Crystal Structures of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and Partial Agonism

Abstract

The X-ray crystal structures of the rat VDR ligand-binding domain complexed with 19-norvitamin D compounds that contain an adamantyl substituent at the side-chain terminus, 2a (ADTT), 2b (ADNY), and 2c (ADMI4) and a coactivator peptide derived from DRIP205 are reported. These compounds show a series of partial agonistic (10-75% efficacy)/antagonistic activities. All of these complexed receptors are crystallized in the canonical active conformation, regardless of their activity profiles. The bulky adamantyl side chain does not crowd helix 12 but protrudes into the gap formed by helix 11, loop 11-12, helix 3, and loop 6-7, thereby widening the ligand binding pocket. We suggest that these structural changes destabilize the active protein conformation and reduce its contribution to equilibrium among the active and inactive conformations. The coactivator peptide traps the minor active conformation, and the equilibrium shifts to the active conformation. As a result, these ligands show partial agonistic activities.

Vitamin D Receptor Activation Enhances Benzo[a]pyrene Metabolism via CYP1A1 Expression in Macrophages

“…1,25(OH) 2 D 3 , BaP, and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) were purchased from Wako Pure Chemical Industries (Osaka, Japan), and ␣-naphthoflavone was obtained from Sigma-Aldrich (St. Louis, MO). LCA acetate, (25R)- 25-adamantyl-1␣,25-dihydroxy-2-methylene-22,23-didehydro-19,26,27-trinor-20-epi-vitamin D 3 (ADTT) and (25S)- 26-adamantyl-1␣,25-dihydroxy-2-methylene-22,23-didehydro-19,27-dinor-20-epi-vitamin D 3 (ADMI3) were synthesized in the Sachiko Yamada laboratory (Igarashi et al, 2007;Ishizawa et al, 2008;Nakabayashi et al, 2008).…”

“…4B). In addition, we examined the effect of VDR antagonists, ADTT and ADMI3 (Igarashi et al, 2007;Nakabayashi et al, 2008). Both ADTT and ADMI3 effectively reduced CYP1A1 expression induced by BaP plus 1,25(OH) 2 D 3 in THP-1 cells (Fig.…”

Dynamic and Ligand-Selective Interactions of Vitamin D Receptor with Retinoid X Receptor and Cofactors in Living Cells

“…1,25(OH) 2 D 3 was purchased from Wako Pure Chemical Industries (Osaka, Japan), and LCA was from Nacalai Tesque, Inc. (Kyoto, Japan). ADTT was synthesized in our laboratory (Nakabayashi et al, 2008).…”

“…ADTT is a synthetic vitamin D derivative that acts as a partial agonist/antagonist for VDR and LCA is a weak endogenous agonist (Makishima et al, 2002;Nakabayashi et al, 2008) (Fig. 4A).…”

“…In this study, we applied FRET in living cells to evaluate the interaction of VDR with RXR␣ and cofactors stimulated by 1,25(OH) 2 D 3 , (25R)-25-adamantyl-1␣,25-dihydroxy-2-methylene-22, 23-didehydro-19,26,27-trinor-20-epivitamin D 3 (ADTT), and lithocholic acid (LCA). ADTT is a synthetic vitamin D derivative that shows partial agonist/antagonist activity (Nakabayashi et al, 2008). LCA is a secondary bile acid that acts as an additional physiological VDR agonist (Makishima et al, 2002).…”