Structure‐Based Calculation of Binding Affinities of α_2A‐Adrenoceptor Agonists

Abstract

Dedicated to Professor E. Sylvester Vizi on the occasion of his 70th birthday.Adrenergic receptors of the a 2 type (a 2 -adrenoceptors) belong to the family of seven transmembrane-spanning G-proteinlinked receptors.[1-9] a 2 -Adrenoceptors can be grouped into three highly homologous subtypes (a 2A , a 2B , and a 2C ) and, because of the difference in pharmacology, [10] a fourth subtype (a 2D ) can be formally distinguished, though this is rather a species orthologue.In general, the a 2 -adrenoceptors are responsible for the presynaptic feedback of the release of adrenaline and noradrenaline, their physiological agonists. Although numerous findings are available on the receptor subtypes from experiments with knockout mice [11] and these results are of some relevance for human pharmacology, the similar patterns of expression of adrenergic receptors in human and mouse tissues do not guarantee similar functions. Thus, the individual roles of the three a 2 -adrenoceptor subtypes in humans have not been completely elucidated. However, the results of the reported studies do indicate (see Supporting Information) that the a 2 -adrenoceptor subtypes are involved in various important physiological processes, and further investigations of the differences in their molecular pharmacology are therefore essential.The identification of subtype-specific functions from pharmacological experiments is currently not possible because of the lack of subtype-specific ligands [3,[6][7][8] and the cross-reactivity with imidazoline receptors.[7] The development of subtype-selective agonists would be useful as it would facilitate further examinations of the molecular pharmacology of the a 2 -adrenoceptors. The rational, structure-based design of such agonists requires a precise knowledge of the molecular structure of the binding site. Unfortunately, because of the difficulties inherent in crystallization, atomic-resolution structures of the a 2 -adrenoceptors are not available in the Protein Databank.In the present study, an atomic-resolution model of the a 2A -adrenoceptor was constructed through use of its amino acid sequence and the crystallographic bovine rhodopsin structure as a template. Similar homology models were earlier constructed by other researchers [12] and successfully used to provide qualitative explanations. The a 2A -adrenoceptor model in the present study is based on a crystallographic template structure with a resolution of 2.2 [13] appropriate for quantitative investigations (for details, refer to the Computational Methods below).In possession of the atomic resolution target structure (a 2A -adrenoceptor), 15 known agonist ligands were automatically docked to the presumed binding region of the receptor (Figure 1 a). Inspection of the results revealed that the docked ligand conformations are in physical contact with the key residues D3.32A C H T U N G T R E N N U N G (113), S5.42A C H T U N G T R E N N U N G (200), and S5.46A C H T U N G T R E N N U N G (204), previously identified by site-directed mutagenesis studies. [1...

Homology Modelling and Docking Studies of Human α2-Adrenergic Receptor Subtypes

“…Later on, it was Bovine rhodopsin and for many years bovine Rhodopsin has been the only GPCR with experimental structural information available, and all the homology modelling efforts were focused on this structure [16,17]. Homology modelling and docking studies were earlier based on bovine Rhodopsin even though it showed lower sequence identity (21%) and lower transmembrane identity (26%) as the availability of high resolution GPCR structures was the limitation [18][19][20][21][22][23][24][25]. This was followed by the availability of other members of GPCR family, Human β2-adrenergic receptor [26], turkey β1-adrenergic receptor [27], squid Rhodopsin [28], Human adenosine A2a receptor [29], chemokine CXCR4 [30], Human Dopamine D3 receptor in complex with a D2/ D3 selective antagonist Eticlopride [31], and most recently histamine H1 (H1R) [32], M3 muscarinic acetylcholine receptor [33], Mu-opioid receptor [34], a lipid G protein-coupled receptor [35], M2 muscarinic receptor [36], Kappa opioid [37], Delta opioid [38], Neurotensin receptor 1 [39], chemokine CXCR1 [40], Protease activated receptor 1 [41], 5-hydroxytryptamine 1b [42], and 5-hydroxytryptamine 2b [43].…”

“…These ligands have been reported by the research studies to bind to and interact with the α2-AR. A set of eight agonists including endogenous ligands such as Dopamine, Adrenaline, known α2 agonists such as Clonidine, Dexmedetomidine and subtype selective agonist Guanfacine were selected from literature for docking studies [23,39,45]. Sixteen antagonists including subtype specific ligands such as BRL-44408, JP-1302, OPC-2836 and others such as ARC239, Clozapine, WB4101 that have been reported to bind to α2 adrenergic receptors were chosen for the docking studies to analyse their interactions with the α2-AR models based on Dopamine receptor (PDB ID:3PBL) [22,46,52].…”