采用基于R基团搜索技术的Topomer Co MFA技术对一系列喹诺酮羧酸类衍生物进行三维定量构效(3D-QSAR)关系研究,所得模型结果的交叉验证相关系数(q2)为0.790,非交互验证系数(r2)为0.890,外部验证的复相关系数(r2pred)为0.878,研究结果表...采用基于R基团搜索技术的Topomer Co MFA技术对一系列喹诺酮羧酸类衍生物进行三维定量构效(3D-QSAR)关系研究,所得模型结果的交叉验证相关系数(q2)为0.790,非交互验证系数(r2)为0.890,外部验证的复相关系数(r2pred)为0.878,研究结果表明该模型具有良好的稳定性和预测能力。采用Topomer search技术在ZINC数据库中进行虚拟筛选,筛选出6个Ra基团和3个Rb基团,进而设计出12个具有更高活性的新型喹诺酮羧酸类化合物。采用分子对接技术对药物与受体的作用机制进行了研究,结果显示,药物与蛋白酶的ASP 30、ASP 29和ASN 25位点作用明显,该QSAR的研究结果可为新药合成提供理论参考。展开更多
In order to understand the chemical-biological interactions governing their activities toward neuraminidase （NA）, QSAR models of 28 thiazolidine-4-carboxylic acid derivatives with inhibitory influenza A virus were d...In order to understand the chemical-biological interactions governing their activities toward neuraminidase （NA）, QSAR models of 28 thiazolidine-4-carboxylic acid derivatives with inhibitory influenza A virus were developed. The obtained HQSAR （hologram quantitative structure activity relationship）, Topomer CoMFA and CoMSIA （comparative molecular similarity indices analysis） models were robust and had good exterior predictive capabilities. Moreover, QSAR modeling results elucidated that hydrogen bonds highly contributed to the inhibitory activity, then electrostatic and hydrophobic factors. Squared multiple correlation coefficients （R2） of HQSAR, Topomer CoMFA and CoMSIA models were 0.994, 0.978 and 0.996, respectively. Squared cross-validated correlation coefficients （Q2） of HQSAR, Topomer CoMFA and CoMSIA models were in turn 0.951, 919 and 0.820. Furthermore, squared multiple correlation coefficients for the test set （R2test） of HQSAR, CoMFA and CoMSIA models were 0.879, 0.912 and 0.953, respectively. Squared cross-validated correlation coefficients for the test set （Q2ext） of HQSAR, Topomer CoMFA and CoMSIA models were 0.867, 0.884 and 0.899, correspondingly.展开更多
Acquired Immunodeficiency Syndrome(AIDS) is a significant human health threat around the world. Therefore, the study of anti-human immunodeficiency virus(HIV) drug design has become an important task for today’s soci...Acquired Immunodeficiency Syndrome(AIDS) is a significant human health threat around the world. Therefore, the study of anti-human immunodeficiency virus(HIV) drug design has become an important task for today’s society. In this paper, a three-dimensional quantitative structure-activity relationships study(3 D-QSAR) was conducted on 53 HIV-1 integrase inhibitors(IN) using random sampling analysis on molecular surface(RASMS) and Topomer comparative molecular field analysis(Topomer CoMFA). The multiple correlation coefficients of fitting, cross-validation, and external validation of two models were 0.926, 0.815 and 0.908 and 0.930, 0.726 and 0.855, respectively. The results indicated that two models obtained had both favorable estimation stability and good prediction capability. Topomer Search was used to search appropriate R groups from ZINC database, and 28 new compounds were designed thereby. The Topomer CoMFA model was subsequently used to predict the biological activity of these compounds, showing that 24 of the new compounds were more active than the template molecule. Ligands of the template molecule and new designed compounds were used for molecular docking to study the interaction of these compounds with the protein receptor. The results show that the ligands would form hydrogen-bonding interactions with the residues LEU58, THR83, GLN62, MET155, LYS119 and ALA154 of the protein receptor generally, thereby providing additional insights for the design of even more effective HIV/AIDS drugs.展开更多
Topomerization of [9] annulen anion （1） and its 2-fluoro-, 2-chloro- and 2- bromo-defivatives （2, 3 and 4, respectively） are studied at the HF/6-31G＊ and B3LYP/6-31 1＋＋G＊＊ levels of theory. The relative ease ...Topomerization of [9] annulen anion （1） and its 2-fluoro-, 2-chloro- and 2- bromo-defivatives （2, 3 and 4, respectively） are studied at the HF/6-31G＊ and B3LYP/6-31 1＋＋G＊＊ levels of theory. The relative ease of topomerization is dependent on the charge distribution and planarity of the ground state and the transition state of 9-membered rings as well as the size and electronegativity of halogen substituent. Consequently, the endo-2-halo-[9] annulen anion topomers become unstable and easily convert to related exo-topomers. Hence, according to the DFT calcu- lations, the order of topomerization energy barrier for endo = exo topomerization is lendo 〉 2endo 〉 3endo.展开更多
