Halogen bonding in complexes of proteins and non-natural amino acids

In this work, we have analyzed the influence of halogen bonding to the stability of 44 complexes of proteins and non-natural amino acids. Fluorine- and chlorine-containing non-natural amino acids are more prevalent in the dataset, and an even larger number of contacts made by iodine-containing ligands are found. Only few halogen bonds with the hydroxyl oxygens and carboxylate side chains are found in the dataset. Halogen bonds with the nitrogen-containing side chains have higher occurrence than other acceptors. Backbone carbonyl oxygens and nitrogens are to a substantial extent involved in our dataset. We have observed a small percentage of interactions involving water as hydrogen bond donors. Additionally, most of the interacting residues comprising the interfaces also show a great degree of conservation. There is a clear interaction hot spot at distances of 3.5–3.7 Å and Θ₁ angles of 100–120°. There is also a cluster of contacts featuring short distances (2.6–2.9 Å) but only nearly optimal Θ₁ angles (140–160°). 51.3% of stabilizing residues are involved in building halogen bonds with the non-natural amino acids. We discovered three types of structural motifs significantly over-represented: beta-turn-ir, beta-turn-il and niche-4r. The halogen-bonding statistics of the dataset do not show any preference for α-helices (36%), β-sheets (36%), or turns/coils (28%) structures. Most of the amino acid residues that were involved in halogen bonds prefer to be in the solvent excluded environment (buried). Furthermore, we have shown that in amino acid–protein complexes halogen atoms can sometimes be involved in hydrogen bonding interactions with hydrogen bonding-donors. The results from this study might be used for the rational design of halogenated ligands as inhibitors and drugs, and in biomolecular engineering.     

Sugar amino acids and related molecules: Some recent developments

To meet the growing demands for the development of new molecular entities for discovering new drugs and materials, organic chemists have started working on many new concepts that can help to assimilate knowledge-based structural diversities more efficiently than ever before. Emulating the basic principles followed by Nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create ‘nature-like’ and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature’s molecular arsenal. In recent years, sugar amino acids have been used extensively in the area of peptidomimetic studies. Advances made in the area of combinatorial chemistry can provide the necessary technological support for rapid compilations of sugar amino acidbased libraries exploiting the diversities of their carbohydrate frameworks and well-developed solid-phase peptide synthesis methods. This perspective article chronicles some of the recent applications of various sugar amino acids, furan amino acids, pyrrole amino acids etc. and many other related building blocks in wide-ranging peptidomimetic studies     

Stereoselective synthesis of the various isomers of 3,4-dideoxy furanoid sugar amino acids with methyl substitution at the C6 position

Various isomers of C6-methyl-containing chiral 3,4-dideoxy furanoid sugar amino acids were synthesized following a common strategy, in which the C2 and C6 chiral centres were derived from the chiralities of the two starting materials, glyceraldehyde acetonide and N,N-dibenzylalaninal, respectively, and the C5 centre was fixed by standard diastereoselective transformations.     

Recent progress of sugar amino acids: Synthetic strategies and applications as glycomimetics and peptidomimetics

In order to meet the increasing demands for the development of large varieties of new molecules for discovering new drugs and materials, organic chemists are developing many novel multifunctional building blocks, which are assembled rationally to create ‘nature-like' and yet unnatural organic molecules with well-defined structures and useful properties. Sugar amino acids(SAAs), the carbohydrate derivatives bearing both amino and carboxylic acid functional groups, are important ones of these multifunctional building blocks, which can be used to create novel materials with potential applications as glycomimetics and peptidomimetics. This review will focus on recent synthetic strategies of SAAs and their applications in creating large number of structurally diverse glycomimetics and peptidomimetics.     

The artificial binaphthyl amino acid 6-amino-6′-carboxyethyl-2-methoxy-2′-hydroxy-1,1′-binaphthyl (Bna): synthesis and assembly of Bna peptides

The new binaphthyl-based amino acid 6-amino-6′-carboxyethyl-2-methoxy-2′-hydroxy-1,1′-binaphthyl (Bna) is presented, which combines the axially chiral binaphthyl core, a phenolic OH-group as well as terminating amino and carboxyl groups in one structure. The large aromatic rings of the compound provide molecular spacing and π-surface attraction in assembled Bna oligoamides. The synthesis of Bna derivatives is reported, both with the (R)- and with the (S)-binaphthyl skeleton. Several dipeptides of (R)- or (S)-Bna units combined with natural amino acids, were prepared as ‘building blocks’ for the synthesis of extended Bna peptides. The tetrapeptide Boc-(S)-Val-(S)-Bna(OH)-(S)-Val-(S)-Bna(OPiv)-O-n-But (12) and the pentapeptide Boc-(S)-Val-(S)-Bna(OH)-(S)-Val-(S)-Bna(OH)-Gly-OH (13) were prepared via conventional solution phase synthesis and solid phase synthetic techniques, respectively. Compound 12 shows an interesting dynamic ¹H NMR spectrum suggesting compact and aggregated forms in dichloromethane. Compound 13 accelerates the enolisation of acetone. The use of more complex Bna peptides as organo catalysts is proposed.     

