title: Recognition of HIV-TAR RNA using neomycin-benzimidazole conjugates.
abstract: Synthesis of a novel class of compounds and their biophysical studies with TAR-RNA are presented. The synthesis of these compounds was achieved by conjugating neomycin, an aminoglycoside, with benzimidazoles modeled from a B-DNA minor groove binder, Hoechst 33258. The neomycin-benzimidazole conjugates have varying linkers that connect the benzimidazole and neomycin units. The linkers of varying length (5-23 atoms) in these conjugates contain one to three triazole units. The UV thermal denaturation experiments showed that the conjugates resulted in greater stabilization of the TAR-RNA than either neomycin or benzimidazole used in the synthesis of conjugates. These results were corroborated by the FID displacement and tat-TAR inhibition assays. The binding of ligands to the TAR-RNA is affected by the length and composition of the linker. Our results show that increasing the number of triazole groups and the linker length in these compounds have diminishing effect on the binding to TAR-RNA. Compounds that have shorter linker length and fewer triazole units in the linker displayed increased affinity towards the TAR RNA.
authors.affiliation: Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States.
authors.forename: Nihar
authors.initials: N
authors.lastname: Ranjan
authors.forename: Sunil
authors.initials: S
authors.lastname: Kumar
authors.forename: Derrick
authors.initials: D
authors.lastname: Watkins
authors.forename: Deyun
authors.initials: D
authors.lastname: Wang
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Appella
authors.forename: Dev P
authors.initials: DP
authors.lastname: Arya
mesh_terms: D001562:Benzimidazoles / Q000737:chemistry*; D006690:Bisbenzimidazole / Q000737:chemistry / Q000378:metabolism; D002942:Circular Dichroism; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D008024:Ligands; D009355:Neomycin / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000037:antagonists & inhibitors / Q000378:metabolism
chemical_list: D001562:Benzimidazoles; D008024:Ligands; D012367:RNA, Viral; D054322:tat Gene Products, Human Immunodeficiency Virus; C031000:benzimidazole; D009355:Neomycin; D006690:Bisbenzimidazole
keywords: Aminoglycosides; Benzimidazole; CD; FID; MALDI-TOF; NA; ND; NMR; Neomycin; TAR; UV; circular dichroism; fluorescent intercalators displacement; matrix assisted laser desorption and ionization-time of flight; not available; not determined; nuclear magnetic resonance; tat-TAR inhibition; trans activating region; ultra violet