【作者】 刘春莉；

【导师】 王存新；

【作者基本信息】 北京工业大学 ， 流体力学， 2005， 硕士

【摘要】 从20 世纪90 年代开始,随着各种理论计算方法和分子模拟技术的发展,药物设计进入了一个崭新的阶段,即合理药物设计的阶段。其内容的核心是,针对酶、受体、离子通道以及核酸等潜在的药物设计靶点,并参考其它内源性配体或天然产物底物的化学结构特征设计出合理的药物分子,以发现选择性作用于某种靶点的新药;其方法的核心是对受体-配体相互作用的研究。合理药物设计已成为国际上十分活跃的科学研究领域。本论文以人体免疫缺陷病毒(HIV-1)整合酶为研究对象,用分子对接方法、分子动力学(MD)模拟方法和结合自由能计算方法研究其与已知抑制剂的结合模式、结合强度、耐药性质,以及与病毒DNA 可能的结合位点,为寻找具有更好活性的抗HIV 药物提供帮助。论文主要包括以下三个方面的工作:用分子模拟方法研究HIV-1 整合酶与咖啡酰基类抑制剂的相互作用;用分子对接方法研究HIV-1 整合酶与病毒DNA的相互作用;HIV-1 整合酶对其抑制剂S-1360 的耐药性研究。X-ray 和NMR 实验已经给出了HIV-1 整合酶三个结构域的结构,这为基于受体结构的药物设计提供了条件。用分子对接和分子动力学(MD)模拟方法研究了一类咖啡酰基和没食子酰基类HIV-1 整合酶抑制剂与整合酶之间的相互作用模式,结果表明该类抑制剂分子上的两个侧链基团(咖啡酰基或没食子酰基)与整合酶的DDE 基序之间的相互作用对抑制整合酶活性起到关键作用。当侧链基团为没食子酰基时,可以提高该类抑制剂与整合酶的结合能力。采用线性相互作用能方法(LIE)计算了该类抑制剂与整合酶之间的结合自由能,预测值与实验值相吻合,均方根偏差(RMSD)为1.39 kJ/mol,以上结果可为基于结构更多还原

【Abstract】 From 1990s, with the development of theoretical and computational methods as well as molecular modeling technology, drug design came into a brand-new era, which mainly involves the rational drug design. The core of the contents of rational drug design is discovery of the new selective drugs against certain targets such as enzyme, receptor, ion channel and nucleic acid, based on some endogenous ligands or characteristic of the chemical structures of some natural products. The kernel of the methodology focus on the studies of the interactions between receptor and ligand. Rational drug design has become an active research area. In this dissertation, molecular docking, molecular dynamics simulation and binding free energy calculation were used to study the binding modes, binding affinity and drug resistance of HIV-1 integrase and its inhibitors. The possible DNA binding sites were also investigated. These studies will be helpful for design and discovery of new active anti-AIDS drugs. The dissertation mainly includes the following three aspects: study on interactions between HIV-1 integrase and its dicaffeoyl inhibitors through molecular modeling approach; investigations on HIV-1 integrase/DNA binding interactions with the molecular docking approach; study on the HIV-1 integrase drug resistance to the clinical trial drug S-1360. X-ray and NMR experiments have revealed the structures of the three domains on HIV-1 integrase, which is important for structure-based drug design. The binding mode of a series of dicaffeoyl-or digalloyl pyrroliding and furan derivatives inhibitors with HIV-1 integrase was proposed by using molecular docking and molecular dynamics simulation methods. The results indicate that the interactions between HIV-1 integrase conserved DDE motif and caffeoyl -or galloyl group of inhibitors play a critical role in the inhibition of integrase activity. The binding affinity between integrase and inhibitors was improved when the side chain groups were galloyls. The linear interaction energy method was used to calculate the binding free energies of HIV-1 integrase and their inhibitors. The predicted values are in good agreement with the experimental data, with a root mean square deviation (RMSD) of 1.39 kJ/mol. The above results provide us useful information for structure-based HIV-1 integrase inhibitor design. HIV-1 integrase (IN) is a key enzyme in the process of HIV-1 replication and can catalyse the insertion of the viral cDNA into host chromosomes. The knowledge of the binding sites between integrase tetramer and viral DNA at atomic level will be very helpful for understanding integrase catalytic mechanism and discovery of inhibitors. Until now, the binding sites and binding modes between HIV-1 IN and viral DNA have not been clarified. In this work, the full length HIV-1 integrase tetramer was obtained by homology modeling. Molecular docking method was used to explore the binding site of integrase with 27bp DNA. The docking results show that the binding sites locate in the saddle-shaped groove produced by two monomers of C-term and N-term domains for each of the IN dimer. In addition, DNA may interact integrase tetramer by contacting with both the C-term and N-term domains from one dimer and the core domain from the other dimer. The 3’end processed DNA and intact DNA interact with integrase in the similar way. The results have good agreement with the known experimental data obtained from the photo-cross-linking and site-directed mutagenesis studies. HIV strain drug resistance to inhibitors is a pivotal problem in anti-HIV therapy.更多还原