Phenylisoserine: a versatile amino acid for the construction of novel beta-peptide structures

Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides

Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.

Assignment of Vibrational Circular Dichroism Cross-Referenced Electronic Circular Dichroism Spectra of Flexible Foldamer Building Blocks: Towards Assigning Pure Chiroptical Properties of Foldamers

Assignment of the most established electronic circular dichroism (ECD) spectra of polypeptides and foldamers is either “evidence based” or relies on the 3D structures of longer oligomers of limited internal dynamics, which are derived from NMR spectroscopy (or X‐ray) data. Critics warn that the use of NMR spectroscopy and ECD side by side has severe limitations for flexible molecules because explicit knowledge of conformational ensembles is a challenge. Herein, an old–new method of comparing ab initio computed and measured vibrational circular dichroism (VCD) data is presented to validate both the structures (conf(i)) and their relative weights (c(i)) that make up the conformational ensemble. Based on the array of {conf(i), c(i)}, the pure ECD spectra, g(i)^conf(i), can be ab initio calculated. The reconstructed spectrum Σc(i)g(i)^conf(i) can thus help to assign any experimental ECD counterparts. Herein, such a protocol is successfully applied to flexible foldamer building blocks of sugar β‐amino acid diamides. The epimeric pair of the model system was selected because these molecules were conformationally tunable by simple chemical modification, and thus, the robustness of the current approach could be probed. The initial hydrogen bond (NH⋅⋅⋅O) eliminated by N‐methylation reorients the amide plain, which influences the chiroptical properties of the foldamer building block; this structural change is successfully monitored by changes to the VCD and ECD transitions, which are now assigned to pure conformers. The current method seems to be general and effective without requiring extensive CPU and spectroscopic resources.

Cooperative 5- and 10-membered ring interactions in the 10-helix folding of oxetin homo-oligomers

Homo-oligomers of the natural product oxetin (cis-3-amino-2-oxetanecarboxylic acid) were prepared and their conformational behaviour studied in solution and solid state and by molecular modelling. The predominant secondary structure was a 10-helix, propiciously stabilized by a network of 5-membered ring H-bonds implicating ring oxygens and neighboring amide hydrogen atoms.

Toward an ab initio potential energy surface for paclitaxel: A C-13 isoserine side chain conformational study

(S)-3-Methyl-3-butenyl-(2R,3S)-N-benzoyl-3-phenylisoserinate is used as a model of the C-13 side chain, an essential subunit for the cytotoxicity of the diterpenoid paclitaxel, a chemotherapeutic drug used in the treatment of cancer. The potential energy surface (PES), calculated using a density functional theory method (DFT) and refined with MP2 single-point energy calculations, based on B3LYP geometries, was evaluated. Twelve intramolecular hydrogen bond patterns were identified for 103 in vacuo conformers. The most stable subset of these structures was found to have cooperative NH ⋯ OH ⋯ OC(O) motifs and six minima of importance that lie within 1.2kcal/mol of each other. The oxygen atoms of the ester groups effectively compete with the 2'-oxygen as a proton acceptor of NH to form stable internal hydrogen bonded structures. Additionally, the conventional OH ⋯ OC(N) hydrogen bond, which is represented by almost one third of the located minima, donates a number of stable conformers. However, the PES of the conformationally flexible model is highly dependent on the polarity of the environment. For example, the OH ⋯ OC(N) feature dominates over the cooperative motif in water. The side chain of the experimental T-taxol shaped structure agrees nicely with the respective theoretical lowest energy minimum. The π-π interactions of the phenyl rings and ethylene moiety of this structure are also discussed.

Synthesis and conformational studies of α/β2,3-peptides derived from alternating β2,3-amino acids and l-Ala repeats

A new class of α/β^2,3-peptides were synthesized from C-linked carbo-β^2,3-amino acids (β^2,3-Caas) and investigated to understand the impact of the side chains (allyl/propargyl) at the Cα-position on their conformations.

