Ambidextrous α,γ‐Hybrid Peptide Foldamers

Molecular chirality is ubiquitous in nature. The natural biopolymers, proteins and DNA, preferred a right‐handed helical bias due to the inherent stereochemistry of the monomer building blocks. Here, we are reporting a rare co‐existence of left‐ and right‐handed helical conformations and helix‐terminating property at the C‐terminus within a single molecule of α,γ‐hybrid peptide foldamers composed of achiral Aib (α‐aminoisobutyric acid) and 3,3‐dimethyl‐substituted γ‐amino acid (Adb; 4‐amino‐3,3‐dimethylbutanoic acid). At the molecular level, the left‐ and right‐handed helical screw sense of α,γ‐hybrid peptides are representing a macroscopic tendril perversion. The pronounced helix‐terminating behaviour of C‐terminal Adb residues was further explored to design helix–Schellman loop mimetics and to study their conformations in solution and single crystals. The stereochemical constraints of dialkyl substitutions on γ‐amino acids showed a marked impact on the folding behaviour of α,γ‐hybrid peptides.     

Multi‐Frequency,Multi‐Technique Pulsed EPR Investigation of the Copper Binding Site of Murine Amyloid β Peptide

Copper‐amyloid peptides are proposed to be the cause of Alzheimer’s disease, presumably by oxidative stress. However, mice do not produce amyloid plaques and thus do not suffer from Alzheimer’s disease. Although much effort has been focused on the structural characterization of the copper‐ human amyloid peptides, little is known regarding the copper‐binding mode in murine amyloid peptides. Thus, we investigated the structure of copper‐murine amyloid peptides through multi‐frequency, multi‐technique pulsed EPR spectroscopy in conjunction with specific isotope labeling. Based on our pulsed EPR results, we found that Ala2, Glu3, His6, and His14 are directly coordinated with the copper ion in murine amyloid β peptides at pH 8.5. This is the first detailed structural characterization of the copper‐binding mode in murine amyloid β peptides. This work may advance the knowledge required for developing inhibitors of Alzheimer’s disease.     

Synthesis and Conformation of Fluorinated β‐Peptidic Compounds

Experimental and theoretical data indicate that, for α‐fluoroamides, the F? C? C(O)? N(H) moiety adopts an antiperiplanar conformation. In addition, a gauche conformation is favoured between the vicinal C? F and C? N(CO) bonds in N‐β‐fluoroethylamides. This study details the synthesis of a series of fluorinated β‐peptides ( 1 – 8 ) designed to use these stereoelectronic effects to control the conformation of β‐peptide bonds. X‐ray crystal structures of these compounds revealed the expected conformations: with fluorine β to a nitrogen adopting a gauche conformation, and fluorine α to a C?O group adopting an antiperiplanar conformation. Thus, the strategic placement of fluorine can control the conformation of a β‐peptide bond, with the possibility of directing the secondary structures of β‐peptides.     

Synthesis and Conformational Analysis of Cyclic Homooligomers from Pyranoid ε‐Sugar Amino Acids

New pyranoid ε‐sugar amino acids were designed as building blocks, in which the carboxylic acid and the amine groups were placed in positions C2 and C3 with respect to the tetrahydropyran oxygen atom. By using standard solution‐phase coupling procedures, cyclic homooligomers containing pyranoid ε‐sugar amino acids were synthesized. Conformation analysis was performed by using NMR spectroscopic experiments, FTIR spectroscopic studies, X‐ray analysis, and a theoretical conformation search. These studies reveal that the presence of a methoxy group in the position C4 of the pyran ring produces an important structural change in the cyclodipeptides. When the methoxy groups are present, the structure collapses through interresidue hydrogen bonds between the oxygen atoms of the pyran ring and the amide protons. However, when the cyclodipeptide lacks the methoxy groups, a U‐shape structure is adopted, in which there is a hydrophilic concave face with four oxygen atoms and two amide protons directed toward the center of the cavity. Additionally, we found important evidence of the key role played by weak electrostatic interactions, such as the five‐membered hydrogen‐bonded pseudocycles (C₅) between the amide protons and the ether oxygen atoms, in the conformation equilibrium of the macrocycles and in the cyclization step of the cyclic tetrapeptides.     