Silicon amino acids

The existence and gas phase stability of silicon analogues of three natural amino acids (i.e., silicon glycine, silicon alanine, and silicon valine) belonging to the novel class of compounds termed silicon amino acids (SiAA) are investigated theoretically on the basis of ab initio QCISD/aug‐cc‐pVTZ and MP2/aug‐cc‐pVTZ calculations. All molecules studied (in their gas phase canonical forms) are structurally comparable to their proteinogenic counterparts (i.e., glycine, l ‐alanine, and l ‐valine) and capable of forming several structural isomers as such. These higher energy isomers are characterized by small relative energies (not exceeding 4 kcal mol⁻¹). The simulated IR spectra of the Si‐Gly, Si‐Ala, and Si‐Val global minima are also presented and discussed.     

Boc-L-甲基苯丙氨酸的合成与拆分

利用Boc-2-氨基丙二酸二乙酯和甲基苄溴为原料, 合成邻位、间位、对位甲基取代的Boc-苯丙氨酸乙酯, 经枯草杆菌蛋白酶拆分得到对应的Boc-L-甲基苯丙氨酸. 通过红外光谱、核磁共振、质谱及旋光度分析对3种物质的结构进行了表征.     

A molecular dynamics study of the pentacyclo-undecane cage amino acid tripeptide

In this paper, we report on the conformational profile of the pentacyclo-undecane (PCU) cage tripeptide carried out by molecular dynamics (MD) simulation using water as an explicit solvent. The MD solution phase studies carried on the model peptide analogues (A)=Ac–Ala–Ala–Ala–NHMe; (B)=Ac–Cage–Cage–Cage–NHMe; (C)=Ac–Ala–Cage–Ala–NHMe and (D)=Ac–Ala–Pro–Ala–NHMe, are used as a complimentary technique to the corresponding gas phase simulated annealing (SA) study previously carried out in our laboratory. No significant structural changes were observed over the MD trajectories. However, the results reported here provide further evidence that the (PCU) cage amino acid exhibits C_7eq, C_7aq, _R and _L conformations, and the theoretical results suggest that the PCU cage amino acid is a strong β-turn inducer. These results support the prediction that when the PCU cage residues are in the (i) and (i+2) positions, the β-turn can be extended in either direction to form anti-parallel β-pleated sheets, thereby forming the basis of the mechanism for the folding back of the chain in a cross-β-turn structure.     

Synthesis and structural studies of peptides containing a glucose-derived furanoid sugar amino acid

Conformational analysis of peptides containing a glucose-derived furanoid sugar amino acid (Gaa) by detailed NMR and constrained MD studies revealed that peptides with repeating Gaa-Leu-Val units had conformational signatures very similar to those of linear homooligomers of Gaa.     

Conformational studies of the linear homooligomers of a glucose-derived furanoid sugar amino acid

Conformational analysis of the linear tetramer of the glucose-derived furanoid sugar amino acid 1 by NMR and constrained molecular dynamics studies revealed that the fully protected tetramer 2a has a well-defined structure in CDCl₃ with repeating β-turns, each involving a 10-membered ring structure with intramolecular hydrogen bonds between NH_i → CO_i−2. Its deprotected versions 2b and 2c showed aggregation in organic solvents with structures similar to that of 2a.     

Synthesis of functionalized guanidino amino acids

We report the synthesis of guanidino amino acids (GuAA), which are structurally related to Arg and resemble a dipeptide consisting of alpha- and gamma-amino acid with a guanidinium group in the main chain. The compounds are available with different protecting groups in gram amounts and are intended as synthetic building blocks for the construction of synthetic oxoanion or peptide receptors. Tyr, Trp or dansyl-functionalized Lys can be introduced as the alpha-amino acid part, which leads to luminescent GuAAs. The compounds signal carboxylate binding in MeOH, DMSO and buffered water by change of the emission intensity. The property may find use in the construction of chemosensors.     

