The β-turn preferential solution conformation of a tetrapeptide containing an azaamino acid residue

A lysine-based 2:1-[α/aza]-pseudopeptide series used as additives in polymeric membranes for CO2 capture: synthesis, structural studies, and application†

The current study presents for the first time the synthesis of a new 2:1-[α/aza]-pseudopeptide series possessing charged amino acids (i.e., lysine) and aims at studying the influences of chirality, backbone length, and the nature of the lysine side chains on the conformation of the 2:1-[α/aza]-oligomers in solution using NMR, FTIR spectroscopy and molecular dynamic calculations. The spectroscopic results emphasized the conservation of the β-turn conformation adopted by the trimers regardless of the chirality which demonstrated a noticeable effect on the conformation of homochiral hexamer (8c) compared with the hetero-analogue (8d). The molecular dynamic calculations predicted that the chirality and the side chain of the lysine residues caused a little distortion from the classical β-turn conformation in the case of short trimer sequences (7c and 7d), while the chirality and the backbone length exerted more distortion on the β-turn adopted by the longer hexamer sequences (8c and 8d). The large disturbance in hexamers from classical β-turn was attributed to increasing the flexibility and the possibility of molecules to adopt a more energetically favorable conformation stabilized by non-classical β-turn intramolecular hydrogen bonds. Thus, alternating d- and l-lysine amino acids in the 2:1-[α/aza]-hexamer (8d) decreases the high steric hindrance between the lysine side chains, as in the homo analogue (8c), and the distortion is less recognized. Finally, short sequences of aza-pseudopeptides containing lysine residues improve CO₂ separation when used as additives in Pebax® 1074 membranes. The best membrane performances were obtained with a pseudopeptidic dimer as an additive (6b′; deprotected lysine side chain), with an increase in both ideal selectivity α_CO2/N2 (from 42.8 to 47.6) and CO₂ permeability (from 132 to 148 Barrer) compared to the virgin Pebax® 1074 membrane.

A new 2:1-[α/aza]-pseudopeptide series based charged lysine amino acid was synthesized. Influences of chirality, backbone length, and lysine side chains on the oligomers conformation were investigated in solution using NMR, FTIR and MD calculations.

Copper-Catalyzed Alkynylation of Hydrazides: An Easy Access to Functionalized Azadipeptides

We report a copper-catalyzed alkynylation of azadipeptides using ethynylbenziodoxolone (EBX) reagents. Nonsymmetrical ynehydrazides could be obtained in 25-97% yield using azaglycine derivatives as nucleophiles. The transformation is compatible with most functional groups naturally occurring on amino acid side chains and allows the transfer of silyl-, alkyl-, and aryl-substituted alkynes. The obtained α-alkynyl azaglycine products could be further functionalized by nucleophilic attack or cycloaddition on the triple bond.

Two consecutive aza-amino acids in peptides promote stable β-turn formation in water

Studies on the synthetic methodologies and the structural propensity of peptides containing consecutive aza-amino acids are still in their infancy. Here, details of the synthesis and conformational analysis of tripeptides containing two consecutive aza-amino acids are provided. The demonstration that the type I β-turn folding is induced, even in aqueous media, by the introduction of one or two lateral chains on the diaza-peptide unit is of particular importance for the design of peptidomimetics of biological interest.

Unnatural Amino Acid: 4-Aminopyrazolonyl Amino Acid Comprising Tri-Peptides Forms Organogel With Co-Solvent (EtOAc:Hexane)

