虚拟原子探针随机采样法用于氨基酸结构描述及其构效关系研究

考虑药物与蛋白质受体的3类非键作用模式, 利用8类虚拟原子探针和Monte Carlo随机采样技术, 得到了一套新的氨基酸侧链表面静电、立体及疏水势能场(ASSPF)参数. 在此基础上对苦味二肽和血管舒缓激五肽进行了结构表征和QSAR研究, 所建模型复相关系数R2和留一法交互检验复相关系数QLOOCV2分别为0.8457, 0.851和0.7688, 0.7952, 同时分析了肽链不同位置上氨基酸侧链对活性的影响, 取得较好的结果.     

Screening nucleotide binding to amino acid-coated supports by surface plasmon resonance and nuclear magnetic resonance

Here, we describe a rapid and efficient screening method using surface plasmon resonance (SPR) and saturation transfer difference–nuclear magnetic resonance (STD-NMR) spectroscopy to yield information regarding the residues involved in nucleotide binding to amino acid-coated supports. The aim of this work was to explore the use of these spectroscopic techniques to study amino acid–nucleotide interactions in order to improve the binding specificity of the amino acid ligands used to purify plasmid DNA. For SPR, we present a strategy that immobilizes arginine and lysine on a surface as model supports, and we analyze binding responses when synthetic homo-deoxyoligonucleotides are injected over the amino acid surface. The binding responses are detectable and reproducible despite the small size of the immobilized amino acids. Using STD-NMR, we performed epitope mapping of homo-deoxyoligonucleotides bound to l-arginine–bisoxyran–Sepharose and l-lysine–Sepharose supports. Polynucleotide binding preferences differed; for example, polyC interacted preferentially through its backbone with the two supports, whereas polyT bound the supports through its thymine moiety. STD-NMR combined with SPR measurements was successfully used to screen amino acid–nucleotide interactions and determine the binding affinities of the complexes.     

Facile syntheses of conformationally constrained analogues of lysine and homoglutamic acid

A facile divergent synthesis of the novel amino acid trans-4-aminoethyl-l-proline and trans-4-carboxymethyl-l-proline from commercially available trans-4-hydroxy-l-proline was developed. These conformationally constrained analogues of l-lysine and l-homoglutamic acid are useful proline templated amino acids (PTAAs) with potential applications in protein engineering and de novo protein design.     

Fluorescent cyclodextrins bearing metal binding sites and their use for chemo- and enantioselective sensing of amino acid derivatives

Ditopic receptors based on cyclodextrins bearing a metal binding site were used as enantioselective fluorescence sensors, which were able to generate different responses in the presence of d- or l-amino acids. The performances of the selectors as a function of their structure were evaluated, and the same analysis was extended to other analytes. In this work, this approach is used for the enantiomers of a series of amino acid derivatives and in particular of 2-aminocaprolactam. The results showed that the ability of these sensors to perform enantiomeric analysis can be extended to other analytes of interest in organic synthesis such as amino acid amides and α-aminolactams.     

Control of the stability of a protein-RNA complex by the position of fluorine in a base analogue

The effects of modifying the electronic characteristics of nonpolar base analogues substituted at positions involved in stacking interactions between SL2 RNA and the U1A protein are described. A surprisingly large difference in the stability between complexes formed with base analogues that differ only in the position of substitution of a single fluorine atom is observed. The results of high-level ab initio calculations of the interactions between the nonpolar base analogue and the amino acid side chain correlate with the experimentally observed trends in complex stability, which suggests that changes in stacking interactions that result from varying the position and degree of fluorine substitution contribute to the effects of fluorine substitution on the stability of the U1A-SL2 RNA complex.     

Using physical chemistry to differentiate nicotinic from cholinergic agonists at the nicotinic acetylcholine receptor

The binding of three distinct agonists-acetylcholine (ACh), nicotine, and epibatidine-to the nicotinic acetylcholine receptor has been probed using unnatural amino acid mutagenesis. ACh makes a cation-pi interaction with Trp alpha149, while nicotine employs a hydrogen bond to a backbone carbonyl in the same region of the agonist binding site. The nicotine analogue epibatidine achieves its high potency by taking advantage of both the cation-pi interaction and the backbone hydrogen bond. A simple structural model that considers only possible interactions with Trp alpha149 suggests that a novel aromatic C-H...O=C hydrogen bond further augments the binding of epibatidine. These studies illustrate the subtleties and complexities of the interactions between drugs and membrane receptors and establish a paradigm for obtaining detailed structural information.     

