The twists and turns of beta-peptides

Conformational analysis of furanoid epsilon-sugar amino acid containing cyclic peptides by NMR spectroscopy, molecular dynamics simulation, and X-ray crystallography: evidence for a novel turn structure

Sugar amino acids (SAAs) are useful building blocks for the design of peptidomimetics and peptide scaffolds. The three-dimensional structures of cyclic hybrid molecules containing the furanoid epsilon-SAA III and several amino acids were elucidated to study the preferred conformation of such an epsilon-SAA and its conformational influence on the backbone of cyclic peptides. NMR-based molecular dynamics simulations and empirical calculations of the cyclic tetramer 1, consisting of two copies of the SAA residue and two amino acids, revealed that it is conformationally restrained. The two SAA residues adopt different conformations. One of them forms an unusual turn, stabilized by an intraresidue nine-member hydrogen bond. The methylene functionalities of the other SAA residue are positioned in such a way that an intraresidue H bond is not possible. The X-ray crystal structure of 1 strongly resembles the solution conformation. Molecular dynamics calculations in combination with NMR analysis were also performed for compounds 2 and 3, which contain the RGD (Arg-Gly-Asp) consensus sequence and were previously shown to inhibit alpha(IIb)beta(3)-receptor-mediated platelet aggregation. The biologically most active compound 2 adopts a preferred conformation with the single SAA residue folded into the nine-member H bond-containing turn. Compound 3, containing an additional valine residue, as compared with compound 2, is conformational flexible. Our studies demonstrate that the furanoid epsilon-SAA III is able to introduce an unusual intraresidue hydrogen bond-stabilized beta-turn-like conformation in two of the three cyclic structures.

Side-chain control of beta-peptide secondary structures

As one of the most important families of non-natural polymers with the propensity to form well-defined secondary structures, the beta-peptides are attracting increasing attention. The compounds incorporating beta-amino acid residues have found various applications in medicinal chemistry and biochemistry. The conformational pool of beta-peptides comprises several periodic folded conformations, which can be classified as helices, and nonpolar and polar strands. The latter two are prone to form pleated sheets. The numerous studies that have been performed on the side-chain dependence of the stability of the folded structures allow certain conclusions concerning the principles of design of the beta-peptide foldamers. The folding propensity is influenced by local torsional, side-chain to backbone and long-range side-chain interactions. Although beta-peptide foldamers are sensitive to solvent, the systematic choice of the side-chain pattern and spatiality allows the design of the desired specific secondary structure. The application of beta-peptide foldamers may open up new directions in the synthesis of highly organized artificial tertiary structures with biochemical functions.

Simple and stereospecific homologation of urethane-protected alpha-amino acids to their higher homologs using HBTU

A simple, efficient and stereospecific approach for the homologation of urethane-protected alpha-amino acids to beta-amino acids by the Arndt-Eistert method employing Fmoc-/Boc-alpha-amino acid and 2-(1H-benzotriazole-1-yl)-1,1,3,3-tetramethyl-uronium hexafluorophosphate mixture for the acylation of diazomethane synthesizing the key intermediates Fmoc-/Boc-alpha-aminodiazomethanes as crystalline solids is described.

Structural and biological effects of a beta2- or beta3-amino acid insertion in a peptide

Molecular mechanics calculations on conformers of Ac-HGly-NHMe, Ac-beta2-HAla-NHMe and Ac-beta3-HAla-NHMe indicate that low-energy conformations of the beta-amino acids backbone, corresponding to gauche rotamers around the Calpha-Cbeta bond, may overlap canonical backbone conformers observed for alpha-amino acids. Therefore, Substance P (SP) was used as a model peptide to analyse the structural and biological consequences of the substitution of Phe7 and Phe8 by (R)-beta2-HPhe and of Gly9 by HGly (R)-beta2-HAla or (S)-beta3-HAla. [(R)-beta2-HAla9]SP has pharmacological potency similar to that of SP while [HGly9]SP and [(S)-beta3-HAla9]SP show a 30- to 50-fold decrease in biological activities. The three analogues modified at position 9 are more resistant to degradation by angiotensin converting enzyme than SP and [Ala9]SP. NMR analysis of these SP analogues suggest that a beta-amino acid insertion in position 9 does not affect the overall backbone conformation. Altogether these data suggest that [HGly9]SP, [(S)-beta3-HAla9]SP and [(R)-beta2-HAla9]SP could adopt backbone conformations similar to that of SP, [Ala9]SP and [Pro9]SP. In contrast, incorporation of beta2-HPhe in position 7 and 8 of SP led to peptides that are almost devoid of biological activity. Thus, a beta-amino acid could replace an alpha-amino acid within the sequence of a bioactive peptide provided that the additional methylene group does not cause steric hindrance and does not confine orientations of the side chain to regions of space different from those permitted in the alpha-amino acid.