Ampyrone is an amino-functionalized heterocyclic pyrazolone derivative that possesses therapeutic values such as analgesic, anti-inflammatory, and antipyretics. The chemical structure of ampyrone exhibits excellent hydrogen bonding sites and is considered as the potential scaffold of supramolecular self-assembly. Recently, this molecule has been derived into unnatural amino acids such as aminopyrazolone amino acid and its peptides. This report describes that one of its amino acids, O-alkylated ampyrone, containing hybrid (α/β) peptides forms organogel after sonication at 50–55°C with 0.7–0.9% (w/v) in ethyl acetate: hexane (1:3). The formation/morphology of such organogels is studied by nuclear magnetic resonance Fourier-transform infrared (FT-IR), circular dichroism (CD), scanning electron microscope (SEM), transmission electron microscopy (TEM), powder X-ray diffraction (Powder-XRD), and thermogravimetric analysis (TGA). Energy-minimized conformation of APA-peptides reveals the possibility of intermolecular hydrogen bonding. Hence, APA-peptides are promising peptidomimetics for the organogel-peptides.

Late-Stage N-Alkylation of Azapeptides

Azapeptides undergo on-resin, late-stage N-alkylations to install side chains with high chemoselectivity for the hydrazide nitrogen atoms. The major product is the N1-alkylated "azapeptoid", with only small amounts (<10%) of alkylation occurring at the other aza-amino acid nitrogen (N2). Dialkylations are also possible and afford highly functionalized, disubstituted azapeptides with side chains installed on both aza-amino acid nitrogen atoms. The site-selectivity was determined using Edman degradation, MS/MS sequencing, and comparative LCMS and NMR analyses.

Conformational preferences of Ac-Pro-azaXaa-NHMe (Xaa = Asn, Asp, Ala) and the effect of intramolecular hydrogen bonds on their stability in gas phase and solution

The conformational preferences of three azadipeptides Ac-Pro-azaXaa-NHMe [Xaa = Asn (1), Asp (2), Ala (3)] have been carried out in gas phase and solution (water) using the density functional method B3LYP/6-311 +  + G(d,p) to explore the effect of the change of side chain of azaamino acids at the i + 2 position on the stability of these components. The most stable conformations of compounds (1), (2), and (3) have an amid bond oriented trans, trans, and cis, respectively, in gas phase, whereas the orientation of amid bond in water solvent of compounds (2) and (3) has changed to cis and trans, respectively. We have also noticed the importance of backbone-side chain hydrogen bonds in the stabilization of the β turn motif in gas phase since this motif is more stable in the case of compounds (1) and (2) and less stable in the case of compound (3) in which these hydrogen bonds are absent. Furthermore, the βII(βII') turn structure is more stable than βI turn for all conformations of the three compounds in gas phase, while it is not true in the case of some conformations in solution. Moreover, the stability of β turn increases from azaAsn to azaAsp which could be due to the side chain's basic nature of azaAsn. In general, hydrogen bonds were found to play a key role in the stabilization of these compounds since most of conformers are lower in energy when they have more than two hydrogen bond interactions while conformations with one or no hydrogen bonds are higher in energy and thus less stable.

Introducing sequential aza-amino acids units induces repeated β-turns and helical conformations in peptides

A major current issue in medicinal chemistry is the design of small peptide analogues resistant to proteolysis and able to adopt preferential conformations, while preserving the selectivity and efficiency of natural peptides. Whereas the introduction of one aza-Gly in peptides has proven numerous biological and structural interest, the conformational effect of sequential aza-Gly or aza-amino acids bearing side chains has not been investigated. In this work, experimental NMR and X-ray data together with in silico conformational studies reveal that the introduction of two consecutive aza-amino acids in pseudotripeptides induces the formation of stable hydrogen-bonded β-turn structures. Notably, this stabilization effect relies on the presence of side chains on aza-amino acids, as more flexible conformations are observed with aza-Gly residues. Remarkably, a longer aza/aza/α/aza/aza/α pseudohexapeptide containing substituted aza-amino acids adopts repeated β-turns conformations which interconvert with a fully helical structure mimicking a 3₁₀ helix.

