Crystal Structures of Aza-β3-peptides, A New Class of Foldamers Relying on a Framework of Hydrazinoturns

Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides

Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.

α-Hydrazino Acid Insertion Governs Peptide Organization in Solution by Local Structure Ordering

In this work, we have applied the concept of α-hydrazino acid insertion in a peptide sequence as a means of structurally organizing a potential protein-protein interactions (PPI) inhibitor. Hydrazino peptides characterized by the incorporation of an α-hydrazino acid at specific positions introduce an additional nitrogen atom into their backbone. This modification leads to a change in the electrostatic properties of the peptide and induces the restructuring of its hydrogen bonding network, resulting in conformational changes toward more stable structural motifs. Despite the successful use of synthetic hydrazino oligomers in binding to nucleic acids, the structural changes due to the incorporation of α-hydrazino acid into short natural peptides in solution are still poorly understood. Based on NMR data, we report structural models of p53-derived hydrazino peptides with elements of localized peptide structuring in the form of an α-, β-, or γ-turn as a result of hydrazino modification in the peptide backbone. The modifications could potentially lead to the preorganization of a helical secondary peptide structure in a solution that is favorable for binding to a biological receptor. Spectroscopically, we observed that the ensemble averaged rapidly interconverting conformations, including isomerization of the E-Z hydrazide bond. This further increases the adaptability by expanding the conformational space of hydrazine peptides as potential protein-protein interaction antagonists.

Consecutive Ribosomal Incorporation of α-Aminoxy/α-Hydrazino Acids with l/d-Configurations into Nascent Peptide Chains

α-Aminoxy and α-hydrazino acids are β-amino acid analogs with β-carbons replaced by oxygen and nitrogen, respectively. Such heteroatoms dictate the folding of peptides into specific secondary structures called pseudo-γ-turns. Achiral α-aminoxyacetic acid (^NOGly) and l-α-hydrazinophenylalanine (l-^NNPhe) have been shown to be suitable for single incorporation during ribosomal translation, but whether ribosomes tolerate other types of α-aminoxy/α-hydrazino acids with l/d-configurations is unknown. Moreover, whether multiple or consecutive incorporations are possible remains unclear. We show, for the first time, multiple and consecutive incorporations of α-aminoxy/α-hydrazino acids with l/d-configurations into various model peptides, including macrocyclic peptide scaffolds.

Local versus Global Control of Helical Folding in β-Peptide Segments Using Hydrazino Turns

Rational control of the self-organization of β-peptides sequences to adopt regular secondary structures is an important challenge in peptidomimetic foldamer science. By replacing the N- and C-terminal residues of homooligomers of trans-2-aminocyclobutanecarboxylic acid (tACBC)_n with N-aminoazetidine-2-carboxylic acid, an 8-helical topology is shown to dominate for sequences up to n = 7. This constitutes an atomic-level tool to override locally the preferred global 12-helix secondary structure of the corresponding tACBC homooligomers of the same length.

Self-Organization Ability of Chiral Nα-Substituted, Nβ-Boc Protected α-Hydrazinoacetamides in the Crystal and Solution States

The limitations of peptides have severely hampered their use in pharmacology, thus prompting the design of new peptidomimetic foldamers. This requires precise knowledge of the secondary structure of new compounds and the ability to predict their folding. Conformational studies of the basic units of these foldamers can be of invaluable assistance in designing new bioactive compounds. To this end, we investigated the conformation of three chiral N^α-substituted, N^β-Boc protected α-hydrazinoacetamide model compounds containing various side chains both on the N^α- and C^α-atoms in both the crystal and solution states. On the basis of IR absorption spectroscopy, NMR, molecular dynamics calculations and X-ray diffraction experiments, we demonstrated that these three models adopt conformational preferences, relying on eight-, six- or five-membered H-bonded pseudocycles (C₈, C₆ or C₅), depending on the steric bulk of both N^α- or C^α-side chains. This study sheds light onto the versatile folding ability of the specific class of α-N^α-hydrazinopeptides and emphasizes the key role of the C^α-side chain on the conformational preference of the folding.

