药物定量构-效关系研究方法概况

定量构-效关系(QSAR)能够产生和优化先导化合物,从分子水平上阐明作用机制,因而广泛应用于药物分子设计中。作者阐述了QSAR方法及其原理、优缺点,包括取代基多参数法(Hansch法)、比较分子力场分析法(CoMFA)、Free-Wilson法。可以预见,QSAR研究中的方法将不断完善,各种方法因出发点和侧重点不同而相互交叉渗透,从而在新药的创制中将发挥更大的作用。

基于定量-构效关系预测含低碳酯二元共沸物的共沸温度

为了能够快速、准确地获取含低碳酯二元共沸物的共沸温度,以102种含低碳酯二元共沸物为研究样本,从分子角度出发,基于定量-构效关系原理对共沸温度与其分子结构信息之间的内在定量关系开展了理论研究,建立了多个共沸温度预测模型。通过对模型的拟合能力、显著性及标准误差进行比较和分析,得到最佳的共沸温度预测模型是由6个分子描述符所构建的模型;再利用留一交叉验证法、测试集及Williams图对该模型进行内部验证、外部验证及应用域分析,并将本文所建的模型与文献报道的同类模型及UNIFAC模型进行比较。研究结果显示:共沸温度预测模型具有稳定性好、预测精度高及泛化推广能力强等优点。

苯基吡咯类杀菌剂的设计合成及三维-定量构效关系(3D-QSAR)研究

为寻找新型吡咯类农药,基于杀菌剂氟咯菌腈设计合成了21个苯基吡咯类化合物,在吡咯环上引入甲基基团,其目的是探究N位取代基对该类化合物活性的影响.通过1H NMR、FTIR、单晶X射线衍射、高分辨质谱、元素分析和熔点测定等对目标化合物结构进行了表征与确认,并通过挥发法培养得到16个目标化合物的单晶结构.5种病原菌抑菌活性测试结果显示:在10 mg/L浓度条件下,4-(2-氯苯基)-1H-吡咯-3-腈(4b),4-(2-溴苯基)-1H-吡咯-3-腈(4c),4-(2-(三氟甲基)苯基)-1H-吡咯-3-腈(4d),4-(2-氯-3-氟苯基)-1H-吡咯-3-腈(4g),4-(2,3-二氯苯基)-1H-吡咯-3-腈(4h)对4种病菌表现出较好甚至高于阳性对照的抑菌效果,其中化合物4g在1 mg/L浓度条件下对3种病菌的抑制效果仍达到80%以上,而氮位甲基取代的目标化合物对水稻纹枯病菌表现出专一的抑菌活性.为了开发出更有效的抗水稻纹枯病菌化合物,采用比较分子力场分析(CoMFA)方法对20个化合物的水稻纹枯病菌活性进行初步的三维-定量构效关系(3D-QSAR)研究,建立了一个有效的CoMFA模型(q^(2)=0.503,r^(2)=0.974),展现了良好的预测能力,为后续该系列化合物的进一步优化提供了理论支持.

A 3D-QSAR Study on a Novel Chromanol Class of I_ (Ks) Potassium Channel Blockers

Aim and Method A novel three-dimensional quantitative structure-activityrelationship (3D-QSAR) method, self-organizing molecular field analysis (SOMFA) , was used toinvestigate the correlation between the molecular properties and a class of chromanol analogs asI_(Ks) blockers. Results The cross-validated correlation coefficient q^2 values (0.698) and noncross-validated correlation coefficient r^2 values (0.701) proved a good conventional statisticalcorrelation. Conclusion The final SOMFA model has therefore good predictive activity for the furthermolecular design of chromanol I_(Ks) potassium channel blockers.

