Design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational study

The present study is aimed at the design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational analysis (NMR, MD, and CD studies). The requisite peptides with heterogeneous backbones were prepared from β-, γ-, and δ-amino acids with carbohydrate side chains and α-amino acid, L-Ala. The α/β-peptides were prepared from (S)-β-Caa(l) (C-linked carbo-β-amino acid with D-lyxo furanoside side chain) and L-Ala with a 1:1 alternation. The α/β-peptides with "helix-turn" motif displayed a 11/9-helix nucleating a 13-atom H-bonding turn. The α/β-octapeptides showed the presence of HTH structures with bifurcated 11/15-H-bonded turn. Further, the α/β-hexapeptide with HT motif, independently on coupling with γ/α/γ/α- and δ/α/δ/α-tetrapeptides at the C-terminus provided access to the decapeptides with "hybrid HTH" motifs. The decapeptide ("α-β-α-β-α-β-γ-α-γ-α") showed a hybrid HTH with "11/9/11/9/11/16/9/12/10" H-bonding, while the decapeptide ("α-β-α-β-α-β-δ-α-δ-α") revealed the presence of a "11/9/11/9/11/17/9/13/11" helical pattern. The above peptides thus have shown compatibility between different types of helices and serendipitous bifurcated 11/16- and 11/17-turns. The present study thus provided the first opportunity for the design and study of "hybrid HTH" motifs with more than one kind of helical structures in them.

Aromatic amide and hydrazide foldamer-based responsive host-guest systems

CONSPECTUS: In host-guest chemistry, a larger host molecule selectively and noncovalently binds to a smaller guest molecule or ion. Early studies of host-guest chemistry focused on the recognition of spherical metal or ammonium ions by macrocyclic hosts, such as cyclic crown ethers. In these systems, preorganization enables their binding sites to cooperatively contact and attract a guest. Although some open-chain crown ether analogues possess similar, but generally lower, binding affinities, the design of acyclic molecular recognition hosts has remained challenging. One of the most successful examples was rigid molecular tweezers, acyclic covalently bonded preorganized host molecules with open cavities that bind tightly as they stiffen. Depending on the length of the atomic backbones, hydrogen bonding-driven aromatic amide foldamers can form open or closed cavities. Through rational design of the backbones and the introduction of added functional groups, researchers can regulate the shape and size of the cavity. The directionality of hydrogen bonding and the inherent rigidity of aromatic amide units allow researchers to predict both the shape and size of the cavity of an aromatic amide foldamer. Therefore, researchers can then design guest molecules with structure that matches the cavity shape, size, and binding sites of the foldamer host. In addition, because hydrogen bonds are dynamic, researchers can design structures that can adapt to outside stimuli to produce responsive supramolecular architectures. In this Account, we discuss how aromatic amide and hydrazide foldamers induced by hydrogen bonding can produce responsive host-guest systems, based on research by our group and others. First we highlight the helical chirality induced as binding occurs in solution, which includes the induction of helicity by chiral guests in oligomeric and polymeric foldamers, the formation of diastereomeric complexes between chiral foldamer hosts and guests, and the induction of helical chirality by chiral guests into inherently flexible backbones. In addition, molecular or ion-pair guests can produce supramolecular helical chirality in the organogel state. Such structures exhibit remarkable time-dependence and a "Sergeants and Soldiers" effect that are not observed for other two-component organogels that have been reported. We further illustrate that the reversible folding behavior of an aromatic amide foldamer segment can modulate the switching behavior of donor-acceptor interaction-based [2]rotaxanes. Finally we show that a folded oligomer can induce folding in one or two attached intrinsically flexible oligomers, an example of a solvent-responsive intramolecular host-guest system.

Targeting the bacteria-host interface: strategies in anti-adhesion therapy

Bacterial infections are a major cause of morbidity and mortality worldwide and are increasingly problematic to treat due to the rise in antibiotic-resistant strains. It becomes more and more challenging to develop new antimicrobials that are able to withstand the ever-increasing repertoire of bacterial resistance mechanisms. This necessitates the development of alternative approaches to prevent and treat bacterial infections. One of the first steps during bacterial infection is adhesion of the pathogen to host cells. A pathogen’s ability to colonize and invade host tissues strictly depends on this process. Thus, interference with adhesion (anti-adhesion therapy) is an efficient way to prevent or treat bacterial infections. As a basis to present different strategies to interfere with pathogen adhesion, this review briefly introduces general concepts of bacterial attachment to host cells. We further discuss advantages and disadvantages of anti-adhesion treatments and issues that are in need of improvement so as to make anti-adhesion compounds a more broadly applicable alternative to conventional antimicrobials.

Supramolecular chemistry with ureido-benzoic acids

A novel, complementary quadruple hydrogen-bonding motif is presented that shows very strong dimerization and is switchable with pH.

