手性辅基法不对称合成特殊结构α-氨基酸——甘氨酸等当体途径

特殊结构的α-氨基酸对于生命过程研究和生物医药开发有重要意义. 不对称合成α-氨基酸的方法学中, 手性辅基方法是较多研究和应用的领域. 介绍了该方法近二十年来的发展, 对近十年的甘氨酸等当体合成策略做了详尽述评.     

1-甲氧基乙基-3-甲基咪唑甘氨酸离子液体的物理化学性质的研究

由于氨基酸基的独特性质,我们以甘氨酸作为阴离子,醚基咪唑基团作为阳离子合成了一种新型离子液体1-甲氧乙基-3-甲基咪唑甘氨酸[MOEMIM][Gly],并经过核磁共振氢谱、核磁共振碳谱和差示扫描量热进行表征。由于离子液体和水之间形成氢键导致传统的方法不能去除水的影响,所以在实验测定中,选用标准加入法在温度范围为298.15–338.15 K,每隔5 K测定离子液体[MOEMIM][Gly]的密度和表面张力。利用密度数据,计算得到离子液体[MOEMIM][Gly]的摩尔体积,并且摩尔体积随着温度的升高而增加,同时得到了热膨胀系数。根据离子液体[MOEMIM][Gly]的摩尔表面Gibbs自由能,改进了传统的Eötvös经验方程,使得方程具有更明确的物理意义,即截距C₀代表摩尔表面焓,它是一个与温度无关的常数,斜率则为摩尔表面熵,这表明改进的Eötvös方程不仅是一个经验方程,而且还是严格的热力学方程。另外,结合摩尔表面Gibbs自由能和改进的Eötvös方程,估算了离子液体的[MOEMIM][Gly]的表面张力,并与实验值进行比较,发现两者很好的一致。     

甘氨酸与间硝基苯甲酸加合物的合成及晶体结构

The title 1:1 adduct, has been prepared and a large single crystal with dimensions of 5 mm×50 mm×20 mm was obtained by slow-cooling method. It produces the green radiation at 532 nm under the irradiation of Nd~3+: YAG laser beam at 1064nm. The crystal structure of this potential non-linear optical material was determined by X-ray diffraction method. The crystal is orthorbombic, space group Pca2_1, with a=2.2701(5) nm, b=0.5852(2) nm, c=0.7815(2) nm, Z=4; final R is 0.054 for 702 observed reflections. The intermolecular hydrogen bonds are formed between the amino and carboxyl groups of glycines, which connect the glycine molecules to form two-dimensional network parallel to the (100) plane, while the intermolecular hydrogen bonds between the carboxyl group of glycine and the carboxyl group of m-nitrobenzoic acid let the latter link to above mentioned two-dimensional network.     

Thermodynamics of amino acid dissociation in mixed solvents. 3: Glycine in aqueous glucose solutions from 5 to 45°C

The first thermodynamic dissociation constants of glycine in 5, 15 mass % glucose+water mixed solvents at five temperatures from 5 to 45°C have been determined from precise emf measrements of a cell without liquid junction using hydrogen and Ag-AgCl electrodes and a new method of polynomial approximation proposed on the basis of Pitzer's electrolytic solution theory in our previous paper. The results obtained from both methods agree within experimental error. The standard free energy of transfer for HCl from water to aqueous mixed solvent have been calculated and the results are discussed.     

The Design of α/β‐Peptides: Study on Three‐Residue Turn Motifs and the Influence of Achiral Glycine on Helix and Turn

Novel three‐residue helix‐turn secondary structures, nucleated by a helix at the N terminus, were generated in peptides that have ‘β‐Caa‐L ‐Ala‐L ‐Ala,’ ‘β‐Caa‐L ‐Ala‐γ‐Caa,’ and ‘β‐Caa‐L ‐Ala‐δ‐Caa’ (in which β‐Caa is C‐linked carbo‐β‐amino acid, γ‐Caa is C‐linked carbo‐γ‐amino acid, and δ‐Caa is C‐linked carbo‐δ‐amino acid) at the C terminus. These turn structures are stabilized by 12‐, 14‐, and 15‐membered (mr) hydrogen bonding between NH(i)/CO(i+2) (i+2 is the last residue in the peptide) along with a 7‐mr hydrogen bond between CO(i)/NH(i+2). In addition, a series of α/β‐peptides were designed and synthesized with alternating glycine (Gly) and (S)‐β‐Caa to study the influence of an achiral α‐residue on the helix and helix‐turn structures. In contrast to previous results, the three ‘β–α–β’ residues at the C terminus (α‐residue being Gly) are stabilized by only a 13‐mr forward hydrogen bond, which resembles an α‐turn. Extensive NMR spectroscopic and molecular dynamics (MD) studies were performed to support these observations. The influence of chirality and side chain is also discussed.     