Efficient synthesis of enantiomerically pure beta2-amino acids via chiral isoxazolidinones

We report a practical and scalable synthetic route for the preparation of alpha-substituted beta-amino acids (beta(2)-amino acids). Michael addition of a chiral hydroxylamine, derived from alpha-methylbenzylamine, to an alpha-alkylacrylate followed by cyclization gives a diastereomeric mixture of alpha-substituted isoxazolidinones. These diastereomers are separable by column chromatography. Subsequent hydrogenation of the purified isoxazolidinones followed by Fmoc protection affords enantiomerically pure Fmoc-beta(2)-amino acids, which are useful for beta-peptide synthesis. This route provides access to both enantiomers of a protected beta(2)-amino acid.

Design and synthesis of a beta-amino phosphotyrosyl mimetic suitably protected for peptide synthesis

Mimetics of phosphotyrosine (pTyr) such as phosphonomethylphenylalanine (Pmp) have traditionally retained alpha-amino functionality. However, beta-amino acids represent isomeric variants, which may exhibit properties that are distinct from the parent. Reported herein is the first beta-amino pTyr mimetic (Pmp(beta)) bearing protection suitable for peptide synthesis. Preparation of Pmp(beta) was accomplished enantioselectively in 43% overall yield from commercially available 4-vinylbenzyl chloride.

Theoretical study of sheets formed by beta-peptides

Structural and thermodynamic features of the sheets formed by beta-peptides have been studied by quantum mechanics calculations using peptide models. Calculations using dipeptide models indicate that the intrinsic hydrogen bond strength is great for both parallel and antiparallel sheets and that it is little affected by proper substituents. Heterochiral-beta(2,3)-peptides have much stronger sheet-forming propensity than other types of peptides because their favored backbone conformation is ideal for sheet formation. A planar or ideally pleated strand has a curved geometry, which is unfavorable for the formation of sheets. Thus, sheets have to adopt twisted geometries. There is a large cooperativity in the formation of the hydrogen bond network in the sheets of beta-peptides in the perpendicular direction due to long-range electrostatic attractions because all carbonyl groups are roughly in the same direction, in contrast to the situation in beta-sheets of alpha-peptides.

Mimicry of bioactive peptides via non-natural, sequence-specific peptidomimetic oligomers

Non-natural, sequence-specific peptidomimetic oligomers are being designed to mimic bioactive peptides, with potential therapeutic application. Cationic, facially amphipathic helical beta-peptide oligomers have been developed as magainin mimetics. Non-natural mimics of HIV-Tat protein, lung surfactant proteins, collagen, and somatostatin are also being developed. Pseudo-tertiary structure in beta-peptides and peptoids may herald the creation of entirely artificial proteins.

Gamma2-, gamma3-, and gamma(2,3,4)-amino acids, coupling to gamma-hexapeptides: CD spectra, NMR solution and X-ray crystal structures of gamma-peptides

