Molecular modeling of G protein-coupled receptors

在本财政年度，我们致力于以下段落所述的气相化学还原系统。其中一些系统在文献中得到了很好的描述，可以找到丰富的信息，包括实验推导的结构。因此，它们构成了开发随后适用于整个超家族的计算方法的理想平台。相反，其他系统的特征不太清楚，但构成了药物制剂开发的有吸引力的目标。 视紫红质视紫红质是由光激活的GPCR，其导致共价结合的11-顺式-视黄醇异构化为全反式-视黄醇，从而触发受体的激活。 β-肾上腺素受体。β-肾上腺素能受体（β-AR）主要存在于平滑肌中，在心脏和气道的生理学中起着至关重要的作用。β-AR的拮抗剂广泛用于各种适应症，特别是治疗高血压和心律失常。β 2-AR激动剂在临床上用于治疗哮喘。 腺苷受体。腺苷受体在人体的几个器官中广泛表达，并介导心脏、肺、血管和血小板中的重要生理功能。 毒蕈碱受体。毒蕈碱受体是由乙酰胆碱刺激的GPCR家族。毒蕈碱受体的配体被广泛用于治疗各种病症，包括帕金森病。 P2 Y受体。P2 Y受体是由细胞外核苷酸激活的GPCR。值得注意的是，P2 Y12受体的拮抗剂广泛用作抗血栓形成剂。 TRH-Rs。促甲状腺激素释放激素（THR）是一种三肽激素，其通过激活称为促甲状腺激素释放激素受体（TRH-R）的特异性GPCR来刺激促甲状腺激素的释放。 特别是在本财政年度，我们进行了研究，并取得了以下段落所述的成果。 1)通过分子建模指导的定点突变实验，阐明了β 2-肾上腺素能受体对氟化儿茶酚胺的选择性的结构基础。实验合作者：Jurgen Wess（NIDDK）和Kenneth Kirk（NIDDK）。 2)完成并发表了一篇独特的综述文章，系统地介绍了全球化学品还原世纪的历史。 3)完成并发表了一篇综述，描述了使用NMR光谱来揭示GPCR的结构-功能关系。 4)从事β 2-肾上腺素能受体配体的后验控制虚拟筛选实验。值得注意的是，我们设计了一种方法，引导筛选对激动剂或阻滞剂的识别。此外，在与克劳迪奥N. Cavasotto（德克萨斯大学），我们通过将受体的灵活性纳入虚拟筛选过程来提高筛选的性能。 5)研究一种策略，通过计算将肾上腺素能受体的配体分为激动剂和阻滞剂。值得注意的是，该研究还提供了激动剂结合机制的深刻见解。 6)综述了G蛋白偶联受体建模的可能性。 7)编写关于气相聚合酶链式反应配体虚拟筛选的一章，将在皇家化学学会编辑的一本书中发表。 8)进行TRH-R受体激动剂的受控虚拟筛选。 9)与卡森C合作进行了一项生物信息学研究。Chow（NIDDK），旨在揭示GPCR超家族的进化。 10)进行腺苷A2 A受体类似物的计算机辅助设计。实验合作者：Kenneth A. Jacobson（NIDDK）和Giampiero Spalluto（的里雅斯特大学，意大利）。 11)通过分子建模指导的核苷酸化学工程，发现了对P2 Y 6受体具有增强选择性的化合物。实验合作者：Kenneth A. Jacobson（NIDDK）. 12)对我们先前通过虚拟筛选鉴定的P2 Y1受体新型拮抗剂类似物进行计算机辅助设计。实验合作者：Kenneth A. Jacobson（NIDDK）和T.肯德尔·哈登（北卡罗来纳州大学）。 13)阐明了P2 Y1激动剂的功能化同源物的结合机制。实验合作者：Kenneth A. Jacobson（NIDDK）. 14)通过生物化学交联实验指导的分子模拟，建立了毒蕈碱M3受体与Gq异源三聚体偶联形成的大分子复合物的结构模型。实验合作者：Jurgen Wess（NIDDK）。 15)进行TRH-R配体的结构设计。实验合作者：Marvin C. Gershengorn（NIDDK）.