A 3D-QSAR Study on C-3 Substituted 4,6-Dichloroindole-2- Carboxylic Acids with Comparative Molecular Field Analysis

Aim and Method Comparative molecular field analysis (CoMFA), a threedimensional quantitative structure-activity relationship (3D-QSAR) method was applied to a novelseries of C-3 substituted 4, 6-dichloioindole-2-carboxylic acids to study the relationship betweentheir structure and the affinity for the glycine site of the NMDA receptor. Result Hie coefficientsof cross-validation q^2 and non cross-validation r^2 for the model established by the study are0.744 and 0.993, respectively, the value of variance ratio F is 261.343, and standard error estimate(SE) is 0.039. Conclusion These values indicate that the CoMFA model may have a good prediction forthe activity of C-3 substituted 4, 6-dichloroin-dole-2-carboxylic acids. As a consequence, thepredicted activity values of new designed compounds supports our conclusion from the model.

3D-QSAR Analysis of DDPH Derivatives for α_1-Adrenoceptor Antagonist Activity

Aim and methods The study of three-dimensional quantitative structure-activity relationship （3D-QSAR） of DDPH and its derivatives has been performed using Apex-3D programme. Results The result indicates that substituents of para- and ortho-positions in phenyl ring of aryloxyalkylamine greatly influence the bioactivity. Conclusion The biophore model and 3D-QSAR equation help us not only further understand receptor-ligand interactions, but also design new compounds with better bioactivity.

Toxicity of Selected Imidazolium-based Ionic Liquids on Caenorhabditis elegans： a Quantitative Structure-Activity Relationship Study

Due to the large number of ionic liquids （ILs） and their potential environmental risk, assessing the toxicity of ILs by ecotoxicological experiment only is insufficient. Quantitative structure- activity relationship （QSAR） has been proven to be a quick and effective method to estimate the viscosity, melting points, and even toxicity of ILs. In this work, the LC50 values of 30 imidazolium-based ILs were determined with Caenorhabditis elegans as a model animal. Four suitable molecular descriptors were selected on the basis of genetic function approximation algorithm to construct a QSAR model with an R^2 value of 0.938. The predicted lgLC50 in this work are in agreement with the experimental values, indicating that the model has good stability and predictive ability. Our study provides a valuable model to predict the potential toxicity of ILs with different sub-structures to the environment and human health.

Structural features of substituted triazole-linked chalcone derivatives as antimalarial activities against D_(10) strains of Plasmodium falciparum: A QSAR approach

A quantitative structure–activity relationship(QSAR) was performed to analyze antimalarial activities against the D10 strains of Plasmodium falciparum of triazole-linked chalcone and dienone hybrid derivatives using partial least squares regression coupled with stepwise forward–backward variable selection method. QSAR analyses were performed on the available IC50 D10 strains of Plasmodium falciparum data based on theoretical molecular descriptors. The QSAR model developed gave good predictive correlation coefficient(r2) of 0.8994, significant cross validated correlation coefficient(q2) of 0.7689, r2 for external test set)(2predr of 0.8256, coefficient of correlation of predicted data set)(2sepred,r of 0.3276. The model shows that antimalarial activity is greatly affected by donor and electron-withdrawing substituents. The study implicates that chalcone and dienone rings should have strong donor and electron-withdrawing substituents as they increase the activity of chalcone. Results show that the predictive ability of the model is satisfactory, and it can be used for designing similar group of antimalarial compounds. The findings derived from this analysis along with other molecular modeling studies will be helpful in designing of the new potent antimalarial activity of clinical utility.

3D-QSAR and Docking Studies of Pyrido[2,3-d]pyrimidine Derivatives as Weel Inhibitors

In order to investigate the inhibiting mechanism and obtain some helpful information for designing functional inhibitors against Wee1, three-dimensional quantitative structure-activity relationship （3D-QSAR） and docking studies have been performed on 45 pyrido[2,3-d] pyrimidine derivatives acting as Wee1 inhibitors. Two optimal 3D-QSAR models with significant statistical quality and satisfactory predictive ability were established, including the CoMFA model （q2=0.707, R2=0.964） and CoMSIA model （q2=0.645, R2=0.972）. The external validation indicated that both CoMFA and CoMSIA models were quite robust and had high predictive power with the predictive correlation coefficient values of 0.707 and 0.794, essen- 2 values of 0.792 and 0.826, the leave-one-out r2m（LOO） values of 0.781 and tim parameter rm2 0.809, r2（ all） values of 0.787 and 0.810, respectively. Moreover, the appropriate binding orientations and conformations of these compounds interacting with Wee1 were revealed by the docking studies. Based on the CoMFA and CoMSIA contour maps and docking analyses, several key structural requirements of these compounds responsible for inhibitory activity were identified as follows： simultaneously introducing high electropositive groups to the sub- stituents R1 and R5 may increase the activity, the substituent R2 should be smaller bulky and higher electronegative, moderate-size and strong electron-withdrawing groups for the substituent R3 is advantageous to the activity, but the substituent X should be medium-size and hydrophilic. These theoretical results help to understand the action mechanism and design novel potential Wee1 inhibitors.