Effect of some amino acids and peptides on silicic acid polymerization

The polymerization of silicic acid in aqueous solutions at different pH was followed by the colorimetric molybdosilicate method. The role of four amino acids (serine, lysine, proline and aspartic acid) and the corresponding homopeptides was studied. All four amino acids behave the same way and favor the condensation of silicic acid. Peptides exhibit a stronger catalytic effect than amino acids but they appear to behave in very different ways depending on the nature of side-groups and pH. Poly-lysine and poly-proline for instance lead to the precipitation of solid phases containing both silica and peptides. The role of these biomolecules on the polymerization of silicic acid is discussed in terms of electrostatic interactions, hydrogen bonds and solubility.     

Dimensionality of amino acid space and solvent accessibility prediction with neural networks

Solvent accessibility prediction from amino acid sequences has been pursued by several researchers. Such a prediction typically starts by transforming the amino acid category (or type) information into numerical representations. All twenty amino acids can be completely and uniquely represented by 20-dimensional vectors. Here, we investigate if the amino acid space defined in this way really requires twenty dimensions. We tried to develop corresponding representations in fewer dimensions. A method for searching optimal codification schema in an arbitrary space using neural networks was developed. The method is used to obtain optimal encoding of amino acids at various levels of dimensionality, and applied to optimize the amino acid codifications for the prediction of the solvent accessibility values of the proteins using feed-forward neural networks. The traditional 20-dimensional codification seems to be redundant in solving the solvent accessibility prediction problem, since a 1-dimensional codification is able to achieve almost the same degree of accuracy as the 20-dimensional codification. Optimal coding in much fewer dimensions could be used to make the predictions of accessible surface area with almost the same degree of accuracy as that obtained by a fully unique 20-dimensional coding. The 1-dimensional amino acid codification for solvent accessibility prediction obtained by a purely mathematical way based on neural networks is highly correlated with a physical property of the amino acids, namely their average solvent accessibility. The method developed to find the optimal codification is general, although the codification thus produced is dependent on the type of estimated property.     

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution

Summary Two new continuum solvation models have been presented recently, and in this paper they are explained and reviewed in detail with further examples. Solvation Model 2 (AM1-SM2) is based on the Austin Model 1 and Solvation Model 3 (PM3-SM3) on the Parameterized Model 3 semiempirical Hamiltonian. In addition to the incorporation of phosphorus parameters, both of these new models address specific deficiencies in the original Solvation Model 1 (AM1-SM1), viz., (1) more accurate account is taken of the hydrophobic effect of hydrocarbons, (2) assignment of heavy-atom surface tensions is based on the presence or absence of bonded hydrogen atoms, and (3) the treatment of specific hydration-shell water molecules is more consistent. The new models offer considerably improved performance compared to AM1-SM1 for neutral molecules and essentially equivalent performance for ions. The solute charges within the Parameterized Model 3 Hamiltonian limit the utility of PM3-SM3 for compounds containing nitrogen and possibly phosphorus. For other systems both AM1-SM2 and PM3-SM3 give realistic results, but AM1-SM2 in general outperforms PM3-SM3. Key features of the models are discussed with respect to alternative approaches.     

Synthesis and pharmacology of glutamate receptor ligands: new isothiazole analogues of ibotenic acid