In the course of this fiscal year, we have worked on the GPCR systems described in the following paragraphs. Some of these systems are very well characterized in the literature, where a wealth of information, including experimentally derived structures, can be found. Thus, they constitute an ideal platform for the development of computational methodologies subsequently applicable to the whole superfamily. Other systems, instead, are less well characterized but constitute attractive targets for the development of pharmaceutical agents. Rhodopsin. Rhodopsin is a GPCR activated by light, which causes the isomerization of the covalently bound 11-cis-retinal to all-trans-retinal, consequently triggering the activation of the receptor. Beta-adrenergic receptors. The beta-adrenergic receptors (beta-ARs) reside predominantly in smooth muscles and play crucial roles in the physiology of heart and airways. Antagonists of the beta-ARs are widely used for various indications, particularly the treatment of hypertension and cardiac arrhythmias. Agonists of the beta2-AR are clinically used in the treatment of asthma. Adenosine receptors. The adenosine receptors are widely expressed in several organs of the human body, and mediate important physiological functions in the heart, lungs, blood vessels, and platelets. Muscarinic receptors. The muscarinic receptors are a family of GPCRs stimulated by acetylcholine. Ligands of the muscarinic receptors are amply used for the treatment of a variety of conditions, including Parkinsons disease. P2Y receptors. P2Y receptors are GPCRs activated by extracellular nucleotides. Of note, antagonists of the P2Y12 receptor are amply used as antithrombotic agents. TRH-Rs. Thyrotropin-releasing hormone (THR) is a tripeptide hormone which stimulates the release of thyrotropin by activating specific GPCRs known as thyrotropin-releasing hormone receptors (TRH-Rs). In particular, during this fiscal year, we have conducted the research and accomplished the results described in the following paragraphs. 1) Rationalized the structural basis of the selectivity of the beta2-adrenergic receptors for fluorinated catecholamines, through molecular modeling-guided site directed mutagenesis experiments. Experimental collaborators: Jurgen Wess (NIDDK) and Kenneth Kirk (NIDDK). 2) Finalized and published a unique review article that covers, in a systematic manner, over a century of GPCR history. 3) Finalized and published a review describing the use of NMR spectroscopy to unravel the structure-function relationships of GPCRs. 4) Worked on controlled a posteriori virtual screening experiments for beta2-adrenergic receptors ligands. Notably, we devised a way of steering the screening towards the identification of agonists or blockers. Moreover, in collaboration with Claudio N. Cavasotto (University of Texas), we improved the performance of the screenings by incorporating the flexibility of the receptor into the virtual screening process. 5) Worked on a strategy to computationally classify ligands of the adrenergic receptors into agonists and blockers. Notably, the study furnished also an insightful view into the mechanism of agonist binding. 6) Reviewed the possibility of modeling G protein-coupled receptors. 7) Work on a chapter on virtual screening for GPCR ligands, to be published in a book edited by the Royal Chemical Society. 8) Conducted a controlled virtual screening for agonists of the TRH-R receptor. 9) Conducted a bioinformatics study, in collaboration with Carson C. Chow (NIDDK), intended to shed light onto the evolution of the GPCR superfamily. 10) Conducted computer-assisted design of analogs of the adenosine A2A receptor. Experimental collaborators: Kenneth A. Jacobson (NIDDK) and Giampiero Spalluto (University of Trieste, Italy). 11) Discovered compounds with enhanced selectivity for the P2Y6 receptor through the molecular modeling-guided chemical engineering of nucleotides. Experimental collaborators: Kenneth A. Jacobson (NIDDK). 12) Conducted computer-assisted design of analogs of novel antagonists of the P2Y1 receptor previously identified by us through virtual screening. Experimental collaborators: Kenneth A. Jacobson (NIDDK) and T. Kendall Harden (University of North Carolina). 13) Rationalized the mechanism of binding of functionalized congeners of P2Y1 agonists. Experimental collaborators: Kenneth A. Jacobson (NIDDK). 14) Generated a structural model of macromolecular complex formed by the muscarinic M3 receptor coupled to the Gq heterotrimer through molecular modeling guided by biochemical cross-linking experiments. Experimental collaborators: Jurgen Wess (NIDDK). 15) Conducted structure-based design of TRH-R ligands. Experimental collaborators: Marvin C. Gershengorn (NIDDK).