An Enhanced Comparative Molecular Field Analysis Method Using Genetic Algorithm

In this study. an automated conformer selection procedure using generic algorithm (GA) has been applied in comparative molecular field analysis (CoMFA) method. Using genetic algorithm. the 3D-QSAR model is optimized to an optimal one. From the calculation results, a group of QSAR models with high predictive ability can be obtained, which is superior than using conventional CoMFA: meanwhile. the active conformers for these compounds in data set can be determined fi om the best model.

3D-QSAR studies on glycogen phosphorylase inhibitors by flexible comparative molecular field analysis

Canceling grids accommodating probes in comparative molecular field analysis (CoMFA), the idea of flexibleness is introduced into the CoMFA, and in combination with swarm intelligent algorithm which attempts to optimize distributions of diverse probes around drug molecules, a new 3D-QSAR method is proposed in this context as flexible comparative molecular field analysis (FCoMFA). In preliminary at-tempts to performing QSAR studies on 47 glycogen phosphorylase inhibitors, FCoMFA is employed and confirmed to be potent to exploring ligand-receptor interaction manners at active positions and thus to generating stable and predictable models. Simultaneously by an intuitive graphics regarding probe distribution patterns, impacts of different substituted groups on activities is also given an insight into.

基于CoMFA研究氟喹诺酮C-3噻唑酮衍生物抗胰腺癌活性

应用比较分子力场分析(Comparative molecular force field analysis,CoMFA)方法研究了18种氟喹诺酮C-3噻唑酮衍生物对胰腺Capan-1细胞的体外抗增殖活性(p A).训练集中14个化合物用于建立预测模型,测试集6个化合物(含模板分子和新设计的1个分子)作为模型验证.通过基于配体的原子契合的叠合方式,获得了训练集的统计显著模型.CoMFA模型使用3个主成分给出交叉验证系数(R 2 cv)值为0.436,非交叉验证系数(R 2)值为0.956,估计F值为72.217.结果显示,模型具有良好的稳健性与预测能力.基于CoMFA等高线图,揭示了该系列化合物抗增殖活性的一些关键结构因素.这些结果为理解其作用机制、设计具有高抗肿瘤活性的新型氟喹诺酮C-3噻唑酮类化合物提供有益的理论参考.

3D-QSAR Study of 7,8-Dialkyl-l,3-diaminopyrrolo-[3,2-f] Quinazolines with Anticancer Activity as DHFR Inhibitors

A three-dimensional quantitative structure-activity relationship （3D-QSAR） study of a series of 7,8-dialkyl-l,3-diaminopyrrolo-[3,2-f] quinazolines with anticancer activity as dihydrofo- late reductase （DHFR） inhibitors was carried out by using the comparative molecular field analysis （CoMFA）, on the basis of our reported 2D-QSAR of these compounds. The es- tablished 3D-QSAR model has good quality of statistics and good prediction ability; the non cross-validation correlation coefficient and the cross-validation value of this model are 0.993 and 0.619, respectively, the F value is 193.4, and the standard deviation SD is 0.208. This model indicates that the steric field factor plays a much more important role than the electrostatic one, in satisfying agreement with the published 2D-QSAR model. However, the 3D-QSAR model offers visual images of the steric field and the electrostatic field. The 3D-QSAR study further suggests the following： to improve the activity, the substituent R^1 should be selected to be a group with an adaptive bulk like Et or i-Pr, and the substituent R should be selected to be a larger alkyl. In particular, based on our present 3D-QSAR as well as the published 2D-QSAR, the experimentMly-proposed hydrophobic binding mechanism on the receptor-binding site of the DHFR can be further explained in theory. Therefore, the QSAR studies help to further understand the ＂hydrophobic binding＂ action mechanism of this kind of compounds, and to direct the molecular design of new drugs with higher activity.

CoMFA Model of Anti-tumor Activity for Fluoroquinolon-3-yl s-Triazole Sulfide-ketone Derivatives and Implications for Molecular Design

Comparative molecular field analysis(CoMFA)techniques were used to perform three-dimensional quantitative structure-activity relationship(3D-QSAR)studies on the anti-tumor activity(pIH and pIC)of 28 fluoroquinolon-3-yl s-triazole sulfide-ketone derivatives(FQTSDs)against two cancer cell lines,including human hepatoma Hep-3B cells and human pancreatic cancer Capan-1 cells.23 compounds were randomly selected as the training set to establish the prediction models,which were verified by the test set of 6 compounds containing template molecule.The obtained cross-validation(Rcv2)and non-cross-validation correlation coefficients(R2)of the CoMFA models were 0.477 and 0.850 for pIH,and 0.421 and 0.836 for pIC,respectively.The contributions of steric and electrostatic fields to pIH were determined to be 48.1%and 51.9%,and those to pIC were 49.4%and 50.6%,respectively.The CoMFA models were then used to predict the activities of the compounds in the training and testing sets,and the models had a strong stability and good predictability.Based on the 3D contour maps,four novel FQTSDs with a higher anti-tumor activity were designed.However,the effectiveness of these novel FQTSDs is still needed to be verified by experimental results.

