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. With rhodopsin, the beta-ARs are the most studied GPCRs and constitute an ideal platform for the development of computational methodologies subsequently applicable to the whole superfamily.? For many years rhodopsin remained the only GPCR with an experimentally elucidated three-dimensional structure. In this context, the structure-based design of GPCR ligands heavily relied on homology modeling. Recently the X-ray structures of the beta1-AR and the beta2-AR have been also solved. In this context, I published a comparison study of rhodopsin-based molecular models and X-ray structures of the beta2-AR, the results of which firmly supported the applicability of homology modeling and ligand docking to the computer-aided discovery of GPCR ligands.? Using P2Y1 antagonists as a case study, we have recently devised LIST-CM, a PLS regression model that combines ligand-based and structure-based techniques for a more robust and accurate prediction of ligand activity. We are currently further developing LIST-CM using agonists and blockers of the beta2-adrenercic receptor as a case study.? We recently established a striking correlation between the flexibility and the basal activity of wild type and mutant TRH receptors by means of Monte Carlo simulations. This work has the potential to lead the way to the development of a computational tool for a rapid prediction of the pharmacological profile of mutants and ligands. Currently we are studying the existence of a similar correlation for the beta2-AR by evaluating modeled complexes of the receptor with ligands with different efficacies.? ? P2Y receptors. P2Y receptors are GPCRs activated by extracellular nucleotides. Of particular interest are P2Y1 antagonists, which have shown the potential of being developed into novel potent antithrombotic agents. In collaboration with the laboratories of Drs. Kenneth Jacobson (NIDDK) and Kendall Harden (University of North Carolina), for the past few years I have been conducting bioinformatics and molecular modeling studies intended to shed light onto the structure-function relationships of the P2Y receptors. A number of compounds computationally identified as potential P2Y1 antagonists are currently being tested in the laboratories of Kendall Harden.? ? FFAR1 (a.k.a. GPR40). FFAR1 (a.k.a. GPR40) is a GPCR activated by long chain free fatty acids (FFAs), which is involved in the regulation of metabolic processes and glucose homeostasis. In particular, FFAR1 is considered an appealing target for the treatment of type two diabetes. Our research, in collaboration with the laboratory of Dr. Marvin Gershengorn (NIDDK), is intended for the elucidation of the structure-function relationships of FFAR1 and for the discovery of novel ligands.? We have recently studied the cross-reactivity between FFAR1 and PPAR-gamma, a nuclear hormone receptor, aiming at the discovery of selective FFAR1 ligands. In this context, seventy compounds formerly computationally identified by us through virtual screening as potential FFAR1 ligands - five of which resulted in true hits after experimental testing - are currently being tested for their ability to stimulate or inhibit PPAR-gamma activity in the laboratory of Dr. Elisabetta Mueller.? Furthermore, we studied the FFAR1 activation mechanism by combining molecular dynamics simulations with site-directed mutagenesis experiments conducted in the laboratory of Dr. Marvin Gershengorn. This interdisciplinary approach led us to the identification of two potential ionic locks between the second extracellular loop and the transmembrane domain, the disruption of which possibly triggers the activation of the receptor.? ? 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). Two different TRH-R subtypes have been identified in rodents. The goal of our research, in collaboration with the laboratory of Dr. Marvin Gershengorn (NIDDK), is the elucidation of the structure-function relationships of the two subtypes and the identification of novel ligands able to discriminate against them.? We recently identified TRH-R ligands through virtual screening and are currently evaluating different strategies for their optimization through structure-based design techniques.? ? Glycoprotein Hormone Receptors. Glycoprotein Hormone Receptors (GPHRs) are GPCRs activated by extracellular hormones that bind to their N-terminal regions. The goal of our research is the identification of small molecules that bind to the transmembrane domain of GPHRs, consequently activating or blocking the receptors. In particular our research, in collaboration with the laboratory of Dr. Marvin Gershengorn (NIDDK), focuses on the identification of agonists and antagonists of the thyroid-stimulating hormone receptor (TSHR).? We recently identified a binding pocket for small molecules within the transmembrane domain of TSHR. Furthermore, combining molecular modeling and functional experiments, we identified a novel antagonist (NIDDK/CEB-52) that selectively inhibits activation of TSHR both by TSH and by antibodies in Graves' hyperthyroidism (TsAbs). Our results suggest that TSHR antagonists could be developed into drugs for the treatment of Graves' disease.? ? 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. ? In collaboration with the research group of Dr. Gerhard Hummer of NIDDK, we used the X-ray structure of Lumirhodopsin (Lumi) together with experimentally derived distance restraints to generate a model of Metarhodopsin II (Meta II), the activated state of rhodopsin. In particular, we generated the model by means of biased molecular dynamics and elastic network models. We then simulated the activation of the receptor in a dynamic model to study the path leading from Lumi to Meta II for the wild type receptor and a series of mutants. Our results led to the conclusion that the lifetimes of the Lumi and Meta II states correspond to the experimental phenotypes of various mutations, suggesting the applicability of dynamics models to the prediction of basal activity.
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