Efficiency of Enhanced Sampling Methods in GPCR Research

描述(申请人提供)：G蛋白偶联受体(GPCRs)是丰富的膜蛋白，具有极其重要的药理学意义，因为它们是目前市场上约30%处方药的主要靶点，并可能成为新治疗药物的潜在靶点。尽管在GPCR领域有大量的研究活动，但由于对配体诱导的与特定生理功能相关的受体构象变化的了解有限，作用于这些受体的强大药物的设计一直滞后。多年来，GPCRs的传统药物设计主要集中在抑制通常定义明确的配体结合部位的单一受体。越来越多的证据表明，GPCRs形成临床相关的二聚体/低聚物，与几种疾病有关，最近增加了该领域的复杂性，使得对受体对和/或高阶低聚物之间相互作用的机制和动力学的理解对成功的合理药物设计同样重要。最近的文献中出现了大量关于GPCRs的新的更高分辨率的结构、生化和生物物理信息，再加上最近在粗粒度建模和改进的采样算法方面的进展，这为有效地探索GPCRs(包括单体和二聚体/低聚物)的构象空间以及产生受体功能潜在的分子机制的新的可测试假说提供了新的途径。在这项拨款申请中，我们建议对理想的膜蛋白系统，即肾上腺素能受体、血糖素A和淀粉样前体蛋白的跨膜结构域二聚体进行基于元动力学的探索性计算研究，以验证改进的采样方法在预测配体特定激活状态和/或与实验数据相一致的二聚化干扰突变方面的效率。 与公共健康相关：作用于G蛋白偶联受体(GPCRs)的强大治疗药物的发现，多年来因对其不同功能的分子机制的有限了解而受到阻碍。GPCRs是最大、最通用、最具药学意义的一组膜蛋白。本次拨款申请中提出的工作的总体目标是探索使用增强抽样方法的先进计算策略在多大程度上可以改进GPCRs的动态分子模型，并生成新的可检验的功能调节假说，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.