Efficiency of Enhanced Sampling Methods in GPCR Research

描述（由申请人提供）：G蛋白偶联受体（GPCR）是具有极端药理学重要性的丰富膜蛋白，因为它们是目前市场上约30%处方药的主要靶点，并且可能是新治疗剂的潜在靶点。尽管在GPCR领域进行了大量的研究活动，但由于对这些受体的配体诱导的与特定生理功能相关的构象变化的理解有限，作用于这些受体的强效药物的设计已经落后。多年来，GPCR的传统药物设计主要集中在通常明确定义的配体结合位点上抑制单个受体。越来越多的证据表明，GPCR形成临床相关的二聚体/寡聚体，在几种疾病的影响，最近增加了一个新的复杂性领域，使机制和动力学的理解控制受体对和/或高阶寡聚体之间的相互作用，同样重要的成功合理的药物设计。在最近的文献中出现了大量关于GPCR的新的更高分辨率的结构、生物化学和生物物理信息，再加上粗粒度建模和增强的采样算法的最新进展，这表明了有效探索GPCR（单体和二聚体/寡聚体）的构象空间的新方法，并产生了关于受体功能的分子机制的新的可测试假设。在这项资助申请中，我们建议进行探索性的基于元粘附学的理想膜蛋白系统的计算研究，即肾上腺素能受体，血型糖蛋白A和淀粉样前体蛋白的跨膜结构域二聚体，以验证增强的采样方法在预测配体特异性激活状态和/或二聚化破坏突变体中的效率，这些突变体与实验数据一致。 公共卫生相关性：G蛋白偶联受体（GPCR）是最大、用途最广、在药学上最重要的一组膜蛋白，其作用于GPCR的强效治疗药物的发现，多年来由于对其多种功能的分子机制的有限理解而受到损害。这项研究的总体目标是探索使用增强采样方法的先进计算策略在多大程度上可以改善GPCR的动态分子模型，并产生新的可测试的功能调节假设，以成功地进行合理的药物设计。

DESCRIPTION (provided by applicant): G protein-coupled receptors (GPCRs) are abundant membrane proteins of extreme pharmacological importance since they are the primary targets for about 30% of prescription drugs that are currently on the market, and are likely to be potential targets for new therapeutic agents. Despite a great deal of research activity in the GPCR field, the design of powerful drugs acting at these receptors has lagged behind due to the limited understanding of the ligand-induced conformational changes of these receptors associated with specific physiological functions. For years, conventional drug design at GPCRs has mainly focused on the inhibition of a single receptor at a usually well-defined ligand-binding site. The growing body of evidence that GPCRs form clinically relevant dimers/oligomers with implications in several disorders has recently added a new complexity to the field, making the understanding of the mechanisms and dynamics governing the interaction between receptor pairs and/or higher-order oligomers equally important for successful rational drug design. The wealth of new higher-resolution structural, biochemical, and biophysical information on GPCRs that has appeared in the recent literature, coupled to recent advancements in coarse-grained modeling and enhanced sampling algorithms, suggests new ways to efficiently explore the conformational space of GPCRs (both monomers and dimers/oligomers), and to generate novel testable hypotheses of molecular mechanisms underlying receptor function. In this grant application, we propose to conduct exploratory metadynamics-based computational studies of ideal membrane protein systems, i.e. ¿-adrenergic receptor, glycophorin A, and the transmembrane domain dimer of the amyloid precursor protein, to validate the efficiency of enhanced sampling methods in predicting ligand-specific activated states and/or dimerization-disrupting mutants that agree with experimental data. PUBLIC HEALTH RELEVANCE: The discovery of powerful therapeutic drugs acting at G-protein coupled receptors (GPCRs), the largest, most versatile, and most pharmaceutically important group of membrane proteins, has been impaired over the years by the limited understanding of the molecular mechanisms underlying their diverse functions. The overall goal of the work proposed in this grant application is to explore the extent to which advanced computational strategies using enhanced sampling methods can improve dynamic molecular models of GPCRs, and generate novel testable hypotheses of functional modulation to pursue rational drug design successfully.