Structural insight into tetrameric hTRPV1 from homology modeling, molecular docking, molecular dynamics simulation, virtual screening, and bioassay validations.
Structural insight into tetrameric hTRPV1 from homology modeling, molecular docking, molecular dynamics simulation, virtual screening, and bioassay validations.
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DOI：
10.1021/ci5007189
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发表时间：
2015-03-23
影响因子：
5.6
通讯作者：
Xie XQ
中科院分区：
文献类型：
--
作者：
Feng Z;Pearce LV;Xu X;Yang X;Yang P;Blumberg PM;Xie XQ
瞬时受体电位香草酸1型（TRPV 1）是一种热激活的阳离子通道蛋白，它有助于炎症，急性和持续性疼痛。人TRPV 1（hTRPV 1）的拮抗剂代表了用于治疗疼痛的新的治疗方法。然而，开发hTRPV 1的各种拮抗剂受到hTRPV 1的3D结构的不可用性的阻碍。最近，大鼠TRPV 1（rTRPV 1）的三维结构的存在和不存在的配体已被报道确定的冷冻电镜。rTRPV 1与hTRPV 1具有85.7%的序列同一性。在本工作中，我们构建并报告了hTRPV 1的三维同源四聚体模型的基础上cryo-EM结构的rTRPV 1。分子动力学（MD）模拟，能量最小化，和预筛选应用于选择和验证的hTRPV 1的最佳模型。预测的hTRPV 1的结合口袋由两个相邻的单体亚基组成，这与实验数据和rTRPV 1的cyro-EM结构一致。利用分子对接技术研究了hTRPV 1与其拮抗剂或激动剂之间的相互作用，确定了其中的重要残基。通过分子动力学模拟研究了hTRPV 1在拮抗剂/激动剂结合后的构象变化。化合物的不同运动导致hTRPV 1中单体的不同构象变化，表明TRPV 1以协同方式工作，类似于其他通道蛋白如水通道蛋白。我们观察到，在MD模拟过程中，当hTRPV 1与激动剂结合时，选择性过滤器是开放的。对于hTRPV 1的下门，我们观察到hTRPV 1与拮抗剂和激动剂结合之间的很大相似性。建立了基于多种拮抗剂的五点药效团模型，并利用该结构模型通过计算机模拟筛选新的hTRPV 1拮抗剂。通过使用上述3D TRPV 1结构模型，初步的计算机筛选已经开始产生具有作为hTRPV 1拮抗剂的活性的有希望的命中物，其中几种显示出相当大的效力。
The transient receptor potential vanilloid type 1 (TRPV1) is a heat-activated cation channel protein, which contributes to inflammation, acute and persistent pain. Antagonists of human TRPV1 (hTRPV1) represent a novel therapeutic approach for the treatment of pain. Developing various antagonists of hTRPV1, however, has been hindered by the unavailability of a 3D structure of hTRPV1. Recently, the 3D structures of rat TRPV1 (rTRPV1) in the presence and absence of ligand have been reported as determined by cryo-EM. rTRPV1 shares 85.7% sequence identity with hTRPV1. In the present work, we constructed and reported the 3D homology tetramer model of hTRPV1 based on the cryo-EM structures of rTRPV1. Molecular dynamics (MD) simulations, energy minimizations, and prescreen were applied to select and validate the best model of hTRPV1. The predicted binding pocket of hTRPV1 consists of two adjacent monomers subunits, which were congruent with the experimental rTRPV1 data and the cyro-EM structures of rTRPV1. The detailed interactions between hTRPV1 and its antagonists or agonists were characterized by molecular docking, which helped us to identify the important residues. Conformational changes of hTRPV1 upon antagonist/agonist binding were also explored by MD simulation. The different movements of compounds led to the different conformational changes of monomers in hTRPV1, indicating that TRPV1 works in a concerted way, resembling some other channel proteins such as aquaporins. We observed that the selective filter was open when hTRPV1 bound with an agonist during MD simulation. For the lower gate of hTRPV1, we observed large similarities between hTRPV1 bound with antagonist and with agonist. A five-point pharmacophore model based on several antagonists was established, and the structural model was used to screen in silico for new antagonists for hTRPV1. By using the 3D TRPV1 structural model above, the pilot in silico screening has begun to yield promising hits with activity as hTRPV1 antagonists, several of which showed substantial potency.