Structural basis for engineering of retinoic acid receptor isotype-selective agonists and antagonists

Selective retinoids and rexinoids in cancer therapy and chemoprevention

Natural and synthetic retinoids are effective inhibitors of tumor cell growth in vitro and in vivo. However, the toxicity of natural derivatives of vitamin A limits their therapeutic use. Recently, synthetic compounds selective for the different retinoid receptor isotypes have been generated that circumvent pan-retinoid toxicity. The tumor-suppressive activity of selective retinoid and/or rexinoid ligands has been established preclinically, and emerging clinical trials are supportive of the chemotherapeutic and chemopreventive potential of these compounds in multiple oncology indications, with reduced toxicity. Moreover, the combination of retinoids and/or rexinoids with chemotherapeutic agents for the synergistic modulation of specific pathways could also be of benefit in cancer therapy.

RAR-RXR selectivity and biological activity of new retinoic acid analogues with heterocyclic or polycyclic aromatic systems

The cell biological activity of novel retinoids and rexinoids is described. The stereochemistry of the new compounds was analyzed and ligand docking experiments revealed the structural basis of their RAR binding characteristics. The new ligands activate nuclear retinoic acid receptors (RAR, RXR) with distinct selectivity patterns, as determined in genetically engineered 'reporter' cells. The biological activity of the novel retinoids was assessed by differentiation of NB4 acute promyelocytic leukemia cells.

Synthetic retinoids dissociate coactivator binding from corepressor release

The ligand-activated retinoid receptors RXR and RAR control development, homeostasis and disease by regulating transcription of retinoic acid (RA) responsive target genes or crosstalk with other signalling pathways. According to the current model ligand-binding triggers an exchange between corepressor- and coactivator-complexes that inhibit or potentiate transcription by deacetylating and acetylating nucleosomal histones, respectively. Additional cofactors may modify the transcriptional regulatory process by linking liganded retinoid receptors to structural components of chromatin or protein degradation. The desire to specifically influence defined events in RA-signalling, while others are left unaffected, motivated the synthesis of retinoid X receptors (RXR)- and retinoid acid receptors (RAR) isoform-selective retinoids. The present study investigates the potential of RARalpha isotype-specific synthetic agonists and antagonists to separate the processes of coactivator recruitment and corepressor release. The synthetic retinoids studied fall into four categories, two of which work according the above model, since they induce surfaces within the RARalpha ligand binding domain (LBD) suitable for either corepressor or coactivator interaction; these retinoids act as pure antagonists and pure agonists, respectively. In contrast, another type of retinoid induces a structure that allows for both, the interaction with corepressors and coactivators (partial RARalpha agonist), and exerts a cell context-specific (ant)agonistic activity. Finally, another type of retinoid, which cannot activate transcription itself but renders heterodimeric RARalpha permissive for signaling by RXR agonists inhibits both, corepressor and coactivator interaction (partial antagonist). Moreover, this retinoid discriminates between the nuclear corepressors SMRT and NCoR, since it efficiently dissociates SMRT but not NCoR from the RARalpha LBD.

Retinoic acid-induced apoptosis in leukemia cells is mediated by paracrine action of tumor-selective death ligand TRAIL

The therapeutic and preventive activities of retinoids in cancer are due to their ability to modulate the growth, differentiation, and survival or apoptosis of cancer cells. Here we show that in NB4 acute promyelocytic leukemia cells, retinoids selective for retinoic-acid receptor-alpha induced an autoregulatory circuitry of survival programs followed by expression of the membrane-bound tumor-selective death ligand, TRAIL (tumor necrosis factor-related apoptosis-inducing ligand, also called Apo-2L). In a paracrine mode of action, TRAIL killed NB4 as well as heterologous and retinoic-acid-resistant cells. In the leukemic blasts of freshly diagnosed acute promyelocytic leukemia patients, retinoic-acid-induced expression of TRAIL most likely caused blast apoptosis. Thus, induction of TRAIL-mediated death signaling appears to contribute to the therapeutic value of retinoids.

