Molecular modeling of G protein-coupled receptors

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G protein-coupled receptors (GPCRs) are a large superfamily of membrane proteins, which act as cellular receivers for extracellular stimuli. GPCRs hold great pharmaceutical interest, given the fact than they are the target of a very large percentage of the drugs currently on the market. From the structural point of view, they consist of a single polypeptide chain that crosses seven times the cell membrane, hence the alternative name of seven transmembrane-spanning receptors. Since crystal structures are available only for bovine rhodopsin, the beta-adrenergic receptors, and the adenosine A2A receptor in the GPCR family, the study of the other receptors heavily relies on homology modeling and docking experiments conducted in an iterative manner with mutagenesis experiments and chemical modification of the ligands. A key focus of this project is GPCR modeling of ligand docking. My models of the adenosine A2A receptors with a bound antagonist were judged the most accurate in a blind assessment organized in coordination with the crystallization of this complex, definitely positioning us at the forefront of the field. My main activities at NIDDK, before leaving NIH on June 1st 2012, concerned the computational study of the structure-function relationships of GPCRs and the identification of low molecular weight compounds capable of modulating their activity through computer-assisted drug discovery (CADD). The latter embodies an ensemble of disciplines and techniques directed toward the rational identification of novel and diverse ligands for biological targets of pharmaceutical interest. Aiming at the structural characterization of the receptors and at lead identification and optimization, I utilized the most advanced techniques in 3-D molecular modeling, bioinformatics, and cheminformatics, some of which are: sequence and phylogenetic analyses, homology modeling, ligand docking, molecular dynamics, QSAR analyses, and virtual screenings. The latter allows a quick virtual evaluation of large databases of compounds in the quest for novel and diverse leads. Only a limited number of compounds are purchased and experimentally evaluated, with a conspicuous saving of time and economical and environmental resources. To achieve our drug discovery objectives and further the field of molecular modeling, I actively developed, improved, and tested novel computational methodologies and research strategies. I operated in strict collaboration with experimental medicinal chemists, molecular pharmacologists, and biologists. In the course of this year, before leaving NIH on June 1st 2012, I 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. Conversely, other systems are less well characterized, but constitute attractive targets for the development of pharmaceutical agents. 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. Muscarinic receptors. The muscarinic receptors are a family of GPCRs stimulated by acetylcholine. Ligands of the muscarinic receptors are widely 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. In particular, during this year, I conducted the research and accomplished the results described in the following paragraphs. 1) Studied the Structural aspects of M3 muscarinic acetylcholine receptor dimer formation and activation. Experimental collaborator: Jrgen Wess (NIDDK). 2) Finalized and published a virtual screening for ligands of the P2Y1 receptor. Notably, we identified novel non-nucleotide receptor antagonists. Experimental collaborators: Kenneth A. Jacobson (NIDDK), T. Kendall Harden (University of North Carolina). 3) Finalized and published a review article on the homology modeling of G protein-coupled receptors. 4) Finalized and published an article on the implications of the use of inactive and activated structures of the beta2 adrenergic receptor on the in silico screening for agonists or blockers. 5) Studied and published an article on the molecular evolution of the transmembrane domains of G protein-coupled receptors. Experimental collaborator: Carson Chow (NIDDK). 6) Reviewed advances in X-ray crystallography of G protein-coupled receptors and their implication for drug design. 7) Within the field of drug discovery, beyond the field of G protein-coupled receptors, I also worked on a model for the detection of adverse drug events in pharmacovigilance databases using molecular structure similarity.