蜂毒溶血肽类似物定量构效关系计算分析

采用HyperChem7．0结构分析软件,对蜂毒溶血肽类似物的分予体积等结构参数进行了计算分析．分别利用多元线性回归、BP-神经网络计算法进行统计分析,获得两个相关性好的QsAR（quantitative structure-function relationship）模型．结果显示,蜂毒肽溶血活性与生成热、键合能、表面积、分予体积、极化能、醇水分配系数、水舍能相关．为降低溶血作用,指出在设计蜂毒肽结构时应尽量避免螺旋状结构．少用疏水性氨基酸．     

QSAR studies on antimalarial 2,4-diamino-6-quinazoline sulfonamides

The present paper discusses QSAR studies on antimalarial 2,4-diamino-6-quinazoline sulfonamide derivatives using electronic parameters, namely energy of highest occupied molecular orbitals (EH), energy of lowest unoccupied molecular orbitals (EL) and charge density (CD). The results have shown that better results are obtained by introducing dummy parameters (indicator parameter), Ip. Excellent results are obtained when all the four parameters (EH, EL, CD and Ip) are used in correlation analysis.     

QSAR-based prediction of anti-HCV activity of thiourea derivatives

Quantitative structure–activity relationship (QSAR) studies were performed on a series of thioureas to explore the physico-chemical parameters responsible for their activity against the hepatitis C virus (HCV)-infected AVa5 cell. The physico-chemical parameters were calculated using WIN CAChe 6.1. Multiple linear regression analysis, after the variables selection by factor analysis, was performed to derive QSAR models which were further evaluated for their statistical significance and predictive power by internal and external validation. The developed QSAR model had the correlation coefficient (R) = 0.928 and cross-validated squared correlation coefficient (Q ²) = 0.751. The selected significant QSAR model indicates that hydrophobicity, dielectric energy, valence connectivity index (order 1), conformational minimum energy and highest occupied molecular orbital of the whole molecule play an important role in the anti-HCV activity of thioureas.     

用分子轨道法探讨油田废水中取代苯系物的毒性效应

采用半经验的分子轨道AM1方法中的MOPAC软件包计算了55种在油田废水中易于检出的取代苯系物的分子轨道能（EHOMO,ELUMO,ENHOMO,ENLUMO）、分子生成熟（△H^f0)和偶极矩（μ）等量化参数,结合一阶价分子连接性指数（^1X^V)和正辛醇／水分配系数(logP)与实验所得发光菌的半数活性浓度（EC50）成功建立了多参数定量－结构活性关系模式,在分类建模的基础上,又获得了仅包含1^X^V和EHOMO两个参数的55种取代苯系物的定量结构－活性相关模式,探讨了不同取代基的毒性作用机制,结果表明,量化参数与物化参数结合能够很好地预测油田废水中具有不同取代基团的取代苯系物的生物活性,预测模式中量子化学参数的出现有利于深入探讨油田废水中有机污染物的毒性效应。     

Three-dimensional quantitative structure–activity relationship (3D-QSAR) of 3-aryloxazolidin-2-one antibacterials

Three-dimensional quantitative structure–activity relationship (3D-QSAR) studies for 3-aryloxazolidin-2-one antibacterials were performed using the genetic function approximation algorithm. This study was performed using 60 compounds, in which the QSAR models were developed using a training set of 50 compounds. The in vitro minimum inhibitory concentration (MIC) against Staphylococcus aureus SFCO-1a was used for the study. The predictive ability of the QSAR model was evaluated by using a test set of 10 compounds. The statistical quality of the QSAR models was assessed using statistical parameters r², r²_cv (cross-validated r²), r²_pred (predictive r²) and lack of fit measure (LOF). The results obtained indicate that the antibacterial activity of the 3-aryloxazolidin-2-ones is strongly dependent on electronic factor as expressed by lowest unoccupied molecular orbital energy (LUMO), spatial factor as expressed by density and thermodynamic factors accounted for by molar refractivity and heat of formation. The model is presently being used to design and predict new potent molecules prior to synthesis.     

