title: Ligand Binding Pathways of Clozapine and Haloperidol in the Dopamine D2 and D3 Receptors.
abstract: The binding of a small molecule ligand to its protein target is most often characterized by binding affinity and is typically viewed as an on/off switch. The more complex reality is that binding involves the ligand passing through a series of intermediate states between the solution phase and the fully bound pose. We have performed a set of 29 unbiased molecular dynamics simulations to model the binding pathways of the dopamine receptor antagonists clozapine and haloperidol binding to the D2 and D3 dopamine receptors. Through these simulations we have captured the binding pathways of clozapine and haloperidol from the extracellular vestibule to the orthosteric binding site and thereby, we also predict the bound pose of each ligand. These are the first long time scale simulations of haloperidol or clozapine binding to dopamine receptors. From these simulations, we have identified several important stages in the binding pathway, including the involvement of Tyr7.35 in a "handover" mechanism that transfers the ligand between the extracellular vestibule and Asp3.32. We have also performed interaction and cluster analyses to determine differences in binding pathways between the D2 and D3 receptors and identified metastable states that may be of use in drug design.
authors.affiliation: Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Pde, Parkville, Victoria 3052, Australia.
authors.forename: Trayder
authors.initials: T
authors.lastname: Thomas
authors.affiliation: Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Pde, Parkville, Victoria 3052, Australia.
authors.forename: Yu
authors.initials: Y
authors.lastname: Fang
authors.affiliation: Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Pde, Parkville, Victoria 3052, Australia.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Yuriev
authors.affiliation: Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Pde, Parkville, Victoria 3052, Australia.
authors.forename: David K
authors.initials: DK
authors.lastname: Chalmers
mesh_terms: D003024:Clozapine / Q000378:metabolism*; D006220:Haloperidol / Q000378:metabolism*; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017448:Receptors, Dopamine D2 / Q000378:metabolism*; D050637:Receptors, Dopamine D3 / Q000378:metabolism*
chemical_list: D008024:Ligands; D017448:Receptors, Dopamine D2; D050637:Receptors, Dopamine D3; D003024:Clozapine; D006220:Haloperidol