Computational development of an α1A-adrenoceptor model in a membrane mimic

Ligand-Receptor Interactions and Structure-Function Relationships in Off-Target Binding of the β3-Adrenergic Agonist Mirabegron to α1A-Adrenergic Receptors

The β3-adrenoceptor agonist mirabegron is available for the treatment of storage symptoms of overactive bladder, including frequency, urgency, and incontinence. The off-target effects of mirabegron include binding to α1-adrenoceptors, which are central in the treatment of voiding symptoms. Here, we examined the structure-function relationships in the binding of mirabegron to a cryo-electron microscopy structure of α1A. The binding was simulated by docking mirabegron to a 3D structure of a human α1A-adrenoceptor (7YMH) using Autodock Vina. The simulations identified two binding states: slope orientation involving 10 positions and horizontal binding to the receptor surface involving 4 positions. No interactions occurred with positions constituting the α1A binding pocket, including Asp-106, Ser-188, or Phe-312, despite the positioning of the phenylethanolamine moiety in transmembrane regions close to the binding pocket by contact with Phe-288, -289, and Val-107. Contact with the unique positions of α1A included the transmembrane Met-292 during slope binding and exosite Phe-86 during horizontal binding. Exosite binding in slope orientation involved contact of the anilino part, rather than the aminothiazol end, to Ile-178, Ala-103, and Asn-179. In conclusion, contact with Met-292 and Phe-86, which are unique positions of α1A, accounts for mirabegron binding to α1A. Because of its lack of interactions with the binding pocket, mirabegron has lower affinity compared to α1A-blockers and no effects on voiding symptoms.

Computational studies of the binding site of alpha1A-adrenoceptor antagonists

Aimed at achieving a good understanding of the 3-dimensional structures of human alpha1A-adrenoceptor (alpha1A-AR), we have successfully developed its homology model based on the crystal structure of beta2-AR. Subsequent structural refinements were performed to mimic the receptor's natural membrane environment by using molecular mechanics (MM) and molecular dynamics (MD) simulations in the GBSW implicit membrane model. Through molecular docking and further simulations, possible binding modes of subtype-selective alpha1A-AR antagonists, Silodosin, RWJ-69736 and (+)SNAP-7915, were examined. Results of the modeling and docking studies are qualitatively consistent with available experimental data from mutagenesis studies. The homology model built should be very useful for designing more potent subtype-selective alpha1A-AR antagonists and for guiding further mutagenesis studies.

Two model system of the alpha1A-adrenoceptor docked with selected ligands

In this study, we have developed a two model system to mimic the active and inactive states of a G-protein coupled receptor specifically the alpha1A adrenergic receptor. We have docked two agonists, epinephrine (phenylamine type) and oxymetazoline (imidazoline type), as well as two antagonists, prazosin and 5-methylurapidil, into two alpha1A receptor models, active and inactive. The best docking complexes for both agonists had hydrophilic interactions with D106, while neither antagonist did. Prazosin and oxymetazoline had hydrophobic interactions with F308 and F312. We predict from our study that the active state is stabilized by the interaction of F193 with I114, L197, V278, F281, and V282. The active state is further stabilized by the interaction of F312 with L75, V79, and L80. We also predict that the inactive state of the receptor is stabilized by the interaction of F312 with W102, F288, and M292.

Computational approach to the basicity of a series of alpha1-adrenoceptor ligands in aqueous solution

In order to design any new potential drug, it is crucial to know their corresponding pK(a) since their protonation state will be critical in the ligand-receptor interaction and it will play an essential role in their pharmacokinetic profile. Several authors have developed approaches for the computational determination of pK(a) which involve the use of a thermodynamic cycle relating pK(a) to the gas-phase proton basicity via the solvation energies of the products and the reactants. Such methods are very dependent on the solvation model used and the nature of the system. The theoretical pK(a) of a number of agonists and antagonists of the alpha1A-adrenoceptor has been computed and the performance of this approach has been tested through comparison with the available and/or measured experimental pK(a) values.

