Dynamic foldamer chemistry

Foldamers can be made more than pieces of static, conformationally uniform molecular architecture by designing into their structure the conformational dynamism characteristic of functional molecular machines. We show that these dynamic foldamers display biomimetic properties reminiscent of allosteric proteins and receptor molecules. They can translate chemical signals into conformational changes, and hence into chemical outputs such as control of reactivity and selectivity. Future developments could see dynamic foldamers operating in the membrane phase providing artificial mechanisms for communication and control that integrate synthetic chemistry into synthetic biology.

Synthesis of a new β-amino acid with a 3-deoxy-L-ara furnaoside side chain: the influence of the side chain on the conformation of α/β-peptides

The important role of side chains in the stabilization of helical folds in peptidic foldamers containing C-linked carbo-β-amino acids (β-Caa), an interesting class of β-amino acids, with carbohydrate side chains has been extensively elaborated. As a pragmatic approach to alleviate the interference of substituents in the side chains on the folding propensities of the peptides, they are often modified or removed. The present study reports the synthesis of a new β-Caa with a 3-deoxy-L-ara furanoside side chain, [(R)-β-Caa(da)], from D-glucose, and its use in the synthesis of α/β-peptides in 1 : 1 alternation with D-Ala. The synthesis of peptides using (R)-β-Caa(da), was facile unlike those from (R)-β-Caa(a) having the L-ara furanoside side chain. The detailed NMR, molecular dynamics (MD) and CD studies on the new α/β-peptides showed the presence of robust left-handed 11/9-mixed helices. The study demonstrates that the new (R)-β-Caa(da), behaves differently compared to the other two related monomers, (R)-β-Caa(x) with the D-xylo furanoside side chain and (R)-β-Caa(a).

Residue dependent hydrogen-bonding preferences in orthanilic acid-based short peptide β-turn motifs

This communication describes the competition between native β-turn (C10) and 2-aminobenzenesulfonic acid (^SAnt)(orthanilic acid)-based pseudo β-turn (C11) in their hybrid peptides.

A remarkable impact of a minor structural variation in the chain-end on the hierarchical self-assembly of a polymeric foldamer

This article elucidates a remarkable end group effect on the macroscopic assembly pathway of chain folded polyurethanes (PU) PU-2 and PU-3, both of which contain a linear PU chain appended with n-type semiconducting naphthalene-diimide (NDI) chromophores.

Synthesis and chiroptical properties of a π-conjugated polymer containing glucose-linked biphenyl units in the main chain capable of folding into a helical conformation

Naturally occurring ellagitannins provide us with inspiration for the development of a chiral π-conjugated polymer bearing glucose-linked biphenyl units in the main chain.

Polar solvent effects on tartaric acid binding by aromatic oligoamide foldamer capsules

Aromatic amide foldamer capsules hold polar guests in protic solvents.

Helix handedness inversion in arylamide foldamers: elucidation and free energy profile of a hopping mechanism

The free energy landscape and conformations of minima and intermediates along the stepwise handedness inversion pathway, proceeding through the simultaneous unfolding/folding of adjacent monomer–monomer linkages, for a helical arylamide foldamer.

Modulation of helix stability of indolocarbazole–pyridine hybrid foldamers

The kinetic stabilities of the helical conformations of indolocarbazole–pyridine hybrid foldamers were modulated through single site modification.

Control of a Chiral Property of a Calix[3]aramide: The Racemization Suppressed by Intramolecular Cyclic Hydrogen Bonds and DMSO-H2O System-Induced Spontaneous Resolution

A calix[3]aramide has been synthesized bearing three triphenylphosphinic amide moieties, which formed intramolecular cyclic hydrogen bonds that suppressed its cone/partial cone inversion. The intramolecular cyclic hydrogen bonds were disrupted by DMSO, and the insertion of H2O into the hydrogen bonds triggered the spontaneous resolution of the calix[3]aramide. Within a chiral environment, such as that afforded by the presence of optically active 2-butanol, the calix[3]aramide underwent a symmetry breaking crystallization process.

Development of protein mimics for intracellular delivery

Designing delivery agents for therapeutics is an ongoing challenge. As treatments and desired cargoes become more complex, the need for improved delivery vehicles becomes critical. Excellent delivery vehicles must ensure the stability of the cargo, maintain the cargo's solubility, and promote efficient delivery and release. In order to address these issues, many research groups have looked to nature for design inspiration. Proteins, such as HIV-1 trans-activator of transcription (TAT) and Antennapedia homeodomain protein, are capable of crossing cellular membranes. However, due to the complexities of their structures, they are synthetically challenging to reproduce in the laboratory setting. Being able to incorporate the key features of these proteins that enable cell entry into simpler scaffolds opens up a wide range of opportunities for the development of new delivery reagents with improved performance. This review charts the development of protein mimics based on cell-penetrating peptides (CPPs) and how structure-activity relationships (SARs) with these molecules and their protein counterparts ultimately led to the use of polymeric scaffolds. These scaffolds deviate from the normal peptide backbone, allowing for simpler, synthetic procedures to make carriers and tune chemical compositions for application specific needs. Successful design of polymeric protein mimics would allow researchers to further understand the key features in proteins and peptides necessary for efficient delivery and to design the next generation of more efficient delivery reagents.