Foldectures: 3D Molecular Architectures from Self-Assembly of Peptide Foldamers

The wide range of fascinating supramolecular architectures found in nature, from DNA double helices to giant protein shells, inspires researchers to mimic the diverse shapes and functions of natural systems. Thus, a variety of artificial molecular platforms have been developed by assembling DNA-, peptide-, and protein-based building blocks for medicinal and biological applications. There has also been a significant interest in the research of non-natural oligomers (i.e., foldamers) that fold into well-defined secondary structures analogous to those found in proteins, because the assemblies of foldamers are expected not only to form biomimetic supramolecular architectures that resemble those of nature but also to display unique functions and unprecedented topologies at the same time due to their different folding propensities from those of natural building blocks. Foldamer-based supramolecular architectures have been reported in the form of nanofibers, nanochannels, nanosheets, and finite three-dimensional (3D) shapes. We have developed a new class of crystalline peptidic materials termed "foldectures" (a compound of foldamer and architecture) with unprecedented topological complexity derived from the rapid and nonequilibrium aqueous phase self-assembly of foldamers. In this Account, we discuss the morphological features, molecular packing structures, physical properties, and potential applications of foldectures. Foldectures exhibit well-defined, microscale, homogeneous, and finite structures with unique morphologies such as windmill, tooth, and trigonal bipyramid shapes. The symmetry elements of the morphologies vary with the foldamer building blocks and are retained upon surfactant-assisted shape evolution. Structural characterization by powder X-ray diffraction (PXRD) revealed the molecular packing structures, suggesting how the foldamer building blocks assembled in the 3D structure. The analysis by PXRD showed that intermolecular hydrogen bonding connects foldamers in head-to-tail fashion, while hydrophobic attraction plays a role in arranging foldamers in parallel, antiparallel, or cholesteric phase-like manners. Each packing structure from the foldamer building blocks possesses distinct symmetry elements that are directly expressed in the 3D morphologies. Because of their well-ordered molecular packing structures, foldectures exhibit facet-dependent surface characteristics and anisotropic magnetic susceptibility. The facet-dependent surface property was harnessed to synthesize anisotropic metal nanoparticle-foldecture composites, and the anisotropic magnetic susceptibility enables foldectures to undergo real-time alignment and rotating motion in response to an external magnetic field. By means of their unusual shapes and properties, foldectures have been demonstrated to mimic the functionality of natural systems such as magnetosomes or carboxysomes. Further development of foldectures using higher-order building units, complicated packing motifs, and functional moieties could provide a novel biocompatible platform rivaling 3D biological architectures in natural systems.

N-Hydroxyimide Ugi Reaction toward α-Hydrazino Amides

The Ugi four-component reaction (U-4CR) with N-hydroxyimides as a novel carboxylic acid isostere has been reported. This reaction provides straightforward access to α-hydrazino amides. A broad range of aldehydes, amines, isocyanides and N-hydroxyimides were employed to give products in moderate to high yields. This reaction displays N-N bond formation by cyclic imide migration in the Ugi reaction. Thus, N-hydroxyimide is added as a new acid component in the Ugi reaction and broadens the scaffold diversity.

Solid Phase Synthesis of Helically Folded Aromatic Oligoamides

Aromatic amide foldamers constitute a growing class of oligomers that adopt remarkably stable folded conformations. The folded structures possess largely predictable shapes and open the way toward the design of synthetic mimics of proteins. Important examples of aromatic amide foldamers include oligomers of 7- or 8-amino-2-quinoline carboxylic acid that have been shown to exist predominantly as well-defined helices, including when they are combined with α-amino acids to which they may impose their folding behavior. To rapidly iterate their synthesis, solid phase synthesis (SPS) protocols have been developed and optimized for overcoming synthetic difficulties inherent to these backbones such as low nucleophilicity of amine groups on electron poor aromatic rings and a strong propensity of even short sequences to fold on the solid phase during synthesis. For example, acid chloride activation and the use of microwaves are required to bring coupling at aromatic amines to completion. Here, we report detailed SPS protocols for the rapid production of: (1) oligomers of 8-amino-2-quinolinecarboxylic acid; (2) oligomers containing 7-amino-8-fluoro-2-quinolinecarboxylic acid; and (3) heteromeric oligomers of 8-amino-2-quinolinecarboxylic acid and α-amino acids. SPS brings the advantage to quickly produce sequences having varied main chain or side chain components without having to purify multiple intermediates as in solution phase synthesis. With these protocols, an octamer could easily be synthesized and purified within one to two weeks from Fmoc protected amino acid monomer precursors.

