Α-amino Acid Side Chain Research Articles

Is Cys(MTSL) the Best α-Amino Acid Residue to Electron Spin Labeling of Synthetically Accessible Peptide Molecules with Nitroxides?

Electron paramagnetic resonance spectroscopy, particularly its pulse technique double electron–electron resonance (DEER) (also termed PELDOR), is rapidly becoming an extremely useful tool for the experimental determination of side chain-to-side chain distances between free radicals in molecules fundamental for life, such as polypeptides. Among appropriate probes, the most popular are undoubtedly nitroxide electron spin labels. In this context, suitable biosynthetically derived, helical regions of proteins, along with synthetic peptides with amphiphilic properties and antibacterial activities, are the most extensively investigated compounds. A strict requirement for a precise distance measurement has been identified in a minimal dynamic flexibility of the two nitroxide-bearing α-amino acid side chains. To this end, in this study, we have experimentally compared in detail the side-chain mobility properties of the two currently most widely utilized residues, namely, Cys(MTSL) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, two double-labeled, chemically synthesized 20-mer peptide molecules have been adopted as appropriate templates for our investigation on the determination of the model intramolecular separations. These double-Cys(MTSL) and double-TOAC compounds are both analogues of the almost completely rigid backbone peptide ruler which we have envisaged and 3D structurally analyzed as our original, unlabeled compound. Here, we have clearly found that the TOAC side-chain labels are largely more 3D structurally restricted than the MTSL labels. From this result, we conclude that the TOAC residue offers more precise information than the Cys(MTSL) residue on the side chain-to-side chain distance distribution in synthetically accessible peptide molecules.

Reliable folding of hybrid tetrapeptides into short β-hairpins

Five hybrid tetrapeptides, each consisting a central dipeptide segment of α-amino acid residues flanked by two aromatic γ-amino acid residues, are found to fold into well-defined β-hairpin conformations as shown by NMR, computational study, and X-ray structures. The turn loop of this β-hairpin motif accommodates different two-residue α-amino acid sequences from the highly flexible Gly-Gly, to the more restricted d-Pro-Gly. The presence of α-amino acid side chains enhances the stabilities of the β-hairpins with the exception of d-Pro-Gly-which results in destabilization. Based on this hairpin/turn motif, a variety of different dipeptide sequences of α-amino acids which rarely occur in β-turns can be introduced and presented as two-residue loops.

Aminomalononitrile inspired prebiotic chemistry as a novel multicomponent tool for the synthesis of imidazole and purine derivatives with anti-influenza A virus activity.

Amino imidazole carbonitrile derivatives decorated with α-amino acid side-chains have been synthesized by a multicomponent microwave assisted reaction inspired by the prebiotic chemistry of aminomalononitrile as a tool for generating high chemical diversity. These compounds were used as annulation synthons for the preparation of 8,9-disubstituted-6,9-dihydro-1H-purin-6-ones by reaction with formic acid as a simple C-1 donor reagent. The novel heterocycles were characterized by significant activity against influenza A virus, amino imidazole carbonitrile derivatives showing the highest activity. Thus, the chemical complexity generated by prebiotic chemistry furnished a general tool for the identification of novel antiviral agents.

Hybrid Sequences that Express both Aromatic Amide and α-Peptidic Folding Features.

Foldamers combining aliphatic and aromatic main‐chain units often produce atypical structures that cannot easily be accessed from purely aromatic or aliphatic sequences. We report solid‐state evidence that sequences comprising α‐amino acids and quinoline‐based monomers adopt conformations that combine the folding propensities of both components. Foldamers 2 and 3 having an XQQ repeat motif (X=α‐amino acid, Q=quinoline) were synthesized. Crystals of 2 (X=Phe, Q with an anionic side chain) obtained from water revealed an aromatic helix where amide groups belonging to the α‐amino acids created a hydrogen‐bond array typical of peptidic helices. Crystals of 3 (X=Ser, Q with a lipophilic side chain) obtained from organic solvents revealed a helix‐turn‐helix structure in which α‐amino acid side chains interfere with main‐chain hydrogen bonding. High sequence‐dependency of the conformation is typical of peptides but is shown here to include aromatic folding features.

