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The Use of in Vitro Peptide Binding Profiles and in Silico Ligand-Receptor Interaction Profiles to Describe Ligand-Induced Conformations of the Retinoid X Receptor Ligand-Binding Domain

Centre for Molecular and Biomolecular Informatics (S.F., G.V., J.d.V.), University of Nijmegen, 6500 GL Nijmegen, The Netherlands; and Organon NV (P.I.v.N., A.d.H., P.C., R.B., A.V., J.d.V.), 5340 BH Oss, The Netherlands

Address all correspondence and requests for reprints to: Jacob de Vlieg, Organon NV, Molenstraat 110, P.O. Box 20, 5340 BH Oss, The Netherlands. E-mail: jacob.devlieg{at}organon.com; or to Simon Folkertsma, Organon NV, Molenstraat 110, P.O. Box 20, 5340 BH Oss, The Netherlands. E-mail: s.folkertsma{at}cmbi.ru.nl.

It is hypothesized that different ligand-induced conformational changes can explain the different interactions of nuclear receptors with regulatory proteins, resulting in specific biological activities. Understanding the mechanism of how ligands regulate cofactor interaction facilitates drug design. To investigate these ligand-induced conformational changes at the surface of proteins, we performed a time-resolved fluorescence resonance energy transfer assay with 52 different cofactor peptides measuring the ligand-induced cofactor recruitment to the retinoid X receptor- (RXR) in the presence of 11 compounds. Simultaneously we analyzed the binding modes of these compounds by molecular docking. An automated method converted the complex three-dimensional data of ligand-protein interactions into two-dimensional fingerprints, the so-called ligand-receptor interaction profiles. For a subset of compounds the conformational changes at the surface, as measured by peptide recruitment, correlate well with the calculated binding modes, suggesting that clustering of ligand-receptor interaction profiles is a very useful tool to discriminate compounds that may induce different conformations and possibly different effects in a cellular environment. In addition, we successfully combined ligand-receptor interaction profiles and peptide recruitment data to reveal structural elements that are possibly involved in the ligand-induced conformations. Interestingly, we could predict a possible binding mode of LG100754, a homodimer antagonist that showed no effect on peptide recruitment. Finally, the extensive analysis of the peptide recruitment profiles provided novel insight in the potential cellular effect of the compound; for the first time, we showed that in addition to the induction of coactivator peptide binding, all well-known RXR agonists also induce binding of corepressor peptides to RXR.

NURSA Molecule Pages Link:

Nuclear Receptors:   DAX1  |  SHP  |  LXRα  |  RXRα

Coregulators:   RIP140  |  TRAP220  |  PGC-1  |  LCoR  |  CBP  |  FHL2  |  SRC-1  |  GRIP1  |  AIB1  |  ARA70  |  ASC-2  |  NCOR  |  SMRT

Ligands:   LGD 100268  |  9-cis-Retinoic acid  |  Arotinoid acid

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