Ligand-dependent conformation change reflects steric structure and interactions of a vitamin D receptor/ligand complex: A fragment molecular orbital study

Abstract

We used an in silico computational method to theoretically analyze important residue-ligand interactions as well as ligand conformation changes in the vitamin D receptor (VDR). The ligand used for analysis was 1α,25-dihydroxy-19-nor-vitamin D 3 [1α,25-19-nor-(OH) 2D 3] [1,2], whose crystal structure has not been solved. To estimate amino acid residue-ligand interactions with chemical accuracy, we adopted the fragment molecular orbital (FMO) method [3,4], which is based on the nonempirical total electronic quantum calculation. The docking of the ligand to the VDR was controlled by hydrophilic and hydrophobic interactions between amino acid residues and the ligand in the ligand binding pocket (LBP) [5–8]. These molecular interactions changed when the conformation of the ligand in the VDR was changed [5,9,10]. This conformation change is important to consider in computational, in silico, approaches for analyzing the mechanism of ligand-docking to the VDR. The position of the 1α,25-19-nor-(OH) 2D 3 ligand in the VDR-LBP was related to the hydrophobic interaction that occurred between the Ile271 residue of the VDR-LBP and the ligand. The interaction between Ile271 and 1α,25-19-nor-(OH) 2D 3 was repulsive, whereas, that between Ile271 and the natural ligand, 1α,25-(OH) 2D 3, is stable. The orientation change in the isopropyl group of Ile271 affected the residue's interaction with 1α,25-19-nor-(OH) 2D 3. We also found that conformation changes in the A-ring affected electrostatic (hydrophilic) interactions between the VDR and the ligand.