Sulfono‐γ‐AApeptides as a New Class of Nonnatural Helical Foldamer

Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono‐γ‐AApeptide foldamers of varying lengths. The crystal structure of the sulfono‐γ‐AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono‐γ‐AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two‐dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right‐handed helical structure. Optical analysis using circular dichroism further supports well‐ defined helical conformation of sulfono‐γ‐AApeptides in solution containing as few as five building blocks. Future development of sulfono‐γ‐AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.     

Orthogonal Halogen‐Bonding‐Driven 3D Supramolecular Assembly of Right‐Handed Synthetic Helical Peptides

Peptide‐mediated self‐assembly is a prevalent method for creating highly ordered supramolecular architectures. Herein, we report the first example of orthogonal C?X???X?C/C?X???π halogen bonding and hydrogen bonding driven crystalline architectures based on synthetic helical peptides bearing hybrids of l ‐sulfono‐γ‐AApeptides and natural amino acids. The combination of halogen bonding, intra‐/intermolecular hydrogen bonding, and intermolecular hydrophobic interactions enabled novel 3D supramolecular assembly. The orthogonal halogen bonding in the supramolecular architecture exerts a novel mechanism for the self‐assembly of synthetic peptide foldamers and gives new insights into molecular recognition, supramolecular design, and rational design of biomimetic structures.     

α‐Aminoxy Oligopeptides: Synthesis,Secondary Structure,and Cytotoxicity of a New Class of Anticancer Foldamers

α‐Aminoxy peptides are peptidomimetic foldamers with high proteolytic and conformational stability. To gain an improved synthetic access to α‐aminoxy oligopeptides we used a straightforward combination of solution‐ and solid‐phase‐supported methods and obtained oligomers that showed a remarkable anticancer activity against a panel of cancer cell lines. We solved the first X‐ray crystal structure of an α‐aminoxy peptide with multiple turns around the helical axis. The crystal structure revealed a right‐handed 2₈‐helical conformation with precisely two residues per turn and a helical pitch of 5.8 Å. By 2D ROESY experiments, molecular dynamics simulations, and CD spectroscopy we were able to identify the 2₈‐helix as the predominant conformation in organic solvents. In aqueous solution, the α‐aminoxy peptides exist in the 2₈‐helical conformation at acidic pH, but exhibit remarkable changes in the secondary structure with increasing pH. The most cytotoxic α‐aminoxy peptides have an increased propensity to take up a 2₈‐helical conformation in the presence of a model membrane. This indicates a correlation between the 2₈‐helical conformation and the membranolytic activity observed in mode of action studies, thereby providing novel insights in the folding properties and the biological activity of α‐aminoxy peptides.     

Helical Folding Competing with Unfolded Aggregation in Phenylene Ethynylene Foldamers

The folding and aggregation behavior of a pair of oligo(phenylene ethynylene) (OPE) foldamers are investigated by means of UV/Vis absorption and circular dichroism spectroscopy. With identical OPE backbones, two foldamers, 1 with alkyl side groups and 2 with triethylene glycol side chains, manifest similar helical conformations in solutions in n‐hexane and methanol, respectively. However, disparate and competing folding and aggregation processes are observed in alternative solvents. In cyclohexane, oligomer 1 initially adopts the helical conformation, but the self‐aggregation of unfolded chains, as a minor component, gradually drives the folding–unfolding transition eventually to the unfolded aggregate state completely. In contrast, in aqueous solution (CH₃OH/H₂O) both folded and unfolded oligomer 2 appear to undergo self‐association; aggregates of the folded chains are thermodynamically more stable. In solutions with a high H₂O content, self‐aggregation among unfolded oligomers is kinetically favored; these oligomers very slowly transform into aggregates of helical structures with greater thermodynamic stability. The folded–unfolded conformational switch thus takes place with the free (nonaggregated) molecules, and the very slow folding transition is due to the low concentration of molecularly dispersed oligomers.     

Structural Properties and Stereochemically Distinct Folding Preferences of 4,5‐cis and trans‐Methano‐L‐Proline Oligomers: The Shortest Crystalline PPII‐Type Helical Proline‐Derived Tetramer

The synthesis, structural properties, and folding patterns of a series of L ‐proline methanologues represented by cis‐ and trans‐4,5‐methano‐L ‐proline amides and their oligomers are reported as revealed by X‐ray crystallography, circular dichroism measurements, and DFT calculations. We disclose the first example of a crystalline tetrameric proline congener to exhibit a polyproline II helical conformation. Experimental evidence of PPII‐type helical arrangement (both in solution and in the solid state) of cis‐4,5‐methano‐L ‐proline oligomers is supported by theoretical calculations reflecting the extent of n→π* stabilization of the trans‐amide conformation.     