3-Aminothiophenecarboxylic acid (3-Atc)-induced folding in peptides

This article demonstrates the consequences of incorporating a constrained β-amino acid into a peptide chain and its effect on conformation of oligomers.

Artificial supersecondary structures based on aromatic oligoamides

With an intelligent design of the monomers, considerable effort has so far focused on the creation of aromatic oligoamide foldamers which are able to mimic the secondary structures of biopolymers. Supersecondary structure is a growing set of known and classifiable protein folding patterns that provides an important organizational context to this complex endeavor. In this article, we highlight the design, chemical synthesis, and structural studies of artificial supersecondary structures based on aromatic oligoamide foldamers in recent years.

Rational design of a low molecular weight, stable, potent, and long-lasting GPR103 aza-β3-pseudopeptide agonist

26RFa, a novel RFamide neuropeptide, is the endogenous ligand of the former orphan receptor GPR103. Intracerebroventricular injection of 26RFa and its C-terminal heptapeptide, 26RFa((20-26)), stimulates food intake in rodents. To develop potent, stable ligands of GPR103 with low molecular weight, we have designed a series of aza-β(3)-containing 26RFa((20-26)) analogues for their propensity to establish intramolecular hydrogen bonds, and we have evaluated their ability to increase [Ca(2+)](i) in GPR103-transfected cells. We have identified a compound, [Cmpi(21),aza-β(3)-Hht(23)]26RFa((21-26)), which was 8-fold more potent than 26RFa((20-26)) in mobilizing [Ca(2+)](i). This pseudopeptide was more stable in serum than 26RFa((20-26)) and exerted a longer lasting orexigenic effect in mice. This study constitutes an important step toward the development of 26RFa analogues that could prove useful for the treatment of feeding disorders.

From a marine neuropeptide to antimicrobial pseudopeptides containing aza-β(3)-amino acids: structure and activity

Incorporation of aza-β(3)-amino acids into an endogenous neuropeptide from mollusks (ALSGDAFLRF-NH(2)) with weak antimicrobial activity allows the design of new AMPs sequences. Depending on the nature of the substitution, this can render the pseudopeptides inactive or lead to a drastic enhancement of the antimicrobial activity without high cytotoxicity. Structural studies of the pseudopeptides carried out by NMR and circular dichroism show the impact of aza-β(3)-amino acids on peptide structure. The first three-dimensional structures of pseudopeptides containing aza-β(3)-amino acids in aqueous micellar SDS were determined and demonstrate that the hydrazino turn can be formed in aqueous solution. Thus, AMP activity can be modulated through structural modifications induced by the nature and the position of such amino acid analogues in the peptide sequences.

Propensity for local folding induced by the urea fragment in short-chain oligomers

Examination of local folding and H-bonding patterns in model compounds can be extremely informative to gain insight into the propensity of longer-chain oligomers to adopt specific folding patterns (i.e. foldamers) based on remote interactions. Using a combination of experimental techniques (i.e. X-ray diffraction, FT-IR absorption and NMR spectroscopy) and theoretical calculations at the density functional theory (DFT) level, we have examined the local folding patterns induced by the urea fragment in short-chain aza analogues of beta- and gamma-amino acid derivatives. We found that the urea-turn, a robust C(8) conformation based on 1<--3 H-bond interaction, is largely populated in model ureidopeptides (I-IV) obtained by replacing the alpha-carbon of a beta-amino acid by a nitrogen. This H-bonding scheme is likely to compete with remote H-bond interactions, thus preventing the formation of secondary structures based on remote intrastrand interactions in longer oligomers. In related oligomers obtained by the addition of a methylene in the main chain (V-VIII), nearest-neighbour H-bonded interactions are unfavourable i.e. the corresponding C9 folding pattern is hardly populated. In this series, folding based on remote intrastrand interactions becomes possible for longer oligomers. We present spectroscopic evidence that tetraurea VIII is likely to be the smallest unit capable of reproducing the H-bonded motif found in 2.5-helical N,N'-linked oligoureas.

