Docking studies of agonists and antagonists suggest an activation pathway of the A3 adenosine receptor

Abstract

Structural determinants of ligand efficacy in the human A(3) adenosine receptor (AR) were studied using pharmacophore and docking analyses of various categories of A(3) selective ligands: inverse agonist, neutral antagonist (nonnucleoside and nucleoside), and agonist (partial and full). The homology modeling of GPCRs was adapted to provide two templates: the rhodopsin-based resting state for antagonist binding and a putative Meta I state, conformationally altered at a key residue (W6.48), for agonist binding. The preferential binding domains and/or local conformational changes associated with docking of three high affinity A(3)AR ligands were compared: inverse agonist PSB-11 1 ((R)-8-ethyl-4-methyl-2-phenyl-imidazo[2,1-i]purin-5-one); neutral antagonist MRE-3008F20 7 (5-[[(4-methoxyphenyl)amino]carbonyl]amino-8-methyl-2-(2-furyl)pyra-zolo[4,3-e]1,2,4-triazolo[1,5-c]pyrimidine), and full agonist Cl-IB-MECA 21 (2-chloro-N(6)-(3-iodobenzyl)-5'-N-methylcarboxamidoadenosine) to define a distinct recognition mode for each. Ribose-containing agonists were more hydrophilic than nonnucleoside antagonists, and H-bonding ability at the ribose 3'- and 5'-positions was required for agonism. From the receptor perspective, common requirements for activation included the destabilization of H-bond networks at W6.48 and H7.43, the specific interactions of the ribose moiety in its putative hydrophilic pocket at T3.36, S7.42, and H7.43, the stabilization of the complex by inward movement of F5.43, and the characteristic rotation of W6.48. By analogy, outward rotation of the W6.48 side-chain upon activation of an internally-crosslinking mutant M(3) muscarinic receptor was indicated by constrained molecular dynamics (MD). Our results are consistent with an anti-clockwise rotation (from the extracellular view) of transmembrane domains 3, 5, 6, and 7, as proposed for other Family A GPCRs. Thus, the putative conformational changes associated with A(3)AR activation indicate a shared mechanism of GPCR activation similar to rhodopsin.

Amino-Pyrrolidine Tricarboxylic Acids Give New Insight into Group III Metabotropic Glutamate Receptor Activation Mechanism

“…These studies are consistent with partial agonists stabilizing a specific conformation of the receptor (Ghanouni et al, 2001;Baneres et al, 2005;Kim et al, 2006;Nikolaev et al, 2006), being able to unlock some but not all the locks that maintain the receptor in its inactive state (Seifert et al, 2001). However, the activation mechanism of class C GPCRs seems more complex, with the agonist binding site located in the VFT, within the large extracellular domain.…”

Molecular Determinants of CGS21680 Binding to the Human Adenosine A2A Receptor

“…The water molecule W2 forms hydrogen bonds with the side chains of amino acid residues Glu169 EL2 , Asn253 , which probably helps to orient the side chain and position it optimally to form hydrogen bonds with the adenine moiety of the ligand. This is supported by mutagenesis data, which suggest that Asn253 6.55 is one of the most important amino acid residues for the binding mode of ligands to human A 2A R (Kim et al, 2006;Lane et al, 2012). The positions of these three water molecules are also conserved between the structures of A 2A R bound to either adenosine, NECA, or ZM241385 (Jaakola et al, 2008;Lebon et al, 2011b) (Supplemental Fig.…”

Molecular dynamics simulation of the human adenosine A3 receptor: agonist induced conformational changes of Trp243

“…We used this receptor model successfully to dock agonists and partial agonists in the putative binding pocket [21]. Recently, Kim et al successfully used a similarly modified receptor model in docking studies [30]. Figure 7 shows the docking result for Cl-IB-MECA.…”