Foldamers Derived From Nucleoside β-Amino Acids: Pna Or Dna? Can We Have Both In One Place?

The synthesis of a modified thymidine (nucleoside β-amino acid) monomer and preliminary investigations into the solid phase peptide synthesis of PNA/DNA chimeras containing a neutral, internucleoside amide linkage are described.     

Glycosylated foldamers: synthesis of carbohydrate-modified beta3hSer and incorporation into beta-peptides.

Fmoc-protected beta(3)hserine (beta(3)hSer) was prepared and O-linked to suitably protected N-acetylgalactosamine (GalNAc) and N-acetylglucosamine (GlcNAc) derivatives. Glycosylation of beta(3)hSer was made by two independent routes: either by direct glycosyl linkage to the beta(3)hSer, or linkage to natural L-Ser and then utilizing the carbohydrate moiety as a protecting group in an Arndt-Eistert homologation. Both procedures gave the novel glycosylated beta(3)-amino acids Fmoc-beta(3)hSer(alpha-D-GalNAc(Ac)(3))-OH (1a), its beta-anomer (1b), and Fmoc-beta(3)hSer(beta-D-GlcNAc(Ac)(3))-OH (2), which were utilized in the solid-phase peptide synthesis of four glycosylated dipeptides (3a-d) and two heptapeptides (4a-b). The preparation of beta-amino acids bearing common post-translational modifiers represents an important step towards functionalized foldamers with broad applications in biomedical research.     

Computationally designed β‐turn foldamers of γ‐peptides based on 2‐(aminomethyl)cyclohexanecarboxylic acid

The γ‐peptide β‐turn structures have been designed computationally by the combination of chirospecific γ 2 , 3 ‐residues of 2‐(aminomethyl)cyclohexanecarboxylic acid (γAmc₆) with a cyclohexyl constraint on the C^α?C^β bond using density functional methods in water. The chirospecific γAmc₆ dipeptide with the (2S,3S)‐(2R,3R) configurations forms a stable turn structure in water, resembling a type II′ turn of α‐peptides, which can be used as a β‐turn motif in β‐hairpins of Ala‐based α‐peptides. The γAmc₆ dipeptide with homochiral (2S,3S)‐(2S,3S) configurations but different cyclohexyl puckerings shows the capability to be incorporated into one of two β‐turn motifs of gramicidin S. The overall structure of this gramicidin S analogue is quite similar to the native gramicidin S with the same patterns and geometries of hydrogen bonds. Our calculated results and the recently observed results may imply the wider applicability of chirospecific γ‐peptides with a cyclohexyl constraint on the backbone to form various peptide foldamers. © 2012 Wiley Periodicals, Inc. Biopolymers 97:1018–1025, 2012.     

Influence of substituents on conformational preferences of helix foldamers of γ‐dipeptides

Conformational preferences of 9‐ and 14‐helix foldamers have been studied for γ‐dipeptides of 2‐aminocyclohexylacetic acid (γAc₆a) residues such as Ac‐(γAc₆a)₂‐NHMe ( 1 ), Ac‐(C^α‐Et‐γAc₆a)₂‐NHMe ( 2 ), Ac‐(γAc₆a)₂‐NHBn ( 3 ), and Ac‐(C^α‐Et‐γAc₆a)₂‐NHBn ( 4 ) at the M06‐2X/cc‐pVTZ//M06‐2X/6‐31 + G(d) level of theory to explore the influence of substituents on their conformational preferences. In the gas phase, the 9‐helix foldamer H9 and 14‐helix foldamer H14‐z are found to be most preferred for dipeptides 2 and 4 , respectively, as for dipeptides 1 and 3 , which indicates no remarkable influence of the C^α‐ethyl substitution on conformational preferences. The benzyl substitution at the C‐terminal end lead H14‐z to be the most preferred conformer for dipeptides 3 and 4 , whereas it is H9 for dipeptides 1 and 2 , which can be ascribed to the favored C? H···π interactions between the cyclohexyl group of the first residue and the C‐terminal benzyl group. There are only marginal changes in backbone structures and the distances and angles of H‐bonds for all local minima by C^α‐ethyl and/or benzyl substitutions. Although vibrational frequencies and intensities of the dipeptide 4 calculated at both M06‐2X/6‐31 + G(d) and M05‐2X/6‐31 + G(d) levels of theory are consistent with observed results in the gas phase, H14‐z is predicted to be most preferred by ΔG only at the former level of theory. Hydration did not bring the significant changes in backbone structures of helix foldamers for both dipeptide 1 and 4 . It is expected that the different substitutions at the C‐terminal end lead to the different helix foldamers, which may increase the resistance of helical structures to proteolysis and provide the more surface to the helical structures suitable for molecular recognition. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 1077–1087, 2014.     

Conformational preferences of helix foldamers of γ‐peptides based on 2‐(aminomethyl)cyclohexanecarboxylic acid

The conformational preferences of helix foldamers having different sizes of the H‐bonded pseudocycles have been studied for di‐ to octa‐γ^2,3‐peptides based on 2‐(aminomethyl)cyclohexanecarboxylic acid (γAmc₆) with a cyclohexyl constraint on the C^α–C^β bond using density functional methods. The helical structures of the γAmc₆ oligopeptides with homochiral configurations are known to be much stable than those with heterochiral configurations in the gas phase and in solution (chloroform and water). In particular, it is found that the (P/M)?2.5₁₄‐helices are most preferred in the gas phase and in chloroform, whereas the (P/M)?2.3₁₂‐helices become most populated in water due to the larger helix dipole moments. As the peptide sequence becomes longer, the helix propensities of 14‐ and 12‐helices are found to increase both in the gas phase and in solution. The γAmc₆ peptides longer than octapeptide are expected to exist as a mixture of 12‐ and 14‐helices with the similar populations in water. The mean backbone torsion angles and helical parameters of the 14‐helix foldamers of γAmc₆ oligopeptides are quite similar to those of 2‐aminocyclohexylacetic acid oligopeptides and γ^2,3,4‐aminobutyric acid tetrapeptide in the solid state, despite the different substituents on the backbone. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 87–95, 2014.