How Computations Can Assist the Rational Design of Drugs for Photodynamic Therapy: Photosensitizing Activity Assessment of a Ru(II)-BODIPY Assembly

Ruthenium-based complexes represent a new frontier in light-mediated therapeutic strategies against cancer. Here, a density functional-theory-based computational investigation, of the photophysical properties of a conjugate BODIPY-Ru(II) complex, is presented. Such a complex was reported to be a good photosensitizer for photodynamic therapy (PDT), successfully integrating the qualities of a NIR-absorbing distyryl-BODIPY dye and a PDT-active [Ru(bpy)₃]²⁺ moiety. Therefore, the behaviour of the conjugate BODIPY-Ru(II) complex was compared with those of the metal-free BODIPY chromophore and the Ru(II) complex. Absorptions spectra, excitation energies of both singlet and triplet states as well as spin–orbit-matrix elements (SOCs) were used to rationalise the experimentally observed different activities of the three potential chromophores. The outcomes evidence a limited participation of the Ru moiety in the ISC processes that justifies the small SOCs obtained for the conjugate. A plausible explanation was provided combining the computational results with the experimental evidences.     

Concise synthetic strategy toward cyclic α,α-disubstituted α-amino acids bearing a δ-nitrogen atom: chiral 1-substituted 4-aminopiperidine-4-carboxylic acids

A concise synthetic strategy toward cyclic α,α-disubstituted α-amino acids, 1-substituted 4-aminopiperidine-4-carboxylic acids have been developed. The synthetic route is a reductive amination of dimethyl bis(dioxolanemethyl)malonate with various amines, followed by Curtius rearrangement. This synthetic route is capable of synthesizing 4-aminopiperidine-4-carboxylic acids bearing a bulky substituent and optically active ones bearing a pendent chiral substituent, by the change of condensed amines.     

An Insight into All Tested Small Molecules against Fusarium oxysporum f. sp. Albedinis: A Comparative Review

Bayoud disease affects date palms in North Africa and the Middle East, and many researchers have used various methods to fight it. One of those methods is the chemical use of synthetic compounds, which raises questions centred around the compounds and common features used to prepare targeted molecules. In this review, 100 compounds of tested small molecules, collected from 2002 to 2022 in Web of Sciences, were divided into ten different classes against the main cause of Bayoud disease pathogen Fusarium oxysporum f. sp. albedinis (F.o.a.) with structure–activity relationship (SAR) interpretations for pharmacophore site predictions as (δ⁻···δ⁻), where 12 compounds are the most efficient (one compound from each group). The compounds, i.e., (Z)-1-(1.5-Dimethyl-1H-pyrazole-3-yl)-3-hydroxy but-2-en-1-one 7, (Z)-3-(phenyl)-1-(1,5-dimethyl-1H-pyrazole-3-yl)-3-hydroxyprop-2-en-1-one 23, (Z)-1-(1,5-Dimethyl-1H-pyrazole-3-yl)-3-hydroxy-3-(pyridine-2-yl)prop-2-en-1-one 29, and 2,3-bis-[(2-hydroxy-2-phenyl)ethenyl]-6-nitro-quinoxaline 61, have antifungal pharmacophore sites (δ⁻···δ⁻) in common in N1---O4, whereas other compounds have only one δ⁻ pharmacophore site pushed by the donor effect of the substituents on the phenyl rings. This specificity interferes in the biological activity against F.o.a. Further understanding of mechanistic drug–target interactions on this subject is currently underway.     

A solvation‐free‐energy functional: A reference‐modified density functional formulation

The three‐dimensional reference interaction site model (3D‐RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation‐free‐energy (SFE) for large solute molecules in water. To improve the free‐energy density functional for the SFE of solute molecules, we propose a reference‐modified density functional theory (RMDFT) that is a general theoretical approach to construct the free‐energy density functional systematically. In the RMDFT formulation, hard‐sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction‐site‐model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side‐chain analogues as well as for 504 small organic molecules. © 2015 Wiley Periodicals, Inc.     

Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: a molecular modeling perspective

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme for splicing a viral DNA (vDNA) replica of its genome into host cell chromosomal DNA (hDNA) and has been recently recognized as a promising therapeutic target for developing anti-AIDS agents. The interaction between HIV-1 IN and vDNA plays an important role in the integration process of the virus. However, a detailed understanding about the mechanism of this interactions as well as the action of the anti-HIV drug raltegravir (RAL, approved by FDA in 2007) targeting HIV-1 IN in the inhibition of the vDNA strand transfer is still absent. In the present work, a molecular modeling study by combining homology modeling, molecular dynamics (MD) simulations with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and molecular mechanics Generalized-Born surface area (MM-GBSA) calculations was performed to investigate the molecular mechanism of HIV-1 IN-vDNA interactions and the inhibition action of vDNA strand transfer inhibitor (INSTI) RAL. The structural analysis showed that RAL did not influence the interaction between vDNA and HIV-1 IN, but rather targeted a special conformation of HIV-1 IN to compete with host DNA and block the function of HIV-1 IN by forcing the 3'-OH of the terminal A17 nucleotide away from the three catalytic residues (Asp64, Asp116, and Glu152) and two Mg(2+) ions. Thus, the obtained results could be helpful for understanding of the integration process of the HIV-1 virus and provide some new clues for the rational design and discovery of potential compounds that would specifically block HIV-1 virus replication.     

Synthesis,experimental and in silico studies of N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine,coupled with CSD data: a survey of interactions in the crystal structures of Fmoc–amino acids

Recently, fluorenylmethoxycarbonyl (Fmoc) amino acids (e.g. Fmoc–tyrosine or Fmoc–phenylalanine) have attracted growing interest in biomedical research and industry, with special emphasis directed towards the design and development of novel effective hydrogelators, biomaterials or therapeutics. With this in mind, a systematic knowledge of the structural and supramolecular features in recognition of those properties is essential. This work is the first comprehensive summary of noncovalent interactions combined with a library of supramolecular synthon patterns in all crystal structures of amino acids with the Fmoc moiety reported so far. Moreover, a new Fmoc‐protected amino acid, namely, 2‐{[(9H‐fluoren‐9‐ylmethoxy)carbonyl](methyl)amino}‐3‐{4‐[(2‐hydroxypropan‐2‐yl)oxy]phenyl}propanoic acid or N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine, Fmoc‐N‐Me‐Tyr(t‐Bu)‐OH, C₂₉H₃₁NO₅, was successfully synthesized and the structure of its unsolvated form was determined by single‐crystal X‐ray diffraction. The structural, conformational and energy landscape was investigated in detail by combined experimental and in silico approaches, and further compared to N‐Fmoc‐phenylalanine [Draper et al. (2015). CrystEngComm, 42 , 8047–8057]. Geometries were optimized by the density functional theory (DFT) method either in vacuo or in solutio. The polarizable conductor calculation model was exploited for the evaluation of the hydration effect. Hirshfeld surface analysis revealed that H…H, C…H/H…C and O…H/H…O interactions constitute the major contributions to the total Hirshfeld surface area in all the investigated systems. The molecular electrostatic potentials mapped over the surfaces identified the electrostatic complementarities in the crystal packing. The prediction of weak hydrogen‐bonded patterns via Full Interaction Maps was computed. Supramolecular motifs formed via C—H…O, C—H…π, (fluorenyl)C—H…Cl(I), C—Br…π(fluorenyl) and C—I…π(fluorenyl) interactions are observed. Basic synthons, in combination with the Long‐Range Synthon Aufbau Modules, further supported by energy‐framework calculations, are discussed. Furthermore, the relevance of Fmoc‐based supramolecular hydrogen‐bonding patterns in biocomplexes are emphasized, for the first time.     

