COMFA of the acute toxicity of phenylsulfonyl carboxylates to Vibrio fischeri

From the Comparative Molecular Field Analysis (CoMFA) method, the paper describes a three-dimentional quantitative structure–activity relationship (3D-QSAR) model for the acute toxicity log EC₅₀ (15min-EC₅₀ in μmoll^-l) of 56 phenylsulfonyl carboxylates on Vibrio fischeri. The achievement of a high leave-one-out (LOO) cross-validated correlation coefficient q² of 0.790 with four optimum components indicates the significance of the correlation of the steric and electrostatic fields with the biological activities. The key features in the CoMFA contour maps are critical to trace the important properties and gain insight into the toxic mechanism of the tested phenylsulfonyl carboxylates.     

Calculation of hydrophobic parameters directly from three-dimensional structures using comparative molecular field analysis

Summary Capacity ratio (log k') values, which are a measure of hydrophobicity, were calculated directly from the three-dimensional structures of 17 furans and 54 triazines using the comparative molecular field analysis approach. The H₂O probe and the GRID force field, including hydrogen-bond potentials, yielded excellent correlations with the log k' values. Moreover, the predicted values of log k' from 14 additional triazine analogs showed excellent agreement with log k' values reported in the literature. Similar results were obtained for the octanol-water partition coefficients (log P) of 17 furans.     

Synthetic modifications in ethyl 2-amino-4-methylthiazole-5-carboxylate: 3D QSAR analysis and antimicrobial study

Ethyl 2-amino-4-methylthiazole-5-carboxylate (1) is a very substantial derivative of the thiazole group. This derivative has been modified and has been synthesized using readily available materials. The structures of synthesized derivatives were confirmed by IR, ¹H NMR, ¹³C NMR, and mass spectral techniques. The newly prepared compounds (5a–k) were studied for their antimicrobial activities against strains of bacteria (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pyogenes) and fungi (Candida albicans, Aspergillus niger, and Aspergillus clavatus) using serial dilution method. Structure-activity relationship was carried out by CoMFA and CoMSIA with the help of 3D-QSAR analysis. As per the database alignment, the CoMFA and CoMSIA models were developed. Information based on these models is useful for structure-activity relationships of the reported molecules.     

Acrosin structure-based design,synthesis and biological activities of 7-azaindol derivatives as new acrosin inhibitors

A series of 7-azaindol derivatives were designed based on the homologous 3D model of human acrosin.These compounds were synthesized and evaluated for their human acrosin inhibitory activities in vitro.Compounds 7a,7i,7j,7k and 7n showed highly inhibitory activity against human acrosin.The three-dimensional structure-activity relationship was investigated through a CoMFA model,which provided valuable information to further study of potential human acrosin inhibitors.     

马来酰胺类糖原合成酶激酶-3β抑制剂的分子对接和三维定量构效关系

通过分子对接和三维定量构效关系(3D-QSAR)两种方法来确定两类马来酰胺类的糖原合成酶激酶-3β(GSK-3β)抑制剂的结合方式. 首先, 用分子对接确定抑制剂与GSK-3β结合模式及其相互作用; 然后用比较分子力场分析法(CoMFA)与比较分子相似性指数分析法(CoMSIA)对48个化合物做三维定量构效关系的分析. 两种方法得出的交互验证回归系数分别为0.669(CoMFA)和0.683(CoMSIA), 证明该模型具有很好的统计相关性, 同时也说明该模型具有较高的预测能力.根据该模型提供的信息, 设计出9个预测活性较好的分子.     

马来酰胺类糖原合成酶激酶-3β抑制剂的分子对接和三维定量构效关系

通过分子对接和三维定量构效关系(3D-QSAR)两种方法来确定两类马来酰胺类的糖原合成酶激酶-3β(GSK-3β)抑制剂的结合方式.首先,用分子对接确定抑制剂与GSK-3β的结合模式及其相互作用;然后用比较分子力场分析法(CoMFA)与比较分子相似性指数分析法(CoMSIA)对48个化合物做三维定量构效关系的分析.两种方法得出的交互验证回归系数分别为0.669(CoMFA)和0.683(CoMSIA),证明该模型具有很好的统计相关性,同时也说明该模型具有较高的预测能力.根据该模型提供的信息,设计出9个预测性较好的分子.     