Short Azapeptides of Folded Structures in Aqueous Solutions

Building folded short peptides that are driven by the intramolecular hydrogen bonding in aqueous solutions remains challenging because of their highly competitive intermolecular hydrogen-bonding interactions with water solvent molecules that would have favored the extended conformations. Here, we show folded β-turn structures in acyl amino acid-based N-amidothioureas, the nonclassic azapeptides, in aqueous solutions, as well as in solid-state and organic solvents, by X-ray crystal structures, DFT calculations, 1D and 2D NMR spectra, and absorption and CD spectra. The achiral phenylthiourea chromophore acts as a CD reporter for the β-turn structure that communicates the chirality of the amino acid residue to the achiral thiourea moiety and the relative intensity of the intramolecular hydrogen bond that stabilizes the turn structure. The amidothiourea moiety represents a versatile structural framework for folded short peptides in aqueous environments.

Azapeptide Synthesis Methods for Expanding Side-Chain Diversity for Biomedical Applications

Mimicry of bioactive conformations is critical for peptide-based medicinal chemistry because such peptidomimetics may augment stability, enhance affinity, and increase specificity. Azapeptides are peptidomimetics in which the α-carbon(s) of one or more amino acid residues are substituted by nitrogen. The resulting semicarbazide analogues have been shown to reinforce β-turn conformation through the combination of lone pair-lone pair repulsion of the adjacent hydrazine nitrogen and urea planarity. Substitution of a semicarbazide for an amino amide residue in a peptide may retain biological activity and add benefits such as improved metabolic stability. The applications of azapeptides include receptor ligands, enzyme inhibitors, prodrugs, probes, and imaging agents. Moreover, azapeptides have proven therapeutic utility. For example, the aza-glycinamide analogue of the luteinizing hormone-releasing hormone analogue Zoladex is a potent long-acting agonist currently used in the clinic for the treatment of prostate and breast cancer. However, the use of azapeptides was hampered by tedious solution-phase synthetic routes for selective hydrazine functionalization. A remarkable stride to overcome this bottleneck was made in 2009 through the introduction of the submonomer procedure for azapeptide synthesis, which enabled addition of diverse side chains onto a common semicarbazone intermediate, providing a means to construct azapeptide libraries by solution- and solid-phase chemistry. In brief, aza residues are introduced into the peptide chain using the submonomer strategy by semicarbazone incorporation, deprotonation, N-alkylation, and orthogonal deprotection. Amino acylation of the resulting semicarbazide and elongation gives the desired azapeptide. Since the initial report, a number of chemical transformations have taken advantage of the orthogonal chemistry of semicarbazone residues (e.g., Michael additions and N-arylations). In addition, libraries have been synthesized from libraries by diversification of aza-propargylglycine (e.g., A³ coupling reactions, [1,3]-dipolar cycloadditions, and 5-exo-dig cyclizations) and aza-chloroalkylglycine residues. In addition, oxidation of aza-glycine residues has afforded azopeptides that react in pericyclic reactions (e.g., Diels-Alder and Alder-ene chemistry). The bulk of these transformations of aza-glycine residues have been developed by the Lubell laboratory, which has applied such chemistry in the synthesis of ligands with promising biological activity for treating diseases such as cancer and age-related macular degeneration. Azapeptide analogues of growth hormone-releasing peptide-6 (His-d-Trp-Ala-Trp-d-Phe-Lys-NH₂, GHRP-6) have for example been pursued as ligands of the cluster of differentiation 36 receptor (CD36) and show promising activity for the development of treatments for angiogenesis-related diseases, such as age-related macular degeneration, as well as for atherosclerosis. Azapeptides have also been employed to make a series of conformationally constrained second mitochondria-derived activator of caspase (Smac) mimetics that exhibit promising apoptosis-inducing activity in cancer cells. The synthesis of cyclic azapeptide derivatives was used to make an aza scan to study the conformation-activity relationships of the anticancer agent cilengitide, cyclo(RGDf-N(Me)V), and its parent counterpart cyclo(RGDfV), which exhibit potency against human tumor metastasis and tumor-induced angiogenesis. Innovations in the synthesis and application of azapeptides will be presented in this Account, focusing on the creation and use of side-chain diversity in medicinal chemistry.