Synthesis and conformational analysis of cyclic homooligomers from pyranoid ε-sugar amino acids

New pyranoid ε-sugar amino acids were designed as building blocks, in which the carboxylic acid and the amine groups were placed in positions C2 and C3 with respect to the tetrahydropyran oxygen atom. By using standard solution-phase coupling procedures, cyclic homooligomers containing pyranoid ε-sugar amino acids were synthesized. Conformation analysis was performed by using NMR spectroscopic experiments, FTIR spectroscopic studies, X-ray analysis, and a theoretical conformation search. These studies reveal that the presence of a methoxy group in the position C4 of the pyran ring produces an important structural change in the cyclodipeptides. When the methoxy groups are present, the structure collapses through interresidue hydrogen bonds between the oxygen atoms of the pyran ring and the amide protons. However, when the cyclodipeptide lacks the methoxy groups, a U-shape structure is adopted, in which there is a hydrophilic concave face with four oxygen atoms and two amide protons directed toward the center of the cavity. Additionally, we found important evidence of the key role played by weak electrostatic interactions, such as the five-membered hydrogen-bonded pseudocycles (C5) between the amide protons and the ether oxygen atoms, in the conformation equilibrium of the macrocycles and in the cyclization step of the cyclic tetrapeptides.

ESTIMATION ON THE INTRAMOLECULAR 8- AND 12-MEMBERED RING N–H…O=C HYDROGEN BONDING ENERGIES IN β-PEPTIDES

Computation of accurate hydrogen bonding energies in peptides is of great importance in understanding the conformational stabilities of peptides. In this paper, the intramolecular 8- and 12-membered ring N – H … O = C hydrogen bonding energies in β-peptide structures were evaluated. The optimal structures of the β-peptide conformers were obtained using MP2/6-31G(d) method. The MP2/6-311++G(d,p) calculations were then carried out to evaluate the single-point energies. The results show that the intramolecular 8-membered ring N – H … O = C hydrogen bonding energies in the five β-dipeptide structures β-di, β-di-R1, β-di-R2, β-di-R3, and β-di-R4 are -5.50, -5.40, -7.28, -4.94, and -6.84 kcal/mol with BSSE correction, respectively; the intramolecular 12-membered ring N – H … O = C hydrogen bonding energies in the nine β-tripeptide structures β-tri, β-tri-R1, β-tri-R2, β-tri-R3, β-tri-R4, β-tri-R1', β-tri-R2', β-tri-R3' and β-tri-R4' are -10.23, -10.32, -9.53, -10.30, -10.32, -10.55, -10.09, -10.51, and -9.60 kcal/mol with BSSE correction, respectively. Our calculation results further indicate that for the intramolecular 8-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "a–a" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "e–e", while for the intramolecular 12-membered ring hydrogen bondings, the structures where the orientation of the side chain methyl group is "e–e" have stronger intramolecular hydrogen bondings than those where the orientation of the side chain methyl group is "a–a". The method is also applied to estimate the individual intermolecular hydrogen bonding energies in the dimers of amino-acetaldehyde, 2-amino-acetamide, 2-oxo-acetamide, and oxalamide, each dimer having two identical intermolecular hydrogen bonds. According to our method, the individual intermolecular hydrogen bonding energies in the four dimers are calculated to be -1.71, -1.50, -4.67, and -3.22 kcal/mol at the MP2/6-311++G(d,p) level, which are in good agreement with the values of -1.84, -1.72, -4.93, and -3.26 kcal/mol predicted by the supermolecular method.

Phenylisoserine in the gas-phase and water: Ab initio studies on neutral and zwitterion conformers

The conformational landscape of phenylisoserine (PhIS) was studied. Trial structures were generated by allowing for all combinations of single-bond rotamers. Based on the B3LYP/aug-cc-pVDZ calculations 54 conformers were found to be stable in the gas phase. The six most stable conformers were further optimized at the B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVDZ levels for which characteristic intramolecular hydrogen bond types were classified. To estimate the influence of water on PhIS conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 51 neutral and six zwitterionic conformers to be stable in water solution. According to DFT calculations, the conformer equilibrium in the gas phase is dominated by one conformer, whereas the MP2 calculations suggest three PhIS structures to be significantly populated. Comparison of DFT and MP2 energies of all 57 structures stable in water indicates that, in practice, one zwitterionic and one neutral conformer determine the equilibrium in water. Based on the AIM calculations, we found that for the neutral conformers in vacuum and in water, d(H...B) is linearly correlated with Laplacian at the H-bond critical point.

