title: Exploratory Study on the RNA-Binding Structural Motifs by Library Screening Targeting pre-miRNA-29 a.
abstract: The metabolic stream of microRNA (miRNA) production, the so-called maturation process of miRNAs, became one of important metabolic paths for drug-targeting to modulate the expression of genes related to a number of diseases. We carried out discovery studies on small molecules binding to the precursor of miR-29a (pre-miR-29a) from a chemical library containing 41,119 compounds (AQ library) by the fluorescent indicator displacement (FID) assay using the xanthone derivative X2SdiMe as a fluorescent indicator. The FID assay provided 1075 compounds, which showed an increase of fluorescence. These compounds were subsequently submitted to a binding analysis in a surface plasmon resonance (SPR) assay on a pre-miR-29a immobilized surface. 21 hit compounds were identified with a good reproducibility in the binding. These compounds have not been reported to bind to RNA until now and can be classified into two groups on the basis of the kinetics in the binding. To gain more information on the motif structures that could be necessary for the binding to pre-miR-29a, 19 substructures were selected from the hit compounds. The substructure library (SS library) which consisted of 362 compounds was prepared from the AQ library. An SPR assay of the SS library on pre-miR-29a-immobilized surface suggested that five substructures could potentially be important structural motifs to bind to pre-miR-29a. These studies demonstrate that the combination of FID-based screening of chemical library and subsequent SPR assay would be one way for obtaining practical solutions for the discovery of molecules which bind to the target pre-miRNAs.
authors.affiliation: Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047 (Japan).
authors.forename: Takeo
authors.initials: T
authors.lastname: Fukuzumi
authors.affiliation: Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047 (Japan).
authors.forename: Asako
authors.initials: A
authors.lastname: Murata
authors.affiliation: Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047 (Japan).
authors.forename: Haruo
authors.initials: H
authors.lastname: Aikawa
authors.affiliation: Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047 (Japan).
authors.forename: Yasue
authors.initials: Y
authors.lastname: Harada
authors.affiliation: Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047 (Japan). nakatani@sanken.osaka-u.ac.jp.
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Nakatani
mesh_terms: D015723:Gene Library; D006801:Humans; D008403:Mass Screening; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism*; D059372:Nucleotide Motifs / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D054852:Small Molecule Libraries; D020349:Surface Plasmon Resonance
chemical_list: D035683:MicroRNAs; D016601:RNA-Binding Proteins; D054852:Small Molecule Libraries
keywords: RNA; displacement assay; screening; small molecule; surface plasmon resonance