3D QSAR Studies,Pharmacophore Modeling and Virtual Screening on a Series of Steroidal Aromatase Inhibitors

Aromatase inhibitors are the most important targets in treatment of estrogen-dependent cancers. In order to search for potent steroidal aromatase inhibitors (SAIs) with lower side effects and overcome cellular resistance, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of SAIs to build 3D QSAR models. The reliable and predictive CoMFA and CoMSIA models were obtained with statistical results (CoMFA: q² = 0.636, r²_ncv = 0.988, r²_pred = 0.658; CoMSIA: q² = 0.843, r²_ncv = 0.989, r²_pred = 0.601). This 3D QSAR approach provides significant insights that can be used to develop novel and potent SAIs. In addition, Genetic algorithm with linear assignment of hypermolecular alignment of database (GALAHAD) was used to derive 3D pharmacophore models. The selected pharmacophore model contains two acceptor atoms and four hydrophobic centers, which was used as a 3D query for virtual screening against NCI2000 database. Six hit compounds were obtained and their biological activities were further predicted by the CoMFA and CoMSIA models, which are expected to design potent and novel SAIs.     

Insight into the Structural Determinants of Imidazole Scaffold-Based Derivatives as TNF-α Release Inhibitors by in Silico Explorations

Presently, 151 widely-diverse pyridinylimidazole-based compounds that show inhibitory activities at the TNF-α release were investigated. By using the distance comparison technique (DISCOtech), comparative molecular field analysis (CoMFA), and comparative molecular similarity index analysis (CoMSIA) methods, the pharmacophore models and the three-dimensional quantitative structure-activity relationships (3D-QSAR) of the compounds were explored. The proposed pharmacophore model, including two hydrophobic sites, two aromatic centers, two H-bond donor atoms, two H-bond acceptor atoms, and two H-bond donor sites characterizes the necessary structural features of TNF-α release inhibitors. Both the resultant CoMFA and CoMSIA models exhibited satisfactory predictability (with Q² (cross-validated correlation coefficient) = 0.557, R²_ncv (non-cross-validated correlation coefficient) = 0.740, R²_pre (predicted correlation coefficient) = 0.749 and Q² = 0.598, R²_ncv = 0.767, R²_pre = 0.860, respectively). Good consistency was observed between the 3D-QSAR models and the pharmacophore model that the hydrophobic interaction and hydrogen bonds play crucial roles in the mechanism of actions. The corresponding contour maps generated by these models provide more diverse information about the key intermolecular interactions of inhibitors with the surrounding environment. All these models have extended the understanding of imidazole-based compounds in the structure-activity relationship, and are useful for rational design and screening of novel 2-thioimidazole-based TNF-α release inhibitors.     

Three Dimensional Quantitative Structure-Activity Relationship of 5H-Pyrido[4,3-b]indol-4-carboxamide JAK2 Inhibitors

Janus kinase 2 (JAK2) is an intracellular nonreceptor tyrosine kinase that belongs to the JAK family of kinases, which play an important role in survival, proliferation, and differentiation of a variety of cells. JAK2 inhibitors are potential drugs for the treatment of myeloproliferative neoplasms. The three dimensional quantitative structure-activity relationships have been studied on a series of JAK2 inhibitors by comparative molecular field analysis (CoMFA), and comparative molecular similarity indices analysis (CoMSIA). The CoMFA model had a cross-validated coefficient q² of 0.633, and the relation non-cross-validated coefficient r² of 0.976. The F value is 225.030. The contributions of steric and electrostatic fields to the activity are 55.2% and 44.8%, respectively. For the CoMSIA study, the q², r², and F values of the model are 0.614, 0.929, and 88.771, respectively. The contributions of steric, electrostatic, hydrophobic, hydrogen bond donor, and hydrogen bond donor fields to the activity are 27.3%, 23.9%, 16.4%, 21.7%, and 10.7%, respectively. The CoMFA and CoMSIA models showed strong predictive ability, and the 3D contour plots give the basis on the structure modification of JAK2 inhibitors.     

部分苯酚化合物对梨型四膜虫毒性的三维定量构效关系

采用比较分子力场分析描述子表征了133个苯酚类化合物对梨型四膜虫的毒性,从133个化合物中随机选取113个作为训练集建立CoMFA模型,其余的20个化合物作为检验集用于评价模型的预测能力,毒性与立体场和静电场的相互关系用三维等高线图直观显示,结果表明苯环上取代基给电子能力的大小和取代基团体积的大小对化合物的毒性均有直接影响.模型的交互验证相关系数(q2)为0.660,相关系数(R2)和标准偏差分别为0.924和0.215,最佳主成分数PC为8,F统计值为158.960,具有较好的预测能力.     

