Conformation of diastereomeric peptide sequences: structural analysis of Z-D-Val-Ac6c-Gly-L-Phe-OMe

Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications

This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.

β-Turn analogues in model αβ-hybrid peptides: structural characterization of peptides containing β(2,2)Ac6c and β(3,3)Ac6c residues

The effect of gem-dialkyl substituents on the backbone conformations of β-amino acid residues in peptides has been investigated by using four model peptides: Boc-Xxx-β(2,2)Ac(6)c(1-aminomethylcyclohexanecarboxylic acid)-NHMe (Xxx = Leu (1), Phe (2); Boc = tert-butyloxycarbonyl) and Boc-Xxx-β(3,3)Ac(6)c(1-aminocyclohexaneacetic acid)-NHMe (Xxx = Leu (3), Phe (4)). Tetrasubstituted carbon atoms restrict the ranges of stereochemically allowed conformations about flanking single bonds. The crystal structure of Boc-Leu-β(2,2)Ac(6)c-NHMe (1) established a C(11) hydrogen-bonded turn in the αβ-hybrid sequence. The observed torsion angles (α(ϕ≈-60°, ψ≈-30°), β(ϕ≈-90°, θ≈60°, ψ≈-90°)) corresponded to a C(11) helical turn, which was a backbone-expanded analogue of the type III β turn in αα sequences. The crystal structure of the peptide Boc-Phe-β(3,3)Ac(6)c-NHMe (4) established a C(11) hydrogen-bonded turn with distinctly different backbone torsion angles (α(ϕ≈-60°, ψ≈120°), β(ϕ≈60°, θ≈60°, ψ≈-60°)), which corresponded to a backbone-expanded analogue of the type II β turn observed in αα sequences. In peptide 4, the two molecules in the asymmetric unit adopted backbone torsion angles of opposite signs. In one of the molecules, the Phe residue adopted an unfavorable backbone conformation, with the energetic penalty being offset by a favorable aromatic interaction between proximal molecules in the crystal. NMR spectroscopy studies provided evidence for the maintenance of folded structures in solution in these αβ-hybrid sequences.

The crystal structure of Afc-containing peptides

A systematic structural analysis of Afc (9-amino-fluorene-9-carboxylic acid) containing peptides is here reported. The crystal structures of four fully protected tripeptides containing the Afc residue in position 2: Z-X(1)-Afc(2)-Y(3)-OMe (peptide a: X = Y = Gly; peptide b: X = Aib, C(alpha, alpha)-dimethylglycine, Y = Gly; peptide c: X = Gly, Y = Aib; peptide d: X = Y = Aib) have been solved by x-ray crystallography. All the results suggest that the Afc residue has a high propensity to assume an extended conformation. In fact, the Afc residue adopts an extended conformation in three peptides examined in this paper (peptides a-c). In contrast, Afc was found in a folded conformation, in the 3(10)-helical region, only in the peptide d, in which it is both preceded and followed by the strong helix promoting Aib.

Mixed conformation in C alpha, alpha-disubstituted tripeptides: x-ray crystal structures of Z-Aib-Dph-Gly-OMe and Bz-Dph-Dph-Gly-OMe

We report here the synthesis and molecular structure in the solid state of fully protected tripeptides containing C alpha, alpha-diphenylglycine (Dph), namely Z-Aib-Dph-Gly-OMe (Aib: C alpha, alpha-dimethylglycine) and Bz-Dph-Dph-Gly-OMe. The molecular conformation around the Dph residue, containing two bulky substituents, is fully extended, while the Aib residue, containing two smaller groups on the C alpha atom, adopts the typical 3(10)/alpha-helical conformation. Gly residues, without substituents on the C alpha atom, show different conformational preferences. Each residue seems to behave, from a conformational point of view, independently from the presence of the other residues, and thus mixed local conformations (folded and extended) are present in the crystals. The nonconventional peptide synthesis, using the Ugi reaction, is also reported.