title: Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors.
abstract: Small molecules targeting allosteric pockets of G protein-coupled receptors (GPCRs) have a great therapeutic potential for the treatment of neurologic and other chronic disorders. Here we performed virtual screening for orthosteric and putative allosteric ligands of the human dopamine D3 receptor (D3R) using two optimized crystal-structure-based models: the receptor with an empty binding pocket (D3R(APO)), and the receptor complex with dopamine (D3R(Dopa)). Subsequent biochemical and functional characterization revealed 14 novel ligands with a binding affinity of better than 10 μM in the D3R(APO) candidate list (56% hit rate), and 8 novel ligands in the D3R(Dopa) list (32% hit rate). Most ligands in the D3R(APO) model span both orthosteric and extended pockets and behave as antagonists at D3R, with compound 7 showing the highest potency of dopamine inhibition (IC₅₀ = 7 nM). In contrast, compounds identified by the D3R(Dopa) model are predicted to occupy an allosteric site at the extracellular extension of the pocket, and they all lack the anchoring amino group. Compounds targeting the allosteric site display a variety of functional activity profiles, where behavior of at least two compounds (23 and 26) is consistent with noncompetitive allosteric modulation of dopamine signaling in the extracellular signal-regulated kinase 1 and 2 phosphorylation and β-arrestin recruitment assays. The high affinity and ligand efficiency of the chemically diverse hits identified in this study suggest utility of structure-based screening targeting allosteric sites of GPCRs.
authors.affiliation: Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (P.C., W.L., V.C., R.C.S., V.K.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (J.R.L., M.C.); and Skaggs School of Pharmacy and Pharmaceutical Sciences, and San Diego Supercomputer Center, University of California, San Diego, La Jolla, California (R.A.).
authors.forename: J Robert
authors.initials: JR
authors.lastname: Lane
authors.forename: Pavel
authors.initials: P
authors.lastname: Chubukov
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.forename: Meritxell
authors.initials: M
authors.lastname: Canals
authors.forename: Vadim
authors.initials: V
authors.lastname: Cherezov
authors.forename: Ruben
authors.initials: R
authors.lastname: Abagyan
authors.forename: Raymond C
authors.initials: RC
authors.lastname: Stevens
authors.forename: Vsevolod
authors.initials: V
authors.lastname: Katritch
mesh_terms: D000495:Allosteric Site; D000818:Animals; D019390:Arrestins / Q000378:metabolism; D001665:Binding Sites; D016466:CHO Cells; D006224:Cricetinae; D003412:Cricetulus; D016208:Databases, Factual; D004298:Dopamine / Q000737:chemistry / Q000494:pharmacology; D057166:High-Throughput Screening Assays; D006801:Humans; D008024:Ligands; D019950:Mitogen-Activated Protein Kinase 1 / Q000378:metabolism; D048052:Mitogen-Activated Protein Kinase 3 / Q000378:metabolism; D008958:Models, Molecular; D010766:Phosphorylation; D011485:Protein Binding; D011487:Protein Conformation; D011869:Radioligand Assay; D050637:Receptors, Dopamine D3 / Q000737:chemistry* / Q000378:metabolism; D061987:Sf9 Cells; D054852:Small Molecule Libraries / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship; D000071557:beta-Arrestins
chemical_list: D019390:Arrestins; D008024:Ligands; D050637:Receptors, Dopamine D3; D054852:Small Molecule Libraries; D000071557:beta-Arrestins; D019950:Mitogen-Activated Protein Kinase 1; D048052:Mitogen-Activated Protein Kinase 3; D004298:Dopamine
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