Synthesis of azabicycloalkanone amino acid and azapeptide mimics and their application as modulators of the prostaglandin F2α receptor for delaying preterm birth

Premature birth (<37 weeks gestation) is the major cause of perinatal mortality and morbidity and has been steadily increasing worldwide. Towards the rational design of more effective therapeutic agents for inhibiting uterine contractions and prolonging gestation (a so-called tocolytic drug), our team has targeted the prostaglandin F2α receptor (FP) employing a peptidomimetic approach designed to provide modulators of this novel target. We identified first a lead peptide (PDC113) (1) based on the sequence of the second extracellular loop of FP on the basis that the loop itself might modulate receptor activation. Systematic study of the structure−activity relationships of 1 generated hypotheses concerning the conformation and side-chains responsible for activity that led to the synthesis of PDC113.31 (2), a potent all d-amino acid peptide, which has successfully completed Phase 1b clinical trials. Employing indolizidinone amino acids, peptide mimics were developed that served to probe the mechanism of FP modulation. For example, PDC113.824 (9) was shown to allosterically regulate FP activity contingent on the presence of prostaglandin F2α by a mechanism implicating biased signalling. Although attempts to understand the turn geometry responsible for the activity of 9 by replacement of its indolizidin-2-one moiety with other azabicycloalkanones failed to produce biologically active analogs, employment of aza-aminoacyl-proline analogs resulted in a series of FP modulators exhibiting distinct effects on different G protein-mediated signalling pathways. Our program has thus contributed novel probes for understanding the chemical biology of FP as well as new therapeutic agents with promise for inhibiting uterine contractions and preventing preterm birth.

Effects and therapeutic potentials of kisspeptin analogs: regulation of the hypothalamic-pituitary-gonadal axis

The hypothalamic peptide kisspeptin (metastin), the endogenous ligand of the G protein-coupled receptor KISS1R, plays a critical role in controlling GnRH release from hypothalamic GnRH neurons and thereby regulates hypothalamic-pituitary-gonadal functions. Although the therapeutic potential of kisspeptin is attractive, its susceptibility to proteolytic degradation limits its utility. To overcome this, KISS1R agonists or antagonists as peptide analogs or small molecules have been investigated. Kisspeptin analogs have been most extensively studied by reducing the length of the peptide from the original 54 amino acids to 10 amino acids or less and by substituting key amino acid residues. Also, 2 investigational kisspeptin agonist analogs have been evaluated in clinical studies in men; in agreement with animal studies, abrupt elevations in gonadotropin and testosterone levels were observed as an acute effect, followed by rapid reductions in these hormones as a chronic effect. Some studies of small-molecule KISS1R antagonists have also been published. In this review, we present a brief overview on kisspeptin/KISS1R physiology in reproductive functions and summarize the available knowledge of both agonists and antagonists. We also focus on the kisspeptin agonist analogs by summarizing key pharmacological findings from both clinical and preclinical studies, and discuss their potential therapeutic utility.

NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water

An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.

Peptide scanning for studying structure-activity relationships in drug discovery

Peptide-based therapeutics have grown in importance over the last few decades. Furthermore, peptides have been extensively used as lead compounds in the drug discovery process to investigate the nature of chemical space required for molecular recognition and activity at a variety of targets. This critical commentary reviews scanning techniques, which employ natural and non-proteinogenic amino acids to facilitate understanding of structural requirements for peptide biological activity. The value of sequence analysis by such methods is highlighted by examples, in which the elements for peptide affinity and activity have been elucidated and employed to prepare peptidomimetic leads for drug development.

