title: Spectroscopic and DFT studies on 6-aminophenanthridine and its derivatives provide insights in their activity towards ribosomal RNA.
abstract: 6-Aminophenanthridine (6AP), a plant alkaloid possessing antiprion activity, inhibits ribosomal RNA dependent protein folding activity of the ribosome (referred as PFAR). We have compared 6AP and its three derivatives 6AP8Cl, 6AP8CF3 and 6APi for their activity in inhibition of PFAR. Since PFAR inhibition requires 6AP and its derivatives to bind to the ribosomal RNA (rRNA), we have measured the binding affinity of these molecules to domain V of 23S rRNA using fluorescence spectroscopy. Our results show that similar to the antiprion activity, both the inhibition of PFAR and the affinity towards rRNA follow the order 6AP8CF3 > 6AP8Cl > 6AP, while 6APi is totally inactive. To have a molecular insight for the difference in activity despite similarities in structure, we have calculated the nucleus independent chemical shift using first principles density functional theory. The result suggests that the deviation of planarity in 6APi and steric hindrance from its bulky side chain are the probable reasons which prevent it from interacting with rRNA. Finally, we suggest a probable mode of action of 6AP, 6AP8CF3 and 6AP8Cl towards rRNA.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124 Uppsala, Sweden.
authors.forename: Debapriya
authors.initials: D
authors.lastname: Banerjee
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124 Uppsala, Sweden; Department of Physics and Astronomy, Uppsala University, Box-516, Ångströmlaboratoriet, 75120 Uppsala, Sweden.
authors.forename: Hakkim
authors.initials: H
authors.lastname: Vovusha
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124 Uppsala, Sweden.
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Pang
authors.affiliation: ManRos Therapeutics, Centre de Perharidy, Roscoff, Bretagne, France.
authors.forename: Nassima
authors.initials: N
authors.lastname: Oumata
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Box-516, Ångströmlaboratoriet, 75120 Uppsala, Sweden. Electronic address: biplab.sanyal@physics.uu.se.
authors.forename: Biplab
authors.initials: B
authors.lastname: Sanyal
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124 Uppsala, Sweden. Electronic address: suparna.sanyal@icm.uu.se.
authors.forename: Suparna
authors.initials: S
authors.lastname: Sanyal
mesh_terms: D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D010617:Phenanthridines / Q000737:chemistry*; D011328:Prions / Q000737:chemistry*; D017510:Protein Folding; D011789:Quantum Theory; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013329:Structure-Activity Relationship
chemical_list: C549408:6-aminophenanthridine; D010617:Phenanthridines; D011328:Prions; D012338:RNA, Ribosomal, 23S
keywords: 6-Amino 8-chloro phenanthridine; 6-Amino 8-trifluoromethyl phenanthridine; 6-Aminophenanthridine; 6AP; 6AP8CF(3); 6AP8Cl; DFT; Fluorescence; PFAR; Ribosomal RNA; density functional theory; protein folding activity of ribosome; rRNA; ribosomal RNA