Reassessment of Hammett σ as an effective parameter representing intermolecular interaction energy-links between traditional and modern QSAR approaches

The Hammett σ constant has for a long time been known to be one of most important linear free-energy related parameters that correlate with biological activity. It is a conventionally used electronic parameter in studies of enzymatic quantitative structure-activity relationships (QSAR). However, it is not necessarily obvious why σ represents variations in the free-energy change associated with the complex formation between a congeneric series of ligands with their target protein. So far, several powerful molecular calculations, such as the ab initio fragment molecular orbital (FMO) one, that are directly applicable to ligand-protein complexes have emerged. In this study, we comprehensively reevaluate experimentally derived parameter σ confirming it represents intermolecular interaction energy terms, by applying molecular orbital (MO) calculations to a simple ligand-protein complex model. The current results provide a rational and quantitative basis for bridging the gap between the traditional QSAR approach and 'the modern QSAR one', which involves the molecular calculations to evaluate the overall free-energy change for complex formation.     

QSAR prediction of toxicity of nitrobenzenes

A QSAR analysis has been carried out on the toxicities of 40 mono-substituted nitrobenzenes using recently introduced PI and Sz indices, as well as older molecular redundancy (MRI) and Balaban indices (J). The results have shown that no statistically significant mono-parametric QSAR models are possible. Also, that along with PI, Sz, MRI and J indices are the appropriate parameters to be used in developing multiparametric QSAR models. The toxicities of nitrobenzenes are well predicted by a penta-parametric model consisting of PI, Sz, J, MRI and Ip(1) (an indicator parameter taking care of the effect of substitution at 2-position) as the correlating parameters. The predictive ability of the model is determined by a cross-validation method.     

Energetics of interactions of aromatic hydrocarbons with water

The thermodynamics of transfer of aromatic (benzene, toluene) and aliphatic (ethane, propane, butane) hydrocarbons from the gas phase into water in the temperature range 5–125°C have been analyzed in order to determine the net hydration effect of these compounds. In the case of the aromatic hydrocarbons the enthalpic contribution predominates over the entropic contribution to the Gibbs energy of hydration. This results in a negative value of the hydration Gibbs energy of aromatic hydrocarbons, in contrast to the positive Gibbs energy of hydration of aliphatic hydrocarbons. The different sign of the hydration Gibbs energies indicates that the mechanism causing hydrophobicity of aromatic hydrocarbons has different nature than that causing the hydrophobicity of aliphatic hydrocarbons. The comparison of hydration of aliphatic and aromatic hydrocarbons leads to the following thermodynamic parameters for these additional interactions between the benzene ring and water at 25°C: enthalpy −5.4 kJ/mol, entropy 26.8 J/K mol and Gibbs energy −13.4 kJ/mol. The large enthalpic contribution to the Gibbs energy of hydration of aromatic hydrocarbons probably comes from the ability of the aromatic ring to accept hydrogens from water, forming hydrogen bonds.     

Human protein tyrosine phosphatase 1B inhibitors: QSAR by genetic function approximation

Protein tyrosine phosphatase 1B (PTP 1B), a negative regulator of insulin receptor signaling system, has emerged as a highly validated, attractive target for the treatment of non-insulin dependent diabetes mellitus (NIDDM) and obesity. As a result there is a growing interest in the development of potent and specific inhibitors for this enzyme. This quantitative structure-activity relationship (QSAR) study for a series of formylchromone derivatives as PTP lB inhibitors was performed using genetic function approximation (GFA) technique. The QSAR models were developed using a training set of 29 compounds and the predictive ability of the QSAR model was evaluated against a test set of 7 compounds. The internal and external consistency of the final QSAR model was 0.766 and 0.785. The statistical quality of QSAR models was assessed by statistical parameters r2, r2 (crossvalidated r2), r2pred (predictive r2) and lack of fit (LOF) measure. The results indicate that PTP lB inhibitory activity of the formylchromone derivatives is strongly dependent on electronic, thermodynamic and shape related parameters.     