Conformationally Programmable Chiral Foldamers with Compact and Extended Domains Controlled by Monomer Structure

Foldamers are an important class of abiotic macromolecules, with potential therapeutic applications in the disruption of protein–protein interactions. The majority adopt a single conformational motif such as a helix. A class of foldamer is now introduced where the choice of heterocycle within each monomer, coupled with a strong conformation‐determining dipole repulsion effect, allows both helical and extended conformations to be selected. Combining these monomers into hetero‐oligomers enables highly controlled exploration of conformational space and projection of side‐chains along multiple vectors. The foldamers were rapidly constructed via an iterative deprotection‐cross‐coupling sequence, and their solid‐ and solution‐phase conformations were analysed by X‐ray crystallography and NMR and CD spectroscopy. These molecules may find applications in protein surface recognition where the interface does not involve canonical peptide secondary structures.     

Amphipathic helices from aromatic amino acid oligomers

Synthetic helical foldamers are of significant interest for mimicking the conformations of naturally occurring molecules while at the same time introducing new structures and properties. In particular, oligoamides of aromatic amino acids are attractive targets, as their folding is highly predictable and stable. Here the design and synthesis of new amphipathic helical oligoamides based on quinoline-derived amino acids having either hydrophobic or cationic side chains are described. Their structures were characterized in the solid state by single-crystal X-ray diffraction and in solution by NMR. Results of these studies suggest that an oligomer as short as a pentamer folds into a stable helical conformation in protic solvents, including MeOH and H(2)O. The introduction of polar proteinogenic side chains to these foldamers, as described here for the first time, promises to provide possibilities for the biological applications of these molecules. In particular, amphipathic helices are versatile targets to explore due to their importance in a variety of biological processes, and the unique structure and properties of the quinoline-derived oligoamides may allow new structure-activity relationships to be developed.     

Oxime Side‐Chain Cross‐Links in an α‐Helical Coiled‐Coil Protein: Structure,Thermodynamics, and Folding‐Templated Synthesis of Bicyclic Species

Covalent side‐chain cross‐links are a versatile method to control peptide folding, particularly when α‐helical secondary structure is the target. Here, we examine the application of oxime bridges, formed by the chemoselective reaction between aminooxy and aldehyde side chains, for the stabilization of a helical peptide involved in a protein–protein complex. A series of sequence variants of the dimeric coiled coil GCN4‐p1 bearing oxime bridges at solvent‐exposed positions were prepared and biophysically characterized. Triggered unmasking of a side‐chain aldehyde in situ and subsequent cyclization proceed rapidly and cleanly at pH 7 in the folded protein complex. Comparison of folding thermodynamics among a series of different oxime bridges show that the cross links are consistently stabilizing to the coiled coil, with the extent of stabilization sensitive to the exact size and structure of the macrocycle. X‐ray crystallographic analysis of a coiled coil with the best cross link in place and a second structure of its linear precursor show how the bridge is accommodated into an α‐helix. Preparation of a bicyclic oligomer by simultaneous formation of two linkages in situ demonstrates the potential use of triggered oxime formation to both trap and stabilize a particular peptide folded conformation in the bound state.     

Synthesis and Self‐assembly of a Helical Polymer Grafted from a Foldable Polyurethane Scaffold

Herein a polyurethane graft poly‐l ‐glutamate amphiphilic copolymer was synthesized from a polyurethane (PU)‐based macro‐initiator (containing pendant primary amine groups) through the ring opening polymerization of N‐carboxy anhydride of γ‐benzyl‐l ‐glutamate ( BLG‐NCA ). On average, twenty two l ‐glutamic acids were grafted from each amino group which was pendant on the polyurethane chain with 10 repeating units. The grafted polymer ( PU‐PP‐1 ) exhibits self‐assembly to produce a hydrogel in a wide pH window ranging from pH 5.0 to 8.0 with a critical gelation concentration (CGC) of 5.0 wt % (w/v) at pH 7.4. Furthermore, circular dichroism study revealed the transition of the α‐helix to a random coil upon increasing the pH. Due to the protonation of side chains at pH 4.0, PU‐PP‐1 adopted an α‐helical conformation whereas at pH >8.0 the side‐chain carboxylic acid groups of the PLGAs were ionized, leading to the formation of an extended random coil conformation as a result of charge repulsion. Conformational switching was also supported by FTIR spectroscopy.     