The naturally occurring heterocyclic amino acid ibotenic acid (Ibo) and the synthetic analogue thioibotenic acid (Thio-Ibo) possess interesting but dissimilar pharmacological activity at ionotropic and metabotropic glutamate receptors (iGluRs and mGluRs). Therefore, a series of Thio-Ibo analogues was synthesized. The synthesis included introduction of substituents by Suzuki and Grignard reactions on 4-halogenated 3-benzyloxyisothiazolols, reduction of the obtained alcohols, followed by introduction of the amino acid moiety by use of 2-(N-tert-butoxycarbonylimino)malonic acid diethyl ester. The obtained Thio-Ibo analogues (1, 2a-g) were characterized in functional assays on recombinant mGluRs and in receptor binding assays on native iGluRs. At mGluRs, the activity at Group II was retained for compounds with small substituents (2a-2d), whereas the Group I and Group III receptor activities for all new compounds were lost. Detection of NMDA receptor affinity prompted further characterization, and two-electrode voltage-clamp recordings at recombinant NMDA receptor subtypes NR1/NR2A-D expressed in Xenopus oocytes were carried out for compounds with small substituents (chloro, bromo, methyl or ethyl, compounds 2a-d). This series of Thio-Ibo analogues defines a structural threshold for NMDA receptor activation and reveals that the individual subtypes have different steric requirements for receptor activation. The compounds 2a and 2c are the first examples of agonists discriminating individual NMDA subtypes.     

Single Amino-Acid Based Self-Assembled Biomaterials with Potent Antimicrobial Activity

The design and development of soft biomaterials based on amino acid and short-peptide have gained much attention due to their potent biomedical applications. A slight alteration in the side-chain of single amino acid in a peptide or protein sequence has a huge impact on the structure and function. Phenylalanine is one of the most studied amino acids, which contains an aromatic phenyl group connected through a flexible −CH₂− unit. In this work, we have examined whether flexibility and aromatic functionality of phenylalanine (Phe) are important in gel formation of model gelator Fmoc-Phe-OH or not. To examine this hypothesis, we synthesized Fmoc-derivatives of three analogues unnatural amino acids including cyclohexylalanine, phenylglycine, and homophenylalanine; which are slightly varied from Phe. Interestingly, all these three new analogues formed hydrogels in phosphate buffer at pH 7.0 having different gelation efficacy and kinetics. This study suggests that the presence of aromatic side-chain and flexibility are not mandatory for the gelation of this model gelator. Newly synthesized unnatural amino acid derivatives have also exhibited promising antimicrobial activity towards gram-positive bacteria by inhibiting cellular oxygen consumption. We further determined the biocompatibility of these amino acid derivatives by using a hemolysis assay on human blood cells. Overall studies described the development of single amino acid-based new injectable biomaterials with improved antimicrobial activity by the slight alteration in the side-chain of amino acid.     

Templated biological synthesis of polymers of abiological monomers

A general method for the in vivo incorporation of amino acid analogues into artificial proteins is described. The method involves the construction of an artificial gene encoding the sequence of interest (with the corresponding natural amino acid encoded in place of the analogue), transformation of a bacterial host strain that cannot synthesize the natural amino acid, and induction of protein synthesis in a host culture enriched in the analogue. Results are described for the amino acid analogues selenomethionine, p-fluorophenylalanine, trifluoroleucine and 3-thienylalanine.     

Synthesis and properties of RNA analogues having amides as interuridine linkages at selected positions

Oligoribonucleotide analogues having amide internucleoside linkages (AM1: 3'-CH(2)CONH-5' and AM2: 3'-CH(2)NHCO-5') at selected positions have been synthesized and the thermal stability of duplexes formed by these analogues with complementary RNA fragments has been evaluated by UV melting experiments. Two series of oligomers with either 2'-OH or 2'-OMe vicinal to the amide linkages were studied. Monomeric synthons (3' and 5'-C amines and carboxylic acids) were synthesized as follows: For synthesis of the AM1 analogue, the known sequence of radical allylation followed by the cleavage of the double bond was adopted. For synthesis of the AM2 analogue, novel routes via addition of nitromethane followed by conversion of the nitro function to either amino or carboxyl groups were developed. Coupling of monomeric amines and carboxylic acids followed by protecting group manipulation and phosphonylation gave dimeric 3'-hydrogenphosphonate building blocks for oligonucleotide synthesis. Monomeric model compounds having 3'-amide and 2'-OH or 2'-OMe groups were also prepared and their conformational equilibrium was determined by (1)H NMR. The AM1 and AM2 models showed equal preferences for the North conformers (at 40 degrees C, 88-89% with 2'-OH, and 92-93% with 2'-OMe). At physiological salt concentration (0.1 M NaCl) the duplexes between AM1 modified oligonucleotides and RNA had stability similar to unmodified RNA-RNA duplexes (Delta t(m)= -0.2 to +0.7 degrees C per modification). However, the AM2 modification resulted in substantial stabilization of duplexes: Delta t(m)= +1 to +2.4 degrees C per modification compared to all RNA. A 2'-O-methyl vicinal to the AM2 linkage further increased the duplex stability. Our results suggest that RNA analogues having amide internucleoside bonds are very promising candidates for medicinal applications.     