Large Enantiospecificity of Step–kink Metal Surfaces: Contributions from the Backbone and Side Chain of α-Amino Acids

Designing step–kink metal surfaces with large enantiospecificity for multiple enantiomers is an important goal for the pharmaceutical industry. Here, we use density functional theory simulations to systematically study the enantiospecificity of the (531) surfaces of Ag, Cu, Pd, and Pt for α-amino acids. This leads us to propose a step–kink metal surface, Pt(531), which presents considerable enantiospecificity for a variety of α-amino acids, such as alanine, α-aminobutyric acid, valine, leucine, phenylalanine, serine, cysteine, and 3-aminoalanine. Further, we explored the role that the molecular backbone and the side chain play in the enantiospecific binding, and found that the backbone dominates the enantiospecificity of step–kink surface for α-amino acids, especially for nonpolar ones.

Selectivity Modulation and Structure of α/aza-β3 Cyclic Antimicrobial Peptides.

Potent and selective antimicrobial cyclic pseudopeptides (ACPPs) mixing α- and aza-β3 -amino acids were developed. Cyclopseudopeptide sequences were designed to investigate the impact of some intrinsic molecular parameters on their biological activities. Fine changes in the nature of the side chains strongly modulated the selectivity of the ACPPs with regard to hemolysis versus antimicrobial activity. The conformational preference of such compounds in various media was extensively studied, and the typical structure of cyclic α/aza-β3 -pseudopeptides is described for the first time. Interestingly, such scaffolds are stabilized by successive inverse γ- and N-N turns (hydrazino turns), a unique feature due to the aza-β3 residues. The α-amino acid side chains form a cluster on one face of the ring, while the aza-β3 -amino acid side chains are projected around the ring in the equatorial orientation. Such structural data are particularly valuable to fine-tune the bioactivity of these ACPPs by a structure-based approach.

Click strategy using disodium salts of amino acids improves the water solubility of plinabulin and KPU-300

Plinabulin and KPU-300 are promising anti-microtubule agents; however, the low water solubility of these compounds (<0.1µg/mL) has limited their pharmaceutical advantages. Here, we developed five water-soluble derivatives of plinabulin and KPU-300 with a click strategy using disodium salts of amino acids. The mother skeleton, diketopiperazine (DKP), was transformed into a monolactim-type alkyne and a copper-catalyzed alkyne azide cycloaddition (CuAAC) combined azides that was derived from amino acids as a water-solubilizing moiety. The conversion of carboxyl groups into disodium salts greatly improved the water solubility by 0.8 million times compared to the solubility of the parent molecules. In addition, the α-amino acid side chains of the water-solubilizing moieties affected both the water solubility and the half-lives of the compounds during enzymatic hydrolysis. Our effort to develop a variety of water-soluble derivatives using the click strategy has revealed that the replaceable water-solubilizing moieties can alter molecular solubility and stability under enzymatic hydrolysis. With this flexibility, we are approaching to the in vivo study using water-soluble derivative.

12/14/14-Helix Formation in 2:1 α/β-Hybrid Peptides Containing Bicyclo[2.2.2]octane Ring Constraints.

The highly constrained β-amino acid ABOC induces different types of helices in β urea and 1:1 α/β amide oligomers. The latter can adopt 11/9- and 18/16-helical folds depending on the chain length in solution. Short peptides alternating proteinogenic α-amino acids and ABOC in a 2:1 α/β repeat pattern adopted an unprecedented and stable 12/14/14-helix. The structure was established through extensive NMR, molecular dynamics, and IR studies. While the 1:1 α-AA/ABOC helices diverged from the canonical α-helix, the helix formed by the 9-mer 2:1 α/β-peptide allowed the projection of the α-amino acid side chains in a spatial arrangement according to the α-helix. Such a finding constitutes an important step toward the conception of functional tools that use the ABOC residue as a potent helix inducer for biological applications.

