Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions

Abstract

Homology model structures of the dopamine D2 receptor (D2R) were generated starting from the active and inactive states of β2-adrenergic crystal structure templates. To the best of our knowledge, the active conformation of D2R was modeled for the first time in this study. The homology models are built and refined using MODELLER and ROSETTA programs. Top-ranked models have been validated with ligand docking simulations and in silico Alanine-scanning mutagenesis studies. The derived extra-cellular loop region of the protein models is directed toward the binding site cavity which is often involved in ligand binding. The binding sites of protein models were refined using induced fit docking to enable the side-chain refinement during ligand docking simulations. The derived models were then tested using molecular modeling techniques on several marketed drugs for schizophrenia. Alanine-scanning mutagenesis and molecular docking studies gave similar results for marketed drugs tested. We believe that these new D2 receptor models will be very useful for a better understanding of the mechanisms of action of drugs to be targeted to the binding sites of D2Rs and they will contribute significantly to drug design studies involving G-protein-coupled receptors in the future.

A Complete Assessment of Dopamine Receptor-Ligand Interactions through Computational Methods

“…Furthermore, by applying Ballesteros & Weinstein numbering (B&W) [42] the position of considered important residues was more easily comparable between all receptors. Mutagenesis studies have shown that for dopamine binding, the endogenous agonist of the DR, a negatively charged aspartate (3.32Asp) is believed to form a ionic bond interaction with the protonable amine of dopamine [2,41,43]. Moreover, it was shown that this effect was crucial for ligand binding and that this amino acid was not only conserved among the DR, but also in all biogenic amine GPCRs [44,45].…”

“…Moreover, it was shown that this effect was crucial for ligand binding and that this amino acid was not only conserved among the DR, but also in all biogenic amine GPCRs [44,45]. Also, a serine microdomain on TM5 (5.42Ser, 5.43Ser, 5.46Ser) was considered as an important feature for dopaminergic binding in all DRs as it is believed that the serines form hydrogenic bonds with the catechol hydroxyls of dopamine, increasing the binding affinity and orienting ligands in the orthosteric binding pocket [38,43,[46][47][48]. While 5.42Ser seems to be critical, 5.43Ser plays a less important role [38].…”

A QM protein–ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R)

“…A combination of MODELLER (Eswar et al, 2007) and the ROSETTA loop-modeling protocol (Das & Baker, 2008) was performed to build and refine the 3D structure of D2R. The details of the modeling process were explained in our previous work (Salmas et al, 2015).…”

“…In the current study, we refine the small molecule binding poses derived from docking and molecular dynamics (MD) trajectory frames in order to obtain an accurate ligand binding energy to the D2R models obtained in our earlier studies (Durdagi, Salmas, Stein, Yurtsever, & Seeman, 2016;Salmas, Yurtsever, Stein, & Durdagi, 2015;Salmas et al, 2017aSalmas et al, , 2017b. The D2R state models were generated by the use of comparative modeling approaches based on the inactive beta-2 adrenergic receptor (β 2 adrenoreceptor) as a template structure (Hanson et al, 2008).…”

“…The D2R state models were generated by the use of comparative modeling approaches based on the inactive beta-2 adrenergic receptor (β 2 adrenoreceptor) as a template structure (Hanson et al, 2008). Since we are investigating the antagonizing binding of molecules to D2R, the inactive form of the D2R was used (Salmas et al, 2015). Here, the binding of six marketed antipsychotic drug molecules into the catalytic domain of the D2R was studied quantum mechanically (QM) using two different approaches.…”