取代三唑-噻二唑类化合物抑菌活性的CoMFA模型

基于比较分子力场(CoMFA)方法建立了21个取代三唑-噻二唑类化合物对大肠杆菌抑菌活性(E_(c))三维定量构效关系(3D-QSAR)模型,训练集中16个化合物用于建立预测模型,测试集中6个化合物(含模板分子)作为模型验证.已建立的CoMFA模型的非交叉验证系数(R 2)、交叉验证系数(R^(2) _(cv))分别为0.938、0.504,说明所建模型具有较强的稳定性和良好的预测能力.该模型中立体场、静电场贡献率依次为90.7%和9.3%,显示以立体场作用为主,对应于位阻与疏水作用.由此推断,影响取代三唑-噻二唑类化合物对大肠杆菌抑菌活性的主要因素是疏水性,电荷分布仅占很次要因素.

CoMFA Model and Molecular Design of Anti-excitatory Activity for Benzodiazepinooxazole Derivatives against Mice

A 3D-QSAR study was conducted to analyze the anti-excitatory activity(p E)of benzodiazepinooxazole derivatives to mice by the comparative molecular field analysis(CoMFA)method.Among the 54 active molecules,a training set of 46 compounds was randomly selected to construct the CoMFA model;the remaining compounds,together with template molecule(No.54)and two newly designed molecules constitute a test set of 17 compounds to validate the model.The obtained cross-validation coefficient(R_(cv)^(2)),the non-cross validation coefficient(R^(2)),and the test value F of the CoMFA model for training set are 0.516,0.899,and 57.57,respectively.The model was used to predict the activities of all compounds in the training and testing sets,and the results indicated that the model had good correlation,strong stability and good predictability.Based on the 3D contour maps,eight novel benzodiazepinooxazole derivatives with higher anti-excitatory activity were designed.However,the effectiveness of these novel benzodiazepinooxazole derivatives is still needed to be verified by the experimental results.

Study on the Biological Activity of 3-Aroyl-5-substituted Thiophene Derivatives Based on the CoMFA Method

A three-dimensional quantitative structure-activity relationship(3 D-QSAR) study was conducted to analyze the A1 AR density(Bmax) of 56 3-aroyl-5-substituted thiophene derivatives(ASTDs) in human A1 Chinese hamster ovary(hA1 CHO) membranes by the comparative molecular field analysis(CoMFA) method. A training set of 45 compounds was used to establish the predictive model, which was verified by the test set of 17 compounds containing template molecule and 5 newly designed molecules. The cross-validation(R2 cv) and non-cross-validation(R2) coefficients of the training set were 0.655 and 0.959, respectively. The model was used to predict the activities of the compounds of the training and test sets, and the results indicated that the models had strong stability and good prediction ability. According to model analysis, the contribution of steric and electrostatic fields was 51.4% and 48.6%, respectively. Based on the 3 D contour maps, five excellent ASTDs agonists were designed, which need to be further verified by biomedical experiments.

3D-QSAR analysis of a new type of acetylcholinesterase inhibitors

Acetylcholinesterase (AChE) inhibitors are an important class of medicinal agents used for the treatment of Alzheimer’s disease. A screening model of AChE inhibitor was used to evaluate the inhibition of a series of phenyl pentenone derivatives. The assay result showed that some compounds displayed higher inhibitory effects. In order to study the relationship between the bioactivities; the structures, 26 compounds with phenyl pentenone scaffold were analyzed. A 3D-QSAR model was constructed using the method of comparative molecular field analysis (CoMFA). The results of cross-validated R[2]cv=0.629, non-cross-validated R[2]=0.972, SE=0.331,; F=72.41 indicate that the 3D-model possesses an ability to predict the activities of new inhibitors,; the CoMFA model would be useful for the future design of new AChE inhibitors.

