Beta-turn Mimic Research Articles

Cooperative Effect of a Classical and a Weak Hydrogen Bond for the Metal‐Induced Construction of a Self‐Assembled β‐Turn Mimic

A novel metal-induced template for the self-assembly of two independent phosphane ligands by means of unprecedented multiple noncovalent interactions (classical hydrogen bond, weak hydrogen bond, metal coordination, pi-stacking interaction) was developed and investigated. Our results address the importance and capability of weak hydrogen bonds (WHBs) as important attractive interactions in self-assembling processes based on molecular recognition. Together with a classical hydrogen bond, WHBs may serve as promoters for the specific self-assembly of complementary monomeric phosphane ligands into supramolecular hybrid structures. The formation of an intermolecular C-H...N hydrogen bond and its persistence in the solid state and in solution was studied by X-ray crystal analysis, mass spectrometry and NMR spectroscopy analysis. Further evidence was demonstrated by DFT calculations, which gave specific geometric parameters for the proposed conformations and allowed us to estimate the energy involved in the hydrogen bonds that are responsible for the molecular recognition process. The presented template can be regarded as a new type of self-assembled beta-turn mimic or supramolecular pseudo amino acid for the nucleation of beta-sheet structures when attached to oligopeptides.

Allosteric Modulation of the Dopamine D2 Receptor by Pro-Leu-Gly-NH2 Peptidomimetics Constrained in Either a Polyproline II Helix or a Type II β-Turn Conformation

Type II beta-turn mimics and polyproline II helix mimics based upon diastereoisomeric 5.6.5 spiro bicyclic scaffolds have provided two pairs of Pro-Leu-Gly-NH(2) (PLG) peptidomimetics with contrasting dopamine receptor modulating activities. Compounds 1a and 3a were found to be positive allosteric modulators of the dopamine receptor, while the corresponding diastereoisomeric compounds 1b and 3b provided the first PLG peptidomimetics with the ability to decrease the binding of agonists to the dopamine receptor. The positive allosteric modulating activity of 3a supported the hypothesis that a polyproline II helix conformation is the bioactive conformation for the PLG analogue Pro-Pro-Pro-NH(2). The results also show that a change in the bridgehead chirality of the 5.6.5 scaffold brings about opposite effects in terms of the modulation of the dopamine receptor.

Allosteric Modulation of the Dopamine Receptor by Conformationally Constrained Type VI β-Turn Peptidomimetics of Pro-Leu-Gly-NH2

A peptidomimetic of Pro-Leu-Pro-NH2, 7, possessing an indolizidinone type VI beta-turn mimic was synthesized via improved high-yielding protocols for the preparation and Cbz protection of alpha-allylproline. Bicyclic peptidomimetic 7 and spirobicylic peptidomimetic 8 enhanced the binding of [3H] N-propylnorapomorphine to dopamine receptors indicating that a type VI beta-turn is a possible bioactive conformation of the homochiral Pro-Leu-Pro-NH2 and Pro-Pro-Pro-NH 2 analogues of Pro-Leu-Gly-NH2 at the dopamine receptor allosteric regulatory site.

β-Turn Mimetic: Synthesis of Cyclic Thioenamino Peptides

[reaction: see text] Following the discovery of callynormine A, a marine metabolite of a new class, the cyclic endiamino peptides, and the synthesis of compounds of this group, we have now prepared an analogue group of compounds, i.e., cyclic thioenamine peptides. The latter peptides contain the alpha-amino-beta-thioacrylamide functionality, a potential new type of beta-turn mimic. The superiority of the SH group over the NH(2) group in the reaction with enol-tosylates was demonstrated.

Synthesis and conformational studies of dipeptides constrained by disubstituted 3-(aminoethoxy)propionic acid linkers.