Controlling the sign and magnitude of screw-sense preference from the C-terminus of an achiral helical foldamer

The global screw-sense preference of an achiral helical oligomer may be controlled by a single chiral monomer located at one terminus. Remarkably, maximal control is induced in oligomers of the achiral quaternary amino acid Aib by a single C-terminal alaninamide residue, probably because the Ala side chain, though small, is compatible with a 310 helical conformation. The presence or absence of a C-terminal hydrogen bond donor determines the screw sense of the entire oligomer.

Reversible Transformation of a One-Handed Helical Foldamer Utilizing a Planarity-Switchable Spacer and C2-Chiral Spirobifluorene Units

Polymeric quaterthiophenes containing optically active C₂-chiral spirobifluorene skeletons were synthesized as a new type of helical foldamers, and their higher-order structures were investigated. Oxidization of quaterthiophene moieties caused the spacer units to be in planar structure, leading the conformation of the polymer to be a coil-shaped, rigid helix. This transformation was reversibly performed.

Flaws in foldamers: conformational uniformity and signal decay in achiral helical peptide oligomers

Although foldamers, by definition, are extended molecular structures with a well-defined conformation, minor conformers must be populated at least to some extent in solution. We present a quantitative analysis of these minor conformers for a series of helical oligomers built from achiral but helicogenic α-amino acids. By measuring the chain length dependence or chain position dependence of NMR or CD quantities that measure screw-sense preference in a helical oligomer, we quantify values for the decay constant of a conformational signal as it passes through the molecular structure. This conformational signal is a perturbation of the racemic mixture of M and P helices that such oligomers typically adopt by the inclusion of an N or C terminal chiral inducer. We show that decay constants may be very low (<1% signal loss per residue) in non-polar solvents, and we evaluate the increase in decay constant that results in polar solvents, at higher temperatures, and with more conformationally flexible residues such as Gly. Decay constants are independent of whether the signal originates from the N or the C terminus. By interpreting the decay constant in terms of the probability with which conformations containing a screw-sense reversal are populated, we quantify the populations of these alternative minor conformers within the overall ensemble of secondary structures adopted by the foldamer. We deduce helical persistence lengths for Aib polymers that allow us to show that in a non-polar solvent a peptide helix, even in the absence of chiral residues, may continue with the same screw sense for approximately 200 residues.

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.

Hydrophobically driven twist sense bias of hollow helical foldamers of aromatic hydrazide polymers in water

Aromatic hydrazide polymers bearingS-chiral tetraethylene glycol chains can fold into M hollow helices in water driven by the hydrophobicity.

Conformational promiscuity in triazolamers derived from quaternary amino acids mimics peptide behaviour

Oligomers made by click chemistry display a duality of secondary structures similar to natural peptides as inferred by NMR spectroscopy and X-ray diffraction experiments.

Solvent assisted structural diversity: supramolecular sheet and double helix of a short aromatic γ-peptide

Solvent interaction has a significant effect on the molecular motions, folding and self-assembly of short aromatic γ-peptides that leads to a change in initial helical conformation.

Bipyridinium radical cation dimerization-driven polymeric pleated foldamers and a homoduplex that undergo ion-tuned interconversion

Radical cation dimerization induces bipyridinium-derived polymers to form pleated secondary structures and a homoduplex which can be tuned by ammonium to interconvert.

Helical folding of an arylamide polymer in water and organic solvents of varying polarity

An arylamide polymer is driven by the solvophobicity and hydrogen bonding to form helical conformation in solvents of different polarity.

The Dynamics, energetics and selectivity of water chain-containing aquapores created by the self-assembly of aquafoldamer molecules

Self-assembled hollow tubular aquapores were found to be stable, very dynamic yet highly selective toward recognition of water molecules.

Synthesis and conformational studies of α/β2,3-peptides derived from alternating β2,3-amino acids and l-Ala repeats

A new class of α/β^2,3-peptides were synthesized from C-linked carbo-β^2,3-amino acids (β^2,3-Caas) and investigated to understand the impact of the side chains (allyl/propargyl) at the Cα-position on their conformations.

Chiral tether-mediated stabilization and helix-sense control of complementary metallo-double helices

A series of novel PtII-linked double helices were prepared by inter- or intrastrand ligand-exchange reactions of the complementary duplexes composed of chiral or achiral amidine dimer and achiral carboxylic acid dimer strands joined by trans-PtII-acetylide complexes with PPh3 ligands using chiral and achiral chelating diphosphines. The structure and stability of the PtII-linked double helices were highly dependent on the diphosphine structures. An interstrand ligand exchange took place with chiral and achiral 1,3-diphosphine-based ligands, resulting in trans-PtII-bridged double helices, whose helical structures were quite stable even in dimethyl sulfoxide (DMSO) due to the interstrand cross-link, whereas a 1,2-diphosphine-based ligand produced non-cross-linked cis-PtII-linked duplexes, resulting from an intrastrand ligand-exchange that readily dissociated into single strands in DMSO. When enantiopure 1,3-diphosphine-based ligands were used, the resulting trans-PtII-bridged double helices adopted a preferred-handed helical sense biased by the chirality of the bridged diphosphines. Interestingly, the interstrand ligand exchange with racemic 1,3-diphosphine toward an optically-active PtII-linked duplex, composed of chiral amidine and achiral carboxylic acid strands, was found to proceed in a diastereoselective manner, thus forming complete homochiral trans-PtII-bridged double helices via a unique chiral self-sorting.