3D-QSAR and action mechanism of potential dual inhibitors towards AP-1 and NF-κB

Three-dimensional quantitative structure-activity relationship （3D-QSAR） and docking studies of a series of novel dioxopyrrolinyl-amino-pyrimidine derivatives, which are potential dual inhibitors mediating a transcriptional activation towards protein-1 （AP-1） and nuclear factor kappa B （NF-κB）, have been carried out. The QS, AR models established by comparative molecular field analysis （CoMFA） and comparative molecular similarity index analysis （CoMSIA） show a good predictive ability with cross-validated coefficients q2 of 0.644 and 0.636, respectively. The docking result shows that there are quite lower average values of the flexible and rigid energy scores on the selected binding sites, meanwhile, it further shows that the binding sites just fall on the joint regions between AP-1 （and NF-κB） and DNA. The reason that these analogues have inhibition function towards AP-I and NF-κB is that their existence on these joint regions can effectively prevent free AP-I and NF-κB from binding to DNA. These results can offer a valuable theoretical reference to the pharmaceutical molecular design as well as the action mechanism analysis.

环境致癌物的计算机预测研究

环境致癌物可诱发人类或哺乳动物体内的肿瘤,建立环境致癌物的计算机预测模型对环境风险评价和生态安全具有重要的意义.通过构建了3 780个化合物的数据集,随机选取其中3 024个作为训练集,其余756个作为外部验证集;基于定量构-效关系(QSAR)方法,采用逐步判别分析和主成分分析建立数学模型.结果表明训练集非致癌物预测正确率为86.0%,可能致癌物的预测正确率为88.0%,而采用主成分建模时,非致癌物和可能致癌物的预测正确率分别为74.2%和73.1%.说明逐步判别分析法的结果优于主成分判别分析.同时确定了可能致癌物和非致癌物的分子结构参数,阐明了两者结构差异.以上结果为预测和评估环境致癌物提供参考依据.

Binding Mechanism and Molecular Design of Benzimidazole/Benzothiazole Derivatives as Potent Abl T3151 Mutant Inhibitors

Despite the efficacy of imatinib therapy in chronic myelogenous leukemia, the development of drug-resistant Abl mutants, especially the most difficult overcoming T3151 mutant, makes the search for new Abl T3151 inhibitors a very interesting challenge in medicinal chem- istry. In this work, a multistep computational framework combining the three dimensional quantitative structure-activity relationship （3D-QSAR）, molecular docking, molecular dy- namics （MD） simulation and binding free energy calculation, was performed to explore the structural requirements for the Abl T315I activities of benzimidazole/benzothiazole derivatives and the binding mechanism between the inhibitors and Abl T315I. The established 3D-QSAR models exhibited satisfactory internal and external predictability. Docking study elucidated the comformations of compounds and the key amino acid residues at the binding pocket, which were confirmed by MD simulation. The binding free energies correlated well with the experimental activities. The MM-GBSA energy decomposition revealed that the van der Waals interaction was the major driving force for the interaction between the ligands and Abl T3151. The hydrogen bond interactions between the inhibitors and Met318 also played an important role in stablizing the binding of compounds to Abl T315I. Finally, four new compounds with rather high Abl T3151 activities were designed and presented to experimenters for reference.