There are numerous possible gamma-amino acids with different degrees of substitution and with various constitutions and configurations. Of these the gamma4- and the like- and unlike-gamma(2,4)-amino acids have been previously used as building blocks in gamma-peptides. The synthesis of gamma2-, gamma3-, and gamma(2,3,4)-peptides is now described. The corresponding amino acids have been prepared by Michael addition of chiral N-acyl-oxazolidinone enolates to nitro-olefins, with subsequent reduction of the NO2 to NH2 groups. Such additions to E-2-methyl-nitropropene provide (2R,3R,4R)-2-alkyl-3-methyl-4-amino-pentanoic acid derivatives (9, 10, 11). Stepwise coupling and fragment coupling lead to gamma-di-, tri-, and hexapeptides (12-23), which were fully characterized. The crystal structures of one of the gamma-amino acids (2,3-dimethyl-4-amino-pentanoic acid x HCl, 9a), of a gamma(2,3,4)-di- and a gamma(2,3,4)-tetrapeptide (20, 22) are described, and the NMR solution structure in MeOH of a gamma(2,3,4)-hexapeptide (3) has been determined (using TOCSY, COSY, HSOC, HMBC and ROESY measurements and a molecular dynamics simulated-annealing protocol). A linear conformation (sheet-like), a novel (M) helix built of nine-membered hydrogen-bonded rings, and (M) 2.6(14) helices have thus been identified. NMR measurements at different temperatures (298-393 K) and H/D-exchange rates obtained for the gamma(2,3,4)-hexapeptide are interpreted as evidence for the stability of the 2.6(14) helix (no "melting") and for its non-cooperative folding mechanism. CD Spectra of the gamma-peptides have been measured in MeOH and CH3CN, indicating that only the protected and unprotected gamma(2,3,4)-hexapeptide is present as the 2.6(14) helix in solution. The structures of the gamma2- and gamma3-hexapeptides (1, 2) could not be determined.

Toward beta-peptide tertiary structure: self-association of an amphiphilic 14-helix in aqueous solution

A major frontier in foldamer research is creation of unnatural oligomers that adopt discrete tertiary structures; at present, only biopolymers are known to fold into such compact conformations. We report an initial step toward helix-bundle tertiary structure in the beta-peptide realm by showing that a 10-residue beta-peptide designed to adopt an amphiphilic helical conformation forms small soluble aggregates in water. Sedimentation equilibrium data indicate that the aggregated state falls in the tetramer-hexamer size range. [structure: see text]

Urethane N-carboxyanhydrides from beta-amino acids

A general method has been developed for the synthesis of N-tert-butyloxycarbonyl N-carboxyanhydrides from beta-amino acids using Vilsmeier complex. These beta-UNCA are stable, and the reactivity with different nucleophiles (alcohol, amine, lithium enolate) was studied.

Influence of hydrophobic interactions on the conformational adaptability of the beta-Ala residue

The chemical synthesis and X-ray crystal structure analysis of a model peptide incorporating a conformationally flexible beta-Ala residue: Boc-beta-Ala-Pda, 1 (C23H46N2O3: molecular weight = 398.62) have been described. The peptide crystallized in the crystal system triclinic with space group P21: a = 5.116(3) A, b = 5.6770(10) A, c = 21.744(5) A; alpha = 87.45 degrees, beta = 86.87 degrees, gamma = 90.0 degrees; Z = 1. An attractive feature of the crystal molecular structure of 1 is the induction of a reasonably extended backbone conformation of the beta-Ala moiety, i.e. the torsion angles phi approximately -115 degrees, mu approximately 173 degrees and psi approximately 122 degrees, correspond to skew-, trans and skew+ conformation, respectively, by an unbranched hydrophobic alkyl chain, Pda, which prefers an all-anti orientation (theta1 approximately -153 degrees, theta2 approximately ellipsis theta14 approximately +/-178 degrees ). The observation is remarkable because, systematic conformational investigations of short linear beta-Ala peptides of the type Boc-beta-Ala-Xaa-OCH3 (Xaa = Aib or Acc6) have shown that the chemical and stereochemical characters of the neighboring moieties may be critical in dictating the overall folded and/or unfolded conformational features of the beta-Ala residue. The overall conformation of 1 is typical of a 'bar'. It appears convincing that, in addition to a number of hydrophobic contacts between the parallel arranged molecules, an array of conventional N-HellipsisO=C intermolecular H-bonding interactions stabilize the crystal molecular structure. Moreover, the resulting 14-membered pseudo-ring motif, generated by the amide-amide interactions between the adjacent molecules, is completely devoid of nonconventional C-HellipsisO interaction. The potentials of the conformational adaptation of the beta-Ala residue, to influence and stabilize different structural characteristics have been highlighted.