On the prediction of equilibrium phase behavior of amino acids in aqueous and aqueous-electrolyte solutions using SAFT equation of state

We present an approach based on the statistical associating fluids theory (SAFT) to predict the solubility of amino acids in aqueous and aqueous-electrolyte solutions. This approach can describe the association interactions and their effects on the solubility of amino acids. Using the experimental data of activity coefficients of amino acids in water, the parameters of SAFT model for amino acids are obtained. The solubility of several amino acids in the temperature range of 273.15–373.15 K is predicted. Results obtained from the model are in a good accordance with the experimental data. Also, we examine the effect of pH on the solubility of dl-methionine. Addition of an extra amino acid to the binary solution of amino acid + water makes the system more complex. To check the accuracy of model, we study the ternary solution of dl-serine + dl-alanine + water and dl-valine + dl-alanine + water. Predicted results depict that the proposed model has the ability to describe the ternary solution of amino acids, accurately. Finally, the solubility of amino acids in aqueous-electrolyte solutions is investigated. The long-range interactions caused by the presence of ions affects the solubility of amino acids, leading them to be salted in or out. To treat this kind of interaction, the restrictive primitive mean spherical approximation (RP-MSA) is coupled with the SAFT equation of state. The proposed model can accurately predict the solubility of amino acids in aqueous-electrolyte solutions.     

Chiral Recognition of Amino Acid Esters in Organic Solvents Using a Glucose-Based Receptor

Due to the chemical and biological relevance of amino acids, efficient methods for the recognition and separation of their enantiomers are highly sought after. Chiral receptors based on extended molecular scaffolds are typically employed for this purpose. These receptors are often effective only in specific environments and towards a narrow scope of amino acid guests. Recently we reported a simple, glucose-based macrocycle capable of enantioselective binding of a broad range of amino acid methyl esters in water. Herein we demonstrate that the same receptor can be used for chiral recognition of amino acid esters in organic solvents. We show that the binding affinity and selectivity of the receptor are highly dependent on the coordinating strength of the solvent. An in-depth analysis of the receptor’s conformation and its interactions with amino acid methyl esters allowed us to propose a binding mode of amino acids to the receptor in CDCl₃. The binding modes in CDCl₃ and D₂O were then compared, highlighting the main interactions responsible for binding affinity and selectivity in each solvent. We envision that the insight provided by this study will facilitate the development of further amino acid receptors based on monosaccharides with improved binding affinities and both enantio- as well as chemoselectivities.     

Neuraminic Acid Derivatives as Anti-Influenza Drugs

Influenza types A and B both cause serious disease in man; vaccines are in use but must be reformulated each year in response to antigenic variation and are frequently ineffective against new influenza variants. Influenza viruses are enveloped RNA viruses which contain two major surface glycoproteins: hemagglutinin (HA) and neuraminidase (NA, EC 3.2.1.18). These proteins are essential for infection and offer potential targets for antiviral drug development. Based upon the knowledge of the most important steps of the whole interaction between virus and host cell, the main purpose of our research was to find a sialic acid analogue for increasing the affinity of the sialic acid cell receptor analogue to the principal binding site of HA. A series of sialic acid analogues were prepared and their structures were designed with the goal to have molecules able to saturate the HA receptor and thereby be potentially useful as anti-influenza drugs.     

Structure-activity relationships of GHRP-6 azapeptide ligands of the CD36 scavenger receptor by solid-phase submonomer azapeptide synthesis