Foldamers as versatile frameworks for the design and evolution of function

Foldamers are sequence-specific oligomers akin to peptides, proteins and oligonucleotides that fold into well-defined three-dimensional structures. They offer the chemical biologist a broad pallet of building blocks for the construction of molecules that test and extend our understanding of protein folding and function. Foldamers also provide templates for presenting complex arrays of functional groups in virtually unlimited geometrical patterns, thereby presenting attractive opportunities for the design of molecules that bind in a sequence- and structure-specific manner to oligosaccharides, nucleic acids, membranes and proteins. We summarize recent advances and highlight the future applications and challenges of this rapidly expanding field.

Aza-β3-Cyclohexapeptides: Pseudopeptidic Macrocycles with Interesting Conformational and Configurational Properties Slow Pyramidal Nitrogen Inversion in 24-Membered Rings!

Among pseudopeptidic foldamers, aza-beta3-peptides have the unique property to possess nitrogen stereocenters instead of carbon stereocenters. As the result of pyramidal inversion at N(alpha)-atoms along the backbone, they behave as a set of C8-based secondary structures in equilibrium. This structural modulation is exploited here to prepare 24-membered macrocycles with great efficiency. Both crystal structures and spectroscopic data establish that aza-beta3-cyclohexapeptides adopt a highly organized conformation where the relative configuration of chiral nitrogen atoms is alternated. This makes them an interesting scaffold as the stereocontrol occurs spontaneously through the cyclization. These compounds reveal an unprecedented slow pyramidal nitrogen inversion in macrocycles. Pyramidal ground state stabilization, hindered rotation, steric crowding, and H-bond cooperativity are proposed to participate in this striking phenomenon. The equilibrium between invertomers of aza-beta3-cyclohexapeptides is reminiscent of the interchange between the two chair forms of cyclohexane.

Helix Formation in α,γ- and β,γ-Hybrid Peptides: Theoretical Insights into Mimicry of α- and β-Peptides

Alpha,gamma- and beta,gamma-hybrid peptides, which are composed of two different homologous amino acid constituents in alternate order, are suggested as novel classes of peptide foldamers. On the basis of a systematic conformational search employing the methods of ab initio MO theory, the possibilities for the formation of periodic secondary structures in these systems are described. The conformational analysis provides a great number of helix conformers widely differing in energy, which can be arranged into three groups: (i) helices with all hydrogen bonds formed in forward direction along the sequence, (ii) helices with all hydrogen bonds in backward direction, and (iii) helices with alternate hydrogen-bond directions (mixed or beta-helices). Most stable are representatives of beta-helices, but their stability decreases considerably in more polar environments in comparison to helix conformers from the other two classes. There is a great similarity between the overall topology of the most stable hybrid peptide helices and typical helices of peptides which are exclusively composed of a single type of homologous amino acids. Thus, the helices of the beta,gamma-hybrid peptides mimic perfectly those of the native alpha-peptides as, for instance, the well-known alpha-helix, whereas the most stable helix conformers of alpha,gamma-hybrid peptides correspond well to the overall structure of beta-peptide helices. The two suggested novel hybrid peptide classes expand considerably the pool of peptide foldamers and may be promising tools in peptide design and in material sciences.

Theoretical prediction of the basic helix types in α,β-hybrid peptides

This study provides a complete overview on all possible helical- folding patterns, their stabilities, and their detailed molecular structure in the novel foldamer class of alpha,beta-hybrid peptides on the basis of ab initio molecular orbital (MO) theory. The results indicate a considerable intrinsic potential of backbone folding. As found for other peptide foldamers, representatives of mixed or beta-helices are most stable in more apolar media, whereas polar environments favor the helices with the hydrogen bonds pointing in only one direction. The theoretical results confirm the hydrogen-bonding patterns found in the first experimental studies on these hybrid peptides. Selecting special backbone substitution patterns, the secondary structure potential of the alpha,beta-hybrid peptides could be of great importance for a rational peptide and protein design.

Helices and other secondary structures of β- and γ-peptides

The principal secondary structural motifs adopted by peptides assembled from beta-amino acid units are discussed: the 14-, 12-, 10-, 12/10-, and 8-helices, as well as the hairpin turn, extended structures, stacks, and sheets. Features that promote a particular folding propensity are outlined and illustrated by structures determined in solution (NMR) and in the solid-state (x-ray). The N-C(beta)-C(alpha)-CO dihedral angles from molecular dynamics simulations, which are indicative of a particular secondary structure, are presented. A brief description of a helix and a turn of gamma-peptides is also given.