3D-QSAR Studies on the Imidazopyrimidine Derivatives

Comparative molecular field analysis(CoMFA) and comparative molecular similarity indices analysis(CoMSIA) for imidazopyrimidine derivatives were performed to get the molecular active conformation selection, molecular alignment, as well as the establishment of corresponding 3 D-QSAR model. The model established by this method has good ability to predict such compounds. For CoMFA model, the cross-validated q2 and non-cross-validated r2 values are 0.665 and 0.872, respectively. The best q2 value for CoMSIA model is 0.632 and r2 value is 0.923. Using this information and the three-dimensional equipotential map for molecular design can theoretically obtain some new antibacterial drugs with higher activity. There are two newly designed molecules with activity values of 7.921 and 7.872, which are higher than that of the template molecule No. 12 with an activity value of 7.850, and the QSAR research results can provide a theoretical reference for the synthesis of new drugs.

CoMFA Study on Anti-proliferative Activity of Fluoroquinolone Amide Derivatives

The in vitro anti-proliferative activity(pICi,i=hp,ca,hl)of fluoroquinolone(rhodanineα,β-unsaturated ketone)amide compounds,referred to as“fluoroquinolone amide derivatives(FQADs)”towards Hep-3B,Capan-1 and HL60 cells,was studied by the 3D-QSAR method of comparative molecular field analysis(CoMFA).Based on the training set of 14 compounds,the prediction model was established,which was further verified by the test set of 5 compounds with template molecule included.It is found that steric and electrostatic fields contribute 66.8%and 33.2%to pIChp,61.4%and 38.6%to pICca,and 61.5%and 38.5%to pIChl,respectively.The Rcv 2(i.e,cross-validation coefficient)is 0.324,0.381,and 0.421 for pIChp,pICca,and pIChl,respectively,while the corresponding R2(i.e,non-cross-validation coefficient)all reach 0.999.Then,the models were employed to estimate the activities of the training and test compounds,and the results show that the stability and predictability of developed models are very satisfactory.According to the contour maps of steric and electronic fields,bulky groups linked to 2-,3-,4-positions of phenyl ring,and electropositive groups near the 4-position and electronegative groups far away may increase the anti-proliferative activity.Using the information provided by the 3D contour maps,four new FQADs owing higher antiproliferative activity were designed,but their effectiveness should be further tested by experiments.

几种酚衍生物对青海弧菌Q67毒性的3D-QSAR研究

测定了16种酚衍生物对青海弧菌(Q67)的半致死浓度EC50(mol·L-1),通过比较分子力场分析方法(CoMFA)和比较分子相似性指数分析方法(CoMSIA),对16种酚衍生物的毒性进行了三维定量结构-活性相关(3D-QSAR)研究,建立了CoMFA和CoMSIA模型.其中CoMFA模型交叉验证相关系数Q2=0.703,非交叉验证相关系数R2=0.983,F检验值F=178.635;CoMSIA模型交叉验证相关系数Q2=0.588,非交叉验证相关系数R2=0.946,F检验值F=52.074,所建立的模型均有较强的稳定性和良好的预测能力.通过分析比较CoMFA和CoMSIA的三维等势图,全面直观地了解了酚衍生物的结构对致毒性的影响.在酚类化合物毒性作用过程中,化合物的氢键供受体特性因素起主要作用,其次是取代基的电负性和疏水性特征.

新型苯环5-(取代)苯甲酰胺基苯磺酰脲类化合物的比较定量构效关系研究

采用比较分子力场分析(CoMFA)方法,对26个新型苯环5-(取代)苯甲酰胺基苯磺酰脲类化合物的除草活性进行了三维定量构效关系(3D-QSAR)研究,建立了三维定量构效关系CoMFA模型(R2=0.948,F=91.364,SE=0.141).结果表明,此类磺酰脲类化合物的除草活性与苯环5位取代基的立体结构和电场性质密切相关.根据CoMFA模型的立体场和静电场三维等值线图不仅直观地解释了结构与活性的关系,而且为进一步设计高活性的目标化合物提供理论依据.

喹唑啉衍生物抗癌活性的比较分子力场研究

运用比较分子力场分析(CoMFA)方法,建立了16种标题化合物对鼠白血病抗癌活性的三维构效模型(3D-QSAR)。在CoMFA研究中,考察了网格结构、步长及探针原子等因素对统计结果的影响。该模型显示立体场、静电场对生物活性贡献依次为61.5%、38.5%,其中立体场是造成这些化合物抗肿瘤活性差异的主要因素。此3D-QSAR模型的交叉验证系数(q2)为0.320,非交互验证系数(R2)为0.992。所建的3D-QSAR模型及其三维等值线图可用于指导新型抗肿瘤喹唑啉衍生物的设计与结构优化。

