Ligand Induced Conformational Changes of the Human Serotonin Transporter Revealed by Molecular Dynamics Simulations

The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.竞争性抑制剂可卡因（cocaine）与非竞争性抑制剂伊博加因（ibogaine）可诱导人类5-羟色胺转运体（human serotonin transporter）产生不同的构象状态。已有可及性实验结果表明，可卡因主要诱导该转运体形成面向外的构象；而非竞争性抑制剂伊博加因及其活性代谢物去甲伊博加因（noribogaine），则被认为可诱导人类5-羟色胺转运体形成面向内的构象，这与内源性底物5-羟色胺（serotonin）所诱导的构象相似。本研究基于人类5-羟色胺转运体的同源建模模型，通过多组全原子分子动力学模拟，探究了底物、非竞争性抑制剂、竞争性抑制剂这三类不同配体诱导的人类5-羟色胺转运体构象变化。模拟结果显示，根据结合配体的类型不同，分子动力学模拟可捕捉到人类5-羟色胺转运体的多种构象。结合去甲伊博加因时，转运体可形成面向内的构象，该状态既与此前通过结合底物的分子动力学模拟所得到的人类5-羟色胺转运体面向内构象一致，也与近期发表的细菌同源蛋白——嗜热水生菌（Aquifex aeolicus）亮氨酸转运体（leucine transporter）的面向内构象相符。研究发现，配体诱导的行为差异源于配体与蛋白质之间不同的相互作用模式。这种从原子层面揭示抑制剂如何通过配体结合决定转运体构象响应的认知，可为未来的药物设计提供重要参考。