Simulation of carbohydrate-protein interactions: Computer-aided design of a second generation GM1 mimic

The oligosaccharide of ganglioside GM1 [Gal1-3GalNAc1-4(NeuAc2-3)Gal1-4Glc1-1Cer] is the cellular target of two bacterial enterotoxins: the cholera toxin (CT) and the heat-labile toxin of E.coli (LT). We recently reported that the pseudosaccharide 2[Gal1-3GalNAc1-4(NeuAc2-3)DCCHD] is a high-affinity ligand for CT, and thus a functional mimic of GM1 (Bernardi, A., Checchia, A., Brocca, P., Sonnino, S. and Zuccotto, F., J. Am. Chem. Soc., 121 (1999) 2032–2036). In this paper we describe the design of a second-generation mimic, formally obtained from 2 by inverting the configuration of a single stereocenter, thus transforming a N-acetyl galactosamine into a N-acetyl glucosamine. The design process involved modeling of the free ligand and its LT complex, followed by qualitative and quantitative comparison with the corresponding structures of 2. The protocol employed relied on both conformational search and molecular dynamics methodologies to account for the flexibility of both the ligand and the protein receptor. The conformational search of the LT:inhibitor complex showed that, compared to 2, the new compound can insert one more hydroxy group within the protein binding site. Molecular dynamics simulations showed that, in turn, this may trigger a series of rearrangements and reorientations of side chains and crystallographic water molecules in the toxin, leading to new H-bond contacts which may result in enhanced affinity of the new inhibitor. FEP calculations were performed by mutating the structure of 2 in solution and in the protein complex, and the prediction was made that the second-generation mimic should be a stronger binder than its parent compound.     

The Glu143 Residue Might Play a Significant Role in T20 Peptide Binding to HIV-1 Receptor gp41: An In Silico Study

Despite the enormous efforts made to develop other fusion inhibitors for HIV, the enfuvirtide (known as T20) peptide is the only approved HIV-1 inhibitory drug so far. Investigating the role of potential residues of the T20 peptide’s conformational dynamics could help us to understand the role of potential residues of the T20 peptide. We investigated T20 peptide conformation and binding interactions with the HIV-1 receptor (i.e., gp41) using MD simulations and docking techniques, respectively. Although the mutation of E143 into alanine decreased the flexibility of the E143A mutant, the conformational compactness of the mutant was increased. This suggests a potential role of E143 in the T20 peptide’s conformation. Interestingly, the free energy landscape showed a significant change in the wild-type T20 minimum, as the E143A mutant produced two observed minima. Finally, the docking results of T20 to the gp41 receptor showed a different binding interaction in comparison to the E143A mutant. This suggests that E143 residue can influence the binding interaction with the gp41 receptor. Overall, the E143 residue showed a significant role in conformation and binding to the HIV-1 receptor. These findings can be helpful in optimizing and developing HIV-1 inhibitor peptides.     

Crystal Structure of a Hydrated Molecular 1 : 2 Complex of Nicotinamide Adenine Dinucleotide (NAD+) and Gallic Acid: Polar Alignment of the Phenolic Partner Molecules

Nicotinamide adenine dinucleotide (oxidized form, free acid, NAD⁺) was utilized as an auxiliary for polar alignment of gallic acid (=3,4,5‐trihydroxybenzoic acid, GA) in the crystalline molecular complex NAD⁺?(GA)₂?(H₂O)₅. In this adduct, NAD⁺ takes up a novel U‐shaped conformation accepting a GA molecule to give rise to a pincer‐type π‐complex. With the assistance of further GA molecules, these pincer assemblies build up infinite donor? acceptor π‐stacks in the crystal. An extended network of H‐bonds among the multitude of pertinent active functional groups and the water molecules supports the crystal structure. These findings may imply noteworthy material properties, in particular nonlinear optical effects, and might also serve to trigger inspiring biochemical connections to be made. The crystal structure of anhydrous GA is also reported, which is centrosymmetric and non‐polar.     

Monolayers (Langmuir films) behavior of multi-component systems composed of a bile acid with different sterols and with their 1:1 mixtures