A series of cyclic compounds with dimethyl-substituted 3-(aminoethoxy)propionic acid linkers have been prepared as potential beta-turn mimics. The desired linkers were prepared from disubstituted pyrones, which were coupled with dipeptides and then subjected to macrocyclization using diethylcyanophosphonate to furnish cyclic compounds 1-5. Conformational analysis was carried out using NMR and X-ray crystallography. All of the five cyclic compounds were found to exist in type I or type II beta-turn conformations.

Hydrogen bond-stabilized helix formation of a m-phenylene ethynylene oligomer.

[reaction: see text] Incorporation of a single hydrogen bonded beta-turn mimic in the backbone of a m-phenylene ethynylene oligomer is shown to affect the thermodynamic properties of the folding reaction. Oligomers 1 and 2 both undergo solvophobic helix formation, but hydrogen bonded oligomer 1 was found to form a more stable helix with a higher tolerance to solvent denaturation than isomeric, non-hydrogen bonded oligomer 2.

Probing opioid receptor interactions with azacycloalkane amino acids. Synthesis of a potent and selective ORL1 antagonist.

Azacycloalkane turn mimics 6-9 were used to explore the relationship between conformation and biological activity of peptide ligands to the opioid receptor-like (ORL1) receptor. Three azabicyclo[x.y.0]alkane amino acids and a 5-tBuPro type VI beta-turn mimic were introduced into peptides 10-13 by solid-phase synthesis on MBHA resin. Biological examination of peptides 10-13 showed two new antagonists (10 and 12) exhibiting increased selectivity for the ORL1 receptor.

The structure of erythromycin enol ether as a model for its activity as a motilide.

Erythromycin enol ether is a potent mimic of the peptide hormone motilin. To understand its biological activity, its three-dimensional structure in CD(2)Cl(2) was determined from constrained molecular mechanics using constraints derived from NMR spectra. The structure of the enol ether is well defined by 10 structures that minimize the energy and satisfy the NMR data. We infer the molecular basis for its activity as a motilide from a comparison of its structure with that of motilin. The macrolide ring of the enol ether is a beta-turn mimic of the peptide. Furthermore, a superposition of the structures of the enol ether and motilin shows a striking overlap of the sugar rings attached to the macrolide ring with essential aromatic side chains in the peptide.

Solid-phase syntheses of beta-turn analogues to mimic or disrupt protein-protein interactions.

Protein-protein interactions are difficult targets in medicinal chemistry, but they will become increasingly important as data from The Human Genome Project is interpreted. Our work focuses on beta-turn mimics that are designed to mimic or disrupt some of these interactions. Solid-phase syntheses and preferred conformations of beta-turn mimics that incorporate dipeptide units are discussed. The activity of one illustrative compound that potentiates the interaction of the nerve growth factor with its transmembrane tyrosine kinase receptor TrkA is outlined. Finally, the importance of dimeric turn mimics and some new approaches to these are described.

Reactivity toward deamidation of asparagine residues in beta-turn structures.

Mimetics of beta-turn structures in proteins have been used to calibrate the relative reactivities toward deamidation of asparagine residues in the two central positions of a beta-turn and in a random coil. N-Acetyl-Asn-Gly-6-aminocaproic acid, an acyclic analog of a beta-turn mimic undergoes deamidation of the asparaginyl residue through a succinimide intermediate to generate N-acetyl-Asp-N-Gly-6-aminocaproic acid (6-aminocaproic acid, hereafter Aca) and N-acetyl-L-iso-aspartyl (isoAsp)-Gly-Aca (pH 8.8, 37 degrees C) approximately 3-fold faster than does the cyclic beta-turn mimic cyclo-[L-Asn-Gly-Aca] with asparagine at position 2 of the beta-turn. The latter compound, in turn, undergoes deamidation approximately 30-fold faster than its positional isomer cyclo-[Gly-Asn-Aca] with asparagine at position 3 of the beta-turn. Both cyclic peptides assume predominantly beta-turn structures in solution, as demonstrated by NMR and circular dichroism characterization. The open-chain compound and its isomer N-acetyl-Gly-Asn-Aca assume predominantly random coil structures. The latter isomer undergoes deamidation 2-fold slower than the former. Thus the order of reactivity toward deamidation is: asparagine in a random coil approximately 3x(asparagine) in position 2 of a beta-turn approximately 30x (asparagine) in position 3 of a beta-turn.

