结核分枝杆菌对抗结核药物耐药机制的分子动力学模拟研究

发布时间：2018-04-28 23:21

本文选题：结核 + 耐药　；参考：《兰州大学》2014年硕士论文

【摘要】：结核病是严重危害人民健康并可致命的一种慢性传染病,其发病原因主要为结核分枝杆菌的感染。到目前为止,对于感染结核分枝杆菌的患者主要的治疗方法就是抗结核化学药物的联合用药。然而,耐多药结核分枝杆菌菌株的出现在很大程度上减弱了药物治疗的有效性,对结核患者的治疗带来严重的影响。理解药物与靶标的相互作用和耐药发生的分子机制对于设计和发现新的有效的抗结核药物具有重要的指导价值。基于此本论文结合分子动力学模拟及结合自由能等方法探究了结核分枝杆菌对抗结核药物利福平以及异烟肼的耐药机制。论文第一部分主要是结合分子动力学模拟以及MM-GBSA结合自由能计算方法探究了结核分枝杆菌RNA聚合酶β-亚单位的突变His526Asp、His526Tyr、 His526Arg、Ser531Trp和Ser531Leu对利福平产生耐药性的分子机制。通过比较计算所得结合自由能的结果,突变体对利福平的耐药性排序为His526Arg Ser531Leu His526Tyr His526Asp。氨基酸残基与利福平分子之间的非极性相互作用的减弱是引起靶标与利福平结合能力变弱的主要因素,其中降低最为明显的为His526Arg和Ser531Leu突变体。另外,对于Ser531Leu和His526Arg突变体来说,两者的气相能中的静电相互作用能也产生明显的减少。通过对复合物结合口袋进行氢键相互作用以及表面性质分析,我们发现第526位组氨酸和531位亮氨酸残基分别发生突变后,不仅影响结合口袋大小以及疏水性强弱,也引起配体分子发生位移,从而在一定程度上影响氢键以及疏水相互作用的形成。论文第二部分主要研究当结核分枝杆菌enoyc-Acp还原酶上发生Ser94Ala、 Ile194Thr以及Ser94Ala/Ile194Thr氨基酸残基突变后,对异烟肼(INH)产生耐药性的分子机理。当异烟肼进入菌体之后被氧化成与烟酰胺腺嘌呤二核苷酸(Nicotinamide Adenine Dinucleotide,NAD)结合的活性形式——INH-NAD。对所有结合有INH-NAD的野生型和突变型复合物体系,根据结合自由能的大小,可将INH-NAD结合enoyc-Acp还原酶的能力从强到弱排列顺序为WT Ile194Thr Ser94Ala Ser94Ala/Ile194Thr。探究其突变引起结合变弱的原因发现突变均能引起极性相互作用能中静电相互作用能与非极性相互作用能的减小,其中非极性相互作用能的减小是引起突变型复合物体系结合自由能减小的最关键因素。另外,极性相互作用能的减小与氢键作用的减弱或消失有着密切的关系。从结构对比的结果来看,若发生Ile194Thr、Ser94Ala以及Ser94Ala/Ile194Thr突变后,会引起enoyc-Acp还原酶上INH-NAD结合口袋发生变化,从而使原有可以存在的enoyc-Acp还原酶上结合口袋与INH-NAD之间的氢键以及范德华相互作用受到影响,亲和力降低。本工作从分子水平探讨了抗结核药物与靶标的相互作用以及靶标突变导致结核分枝杆菌耐药性发生的分子机制,得到的结果将为发现和设计针对耐药结核的抗结核药物提供重要的理论指导。
[Abstract]:Tuberculosis is a chronic infectious disease that seriously endangers the people's health and can be fatal, the main cause of which is Mycobacterium tuberculosis infection. So far, the main treatment for Mycobacterium tuberculosis patients is the combination of anti tuberculosis chemical drugs. However, the emergence of multi drug resistant Mycobacterium tuberculosis strains is very important. The understanding of the interaction between drug and target and the molecular mechanism of drug resistance have important guiding value for the design and discovery of new and effective anti tuberculosis drugs. Based on this theory, it combines molecular dynamics simulation and freedom. The resistance mechanism of Mycobacterium tuberculosis to rifampicin and isoniazid can be explored by other methods.
The first part of the thesis is to explore the molecular mechanism of the mutation of His526Asp, His526Tyr, His526Arg, Ser531Trp and Ser531Leu to rifampin, combined with molecular dynamics simulation and MM-GBSA binding free energy calculation method. The results of the combination of free energy are calculated by comparing the results of the comparison of the resistance to rifampin, His526Tyr, His526Arg, Ser531Trp and Ser531Leu. The resistance of the mutant to Li Fuping was sorted by the reduction of the non polar interaction between the His526Arg Ser531Leu His526Tyr His526Asp. amino acid residues and the Li Fuping molecule, which was the main factor causing the weakening of the binding ability of the target and Li Fuping, among which the most obvious was the His526Arg and Ser531Leu mutants. In addition, for Ser531Leu With the His526Arg mutants, the electrostatic interaction in the gas phase can also be significantly reduced. By hydrogen bonding interaction and surface properties analysis of the composite binding pockets, we found that the 526th - and 531 - bit leucine residues mutated respectively, not only affecting the size and hydrophobicity of the binding pockets. Strong and weak also cause the displacement of ligand molecules, thus affecting the formation of hydrogen bonds and hydrophobic interactions to a certain extent.
The second part of the paper mainly studies the molecular mechanism of drug resistance to isoniazid (INH) when Ser94Ala, Ile194Thr, and Ser94Ala/Ile194Thr amino acid residues are mutated on enoyc-Acp reductase of Mycobacterium tuberculosis. When isoniazid enters the fungus, it is oxidized to nicotinamide adenine dinucleotide (Nicotinamide Adenine Dinucleo). Tide, NAD) combining the active form of INH-NAD. to all the wild and mutant complexes with INH-NAD, based on the size of the binding free energy, the ability of INH-NAD to bind enoyc-Acp reductase from strong to weak sequence to WT Ile194Thr Ser94Ala Ser94Ala/ Ile194Thr. explores the cause of the mutation caused by the mutation. The present mutation can cause the decrease of the energy between the electrostatic interaction energy and the non polar interaction energy in the polar interaction energy, and the decrease of the non polar interaction energy is the most important factor causing the decrease of the free energy of the mutant complex system. From the results of structural contrast, if Ile194Thr, Ser94Ala, and Ser94Ala/Ile194Thr mutations occur, the INH-NAD binding pocket on the enoyc-Acp reductase can be changed, thus making the existing enoyc-Acp reductase binding to the hydrogen bond between the pocket and INH-NAD and the influence of the Fan Dehua interaction on the original enoyc-Acp reductase, and the affinity. The force is reduced.
In this work, the molecular mechanism of the interaction of anti tuberculosis drugs and targets and the molecular mechanism of the drug resistance of Mycobacterium tuberculosis caused by the target mutation are discussed. The results will provide important theoretical guidance for the discovery and design of anti tuberculosis drugs for drug-resistant tuberculosis.

【学位授予单位】：兰州大学
【学位级别】：硕士
【学位授予年份】：2014
【分类号】：R52

【参考文献】