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HEPT类HIV-1逆转录酶衍生物的CoMFA、CoMSIA及HQSAR分析 被引量:4
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作者 仝建波 雷珊 +1 位作者 王洋 秦尚尚 《精细化工》 EI CAS CSCD 北大核心 2019年第1期57-65,73,共10页
采用比较分子力场分析法(CoMFA)、比较分子相似因子分析法(CoMSIA)和分子全息定量结构关系(HQSAR)对1-[(2-羟乙氧)甲基]-6-苯硫基胸腺嘧啶(HEPT)类衍生物进行了分子活性构象选择、分子叠合、空间力场范围建立以及相应3D-QSAR模型建立。... 采用比较分子力场分析法(CoMFA)、比较分子相似因子分析法(CoMSIA)和分子全息定量结构关系(HQSAR)对1-[(2-羟乙氧)甲基]-6-苯硫基胸腺嘧啶(HEPT)类衍生物进行了分子活性构象选择、分子叠合、空间力场范围建立以及相应3D-QSAR模型建立。结果表明:该法所建模型对此类化合物具有良好的预测能力。CoMFA模型显示,交叉验证系数(q2)为0.565,非交互验证系数(r2)为0.892;CoMSIA模型显示,最佳q2为0.636,r2为0.953;最佳的HQSAR模型显示,q2为0.876,r2为0.929,最佳全息长度为97。根据三维等势图和HQSAR色码图设计了7个有较高活性的HEPT类化合物。 展开更多
关键词 COMFA COMSIA HQSAR HEPT类衍生物 生物工程
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基于Topomer CoMFA方法的喹诺酮羧酸类衍生物的QSAR研究及分子设计 被引量:5
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作者 仝建波 雷珊 +1 位作者 秦尚尚 王洋 《分析测试学报》 CAS CSCD 北大核心 2018年第5期517-524,共8页
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
关键词 三维定量构效(3D-QSAR) 喹诺酮羧酸类衍生物 Topomer COMFA 分子设计 分子对接
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A 3D-QSAR Study of HIV-1 Integrase Inhibitors Using RASMS and Topomer CoMFA 被引量:6
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作者 TONG Jian-Bo QIN Shang-Shang +1 位作者 LEI Shan WANG Yang 《Chinese Journal of Structural Chemistry》 SCIE CAS CSCD 2019年第6期867-881,共15页
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
关键词 3D-QSAR INTEGRASE INHIBITORS RASMS Topomer COMFA molecular DOCKING
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3D-QSAR Study of Melittin and Amoebapore Analogues by CoMFA and CoMSIA Methods 被引量:3
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作者 TONG Jian-Bo QIN Shang-Shang JIANG Guo-Yan 《Chinese Journal of Structural Chemistry》 SCIE CAS CSCD 2019年第2期201-210,165,共11页
Peptides are one of the indispensable substances in life. The use of computer aided drug design(CADD) methods to design peptides and peptiodmimetics can short the design cycle, save research funding, improve the level... Peptides are one of the indispensable substances in life. The use of computer aided drug design(CADD) methods to design peptides and peptiodmimetics can short the design cycle, save research funding, improve the level of whole research to a large extent and guide the discovery of new drugs. In this paper, Melittin and amoebapore three-dimensional quantitative structureactivity relationship(3D-QSAR) models were established by using comparative molecular field analysis(CoMFA) and comparative molecular similarity indices analysis(CoMSIA) method. The result shows that, the correlation coefficient(q^2) was 0.583 and non-cross-validation correlation coefficient(r^2) was 0.972 for the melittin CoMFA model. The q^2 and r^2 were 0.630 and 0.995 for the best CoMSIA model, 0.645 and 0.993 for the amoebapore CoMFA model, and 0.738 and 0.996 for the best CoMSIA model. The statistical parameters demonstrated that the CoMFA and CoMSIA models had both good predictive ability and high statistical stability, and can provide theoretical basis for designing new high activity polypeptide drugs. 展开更多
关键词 3D-QSAR MELITTIN ANALOGUES amoebapore ANALOGUES COMFA COMSIA
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S-DABO类逆转录酶抑制剂的Topomer CoMFA及分子对接 被引量:1
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作者 仝建波 王洋 +1 位作者 雷珊 秦尚尚 《陕西科技大学学报》 CAS 2018年第6期63-70,92,共9页
采用Topomer CoMFA方法对21个6-(1-萘甲基)取代S-DABO类化合物进行三维定量构效关系研究,建立了3D-QSAR模型,所得优化模型的主要参数分别为N=3,q^2=0.659,r^2=0.917,F=44.418,SEE=0.222,q_(stderr)~2=0.45,r_(stderr)~2=0.22.结果表明,... 采用Topomer CoMFA方法对21个6-(1-萘甲基)取代S-DABO类化合物进行三维定量构效关系研究,建立了3D-QSAR模型,所得优化模型的主要参数分别为N=3,q^2=0.659,r^2=0.917,F=44.418,SEE=0.222,q_(stderr)~2=0.45,r_(stderr)~2=0.22.结果表明,该模型具有良好的稳定性及预测能力.采用Topomer search在ZINC分子数据库中进行R基团的虚拟筛选,设计了8个活性优于模板分子的新化合物.借助Surflex-dock分子对接研究了新化合物与HIV-1逆转录酶作用模式与机制.结果显示,新化合物与HIV-1逆转录酶的LYS101、LYS103、TYR318位点作用显著. 展开更多
关键词 Topomer COMFA 6-(1-萘甲基)取代S-DABO 3D-QSAR Topomer SEARCH Surflex-dock
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R基团搜索技术用于硫代氨基甲酸酯类非核苷类逆转录酶抑制剂的分子设计 被引量:1
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作者 仝建波 王洋 +1 位作者 雷珊 秦尚尚 《计算机与应用化学》 CAS 北大核心 2018年第2期115-125,共11页
硫代氨基甲酸酯(TCS)被确认为一种新的非核苷类HIV-1逆转录酶抑制剂。本文采用基于R基团搜索技术的Topomer Co MFA方法。实验一对111个硫代氨基甲酸酯衍生物分子进行了三维定量构效关系分析,得到3D-QSAR模型的q^2为0.616,r^2为0.751,... 硫代氨基甲酸酯(TCS)被确认为一种新的非核苷类HIV-1逆转录酶抑制剂。本文采用基于R基团搜索技术的Topomer Co MFA方法。实验一对111个硫代氨基甲酸酯衍生物分子进行了三维定量构效关系分析,得到3D-QSAR模型的q^2为0.616,r^2为0.751,实验二对前60个分子进行同样的分析,得到q^2为0.777,r^2为0.913。两次实验结果表明所建立的模型在统计上都有较好的稳定性和预测能力,但相比之下,实验二更有利于抗艾滋病药物的设计。 展开更多
关键词 Topomer COMFA 3D-QSAR 硫代氨基甲酸酯(TCS)
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