A Genetic-Function-Approximation-Based QSAR Model for the Affinity of Arylpiperazines toward α1 Adrenoceptors

The genetic function approximation (GFA) algorithm has been used to derive a three-term QSAR equation able to correlate the structural properties of arylpiperazine derivatives with their affinity toward the alpha1 adrenoceptor (alpha1-AR). The number of rotatable bonds, the hydrogen-bond properties, and a variable belonging to a topological family of descriptors (chi) showed significant roles in the binding process toward alpha1-AR. The new model was also compared to a previous pharmacophore for alpha1-AR antagonists and a QSAR model for alpha2-AR antagonists with the aim of finding common or different key determinants influencing both affinity and selectivity toward alpha1- and alpha2-AR.

Theoretical proton affinities of α1 adrenoceptor ligands

A systematic study has been performed of the proton affinity of a large family of agonists and antagonists of the alpha1-adrenoceptor at the B3LYP/6-31G* level of theory. After a conformational search, all the N atoms were considered as protonation sites and protonation energy values were determined. The inclusion of solvation by means of the Onsager model yielded stabilization in the proton affinity values obtained. In addition, a good correlation was found between the proton affinity values corresponding to the first protonation in gas phase of some of the compounds and their corresponding experimental affinity constants K(i) for the alpha1A adrenergic receptor.

Computational Study of Antagonist/α1A Adrenoceptor ComplexesObservations of Conformational Variations on the Formation of Ligand/Receptor Complexes

As selective antagonist inhibition may relieve the symptoms of benign prostatic hyperplasia, we have examined the interactions of antagonists including quinazoline and imidazolidinium/guanidinium compounds complexed with a homology model of the alpha(1A) adrenoceptor. Our approach involves docking of ligands of various structural classes followed by molecular dynamics simulations of antagonist/receptor complexes, which demonstrates that different structural classes of antagonist induce different receptor conformations upon binding with particular variations noted in the conformation of TM-V. Subsequently, we examined the interactions and the conformational flexibility of alpha(1) and alpha(1A) adrenoceptor antagonists, with the ligand-induced receptor conformers. This study indicated that a receptor conformation induced by one structural class of antagonist is not suitable for direct screening of another class. Our analysis indicates that computational high-throughput screening is likely to give inaccurate data on binding and selectivity and such studies need to consider conformational changes in the receptor.

Comparative molecular dynamics simulations of uncomplexed, 'agonist-bound' and 'antagonist-bound' alpha1A adrenoceptor models

Molecular dynamics simulations (2 ns) were conducted on a homology model of the alpha1A adrenoceptor complexed with agonists and antagonists to examine the various receptor conformations induced. These simulations yield insights into the binding site interactions of the active and inactive states of the receptor. Furthermore, our analysis allowed for the selection of candidate sites for future mutagenesis experiments such as of Glu-180, which may be important for antagonist binding. The interactions of conserved residues of the DRY motif in TM-III and the NPxxY motif in TM-VII in the alpha1A adrenoceptor complexes were also examined. The major differences lie in the role of residue Arg-124, which for the agonist complexes formed additional interactions with residues of intracellular loops I and II. Alternatively, for the antagonist complexes, additional interactions were observed for Asn-322 with residues of TM-II and TM-VII.

Modelling the Interaction of Catecholamines with the α1A Adrenoceptor Towards a Ligand-induced Receptor Structure

Adrenoceptors are members of the important G protein coupled receptor family for which the detailed mechanism of activation remains unclear. In this study, we have combined docking and molecular dynamics simulations to model the ligand induced effect on an homology derived human alpha1A adrenoceptor. Analysis of agonist/alpha1A adrenoceptor complex interactions focused on the role of the charged amine group, the aromatic ring, the N-methyl group of adrenaline, the beta hydroxyl group and the catechol meta and para hydroxyl groups of the catecholamines. The most critical interactions for the binding of the agonists are consistent with many earlier reports and our study suggests new residues possibly involved in the agonist-binding site, namely Thr-174 and Cys-176. We further observe a number of structural changes that occur upon agonist binding including a movement of TM-V away from TM-III and a change in the interactions of Asp-123 of the conserved DRY motif. This may cause Arg-124 to move out of the TM helical bundle and change the orientation of residues in IC-II and IC-III, allowing for increased affinity of coupling to the G-protein.