基于系统药理学的多靶标弱结合药物发现方法与应用

发布时间：2017-12-28 20:41

本文关键词：基于系统药理学的多靶标弱结合药物发现方法与应用　出处：《西北农林科技大学》2017年博士论文　论文类型：学位论文

【摘要】：药物-靶标亲和力是药物开发中的重要指标,传统药物设计开发的中心法则即针对单个靶标设计高选择性、高亲和力的小分子配体,认为靶标越单一、亲和力越高,药效就越好。然而,人们逐渐发现面对复杂疾病时(例如肿瘤、心血管病、阿尔兹海默病),靶向多个靶标的低亲和力药物比单一靶标的高亲和力药物更优秀。近年来网络药理学、多向药理学、系统药理学等新兴学科蓬勃发展,为多靶标弱结合药物的开发奠定了基础。但是目前仍然缺乏行之有效的多靶标弱结合药物的发现方法。为了解决多靶标弱结合药物发现中的基本问题,本研究工作基于药物靶标之间的网络拓扑结构和动力学参数,以及多靶标弱结合药物对网络的扰动特点,提出了一整套药物发现新方法,并与药物发现实践相结合,开展了系统性的研究工作。主要发现如下:(1)提出一种系统动力学方法推理网络基元模块,并模拟网络基元模块对多点扰动的响应。归纳总结出了33个基元模块,采用动力学模拟研究了它们在多点扰动下的拓扑结构和动力学参数变化。结果表明基元模块的协同/拮抗效果可以由拓扑结构单独决定,或者由拓扑结构和动力学参数共同决定。(2)利用生物范围合理的参数集以及常微分方程数值积分重新构建了浓缩的MAPK信号网络,并将基元模块应用于重建的网络中。重建的系统可以由LPS诱导激活,并且对不同模块的扰动效果可由IL-6和TNF-α的信号水平来评价。模拟了单靶标强结合药物以及多靶标弱结合药物对网络的扰动情况,从而筛选最优靶标组合。结果表明,为了降低MAPK信号通路对炎性刺激的响应水平,设计多靶标弱结合药物应该优先考虑含有p38激酶的靶标组合。(3)以最优靶标组合为基础,采用系统药理学方法,从中药系统药理学数据库中的所有天然产物以及Drugbank数据库中的小分子药物里反向筛选出32个多靶标化合物,运用分子动力学模拟与结合自由能计算评价了这些化合物的亲和力。随后选取木犀草素与丹参酮IIA作为多靶标弱结合化合物,以几种激酶抑制剂作为单靶标强结合化合物对照,进行了体外实验验证。结果表明,在酶学水平上木犀草素和丹参酮IIA对其靶标的IC50在微摩尔浓度范围,远大于现有的激酶抑制剂,但是在细胞抗炎实验中显示出与激酶抑制剂相当甚至更好的药效。综上所述,本研究系统地分析了网络基元模块的性质以及如何利用基元模块选取信号通路中的最优靶标组合。同时,基于系统药理学提出了多靶标弱结合药物的发现方法,为新药开发,老药新用,天然产物开发利用提供了新思路。
[Abstract]:Drug target affinity is an important index in drug development. The central rule of traditional drug design and development is to design high selectivity and high affinity small molecule ligands for single target. It is considered that the more single target and the higher affinity, the better the efficacy. However, it has been found that when facing complex diseases, such as tumor, cardiovascular disease, Alzheimer's disease, low affinity drugs targeting multiple targets are better than single target high affinity drugs. In recent years, new disciplines such as network pharmacology, multidirectional pharmacology and systematic pharmacology have developed vigorously, which has laid a foundation for the development of multi targets and weak combination drugs. However, there is still a lack of effective methods for the discovery of multiple targets and weak combination drugs. In order to solve the basic problem of multi target weak combined with drug discovery, this research work based on the drug target between the network topology and the dynamic parameters, and combined with the features of disturbance of multi target weak drugs on the network, puts forward a series of new drug discovery methods, and found that the practice of combining with drugs, carried out the research work of the system. The main findings are as follows: (1) a system dynamics method is proposed to reasoning network primitives and to simulate the response of network primitives to multipoint disturbances. 33 elementary modules are summed up and the dynamics simulation is used to study their topological structure and dynamic parameters. The results show that the synergistic / antagonistic effects of the primitives can be determined solely by the topology or by the topology and dynamic parameters. (2) reconstruct the condensed MAPK signal network by using the reasonable parameter set of biological range and numerical integration of ordinary differential equations, and apply the primitive module to the reconstructed network. The reconstructed system can be activated by LPS, and the disturbance effect on different modules can be evaluated by the signal level of IL-6 and TNF- alpha. The disturbance of the single target strong combination drug and the multi target weak combination drug on the network is simulated, so as to screen the optimal target combination. The results showed that in order to reduce the response level of MAPK signaling pathway to inflammatory stimuli, we should first consider the target combinations containing p38 kinase when designing multi target weak binding drugs. (3) to the optimal target portfolio based system, using pharmacological methods, from small molecule drugs of traditional Chinese medicine pharmacology system database of all natural products as well as in the Drugbank database in reverse screening more than 32 target compounds by molecular dynamics simulation and combining self by the calculation and evaluation of the affinity of these compounds. Subsequently, luteolin and tanshinone IIA were selected as multi target weak binding compounds. Several kinase inhibitors were used as single target strong binding compound control, and were verified in vitro. The results showed that luteolin and tanshinone IIA had higher IC50 concentration in the micromolar range than the existing kinase inhibitors at the enzymology level. But in cell anti-inflammatory experiments, it showed a comparable or even better efficacy than kinase inhibitors. To sum up, this research systematically analyzes the nature of the network primitives module and how to select the optimal target combination in the signal path by using the basic module. At the same time, based on System Pharmacology, the discovery method of multi target weak binding drugs is put forward, which provides a new idea for new drug development, new use of old drugs and natural products development and utilization.
【学位授予单位】：西北农林科技大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：R96

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