Refoldable Foldamers: Global Conformational Switching by Deletion or Insertion of a Single Hydrogen Bond

Small changes in the structure of a foldamer may lead to gross changes in conformational preference. We show that the simple insertion or deletion of a single hydrogen bond by changes in pH or by photochemical deprotection is sufficient to refold a helical oligomer, interconverting M and P screw-sense preference. As a consequence of the switch, information may be transmitted to a remote catalytic site, selectively directing the formation of either of two enantiomeric products by a reaction involving 1,22-remote intermolecular asymmetric induction.

Peptide Backbone Composition and Protease Susceptibility: Impact of Modification Type, Position, and Tandem Substitution

The clinical utility of peptides is limited by their rapid degradation by endogenous proteases. Modification of the peptide backbone can generate functional analogues with enhanced proteolytic stability. Existing principles for the design of such oligomers have focused primarily on effective structural mimicry. A more robust strategy would incorporate a rational approach for engineering maximal proteolytic stability with minimal unnatural residue content. We report here the systematic comparison of the proteolytic resistance imparted by four backbone modifications commonly employed in the design of protease-stable analogues of peptides with complex folding patterns. The degree of protection was quantified as a function of modification type, position, and tandem substitution in the context of a long, unstructured host sequence and a canonical serine protease. These results promise to inform ongoing work to develop biostable mimics of increasingly complex peptides and proteins.

A cell-penetrating foldamer with a bioreducible linkage for intracellular delivery of DNA

Despite significant advances in foldamer chemistry, tailored delivery systems based on foldamer architectures, which provide a high level of control over secondary structure, are curiously rare among non-viral technologies for transporting nucleic acids into cells. A potent pH-responsive, bioreducible cell-penetrating foldamer (CPF) was developed through covalent dimerization of a short (8-mer) amphipathic oligourea sequence bearing histidine-type units. This CPF exhibits a high capacity to assemble with pDNA and mediates efficient delivery of nucleic acids into the cell. Furthermore, it does not adversely affect cellular viability and was shown to compare favorably with a cognate peptide transfection agent based on His-rich sequences.

Can Helical Peptides Unwind One Turn at a Time? - Controlled Conformational Transitions in α,β(2,3)-Hybrid Peptides

Unfolding of helical trans-β(2,3) -hybrid peptides with (α-β)n α composition, when executed by increasing solvent polarity or temperature, proceeded in a systematic manner with the turns unwinding sequentially; C-terminal region of these peptides were first to unwind and the process propagated towards N terminus with more and more β residues equilibrating from the gauche to the anti rotameric state across Cα-Cβ . This is evidenced by clear change in their Cβ H signal splitting, (3)JCαH-CβH values, and sequential disappearance of i,i+2 NOEs.

Antiparallel Self-Association of a γ,α-Hybrid Peptide: More Relevance of Weak Interactions

To learn how a preorganized peptide-based molecular template, together with diverse weak non-covalent interactions, leads to an effective self-association, we investigated the conformational characteristics of a simple γ,α-hybrid model peptide, Boc-γ-Abz-Gly-OMe. The single-crystal X-ray diffraction analysis revealed the existence of a fully extended β-strand-like structure stabilized by two non-conventional C-H⋅⋅⋅O=C intramolecular H-bonds. The 2D (1) H NMR ROESY experiment led us to propose that the flat topology of the urethane-γ-Abz-amide moiety is predominantly preserved in a non-polar environment. The self-association of the energetically more favorable antiparallel β-strand-mimic in solid-state engenders an unusual 'flight of stairs' fabricated through face-to-face and edge-to-edge Ar⋅⋅⋅Ar interactions. In conjunction with FT-IR spectroscopic analysis in chloroform, we highlight that conformationally semi-rigid γ-Abz foldamer in appositely designed peptides may encourage unusual β-strand or β-sheet-like self-association and supramolecular organization stabilized via weak attractive forces.

Folding Patterns in a Family of Oligoamide Foldamers

A series of small, unsymmetrical pyridine-2,6-dicarboxylamide oligoamide foldamers with varying lengths and substituents at the end groups were synthetized to study their conformational properties and folding patterns. The @-type folding pattern resembled the oxyanion-hole motifs of enzymes, but several alternative folding patterns could also be characterized. Computational studies revealed several alternative conformers of nearly equal stability. These folding patterns differed from each other in their intramolecular hydrogen-bonding patterns and aryl-aryl interactions. In the solid state, the foldamers adopted either the globular @-type fold or the more extended S-type conformers, which were very similar to those foldamers obtained computationally. In some cases, the same foldamer molecule could even crystallize into two different folding patterns, thus confirming that the different folding patterns are very close in energy in spite of their completely different shapes. Finally, the best match for the observed NOE interactions in the liquid state was a conformation that matched the computationally characterized helix-type fold.