A Designed Three‐Stranded β‐Sheet in an α/β Hybrid Peptide

The incorporation of β‐amino acid residues into the antiparallel β‐strand segments of a multi‐stranded β‐sheet peptide is demonstrated for a 19‐residue peptide, Boc‐LV^βFV^DPGL^βFVVL^DPGLVL^βFVV‐OMe (BBH19). Two centrally positioned ^DPro–Gly segments facilitate formation of a stable three‐stranded β‐sheet, in which β‐phenylalanine (^βPhe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR‐derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well‐defined three‐stranded β‐sheet structure in solution. Cross‐strand interactions between ^βPhe3/^βPhe17 and ^βPhe3/Val15 residues define orientations of these side‐chains. The observation of close contact distances between the side‐chains on the N‐ and C‐terminal strands of the three‐stranded β‐sheet provides strong support for the designed structure. Evidence is presented for multiple side‐chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three‐stranded β‐sheet structures, which in turn influences the conformational interconversion between type I′ and type II′ β‐turns at the two ^DPro–Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc‐LV^βFV^DPGL^βFVV‐OMe (BBH10), which has been previously characterized as a type I′ β‐turn nucleated hairpin, is shown to favour a type II′ β‐turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.     

β‐Turn Analogues in Model αβ‐Hybrid Peptides: Structural Characterization of Peptides Containing β2,2Ac6c and β3,3Ac6c Residues

The effect of gem‐dialkyl substituents on the backbone conformations of β‐amino acid residues in peptides has been investigated by using four model peptides: Boc‐Xxx‐β^2,2Ac₆c(1‐aminomethylcyclohexanecarboxylic acid)‐NHMe (Xxx=Leu ( 1 ), Phe ( 2 ); Boc=tert‐butyloxycarbonyl) and Boc‐Xxx‐β^3,3Ac₆c(1‐aminocyclohexaneacetic acid)‐NHMe (Xxx=Leu ( 3 ), Phe ( 4 )). Tetrasubstituted carbon atoms restrict the ranges of stereochemically allowed conformations about flanking single bonds. The crystal structure of Boc‐Leu‐β^2,2Ac₆c‐NHMe ( 1 ) established a C₁₁ hydrogen‐bonded turn in the αβ‐hybrid sequence. The observed torsion angles (α(?≈?60°, ψ≈?30°), β(?≈?90°, θ≈60°, ψ≈?90°)) corresponded to a C₁₁ helical turn, which was a backbone‐expanded analogue of the type III β turn in αα sequences. The crystal structure of the peptide Boc‐Phe‐β^3,3Ac₆c‐NHMe ( 4 ) established a C₁₁ hydrogen‐bonded turn with distinctly different backbone torsion angles (α(?≈?60°, ψ≈120°), β(?≈60°, θ≈60°, ψ≈?60°)), which corresponded to a backbone‐expanded analogue of the type II β turn observed in αα sequences. In peptide 4 , the two molecules in the asymmetric unit adopted backbone torsion angles of opposite signs. In one of the molecules, the Phe residue adopted an unfavorable backbone conformation, with the energetic penalty being offset by a favorable aromatic interaction between proximal molecules in the crystal. NMR spectroscopy studies provided evidence for the maintenance of folded structures in solution in these αβ‐hybrid sequences.     

Conformational Studies on Peptides of α‐Aminoxy Acids with Functionalized Side‐Chains

Peptides of homochiral α‐aminoxy acids of nonpolar side chains can form a 1.8₈‐helix. In this paper, we report the conformational studies of α‐aminoxy peptides 1 , 2 , 3 , which have functionalized side chains, in both nonpolar and polar solvents. ¹H NMR, XRD, and FTIR absorption studies confirm the presence of the eight‐membered‐ring intramolecular hydrogen bonds (the N‐O turns) in nonpolar solvents as well as in methanol. CD studies of peptides 1 , 2 , 3 in different solvents indicate that a substantial degree of helical content is retained in methanol and acidic aqueous buffers. The introduction of functionalized side chains in α‐aminoxy peptides provides opportunities for designing biologically active peptides.     

Gas‐Phase Peptide Structures Unraveled by Far‐IR Spectroscopy: Combining IR‐UV Ion‐Dip Experiments with Born–Oppenheimer Molecular Dynamics Simulations

Vibrational spectroscopy provides an important probe of the three‐dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides. ¹ Although the far‐IR region (<500 cm^?1) may contain a wealth of structural information, as recognized in condensed phase studies, ² DFT often performs poorly in predicting the far‐IR spectra of peptides. Here, Born–Oppenheimer molecular dynamics (BOMD) is applied to predict the far‐IR signatures of two γ‐turn peptides. Combining experiments and simulations, far‐IR spectra can provide structural information on gas‐phase peptides superior to that extracted from mid‐IR and amide A features.     

