title: Identification of ligand binding site on RXRγ using molecular docking and dynamics methods.
abstract: Retinoid X receptors (RXRα, β and γ) are recently known to be cancer chemotherapies targets. The ligand binding domains of RXRs have been crystallized, but the information of RXRγ ligand binding site is not yet available due to the lack of liganded complex. A thorough understanding of the ligand binding sites is essential to study RXRs and may result in cancer therapeutic breakthrough. Thus we aimed to study the RXRγ ligand binding site and find out the differences between the three subtypes. Alignment and molecular simulation were carried out for identifying the RXRγ ligand binding site, characterizing the RXRγ ligand binding mode and comparing the three RXRs. The result has indicated that the RXRγ ligand binding site is defined by helices H5, H10, β-sheet s1 and the end loop. Besides hydrophobic interactions, the ligand 9-cis retinoic acid interacts with RXRγ through a hydrogen bond with Ala106, a salt bridge with Arg95 and the π-π interactions with Phe217 and Phe218. The binding modes exhibit some similarities among RXRs, such as the interactions with Arg95 and Ala106. Nonetheless, owing to the absence of Ile47, Cys48, Ala50, Ala51 and residues 225∼237 in the active site, the binding pocket in RXRγ is two times larger than those of RXRα and RXRβ. Meanwhile, spatial effects of Trp84, Arg95, Ala106, Phe217 and Phe218 help to create a differently shaped binding pocket as compared to those of RXRα and RXRβ. Consequently, the ligand in RXRγ undergoes a "standing" posing which is distinct from the other two RXRs.
authors.affiliation: Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, Tianjin, People's Republic of China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhao
authors.forename: Qing-hua
authors.initials: QH
authors.lastname: Liao
authors.forename: Cheng-Feng
authors.initials: CF
authors.lastname: Ren
authors.forename: Jing
authors.initials: J
authors.lastname: Wei
mesh_terms: D000077556:Alitretinoin; D000595:Amino Acid Sequence; D001665:Binding Sites; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D047490:Retinoid X Receptor alpha / Q000737:chemistry; D049230:Retinoid X Receptor beta / Q000737:chemistry; D047491:Retinoid X Receptor gamma / Q000737:chemistry*; D016415:Sequence Alignment; D014212:Tretinoin / Q000737:chemistry*
chemical_list: D047490:Retinoid X Receptor alpha; D049230:Retinoid X Receptor beta; D047491:Retinoid X Receptor gamma; D000077556:Alitretinoin; D014212:Tretinoin