类黄酮抑制P糖蛋白的三维定量构效关系与作用模式

采用基于R基团搜索技术的Topomer CoMFA建立了30个类黄酮类P糖蛋白抑制剂的三维定量构效关系(3D-QSAR)模型, 并用包括9个样本的测试集验证模型的外部预测能力. 所得模型的拟合、 交互验证以及外部验证的复相关系数分别为r²=0.971, q²=0.728和\begin{array}{c}{r}_{\mathit{pred}}^2\end{array}=0.816. 在此基础上, 运用Surflex-dock分子对接法研究了白杨素及其异戊烯化衍生物与P糖蛋白的作用模式. 结果表明, 异戊烯化修饰可显著提高类黄酮的亲脂性, 修饰产物能更好地与P糖蛋白的疏水性口袋契合, 二者结合程度高.     

应用CoMFA研究抗菌肽的三维定量构效关系

采用比较分子场分析(CoMFA)方法对抗菌九肽、抗菌十四肽、抗菌十八肽进行三维定量构效关系(3D-QSAR)分析,建立了预测力强的3D-QSAR模型.结果表明,所建立的3D-QSAR模型对三种抗菌肽均有较好的统计学稳定性及预测能力(抗菌九肽:交叉验证系数q~2=0.537,非交叉验证相关系数r~2=0.961,外部样本检验复相关系数Q_(ext)~2=0.883;抗菌十四肽:q~2=0.502,r~2=0.718,Q_(ext)~2=0.645;抗菌十八肽:q~2=0.550,r~2=0.967,Q_(ext)~2=0.989).三维等势图不仅解释了抗菌肽结构与活性的关系,而且为抗菌肽的进一步合成提供了理论依据.     

具有除草活性的大环内酯类衍生物的定量构效关系

研究了一系列结构新颖的具有除草活性的大环内酯衍生物的定量构效关系(QSAR). 构建的比较分子力场分析(CoMFA)、比较分子近似指数分析(CoMSIA)和全息定量构效关系(HQSAR)分子模型的交叉验证系数r2cv均大于0.5, 非交叉验证系数r2都超过0.8, 表明获取的QSAR模型具有可信的预测能力. 对CoMFA、CoMSIA模型的三维(3D)等势图分析, 发现除了立体场和静电场外, 疏水场和氢键受体场也是影响大环内酯类化合物除草活性的重要因素. 构建的HQSAR模型的原子贡献图提示的结构改造信息与三维QSAR的结果基本一致. 利用CoMFA、CoMSIA模型提供的信息,对目前已合成的活性最高化合物B1-3进行分子结构改造, 预测结果发现部分化合物可能具有更好的除草活性.     

Design of new CD38 inhibitors based on CoMFA modelling and molecular docking analysis of 4‑amino-8-quinoline carboxamides and 2,4-diamino-8-quinazoline carboxamides

In this study, based on molecular docking analysis and comparative molecular field analysis (CoMFA) modelling of a series of 71 CD38 inhibitors including 4?amino-8-quinoline carboxamides and 2,4-diamino-8-quinazoline carboxamides, new CD38 inhibitors were designed. The interactions of the molecules with the greatest and the lowest activities with the nicotinamide mononucleotide (NMN) binding site were investigated by molecular docking analysis. A CoMFA model with four partial least squares regression (PLSR) components was developed to predict the CD38 inhibitory activity of the molecules. The r² values for the training and test sets were 0.89 and 0.82, respectively. The Q² values for leave-one-out cross-validation (LOO-CV) and leave-many-out cross-validation (LMO-CV) tests on the training set were 0.65 and 0.64, respectively. The CoMFA model was validated by calculating several statistical parameters. CoMFA contour maps were interpreted, and structural features that influence the CD38 inhibitory activity of molecules were determined. Finally, seven new CD38 inhibitors with greater activity with respect to the greatest active molecules were designed.