Synthesis, conformation, and chemical properties of new mini parallel double-stranded peptides conjugated with -Phe-Phe- and -Phe-Phe-X-sequences.

To investigate the chemical conformations and functions of the -Phe-Phe-Val- or -Phe-Phe- sequences contained in the Alzheimer's disease related beta-amyloid peptide, a series of mini parallel double-stranded peptides conjugated with two peptide residues to one spacer were designed and prepared. The structure of the compounds was elucidated by circular dichroism (CD) spectrum and NMR two dimensional (2D) nuclear Overhauser enhancement and exchange spectroscopy (NOESY) measurments. The structure of 1,2-ethano-bis(L-Phe-L-Phe-L-Leu), 1,12-dodecano-bis(L-Phe-L-Phe-L-Leu), 1,12-dodecano-bis(L-Phe-L-Phe-L-Val), and 1,12-dodecano (D-Phe-D-Phe-D-Leu) conjugated with L-Leu and L-Val residues show a beta-turn-like nucleation. The dihedral angles (theta = +75 degrees, omega = +180 degrees, phi = +90 degrees, phi = -87 degrees, psi = +180 degrees) obtained from experimental coupling constant (J) data, etc. support that 1,12-dodecano-bis(L-Phe-L-Phe) adopts beta-turn mimic nucleation. The 1,12-dodecano- bis(L-Leu-L-Leu-L-Phe), 1,12-dodecano-bis(L-lle-L-Phe-L-Leu), and 1,12-dodecano-bis(L-Phe-L-Val-L-Leu), etc. adopt most probably a random structure by CD studies. It was found by titration spectrum that an inclusion complex of 1:1 ratio (association constant; azobenzene (guest, Ka=1.0 x 10(4)M-1) is formed between 1,12-dodecano-bis(L.-Phe-L-Phe-L-Leu) and [L0]=1.758 x 10(-5)M-1). Moreover, the stability of the complexes was increased in order of 1,12-dodecano-bis(L-Phe-L-Phe-L-Leu) x azobenzene> 1,12-dodecano-bis(L-Phe-L-Phe-L-Val) x azobenzene> 1,12-dodecano-bis(L-Phe-L-Val-L-Leu) azobenzene. The data show that X-Phe-L-Phe-L-spacer(S)-L-Phe-L-Phe-X (X=amino acids; S = 1,2-ethano- and 1,12-dodecano-) plays an important role as a binding site of the artificial receptor. The hydrophobic interaction of the four Phes in the two strands is a very interesting issue in the physiological action of proteins as well as the conformation of the backbone of X-L-Phe-L-Phe-spacer(S)-iL-Phe-l.-Phe-X.

Use of Steric Interactions To Control Peptide Turn Geometry. Synthesis of Type VI beta-Turn Mimics with 5-tert-Butylproline.

The influences of steric interactions on peptide geometry were studied to develop a novel means for generating type VIa beta-turn mimics. (2S,5R)-5-tert-Butylproline and L-proline were respectively introduced at the C-terminal residue of N-(acetyl)dipeptide N'-methylamides 1 and 2. The relative populations of prolyl cis- and trans-amide isomers in dipeptides 1 and 2 were measured in chloroform, DMSO, and water by proton NMR spectroscopy. Although the trans-amide isomer was favored in prolyl peptide 2, the Xaa-Pro peptide bond adopted preferably the cis-amide isomer in the case of 5-tert-butylprolyl peptide 1. Measurements of the influence of solvent and temperature on the chemical shift values for the amide proton signals of 1 in the cis-amide conformer indicated that the N'-methylamide was engaged in a hydrogen bond with the acetamide carbonyl in a type VIa beta-turn conformation. Analysis of N-(acetyl)leucyl-5-tert-butylproline N'-methylamide (1d) in the solid state by X-ray diffraction showed the cis-amide conformer which adopted a geometry characteristic of the central, i + 1 and i + 2 residues of an ideal type VIa beta-turn. In contrast to prolyl peptides 2b and 2d, N-(acetyl)alanyl- and N-(acetyl)leucyl-5-tert-butylproline N'-methylamides (1b and 1d) maintained ordered beta-turn conformations in solution that were shown to be independent of solvent composition by a comparison of their circular dichroism spectra obtained in water and acetonitrile. The NMR, X-ray, and CD data all confirm that the steric interactions of the 5-tert-butylprolyl residue induced dipeptide 1 to adopt a type VIa beta-turn conformation.