新型肟醚拟除虫菊酯化合物杀粘虫活性3D-QSAR研究

用比较分子力场分析（CoMFA）方法对50个自主设计并合成的新型芳基烷基肟醚化合物杀粘虫活性的定量构效关系进行了研究。所得模型交叉验证参数q^2为0．598，非交叉验证相关系数r^2为0．949，标准偏差SE=0．136，F=92．419，影响药效的立体场与静电场的贡献分别50．6％和49．4％。CoMFA等值线图表明化合物肟苯环对位取代基是影响其杀粘虫活性的主要因素，体积和电性增加有利于提高化合物的杀粘虫活性。该模型三维等值线图为该类化合物的结构改造提供了理论依据。     

两类促肾上腺皮质释放因子(CRF)抑制剂的CoMFA研究

Fipronil and related analogs, a set of new noncompetitive GABAA receptor antagonists, were investigated using comparative molecular field analysis (CoMFA) to explore their three-dimensional quantitative structure-activity relationships (3D-QSAR).Considering the structural complexity of molecules of fipronil and related analogs, three different alignments were performed in this paper. CoMFA model for housefly receptor yield the leave-one-out and cross-validated correlation coefficient q2 value of 0.511 and the conventional correlation coefficient r2 value of 0.997. The new compounds with higher activity would be designed from this model.CoMFA model for rat receptor was not successful using all these three alignments, the reason of which maybe that some molecules adopt different conformations for rat receptor.     

Pharmacophore and docking-based combined in-silico study of KDR inhibitors

The growth and metastasis of solid tumors is dependent on angiogenesis. The vascular endothelial growth factor (VEGF) and its cell surface receptor in human KDR (kinase domain containing receptor or VEGFR-2) have particular interest because of their importance in angiogenesis. The development of novel inhibitors of VEGFR-2 would be helpful to check the growth of tumors. Quantitative structure activity relationship (QSAR) analyses used to understand the structural factors affecting inhibitory potency of thiazole-substituted pyrazolone derivatives. Several pharmacophore-based models indicated the importance of steric, hydrophobic and hydrogen bond acceptor groups to inhibitory activity. The comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analyses (CoMSIA) based 3D-QSAR models were derived using pharmacophore-based alignment. Both CoMFA (q² = 0.70, r² = 0.97 and ) and CoMSIA (q² = 0.54, r² = 0.82 and ) gave reasonable results. The molecular docking (receptor-guided technique) with a recently reported receptor structure (PDB = 1YWN) were performed. The docked alignment was subsequently used for 3D-QSAR (CoMFA; q² = 0.56, r² = 0.97, , CoMSIA; q² = 0.58 r² = 0.91, ). The overall both studies were indicated, steric, electrostatic and hydrogen bond acceptor effects contribute to the inhibitory activity. CoMFA and CoMSIA models suggested that a positive bulk with hydrophobic effect is desirable around position 4 and 5 and hydrogen bond acceptor groups around pyrazolones ring will be helpful.     

应用比较分子力场分析法研究氯代苯酚化合物结构与活性的相关性

苯酚是一类对水生生物有严重危害作用的工业化合物。通过比较分子力场分析(CoMFA)法建立标题化合物对发光菌和浮萍活性的三维定量结构-活性关系(3D-QSAR)模型。其中,对发光菌的研究结果为:交叉验证系数q2=0．921,传统的相关系数(非交叉验证系数)R2=0．990。对浮萍的研究结果为:交叉验证系数q2=0．931,传统的相关系数(非交叉验证系数)R2= 0．995。取得优于文献的结果。     

苯并呋喃类组胺H_3受体拮抗剂的构效关系研究

绢胺H3受体在体内参与调节很多神经递质的释放.人们预期,H3受体拮抗剂将临床应用于老年性痴呆症、抑郁症、精神分裂症等中枢性疾病.本文使用三维定量构效关系研究方法,包括比较分子场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA),研究芳基苯并呋喃类H3受体拮抗剂的分子结构与生物活性之间的定量关系.本文使用CoMSIA法所获建三维定量构效关系模型,其交叉验证系数q2为0.646,非交叉验证相关系数R2为0.920,表明模型预测能力较好,同时使用"留八法"证实模型的稳定和可靠.模型中各分子场的贡献为:立体场10.4%、静电场56.9%和疏水场32.7%.三维系数等势图和静电势图显示:母核3'和4'位上的取代基对活性影响较大,估计它们是配体与受体作用的位点.本研究结果可为设计和开发活性更高的该类拮抗剂提供理论参考.     

N，N-二甲基二2-溴苯乙胺类衍生物活性与CoMFA、CoMSIA的研究

用比较分子力场分析（CoMFA）法和比较分子相似性指数分析（CoMSIA）法，建立N，N-二甲基-2-溴苯乙胺类化合物的3D—QSAR模型。CoMFA模型中，其交叉验证系数q^2=0．792，传统的相关系数R^2=0．955（R=0．978），相应立体场贡献为77．4％、静电场贡献为22．6％，优于文献的报导。CoMSIA研究中，其交叉验证系数q^2=0．757，传统的相关系数R^2=0．917（R=0．958），其疏水场、立体场、静电场贡献依次为：42．9％、39．5％、17．6％。用两种模型分别预测检测集分子的活性，结果与实验值较吻合。说明所建的模型具有较好的预测能力。通过分析CoMFA分子场等值线图，可为优化N，N-二甲基-2-溴苯乙胺类衍生物的结构提供理论指导。