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The chirality of a compound affects its biochemical and pharmaceutical properties. It was found that the binding affinity between vitamin D receptor (VDR) and its ligand depends significantly on the chirality of the ligand. To elucidate the reason for this dependence, we here investigated the specific interactions between VDR and two types of ligands with different chirality, using ab initio fragment molecular orbital (FMO) calculations. The FMO results reveal that the part of ligand with different chirality interacts strongly with the imidazole ring of histidine side-chain in VDR, and that the binding affinity between VDR and the ligands depends on the protonation state of the histidine. This finding indicates the possibility that ligands with different chirality can assign the protonation state of VDR histidine residues existing near the ligand.

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