Acid/Base-mediated uptake and release of halide anions with a preorganized aryl-triazole foldamer

A new approach for the construction of artificial receptors capable of selectively uptake and release of halides to mimic the biological halide ions pumps is developed, in which the preorganized aryl-triazole foldamer was designed to bear a resorcinolic group in the central strand as a switch regulator. By using 1,8-diazabicyclo[5.4.0]undec-7-ene/picric acid as the trigger, the foldamer can be switched between "w"-shape and helical conformation. Due to the large, half-open cavity as well as the additional electrostatic repulsion between oxyanions and guest halide, the foldamer in "w"-shape possesses a much weaker affinity for chloride, bromide, and iodide anions than those in the helical conformation in 6:94 (v/v) [D6 ]DMSO/CDCl3 . When the foldamer and chloride ions have the same initial concentrations of 1 mM, 70 % chloride ions in the solution could be reversibly bound or released upon switching.

Targeting diverse protein-protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold

Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. Here, we describe a strategy for designing oligomers containing both α- and β-amino acid residues ("α/β-peptides") that mimic several peptides derived from the three-helix bundle "Z-domain" scaffold. We show that α/β-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding α/β-peptide inhibits the VEGF165-induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain-mimetic α/β-peptides that bind to two other protein partners, IgG and tumor necrosis factor-α. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable α/β-peptides that bind tightly and specifically to diverse targets of biomedical interest. Such reagents would be useful for diagnostic and therapeutic applications.

Imidazole-peptide foldamers: parabolic dependence of the folding process on the water content of the solvent

Oligomers of azole peptides have been isolated from a multitude of marine organisms. Up to now, these azole-containing dipeptide-analogue oligomers have only been found as cyclic n-mers (mostly tri- and tetramers) in nature. Herein, we show that imidazole-containing pseudopeptides form helixlike secondary structures in different solvents. The screw sense of the helix can be determined by attaching a single chiral imidazole unit to the N terminus of the oligomer. Investigation by means of circular dichroism (CD) spectroscopy showed that the folding process of the helix depends on the water content of the solvent in a parabolic way. In a pure organic medium, the helix is stabilized by hydrogen bonds between the hydrogen atoms of the amide groups and the nitrogen atoms of the azole ring. In aqueous solution, the formation of the helix is driven by dispersion interactions. The formation of the helix is more pronounced in aqueous solution than in organic solvents.

Selective and potent proteomimetic inhibitors of intracellular protein-protein interactions

Inhibition of protein–protein interactions (PPIs) represents a major challenge in chemical biology and drug discovery. α-Helix mediated PPIs may be amenable to modulation using generic chemotypes, termed “proteomimetics”, which can be assembled in a modular manner to reproduce the vectoral presentation of key side chains found on a helical motif from one partner within the PPI. In this work, it is demonstrated that by using a library of N-alkylated aromatic oligoamide helix mimetics, potent helix mimetics which reproduce their biophysical binding selectivity in a cellular context can be identified.

Targeting DNA G-quadruplexes with helical small molecules

We previously identified quinoline-based oligoamide helical foldamers and a trimeric macrocycle as selective ligands of DNA quadruplexes. Their helical structures might permit targeting of the backbone loops and grooves of G-quadruplexes instead of the G-tetrads. Given the vast array of morphologies G-quadruplex structures can adopt, this might be a way to achieve sequence selective binding. Here, we describe the design and synthesis of molecules based on macrocyclic and helically folded oligoamides. We tested their ability to interact with the human telomeric G-quadruplex and an array of promoter G-quadruplexes by using FRET melting assay and single-molecule FRET. Our results show that they constitute very potent ligands--comparable to the best so far reported. Their modes of interaction differ from those of traditional tetrad binders, thus opening avenues for the development of molecules specific for certain G-quadruplex conformations.

