Conformationally Constrained Aliphatic−Aromatic Amino-Acid-Conjugated Hybrid Foldamers with Periodic β-Turn Motifs

Hybrid Sequences that Express both Aromatic Amide and α-Peptidic Folding Features

Foldamers combining aliphatic and aromatic main-chain units often produce atypical structures that cannot easily be accessed from purely aromatic or aliphatic sequences. We report solid-state evidence that sequences comprising α-amino acids and quinoline-based monomers adopt conformations that combine the folding propensities of both components. Foldamers 2 and 3 having an XQQ repeat motif (X=α-amino acid, Q=quinoline) were synthesized. Crystals of 2 (X=Phe, Q with an anionic side chain) obtained from water revealed an aromatic helix where amide groups belonging to the α-amino acids created a hydrogen-bond array typical of peptidic helices. Crystals of 3 (X=Ser, Q with a lipophilic side chain) obtained from organic solvents revealed a helix-turn-helix structure in which α-amino acid side chains interfere with main-chain hydrogen bonding. High sequence-dependency of the conformation is typical of peptides but is shown here to include aromatic folding features.

Indoloazepinone-Constrained Oligomers as Cell-Penetrating and Blood-Brain-Barrier-Permeating Compounds

Non-cationic and amphipathic indoloazepinone-constrained (Aia) oligomers have been synthesized as new vectors for intracellular delivery. The conformational preferences of the [l-Aia-Xxx]_n oligomers were investigated by circular dichroism (CD) and NMR spectroscopy. Whereas Boc-[l-Aia-Gly]_2,4 -OBn oligomers 12 and 13 and Boc-[l-Aia-β³ -h-l-Ala]_2,4 -OBn oligomers 16 and 17 were totally or partially disordered, Boc-[l-Aia-l-Ala]₂ -OBn (14) induced a typical turn stabilized by C₅ - and C₇ -membered H-bond pseudo-cycles and aromatic interactions. Boc-[l-Aia-l-Ala]₄ -OBn (15) exhibited a unique structure with remarkable T-shaped π-stacking interactions involving the indole rings of the four l-Aia residues forming a dense hydrophobic cluster. All of the proposed FITC-6-Ahx-[l-Aia-Xxx]₄ -NH₂ oligomers 19-23, with the exception of FITC-6-Ahx-[l-Aia-Gly]₄ -NH₂ (18), were internalized by MDA-MB-231 cells with higher efficiency than the positive references penetratin and Arg₈ . In parallel, the compounds of this series were successfully explored in an in vitro blood-brain barrier (BBB) permeation assay. Although no passive diffusion permeability was observed for any of the tested Ac-[l-Aia-Xxx]₄ -NH₂ oligomers in the PAMPA model, Ac-[l-Aia-l-Arg]₄ -NH₂ (26) showed significant permeation in the in vitro cell-based human model of the BBB, suggesting an active mechanism of cell penetration.

Exploring the gem-dimethyl effect in the formation of imine-based macrocycles and cages

A series of imine-based macrocycles and cages has been synthesized using the gem-dimethyl effect as a platform. Following this strategy, imine-based macrocyclization could be performed even at higher concentration.

Solid-Phase Synthesis of Water-Soluble Helically Folded Hybrid α-Amino Acid/Quinoline Oligoamides

We report here a solid phase synthesis methodology that allows the incorporation of α-amino acids (X) into quinoline (Q) oligoamide foldamer sequences. Water-soluble hybrid oligoamides based on the XQ2 trimer repeat motif were shown to adopt helical conformations presenting α-amino acid side chains in a predictable linear array on one face of the helix. In contrast, sequences based on the XQ dimer motif expressed less well-defined behavior, most likely due to local conformational variability precluding long-range order. Also presented is a full structural investigation by NMR of a dodecameric XQ2-type foldamer containing four different amino acid residues (Lys, Ala, Asp, and Ser).

Structural elucidation of foldamers with no long range conformational order

The synthesis and structural investigation of aromatic-aliphatic oligoamide foldamers reveals a zig-zag tape conformation with local conformational variability that precludes long range order.

Synthetic turn mimetics and hairpin nucleators: Quo Vadimus?

Structural mimicry of peptides has witnessed perceptible progress in the last three decades. Reverse turn and β-hairpin units are the smallest secondary structural motifs that are some of the most scrutinized functional cores of peptides and proteins. The practice of mimicking, without altering the function of the bioactive core, ranges from conformational locking of the basic skeleton to total replacement of structural architecture using synthetic analogues. Development of heterogeneous backbones--using unnatural residues in place of natural ones--has broadened further opportunities for efficient structural rigidification. This feature article endeavours to trail the path of progress achieved hitherto and envisage the possibilities that lie ahead in the development of synthetic turn mimetics and hairpin nucleators.

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.

Artificial supersecondary structures based on aromatic oligoamides

With an intelligent design of the monomers, considerable effort has so far focused on the creation of aromatic oligoamide foldamers which are able to mimic the secondary structures of biopolymers. Supersecondary structure is a growing set of known and classifiable protein folding patterns that provides an important organizational context to this complex endeavor. In this article, we highlight the design, chemical synthesis, and structural studies of artificial supersecondary structures based on aromatic oligoamide foldamers in recent years.

Nanosized hybrid oligoamide foldamers: aromatic templates for the folding of multiple aliphatic units

Oligoamide sequences comprised of both 8-amino-2-quinolinecarboxylic acid "Q" and 6-aminomethyl-2-pyridinecarboxylic acid "P" have been synthesized. It was found that the aliphatic amine of P greatly facilitates amide couplings, as opposed to the aromatic amine of Q, which enabled us to prepare sequences having up to 40 units. The conformation and conformational stability of these oligomers were characterized in the solid state using X-ray crystallography and in solution using NMR and various chromatographic techniques. Q(n) oligomers adopt very stable helically folded conformations whereas P(n) oligomers do not fold and impart conformational preferences distinct from those of Q units. When a P(n) segments is attached at the end of a Q(4) segment, a couple P units appear to follow the folding pattern imposed by the Q(n) segment, but P units remote from the Q(n) segment do not fold. When a P(n) segment is inserted between two Q(4) segments, the P(n) segment adopts the canonical helical conformation imposed by the Q units at least up to two full helical turns (n = 5). However, the overall stability of the helix tends to decrease as the number of P units increases. When noncontiguous P units separated by Q(4) segments are incorporated in a sequence, they all adopt the helical conformation imposed by Q monomers and the overall helix stability increases when helix length increases. For example, a 40mer with a sequence (PQ(4))(8) folds into a rod-like helix spanning over 16 turns with a length of 5.6 nm. This investigation thus demonstrates that remarkably long (nanometers) yet well-defined foldamers can be efficiently synthesized stepwise and that their helical stability may be continuously tuned upon controlling the ratio and sequence of P and Q monomers.