ω-amino acids in peptide design. Crystal structures and solution conformations of peptide helices containing a β-alanyl-γ-aminobutyryl segment

Abstract

Insertion of achiral ω-amino acids into peptide sequences results in replacement of scissile peptide bonds by proteolytically stable C-C bonds. This provides a convenient means of creating peptidomimetics. The present study establishes the preservation of helical structures in octa- and undecapeptides with centrally located β- and γ-amino acids in the sequence. X-ray diffraction analyses of single crystals and NMR studies have been used to investigate the extent of perturbations of a regular 3₁₀- or α-helix by the introduction of (-CH₂-)_n groups into the backbone by the use of the β-Ala-γ-Abu segment (β-Ala = β-alanine, γ-Abu = γ-aminobutyric acid), which is formally homomorphous with a (Gly)₃ segment. In crystals, the octapeptide Boc-Leu-Aib-Val-β-Ala-γ-Abu-Leu-Aib-Val-OMe (1) and the undecapeptide Boc-Leu-Aib-Val-β-Ala-γ-Abu-Leu-Aib-Val-Ala-Leu-Aib-OMe (2) retain their helical motifs with minor bulges. Five new types of 4 → 1, 5 → 1, and 6 → 1 hydrogen bond rings are formed with up to three extra CH₂ moieties. Cell parameters for peptide 1 are space group P2₁2₁2₁ with a = 11.506 (1) Å, b = 16.600 (1) Å, c = 27.362(1) Å, and R = 6.1% for 2696 data measured >4σ(F); for the undecapeptide 2, the space group is P2₁ with a = 8.605 (3) Å, b = 22.806 (4) Å, c = 19.014 (3) Å, β = 101.47(2)°, and R = 7.5% for 3797 data measured >4σ(F). Helical conformations in solution are also maintained for peptide 2 as is evident from NMR studies in CDCl₃, which suggest that the centrally positioned, flexible β-Ala-γ-Abu segment can be comfortably accommodated into helical structures adopting gauche conformations about specific C-C bonds of the poly(methylene) units. Twenty structures for backbone conformations generated from MD simulations using NMR-derived contraints, superpose with a low RMSD value (0.78 ± 0.05 Å), further indicating that in these peptides the conformational flexibility of the β-Ala-γ-Abu segment is limited and confined to largely helical conformations.