Synthesis, folding, and structure of the beta-turn mimic modified B1 domain of streptococcal protein G.

The mechanism of beta-sheet formation remains a fundamental issue in our understanding of the protein folding process, but is hampered by the often encountered kinetic competition between folding and aggregation. The role of local versus nonlocal interactions has been probed traditionally by mutagenesis of both turn and strand residues. Recently, rigid organic molecules that impose a correct chain reversal have been introduced in several small peptides to isolate the importance of the long-range interactions. Here, we present the incorporation of a well-studied beta-turn mimic, designated as the dibenzofuran-based (DBF) amino acid, in the B1 domain of streptococcal protein G (B1G), and compare our results with those obtained upon insertion of the same mimic into the N-terminal beta-hairpin of B1G (O Melnyk et al., 1998, Lett Pept Sci 5:147-150). The DBF-B1G domain conserves the structure and the functional and thermodynamical properties of the native protein, whereas the modified peptide does not adopt a native-like conformation. The nature of the DBF flanking residues in the modified B1G domain prevents the beta-turn mimic from acting as a strong beta-sheet nucleator, which reinforces the idea that the native beta-hairpin formation is not driven by the beta-turn formation, but by tertiary interactions.

Preparation of head-to-tail cyclic peptides via side-chain attachment: implications for library synthesis.

Cyclic peptide mixtures represent a promising approach for drug lead discovery. Diversity can be expanded via changes in ring size, amide bond replacements, D- and L-natural and unnatural amino acids, and by the incorporation of beta-turn mimics and related conformational constraints. We expand the scope of our side-chain attachment/resin-bound cyclization strategy first developed using aspartic acid, asparagine, and elated acid-based attachments. In this report, we describe the preparation and use of Boc-Lys-OFm, Boc-Orn-OFm, and Boc-Dab-OFm. The synthetic strategies were verified by the independent synthesis of two small RGD-based cyclic mixtures, cyclo(Pro-Xxx-Lys-Arg-Gly-Asp), where Xxx = Ala, Ser, Leu, Tyr, using Boc-Asp-OFm, and then Boc-Lys-OFm for the initial resin-bound side-chain linkage. A new orthogonal synthetic approach to cyclic peptides, based on the use of the paranitrobenzyl (ONB) ester for alpha-carboxyl protection (selectively cleaved via SnCl2 reduction), was developed. It led to the successful synthesis of individual cyclic pentapeptides using serine (Boc-Ser-ONB), and tyrosine (Fmoc-Tyr-ONB) as the side chain-linked residues.

Peptides Constrained to Type VI beta-Turns. 2. Antiparallel beta-Ladder Formation.

The preparation and characterization of an extensive series of bis-amino acid conjugates of a novel beta-turn mimic are described. The conjugates were prepared by coupling amino acid residues to the amino and carboxyl groups of the mimic, which represented the central two residues of a peptide constrained to the type VI turn conformation. The resultant adducts had the capability to form either singly or doubly hydrogen-bonded conformations, which represented beta-turn or antiparallel beta-ladder structures, respectively. In the majority of the bis-amino acid conjugates of the cis-lactam 1 (or its enantiomer), only the interior hydrogen bond, characteristic of the singly hydrogen-bonded conformation, was present, according to NMR and IR spectra. When the lactam 1 or its enantiomer were coupled to L-Phe at its carboxyl group and N-AcGly at its amino group, the spectral properties indicated the presence of the doubly hydrogen-bonded form. The results are consistent with other workers' studies that demonstrated that aryl residues following Pro stabilize antiparallel type VI turn structures and that the propensity of an amino acid to adopt a beta-conformation in proteins is highly dependent on context.