Solid-Phase Synthesis of Water-Soluble Helically Folded Hybrid α-Amino Acid/Quinoline Oligoamides

We report here a solid phase synthesis methodology that allows the incorporation of α-amino acids (X) into quinoline (Q) oligoamide foldamer sequences. Water-soluble hybrid oligoamides based on the XQ2 trimer repeat motif were shown to adopt helical conformations presenting α-amino acid side chains in a predictable linear array on one face of the helix. In contrast, sequences based on the XQ dimer motif expressed less well-defined behavior, most likely due to local conformational variability precluding long-range order. Also presented is a full structural investigation by NMR of a dodecameric XQ2-type foldamer containing four different amino acid residues (Lys, Ala, Asp, and Ser).

Poly(ester amide)s based on (L)-lactic acid oligomers and α-amino acids: influence of the α-amino acid side chain in the poly(ester amide)s properties

Novel biodegradable and low cytotoxic poly(ester amide)s (PEAs) based on α-amino acids and (L)-lactic acid (L-LA) oligomers were successfully synthesized by interfacial polymerization. The chemical structure of the new polymers was confirmed by spectroscopic analyses. Further characterization suggests that the α-amino acid plays a critical role on the final properties of the PEA. L-phenylalanine provides PEAs with higher glass transition temperature, whereas glycine enhances the crystallinity. The hydrolytic degradation in PBS (pH = 7.4) at 37 °C also depends on the α-amino acid, being faster for glycine-based PEAs. The cytotoxic profiles using fibroblast human cells indicate that the PEAs did not elicit an acute cytotoxic effect. The strategy presented in this work opens the possibility of synthesizing biodegradable PEAs with low citotoxicity by an easy and fast method. It is worth to mention also that the properties of these materials can be fine-tuned only by changing the α-amino acid.

Bicyclic amino acid-carbohydrate-conjugates as conformationally restricted hydroxyethylamine (HEA) transition-state isosteres

This communication describes a general synthetic route to bicyclic amino acid-carbohydrate-conjugates, which would be useful as conformationally restricted hydroxyethylamine (HEA) transition-state isosteres. The synthesis was achieved in 12 steps starting from D-glucose. The striking features of this system are the bicyclic rigid core displaying an α-amino acid side chain and hydroxyethylamine moiety--both of which would be potentially important for receptor interactions, leading to various biomedical responses, as described in the literature. Crystal structure investigation suggested extensive intermolecular hydrogen-bonding interactions in this system, involving the backbone amide and hydroxyl groups.

Tandem chain extension–iodomethylation reactions: formation of α-functionalized γ-keto carbonyls

Sequential exposure of a zinc-organometallic intermediate, generated through a zinc carbenoid-mediated chain extension reaction of a β-keto carbonyl, to trimethylsilylchloride and iodine provided regioselective formation of an α-iodomethyl-γ-keto carbonyl. The iodomethyl functionality can be further manipulated to provide side chains that are potential mimics of α-amino acid side chains.

Highly diastereoselective preparation of anti-α,β-dialkyl β-amino acids containing natural α-amino acid side chains

An efficient synthesis of anti-2-alkyl β 3-amino acids was developed starting from the fully protected β 3-amino acids. The strategy allows the introduction of the side chain of natural α-amino acids such as Ala, Phe and Ser at the C-2 position, with high diastereoselectivity. The preparation of 2-methyliden-β 3-amino acids is also reported. This methodology does not need the use of expensive chiral reagents and/or chiral auxiliaries, and leads to compounds with orthogonal protecting groups.

