Molecular modeling of A₁ and A_2A adenosine receptors: Comparison of rhodopsin‐ and β₂‐adrenergic‐based homology models through the docking studies

Abstract

Adenosine receptors (ARs) are members of the superfamily of G protein-coupled receptors. The homology models of adenosine A1 and A2A receptors were constructed. The high-resolution X-ray structure of bovine rhodopsin and crystal structure of beta2-adrenergic receptor were used as templates. The binding sites of the A1 and A2A ARs were constructed by using data obtained from mutagenesis experiments as well as docking simulations of the respective AR antagonsists DPCPX and XAC. To compare rhodopsin- and beta2-adrenergic-based models, the binding mode of A1 (KW-3902, LUF-5437) and A2A (KW-6002, ZM-241385) ARs antagonists were also examined. The differences in the binding ability of both models were noted during the study. The beta2-adrenergic-based A2A AR model was much more capable to stabilize the ligand in the binding site cavity than the corresponding rhodopsin-based A2A AR model, however, such differences were not so clear in case of A1 AR models. It was suggested that for the A1 AR it is possible to use the crystal structure of rhodopsin as a template as well as beta2-adrenergic receptor, but for A2A AR, with the now available beta2-adrenergic receptor X-ray structure, docking studies should be avoided on the rhodopsin-based model. However, taking into account that the beta2AR shares about 31% of the residues with the AR in comparison to 21% in case of bRho, we suggest using beta2-adrenergic-based models for the A1 and A2A ARs for further in silico ligand screening also because of their generally better ability to stabilize ligands inside the binding pocket.

Ligand Binding and Subtype Selectivity of the Human A2A Adenosine Receptor

“…The recently solved human A 2A AR-ZM241385 co-crystal structure revealed that the prototypical non-xanthine antagonist, ZM241385, binds very differently to the receptor than had been predicted by models based on rhodopsin binding to retinal (7,8). The long axis of ZM241385 lies orthogonal to the membrane plane and has a large number of interactions with residues in TM domains 5-7, and extracellular loops 2 and 3 (3).…”

“…Surprisingly, we found that the binding mode of ZM241385 to its receptor is very different from the binding of ligand to other GPCRs with known crystal structures, the beta-blockers timolol, carazolol, and cyanopindolol co-crystallized with turkey ␤ 1 -adrenoreceptor or human ␤ 2 -adrenoceptors and retinal cocrystallized with bovine and squid rhodopsin, and binding of these ligands to their cognate receptors has very little overlap with ZM241385 binding to A 2A AR when all available receptor structures are superimposed (6). In addition, the orientation of ZM241385 in the binding pocket deviates greatly from that of homology models, which used the rhodopsin structure as a template (7)(8). Therefore, models for ligand-A 2A AR interac-tions based upon these other GPCR-ligand structures can give only rough picture of ligand binding (9).…”

Challenges and advances in computational docking: 2009 in review

“…Katritch et al (155) have demonstrated such potential by b 2 -AR receptor optimization in the presence of docked ligands and the resultant improved prediction of agonist binding affinities. Generally, optimization of GPCR binding sites by flexible receptor docking, particularly as a measure to improve and test the quality of GPCR homology model, has evolved as a mainstream theme in the GPCR field as exemplified by a number of recent studies (156)(157)(158)(159).…”

The Structure of the Adenosine Receptors

“…Further, in a recent study by Mantri and coworkers on new antagonists for the A 2A AR, it was demonstrated that tremendous substituent flexibility exists in this area of the pharmacophore (Mantri et al, 2008). This observation correlates well with the directionality of the phenylethylamine substituent in ZM241385 because it extends toward the more solvent-exposed extracellular region (ECL2 and ECL3) rather than toward the transmembrane domain of the receptor, as was previously proposed (Martinelli & Tuccinardi, 2008;Yuzlenko & Kiec-Kononowicz, 2009). …”

“…3A). This cannot be reconciled with earlier molecular modeling studies based on rhodopsin homology models in which ZM241385 and other antagonists were docked into a binding site emulating that of the b 2 -adrenoceptor and rhodopsin (Martinelli & Tuccinardi, 2008;Yuzlenko & Kiec-Kononowicz, 2009). Second, the organization of the extracellular loops is markedly different from those of the b 1 -adrenoceptor, the b 2 -adrenoceptor, or the bovine and squid rhodopsins.…”