Antagonist and agonist binding models of the human gonadotropin-releasing hormone receptor

G-protein-coupled receptors (GPCRs) constitute one of the most important classes of drug targets. Since the first high-resolution structure of a GPCR was determined by Palczewski and co-workers [K. Palczewski, T. Kumasaka, T. Hori, C.A. Behnke, H. Motoshima, B.A. Fox, I. Le Trong, D.C. Teller, T. Okada, R.E. Stenkamp, M. Yamamoto, M. Miyano, Crystal structure of rhodopsin: a G-protein-coupled receptor, Science 289 (2000) 739-745], development of in silico models of rhodopsin-like GPCRs could be rationally founded. In this work, we present a model of the human gonadotropin-releasing hormone receptor based on the rhodopsin structure. The transmembrane helices are modeled by homology, while the extra- and intra-cellular loops are modeled in such a way that experimentally determined interactions and microdomains (e.g., hydrophobic cores) are retained. We conclude that specifically tailored models, compared to more automatic approaches, have the benefit that known interactions are easily introduced early in the homology modeling. Furthermore, tailored models, although more tedious to construct, are better suited for drug lead finding and for compound optimization. To test the stability of the receptor, we performed a 1 ns molecular dynamics simulation. Moreover, we docked two agonists (native GnRH and Triptorelin, [dTrp(6)]-GnRH) and two antagonists (Cetrorelix, dNal(1)-dCpa(2)-dPal(3)-Ser(4)-Tyr(5)-dCit(6)-Leu(7)-Arg(8)-Pro(9)-dAla(10)), and the covalently constrained dicyclic decapeptide dicyclo(1,1'-5/4-10)[Ac-Glu(1)(Gly(1)')-dCpa(2)-dTrp(3)-Asp(4)-dbu(5)-dNal(6)-Leu(7)-Arg(8)-Pro(9)-dpr(10)-NH(2)] into the putative receptor binding site. The docked ligand conformations result in ligand-receptor interactions that are generally in good agreement with site-directed mutagenesis and ligand-binding studies presented in the literature. Our results indicate that the binding conformation of the antagonists differs from that of the agonists. This difference can be linked to the activation or inhibition of the receptor.