Conformational changes and coactivator recruitment by novel ligands for estrogen receptor-alpha and estrogen receptor-beta: correlations with biological character and distinct differences among SRC coactivator family members

Ligands for the estrogen receptor (ER) that have the capacity to selectively bind to or activate the ER subtypes ERalpha or ERbeta would be useful in elucidating the biology of these two receptors and might assist in the development of estrogen pharmaceuticals with improved tissue selectivity. In this study, we examine three compounds of novel structure that act as ER subtype-selective ligands. These are a propyl pyrazole triol (PPT), which is a potent agonist on ERalpha but is inactive on ERbeta, and a pair of substituted tetrahydrochrysenes (THC), one enantiomer of which (S,S-THC) is an agonist on both ERalpha and ERbeta, the other (R,R-THC) being an agonist on ERalpha but an antagonist on ERbeta. To investigate the molecular mechanisms underlying the ER subtype-selective actions of these compounds, we have determined the conformational changes induced in ERalpha and ERbeta by these ligands using protease digestion sensitivity, and we have tested the ability of these ligands to promote the recruitment of representatives of the three SRC/p160 coactivator protein family members (SRC-1, GRIP-1, ACTR, respectively) to ERalpha and ERbeta using yeast two-hybrid and glutathione-S-transferase (GST) pull-down assays. We find that the ligand-ER protease digestion pattern is distinctly different for stimulatory and inhibitory ligands, and that this assay, as well as coactivator recruitment, are excellent indicators of their agonist/antagonist character. Interestingly however, compared with estradiol, the novel agonist ligands show some quantitative differences in their ability to recruit SRC-1, -2, and -3. This implies that while generally similar to estradiol, these ligands induce ER conformations that differ somewhat from that induced by estradiol, differences that are illustrative of the nature of their biological character. The application of methods to characterize the conformations induced in ER subtypes by novel ligands, as done in this study, enables a greater understanding of how ligand-receptor conformations relate to estrogen agonist or antagonist behavior.

Nuclear receptor ligand-binding domains: three-dimensional structures, molecular interactions and pharmacological implications

Nuclear receptors are members of a large family of ligand-inducible transcription factors that regulate gene programs underlying a plethora of (patho)physiological phenomena. The recent determination of the crystal structures of nuclear receptor ligand-binding domains has provided an extremely detailed insight into the intra- and intermolecular mechanisms that constitute the initial events of receptor activation and signal transduction. Here, a comprehensive mechanistic view of agonist and antagonist action will be presented. Furthermore, the novel class of partial agonists-antagonists will be described and the multiple challenges and novel perspectives for nuclear-receptor-based drug design will be discussed.

Structural basis for isotype selectivity of the human retinoic acid nuclear receptor

The human retinoic acid receptor (hRAR) belongs to the family of nuclear receptors that regulate transcription in a ligand-dependent way. The isotypes RARalpha,beta and gamma are distinct pharmacological targets for retinoids that are involved in the treatment of various skin diseases and cancers, in particular breast cancer and acute promyelocytic leukemia. Therefore, synthetic retinoids have been developed aiming at isotype selectivity and reduced side-effects. We report the crystal structures of three complexes of the hRARgamma ligand-binding domain (LBD) bound to agonist retinoids that possess selectivity either for RARgamma (BMS184394) or for RARbeta/gamma (CD564), or that are potent for all RAR-isotypes (panagonist BMS181156). The high resolution data (1.3-1. 5 A) provide a description at the atomic level of the ligand pocket revealing the molecular determinants for the different degrees of ligand selectivity. The comparison of the complexes of the chemically closely related retinoids BMS184394 and CD564 shows that the side-chain of Met272 adopts different conformations depending on the presence of a hydrogen bond between its sulfur atom and the ligand. This accounts for their different isotype selectivity. On the other hand, the difference between the pan- and the RARbeta, gamma-selective agonist is probably due to a steric discrimination at the level of the 2-naphthoic acid moiety of CD564. Based on this study, we propose a model for a complex with the RARgamma-specific agonist CD666 that shows the possible applications for structure-based drug design of RAR isotype-selective retinoids.

