Designed Spiroketal Protein Modulation

Abstract

Spiroketals are structural motifs found in many biologically active natural products,w hich has stimulated considerable efforts towardtheir synthesis and interest in their use as drug lead compounds.D espite this,t he use of spiroketals,a nd especially bisbenzanulated spiroketals,i n astructure-based drug discovery setting has not been convincingly demonstrated. Herein, we report the rational design of ab isbenzannulated spiroketal that potently binds to the retinoid Xr eceptor (RXR) therebyi nducing partial coactivator recruitment. We solved the crystal structure of the spiroketal-hRXRa-TIF2 ternary complex, and identified ac anonical allosteric mechanism as ap ossible explanation for the partial agonist behavior of our spiroketal. Our cocrystal structure,t he first of ad esigned spiroketal-protein complex, suggests that spiroketals can be designed to selectively target other nuclear receptor subtypes.

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

“…The binding of agonists to NRs induces the structural changes in the C-terminal region, especially in helix 12, and bring it to the folded form to recruit a coactivator efficiently [6], whereas an antagonist binding stabilizes the same region in the extended form by establishing a tetrameric structure [21]. Unlike a 'folded' type homodimer structure identified for a partial agonist-bound hRXRa-LBD in a recent study [25], the crystal structure of the hRXRa-LBD/CBt-PMN complex reported here has a tetrameric structure with an extended form of C-terminal helix with the ligand in two different rotational conformations. The conformation of CBt-PMN in subunit A1 is similar to that of bexarotene in the 'folded' form of hRXRa and the MD simulations clearly indicate that the conformation of the C-terminal helix changes to the folded form immediately in this subunit (Fig.…”

“…Meanwhile, hRXRα‐LBD bound to partial agonists have been shown to have a dimer form with a ‘folded’ AF‐2 interface , similar to that of the typical agonist‐bound structure. Unfortunately, the dynamics of the AF‐2 interface, whose conformation plays the most important role in the transactivity of RXR, remains not completely clear although a few studies in the past made considerable progress .…”

“…Crystal structures of apo and various modulatorbound ligand-binding domain (LBD) of human RXRa (hRXRa) were reported in the past [16][17][18][19][20][21][22][23][24][25]. They can largely be classified into two types according to their conformation of the AF-2 interface in the C-terminal region; the 'folded' or 'extended' form.…”