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bioRxiv · 10.1101/2023.09.05.556418

Unraveling the Structure of Meclizine Dihydrochloride with MicroED

Lin, J.·Unge, J.·Gonen, T.
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Abstract

Meclizine (Antivert, Bonine) is a first-generation H1 antihistamine used in the treatment of motion sickness and vertigo. Despite its wide medical use for over 70 years, its crystal structure and the details of protein-drug interactions remained unknown. In this study, we used microcrystal electron diffraction (MicroED) to determine the three-dimensional (3D) crystal structure of meclizine dihydrochloride directly from a seemingly amorphous powder. Two racemic enantiomers (R/S) were found in the unit cell, which packed as repetitive double layers in the crystal lattice. The packing was made of multiple strong N-H{middle dot}{middle dot}{middle dot}Cl- hydrogen bonding interactions and weak interactions like C-H{middle dot}{middle dot}{middle dot}Cl- and pi-stacking. Molecular docking revealed the binding mechanism of meclizine to the histamine H1 receptor. A comparison of the docking complexes between histamine H1 receptor and meclizine or levocetirizine (a second-generation antihistamine) showed the conserved binding sites. This research illustrates the combined use of MicroED and molecular docking in unraveling protein-drug interactions for precision drug design and optimization.

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Lin, J., Unge, J., Gonen, T.. 2023-09-06. Unraveling the Structure of Meclizine Dihydrochloride with MicroED. https://doi.org/10.1101/2023.09.05.556418

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