Helical arrangement of a hydrogen‐bonded columnar liquid crystal induced by a centered triphenylene derivative bearing chiral side‐chains

A hydrogen‐bonded helical columnar liquid crystal was synthesized, in which the helical structure is induced by a centered triphenylene derivative bearing chiral side‐chains. The triphenylene derivative, 2,6,10‐tris(carboxymethoxy)‐3,7,11‐tris((S)‐(‐)‐2‐methyl‐1‐butanoxy)triphenylene ( TPC4(S) ), and a dendric amphiphile, 3,5‐bis‐(3,4‐bis‐dodecyloxy‐benzyloxy)‐N‐pyridine‐4‐yl‐benzamide ( DenC12 ), were mixed in a 1:3 ratio to obtain a complex, TPC4(S)‐DenC12 . Analyses by ¹H‐NMR spectroscopy, diffusion ordered spectroscopy (DOSY), CD spectroscopy, infrared (IR) spectroscopy, polarized optical microscopy (POM), differential scanning calorimetry (DSC), and X‐ray diffractometry revealed that TPC4(S)‐DenC12 self‐assembles to form helical columnar stacks in solution and a helical columnar liquid crystal in bulk. The hydrogen bonding between TPC4(S) and DenC12 is essential for the helical columnar organization, and the preference for a one‐handed helical conformation is likely derived from the steric interaction between the chiral side‐chains and the dendric amphiphiles in the packing of the hydrogen‐bonded columnar assemblies. Copyright © 2008 John Wiley & Sons, Ltd.     

Helical Folding of Conjugated Oligo(phenyleneethynylene): Chain‐Length Dependence,Solvent Effects,and Intermolecular Assembly

As a representative folding system that features a conjugated backbone, a series of monodispersed (o‐phenyleneethynylene)‐alt‐(p‐phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side‐chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain‐length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light‐scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self‐assembling into hierarchical supramolecular structures promises application potential for the system.     

Isosteric Substitutions of Urea to Thiourea and Selenourea in Aliphatic Oligourea Foldamers: Site‐Specific Perturbation of the Helix Geometry

Nearly isosteric oxo to thioxo substitution was employed to interrogate the structure of foldamers with a urea backbone and explore the relationship between helical folding and hydrogen‐bonding interactions. A series of oligomers with urea bonds substituted by thiourea bonds at discrete or all positions in the sequence have been prepared and their folding propensity was studied by using a combination of spectroscopic methods and X‐ray diffraction. The outcome of oxo to thioxo replacements on the helical folding was found to depend on whether central or terminal ureas were modified. The canonical helix geometry was not affected upon insertion of thioureas close to the negative end of the helix dipole, whereas thioureas close to the positive pole were found to increase the terminal flexibility and cause helix fraying. Perturbation was amplified when a selenourea was incorporated instead, leading to a structure that is only partly folded.     

Structure and mechanical properties of poly(L‐lactic acid) crystals and fibers

The elastic constants of poly(L ‐lactic acid) (PLLA) crystals are reported on the basis of a commercial software package and the published crystal structure of the α form. A chain modulus of 36 GPa and a shear modulus of 3 GPa have been obtained for cylindrically symmetric aggregates of perfectly oriented crystals. The helical conformation of the PLLA molecule reduces the stiffness in the chain axis direction because bond rotation plays a significant role in the deformation. X‐ray crystal strain measurements suggest that shear of the α crystal parallel to the helix axis is the easiest mode of deformation, in agreement with the expectations obtained from the low shear modulus of 3 GPa obtained from the theoretical calculations. A combination of small‐ and wide‐angle X‐ray scattering, differential scanning calorimetry, dynamic mechanical thermal analysis, and shrinkage measurements has been used to characterize the structure that develops and the crystal transformation that occurs during fiber processing. The structure that develops during processing very much depends on the crystal transformation, and a structural model is proposed for fibers at different degrees of plastic deformation. The transformation of the α crystal into the β form and vice versa is governed primarily by shear along the helix axis because the chains must shear past each other during the crystal transformation, disrupting the lamellar packing. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 892–902, 2007     

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.     

Design and Synthesis of Urea‐Linked Aromatic Oligomers—A Route Towards Convoluted Foldamers

Herein we report the design and synthesis of crescent‐shaped and helical urea‐based foldamers, the curvature of which is controlled by varying the constituent building blocks and their connectivity. These oligomers are comprised of two, three or five alternating aromatic heterocycles (pyridazine, pyrimidine or pyrazine) and methyl‐substituted aromatic carbocycles (tolyl, o‐xylyl or m‐xylyl) connected together through urea linkages. A crescent‐shaped conformational preference is encoded within these π‐conjugated urea‐linked oligomers based on intramolecular hydrogen bonding and steric interactions; the degree of curvature is tuned by the urea connectivity to the heterocycles and the aryl groups. NMR characterization of these foldamers confirms the intramolecular hydrogen‐bonded conformation expected (Z,E configuration of the urea bond) in both the pyridazyl and pyrimidyl foldamers in solution. An X‐ray crystal structure of the N³,N⁶‐diisobutylpyridazine‐4,6‐diamine–o‐tolyl urea‐linked foldamer ( 4 ) confirms the presence of N? H???N hydrogen bonds between the heterocyclic nitrogen atom and the free hydrogen of the urea linkage. Additionally, the tolyl methyl group interacts unfavourably with the urea carbonyl oxygen, thus destabilising the alternate planar conformation.     