Different physicochemical properties of Langmuir films (monolayers) composed of 10 mixed systems of a bile acid, deoxycholic acid (DC) with various plant sterols, such as stigmasterol (Stig), beta-sitosterol (Sito) and campesterol (Camp) and a stanol, cholestanol (Chsta) in addition to an animal sterol, cholesterol (Ch) [these sterols and Chsta are abbreviated as St] and DC with 1:1 St mixtures; (Ch+Chsta), (Ch+Stig), (Stig+Chsta), (Ch+Sito) and (Ch+Camp) on the substrate of 5M aqueous NaCl solution (pH 1.2) at 25 degrees C, were investigated in terms of mean surface area per molecule (A(m)), the partial molecular area (PMA), surface excess Gibbs energy (DeltaG((ex))), interaction parameter (I(p)) as well as activity coefficients (f(1) and f(2)) in 2-D phase of each binary (or ternary) component system and elasticity (Cs(-1)) of formed films; these were analyzed on the basis of the respective surface pressure (pi) versus A(m) isotherms as a function of mole fraction of Sts (X(st)) in the DC/St(s) mixtures at discrete surface pressures. Notable findings are: (i) all the binary component systems did form patched film type monolayers consisting of (a) DC-dominant film solubilizing a trace amount of St molecules and (b) St dominant film dissolving a small amount of DC molecules, (ii) DC in 2-D phase exhibited a transition from LE film to LC film at a constant pressure (pi(C)(1)) accompanied by compression and (iii) DeltaG((ex)) as well as I(p) was found to be greatly dependent on (a) the combinations of DC with different St species and (b) to be markedly varied by a difference in mixing ratio of DC to Sts. Compressibility (or elasticity) analyses and fluorescence microscopy images could support the above findings as well as interpretation.     

Catalyst‐ and solvent‐free synthesis of 2‐fluoro‐N‐(3‐methylsulfanyl‐1H‐1,2,4‐triazol‐5‐yl)benzamide through a microwave‐assisted Fries rearrangement: X‐ray structural and theoretical studies

An efficient approach for the regioselective synthesis of (5‐amino‐3‐methylsulfanyl‐1H‐1,2,4‐triazol‐1‐yl)(2‐fluorophenyl)methanone, C₁₀H₉FN₄OS, (3), from the N‐acylation of 3‐amino‐5‐methylsulfanyl‐1H‐1,2,4‐triazole, (1), with 2‐fluorobenzoyl chloride has been developed. Heterocyclic amide (3) was used successfully as a strategic intermediate for the preparation of 2‐fluoro‐N‐(3‐methylsulfanyl‐1H‐1,2,4‐triazol‐5‐yl)benzamide, C₁₀H₉FN₄OS, (4), through a microwave‐assisted Fries rearrangement under catalyst‐ and solvent‐free conditions. Theoretical studies of the prototropy process of (1) and the Fries rearrangement of (3) to provide (4), involving the formation of an intimate ion pair as the key step, were carried out by density functional theory (DFT) calculations. The crystallographic analysis of the intermolecular interactions and the energy frameworks based on the effects of the different molecular conformations of (3) and (4) are described.     

A new dinuclear copper (II) complex of 2,5–Furandicarboxyclic acid with 4(5)‐Methylimidazole as a high potential α‐glucosidase inhibitor: Synthesis,Crystal structure,Cytotoxicity study,and TD/DFT calculations

A new dinuclear copper (II) complex of 2,5–furandicarboxyclic acid with 4(5)‐methylimidazole, [Cu (FDCA)((4(5)MeI)₂]₂·2H₂O, was synthesized, and its structure characterized by XRD, FT–IR and UV–Vis spectroscopic techniques. The α‐glucosidase inhibition and cytotoxicity study of the synthesized Cu (II) complex were determined by IC₅₀ values. The optimized geometry and vibrational harmonic frequencies for the Cu (II) complex were obtained by using Density Functional Theory (DFT) of HSEh1PBE/6–311++G(d,p)/LanL2DZ level. TD‐DFT/HSEh1PBE/6–311++G(d,p)/LanL2DZ level with CPCM model was applied to examine the electronic spectral properties and major contributions were determined via Swizard program. To investigate linear and nonlinear optical behavior of the synthesized Cu (II) complex, the α, Δα and χ⁽¹⁾/β, γ and χ⁽³⁾ parameters called linear/nonlinear optical parameters in gas phase and ethanol solvent were computed at the same level and basis set. Furthermore, molecular electrostatic potential (MEP) surface was determined by using the same level. The docking study of the Cu (II) complex to the binding site of the target protein (the template structure S. cerevisiae isomaltase) is fulfilled. Natural bond orbital (NBO) analysis was used to investigate the hyperconjugative interactions, inter‐ and intra‐molecular bonding and to determine coordination around Cu (II) ion. Finally, present work is the first remarkable scientific report of mixed‐ligand (H₂FDCA and 4(5)MeI) Cu (II) complex as novel drug candidate for DM II. It is also determined that microscopic third?NLO parameters for the Cu (II) complex is remarkable.