New enantiopure 7-azanorbornane β-substituted prolines by S N2 displacements at the Cγ of the side chain

Continuing our work on building new β-substituted prolines in enantiomerically pure form as new surrogates to be incorporated into model peptides, we describe functional group conversions and carbon–carbon bond forming reactions by S N2 displacements at the γ-position of the α-amino acid side chain of an azanorbornane derivative. This work extends efforts on the elaboration of the side arm at carbon C2 of the 7-azabicyclo[2.2.1]heptane core.

Synthesis of 2,6‐Disubstituted Piperidine‐Bearing α‐Amino Acid Side‐Chains.

AbstractFor Abstract see ChemInform Abstract in Full Text.

β-Aminocyclopropanecarboxylic acids with α-amino acid side chain functionality

The synthesis of conformationally restricted trans-β-aminocyclopropanecarboxylic acids (β-ACCs) having α-amino acid side chain functionality of asparagine, arginine, cysteine, or serine is described.

Synthesis of a series of stromelysin-selective thiadiazole urea matrix metalloproteinase inhibitors.

The synthesis and enzyme inhibition data for a series of thiadiazole urea matrix metalloproteinase (MMP) inhibitors are described. A broad screening effort was utilized to identify several thiadiazoles which were weak inhibitors of stromelysin. Optimization of the thiadiazole leads to include an alpha-amino acid side chain with variable terminal amide substituents provided a series of ureas which were moderately effective stromelysin inhibitors, with Ki's between 0.3 and 1.0 microM. The most effective analogues utilized an L-phenylalanine as the amino acid component. In particular, unsubstituted 46 had a Ki of 710 nM, while the p-fluoro analogue 52 displayed increased potency (100 nM). Stromelysin inhibition was further improved using a pentafluorophenylalanine substituent which resulted in 70, a 14 nM inhibitor. While gelatinase inhibition was generally poor, the use of 1-(2-pyridyl)piperazine as the amide component usually provided for enhanced activity, with 71 inhibiting gelatinase with a Ki of 770 nM. The combination of this heterocycle with a p-fluorophenylalanine substituent provided the only analogue, 69, with collagenase activity (13 microM). The SAR for analogues described within this series can be rationalized through consideration of the X-ray structure recently attained for70 complexed to stromelysin. Uniquely, this structure showed the inhibitor to be completely orientated on the left side of the enzyme cleft. These results suggest that thiadiazole urea heterocycles which incorporate a substituted phenylalanine can provide selective inhibitors of stromelysin. Careful selection of the amide substituent can also provide for analogues with modest gelatinase inhibition.

Cα-Methyl, Cα-phenylglycine peptides: A structural study

In order to obtain further information on the role played by phenyl ring position in the Cα-methylated α-amino acid side chain on peptide preferred conformation, the crystal-state structural preferences of Cα-methyl, Cα-phenylglycine peptides have been determined by X-ray diffraction. This study shows that either the fully extended conformation or the β-bend/310-helical structures are adopted by peptides characterized by this Cα-methylated, β-branched, aromatic α-amino acid.

Effect of phenyl ring position in the Cα-methylated α-amino acid side chain on peptide preferred conformation

The preferred conformations of Cα-methyl phenylglycine, Cα-methyl phenylalanine, and Cα-methyl homophenylalanine residues, as determined in model peptides (including homopeptides) by Fourier transform ir absorption, 1H-nmr, CD, and x-ray diffraction techniques, are compared with the aim of investigating the effect of phenyl ring position in the Cα-methylated amino acid side chain. This study shows that (a) β-turn and 310-helical structures are preferentially adopted by peptides rich in these Cα-methylated, aromatic α-amino acids and (b) turn and helix handedness is critically biased by the position of side-chain branching. © 1997 John Wiley & Sons, Inc. Biopoly 40: 523–527, 1996

Elaboration of the side chain of α-amino acids by palladium-catalysed stille couplings

The palladium-catalysed couplings of a γ-tri- n-butylstannylallylglycine derivative and an E-δ-tri- n-butylstannylallylglycine derivative with various organic electrophiles are described.