2D-QSAR model development and analysis on variant groups of anti-tuberculosis drugs

A quantitative structure activity relationship study was performed on different groups of anti-tuberculosis drug compound for establishing quantitative relationship between biological activity and their physicochemical /structural properties. In recent years, a large number of herbal drugs are promoted in treatment of tuberculosis especially due to the emergence of MDR (multi drug resistance) and XDR (extensive drug resistance) tuberculosis. Multidrug-resistant TB (MDR-TB) is resistant to front-line drugs (isoniazid and rifampicin, the most powerful anti-TB drugs) and extensively drug-resistant TB (XDR-TB) is resistant to front-line and second-line drugs. The possibility of drug resistance TB increases when patient does not take prescribed drugs for defined time period. Natural products (secondary metabolites) isolated from the variety of sources including terrestrial and marine plants and animals, and microorganisms, have been recognized as having antituberculosis action and have recently been tested preclinically for their growth inhibitory activity towards Mycobacterium tuberculosis or related organisms. A quantitative structure activity relationship (QSAR) studies were performed to explore the antituberculosis compound from the derivatives of natural products . Theoretical results are in accord with the in vitro experimental data with reported growth inhibitory activity towards Mycobacterium tuberculosis or related organisms. Antitubercular activity was predicted through QSAR model, developed by forward feed multiple linear regression method with leave-one-out approach. Relationship correlating measure of QSAR model was 74% (R(2) = 0.74) and predictive accuracy was 72% (RCV(2) = 0.72). QSAR studies indicate that dipole energy and heat of formation correlate well with anti-tubercular activity. These results could offer useful references for understanding mechanisms and directing the molecular design of new lead compounds with improved anti-tubercular activity. The generated QSAR model revealed the importance of structural, thermodynamic and electro topological parameters. The quantitative structure activity relationship provides important structural insight in designing of potent antitubercular agent.     

基于支持向量回归的酚类化合物QSAR建模

目的：采用定量构效关系（QSAR）方法探索酚类化合物的毒性与分子结构参数的关系。方法：基于支持向量回归（SVR）、依均方误差最小原则选择最优核函数,对酚类化合物及其衍生物进行了QSAR研究。结果：不同数据集选取的最优核函数有异,对小样本、非线性等问题,SVR具有较优的稳定性及预测能力,在酚类化合物及其衍生物的QSAR研究中得到了优于原文献方法的独立预测结果。结论：SVR模型具有较好的预测能力,在QSAR及相关研究中可得到更广泛应用。     

Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

We consider whether the continuum model of hydration optimized to reproduce vacuum-to-water transfer free energies simultaneously describes the hydration free energy contributions to conformational equilibria of the same solutes in water. To this end, transfer and conformational free energies of idealized hydrophobic and amphiphilic solutes in water are calculated from explicit water simulations and compared to continuum model predictions. As benchmark hydrophobic solutes, we examine the hydration of linear alkanes from methane through hexane. Amphiphilic solutes were created by adding a charge of +/-1e to a terminal methyl group of butane. We find that phenomenological continuum parameters fit to transfer free energies are significantly different from those fit to conformational free energies of our model solutes. This difference is attributed to continuum model parameters that depend on solute conformation in water, and leads to effective values for the free energy/surface area coefficient and Born radii that best describe conformational equilibrium. In light of these results, we believe that continuum models of hydration optimized to fit transfer free energies do not accurately capture the balance between hydrophobic and electrostatic contributions that determines the solute conformational state in aqueous solution.     

Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor.

