The influence of backbone fluorination on the helicity of α/γ-hybrid peptides

Peptides that are composed of an alternating pattern of α- and γ-amino acids are potentially valuable as metabolism-resistant bioactive agents. For optimal function, some kind of conformational restriction is usually required to either stabilize the dominant 12-helix, or else to divert the peptide away from this conformation in a controlled way. Herein, we explore stereoselective fluorination as a method for controlling the conformations of α/γ-hybrid peptides. We show through a combination of X-ray, NMR and CD analyses that fluorination can either stabilize or disrupt the 12-helix, depending on the fluorine stereochemistry. These findings could inform the ongoing development of diverse functional hybrid peptides.

Herringbone Helical Foldamers from Aromatic Ether Derived ϵ-Amino Acid Peptides

Oligomers based on an aromatic ether derived ϵ-amino acid peptides folded into herringbone helical structures, induced by successive NH-O-NH & O-NH-O bifurcated hydrogen bonding interactions and reinforced by π-π stacking between aryls from adjacent layers. The diaryl ether bonds -O- worked both as structural units to provide turn motifs for changing the amplitude of the slope along the axis of helix for herringbone formation, and also as acceptors for hydrogen bonding. Attachment of a single chiral carbon to the C-termini of the peptides induced excess of single-handed screw sense and amplification through the chain propagation as exemplified by chain length dependent circular dichroism (CD) investigations.

Proteolytically Stable ααγ-Hybrid Peptides Inhibit the Aggregation and Cytotoxicity of Aβ42

The recent approval of antibody-based therapy for targeting the clearance of amyloid plaques fuels the research in designing small molecules and peptide inhibitors to target the aggregation of Aβ-peptides. Here, we report that the 15-residue ααγ-hybrid peptide not only inhibits the aggregation of soluble Aβ42 into fibrils but also disintegrates the aggregated Aβ42 fibrils into smaller assemblies. Further, the hybrid peptide completely rescues neuronal cells from the toxicity of Aβ42 at equimolar concentrations. The shorter 10- and 12-mer peptides showed weak aggregation inhibition activity, while the fully hydrophobic 15-mer ααγ-hybrid peptide analogue showed no aggregation inhibition activity. Further, the 15-mer ααγ-hybrid peptide showed resistance against trypsin digestion and also nontoxic to the neuronal cells. The CD revealed that the peptide upon interaction induces a helix-type conformation in the Aβ42. This is in sharp contrast to the β-sheet conformation of Aβ42 upon incubation. The two-dimensional-NMR (2D-NMR) analysis revealed a large perturbation in the chemical shifts of residues at the N-terminus. The presence of 15-mer peptide at an equimolar concentration of Aβ42 showed less tendency for aggregation and also exhibited nontoxicity to the neuronal cells. The results reported here may be useful in designing new therapeutics for Alzheimer's disease.

Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

Unnatural helical peptidic foldamers as protein segment mimics

Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.

Cyclization of N-Boc-(E)-α,β-unsaturated γ-amino acid active esters into N-Boc-(Z)-α,β-unsaturated γ-lactams through E → Z isomerization

Here, we are reporting the spontaneous transformation of the active esters of N-Boc protected E-α,β-unsaturated γ-amino acids into the corresponding Z-α,β-unsaturated γ-lactams with concomitant E → Z isomerization in the presence of a weak base. No cyclization was observed in the absence of the base. Analysis revealed that amide γ-NH is crucial for both lactamization and E → Z isomerization. This mild transformation provides easy access to the synthetically challenging α,β-unsaturated γ-lactams and also gives new insights into the E → Z isomerization of double bonds.

α,ε-Hybrid Peptide-Stabilized Magnetic Nanoparticle-Coated Paper-Based Actuators

The development of α,ε-hybrid peptide-stabilized magnetic nanoparticles and their application to fabricate a paper-based actuator has been reported. From single-crystal diffraction analysis, the nitropeptide 2 has an extended structure with a trans geometry. The one-pot in situ multiple oxidation-reduction reaction of a synthetic nitropeptide solution in ammonium hydroxide and FeCl₂ leads to the formation of Fe₃O₄ nanoparticles. The reduction reaction replaces the nitro group with an amine group, which finally acts as capping agent for the stabilization of the Fe₃O₄ nanoparticles. Paper-based soft magneto machines with multivariant actuation modes such as contraction-expansion, bending, and uplifting locomotion have been studied. The device has potential as controllable paper-based soft robots.

α,β-Unsaturated γ-Peptide Foldamers

Despite their concomitant emergence in the 1990s, γ-peptide foldamers have not developed as fast as β-peptide foldamers and to date, only a few γ-oligomer structures have been reported, and with sparse applications. Among these examples, sequences containing α,β-unsaturated γ-amino acids have recently drawn attention since the Z/E configurations of the double bond provide opposite planar restrictions leading to divergent conformational behaviors, from helix to extended structures. In this Review, we give a comprehensive overview of the developments of γ-peptide foldamers containing α,β-unsaturated γ-amino acids with examples of applications for health and catalysis, as well as materials science.