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Toward a rational design of beta-peptide structures

Intrinsic conformational characteristics of beta-peptides built up from simple achiral and chiral beta-amino acid residues (i.e., HCO-beta-Ala-NH2, HCO-beta-Abu-NH2) were studied using quantum chemical calculations and 1H-NMR spectroscopy. A conformer-based systematic and uniform nomenclature was introduced to differentiate conformers. Geometry optimizations were performed on all homoconformers of both HCO-(beta-Ala)(k)-NH2 and HCO-(beta-Abu)(k)-NH2 (1 < or = k < or = 6) model systems at the RHF/3-21G and RHF/6-311++G(d, p) levels of theory. To test for accuracy and precision, additional computations were carried out at several levels of theory [e.g., RHF/6-31G(d), and B3LYP/6-311++G(d, p)]. To display the folding preference, the relative stability of selected conformers as function of the length of the polypeptide chain was determined. Ab initio population distribution of hexapeptides and the conformational ensemble of synthetic models composed of beta-Ala and beta-Abu studied using 1H-NMR in different solvents were compared at a range of temperatures. Helical preference induced by various steric effects of nonpolar side chains was tested using higher level ab initio methods for well-known model systems such as: HCO-(beta-HVal-beta-HAla-beta-HLeu)2-NH2, HCO-(ACHC)6-NH2, HCO-(trans-ACPC)6-NH2, and HCO-(cis-ACPC)6-NH2. The relative stabilities determined by theoretical methods agreed well with most experimental data, supporting the theory that the local conformational preference influenced by steric effects is a key determining factor of the global fold both in solution and in the gas phase.

Control of Helix Formation in Vinylogous γ-Peptides by (E)- and (Z)-Double Bonds: A Way to Ion Channels and Monomolecular Nanotubes

[structure: see text] A complete overview on the alternative and competitive helices in vinylogous gamma-peptides is given, which was obtained on the basis of a systematic conformational analysis at various levels of ab initio MO theory (HF/6-31G*, DFT/B3LYP/6-31G*, PCM/HF/6-31G*). Contrary to the parent gamma-peptides, there is a strict control of helix formation by the configuration of the double bond between the C(alpha) and C(beta) atoms of the monomer constituents. (E)-Double bonds favor helices with larger pseudocycles beginning with 14- up to 27-membered hydrogen-bonded rings, whereas the (Z)-configuration of the double bonds supports a distinct preference of helices with smaller seven- and nine-membered pseudocycles showing interactions between nearest-neighbor peptide bonds. The rather stable helices of the (E)-vinylogous peptides with 22-, 24-, and 27-membered hydrogen-bonded pseudocycles have inner diameters large enough to let molecules or ions pass. Thus, they could be interesting model compounds for the design of membrane channels and monomolecular nanotubes. Since (E)- and (Z)-vinylogous gamma-amino acids and their oligomers are synthetically accessible, our study may stimulate structure research in this novel field of foldamers.

δ-Peptides and δ-Amino Acids as Tools for Peptide Structure DesignA Theoretical Study

An overview on all possible helix types in oligomers of delta-amino acids (delta-peptides) and their stabilities is given on the basis of a systematic conformational analysis employing various methods of ab initio MO theory (HF/6-31G*, B3LYP/6-31G*, PCM//HF/6-31G*). A wide variety of novel helical structures with hydrogen-bonded pseudocycles of different size are predicted. Since a delta-amino acid constituent may replace a dipeptide unit in alpha-peptides, there are close relationships between the secondary structures of peptides with delta-amino acid residues and typical secondary structures of alpha-peptides. However, the preference of gauche conformations at the central C(beta)-C(gamma) bonds of delta-amino acids, which correspond to the peptide linkages in alpha-peptides, over staggered ones makes completely novel structure alternatives for helices and turns more probable. The peculiarities of beta-turn formation by sugar amino acids derived from delta-amino acids are compared with the turn formation in delta-amino acid residues and in alpha-peptides. The considerable potential of secondary structure formation in delta-peptides and single delta-amino acid constituents predicted by ab initio MO theory may stimulate experimental work in the field of peptide and foldamer design.

Stereoselective Iodocyclization of 3-Acylamino-2-methylene Alkanoates: Synthesis of Analogues of N-Benzoyl-syn-phenylisoserine

[reaction: see text] A convenient approach to racemic analogues of N-benzoyl-syn-phenylisoserine was realized via the stereoselective iodocyclization of amides obtained from Baylis-Hillman adducts.

A New Class of Foldamers Based on cis-γ-Amino-l-proline1,2

A synthetic method for the preparation of conformationally constrained gamma-peptides derived from gamma-amino-L-proline is described. The methodology allows the independent buildup of the peptide backbone and the introduction of sequential variations by reactions with the alpha-amino group of gamma-aminoproline. Both alkyl- and acyl-substituted gamma-peptides have been prepared and studied by CD and NMR. Conformational restrictions due to the cyclic structure of the monomer give rise to long-range interactions that are indicative of secondary structures even in aqueous solution. Interresidue NOEs suggest a concatenation of turns that, in a permissive solvent, could give rise to an isolated hydrogen bond ribbon, flanked and protected by proline rings.