title: An extended pyrrolobenzodiazepine-polyamide conjugate with selectivity for a DNA sequence containing the ICB2 transcription factor binding site.
abstract: The binding of nuclear factor Y (NF-Y) to inverted CCAAT boxes (ICBs) within the promoter region of DNA topoisomerase IIα results in control of cell differentiation and cell cycle progression. Thus, NF-Y inhibitory small molecules could be employed to inhibit the replication of cancer cells. A library of pyrrolobenzodiazepine (PBD) C8-conjugates consisting of one PBD unit attached to tri-heterocyclic polyamide fragments was designed and synthesized. The DNA-binding affinity and sequence selectivity of each compound were evaluated in DNA thermal denaturation and DNase I footprinting assays, and the ability to inhibit binding of NF-Y to ICB1 and ICB2 was studied using an electrophoretic mobility shift assay (EMSA). 3a was found to be a potent inhibitor of NF-Y binding, exhibiting a 10-fold selectivity for an ICB2 site compared to an ICB1-containing sequence, and showing low nanomolar cytotoxicity toward human tumor cell lines. Molecular modeling and computational studies have provided details of the covalent attachment process that leads to formation of the PBD-DNA adduct, and have allowed the preference of 3a for ICB2 to be rationalized.
authors.affiliation: School of Science, University of the West of Scotland, Paisley, Scotland, U.K.
authors.forename: Federico
authors.initials: F
authors.lastname: Brucoli
authors.forename: Rachel M
authors.initials: RM
authors.lastname: Hawkins
authors.forename: Colin H
authors.initials: CH
authors.lastname: James
authors.forename: Paul J M
authors.initials: PJ
authors.lastname: Jackson
authors.forename: Geoff
authors.initials: G
authors.lastname: Wells
authors.forename: Terence C
authors.initials: TC
authors.lastname: Jenkins
authors.forename: Tom
authors.initials: T
authors.lastname: Ellis
authors.forename: Minal
authors.initials: M
authors.lastname: Kotecha
authors.forename: Daniel
authors.initials: D
authors.lastname: Hochhauser
authors.forename: John A
authors.initials: JA
authors.lastname: Hartley
authors.forename: Philip W
authors.initials: PW
authors.lastname: Howard
authors.forename: David E
authors.initials: DE
authors.lastname: Thurston
mesh_terms: D000818:Animals; D001569:Benzodiazepines / Q000737:chemistry*; D001665:Binding Sites; D045744:Cell Line, Tumor; D002851:Chromatography, High Pressure Liquid; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D041681:NIH 3T3 Cells; D009757:Nylons / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D009757:Nylons; D014157:Transcription Factors; D001569:Benzodiazepines; D004247:DNA