Several hydration models for peptides and proteins based on solvent accessible surface area have been proposed previously. We have evaluated some of these models as well as four new ones in the context of near-native conformations of a protein. In addition, we propose an empirical site-site distance-dependent correction that can be used in conjunction with any of these models. The set of near-native structures consisted of 39 conformations of bovine pancreatic trypsin inhibitor (BPTI) each of which was a local minimum of an empirical energy function (ECEPP) in the absence of solvent. Root-mean-square (rms) deviations from the crystallographically determined structure were in the following ranges: 1.06-1.94 A for all heavy atoms, 0.77-1.36 A for all backbone heavy atoms, 0.68-1.33 A for all alpha-carbon atoms, and 1.41-2.72 A for all side-chain heavy atoms. We have found that there is considerable variation among the solvent models when evaluated in terms of concordance between the solvation free energy and the rms deviations from the crystallographically determined conformation. The solvation model for which the best concordance (0.939) with the rms deviations of the C alpha atoms was found was derived from NMR coupling constants of peptides in water combined with an exponential site-site distance dependence of the potential of mean force. Our results indicate that solvation free energy parameters derived from nonpeptide free energies of hydration may not be transferrable to peptides. Parameters derived from peptide and protein data may be more applicable to conformational analysis of proteins. A general approach to derive parameters for free energy of hydration from ensemble-averaged properties of peptides in solution is described.     

Chiral configuration of the hydration layers of D‐ and L‐alanine in water implied from dilution calorimetry

The size and configuration of the hydration layer of solutes play a major role in their thermodynamic features. With respect to amino acids in water, a series of indirect evidence strongly suggest that their hydration layer acquires a chiral configuration induced by their chiral centers. Such a chiral hydration may act as a recognition factor in the various biochemical interactions, but information on it remains rather scarce. In this study, we determined by dilution microcalorimetry the fraction of the hydration energy invested in the chiral distortion of the hydration layer surrounding D ‐ and I ‐alanine in water. The results indicate that in dilute solutions, a multilayered chiral hydration surrounds each of these solutes and amounts to over 100 water molecules. In concentrated solutions, the immediate chiral hydration layer decreases to ～30 water molecules. The energy invested in the induction of the chiral twist in the hydration layer is predominantly attributed to TΔS, the energy associated with “configurational entropy,” which amounts to only several cal/mol, about a thousandth of the total energy of the hydration shell. Chirality 2010. © 2009 Wiley‐Liss, Inc.     

定量计算萜类驱避化合物与二氧化碳缔合对其蚊虫驱避活性的影响

为验证萜类驱避化合物与嗅觉引诱物二氧化碳存在缔合作用, 并研究缔合作用对蚊虫驱避活性的影响。本研究借助计算化学的方法获得缔合体和缔合能量, 利用Gaussian View和Gaussian 03W软件分别构建和优化二氧化碳、 22个萜类蚊虫驱避化合物以及它们与二氧化碳缔合后的三维分子结构, 经Ampac 8.16转化后, 获得它们的缔合能量。借助定量构效关系计算方法研究缔合作用对驱避活性的影响, 利用Codessa 2.7.10计算获得驱避剂和缔合体的各类结构描述符, 从包括缔合体结构描述符及特征描述符在内的各类结构参数中筛选显著性参数, 以萜类驱避化合物对白纹伊蚊Aedes albopictus的校正驱避率的对数值为活性数据, 建立结构描述符与驱避活性的定量构效关系（quantitative structure-activity relationship, QSAR）模型。结果获得了22个萜类驱避化合物与二氧化碳缔合的缔合能量, 计算显示它们之间存在缔合作用并且可以形成缔合体; 获得1个R²为0.9643的4参数QSAR模型, 这4个参数所对应的结构描述符分别是COM-WNSA 3 Weighted PNSA (PNSA3*TMSA/1 000) ［Zefirov’s PC］, f-TerCO₂-Min e-n attraction for a C-O bond, M-Max 1-electron reaction index for an O atom, M-Min (>0.1) bond order of an H atom, 前2个参数分别为缔合体的整体结构描述符和碎片特征描述符。计算化学结果表明, 萜类驱避化合物与二氧化碳存在缔合作用, 该缔合作用对驱避活性的影响显著。