A molecular description of ligand binding to the two overlapping binding pockets of the nuclear vitamin D receptor (VDR): Structure-function implications

Abstract

Molecular modeling results indicate that the VDR contains two overlapping ligand binding pockets (LBP). Differential ligand stability and fractional occupancy of the two LBP has been physiochemically linked to the regulation of VDR-dependent genomic and non-genomic cellular responses. The purpose of this report is to develop an unbiased molecular modeling protocol that serves as a good starting point in simulating the dynamic interaction between 1α,25(OH) 2-vitamin D 3 (1,25D3) and the VDR LBP. To accomplish this goal, the flexible docking protocol developed allowed for flexibility in the VDR ligand and the VDR atoms that form the surfaces of the VDR LBP. This approach blindly replicated the 1,25D3 conformation and side-chain dynamics observed in the VDR X-ray structure. The results are also consistent with the previously published tenants of the vitamin D sterol (VDS)–VDR conformational ensemble model. Furthermore, we used flexible docking in combination with whole-cell patch-clamp electrophysiology and steroid competition assays to demonstrate that (a) new non-vitamin D VDR ligands show a different pocket selectivity when compared to 1,25D3 that is qualitatively consistent with their ability to stimulate chloride channels and (b) a new route of ligand binding provides a novel hypothesis describing the structural nuances that underlie hypercalceamia.