomers that contain both α- and β-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of α-helix-forming conventional peptides (composed exclusively of α-amino acid residues). Here we describe a comprehensive evaluation of diverse α/β-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-xL and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All α/β-peptide homologues retain the side chain sequence of the Bim BH3 domain, but each homologue contains periodic α-residue → β3-residue substitutions. Previous work has shown that the ααβαααβ pattern, which aligns the β3-residues in a 'stripe' along one side of the helix, can support functional α-helix mimicry, and the results reported here support this conclusion. The present study provides the first evaluation of functional mimicry by ααβ and αααβ patterns, which cause the β3-residues to spiral around the helix periphery. We find that the αααβ pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an α/β-peptide bound to Bcl-xL, affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best αααβ homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 α-peptide.