Ligand Dependent Switch from RXR Homo- to RXR-NURR1 Heterodimerization

Abstract

Retinoid X receptors (RXRs) play key roles in many physiological processes in both the periphery and central nervous system. In addition, RXRs form heterodimers with other nuclear receptors to exert their physiological effects. The nuclear receptor related 1 protein (NURR1) is particularly interesting because of its role in promoting differentiation and survival of dopamine neurons. However, only a small number of RXR-heterodimer selective modulators are available, with limited chemical diversity. This work describes the synthesis, biochemical evaluation, and structural elucidation of a novel series of RXR ligands with strongly biased interactions with RXRα–NURR1 heterodimers. Targeted modifications to the small molecule biaryl scaffold caused local RXRα side-chain disturbances and displacement of secondary structural elements upon ligand binding. This resulted in the repositioning of protein helices in the heterodimer interface of RXRα, alterations in homo- versus heterodimer formation, and modulation of activation function 2 (AF2). The data provide a rationale for the design of RXR ligands consisting of a highly conserved hydrophilic region, strongly contributing to the ligand affinity, and a variable hydrophobic region, which efficiently probes the effects of structural changes at the level of the ligand on co-regulator recruitment or the RXRα–NURR1 dimerization interface.

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

“…Heterodimer- and subtype-specific targeting has been proposed as a strategy to overcome this, yet high sequence similarity between the three human RXR isoforms presents a challenge for the design of such selective modulators. Several examples demonstrate that RXR ligands can exhibit heterodimer preference (e.g., for RXR:PPAR [ 31 , 38 , 39 , 40 ], RXR:LXR [ 41 ] and RXR:Nurr1 [ 42 ]) and even subtype preference [ 30 , 31 ] but while some structural insights in heterodimer-preference mechanisms are available, subtype preference among RXRs remains elusive. As a basis for better understanding of the three RXR isoforms and potential selectivity mechanisms, we presented here a uniform set of the crystal structures for all three RXR isoform LBDs in activated conformation, providing improved structural insights for the design of RXR modulators.…”

“…This notion was in line with previous structure–activity relationship studies on biphenyl-based RXR agonists [ 31 ], where an introduction of bulkier moieties at the terminal ring or substituents at the ortho position of the phenylacetic acid motif binding in the vicinity of helix 5, which forms an interface with helix 8, was observed to result in different affinities to the three RXR isoforms. In addition, various RXR-ligand complexes, including RXRα-LG100754 (PDB ID: 6sti) [ 43 ], RXRα-JP175 (PDB ID: 6sjm) [ 31 ], RXRα-honokiol derivative (PDB ID: 5mku) [ 42 ], RXRβ-LG100268 (PDB ID: 1h9u) [ 44 ] and RXRγ-PA, have demonstrated different conformations of helix 12 and the loop preceding this helix, feasibly required for accommodation of different ligands. Since this helix and the loop form a direct interface with helix 2, the small change from Gln270/341 in RXRα/β to His271 in RXRγ, leading to a hydrogen bond with helix 12 Asp449 in the latter, could result in a different degree of flexibility of this region, which may have an indirect effect toward the properties of the ligand-binding pockets.…”

Targeting Nuclear Receptors in Neurodegeneration and Neuroinflammation

“…423 Through N-terminal Nurr1 modulation, C-DIM derivatives may hence exhibit direct effects on Nurr1 for Scheme 9. Nurr1-RXR Heterodimer-Specific RXR Agonists Reported in the Literature 402,403,435,436,438,439 Journal of Medicinal Chemistry example in NFκB transrepression 429 (Figure 4b), but altered Nurr1 protein levels 426 and indirect mechanisms rather than direct Nurr1 transactivation via its LBD appear to dominate the effects. 351 In addition, the antimetabolite 6-MP (91) was identified as a Nurr1 activator from an HTS utilizing a full-length reporter gene assay under the control of the homodimer responsive element in CV1 cells.…”

“…The synthetic honokiol derivative 89 with a biaryl scaffold demonstrated a greater 25fold selectivity for the Nurr1-RXRα heterodimer (pEC 50 9.1, 129% efficacy) compared to the RXRα homodimer (pEC 50 7.7, 291% efficacy) determined in a BRET assay. 439 The respective cocrystal structure analysis indicated that compact ligands, allowing movement of helix 7 and 11, favor RXRα heterodimerization with Nurr1 (pdb 5MKU), whereas ligands with substituents in the 2′ position on the biaryl scaffold induced pocket expansion with helix 12 movement, resulting in lower binding affinity or antagonistic behavior (pdb 5MKJ) and promoting RXRα homodimerization.…”

Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor α (RXRα)

“…Retinoid X receptor (RXR) is a member of nuclear receptor (NR) superfamily, which regulates various physiological metabolism, such as dietary lipid metabolism and nervous system , via forming homodimer or heterodimers with other NRs . Binding of small molecules to the ligand‐binding pocket (LBP) induces the conformational change of ‘AF‐2 interface’, which plays a key role in recognizing the L XX LL motifs located in coactivators .…”