Comprehensive Set of Tertiary Complex Structures and Palmitic Acid Binding Provide Molecular Insights into Ligand Design for RXR Isoforms

Abstract

The retinoid X receptor (RXR) is a ligand-sensing transcription factor acting mainly as a universal heterodimer partner for other nuclear receptors. Despite presenting as a potential therapeutic target for cancer and neurodegeneration, adverse effects typically observed for RXR agonists, likely due to the lack of isoform selectivity, limit chemotherapeutic application of currently available RXR ligands. The three human RXR isoforms exhibit different expression patterns; however, they share high sequence similarity, presenting a major obstacle toward the development of subtype-selective ligands. Here, we report the discovery of the saturated fatty acid, palmitic acid, as an RXR ligand and disclose a uniform set of crystal structures of all three RXR isoforms in an active conformation induced by palmitic acid. A structural comparison revealed subtle differences among the RXR subtypes. We also observed an ability of palmitic acid as well as myristic acid and stearic acid to induce recruitment of steroid receptor co-activator 1 to the RXR ligand-binding domain with low micromolar potencies. With the high, millimolar endogenous concentrations of these highly abundant lipids, our results suggest their potential involvement in RXR signaling.

Oxaprozin Analogues as Selective RXR Agonists with Superior Properties and Pharmacokinetics

“…Recombinant RXRα LBD was purified as previously described . The protein was incubated with the inhibitors and GRIP-1 peptide prior to crystallization using sitting drop vapor diffusion at 20 °C and the conditions described in Table S1.…”

“…Diffraction data were collected at SLS X06SA and were processed and scaled with XDS and aimless, respectively. Molecular replacement was performed using Phaser and the published coordinates of RXRα . Manual model rebuilding alternated with refinement was performed in COOT and REFMAC5 .…”

“…The nuclear retinoid X receptor (RXR) comprises a ligand-activated transcription factor family existing in three highly conserved isoforms (RXRα, NR2B1; RXRβ, NR2B2; and RXRγ, NR2B3). , The RXRs fulfill a central role in the nuclear receptor superfamily acting not only as universal heterodimer partners but also as homodimers regulating gene expression. Several fatty acids and vitamin A metabolites have been discovered as RXR agonists among which 9- cis retinoic acid ( 1 , Chart ) is the most potent ligand. − As the only approved synthetic rexinoid, bexarotene ( 2 ) is used as second-line treatment in cancer; ,, however, its use has been associated with severe adverse effects. , Considerable preclinical evidence suggests a high therapeutic potential of RXR activation to counteract neurodegenerative diseases such as multiple sclerosis − and Alzheimer’s disease. − Despite recent progress in targeting RXRs, ,− new potent RXR agonists are needed to overcome the limitations of traditional rexinoids, such as exceptional lipophilicity, poor pharmacokinetics (PK), and pronounced toxicity, ,− to further probe and exploit the highly promising pharmacological potential of RXR modulation.…”

“…The nuclear retinoid X receptor (RXR) comprises a ligandactivated transcription factor family existing in three highly conserved isoforms (RXRα, NR2B1; RXRβ, NR2B2; and RXRγ, NR2B3). 1,2 The RXRs fulfill a central role in the nuclear receptor superfamily acting not only as universal heterodimer partners but also as homodimers regulating gene expression. Several fatty acids and vitamin A metabolites have been discovered as RXR agonists among which 9-cis retinoic acid (1, Chart 1) is the most potent ligand.…”

“…It has preferable aqueous solubility (3: 13.3 mg/L; bexarotene (2): 0.3 mg/L 20 ), favorable PK, and clinically confirmed safety. These features render 3 a superior lead to develop potent RXR activators with improved characteristics compared to bexarotene (2) and other known RXR ligand chemotypes. Following the concept of selective optimization of side-activities (SOSA), 27 bexarotene (2) in terms of lipophilicity, cytotoxicity, and pharmakokinetic parameters.…”