The cluster of differentiation 36 (CD36) class B scavenger receptor binds a variety of biologically endogenous ligands in addition to synthetic peptides (i.e., growth hormone-releasing peptides, GHRPs), which modulate biological function related to anti-angiogenic and anti-atherosclerotic activities. Affinity labeling had previously shown that GHRP-6 analogues such as hexarelin, [2-Me-W(2)]GHRP-6 (1), bind to the lysine-rich domain of the CD36 receptor. Moreover, the azapeptide analogue [aza-F(4)]GHRP-6, 2, exhibited a characteristic β-turn conformation as described by CD and NMR spectroscopy and a slightly higher CD36 binding affinity relative to hexarelin (1.34 and 2.37 μM, respectively), suggesting receptor binding was mediated by the conformation and the aromatic residues of these peptide sequences. Ligand-receptor binding interactions were thus explored using azapeptides to examine influences of side-chain diversity and backbone conformation. In particular, considering that aromatic cation interactions may contribute to binding affinity, we have explored the potential of introducing salt bridges to furnish GHRP-6 azapeptide ligands of the CD36 receptor. Fifteen aza-glutamic acid analogues related to 2 were prepared by submonomer solid-phase synthesis. The azapeptide side chains were installed by novel approaches featuring alkylation of resin-bound semicarbazone with Michael acceptors and activated allylic acetates in the presence of phosphazene base (BTPP). Moreover, certain Michael adducts underwent intramolecular cyclization during semicarbazone deprotection, leading to novel pyrrazoline and aza-pyroglutamate N-terminal residues. Structural studies indicated that contingent on sequence the [aza-Glu]GHRP-6 analogues exhibited CD spectra characteristic of random coil, polyproline type II and β-turn secondary structures in aqueous media. In covalent competition binding studies with the GHRP-6 prototype hexarelin bearing a radiotracer, certain [aza-Glu]GHRP-6 azapeptides retained relatively high (2-27 μM) affinity for the CD36 scavenger receptor.     

Evaluation of the synergistic effect with amino acids for enantioseparation of basic drugs using capillary electrophoresis

The synergistic effect of two acidic amino acids, aspartic and glutamic acid, on the electrophoretic enantioseparation of four basic drugs was evaluated in the BGE containing a CD and at different pHs. Chlorpheniramine, hydroxyzine, propranolol and tramadol were used as the basic model drugs. However, no enantioseparations were achieved with a BGE containing sole amino acid, but the combined use of an acidic amino acid and a CD showed improved enantioseparations (synergistic effect) compared with the single CD system. The results demonstrated that at optimized pH, the electrostatic interactions of the anionic amino acids with the positively charged basic drugs could result in a decrease of the analyte migration velocity and it consequently improved the enantioseparation. The effective parameters such as the amino acid and chiral selector type and concentration, buffer pH, applied voltage, and capillary temperature were optimized. Favorable enantiomeric resolution and migration times of the model drugs were achieved with a 100 mM phosphate buffer solution (pH 3.0) containing 5.0 mM HP‐α‐CD/HP‐β‐CD and 20 mM aspartic acid with an 18 kV applied voltage at 25°C. ¹H NMR experiments were also carried out in a mixture of an analyte and CD in the absence and presence of aspartic acid. The NMR results were consistent with the results obtained by CE which showed the synergistic effect of amino acid.     

Investigation of Non-covalent Interactions of 18-Crown-6 with Amino Acids in Gas Phase by Mass Spectrometry

The non-covalent interactions between 18-Crown-6 (18c6) and 20 common types of protonated amino acids were explored by electrospray ionization mass spectrometry. The mass spectra showed that 18c6 could react with amino acids to form a non-covalent complexe in a stoichiometric ratio of 1:1. The calibration curves and linear equations for the complexes of L-Phe, L-Tyr, L-Lys and L-Asp with 18c6 were established by mass spectrometric titration and used as reference values for competitive ESI-MS. Through competitive equilibria, the binding constants for the complexes of 18c6 with other L-amino acids and their D-isomers were derived. It was found that, as a general trend, lgK_a for the complexes of 18c6 with the basic amino acid and the amino acid with alkyl side chain were larger than other complexes, and among the amino acid with alkyl side chain, Gly and Ala exhibited greater 18c6 binding affinities. As for Ser and Thr, the intramolecular hydrogen bond between the nitrogen atom from terminal –NH₂ and the oxygen atom from carboxyl might impede their protonated amino-group to attack the 18c6. Furthermore, Gln and Asn exhibited lower binding affinities to 18c6, probably due to effects of electron-withdrawing group of acylamide. Finally, the chiral selectivity of 18c6 for L-amino or D-amino acids were measured by ESI-MS, and the result showed that 18c6 could only recognize some neutral amino acid isomers.