title: Docking simulations suggest that all-trans retinoic acid could bind to retinoid X receptors.
abstract: Retinoid X receptors (RXRs) are ligand-controlled transcription factors which heterodimerize with other nuclear receptors to regulate gene transcriptions associated with crucial biological events. 9-cis retinoic acid (9cRA), which transactivates RXRs, is believed to be an endogenous RXR ligand. All-trans retinoic acid (ATRA) is a natural ligand for retinoic acid receptors (RARs), which heterodimerize with RXRs. Although the concentration of 9cRA in tissues is very low, ATRA is relatively abundant and some reports show that ATRA activates RXRs. We computationally studied the possibility of ATRA binding to RXRs using two different docking methods with our developed programs to assess the binding affinities of naturally occurring retinoids. The simulations showed good correlations to the reported binding affinities of these molecules for RXRs and RARs.
authors.affiliation: Institute of Molecular Function, 2-105-14 Takasu, Misato-shi, Saitama, 341-0037, Japan. motonori@molfunction.com.
authors.forename: Motonori
authors.initials: M
authors.lastname: Tsuji
authors.affiliation: Japan Pharmaceutical Information Center, 2-12-15 Shibuya, Shibuya-ku, Tokyo, 150-0002, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Shudo
authors.affiliation: Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kagechika
mesh_terms: D000077556:Alitretinoin; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D006801:Humans; D015474:Isotretinoin / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D051379:Mice; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D018168:Receptors, Retinoic Acid / Q000737:chemistry / Q000378:metabolism*; D015203:Reproducibility of Results; D047488:Retinoid X Receptors / Q000737:chemistry / Q000378:metabolism*; D014212:Tretinoin / Q000737:chemistry / Q000378:metabolism*
chemical_list: D008024:Ligands; D018168:Receptors, Retinoic Acid; D047488:Retinoid X Receptors; D000077556:Alitretinoin; D014212:Tretinoin; D015474:Isotretinoin
keywords: 13-cis retinoic acid; 9-cis retinoic acid; All-trans retinoic acid; Docking simulation; Retinoic acid receptors; Retinoid X receptors