Structure–mechanical property relationship of a pentapeptide crystal

A peptide having miniature (P)310/α-helix conformation, forms intermolecular H-bonded supramolecular helical bundle structure which further self-assembled to interdigited supramolecular sheet-like structure that eventually from the brittle crystal.

Conformational Heterogeneity and Self-Assembly of α,β,γ-Hybrid Peptides Containing Fenamic Acid: Multistimuli-Responsive Phase-Selective Gelation

The effect of fenamic acid-α-aminoisobutyric acid corner motif in α,β,γ-hybrid peptides has been reported. From X-ray single-crystal diffraction studies, it is observed that Phe-containing peptide 1 has an "S"-shaped conformation that is stabilized by two consecutive intramolecular N-H···N hydrogen bonds. However, the tyrosine analogue peptide 2 has an "S"-shaped conformation, which is stabilized by consecutive intramolecular six-member N-H···N and seven-member N-H···O hydrogen bonds. The asymmetric unit of peptide 3 containing m-aminobenzoic acid has two molecules which are stabilized by multiple intermolecular hydrogen-bonding interactions. There are also π-π stacking interactions between the aromatic rings of fenamic acid. The peptides 1 and 2 have a polydisperse microsphere morphology, but peptide 3 has an entangled fiber-like morphology. Peptides 1-3 do not form organogels. However, in the presence of water, the peptide 3 forms a phase-selective instant gel in xylene. The gel exhibits high stability and thermal reversibility. The phase-selective gel of peptide 3 is highly responsive to H₂SO₄.

Direct Transformation of N-Protected α,β-Unsaturated γ-Amino Amides into γ-Lactams through a Base-Mediated Molecular Rearrangement

Here, we are reporting a single-step transformation of N-protected α,β-unsaturated γ-amino amides into 5,5-disubstituted γ-lactams through a base-mediated new molecular rearrangement. In contrast to the known N- to C(O) cyclization of saturated γ-amino acids into corresponding γ-lactams, the new rearrangement involves the cyclization between N-terminal C^γ- to C-terminal amide N. The cyclization process was initiated by the migration of double bond from α,β → β,γ position. The enamine-imine tautomerization of the new β,γ-double bond and subsequent 5-exo-trig cyclization of terminal amide leads to the formation of N-protected 5,5-disubstituted γ-lactam. The structures of various γ-lactams obtained from the rearrangement were studied in single crystals. Overall, the results reported here demonstrate the facile and single-step transformation of N-protected α,β-unsaturated γ-amino amides into γ-lactams and provided an excellent opportunity to construct small-molecule peptidomimetics.

Flow-chemistry enabled efficient synthesis of β-peptides: backbone topology vs. helix formation

Enantiodiscriminative helix formation was observed for β-peptide H14 helices when enantiomers of bridged bicyclic residues were introduced.

α,ε-Hybrid Peptide Foldamers: Self-Assembly of Peptide with Trans Carbon-Carbon Double Bonds in the Backbone and Its Saturated Analogue

The effect of geometrically rigid trans α,β-unsaturated ε-amino acids on the structure, folding, and assembly of α,ε-hybrid peptide foldamers has been reported. From single-crystal diffraction analysis, the unsaturated tetrapeptide 1 has stapler-pin-like structure but without intramolecular hydrogen bond. The asymmetric unit has two molecules that are stabilized by multiple intermolecular hydrogen bonding interactions as well as π-π stacking interactions between the aromatic rings of 3-aminocinnamic acid. Peptide 1 does not form organogel. But on hydrogenation, peptide 1 provides the saturated α,ε-hybrid peptide foldamer 2, which forms instant gel in most of the aromatic solvents. The gel exhibits high stability. The unsaturated peptide 1 has porous microsphere morphology, but saturated analogue 2 has ribbonlike morphology. The gel has been used efficiently for removal of cationic organic pollutants from waste water.

Understanding the conformational analysis of gababutin based hybrid peptides

A new class of gababutin-based tetrapeptide shows a C₁₂/C₁₀ hydrogen-bonded hybrid turn.

Artificial β-Double Helices from Achiral γ-Peptides

Double helices are not common in polypeptides and proteins except in the peptide antibiotic gramicidin A and analogous l,d-peptides. In contrast to natural polypeptides, remarkable β-double-helical structures from achiral γ-peptides built from α,β-unsaturated γ-amino acids have been observed. The crystal structures suggest that they adopted parallel β-double helical structures and these structures are stabilized by the interstrand backbone amide H-bonds. Furthermore, both NMR spectroscopy and fluorescence studies support the existence of double-helical conformations in solution. Although a variety of folded architectures featuring distinct H-bonds have been discovered from the β- and γ-peptide foldamers, this is the first report to show that achiral γ-peptides can spontaneously intertwine into β-double helical structures.

Foldamers in Medicinal Chemistry

Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.