Evaluation of Homology Modeling of G-Protein-Coupled Receptors in Light of the A_2A Adenosine Receptor Crystallographic Structure

Abstract

Homology modeling of the human A2A adenosine receptor (AR) based on bovine rhodopsin predicted a protein structure that was very similar to the recently determined crystallographic structure. The inaccuracy of previous antagonist docking is related to the loop structure of rhodopsin being carried over to the model of the A2A AR and was rectified when the β2-adrenergic receptor was used as a template is used for homology modeling. Docking of the triazolotriazine antagonist ligand ZM241385 1 was greatly improved by including water molecules of the X-ray structure or by using a constraint from mutagenesis. Automatic agonists docking to both a new homology modeled receptor and the A2A AR crystallographic structure produced similar results. Heterocyclic nitrogen atoms closely corresponded when the docked adenine moiety of agonists and 1 were overlayed. The cumulative mutagenesis data, which support the proposed mode of agonist docking, can be reexamined in light of the crystallographic structure. Thus, homology modeling of GPCRs remains a useful technique in probing the structure of the protein and predicting modes of ligand docking.

A Novel Nonribose Agonist, LUF5834, Engages Residues That Are Distinct from Those of Adenosine-Like Ligands to Activate the Adenosine A2a Receptor

“…Mutation of Ser277 7.42 , Thr88 3.36 ,and Leu85 3.33 to alanine abrogated this agonist interaction and reduced the potency and affinity of CGS21680 by at least 100-fold in agreement with previous studies (Kim et al, 1995;Gao et al, 2000;Ivanov et al, 2009). In contrast, the potency and affinity of LUF5834 were unaffected by the mutation of either Ser277 7.42 or Thr88 3.36 to alanine.…”

“…As a partial agonist, LUF5834 will bind with a similar affinity to this mutated receptor, although a loss of efficacy will be observed (Christopoulos and Kenakin, 2002). Glu169 5.30 in ECL2 was highlighted as having a key role in ligand binding by ligand docking, mutagenesis studies, and finally the antagonist-bound crystal structure Jaakola et al, 2008;Ivanov et al, 2009). Consistent with these observations, we observed a Ͼ20-fold reduction in the affinity of [ 3 H]ZM241385.…”

“…The adenine core of such agonists is a common scaffold and is present in nearly all major types of AR agonists and a number of antagonists. This moiety aligns to the heterocyclic core of ZM241385 when the two complex structures are superimposed together, as already predicted in modeling studies (Ivanov et al, 2009;Jaakola et al, 2010). The molecular interactions that anchor ZM241385 in this region are also conserved in the agonist-bound cavity, including aromatic stacking with Phe168 in extracellular loop 2 (ECL2), nonpolar interaction with Ile274 7.39 , and two hydrogen bonds with Asn253 6.55 (Lebon et al, 2011;Xu et al, 2011).…”

International Union of Basic and Clinical Pharmacology. LXXXI. Nomenclature and Classification of Adenosine Receptors—An Update

“…The majority of models had root-mean-square deviation values of more than 10 Å for the ligand binding site, and only one predicted the typical perpendicular orientation of ZM241385 halfway the extracellular and transmembrane domains. The reasons for this generally large divergence were implicitly examined by Ivanov et al (2009). The authors noted that domain knowledge such as mutagenesis data yielded useful constraints when docking ZM241385 into a receptor homology model.…”

New Insights for Drug Design from the X-Ray Crystallographic Structures of G-Protein-Coupled Receptors

“…at ASPET Journals on May 11, 2018 molpharm.aspetjournals.org rically opposed modes of ligand binding for the same receptor-ligand complex), there were examples of well supported modeling that was later validated crystallographically (among others, see Ivanov et al, 2009;Michino et al, 2009;Kufareva et al, 2011). Comparisons of crystal structures and homology models revealed that, for some GPCRs, reasonably accurate receptor-ligand complexes can be constructed through homology modeling followed by molecular docking (Costanzi, 2008(Costanzi, , 2010(Costanzi, , 2012Reynolds et al, 2009).…”