多巴胺转运体微观机理的多层次分子模拟研究

Dopamine transporter is a kind of membrane protein, which controls the signal communication between neurons. Dysfunction of Dopamine Transporter is associated with various mental disordered diseases. However, drug design targeting dopamine transporter is quit random, because the atomic-level details of substrate selectivity mechanism and transport inhibition mechanism remain unknown. .In this project, we plan to focus on theoretical/computational study of Dopamine Transporter, aiming to understand and predict its binding and inhibition mechanism. In 2015, there are eight essential crystal structures for dopamine transporter newly released, including its substrate dopamine, and several inhibitors like cocaine, amphetamines, and antidepressant drugs. The rich information in these crystal structures provides a solid basis of comparison of structural and dynamic properties between substrates and inhibitors. We plan to exert our endeavor in the following three aspects: 1) Develop a polarized force filed for membrane protein system to monitor the effect of electrostatic polarization played on the structures and functions of Dopamine Transporters. 2) Use enhanced sampling techniques to elucidate the dynamics of dopamine transporters soaked in multi-components lipid molecules, especially cholesterol. 3) Use pocket-based bioinformatics method and Markov State Model to analyze the simulations results and to elucidate the regulation mechanisms under neurotransmitter transport of Dopamine Transporter. The final goal is to provide critical information for new generation of drugs on cures of the diseases in nervous systems.

多巴胺转运体是一类调控神经元细胞间信号传导的膜蛋白，其功能失调会导致多种严重神经类疾病。但是目前对其底物选择机理、抗抑郁药等抑制剂的拮抗机理尚缺乏原子水平的认识，导致针对多巴胺转运体的药物开发具有盲目性。本项目基于2015年新发现的多巴胺转运体的系列晶体结构，通过理论模拟，研究其微观运动性质，探索其控病机制。本项目围绕以下三方面工作展开：1）开发针对膜蛋白体系的极化分子力场，探索静电极化效应对研究体系结构和功能的影响。2）引入包含胆固醇分子以及多种磷脂分子的多组分膜，配合增强抽样方法，探究在真实生物膜环境内，多巴胺转运体行使生理功能过程中的大尺度构象变化。3）采用先进的结合位点分块分析方法和马尔科夫态模型，提取分子模拟中的热力学动力学信息，对比实验数据，揭示多巴胺转运体的微观机理，为今后针对神经系统疾病的新药开发作出贡献。

神经元细胞间信号传导的终止主要由神经递质钠协同转运体NSSs家族调控。此家族功能失调会导致多种严重神经类疾病，如抑郁症、多动症、帕金森综合症、癫痫症等。NSSs家族是目前开发新颖治疗神经类疾病药物的重要靶标。对NSSs家族的控病机制开展研究，具有重要的经济价值和社会意义。本项目计划对NSSs家族最新的也是首批晶体结构多巴胺转运体开展微观机理方面的分子模拟和药物设计研究。这些晶体结构包括转运体同底物多巴胺、抑制剂可卡因、安非他命和知名抗抑郁药去甲阿米替林等8个配体形成的复合物。基于这些实验结构，我们利用生物信息学方法、分子动力学模拟和增强采样等先进的理论技术对多巴胺转运体的底物结合机理和抑制剂抑制机理开展研究，并对比利用获得的机理开展针对多巴胺转运体的新型神经类药物设计。我们也进一步将这一套研究方法推广到另一类膜蛋白--能量耦合因子的模拟。.本报告中，我们也针对药物开发的一般性问题，设计了一种新型的自由能计算方法，相互作用熵方法，并应用这种方法计算了蛋白质蛋白质相互作用能和水的过量自由能。