Molecular modeling of G protein-coupled receptors

在本财政年度的过程中，我们对以下各段所述的GPCR系统进行了研究。其中一些系统在文献中得到了很好的描述，在这些文献中可以找到丰富的信息，包括实验推导的结构。因此，它们构成了一个理想的平台，用于开发随后适用于整个超族的计算方法。相反，其他系统的特性不太好，但构成了开发药物制剂的有吸引力的目标。

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).