Increased Molecular Flexibility Widens the Gap between and values in Screening for Retinoid X Receptor Modulators.

Screening for small-molecule modulators targeting a particular receptor is frequently based on measurement of , i.e., the binding constant between the receptor and the compound of interest. However, values also reflect binding at receptor protein sites other than the modulatory site. We designed derivatives of retinoid X receptor (RXR) antagonist CBTF-EE () with modifications that altered their conformational flexibility. Compounds , and , showed quite similar values, but , exhibited 10-fold higher values than those of ,. Further, , showed potent RXR-antagonistic activity, while , were inactive. These results suggest that increased conformational flexibility promotes binding at nontarget receptor sites. In this situation, conventional determination of is less effective for screening purposes than the determination of using a ligand that binds specifically to the site regulating transcriptional activity. Thus, the use of values for orthosteric ligands may increase the hit rate in screening active regulatory molecules.