N,N'-linked oligoureas as foldamers: chain length requirements for helix formation in protic solvent investigated by circular dichroism, NMR spectroscopy, and molecular dynamics

N,N'-linked oligoureas with proteinogenic side chains are peptide backbone mimetics belonging to the gamma-peptide lineage. In pyridine, heptamer 4 adopts a stable helical fold reminiscent of the 2.6(14) helical structure proposed for gamma-peptide foldamers. In the present study, we have used a combination of CD and NMR spectroscopies to correlate far-UV chiroptical properties and conformational preferences of oligoureas as a function of chain length from tetramer to nonamer. Both the intensity of the CD spectra and NMR chemical shift differences between alphaCH2 diastereotopic protons experienced a marked increase for oligomers between four and seven residues. No major change in CD spectra occurred between seven and nine residues, thus suggesting that seven residues could be the minimum length required for stabilizing a dominant conformation. Unexpectedly, in-depth NMR conformational investigation of heptamer 4 in CD3OH revealed that the 2.5 helix probably coexists with partially (un)folded conformations and that Z-E urea isomerization occurs, to some degree, along the backbone. Removing unfavorable electrostatic interactions at the amino terminal end of 4 and adding one H-bond acceptor by acylation with alkyl isocyanate (4 --> 7) was found to reinforce the 2.5 helical population. The stability of the 2.5 helical fold in MeOH is further discussed in light of unrestrained molecular dynamics (MD) simulation. Taken together, these new data provide additional insight into the folding propensity of oligoureas in protic solvent and should be of practical value for the design of helical bioactive oligoureas.     

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.     

The meso Helix: Symmetry and Symmetry‐Breaking in Dynamic Oligourea Foldamers with Reversible Hydrogen‐Bond Polarity

Oligoureas (up to n=6) of meso cyclohexane‐1,2‐diamine were synthesized by chain extension with an enzymatically desymmetrized monomer 2 . Despite being achiral, the meso oligomers adopt chiral canonical 2.5‐helical conformations, the equally populated enantiomeric screw‐sense conformers of which are in slow exchange on the NMR timescale, with a barrier to screw‐sense inversion of about 70 kJ mol^?1. Screw‐sense inversion in these helical foldamers is coupled with cyclohexane ring‐flipping, and results in a reversal of the directionality of the hydrogen bonding in the helix. The termini of the meso oligomers are enantiotopic, and desymmetrized analogues of the oligoureas with differentially and enantioselectively protected termini display moderate screw‐sense preferences. A screw‐sense preference may furthermore be induced in the achiral, meso oligoureas by formation of a 1:1 hydrogen‐bonded complex with the carboxylate anion of Boc‐d ‐proline. The meso oligoureas are the first examples of hydrogen‐bonded foldamers with reversible hydrogen‐bond directionality.     

Anion Recognition by Aliphatic Helical Oligoureas

Anion binding properties of neutral helical foldamers consisting of urea type units in their backbone have been investigated. ¹H NMR titration studies in various organic solvents including DMSO suggest that the interaction between aliphatic oligoureas and anions (CH₃COO^?, H₂PO₄^?, Cl^?) is site‐specific, as it largely involves the urea NHs located at the terminal end of the helix (positive pole of the helix), which do not participate to the helical intramolecular hydrogen‐bonding network. This mode of binding parallels that found in proteins in which anion‐binding sites are frequently found at the N‐terminus of an α‐helix. ¹H NMR studies suggest that the helix of oligoureas remains largely folded upon anion binding, even in the presence of a large excess of the anion. This study points to potentially useful applications of oligourea helices for the selective recognition of small guest molecules.     

Synthesis and helical properties of aromatic multilayered oligoureas

Several aromatic multilayered oligoureas with different chain lengths and different numbers of chiral N-substituents were synthesized, and their helical conformation and induced handedness were examined by means of CD spectroscopy. Introduction of one chiral N-substituent is enough to induce handedness, and all the oligoureas examined exist predominantly as helical structures with all-S axial chirality. The hexaureas 6 and 7 had similar CD intensity to the tetraureas 4 and 5, and had larger CD intensity than diurea 8. The results indicate that the effect of a chiral N-substituent at the central benzene ring in inducing well-ordered handedness at the terminal positions of hexaureas 6 and 7 is relatively weak, even though these compounds mainly take the form of aromatic multilayered foldamers.     