Serum stability of selected decapeptide agonists of KISS1R using pseudopeptides

Metastin/kisspeptin, a 54-amino acid peptide, is the ligand of the G-protein-coupled receptor KISS1R which plays a key role in pathways that regulate reproduction and cell migration in many endocrine and gonadal tissues. The N-terminally truncated decapeptide, metastin(45-54), has 3-10 times higher receptor affinity and intracellular calcium ion-mobilizing activity but is rapidly inactivated in serum. In this study we designed and synthesized stable KISS1R agonistic decapeptide analogs with selected substitutions at positions 47, 50, and 51. Replacement of glycine with azaglycine (azaGly) in which the α-carbon is replaced with a nitrogen atom at position 51 improved the stability of amide bonds between Phe(50)-Gly(51) and Gly(51)-Leu(52) as determined by in vitro mouse serum stability studies. Substitution for tryptophan at position 47 with other amino acids such as serine, threonine, β-(3-pyridyl)alanine, and D-tryptophan (D-Trp), produced analogs that were highly stable in mouse serum. D-Trp(47) analog 13 showed not only high metabolic stability but also excellent KISS1R agonistic activity. Other labile peptides may have increased serum stability using amino acid substitution.

Induction of chirality: experimental evidence of atropisomerism in azapeptides

Methylation of the peptide bond in model azadipeptides leads to the E configuration and hence to atropisomerism due to a restricted rotation around the N-N axis.

THE ϕ, ψ SPACE OF BORON ISOSTERES OF AMINO ACIDS: ANAB INITIOSTUDY

Boron isosteres [ CH3- CO - BH - CH(R) - CONHCH3; R = CH3, CH2OH , CH2SH ] of natural amino acids have been designed as inhibitors of serine protease based on boron's ability to mimic the transition state of the normal enzyme catalyzed reaction. The conformation and electronic properties of these isosteres have been determined by ab initio calculations at the HF/6-31G** level of theory. The global minimum energy structures of the boron isosteres (which are all identical) and the natural amino acids are radically different. Interestingly, the boron isosteres have favorable conformations with positive values for the ϕ dihedral, which are "disallowed states" for the natural amino acids. This is possible because of the smaller atomic size of boron compared to nitrogen. The molecular electrostatic potential of the boron isosteres is also very different from the natural amino acids. There is a positive potential around the boron atom, which provokes the attack of the Ser195– OH group in the enzyme, resulting in formation of an irreversible enzyme-inhibitor adduct.

Azapeptides and their therapeutic potential

Azapeptides are peptide analogs in which one or more of the amino residues is replaced by a semicarbazide. This substitution of a nitrogen for the α-carbon center results in conformational restrictions, which bend the peptide about the aza-amino acid residue away from a linear geometry. The resulting azapeptide turn conformations have been observed by x-ray crystallography and spectroscopy, as well as predicted based on computational models. In biologically active peptide analogs, the aza-substitution has led to enhanced activity and selectivity as well as improved properties, such as prolonged duration of action and metabolic stability. In light of these characteristics, azapeptides have found important uses as receptor ligands, enzyme inhibitors, drugs, pro-drugs, probes and imaging agents. Recent improvements in synthetic methods for their procurement have ushered in a new era of azapeptide chemistry. This review aims to provide a historical look at the development of azapeptide science along with a focus on recent developments and perspectives on the future of this useful tool for medicinal chemistry.