Role of Ser(289) in RARgamma and its homologous amino acid residue of RARalpha and RARbeta in the binding of retinoic acid

The biological actions of retinoic acid (RA) are mediated by retinoic acid receptors (RARalpha, -beta, and -gamma) and retinoid X receptors (RXRalpha, -beta, and -gamma). Although the ligand-binding domains of RARs and RXRs have been suggested to share the same novel folding pattern, the ligand-binding pockets of each of the retinoid receptors must have unique structural features since it has been possible to develop RAR subtype-selective and RXR-selective retinoids. We have previously demonstrated the importance for RA binding and RA-dependent transactivation of Arg(276) in RARalpha and Arg(278) in RARgamma; however, in RARbeta Arg(269) functions in conjunction with Lys(220). Here we have examined the role of the hydroxyl group of RARgamma Ser(289) and its homologous amino acid residues in RARalpha (Ser(287)) and RARbeta (Ser(280)) alone and in conjunction with their respective RARgamma Arg(278) homologs for RA binding and RA-dependent transactivation activity. The hydroxyl group of this Ser in all three RARs was found by itself not to be important for RA binding and RA-dependent transactivation activity. However, in RARalpha and RARgamma this Ser appears to play a small role in conjunction with Arg(276) and Arg(278), respectively, for these activities. Alternatively, strong synergism was observed in RARbeta between Ser(280) and Arg(269) for RA-binding and RA-dependent transactivation activity. This provides further evidence that the mechanism of interaction between the carboxylate group of retinoids and the amino acid residues in the ligand binding pocket of RARbeta is different from that of RARalpha and RARgamma.

Heterodimeric complex of RAR and RXR nuclear receptor ligand-binding domains: purification, crystallization, and preliminary X-ray diffraction analysis

Both the human retinoic acid receptor alpha (hRARalpha) and a constitutively active mutant (F318A) of the mouse retinoid X receptor alpha (mRXR alpha F318A) ligand-binding domains were separately overexpressed in Escherichia coli, copurified as a heterodimer in a two-step procedure, and cocrystallized with an RAR alpha-specific antagonist by using polyethylene glycol 10,000 as precipitant. The crystals grew in the hexagonal space group P6(1)22 displaying the unit cell parameters a = b = 116.6 A and c = 207.8 A. They diffracted X-ray to a limit of 2.2-A resolution. The asymmetric unit comprises one heterodimer and the crystal contains 60% solvent. The structure was determined by molecular replacement and is currently being refined.

Ligand-protein interactions in nuclear receptors of hormones

Nuclear hormone receptors are transcription factors regulated by lipophilic ligands. These hormones bind to their nuclear receptor targets using an induced fit mechanism that triggers a large conformational change and generates the proper surface for the binding of protein coactivators. The molecular details of the various steps of this activation process or its inhibition by antagonists are now understood for several nuclear receptors.

Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains

The crystal structure of a heterodimer between the ligand-binding domains (LBDs) of the human RARalpha bound to a selective antagonist and the constitutively active mouse RXRalphaF318A mutant shows that, pushed by a bulky extension of the ligand, RARalpha helix H12 adopts an antagonist position. The unexpected presence of a fatty acid in the ligand-binding pocket of RXRalpha(F318A is likely to account for its apparent "constitutivity." Specific conformational changes suggest the structural basis of pure and partial antagonism. The RAR-RXR heterodimer interface is similar to that observed in most nuclear receptor (NR) homodimers. A correlative analysis of 3D structures and sequences provides a novel view on dimerization among members of the nuclear receptor superfamily.

Ligand selectivity by nuclear hormone receptors

Abstract Numerous crystal structures of nuclear receptor ligand binding domains (LBDs) are known. The retinoic acid (RAR) and estrogen (ER) receptors are the two members for which a large set of agonists and antagonist complexes are available. Their analysis reveals key features of the RAR and ER ligand binding pocket (LBP) responsible for ligand selectivity. The RAR LBD exhibits a rigid architecture to which the ligand has to adapt, whereas the ER LBD can accomodate numerous ligands of variable shapes.