A Quantitative Structure Property Relationship for Prediction of Flash Point of Alkanes Using Molecular Connectivity Indices

Many structure-property/activity studies use graph theoretical indices, which are based on the topological properties of a molecule viewed as a graph. Since topological indices can be derived directly from the molecular structure without any experimental effort, they provide a simple and straightforward method for property prediction. In this work the flash point of alkanes was modeled by a set of molecular connectivity indices （Х）, modified molecular connectivity indices （ ^mХ^v ） and valance molecular connectivity indices （ ^mХ^v ）, with ^mХ^v calculated using the hydrogen perturbation. A stepwise Multiple Linear Regression （MLR） method was used to select the best indices. The predicted flash points are in good agreement with the experimental data, with the average absolute deviation 4.3 K.

Synthesis,algal inhibition activities and QSAR studies of novel gramine compounds containing ester functional groups

2,5,6-Tribromo-l-methylgramine （TBG）, isolated from bryozoan Zoobotryon pellucidum was shown to be very efficient in preventing recruitment of larval settlement. In order to improve the compatibility of TBG and its analogues with other ingredients in antifouling paints, structural modification of TBG was focused mainly on halogen substitution and N-substitution. Two halogen-substitute gramines and their derivatives which contain ester functional groups at N-position of gramines were synthesized. Algal inhibition activities of the synthesized compounds against algae Nitzschia cIosterium were evaluated and the Median Effective Concentration （EC50） range was 1.06-6.74 lag ml^-1. Compounds that had a long chain ester group exhibited extremely high antifouling activity. Quantitive Structure Activity Relationship （QSAR） studies with multiple linear regression analysis were applied to fred correlation between different calculated molecular descriptors and biological activity of the synthesized compounds. The results show that the toxicity （log （I/EC50）） is correlated well with the partition coefficient log P. Thus, these products have potential function as antifouling agents.

Molecular Modeling and Design of Arylthioindole Derivatives as Tubulin Inhibitors

Three-dimensional quantitative structure activity relationship （3D-QSAR） and docking studies of a series of arylthioindole derivatives as tubulin inhibitors against human breast cancer cell line MCF-7 have been carried out. An optimal 3D-QSAR model from the comparative molecular field analysis （CoMFA） for training set with significant statistical quality （R2=0.898） and predictive ability （q2=0.654） was established. The same model was further applied to predict pIC50 values of the compounds in test set, and the resulting predictive correlation coefficient R2（pred） reaches 0.816, further showing that this CoMFA model has high predictive ability. Moreover, the appropriate binding orientations and conformations of these compounds interacting with tubulin are located by docking study, and it is very interesting to find the consistency between the CoMFA field distribution and the 3D topology structure of active site of tubulin. Based on CoMFA along with docking results, some important factors improving the activities of these compounds were discussed in detail and were summarized as follows： the substituents R3-R5 （on the phenyl ring） with higher electronegativity, the substituent R6 with higher eleetropositivity and bigger bulk, the substituent R7 with smaller bulk, and so on. In addition, five new compounds with higher activities have been designed. Such results can offer useful theoretical references for experimental works.

Estimation of thermal decomposition temperatures of organic peroxides by means of novel local and global descriptors

The thermal decomposition temperature is one of the most important parameters to evaluate fire hazard of organic peroxide. A quantitative structure-property relationship model was proposed for estimating the thermal decomposition temperatures of organic peroxides. The entire set of 38 organic peroxides was at random divided into a training set for model development and a prediction set for external model validation. The novel local molecular descriptors of AT1, AT2, AT3, AT4, AT5, AT6 and global molecular descriptor of ATC have been proposed in order to character organic peroxides’ molecular structures. An accurate quantitative structure-property relationship （QSPR） equation is developed for the thermal decomposition temperatures of organic peroxides. The statistical results showed that the QSPR model was obtained using the multiple linear regression （MLR） method with correlation coefficient （R）, standard deviation （S）, leave-one-out validation correlation coefficient （RCV） values of 0.9795, 6.5676 ℃ and 0.9328, respectively. The average absolute relative deviation （AARD） is only 3.86% for the experimental values. Model test by internal leave-one-out cross validation and external validation and molecular descriptor interpretation were discussed. Comparison with literature results demonstrated that novel local and global descriptors were useful molecular descriptors for predicting the thermal decomposition temperatures of organic peroxides.

