Synthesis and conformational studies of peptides from new C-linked carbo-beta-amino acids (beta-Caas) with anomeric methylamino- and difluorophenyl moieties.

New C-linked carbo-beta-amino acids (beta-Caas), Cbz-(S)-beta-Caa-(NHBoc)-OMe (1) and Cbz-(R)-beta-Caa-(NHBoc)-OMe (2), with an additional amine group (methylamino group of NHBoc) at the C-1 position of the lyxofuranoside side chain and Boc-(S)-beta-Caa-(diFP)-OMe (3) and Boc-(R)-beta-Caa-(diFP)-OMe (4), with a C-difluorophenyl (diFP) moiety at the anomeric position of the lyxofuranoside side chain were prepared from D-mannose. Beta-peptides [tetra- and hexapeptides] were synthesized from these beta-Caas, 'epimeric' [at the amine stereocentre (C(beta))], using the concept of 'alternating chirality' to carry out their conformational studies [NMR (CDCl(3)), CD and MD]. In the monomer design, it was envisaged that the presence of an additional amine group in 1 or 2 would help in solubilizing the peptides in water, while, the C-difluorophenyl (diFP) moiety of 3 and 4 is expected to enhance the biological activity. The peptides having 1 and 2, though could not retain their 12-10-mixed helices in water, have shown moderate activity against gram positive and gram negative bacterial strains. The peptides prepared from 3 and 4, much against our expectations, did not display any biological activity.

Positive and negative ion electrospray tandem mass spectrometry (ESI MS/MS) of Boc-protected peptides containing repeats of L-Ala-gamma4Caa/gamma4Caa-L-Ala: differentiation of some positional isomeric peptides.

High-resolution electrospray ionization (ESI) quadrupole time-of-flight and ion trap tandem mass spectrometry has been used to distinguish the positional isomers of a new class of N-blocked hybrid peptides containing repeats of the amino acids, L-Ala-gamma(4)Caa ((l))/gamma(4)Caa((l))-L-Ala [Caa((l)) = Carbo (lyxose) amino acid, derived from D-mannose]. Both MS/MS and MS(3) of protonated isomeric peptides produce characteristic fragmentation involving the peptide backbone, Boc-group, and the side-chain. It is interesting to observe that the abundant y(n)(+) ions are formed when the corresponding amide -NH does not participate in the helical structures in solution phase and relatively low abundance y(n)(+) ions resulted when the amide -NH involves in the H-bonding. Thus, it was possible to identify the amide -NH hydrogens that participate in the helical structures through H-bonding in solution phase. Further, negative ion ESI MS/MS has also been found to be useful for differentiating these isomeric peptide acids.

12/10- and 11/13-mixed helices in alpha/gamma- and beta/gamma-hybrid peptides containing C-linked carbo-gamma-amino acids with alternating alpha- and beta-amino acids.

New classes of alpha/gamma- and beta/gamma-hybrid peptides have been synthesized with novel 12/10- and 11/13-mixed helical patterns, respectively. The alpha/gamma-peptides were derived from the dipeptide repeats with alternating arrays of l-Ala and gamma-Caa((l)) (C-linked carbo-gamma-amino acid from d-mannose), which generated a new 12/10-mixed helix, for the first time, without a beta-amino acid. The beta/gamma-peptides made from an alternating arrangement of beta-Caa((x)) (C-linked carbo-beta-amino acid) and gamma-Caa((x)) (C-linked carbo-gamma-amino acid from d-xylose), on the other hand, resulted in an unprecedented 11/13-helix. The secondary structures in these peptides have been ascertained from detailed NMR studies, and CD spectroscopy and molecular dynamics investigations provided additional support for the structures derived.