Modeling human D4 receptor structure and ligands

The 3D structure of the human dopamine D4 receptor was downloaded from the Protein Data Bank database [47 (link)] (PDB ID: 5WIU). It is a protein crystal in complex with the antagonist nemonapride [37 (link)]. After removing all co-crystallized small molecules, this structure served as a model for the inactive conformation of the receptor. In this work, the active conformation of the D4 receptor was used as a homology model built on a template of the active form of the D2 receptor with PDBID 6VMS. The pre-prepared one was downloaded courtesy of the GPCRdb [48 (link),49 (link),50 (link),51 (link)] just before the 2023 update, where AlphaFold2 was used [52 (link)]. The agonists and antagonists of the human D4 receptor sets of compounds were constructed using affinity results for 5997 compounds found in the ChEMBL database [53 (link),54 (link)]. From this set, 77 compounds showing agonist or partial agonist activity and 25 antagonists were extracted manually by verifying the results of the source studies. All compounds were hierarchically clustered using Molprint2D, the Tanimoto metric, and the complete cluster linking method implemented in Canvas from the Schrödinger [55 (link),56 (link)]. The centroid was selected from each cluster containing more than two members to constitute representative structures to further study. Two sets of test compounds were created, enlisting seven agonists and ten antagonists of the human dopamine D4 receptor, respectively (Figures S1 and S2).