Topomer CoMFA models have been used to optimize the potency of 15 biologically active acridone derivatives se- lected from the literature. Their 3D chemical structures were sliced into three acyclic R groups, to produ...Topomer CoMFA models have been used to optimize the potency of 15 biologically active acridone derivatives se- lected from the literature. Their 3D chemical structures were sliced into three acyclic R groups, to produce a fragment that is present in each training set. The analysis was successful with 3 as the number of components that provided the highest q2 results: q2 is 0.56, which is the cross-validated coefficient for the specified number of components, giving rise to 0.37 standard error of estimate (q2 stderr), and a conventional coefficient (r2) of 0.82, whose standard error of estimate is 0.24. These results provide structure-activity relationship (sar) among the compounds. The result of the To-pomer CoMFA studies was used to design novel derivatives for future studies.展开更多
目的:为了定量解释12-LOX抑制剂活性和结构的关系,得到分子优化的方向。方法:从文献中得到一系列化合物,进行Topomer Co MFA研究。结果:模型具有良好统计学意义,分别为N=7,Q2=0.540,R2=0.952,F=162.3,SEE=0.14,Stderr=0.44,R2pred=5.52...目的:为了定量解释12-LOX抑制剂活性和结构的关系,得到分子优化的方向。方法:从文献中得到一系列化合物,进行Topomer Co MFA研究。结果:模型具有良好统计学意义,分别为N=7,Q2=0.540,R2=0.952,F=162.3,SEE=0.14,Stderr=0.44,R2pred=5.52。结论:计算值与测量值的低偏差表示模型具有较强的预测能力,等势图和假设的结合模式提供了选择性的合理解释,这将指导进一步的研究。展开更多
Topomer comparative molecular field analysis(Topomer Co MFA)and holographic quantitative structure-activity relationship(HQSAR)for 1302,5-diketopiperazine derivatives were used to build a three-dimensional quantitativ...Topomer comparative molecular field analysis(Topomer Co MFA)and holographic quantitative structure-activity relationship(HQSAR)for 1302,5-diketopiperazine derivatives were used to build a three-dimensional quantitative structure-activity relationship(3D-QSAR)model.The results show that the models have high predictive ability.For Topomer CoMFA,the cross-validated q^2 value is 0.710 and the non-cross-validated r^2 value is 0.834.The most effective HQSAR model shows that the cross-validation q^2 value is 0.700,the non-cross-validated r^2 value is 0.815,and the best hologram length value is 353 using connections and bonds as fragment distinctions.50 highly active 2,5-diketopiperazine derivatives were designed based on the three-dimensional equipotential map and HQSAR color code map.Finally,the molecular docking method was also used to study the interactions of these new molecules by docking the ligands into the diketopiperazine active site,which revealed the likely bioactive conformations.This study showed that there are extensive interactions between the new molecule and Arg156,Arg122 residues in the active site of diketopiperazine.These results provide useful insights for the design of potent of the new 2,5-diketopiperazine derivatives.展开更多
基金supported by the National Natural Science Foundation of China (No. 21202110)
文摘In order to understand the chemical-biological interactions governing their activities toward neuraminidase （NA）, QSAR models of 28 thiazolidine-4-carboxylic acid derivatives with inhibitory influenza A virus were developed. The obtained HQSAR （hologram quantitative structure activity relationship）, Topomer CoMFA and CoMSIA （comparative molecular similarity indices analysis） models were robust and had good exterior predictive capabilities. Moreover, QSAR modeling results elucidated that hydrogen bonds highly contributed to the inhibitory activity, then electrostatic and hydrophobic factors. Squared multiple correlation coefficients （R2） of HQSAR, Topomer CoMFA and CoMSIA models were 0.994, 0.978 and 0.996, respectively. Squared cross-validated correlation coefficients （Q2） of HQSAR, Topomer CoMFA and CoMSIA models were in turn 0.951, 919 and 0.820. Furthermore, squared multiple correlation coefficients for the test set （R2test） of HQSAR, CoMFA and CoMSIA models were 0.879, 0.912 and 0.953, respectively. Squared cross-validated correlation coefficients for the test set （Q2ext） of HQSAR, Topomer CoMFA and CoMSIA models were 0.867, 0.884 and 0.899, correspondingly.