靛玉红类衍生物的三维定量构效关系研究

采用比较分子场方法(CoMFA)对16个靛玉红类衍生物进行三维定量构效关系(3D-QSAR)研究,探讨靛玉红类衍生物的抗癌活性与其结构的关系。建立了3D-QSAR的CoMFA模型,得到了非交叉验证相关系数r2=0.987,标准偏差SD=2.141,统计方差比F=117.136,交叉验证相关系数q2=0.496。该模型合理、可信,具有一定的预测能力,表明改变取代基R1基团的体积才是提高靛玉红类衍生物抗癌活性的主要途径,为开发活性更好的抗癌药物提供一定的理论参考。

黄酮类化合物的3D-QSAR研究

从NCI数据库中,筛选出67个与矢车菊黄素类似的天然黄酮化合物。采用CoMFA方法研究其构效关系,构建CoMFA模型,其模型相关系数为q^2=0.599,r^2=0.919,验证模型的预测能力和拟合能力较好。通过分子场等势图,可直观分子周围立体和静电特征对化合物活性的影响,为设计高活性黄酮衍生物提供理论依据。

(E)-4-取代酰氧基-3-甲氧基苯乙烯侧链类衍生物的比较分子力场(CoMFA)研究

利用比较分子力场方法,建立5-脂氧合酶/环氧合酶抑制剂的三维定量构效关系,为设计新的更有效的酶抑制剂提供理论依据.在CoMFA分析中,交叉验证回归系数R2CV、非交叉验证回归系数r2和标准偏差(SEE)分别为0.639,0.744,0.148.说明系列化合物分子周围立体场和静电场的分布与抗炎活性间有良好的相关性.利用该模型对自行合成的24个化合物进行活性预测,结果与实测值相符.所得模型支持了假设的抑制剂作用机理和作用模型.所得CoMFA模型具有一定的预测能力,可用来指导设计新的5-脂氧合酶/环氧合酶抑制剂.

3D-QSAR Models of Anti-tumor Activity for Histone Deacetylase Inhibitors Containing Dihydropyridin-2-one

A 3D-QSAR study was conducted to analyze the anti-tumor activity(pHs,s=1,6)of dihydropyridin-2-one containing histone deacetylase inhibitor(DHDACi)to histone deacetylase(HDACs,s=1,6)by the comparative molecular field analysis(CoMFA)method.The predicting model was established based on the training set of 22 compounds,which was verified by the test set of 6 compounds containing template molecule.The results showed that the contributions of steric and electrostatic fields to pH1 are 37.6%and 62.4%,and those to pH6 are 44.6%and 55.4%,respectively.The coefficients of the cross-validation(Rcv2)and the non cross-validation(R2)are 0.574 and 0.947 for pH1,and 0.488 and 0.884 for pH6,respectively.The models were then used to predict the activities of the compounds for the training and testing sets.The results indicated that the models had strong stability and good predictability.Based on the 3D contour maps,several new potential inhibitors with higher anti-tumor activity were designed.However,the effectiveness of these potential inhibitors is still needed to be verified by the experimental results.

GABA_A/BZ受体激动剂4-喹啉酮衍生物的DISCOtech及CoMFA研究

γ-氨基丁酸是重要的抑制性神经传递物质,4-喹啉酮衍生物作用于GABA_A受体具有广泛的生物活性。本文采用DIS- COtech法构建大鼠GABA_A/BZ受体4-喹啉酮衍生物激动剂的药效团模型,同时根据分子骨架叠合规则构建CoMFA模型,模型的交叉验证系数为0.681,非交叉验证系数为0.967,药效团模型和CoMFA模型具有一致性。根据模型分析配体-受体间的相互作用,设计一系列化合物并预报了其活性,为设计高活性的化合物提供参考。

Study on the Three-dimensional Quantitative Structure-activity Relationship of Pyridazinonyl-substituted 1,3,4-Thiadiazoles

The three-dimensional quantitative structure-activity relationships of a series of 5-[ 1-aryl-1,4-dihydro-6-methylpyridazin-4-one-3-yl]-2-arylamino-1,3,4-thiadiazoles, related to the fungicidal activity, were studied using the comparative molecular field analysis （CoMFA）. The results show that the contributions of steric and electrostatic fields to the activity are 0.505 and 0.495, respectively. The cross-validated q^2 and the correlation coefficient r^2 for the model established by the study are 0.769 and 0.938, respectively, with the F value of 60.996, and the standard deviation s of 0.074. These values indicate that the model is significant and has good predictability. The analysis results are in good agreement well with the study of 2D-QSAR, and offered important structural insights into designing highly active compounds prior to synthesis.