Supramolecular interactions between ethylene-bridged oligoureas: nanorings and chains formed by cooperative positive allostery

Ethylene-bridged oligoureas are dynamic foldamers in which the polarity of a coherent chain of intramolecular hydrogen bonds may be controlled by intra- or intermolecular interactions with hydrogen-bond donors or acceptors. In this paper, we describe the way that supramolecular interactions between ethylene-bridged oligoureas bearing a 3,5-bis(trifluoromethyl)phenylurea (BTMP) terminus leads to higher-order structures both in the crystalline state and in solution. The oligoureas self-assemble by head-to-tail hydrogen bonding interactions to form either supramolecular ‘nanorings’ with cyclic hydrogen bond chain directionality, or supramolecular helical chains of hydrogen bonds. The self-assembly process features a cascade of cooperative positive allostery, in which each intermolecular hydrogen bond formation at the BTMP terminus switches the native hydrogen bond chain directionality of monomers, favouring further assembly. Monomers with a benzyl urea terminus self-assemble into nanorings, whereas monomers with a N-ethyl urea terminus form helical chains. In the crystal state, parallel helices have identical handedness and polarity, whereas antiparallel helices have opposite handedness. The overall dipole moment of crystals is zero due to the antiparallel arrangements of local dipoles in the crystal packing. Supramolecular interactions in solution were also examined by VT and DOSY NMR spectroscopy, up to the point of crystal formation. The size of higher aggregates in dichloromethane was estimated by their hydrodynamic radius. The relative orientation of the monomers within the aggregates, determined by 2D ROESY NMR, was the same as in the crystals, where syn-orientations lead to the formation of rings and anti-orientations result in chains. Overall, the switch of hydrogen bond polarity propagates intermolecularly in crystal and solution states, constituting an example of intermolecular communication within supramolecular polymers.

Hydrogen-bonded urea oligomers form supramolecular aggregates in the crystalline state. Intermolecular hydrogen bonding generates nano-rings or chains, according to the length and substitution pattern of the oligomers.     

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N′H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.      

Mixed Oligoureas Based on Constrained Bicyclic and Acyclic β‐Amino Acids Derivatives: On the Significance of the Subunit Configuration for Folding

The combination of a non‐functionalized constrained bicyclo[2.2.2]octane motif along with urea linkages allowed the formation of a highly rigid 2.5_12/14 helical system both in solution and the solid state. In this work, we aimed at developing stable and functionalized systems as promising materials for biological applications in investigating the impact of this constrained motif and its configuration on homo and heterochiral mixed‐oligourea helix formation. Di‐, tetra‐, hexa‐, and octa‐oligoureas alternating the highly constrained bicyclic motif of (R) or (S) configuration with acyclic (S)‐β³‐amino acid derivatives were constructed. Circular dichroism (CD), NMR experiments, and the X‐ray crystal structure of the octamer unequivocally proved that the alternating heterochiral R/S sequences form a stable left‐handed 2.5‐helix in contrast to the mixed (S/S)‐oligoureas, which did not adopt any defined secondary structure. We observed that the (?)‐synclinal conformation around the C_α? C_β bond of the acyclic residues, although sterically less favorable than the (+)‐synclinal conformation, was imposed by the (R)‐bicyclic amino carbamoyl (BAC) residue. This highlighted the strong ability of the BAC residue to drive helical folding in heterochiral compounds. The role of the stereochemistry of the BAC unit was assessed and a model was proposed to explain the misfolding of the S/S sequences.     

Helix persistence and breakdown in oligoureas of metaphenylenediamine: apparent diastereotopicity as a spectroscopic marker of helix length in solution

Oligomeric ureas derived from m-phenylenediamine with chain lengths of up to seven urea linkages were made by iterative synthetic pathways. Three families were synthesized: 4 and 20, bearing a terminal chiral sulfinyl group; 24, bearing a terminal rotationally restricted amide group, and 30 bearing a terminal achiral bromophenyl group. The distal end of the oligomers was capped with an N-benzyl group to act as a diastereotopic probe. With a terminal sulfinyl group, the 1H NMR signals arising from the CH2 group of the diastereotopic probe remained anisochronous even when separated from the stereogenic center by up to 24 bonds (in 20c). With a rotationally restricted amide, anisochronicity was no longer apparent beyond 17 bond lengths (in 24c). No anisochronicity was observable with a terminal bromophenyl group. We interpret these results as indicating that the oligoureas of short lengths adopt a defined helical secondary structure in solution, but that in longer oligomers the helicity breaks down and transmission of chirality in these systems is limited to about 24 bond lengths. We propose that "apparent diastereotopicity" (anisochronicity) provides a general empirical method for identifying secondary structure in solution.     

Microwave-enhanced solid-phase synthesis of N,N'-linked aliphatic oligoureas and related hybrids

A practical and efficient microwave-assisted solid-phase method for the synthesis of N,N'-linked oligoureas and related amide/urea hybrid oligomers, featuring the use of succinimidyl (2-azido-2-substituted ethyl) carbamate monomers, is reported. The rate enhancement of urea formation under microwave irradiation combined with the mild conditions of the phosphine-based azide reduction makes this approach very effective for routine synthesis of oligoureas and possibly for library production.     

