Levit Anat, Barak Dov, Behrens Maik, Meyerhof Wolfgang, Niv Masha Y
Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, Israel.
Methods Mol Biol. 2012;914:179-205. doi: 10.1007/978-1-62703-023-6_11.
G protein-coupled receptors (GPCRs) are important mediators of cell signaling and a major family of drug targets. Despite recent breakthroughs, experimental elucidation of GPCR structures remains a formidable challenge. Homology modeling of 3D structures of GPCRs provides a practical tool for elucidating the structural determinants governing the interactions of these important receptors with their ligands. The working model of the binding site can then be used for virtual screening of additional ligands that may fit this site, for determining and comparing specificity profiles of related receptors, and for structure-based design of agonists and antagonists. The current review presents the protocol and enumerates the steps for modeling and validating the residues involved in ligand binding. The main stages include (a) modeling the receptor structure using an automated fragment-based approach, (b) predicting potential binding pockets, (c) docking known binders, (d) analyzing predicted interactions and comparing with positions that have been shown to bind ligands in other receptors, (e) validating the structural model by mutagenesis.
G蛋白偶联受体（GPCRs）是细胞信号传导的重要介质，也是一大类药物靶点。尽管最近取得了突破，但GPCR结构的实验解析仍然是一项艰巨的挑战。GPCR三维结构的同源建模为阐明控制这些重要受体与其配体相互作用的结构决定因素提供了一种实用工具。然后，结合位点的工作模型可用于虚拟筛选可能适合该位点的其他配体，用于确定和比较相关受体的特异性概况，以及用于基于结构的激动剂和拮抗剂设计。本综述介绍了该方案，并列举了对参与配体结合的残基进行建模和验证的步骤。主要阶段包括：（a）使用基于片段的自动化方法对受体结构进行建模；（b）预测潜在的结合口袋；（c）对接已知的结合剂；（d）分析预测的相互作用，并与已显示在其他受体中结合配体的位置进行比较；（e）通过诱变验证结构模型。