Docking and 3D-QSAR studies of N-benzyl isatin oximes as JNK3 inhibitors

The c-Jun N-terminal kinase （JNK） is involved in a variety of important cellular processes and aberrant JNK activity is associated with many human diseases.The ligand-based and receptor-based alignment rules were used to build 3D-QSAR models for a series of N-benzyl isatin oximes JNK inhibitors. The best models were obtained for the receptor-based alignment with CoMSIA combining steric （S）, electrostatic （E）, and hydrogen bond donor （D） and hydrogen bond acceptor （A） fields （q2 = 0.759, r2 = 0.966, r2 pred = 0.703）. Based on the contour maps of RB CoMSIA model, some key structural factors responsible for inhibitory activity were investigated. Large groups at N-substituent or R6 position are preferred to interact with hydrophobic residues Ile70, Asp150, Ala151, Asn152 and Ser193. Electron-donating or hydrogen bond donor groups on the isatin ring would form polar and hydrogen bond with the negative-charged residue Glu147. In addition, electron-withdrawing groups or hydrogen bond acceptor group near the N-substituent would enhance inhibitory activity. The results are in good accordance and complementary to each other. The developed models could provide guidance in the rational design of more potent and selective JNK inhibitors.

Docking and field-based QSAR studies of S-DABOs as HIV-1 reverse transcriptase inhibitors

HIV-1 reverse transcriptase（RT） inhibitors are major components of HAART（highly active antiviral therapy）. The S-DABOs（dihydro-alkylthio-benzyl-oxopyrimidines） series and their similar skeletons have exhibited preferable activities to inhibit HIV-1 RT. In the present study, we generated field-based QSAR models using common structure alignment, which was characterized by Gaussian steric, electrostatic, hydrophobic, hydrogen bond donor, hydrogen bond acceptor and aromatic ring fields（R2 = 0.8421, RCV2 = 0.5949 for the training set, Q2 = 0.5486, Pearson-r = 0.7460 for the test set）. Docking, pocket surface and contour map analyses were carried out. Key pharmacophore features were investigated, including（i） π-π interaction with residue Tyr181, Tyr188 and Trp229, σ-π interaction with His236,（ii） hydrogen bond with residue Lys101 and halogen bond with residue Tyr188. The docking analysis and field-based QSAR models could provide reasonable guidance in the rational design of potent HIV-1 RT inhibitors.

Synthesis, anti-fibrosis activity, and quantitative structure-activity relationship studies of 1,3-disubstituted-pyridin-4(1H)-one derivatives

A series of 1,3-disubstituted-pyridin-4（1H）-one derivatives were synthesized. The results of a viability assay on NIH_T3 cells indicated that compound 3m potently inhibited the cell viability with an IC50 value of 2.0 μM. The 3D-quantitative structure-activity relationship analyses of 30 final molecules applying topomer CoMFA and AutoGPA methods gave two reasonable models with a cross-validated correlation coefficient q^2 of 0.662 and 0.787, respectively. The achievement herein suggested the application of 3-hydroxypyridin-4（1H）-one as a novel scaffold for the discovery of anti-fibrosis agents. In addition, the QSAR and pharmacophore models established with the activity data may provide new insights into the structure optimization of pyridin-4（1H）-one derivative with potent anti-fibrotic effects.

Quantitative structure-activity relationship of compounds binding to estrogen receptor β based on heuristic method

Estrogen compounds may pose a serious threat to the health of humans and wildlife. The estrogen receptor （ER） exists as two subtypes, ERα and ERβ. Compounds might have different relative affinities and binding modes for ERα and ERβ. In this study, the heuristic method was performed on 31 compounds binding to ERβ to select 5 variances most related to the activity （LogRBA） from 1524 variances, which were then employed to develop the best model with the significant correlation and the best predictive power （γ^2 = 0.829, q^2LOO = 0.742, γ^2pred = 0.772, q^2ext = 0.724, RMSEE = 0.395） using multiple linear regression （MLR）. The model derived identified critical structural features related to the activity of binding to ERβ. The applicability domain （AD） of the model was assessed by Williams plot.