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Histamine H(3) receptor (H(3)R) is a promising target for the development of new drugs to treat several diseases. In this work, molecular docking and dynamics approaches were applied to predict binding modes and activities of 13 quinazoline derivatives at the H(3)R. A systematic study on binding modes of these derivatives suggested that two 4-methoxy-2-methylquinazoline derivatives (compounds 22 and 29) fit into the orthosteric binding site (OTBS) of H(3)R, interacting with Asn109, Glu110, Gln127, Phe128, Trp82, and Tyr71. The predicted binding free energies were well correlated with experimental values. The modes of these two derivatives were further confirmed by MD simulations. The 1-naphthyl ring of quinazoline derivatives showed possible interactions with Tyr71, Leu109, Asn109, Glu110, and Leu118. In addition, the optimized molecular structures of ligands were found to be consistent with the NMR data. These results indicate that compound 22 is a potent H(3)R antagonist and compound 29 is a potential H(3)R agonist, which may provide a useful guide to the design of novel H(3)R ligands.Q:
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