Minireview: Not picking pockets: nuclear receptor alternate-site modulators (NRAMs)

Abstract

Because of their central importance in gene regulation and mediating the actions of many hormones, the nuclear receptors (NRs) have long been recognized as very important biological and pharmaceutical targets. Of all the surfaces available on a given NR, the singular site for regulation of receptor activity has almost invariably been the ligand-binding pocket of the receptor, the site where agonists, antagonists, and selective NR modulators interact. With our increasing understanding of the multiple molecular components involved in NR action, researchers have recently begun to look to additional interaction sites on NRs for regulating their activities by novel mechanisms. The alternate NR-associated interaction sites that have been targeted include the coactivator-binding groove and allosteric sites in the ligand-binding domain, the zinc fingers of the DNA-binding domain, and the NR response element in DNA. The studies thus far have been performed with the estrogen receptors, the androgen receptor (AR), the thyroid hormone receptors, and the pregnane X receptor. Phenotypic and conformation-based screens have also identified small molecule modulators that are believed to function through the NRs but have, as yet, unknown sites and mechanisms of action. The rewards from investigation of these NR alternate-site modulators should be the discovery of new therapeutic approaches and novel agents for regulating the activities of these important NR proteins.

Figure 1

Illustration of the different interaction sites for the regulation of NR activity. Multicolor and multimode rendered diagram of a representative NR heterodimer [retinoid X receptor α (yellow)/peroxisome proliferator-activated receptor γ (black)], showing one of two ligands [rosiglitazone (blue)], two of four zinc ions (red) in the zinc fingers, a DNA response element (green), and sequences from a NR interaction box [NR-box (violet)] of SRC 2. (Figure prepared from PDB accession code 3DZY).

Figure 2

Ribbon diagrams of three NR ligand-binding domains illustrating different interaction sites. A, ERα (blue) liganded with diethylstilbestrol (red) in the ligand-binding pocket showing interaction of an SRC coactivator peptide (magenta) in the coactivator-binding groove. B, TRβ (green) liganded with T₃ (red) and Michael acceptor HPPE (gray/cyan). The sulfhydryl group of cysteine residue 298 (yellow) later forms a covalent bond with the α,β-unsaturated ketone group (shown in cyan) of HPPE. C, AR (lavender) liganded with DHT (red), with flufenamic acid (orange) located at binding function 3. (Panels A, B, and C prepared from PDB accession codes 3ERD, 2PIN, and 2PIX, respectively).

Figure 3

ER coactivator-binding inhibitors.

Figure 4

TR coactivator-binding inhibitors.

Figure 5

Representation of coactivator-binding grooves of ERα ligand-binding domain (A) bound to an LXXLL motif (yellow) and AR ligand-binding domain (B) bound to an FXXLF motif (green). A distance map (red = 0.5 Å; dark gray > 7 Å) from the backbone of the coactivator helix has been applied to the surface of each receptor, demonstrating that the interior of the ER groove is shallower (pink), on average, than that of the AR (gray). The charge clamp residues (K362/E542 for ER and K720/E897 for androgen receptor) are denoted. (Figure prepared using PDB accession codes 3ERD and 1XOW.)

Figure 6

PXR coactivator-binding inhibitors.

Figure 7

AR-binding function 3 inhibitors.

Figure 8

ERE- and ARE-binding inhibitors.

Figure 9

ER zinc finger-binding inhibitors.

Figure 10

AR antagonists/inverse agonists that function at unknown binding sites.