Chiral Photoresponsive Tetrathiazoles That Provide Snapshots of Folding States

Herein, we designed chiral photoresponsive tetra(2‐phenylthiazole)s, which induce a diastereoselective 6π‐electrocyclization reaction in a helically folded structure to freeze the conformational interconversions. The folding conformation with one helical turn of tetra(2‐phenylthiazole)s was supported by multiple intramolecular noncovalent interactions including vicinal S???N interheteroatom interactions and CH–π and π–π stacking interactions between nonadjacent units, as found in X‐ray crystal structures as well as quantum chemical calculations. The introduction of a chiral group at both ends of tetra(2‐phenylthiazole) dictates the preferential folding into a one‐handed helix conformation by the simultaneous operation of S???O and multiple CH–π interactions that involve the chiral end groups. Since the tetra(2‐phenylthiazole)s possess two equivalent photoreactive 6π‐electron systems and the folded conformation is suitable for photoinduced electrocyclization reaction, they undergo a photocyclization reaction in a stereoselective manner to memorize the chirality of the helix in a resulting diastereomeric closed form.     

Do Valine Side Chains Have an Influence on the Folding Behavior of β‐Substituted β‐Peptides?

The influence of valine side chains on the folding/unfolding equilibrium and, in particular, on the 3₁₄‐helical propensity of β³‐peptides were investigated by means of molecular‐dynamics (MD) simulation. To that end, the valine side chains in two different β³‐peptides were substituted by leucine side chains. The resulting four peptides, of which three have never been synthesized, were simulated for 150 to 200 ns at 298 and 340 K, starting from a fully extended conformation. The simulation trajectories obtained were compared with respect to structural preferences and folding behavior. All four peptides showed a similar folding behavior and were found to predominantly adopt 3₁₄‐helical conformations, irrespective of the presence of valine side chains. No other well‐defined conformation was observed at significant population in any of the simulations. Our results imply that β³‐peptides show a structural preference for 3₁₄‐helices independent of the branching nature of the side chains, in contrast to what has been previously proposed on the basis of circular‐dichroism (CD) measurements.     

Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution

In the search of molecules that could recognize sizeable areas of protein surfaces, a series of ten helical aromatic oligoamide foldamers was synthesized on solid phase. The foldamers comprise three to five monomers carrying various proteinogenic side chains, and exist as racemic mixtures of interconverting right‐handed and left‐handed helices. Functionalization of the foldamers by a nanomolar ligand of human carbonic anhydrase II (HCA) ensured that they would be held in close proximity to the protein surface. Foldamer–protein interactions were screened by circular dichroism (CD). One foldamer displayed intense CD bands indicating that a preferred helix handedness is induced upon interacting with the protein surface. The crystal structure of the complex between this foldamer and HCA could be resolved at 2.1 Å resolution and revealed a number of unanticipated protein–foldamer, foldamer–foldamer, and protein–protein interactions.     

Structure Elucidation of Helical Aromatic Foldamer–Protein Complexes with Large Contact Surface Areas

The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein–protein interactions. Herein, we present long helical aromatic oligoamide foldamers bearing proteinogenic side chains that cover up to 450 Ų of the human carbonic anhydrase II (HCA) surface. The foldamers are composed of aminoquinolinecarboxylic acids bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids that enhance helix handedness dynamics. Crystal structures of HCA-foldamer complexes were obtained with a 9- and a 14-mer both showing extensive protein–foldamer hydrophobic contacts. In addition, foldamer–foldamer interactions seem to be prevalent in the crystal packing, leading to the peculiar formation of an HCA superhelix wound around a rod of stacked foldamers. Solution studies confirm the positioning of the foldamer at the protein surface as well as a dimerization of the complexes.     

Conformational analysis of dipeptide‐derived polyisocyanides

The conformational properties of polymers derived from isocyanodipeptides have been investigated with a combination of model calculations, X‐ray diffraction, and circular dichroism spectroscopy. Depending on the configuration of the side chains, defined arrays of hydrogen bonds along the polymeric backbone are formed. This leads to a well‐defined conformation as, for example, expressed in the formation of lyotropic liquid‐crystalline phases and increased helical stability. Upon the disruption of the hydrogen bonds by a strong acid, a less well‐defined macromolecular conformation is observed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1725–1736, 2003