Insights into the binding modes of human β₃-adrenergic receptor agonists with ligand-based and receptor-based methods

Agonists of β(3)-adrenergic receptor (AR) have been thought as potential drugs for the treatment of obesity, type II diabetes, and overactive bladder. In order to clarify the essential structure-activity relationship and the detailed binding modes of β(3)-AR agonists as well as to identify new lead compounds activating β(3)-AR, ligand-based and receptor-based methods were applied. The pharmacophore models were developed based on 144 β(3)-AR agonists. Meanwhile, the homology model of the β(3)-AR was built based on the crystal structure of β(2)-AR. The pharmacophore model and the homology model mapped with each other very well, and some important information was obtained from the docking result. For example, agonists formed similar hydrogen-bonding interactions with residues Asp117, Arg315, and Asn332, π-π stacking interaction with residues Phe308, and hydrophobic interactions with residues Val118, Val121, Ala197, Phe198, Ala199, Phe309, and Phe328 of β(3)-AR. And the major difference about binding mode from the crystal structures of β(1)- and β(2)-ARs is the hydrogen-bonding interaction with the residue Arg315, which corresponds to the residue Asn313 of β(1)-AR and the residue His296 of β(2)-AR, respectively. Our findings may be crucial for the design and development of novel selective and potent β(3)-AR agonists.