title: Rational ligand design for RNA: the role of static structure and conformational flexibility in target recognition.
abstract: The role of static structure and conformational flexibility in the recognition of RNA targets by small molecule ligands is discussed with emphasis on the natural aminoglycoside antibiotics and their promiscuity in RNA target binding. A brief overview is given of previous efforts to design simplified aminoglycoside derivatives targeted at the bacterial decoding site RNA.
authors.affiliation: Department of Computational Chemistry and Structure, Anadys Pharmaceuticals, Inc., 9050 Camino Santa Fe, San Diego, CA 92121, USA. thermann@anadyspharma.com
authors.forename: Thomas
authors.initials: T
authors.lastname: Hermann
mesh_terms: D000617:Aminoglycosides; D000818:Animals; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology*; D001665:Binding Sites; D015195:Drug Design; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000187:drug effects / Q000378:metabolism; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D008024:Ligands; D012335:RNA, Ribosomal; D014867:Water; D012313:RNA