Designing foldamer-foldamer interactions in solution: the roles of helix length and terminus functionality in promoting the self-association of aminoisobutyric acid oligomers

The biological activity of antibiotic peptaibols has been linked to their ability to aggregate, but the structure-activity relationship for aggregation is not well understood. Herein, we report a systematic study of a class of synthetic helical oligomer (foldamer) composed of aminoisobutyric acid (Aib) residues, which mimic the folding behavior of peptaibols. NMR spectroscopic analysis was used to quantify the dimerization constants in solution, which showed hydrogen-bond donors at the N terminus promoted aggregation more effectively than similar modifications at the C terminus. Elongation of the peptide chain also favored aggregation. The geometry of aggregation in solution was investigated by means of titrations with [D6]DMSO and 2D NOE NMR spectroscopy, which allowed the NH protons most involved in intermolecular hydrogen bonds in solution to be identified. X-ray crystallography studies of two oligomers allowed a comparison of the inter- and intramolecular hydrogen-bonding interactions in the solid state and in solution and gave further insight into the geometry of foldamer-foldamer interactions. These solution-based and solid-state studies indicated that the preferred geometry for aggregation is through head-to-tail interactions between the N and C termini of adjacent Aib oligomers.

Building proficient enzymes with foldamer prostheses

Foldamers are non-natural oligomers that adopt stable conformations reminiscent of those found in proteins. To evaluate the potential of foldameric subunits for catalysis, semisynthetic enzymes containing foldamer fragments constructed from α- and β-amino acid residues were designed and characterized. Systematic variation of the α→β substitution pattern and types of β-residue afforded highly proficient hybrid catalysts, thus demonstrating the feasibility of expanding the enzyme-engineering toolkit with non-natural backbones.

Exploiting aromatic interactions for β-peptide foldamer helix stabilization: a significant design element

Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side-chains in β-peptide oligomers by intramolecular backbone-side chain CH-π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self-assembly in a polar medium for the β-peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis-[1S,2S]- or cis-[1R,2R]-1-amino-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (ATENAC) and cis-[1R,2S]- or cis-[1S,2R]-2-aminocyclohex-3-enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side-chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain-length. The hydrophobically driven self-assembly was achieved for the helix-forming oligomers, seen as vesicles in transmission electron microscopy images. The self-association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side-chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side-chains may yield important receptor-ligand interaction surfaces, which can provide amplified binding strength.

Comparison of design strategies for promotion of beta-peptide 14-helix stability in water

Many short beta-peptides adopt well-defined conformations in organic solvents, but specialized stabilizing elements are required for folding to occur in aqueous solution. Several different strategies to stabilize the 14-helical secondary structure in water have been developed, and here we provide a direct comparison of three such strategies. We have synthesized and characterized beta-peptide heptamers in which variously a salt bridge between side chains, a covalent link between side chains, or two cyclically constrained residues have been incorporated to promote 14-helicity. The incorporation of a salt bridge does not generate significant 14-helicity in water, according to CD and 2D NMR data. In contrast, incorporation either of a lactam bridge between side chains or of cyclic residues results in stable 14-helices in water. The beta-peptides featuring trans-2-aminocyclohexanecarboxylic acid (ACHC) residues show the highest 14-helical backbone stability, with hardly any sensitivity to pH or ionic strength. The beta-peptides featuring side-chain-to-side-chain cyclization show lower 14-helical backbone stability and higher sensitivity to pH and ionic strength, but increased order between the side chains because of the cyclization.

Folding of a donor-acceptor polyrotaxane by using noncovalent bonding interactions

Mechanically interlocked compounds, such as bistable catenanes and bistable rotaxanes, have been used to bring about actuation in nanoelectromechanical systems (NEMS) and molecular electronic devices (MEDs). The elaboration of the structural features of such rotaxanes into macromolecular materials might allow the utilization of molecular motion to impact their bulk properties. We report here the synthesis and characterization of polymers that contain pi electron-donating 1,5-dioxynaphthalene (DNP) units encircled by cyclobis(paraquat-p-phenylene) (CBPQT(4+)), a pi electron-accepting tetracationic cyclophane, synthesized by using the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The polyrotaxanes adopt a well defined "folded" secondary structure by virtue of the judicious design of two DNP-containing monomers with different binding affinities for CBPQT(4+). This efficient approach to the preparation of polyrotaxanes, taken alongside the initial investigations of their chemical properties, sets the stage for the preparation of a previously undescribed class of macromolecular architectures.