Synthesis of a new dipeptide template, its X-ray structure, and modeling studies on its conformational features.

The diastereoselective synthesis is reported of a dipeptide template which is closely related to H-Gly-Trp-OH. Intramolecular bond formation between alpha-C of Gly and ring position 2 of the Trp unit has been achieved by a Pictet-Spengler-type electrophilic aromatic substitution. The absolute configuration of the N-Moc protected dipeptide template 9.2H2O was determined by single-crystal X-ray crystallography and found to be (2S,5S). The cis orientation of the amino and carboxy termini prompted us to investigate the potential of 9 as a beta-turn mimic. MD calculations on the model pseudopeptide Ac-Ala-Gly-Trp-Ala-NHMe 11 suggest that an unusually tight turn should be favoured rather than a beta-turn. The proper protective situation as a pre-requisite for the incorporation of the template into a peptide has been established, and comments about its chemical properties are given.

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Design, synthesis and evaluation of a novel bicyclic lactam as a gly-pro type vi beta-turn mimic

The stereoselective synthesis and conformational evaluation of Gly-Pro type VI turn mimic 7, the first mimetic to constrain the central three bonds and incorporate the side chain groups of a beta-turn, is described. A superimposition of the crystallographically determined structure of 7 with the structure of a typical type VI turn revealed exceptional similarity in backbone and side chain atom positions. The temperature dependence of the chemical shift of the amide proton of the derivative 8 in DMSO confirmed the presence of a remarkably stable i, i+3 intramolecular hydrogen bond.

Dopamine receptor modulation by a highly rigid spiro bicyclic peptidomimetic of Pro-Leu-Gly-NH2.

A peptidomimetic analogue of Pro-Leu-Gly-NH2 (PLG), compound 3, has been synthesized that contains a highly constrained spiro bicyclic type-II beta-turn mimic. Peptidomimetic 3 enhanced the binding of the dopamine receptor agonist ADTN to dopamine receptors by 40% at 10(-6) M. At this same concentration PLG enhanced the binding of ADTN by 26%. Like PLG, 3 exhibited a bell-shaped dose-response curve with the maximum effect occurring at a concentration of 10(-6) M. Because of the highly rigid nature of the spiro bicyclic type-II beta-turn constraint found in 3, these results lend strong support for the hypothesis that the biologically active conformation of PLG is a type-II beta-turn.

Structural engineering of the HIV‐1 protease molecule with a β‐turn mimic of fixed geometry

An important goal in the de novo design of enzymes is the control of molecular geometry. To this end, an analog of the protease from human immunodeficiency virus 1 (HIV-1 protease) was prepared by total chemical synthesis, containing a constrained, nonpeptidic type II' beta-turn mimic of predetermined three-dimensional structure. The mimic beta-turn replaced residues Gly16,17 in each subunit of the homodimeric molecule. These residues constitute the central amino acids of two symmetry-related type I' beta-turns in the native, unliganded enzyme. The beta-turn mimic-containing enzyme analog was fully active, possessed the same substrate specificity as the Gly16,17-containing enzyme, and showed enhanced resistance to thermal inactivation. These results indicate that the precise geometry of the beta-turn at residues 15-18 in each subunit is not critical for activity, and that replacement of the native sequence with a rigid beta-turn mimic can lead to enhanced protein stability. Finally, the successful incorporation of a fixed element of secondary structure illustrates the potential of a "molecular kit set" approach to protein design and synthesis.