Hydrazino peptides as foldamers: an extension of the beta-peptide concept

Replacing the C(beta) atoms in the beta-amino acid constituents of beta-peptides by nitrogen atoms leads to hydrazino peptides. A systematic conformation analysis of blocked hydrazino peptide oligomers of the general type I at the HF/6-31G, MP2/6-31G, and DFT/B3LYP/6-31G levels of ab initio MO theory and on the basis of molecular mechanics reveals a wide variety of secondary structures, as for instance various helices and sheet- and turnlike conformers. Some of them are closely related to secondary structure types found in beta-peptides; others represent novel types. Thus, a very stable, novel helix with 14-membered hydrogen-bonded pseudocycles, which occupies a conformation space different from that of helices with 14-membered rings found among the most stable conformers in beta-peptides, is indicated. The most important secondary structure elements are characterized by interactions between peptidic NH and CO groups. The additional hydrazino N(alpha)H group takes part in special structuring effects but is of lesser importance for secondary structure formation. The influence of environmental effects on the existence and stability of the various structure types is discussed. Due to the wide variety of structural possibilities, hydrazino peptides might be a useful tool for peptide and protein design.

Synthesis of (3R)-carboxy pyrrolidine (a beta-proline analogue) and its oligomer

A decamer of a beta-amino acid analogue of L-proline, (3R)-carboxy pyrrolidine (beta-proline), was synthesized from a readily available (R)-glycidol. It was found to possess a rigid secondary structure, as evidenced by its CD spectrum. The beta-proline decamer, however, failed to bind to profilin, whereas the corresponding alpha-L-proline decamer bound tightly to this protein.

Collateral existence of folded and extended conformations of the beta-Ala moiety in a model peptide

The single-crystal X-ray diffraction analysis of a nonchiral beta-Ala-containing model peptide, Boc-beta-Ala-Aib-OCH(3) 1 (beta-Ala, 3-aminopropionic acid; Aib, alpha-aminoisobutyric acid), establishes the coexistence of distinctly different backbone conformations in two crystallographically independent molecules, A and B, in the asymmetric unit. Interestingly, the central mu torsion angle around the -C(beta)-C(alpha)- bond of the conformationally flexible beta-Ala residue appears to be critical in dictating the overall distinct structural features, i.e., in molecule A it adopts a folded gauche conformation: mu = -71.0 degrees, whereas it favors an extended trans conformation, mu = 161.2 degrees, in molecule B. As expected, the stereochemically constrained Aib residue preferred an energetically favorable folded backbone conformation, the torsion angles being phi = 46.2 degrees and psi = 48.3 degrees for molecule A and phi = -43.6 degrees and psi = -45.5 degrees for molecule B, lying in the left-handed and right-handed helical regions of the Ramachandran map, respectively. Considering the signs as well as the magnitudes of the backbone torsional angles, molecule A typically folds into a pseudo type III' beta-turn-like structure while molecule B prefers an overall extended conformation. Entrapping the two dramatically distinct conformational characteristics in the crystalline state clearly suggests that the gauche and the trans effects of the beta-Ala moieties are indeed energetically accessible to a short linear peptide and receive strong experimental support. The analyses permitted us to emphasize that in addition to conformational constraints of the neighboring residue, the chemical nature of the side-chain acyclic substituents and the "local environments" collectively seem to influence the stabilization of the folding-unfolding behavior of the two methylene units (-CONH-CH(2)-CH(2)-CONH-) in 1.

Entrapping unusual folding characteristics of the beta-Ala residues in a model peptide: Boc-beta-Ala-Aib-beta-Ala-NHCH3

Crystal structure analysis of a model peptide: Boc-beta-Ala-Aib-beta-Ala-NHCH3 (beta-Ala: 3-amino propionic acid; Aib: alpha-aminoisobutyric acid) revealed distinct conformational preferences for folded [phi approximately 136 degrees, mu approximately -62 degrees, psi approximately 100 degrees] and semifolded [phi approximately 83 degrees, mu approximately -177 degrees, psi approximately -117 degrees] structures of the N-and C-terminus beta-Ala residues, respectively. The overall folded conformation is stabilized by unusual Ni...H-Ni+1 and nonconventional C-H...O intramolecular hydrogen bonding interactions.