基金supported by the National Natural Science Foundation of China(21475081)Natural Science Foundation of Shaanxi Province(2015JM2057)Graduate Innovation Fund of Shaanxi University of Science and Technology
文摘Acquired Immunodeficiency Syndrome(AIDS) is a significant human health threat around the world. Therefore, the study of anti-human immunodeficiency virus(HIV) drug design has become an important task for today’s society. In this paper, a three-dimensional quantitative structure-activity relationships study(3 D-QSAR) was conducted on 53 HIV-1 integrase inhibitors(IN) using random sampling analysis on molecular surface(RASMS) and Topomer comparative molecular field analysis(Topomer CoMFA). The multiple correlation coefficients of fitting, cross-validation, and external validation of two models were 0.926, 0.815 and 0.908 and 0.930, 0.726 and 0.855, respectively. The results indicated that two models obtained had both favorable estimation stability and good prediction capability. Topomer Search was used to search appropriate R groups from ZINC database, and 28 new compounds were designed thereby. The Topomer CoMFA model was subsequently used to predict the biological activity of these compounds, showing that 24 of the new compounds were more active than the template molecule. Ligands of the template molecule and new designed compounds were used for molecular docking to study the interaction of these compounds with the protein receptor. The results show that the ligands would form hydrogen-bonding interactions with the residues LEU58, THR83, GLN62, MET155, LYS119 and ALA154 of the protein receptor generally, thereby providing additional insights for the design of even more effective HIV/AIDS drugs.
文摘Topomerization of [9] annulen anion （1） and its 2-fluoro-, 2-chloro- and 2- bromo-defivatives （2, 3 and 4, respectively） are studied at the HF/6-31G＊ and B3LYP/6-31 1＋＋G＊＊ levels of theory. The relative ease of topomerization is dependent on the charge distribution and planarity of the ground state and the transition state of 9-membered rings as well as the size and electronegativity of halogen substituent. Consequently, the endo-2-halo-[9] annulen anion topomers become unstable and easily convert to related exo-topomers. Hence, according to the DFT calcu- lations, the order of topomerization energy barrier for endo = exo topomerization is lendo 〉 2endo 〉 3endo.
文摘Topomer CoMFA models have been used to optimize the potency of 15 biologically active acridone derivatives se- lected from the literature. Their 3D chemical structures were sliced into three acyclic R groups, to produce a fragment that is present in each training set. The analysis was successful with 3 as the number of components that provided the highest q2 results: q2 is 0.56, which is the cross-validated coefficient for the specified number of components, giving rise to 0.37 standard error of estimate (q2 stderr), and a conventional coefficient (r2) of 0.82, whose standard error of estimate is 0.24. These results provide structure-activity relationship (sar) among the compounds. The result of the To-pomer CoMFA studies was used to design novel derivatives for future studies.
文摘目的:为了定量解释12-LOX抑制剂活性和结构的关系,得到分子优化的方向。方法:从文献中得到一系列化合物,进行Topomer Co MFA研究。结果:模型具有良好统计学意义,分别为N=7,Q2=0.540,R2=0.952,F=162.3,SEE=0.14,Stderr=0.44,R2pred=5.52。结论:计算值与测量值的低偏差表示模型具有较强的预测能力,等势图和假设的结合模式提供了选择性的合理解释,这将指导进一步的研究。
基金supported by the National Natural Science Funds of China(21475081)the Natural Science Foundation of Shaanxi Province(2019JM-237)the Graduate Innovation Fund of Shaanxi University of Science and Technology。
文摘Topomer comparative molecular field analysis(Topomer Co MFA)and holographic quantitative structure-activity relationship(HQSAR)for 1302,5-diketopiperazine derivatives were used to build a three-dimensional quantitative structure-activity relationship(3D-QSAR)model.The results show that the models have high predictive ability.For Topomer CoMFA,the cross-validated q^2 value is 0.710 and the non-cross-validated r^2 value is 0.834.The most effective HQSAR model shows that the cross-validation q^2 value is 0.700,the non-cross-validated r^2 value is 0.815,and the best hologram length value is 353 using connections and bonds as fragment distinctions.50 highly active 2,5-diketopiperazine derivatives were designed based on the three-dimensional equipotential map and HQSAR color code map.Finally,the molecular docking method was also used to study the interactions of these new molecules by docking the ligands into the diketopiperazine active site,which revealed the likely bioactive conformations.This study showed that there are extensive interactions between the new molecule and Arg156,Arg122 residues in the active site of diketopiperazine.These results provide useful insights for the design of potent of the new 2,5-diketopiperazine derivatives.