Aromatic oligoureas: enforced folding and assisted cyclization

[STRUCTURE: SEE TEXT] Aromatic oligoureas are forced into well-defined conformation by incorporated intramolecular hydrogen bonds. Shape-persistent tetraureas macrocycles were obtained in a one-step [2+2] reaction in good yields.     

Helix‐Forming Oligoureas: Temperature‐Dependent NMR,Structure Determination,and Circular Dichroism of a Nonamer with Functionalized Side Chains

To further investigate the degree of structural homology between γ‐peptides A and N,N′‐linked oligoureas B , we prepared oligourea nonamer 2 containing Ala, Val, Leu, Phe, Tyr and Lys side chains. Oligomer 2 was synthesized on solid support from activated monomers, i.e., from enantiomerically pure succinimidyl {2‐{[(9H‐fluoren‐9‐ylmethoxy)carbonyl]amino}ethyl}carbamates 3a – f that are further substituted at C(2) of the ethyl moiety. These precursors were conveniently prepared from N‐Fmoc‐protected β³‐amino acids with corresponding side chains. Detailed NMR studies (DQF‐COSY, TOCSY, and ROESY) in (D₅)pyridine revealed that 2 adopts a regular (P)‐2.5 helical secondary structure very similar to that previously determined for oligourea heptamer 1 and closely related to the (P)‐2.6₁₄ helix of γ‐peptides. Temperature‐dependent NMR further demonstrated the conformational homogeneity and remarkable stability of the structure of 2 in pyridine. The CD spectrum of 2 (0.2 mM ) was recorded in MeOH with the aim to gain more information about the conformation of oligoureas. In contrast to 2.6‐helical γ‐peptides, which display only a weak or no Cotton effect, oligourea 2 exhibits an intense positive Cotton effect at ca. 203 nm ([Θ]=+373000 deg cm² dmol⁻¹) that decreases only slowly upon increasing the temperature.     

Solid state NMR studies of oligourea foldamers: interaction of 15N-labelled amphiphilic helices with oriented lipid membranes

Synthetic oligomers that are derived from natural polypeptide sequences, albeit with unnatural building blocks, have attracted considerable interest in mimicking bioactive peptides and proteins. Many of those compounds adopt stable folds in aqueous environments that resemble protein structural elements. Here we have chemically prepared aliphatic oligoureas and labeled them at selected positions with (15)N for structural investigations using solid-state NMR spectroscopy. In the first step, the main tensor elements and the molecular alignment of the (15)N chemical shift tensor were analyzed. This was possible by using a two-dimensional heteronuclear chemical shift/dipolar coupling correlation experiment on a model compound that represents the chemical, and thereby also the chemical shift characteristics, of the urea bond. In the next step (15)N labeled versions of an amphipathic oligourea, that exert potent antimicrobial activities and that adopt stable helical structures in aqueous environments, were prepared. These compounds were reconstituted into oriented phospholipid bilayers and the (15)N chemical shift and (1)H-(15)N dipolar couplings of two labeled sites were determined by solid-state NMR spectroscopy. The data are indicative of an alignment of this helix parallel to the membrane surface in excellent agreement with the amphipathic character of the foldamer and consistent with previous models explaining the antimicrobial activities of α-peptides.     

β-Sheet to Helical-Sheet Evolution Induced by Topochemical Polymerization: Cross-α-Amyloid-like Packing in a Pseudoprotein with Gly-Phe-Gly Repeats

Protein-mimics are of great interest for their structure, stability, and properties. We are interested in the synthesis of protein-mimics containing triazole linkages as peptide-bond surrogate by topochemical azide-alkyne cycloaddition (TAAC) polymerization of azide- and alkyne-modified peptides. The rationally designed dipeptide N₃-CH₂CO-Phe-NHCH₂CCH ( 1 ) crystallized in a parallel β-sheet arrangement and are head-to-tail aligned in a direction perpendicular to the β-sheet-direction. Upon heating, crystals of 1 underwent single-crystal-to-single-crystal polymerization forming a triazole-linked pseudoprotein with Gly-Phe-Gly repeats. During TAAC polymerization, the pseudoprotein evolved as helical chains. These helical chains are laterally assembled by backbone hydrogen bonding in a direction perpendicular to the helical axis to form helical sheets. This interesting helical-sheet orientation in the crystal resembles the cross-α-amyloids, where α-helices are arranged laterally as sheets.     