Self‐Association of an Enantiopure β‐Pentapeptide in Nematic Liquid Crystals

Herein, we report for the first time that nematic liquid‐crystalline environments drive the reversible self‐aggregation of an enantiopure β‐pentapeptide into oligomers with a well‐defined structure. The peptide contains four (1S,2S)‐2‐aminocyclopentane carboxylic acid (ACPC) residues and the paramagnetic β‐amino acid (3R,4R)‐4‐amino‐1‐oxyl‐2,2,5,5‐tetramethylpyrrolidine‐3‐carboxylic acid (POAC). The structure of the oligomers was investigated by electron paramagnetic resonance (EPR) spectroscopy, which allowed us to obtain the intermonomer distance distribution in the aggregates as a function of peptide concentration in two nematic liquid crystals, E7 and ZLI‐4792. The aggregates were modeled on the basis of the EPR data, and their orientation and order in the nematic phase were studied by the surface tensor method.     

Effect of β3‐Amino Acids on the Performance of the Peptidic Catalyst H‐dPro‐Pro‐Glu‐NH2

The effect of β³‐amino acids on the conformation and catalytic performance of the peptidic catalyst H‐d Pro‐Pro‐Glu‐NH₂ was investigated. Analogues of the peptidic catalyst bearing instead of the α‐amino acids the respective β³‐amino acids were prepared and their reactivity and stereoselectivity was investigated in conjugate addition reactions of aldehydes to nitroolefins. Additional computational studies provided insights into the preferred conformations of the peptidic catalysts. The results show that conformational flexibility at the N‐terminus has a severe effect on the stereoselectivity but is tolerated at the C‐terminus.     

α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers

Short α‐peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non‐peptide helical foldamers to stabilize α‐helices when fused to short α‐peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C‐ or N‐termini of α‐peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α‐helical conformation in the fused peptide segment. The remarkable compatibility of α‐peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non‐peptide backbones as a means to further control the behavior of α‐peptides.     

A Hexameric Peptide Barrel as Building Block of Amyloid‐β Protofibrils

Oligomeric and protofibrillar aggregates formed by the amyloid‐β peptide (Aβ) are believed to be involved in the pathology of Alzheimer’s disease. Central to Alzheimer pathology is also the fact that the longer Aβ₄₂ peptide is more prone to aggregation than the more prevalent Aβ₄₀. Detailed structural studies of Aβ oligomers and protofibrils have been impeded by aggregate heterogeneity and instability. We previously engineered a variant of Aβ that forms stable protofibrils and here we use solid‐state NMR spectroscopy and molecular modeling to derive a structural model of these. NMR data are consistent with packing of residues 16 to 42 of Aβ protomers into hexameric barrel‐like oligomers within the protofibril. The core of the oligomers consists of all residues of the central and C‐terminal hydrophobic regions of Aβ, and hairpin loops extend from the core. The model accounts for why Aβ₄₂ forms oligomers and protofibrils more easily than Aβ₄₀.     

Mimicking Chitin: Chemical Synthesis,Conformational Analysis,and Molecular Recognition of the β(1→3) N‐Acetylchitopentaose Analogue

Mimicking Nature by using synthetic molecules that resemble natural products may open avenues to key knowledge that is difficult to access by using substances from natural sources. In this context, a novel N‐acetylchitooligosaccharide analogue, β‐1,3‐N‐acetamido‐gluco‐pentasaccharide, has been designed and synthesized by using aminoglucose as the starting material. A phthalic group has been employed as the protecting group of the amine moiety, whereas a thioalkyl was used as the leaving group on the reducing end. The conformational properties of this new molecule have been explored and compared to those of the its chito analogue, with the β‐1,3 linkages, by a combined NMR spectroscopic/molecular modeling approach. Furthermore, the study of its molecular recognition properties towards two proteins, a lectin (wheat germ agglutinin) and one enzyme (a chitinase) have also been performed by using NMR spectroscopy and docking protocols. There are subtle differences in the conformational behavior of the mimetic versus the natural chitooligosaccharide, whereas this mimetic is still recognized by these two proteins and can act as a moderate inhibitor of chitin hydrolysis.     

Total Synthesis and Conformational Study of Callyaerin A: Anti‐Tubercular Cyclic Peptide Bearing a Rare Rigidifying (Z)‐2,3‐ Diaminoacrylamide Moiety

The first synthesis of the anti‐TB cyclic peptide callyaerin A ( 1 ), containing a rare (Z)‐2,3‐diaminoacrylamide bridging motif, is reported. Fmoc‐formylglycine‐diethylacetal was used as a masked equivalent of formylglycine in the synthesis of the linear precursor to 1 . Intramolecular cyclization between the formylglycine residue and the N‐terminal amine in the linear peptide precursor afforded the macrocyclic natural product 1 . Synthetic 1 possessed potent anti‐TB activity (MIC₁₀₀=32 μm ) while its all‐amide congener was inactive. Variable‐temperature NMR studies of both the natural product and its all‐amide analogue revealed the extraordinary rigidity imposed by this diaminoacrylamide unit on peptide conformation. The work reported herein pinpoints the intrinsic role that the (Z)‐2,3‐diaminoacrylamide moiety confers on peptide bioactivity.     