Formation of a pseudo-β-hairpin motif utilizing the Ant–Pro reverse turn: consequences of stereochemical reordering

Herein, we report a special case of pseudo-β-hairpin formation by tetrapeptide sequences featuring a two-residue Ant–Pro dipeptide motif (Ant = anthranilic acid and Pro = proline) at the loop region.

Stretching single polymer chains of donor-acceptor foldamers: toward the quantitative study on the extent of folding

Single-molecule force spectroscopy has proven to be an efficient tool for the quantitative characterization of flexible foldamers on the single-molecule level in this study. The extent of folding has been estimated quantitatively for the first time to the best of our knowledge, which is crucial for a better understanding of the "folding-process" on single-molecule level. Therefore, this study may provide a guidance to regulate folding for realizing rational control over the functions of bulk materials.

Hydrophobic collapse of foldamer capsules drives picomolar-level chloride binding in aqueous acetonitrile solutions

Aqueous media are competitive environments in which to perform host-guest chemistry, particularly when the guest is highly charged. While hydrophobic binding is a recognized approach to this challenge in which apolar pockets can be designed to recognize apolar guests in water, complementary strategies are required for hydrophilic anions like chloride. Here, we present evidence of such an alternative mechanism, used everyday by proteins yet rare for artificial receptors, wherein hydrophobic interactions are shown to be responsible for organizing and stabilizing an aryl-triazole foldamer to help extract hydrophilic chloride ions from increasingly aqueous solutions. Therein, a double-helical complex gains stability upon burial of ∼80% of the π surfaces that simultaneously creates a potent, solvent-excluding microenvironment for hydrogen bonding. The chloride's overall affinity to the duplex is substantial in 25% water v/v in acetonitrile (log β2 = 12.6), and it remains strong (log β2 = 13.0) as the water content is increased to 50%. With the rise in predictable designs of abiological foldamers, this water-assisted strategy can, in principle, be utilized for binding other hydrophilic guests.

Chirality transfer in propeller-shaped cyclen-calcium(II) complexes: metal-coordinating and ion-pairing anion procedures

A series of quadruple-stranded Na(+) and Ca(2+) complexes with octadentate cyclen ligands was synthesized to produce complexes that contained four different side-arm combinations (one triazole-coumarin group and three pyridine groups (1), four pyridine groups (2), one triazole-coumarin group and three quinoline groups (3), and four quinoline groups (4)). X-ray crystallographic analysis revealed that no significant changes occurred in the stereostructure of these complexes upon replacing one pyridine group with a triazole-coumarin moiety, or by replacing Na(+) ions with Ca(2+) ions, although the coordination number of the complexes in the solid state decreased when pyridine groups were replaced by quinoline groups. In solution, all of the side arms were arranged in a propeller-like pattern to yield an enantiomer pair of Δ and Λ forms in each metal complex. The addition of a tert-butoxycarbonyl (Boc)-protected amino acid anion, that is, a coordinative chiral carboxylate anion, to the cyclen-Ca(2+) complex induced circular dichroism (CD) signals in the aromatic region by forming a 1:1 mixture of diastereomeric ternary complexes with opposite complex chirality, whilst the corresponding Na(+) complexes rarely showed any response. In complexes 1-Ca(2+) and 3-Ca(2+), this chirality-transfer process was efficiently followed by considering the induction of the CD signals at two different wavelengths, that is, the coumarin-chromophore region and the aza-aromatic region. The sign and intensity of the CD signal were significantly dependent on both the nature of the aza-aromatic moiety and the enantiomeric purity of the external anion. These Ca(2+) complexes worked as effective probes for the determination of the enantiomeric excess of the chiral anion. The cyclen-Ca(2+) complexes also interacted with the non-coordinative Δ-TRISPHAT anion through an ion-pairing mechanism to achieve chirality transfer from the anion to the metal complex; both complexes 1-Ca(2+) and 3-Ca(2+) clearly showed induced CD signals in the coumarin-chromophore region, owing to ion-paring interactions with the Δ-TRISPHAT anion. Thus, the proper combination of an octadentate cyclen ligand and a metal center demonstrated effective chirality transfer.

Ion permeation by a folded multiblock amphiphilic oligomer achieved by hierarchical construction of self-assembled nanopores

A multiblock amphiphilic molecule 1, with a tetrameric alternating sequence of hydrophilic and hydrophobic units, adopts a folded structure in a liposomal membrane like a multipass transmembrane protein, and is able to transport alkali metal cations through the membrane. Hill's analysis and conductance measurements, analyzed by the Hille equation, revealed that the tetrameric assembly of 1 forms a 0.53 nm channel allowing for permeation of cations. Since neither 3, bearing flexible hydrophobic units and forming no stacked structures in the membrane, nor 2, a monomeric version of 1, is able to transport cations, the folded conformation of 1 in the membrane is likely essential for realizing its function. Thus, function and hierarchically formed higher-order structures of 1, is strongly correlated with each other like proteins and other biological macromolecules.