Homology Model-Based Histamine H3 Receptor Docking

The three-dimensional structures for ligands were prepared with LigPrep (Schrodinger Suite) from SMILES strings, using an ionizer for the prediction of protonation states at pH 7.4 ± 0.2. The previously prepared homology model of the histamine H₃ receptor was utilized for docking studies [32 (link)]. This model was built with Modeller 9.14 based on a template of M₃ muscarinic receptor (PDB code: 4U15) using automodel class and very fast refinement option. Recently, the crystal structure of H₃R was obtained [38 (link)]. Comparing this experimental structure with our homology model, it is worth noting that the model is very consistent with the X-ray structure. Therefore, the application of our homology model in presented docking studies was fully justified. All dockings were performed using the Induced Fit Docking procedure (Schrodinger Suite) with the standard protocol. Binding site box with a center at Asp3.32 and size, adjusted for docking of ligands with length ≤25 Å, was applied. The obtained ligand–receptor complexes were analyzed concerning IFDScore as well as interaction networks with Maestro (Schrodinger Suite) and PyMOL 0.99rc6 (DeLano Scientific LLC).

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Staszewski M., Iwan M., Werner T., Bajda M., Godyń J., Latacz G., Korga-Plewko A., Kubik J., Szałaj N., Stark H., Malawska B., Więckowska A, & Walczyński K. (2023). Guanidines: Synthesis of Novel Histamine H3R Antagonists with Additional Breast Anticancer Activity and Cholinesterases Inhibitory Effect. Pharmaceuticals, 16(5), 675.

Publication 2023

LigPrep PyMOL 0.99rc6

Binding site Histamine h3 receptor Ligand M3 muscarinic receptor X ray

Corresponding Organization : Medical University of Lodz

Other organizations : Medical University of Lublin, Heinrich Heine University Düsseldorf, Jagiellonian University

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Variable analysis

independent variables

Ligand structures prepared using LigPrep
Homology model of the histamine H3 receptor used for docking studies

dependent variables

Binding interactions and complex formation between ligands and the histamine H3 receptor
IFDScore (Induced Fit Docking Score) of the ligand-receptor complexes

control variables

Ionizer used for prediction of ligand protonation states at pH 7.4 ± 0.2
Binding site box with a center at Asp3.32 and size adjusted for docking of ligands with length ≤25 Å

positive controls

Comparison of the homology model with the recently obtained crystal structure of the histamine H3 receptor, which showed the model is very consistent with the experimental structure

negative controls

No negative controls were explicitly mentioned in the provided information.

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