Three‐Residue Turns in α/β‐Peptides and Their Application in the Design of Tertiary Structures

A new three‐residue turn was serendipitously discovered in α/β hybrid peptides derived from alternating C‐linked carbo‐β‐amino acids (β‐Caa) and L ‐Ala residues. The three‐residue β‐α‐β turn at the C termini, nucleated by a helix at the N termini, resulted in helix‐turn (HT) supersecondary structures in these peptides. The turn in the HT motif is stabilized by two H bonds—CO(i?2)–NH(i), with a seven‐membered pseudoring (γ turn) in the backward direction, and NH(i?2)–CO(i), with a 13‐membered pseudoring in the forward direction (i being the last residue)—at the C termini. The study was extended to generalize the new three‐residue turn (β‐α‐β) by using different α‐ and β‐amino acids. Furthermore, the HT motifs were efficiently converted, by an extension with helical oligomers at the C termini, into peptides with novel helix‐turn‐helix (HTH) tertiary structures. However, this resulted in the destabilization of the β‐α‐β turn with the concomitant nucleation of another three‐residue turn, α‐β‐β, which is stabilized by 11‐ and 15‐membered bifurcated H bonds. Extensive NMR spectroscopic studies were carried out to delineate the secondary and tertiary structures in these peptides, which are further supported by molecular dynamics (MD) investigations.     

Synthesis and Analysis of the Conformational Preferences of 5‐Aminomethyloxazolidine‐2,4‐dione Scaffolds: First Examples of β2‐ and β2, 2‐Homo‐Freidinger Lactam Analogues

Constrained peptidomimetic scaffolds are of considerable interest for the design of therapeutically useful analogues of bioactive peptides. We present the single‐step cyclization of (S)‐ or (R)‐α‐hydroxy‐β²‐ or α‐substituted‐α‐hydroxy‐β^{2, 2}‐amino acids already incorporated within oligopeptides to 5‐aminomethyl‐oxazolidine‐2,4‐dione (Amo) rings. These scaffolds can be regarded as unprecedented β²‐ or β^{2, 2}‐homo‐Freidinger lactam analogues, and can be equipped with a proteinogenic side chain at each residue. In a biomimetic environment, Amo rings act as inducers of extended, semi‐bent or folded geometries, depending on the relative stereochemistry and the presence of α‐substituents.     

Isolated β‐Turn Model Systems Investigated by Combined IR/UV Spectroscopy

The functionality of bioactive molecules sensitively depends on their structure. For the investigation of intrinsic structural properties, molecular beam experiments combined with laser spectroscopy have proven to be a suitable tool. Herein we present an analysis of the two isolated tripeptide model systems Ac‐Phe‐Tyr(Me)‐NHMe and Boc‐Phe‐Tyr(Me)‐NHMe. For this purpose, mass‐selective combined IR/UV spectroscopy is applied to both substances in a molecular beam experiment. The comparison of the experimental data with DFT calculations, including different functionals as well as dispersion corrections, allows an assignment of both tripeptide models to β‐turns formed independently from the protection groups and supported by the interaction of the two aromatic chromophores.     

Spectroscopic Evidence for Polymorphic Aggregates Formed by Amyloid‐β Fragments

Understanding the structure of amyloid‐β (Aβ) aggregates is a key step towards elucidating the pathology of Alzheimer’s disease. In this work, three fragments of the Aβ_1–42 protein, Aβ_1–25 (DAEFRHDSGYEVHHQKLVFFAEDVG), Aβ_25–35 (GSNKGAIIGLM), and Aβ_33–42 (GLMVGGVVIA), were synthesized, and their aggregated structures were examined by linear infrared spectroscopy in the amide‐I (mainly the C?O stretching) region. The structures of the formed aggregates were found to be both sequence and pH dependent. The results suggest that instead of forming matured fibrils, as in the case of full‐length Aβ_1–42, both Aβ_1–25 and Aβ_33–42 form a mixture of threadlike β‐sheet fibril, soluble β‐sheet oligomer, and random coil structures. The β‐sheet conformations were found to be mainly antiparallel for the former and both parallel and antiparallel for the latter. However, the Aβ_25–35 fragment was found to form assembled fibrils containing predominantly parallel β‐sheets. The conformation and morphology of the aggregates were also confirmed by circular dichroism measurements and transmission electron microscopy. Factors influencing the structures of the aggregates formed by the Aβ fragments were discussed.