Synthesis of phosphinic and phosphonic analogs of aromatic amino acids

The reaction of aryl and aralkyl aldoximes with hypophosphorous acid resulted in aminophosphinic acids, which were oxidized into the corresponding aminophosphonic acids. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 137–140, January, 1997.     

A halide-initiated aza-Baylis-Hillman reaction: generation of unnatural amino acids

A series of allenic ketones react with a glyoxylate-derived imine in the presence of MgBr₂ through an aza-Morita-Baylis-Hillman (MBH) reaction. The isolation of a variety of unnatural amino acids with unique allene-containing functional groups provides a conceptually new application of the aza-MBH. The reaction scope and preliminary mechanistic investigations are discussed.     

Alumina catalyzed reactions of amino acids

Thermal reactions of glycine (Gly), alanine (Ala), leucine (Leu), valine (Val) and proline (Pro) adsorbed on activated alumina were studied by means of thermal analysis. In the absence of alumina, decomposition of amino acids was detected as a sharp endotherm above 200°C, whereas no thermal effects were detectable by differential thermal analysis (DTA) and differential scanning calorimetry (DSC) for amino acid/alumina mixtures. This could be explained by a continuous amino acid condensation to peptides and simultaneous absorption of formed water by alumina, the latter being gradually released at higher temperatures. Thermogravimetry (TG) and differential thermogravimetry (DTG) measurements revealed that the reactions of the amino acids adsorbed on alumina surface were spread over a wide range of temperatures. The catalysis of peptide bond formation on alumina surface at 85°C was proven directly by the identification of the reaction products, mainly dipeptides and cyclic anhydrides. This revised version was published online in August 2006 with corrections to the Cover Date.     

Fluoroalkyl substituted (Z)-dehydro α-amino ester as a building block for the fluorine-containing cyclopropyl α-amino esters and dihydrooxazole

Multi-functionalized β-trifluoromethyl and β-difluoromethyl substituted (Z)-α,β-dehydro α-amino esters have been successfully prepared from N-protected fluorinated threonine ester. Applications of this new fluorine-containing building block to the synthesis of biologically important fluorinated cylcopropyl α-amino esters and dihydrooxazole ester have also been reported.     

Chromatography of amino acids and short peptides. New advances

The newest results in the application of various chromatographic methods (gas-liquid chromatography, liquid chromatographic techniques, electrically driven systems) for the separation and quantitative determination of amino acids and short peptides in pure state and in complicated matrices are compiled. The results are concisely described and critically evaluated. The future trends of the chromatographic analysis of amino acids and short peptides are briefly discussed.     

Complexation of thiacalix[4]arene methylphosphonic and sulphonic acids with amino acids

In this paper, host–guest complexation process of thiacalix[4]arene tetrakis–methylphosphonic and tetrakis–sulphonic acids with amino acids by HPLC and molecular modelling methods has been studied. It was shown that thiacalix[4]arene tetrakis–methylphosphonic acid due to transformability of macrocyclic skeleton and flexibility of methylphosphonic substituents can adopt its conformation for strong multicentre binding of the amino acids with association constant values 530–10,140 M^? 1 in water.     

Isotope effect on the solubility of amino acids in water

The solubilities of glycine, alanine, phenylalanine, and proline in H₂O and D₂O from 283 K to 335 K were determined. It was found that glycine and alanine are less soluble in heavy water than in light water but proline is more soluble in heavy water over the whole temperature range studied. Phenylalanine is more soluble in H₂O than D₂O below 310 K but above that temperature heavy water becomes a better solvent. An influence of H/D isotope substitution on the enthalpies of solution is also observed. In the case of glycine and alanine enthalpies of solution in heavy water increase by a small amount and in the same time the solution enthalpy for phenylalanine in D₂O increases markedly. No change in the solution enthalpy for proline was observed. The isotope effects on solubility and the solution enthalpy are qualitatively discussed.     

Synthesis of tetrazole analogues of amino acids using Fmoc chemistry: isolation of amino free tetrazoles and their incorporation into peptides

An efficient synthesis of tetrazole analogues of amino acids starting from N^α-Fmoc amino acid in a three-step protocol is reported. The free amino tetrazoles were obtained in good yields and with excellent purity after removal of the Fmoc group. The synthesis of analogues of aspartic and glutamic acids in which the 5-tetrazolyl moiety is inserted at the β/γ carboxyl group starting from Fmoc-Asn and Fmoc-Gln and the incorporation of these tetrazoles into peptides are also described.