Rational design of RAR‐selective ligands revealed by RARβ crystal stucture

Abstract

The crystal structure of the ligand-binding domain of RARb, a suspect tumour suppressor, reveals important features that distinguish it from the two other RAR isotypes. The most striking difference is an extra cavity allowing RARb to bind more bulky agonists. Accordingly, we identified a ligand that shows RARb selectivity with a 100-fold higher affinity to RARb than to a or c isotypes. The structural differences between the three RAR ligand-binding pockets revealed a rationale explaining how a single retinoid can be at the same time an RARa, c antagonist and an RARb agonist. In addition, we demonstrate how to generate an RARb antagonist by gradually modifying the bulkiness of a single substitution. Together, our results provide structural guidelines for the synthesis of RARb-selective agonists and antagonists, allowing for the first time to address pharmacologically the tumour suppressor role of RARb in vitro and in animal models.

The molecular basis of the interactions between synthetic retinoic acid analogues and the retinoic acid receptors

“…Therefore, given the orientation of EC19 towards this cavity, as predicted by docking, one can predict that the molecule exhibits specificity towards RARβ. 20,43 10 | J. Name., 2012, 00, 1-3 This journal is © The Royal Society of Chemistry 20xx…”

“…13,20,42 This was then used to assign a predicted ranking for each retinoid that could be tested experimentally. a A ranking for each retinoid was determined based upon: 1) the observed flexibility within the binding pocket (number of binding conformations); 2) whether the retinoid interacts with the top, bottom or both areas of the pocket around H12; 3) the perceived strength of polar contacts based on the number and distance to the polar cluster; and 4) the overall fit.…”

“…29 Accordingly, rather than docking only the lowest energy structures, all of the output conformations from the conformer distribution calculations of ATRA, 9CRA, EC23, EC23Me, EC19 and EC19Me were prepared for docking using GOLD. 30 Crystal structures were retrieved from the RCSB protein data bank as PDB files (3KMR 31 for RARα, 1XAP 20 for RARβ and 2LBD 13 for RARγ). The bound ligands were removed from the structures, and used only as a positional reference.…”

“…18,19 These divergent residues account for the observed selectivity of the different retinoic acids towards binding with RARα, β and γ, and have been exploited to inform the design of a variety of isotype-specific synthetic retinoids. 3,20,21 The second endogenous ligand for the RARs is 9CRA, a cisisomer of ATRA, which acts as an agonist for both RARs and a second class of retinoic acid receptor, the retinoid X-receptors, (RXR). [22][23][24] Crystallographic studies of the LBDs of both types of receptor show that although the overall architecture of RARs and RXRs is very similar, the shape of the ligand binding pocket differs markedly between RARs and RXRs.…”

Synthesis and applications of 2,4-disubstituted thiazole derivatives as small molecule modulators of cellular development

“…7 A 3D comparison of the RAR LBDs found that the RARβ binding site was significantly larger due to the presence of 20 an additional cavity between H5 and H10 caused by the position of the I 263 side chain. 8 It may be postulated, therefore, that ligands with larger side-chains are able to occupy the additional space within the RARβ retinoid binding site and hence, may acquire selectivity for this subtype. 25 Differential promoter usage and alternative splicing produce the different isoforms observed with each RAR subtype; the RARβ gene has four isoforms: β1-4.…”