Structural Basis for the Accommodation of Bis- and Tris-Aromatic Derivatives in Vitamin D Nuclear Receptor

Actual use of the active form of vitamin D (calcitriol or 1α,25-dihydroxyvitamin D₃) to treat hyperproliferative disorders is hampered by calcemic effects, hence the continuous development of chemically modified analogues with dissociated profiles. Structurally distinct nonsecosteroidal analogues have been developed to mimic calcitriol activity profiles with low calcium serum levels. Here, we report the crystallographic study of vitamin D nuclear receptor (VDR) ligand binding domain in complexes with six nonsecosteroidal analogues harboring two or three phenyl rings. These compounds induce a stimulated transcription in the nanomolar range, similar to calcitriol. Examination of the protein–ligand interactions reveals the mode of binding of these nonsecosteroidal compounds and highlights the role of the various chemical modifications of the ligands to VDR binding and activity, notably (de)­solvation effects. The structures with the tris-aromatic ligands exhibit a rearrangement of a novel region of the VDR ligand binding pocket, helix H6

Diastereotopic and Deuterium Effects in Gemini

Changing the geminal methyl groups on 1α,25-dihydroxyvitamin D₃ and its analogues to the deuterio versions generally improves the bioactivity. Derivatives of 1α,25-dihydroxyvitamin D₃ with two chains emanating at C20, commonly referred to as gemini, are subject to the same phenomenon. Additionally, gemini with different side chains are susceptible to bioactivity differentials where the C17–C20 threo configuration usually imparts higher activity than the corresponding erythro arrangement. In an effort to analyze the deuterium effect on gemini with minimal diastereotopic distortion, we synthesized gemini with equal side chains but introduced deuterium diastereospecifically on either chain. We solved the crystal structures of these compounds in the zebra fish zVDR ligand binding domain as complexes with NCoA-2 coactivator peptide and correlated the findings with growth inhibition in a breast cancer cell line

Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics

<div><p>Nuclear receptor proteins constitute a superfamily of proteins that function as ligand dependent transcription factors. They are implicated in the transcriptional cascades underlying many physiological phenomena, such as embryogenesis, cell growth and differentiation, and apoptosis, making them one of the major signal transduction paradigms in metazoans. Regulation of these receptors occurs through the binding of hormones, and in the case of the retinoic acid receptor (RAR), through the binding of retinoic acid (RA). In addition to this canonical scenario of RAR activity, recent discoveries have shown that RAR regulation also occurs as a result of phosphorylation. In fact, RA induces non-genomic effects, such as the activation of kinase signaling pathways, resulting in the phosphorylation of several targets including RARs themselves. In the case of RARα, phosphorylation of Ser369 located in loop L9–10 of the ligand-binding domain leads to an increase in the affinity for the protein cyclin H, which is part of the Cdk-activating kinase complex of the general transcription factor TFIIH. The cyclin H binding site in RARα is situated more than 40 Å from the phosphorylated serine. Using molecular dynamics simulations of the unphosphorylated and phosphorylated forms of the receptor RARα, we analyzed the structural implications of receptor phosphorylation, which led to the identification of a structural mechanism for the allosteric coupling between the two remote sites of interest. The results show that phosphorylation leads to a reorganization of a local salt bridge network, which induces changes in helix extension and orientation that affects the cyclin H binding site. This results in changes in conformation and flexibility of the latter. The high conservation of the residues implicated in this signal transduction suggests a mechanism that could be applied to other nuclear receptor proteins.</p></div

Distribution of the angle values in the unphosphorylated (in black) and the phosphorylated (in grey) simulations of RARα between H9–H10 (A) and H4–H9 (B).

<p>Distribution of the angle values in the unphosphorylated (in black) and the phosphorylated (in grey) simulations of RARα between H9–H10 (A) and H4–H9 (B).</p

Histograms of the following four distances: S369-R367 (A), E325-R367 (B), D323-R192 (C), E320-R367 (D), and R347-D256 (E), for the unphosphorylated RARα (in black) and the phosphorylated RARα (in grey).

<p>Histograms of the following four distances: S369-R367 (A), E325-R367 (B), D323-R192 (C), E320-R367 (D), and R347-D256 (E), for the unphosphorylated RARα (in black) and the phosphorylated RARα (in grey).</p

Structural Insights into the Molecular Mechanism of Vitamin D Receptor Activation by Lithocholic Acid Involving a New Mode of Ligand Recognition

The vitamin D receptor (VDR), an endocrine nuclear receptor for 1α,25-dihydroxyvitamin D3, acts also as a bile acid sensor by binding lithocholic acid (LCA). The crystal structure of the zebrafish VDR ligand binding domain in complex with LCA and the SRC-2 coactivator peptide reveals the binding of two LCA molecules by VDR. One LCA binds to the canonical ligand-binding pocket, and the second one, which is not fully buried, is anchored to a site located on the VDR surface. Despite the low affinity of the alternative site, the binding of the second molecule promotes stabilization of the active receptor conformation. Biological activity assays, structural analysis, and molecular dynamics simulations indicate that the recognition of two ligand molecules is crucial for VDR agonism by LCA. The unique binding mode of LCA provides clues for the development of new chemical compounds that target alternative binding sites for therapeutic applications

Backbone RMS fluctuations as a function of residue number calculated from the last 40 ns of the molecular dynamics simulations (A) and from the ten lowest frequency modes of the quasi-harmonic analysis (B).

<p>Black lines correspond to the average over the three unphosphorylated RARα, dashed lines to the three phosphorylated RARα. In <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003012#pcbi-1003012-g007" target="_blank">Figure 7.A</a>, dotted lines correspond to the experimental B-factor values. Similar behavior is observed for the fluctuations calculated from simulations and the experimental values. The RMS fluctuations are averaged and displayed by residue. Fluctuations of loop L8–9 are highlighted in purple color.</p

Distribution of the radius of the circle fitted to the α-carbons (Å) of helix H9 in the unphosphorylated (in black) and the phosphorylated (in grey) simulations of RARα.

<p>A decrease in the radius of the circle corresponds to an increase in the bend of the helix.</p

Structural representation of the ligand-binding domain of RARα illustrating the cyclin H docking site (CDS) and the phosphorylation site (S369).

<p>Structural representation of the ligand-binding domain of RARα illustrating the cyclin H docking site (CDS) and the phosphorylation site (S369).</p

Cross-correlation networks in the unphosphorylated (A) and phosphorylated (B) forms of RARα.

<p>The figures show cross-correlations between loops L9–10 and L8–9 and the other structural elements of the LBD by drawing a specific line between two residues if their motion is correlated. The color code corresponds to the value of the cross-correlation coefficient (ccc, see also <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003012#pcbi.1003012.s005" target="_blank">Figure S5</a>). Marine blue is used for anti-correlated motions (ccc between −0.2 to −0.1), whereas orange (ccc 0.2 to 0.3), salmon (ccc 0.3 to 0.4), light red (ccc 0.4 to 0.7) and red (ccc 0.7 to 1) are used for correlated motions. The changes in the dynamics upon phosphorylation are reflected by the loss of anti-correlated motions connecting loop L8–9 with H11 and the increased anti-correlations of loop L9–10.</p