β‐Sheet to Helical‐Sheet Evolution Induced by Topochemical Polymerization: Cross‐α‐Amyloid‐like Packing in a Pseudoprotein with Gly‐Phe‐Gly Repeats

Protein‐mimics are of great interest for their structure, stability, and properties. We are interested in the synthesis of protein‐mimics containing triazole linkages as peptide‐bond surrogate by topochemical azide‐alkyne cycloaddition (TAAC) polymerization of azide‐ and alkyne‐modified peptides. The rationally designed dipeptide N₃‐CH₂CO‐Phe‐NHCH₂CCH ( 1 ) crystallized in a parallel β‐sheet arrangement and are head‐to‐tail aligned in a direction perpendicular to the β‐sheet‐direction. Upon heating, crystals of 1 underwent single‐crystal‐to‐single‐crystal polymerization forming a triazole‐linked pseudoprotein with Gly‐Phe‐Gly repeats. During TAAC polymerization, the pseudoprotein evolved as helical chains. These helical chains are laterally assembled by backbone hydrogen bonding in a direction perpendicular to the helical axis to form helical sheets. This interesting helical‐sheet orientation in the crystal resembles the cross‐α‐amyloids, where α‐helices are arranged laterally as sheets.     

Design of a novel co‐electrospinning system with flat spinneret for producing helical nanofibers

A kind of biomimetic fibers of helical structures at nanoscale has attracted increasing interest. In this study, a novel co‐electrospinning setup with a designed flat spinneret, used for the fabrication of helical nanofibers, is reported in this study. Poly(m‐phenylene isophthalamide) (Nomex) and Thermoplastic polyurethane (TPU) are chosen as the two components in co‐electrospinning. To display the efficiency for producing helical fibers, a generally used core–shell needle spinneret is used for comparison. The effect of the uniformity of electric field distribution created by these two types of spinnerets on the jet motion and the resultant helical fibers is developed, with systematical simulation and experimental research. The results showed that the co‐electrospinning system with the newly designed flat spinneret can produce helical nanofibers efficiently. Compared with the needle spinneret, the flat spinneret created more uniform electric field, leading to better morphology and structure of the resultant helical fibers. In addition, an approach to achieve the scale‐up of this co‐electrospinning system is developed. This novel design is expected to provide a promising method to fabricate nanofiber materials with helical structures. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1496–1505     

Helical supramolecular self-assembly by prolamide thymidine/uridine analogues

This report describes the syntheses of rationally designed non-sugar nucleoside as prolamide nucleosides which contain prolyl ring and pyrimidine nucleobases (uracil/thymine) via acetamide bonds. These nucleosides have propensity to form distinctive self-assembly supramolecular helical structures ubiquitously through Watson-Crick/reverse type of hydrogen bonding with nucleobases. Moreover, the prolyl acetamide backbone groups- carbonyl (-C = O) and hydroxyl (-OH) group, are also involved in strengthening of self-assembled helical structures. Importantly, both prolamide thymidine and prolamide uridine have shown two distinctive helical structural patterns, in spite of containing the same backbone. Hence thymine and uracil moieties of prolamide nucleosides are responsible for unique supramolecular helical structural architectures.     

Probing the helical content of growth hormone-releasing factor analogs using electrospray ionization mass spectrometry

A series of growth hormone-releasing factor analogs have been studied by both circular dichroism and electrospray ionization mass spectrometry (ESI/MS). The peptides are 32 residues long and are known to adopt a random-coil structure in aqueous solution but become increasingly helical as the proportion of organic solvent is increased. Deuterium exchange was observed as an increase in mass of the peptide, as measured by ESI/MS. Rates of exchange were measured and half-lives calculated for analogs containing amino acid substitutions designed to promote or discourage helix formation. Exchange was slower in peptides that are helical (as shown by circular dichroism) than in randomly coiled peptides. Solution conditions that favor helix formation also produced slower exchange rates. These studies suggest that ESI/MS can provide date about the extent and stability of helix formation.     

Chiroptical transcription of helical information through supramolecular harmonization with dynamic helices

With biologically important "peptide bundling" as the motif, new chromophoric cyclic host 1 was designed, which consists of two zinc porphyrin units that are connected by dynamic peptide helices of nonameric aminoisobutyric acid (Aib) units. Upon inclusion of pyridine-anchored helical peptides between the zinc porphyrin units, 1 displayed an intense exciton-coupled circular dichroism (CD) band at 410-450 nm, whose sign reflected the helical sense of the guest peptides. Studies with conformationally defined dehydrophenylalanine-containing analogues indicated that the dynamic helical chains in the host are stereochemically harmonized with right- or left-handed helices of the guest peptides in a confined nano space, leading to either clockwise- or anticlockwise-twisted geometry (chiroptical output) of the connecting zinc porphyrin chromophores.