Browsing by Subject "docking"
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Item Advancing the Role of Thyrotropin-releasing Hormone as a Central Nervous System Agent(2022-05) De La Cruz, Daniel L.; Prokai-Tatrai, Katalin; Prokai, Laszlo; Lacko, Andras G.; Forster, Michael J.Item Interaction of Ligands for PET with the Dopamine D3 Receptor: In Silico and In Vitro Methods(MDPI, 2021-04-02) Hsieh, Chia-JI; Riad, Aladdin; Lee, Ji Youn; Sahlholm, Kristoffer; Xu, Kuiying; Luedtke, Robert R.; Mach, Robert H.[(18)F]Fallypride and [(18)F]Fluortriopride (FTP) are two different PET radiotracers that bind with sub-nanomolar affinity to the dopamine D3 receptor (D3R). In spite of their similar D3 affinities, the two PET ligands display very different properties for labeling the D3R in vivo: [(18)F]Fallypride is capable of binding to D3R under "baseline" conditions, whereas [(18)F]FTP requires the depletion of synaptic dopamine in order to image the receptor in vivo. These data suggest that [(18)F]Fallypride is able to compete with synaptic dopamine for binding to the D3R, whereas [(18)F]FTP is not. The goal of this study was to conduct a series of docking and molecular dynamic simulation studies to identify differences in the ability of each molecule to interact with the D3R that could explain these differences with respect to competition with synaptic dopamine. Competition studies measuring the ability of each ligand to compete with dopamine in the beta-arrestin assay were also conducted. The results of the in silico studies indicate that FTP has a weaker interaction with the orthosteric binding site of the D3R versus that of Fallypride. The results of the in silico studies were also consistent with the IC50 values of each compound in the dopamine beta-arrestin competition assays. The results of this study indicate that in silico methods may be able to predict the ability of a small molecule to compete with synaptic dopamine for binding to the D3R.Item The Antagonist pGlu-betaGlu-Pro-NH2 Binds to an Allosteric Site of the Thyrotropin-Releasing Hormone Receptor(MDPI, 2021-09-05) De La Cruz, Daniel L.; Prokai, Laszlo; Prokai-Tatrai, KatalinAfter we identified pGlu-betaGlu-Pro-NH2 as the first functional antagonist of the cholinergic central actions of the thyrotropin-releasing hormone (TRH, pGlu-His-Pro-NH2), we became interested in finding the receptor-associated mechanism responsible for this antagonism. By utilizing a human TRH receptor (hTRH-R) homology model, we first refined the active binding site within the transmembrane bundle of this receptor to enhance TRH's binding affinity. However, this binding site did not accommodate the TRH antagonist. This directed us to consider a potential allosteric binding site in the extracellular domain (ECD). Searches for ECD binding pockets prompted the remodeling of the extracellular loops and the N-terminus. We found that different trajectories of ECDs produced novel binding cavities that were then systematically probed with TRH, as well as its antagonist. This led us to establish not only a surface-recognition binding site for TRH, but also an allosteric site that exhibited a selective and high-affinity binding for pGlu-betaGlu-Pro-NH2. The allosteric binding of this TRH antagonist is more robust than TRH's binding to its own active site. The findings reported here may shed light on the mechanisms and the multimodal roles by which the ECD of a TRH receptor is involved in agonist and/or antagonist actions.