Molecular modeling of histamine H3 receptor and QSAR studies on arylbenzofuran derived H3 antagonists

Histamine H3 receptors are presynaptic autoreceptors found in both central and peripheral nervous systems of many species. The central effects

of these receptors suggest a potential therapeutic role for their antagonists in treatment of several neurological disorders such as epilepsy,

schizophrenia, Alzheimer’s and Parkinson’s diseases. The purpose of this study was to identify the structural requirements for H3 antagonistic

activity via quantitative structure–activity relationship (QSAR) studies and receptor modeling/docking techniques. A combination of partial least

squares (PLS) and genetic algorithm (GA) was used in the QSAR approach to select the structural descriptors relevant to the receptor binding

affinity of a series of 58 H3 antagonists. The descriptors were selected out of a pool of >1000 descriptors calculated by DRAGON, Hyperchem and

ACD labs suite of programs. The resulting QSAR models for rat and human H3 binding affinities were validated using different strategies. QSAR

models generated in the current work suggested the role of charge transfer interactions in the ligand–receptor interaction verified using the

molecular modeling of the receptor and docking two antagonists to the binding site. The 3D model of human H3 receptor was built based on bovine

rhodopsin structure and evaluated by molecular dynamics (MD) simulation in a mixed water–vacuum–water environment. The results were

indicative of the stability of the model relating the observed structural changes during the MD simulation to the suggested ligand–receptor

interactions. The results of this investigation are expected to be useful in the process of design and development of new potent H3 receptor

antagonists.