Efficiency of Enhanced Sampling Methods in GPCR Research

描述（由申请人提供）：G蛋白偶联受体（gpcr）是丰富的膜蛋白，具有极高的药理学重要性，因为它们是目前市场上约30%处方药的主要靶点，并且可能成为新治疗药物的潜在靶点。尽管在GPCR领域进行了大量的研究活动，但由于对这些受体与特定生理功能相关的配体诱导的构象变化的了解有限，因此作用于这些受体的强效药物的设计滞后。多年来，传统的gpcr药物设计主要集中在抑制单个受体在通常明确的配体结合位点上。越来越多的证据表明，GPCRs形成临床相关的二聚体/低聚体与几种疾病有关，最近为该领域增添了新的复杂性，使得理解受体对和/或高阶低聚体之间相互作用的机制和动力学对成功合理的药物设计同样重要。最近文献中出现的关于gpcr的大量新的高分辨率结构、生化和生物物理信息，加上粗粒度建模和增强的采样算法的最新进展，为有效探索gpcr（包括单聚体和二聚体/低聚体）的构象空间提供了新的方法，并为受体功能的分子机制产生了新的可测试的假设。在这项拨款申请中，我们提议对理想膜蛋白系统进行探索性的基于元动力学的计算研究，即-肾上腺素能受体、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方面的效率，这些突变体与实验数据一致。

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.