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.

Vitamin D Sterol/VDR Conformational Dynamics and Nongenomic Actions

“…This rotomer is favored by the VDR-AP and is observed 73% of the time in the 1,25(OH) 2 D 3 dot map calculation (262 total conformers Specific C5-C6-C7-C8 dihedral angles are highlighted in the figure that have been observed in the DBP and VDR X-ray complexes and also in the in silico flexible docking complexes obtained when 1,25(OH) 2 D 3 was docked to the VDR genomic pocket (VDR-GP) and the VDR alternative ligand-binding pocket (VDR-AP, see text for more details). These conformations were first generated by a conformational search calculation using a modified PC_Model v9.2 GMMX protocol (see [1,44,45]). Thus the "active" seco-B-ring conformations of 25(OH)D 3 and 1,25(OH) 2 D 3 and other vitamin D sterols, can be produced in silico [1,37,44].…”

“…Fortunately, since the dot map protocols were first published, advancements in computational hardware/software have allowed for inclusion of the entire VDS molecule in the same type of conformational search calculation [44,45]. This type of calculation allows for all combinations of A-ring, seco-B-ring, and sidechain rotomers to be generated that range from 6-s-cis planar-like to 6-s-trans bowl and planar-like shapes ( Fig.…”

“…15.4). In fact, the 1,25(OH) 2 D 3 conformational ensemble generated using PC_Model v9.2 was recently combined with a flexible docking simulation (Discovery Studio v2.0) to blindly replicating the 1,25(OH) 2 D 3 pose, energetics in molecular dynamics observed in the 1,25 (OH) 2 D 3 -VDR (aa118-427; D165-215) X-ray co-crystal [44,45]. Thus, the combination of PC_Model and DS2.0 may be useful in future VDR drug design efforts.…”

“…Figure 15.5 and Table 15.1 highlight the ion channel blockers used to attenuate 1,25 (OH) 2 D 3 , JN and 25(OH)D 3 potentiation of outwardly rectifying chloride and L-type calcium channels. Of these four blockers we recently showed that DIDS is a VDR ligand with approximately 10 mM affinity [45].…”

“…15.9C). Based on the computational results that show the VDR-AP accepts more conformational isomers of 1,25(OH) 2 D 3 when compared to the VDR-GP [37,45] and the evidence that the potential interaction energy and Gibbs free energy of binding (DG binding ) are better for the VDR-GP for nearly all VDS (Table 15.2), the VDR-AP has been described as being kinetically favored while the VDR-GP is the thermodynamically favored ligand-binding pocket for 1,25 (OH) 2 D 3 , if not all 1-OH vitamin D sterols (Table 15.2 and Fig. 15.9A legend).…”