The β-turn scaffold of tripeptide containing an azaphenylalanine residue

The conformational preferences of azaphenylalanine-containing peptide were investigated using a model compound, Ac-azaPhe-NHMe with ab initio method at the HF/3-21G and HF/6-31G(*) levels, and the seven minimum energy conformations with trans orientation of acetyl group and the 4 minimum energy conformations with cis orientation of acetyl group were found at the HF/6-31G(*) level if their mirror images were not considered. An average backbone dihedral angle of the 11 minimum energy conformations is phi=+/-91 degrees +/-24 degrees , psi =+/-18 degrees +/-10 degrees (or +/-169 degrees +/-8 degrees ), corresponding to the i+2 position of beta-turn (delta(R)) or polyproline II (beta(P)) structure, respectively. The chi(1) angle in the aromatic side chain of azaPhe residue adopts preferentially between +/-60 degrees and +/-130 degrees, which reflect a steric hindrance between the N-terminal carbonyl group or the C-terminal amide group and the aromatic side chain with respect to the configuration of the acetyl group. These conformational preferences of Ac-azaPhe-NHMe predicted theoretically were compared with those of For-Phe-NHMe to characterize the structural role of azaPhe residue. Four tripeptides containing azaPhe residue, Boc-Xaa-azaPhe-Ala-OMe [Xaa=Gly(1), Ala(2), Phe(3), Asn(4)] were designed and synthesized to verify whether the backbone torsion angles of azaPhe reside are still the same as compared with theoretical conformations and how the preceding amino acids of azaPhe residue perturb the beta-turn skeleton in solution. The solution conformations of these tripeptide models containing azaPhe residue were determined in CDCl(3) and DMSO solvents using NMR and molecular modeling techniques. The characteristic NOE patterns, the temperature coefficients of amide protons and small solvent accessibility for the azapeptides 1-4 reveal to adopt the beta-turn structure. The structures of azapeptides containing azaPhe residue from a restrained molecular dynamics simulation indicated that average dihedral angles [(phi(1), psi(1)), (phi(2), psi(2))] of Xaa-azaPhe fragment in azapeptide, Boc-Xaa-azaPhe-Ala-OMe were [(-68 degrees, 135 degrees ), (116 degrees, -1 degrees )], and this implies that the intercalation of an azaPhe residue in tripeptide induces the betaII-turn conformation, and the volume change of a preceding amino acid of azaPhe residue in tripeptides would not perturb seriously the backbone dihedral angle of beta-turn conformation. We believe such information could be critical in designing useful molecules containing azaPhe residue for drug discovery and peptide engineering.

Aza-scanning of the Potent Melanocortin Receptor Agonist Ac-His-d-Phe-Arg-Trp-NH2

The melanocortin pathway is an important participant in the regulation of skin pigmentation, steroidogenesis, obesity, energy homeostasis, and exocrine gland function. Melanocortin agonists contain the putative sequence 'His-Phe-Arg-Trp', which has been designated as the 'message' sequence for melanocortin peptides, and this sequence has been hypothesized to adopt a bioactive reverse turn conformation. Exploring the relationship between its structure and biological activity, we report the synthesis and evaluation of seven aza-analogs of the potent melanocortin receptor agonist Ac-His-D-Phe-Arg-Trp-NH2. Aza-amino acids, in which the alpha-carbon was replaced by nitrogen, were inserted along the peptide sequence to probe the importance of local configuration and turn conformation on the biology of this tetrapeptide. Although systematic substitution of aza-amino acids for the D-Phe and Arg residues led to a significant loss of activity relative to the parent peptide for all melanocortin receptor subtypes examined, substitution of aza-amino acids at the C-terminal Trp residue gave analogs equipotent to the parent peptide. In summary, the aza-scan has demonstrated that recognition of this tetrapeptide by the melanocortin receptors is particularly sensitive to modifications of configuration and conformation at the D-Phe and Arg residues versus the Trp amino acid. In light of aza-residues imparting resistance from enzymatic degradation, C-terminal aza-amino acid analogs may be used to design new peptide mimics with enhanced metabolic stability.

Aza-Amino Acid Scanning of Secondary Structure Suited for Solid-Phase Peptide Synthesis with Fmoc Chemistry and Aza-Amino Acids with Heteroatomic Side Chains

