Molecular modeling of G protein-coupled receptors

在本财政年度期间，我们致力于以下各段所述的GPCR制。其中一些系统在文献中有很好的特征，其中可以找到丰富的信息，包括实验得出的结构。因此，它们构成了开发随后适用于整个超级家族的计算方法的理想平台。相反，其他系统没有那么好的特征，但构成了药物制剂发展的有吸引力的目标。 视紫红质。视紫红质是一种被光激活的GPCRs，它导致11-顺式视网膜的共价结合异构化为全反式视网膜，从而触发受体的激活。 β肾上腺素能受体。β-肾上腺素能受体(β-AR)主要存在于平滑的肌肉中，在心脏和呼吸道的生理中起着至关重要的作用。β-受体拮抗剂被广泛用于各种适应症，特别是治疗高血压和心律失常。β2-AR激动剂在临床上用于哮喘的治疗。 腺苷受体。腺苷受体广泛表达于人体的几个器官，在心脏、肺、血管和血小板中发挥重要的生理功能。 毒鼠碱受体。M受体是一个受乙酰胆碱刺激的GPCRs家族。M受体的配体被大量用于治疗各种疾病，包括帕金森氏病。 P2Y受体。P2Y受体是由胞外核苷酸激活的GPCRs。值得注意的是，P2Y12受体的拮抗剂被广泛用作抗血栓药。 TRH-R。促甲状腺激素释放激素(THR)是一种三肽类激素，通过激活被称为促甲状腺激素释放激素受体(TRH-Rs)的特异性GPCRs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，并取得了以下各段所述的成果。 1)通过分子模型引导的定点突变实验，使β2-肾上腺素能受体对氟化儿茶酚胺选择性的结构基础合理化。实验合作者：尤尔根·韦斯(NIDDK)和肯尼斯·柯克(NIDDK)。 2)完成并发表了一篇独特的评论文章，系统地涵盖了GPCR一百多年的历史。 3)完成并发表了一篇综述，描述了利用核磁共振光谱学来解开GPCRs的结构-功能关系。 4)进行了β2-肾上腺素能受体配体的后验虚拟筛选实验。值得注意的是，我们设计了一种方法来指导筛选以识别激动剂或阻滞剂。此外，我们与克劳迪奥·N·卡瓦索托(德克萨斯大学)合作，通过将受体的灵活性纳入虚拟筛选过程，提高了筛选的性能。 5)研究了一种策略，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，这项研究还为激动剂结合的机制提供了一个有洞察力的观点。 6)综述了建立G蛋白偶联受体模型的可能性。 7)编写关于GPCR配体虚拟筛选的一章，将在皇家化学学会编辑的一本书中出版。 8)进行了TRH-R受体激动剂的虚拟对照筛选。 9)与Carson C.Chow(NIDDK)合作进行了一项生物信息学研究，旨在揭示GPCR超家族的进化。 10)进行了腺苷A2a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(意大利的里雅斯特大学)。 11)通过分子建模指导的核苷酸化学工程发现了对P2Y6受体具有更高选择性的化合物。实验合作者：Kenneth A.Jacobson(NIDDK)。 12)对我们先前通过虚拟筛选鉴定的新型P2Y1受体拮抗剂的类似物进行了计算机辅助设计。实验合作者：肯尼斯·A·雅各布森(NIDDK)和T·肯德尔·哈登(北卡罗来纳大学)。 13)理顺了P2Y1激动剂官能化同系物的结合机制。实验合作者：Kenneth A.Jacobson(NIDDK)。 14)以生化交联实验为指导，通过分子模拟，建立了M3受体与GQ杂三聚体偶联形成的大分子复合体的结构模型。实验合作者：尤尔根·韦斯(NIDDK)。 15)进行了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).