Aza-peptides, peptide analogues in which the alpha-carbon of one or more of the amino acid residues is replaced with a nitrogen atom, exhibit a propensity for adopting beta-turn conformations. A general Fmoc-protection protocol for the stepwise solid-phase synthesis of aza-peptides has now been developed based on the activation of N'-alkyl fluoren-9-ylmethyl carbazates with phosgene for coupling the aza-amino acid residues. This method has proven effective for introducing aza-amino acid residues with aliphatic (Ala, Leu, Val, and Gly) and aromatic (Phe, Tyr, and Trp) side chains. Acid promoted loss of aromatic side chains was noted with aza-Trp and aza-Tyr residues during peptide cleavage and suppressed by temperature control in the case of the latter. In addition, aza-peptides with heteroatomic side chain residues (Lys, Orn, Arg, and Asp) were conveniently synthesized using this protocol. Partial aza-amino acid scans were performed on three biologically active peptides: the potent tetrapeptide melanocortin receptor agonist, Ac-His-d-Phe-Arg-Trp-NH2; the growth hormone secretagogue hexapeptide, GHRP-6, His-d-Trp-Ala-Trp-d-Phe-Lys-NH2; and the human calcitonin gene-related peptide (hCGRP) antagonist, FVPTDVGPFAF-NH2. This practical procedure for aza-amino acid scanning using Fmoc-based solid-phase synthesis should find general utility for probing the existence and importance of beta-turn conformations in bioactive peptides.

Computational study of conformational preferences of thioamide-containing azaglycine peptides

The effect of thioamide substitution on the conformational stability of an azaglycine-containing peptide, For-AzaGly-NH2 (1), was investigated for the sake of finding possible applications by using ab initio and DFT methods. As model compounds, For-[psiCSNH]-AzaGly-NH2 (2), For-AzaGly-[psiCSNH]-NH2 (3), and For-[psiCSNH]-AzaGly-[psiCSNH]-NH2 (4) were used. Two-dimensional phi-psi potential energy surfaces (PESs) for 2-4 were calculated at the B3LYP/6-31G*//HF/6-31G* level in gas (epsilon = 1.0) and in water (epsilon = 78.4) by applying the isodensity polarizable continuum model (IPCM) method. On the basis of these PESs, the minimum energy conformations for 2-4 were characterized at the B3LYP level with 6-31G*, 6-311G**, and 6-31+G** basis sets. The remarkable structural effect of thioamide substitution for 2-4 is that beta-strand structure is observed as a global or local minimum. The minima of 2-4 are also compared with those for glycine and thioamide-containing glycine peptides. Our theoretical results demonstrate that compounds 2-4 would be used to design controllable secondary structures.

A theoretical study of conformational properties of N-methyl azapeptide derivatives

The conformational properties of azapeptide derivatives, Ac-azaGly-NHMe (1), Ac-azaAla-NHMe (2), Ac-NMe-azaGly-NHMe (3), Ac-NMe-azaAla-NHMe (4), Ac-azaGly-NMe(2) (5), Ac-azaAla-NMe(2) (6), Ac-NMe-azaGly-NMe(2) (7), and Ac-NMe-azaAla-NMe(2) (8), were systematically examined by using ab initio MO and DFT methods. Structural perturbations in azapeptides resulting from cyclic substitution of a methyl group at three N-positions of an azaamino acid were studied on the basis of the structure of the simplest model azapeptide, 1. Potential energy surfaces were generated at the HF/6-31G level for 1-4 and at the HF/6-31G//HF/3-21G level for 5-8 by rotating two key dihedral angles (phi, psi) in increments of 30 degrees. The backbone (phi, psi) angles of the minima for 1-4 are observed at the i + 2 position to form the betaI(I')-, betaII(II')-, betaVI-turns or the polyproline II structure according to the orientation of the acetyl group and the positions of the N-methyl groups. Compounds 5-8 coupled to a secondary amine were found to preferentially adopt polyproline II, betaI(III)-turn, or alpha-helical structure or even extended conformations depending on the orientation of the acetyl group and the positions of the N-methyl groups. Furthermore, N-methyl groups, depending on their positions, were found to affect the orientation of the amide group in the lowest energy conformations, the pyramidality of the N2 atom, and the bond length in azapeptide derivatives. These unique theoretical conformations of N-methyl azapeptide derivatives could be utilized in the definite design of secondary structure for peptides and proteins, and in the development of new drugs and molecular machines.