Design, Synthesis, and Biophysical and Biological Evaluation of a Series of Pyrrolobenzodiazepine−Poly(N-methylpyrrole) Conjugates

Abstract

A novel series of methyl ester-terminated C8-linked pyrrolobenzodiazepine (PBD)-poly(N-methylpyrrole) conjugates (50a-f) has been synthesized and their DNA interaction evaluated by thermal denaturation, DNA footprinting, and in vitro transcription stop assays. The synergistic effect of attaching a PBD unit to a polypyrrole fragment is illustrated by the large increase in DNA binding affinity (up to 50-fold) compared to the individual PBD and pyrrole components. 50a-f were found to bind mainly to identical DNA sequences but with apparent binding site widths increasing with molecular length and the majority of sites conforming to the consensus motif 5'-XGXWz (z = 3 +/- 1; W = A or T; X = any base but preferably a purine). They also provided robust sequence-selective blockade of transcription at sites corresponding approximately to their DNA footprints. 50a-f were shown to have good cellular/nuclear penetration properties, and a degree of correlation between cytotoxicity and DNA-binding affinity was observed.

Inhibition of DNA binding of the NF-Y transcription factor by the pyrrolobenzodiazepine-polyamide conjugate GWL-78

“…Several potential binding sites, which fit the consensus motif for GWL-78 as reported by Wells et al (18) (that is, 5 ¶-XGXWz, where z = 3 F 1, W = A or T, X = any base but preferably a purine), are evident in the DNA sequences relating to ICB1 to ICB3. One binding site example from each ICB is highlighted in bold in the sequence labels of the footprints in Fig.…”

“…The structure and chemical properties of GWL-78 have been described (18). DNA footprinting and in vitro transcription stop assay results suggest that it binds preferentially to the consensus motif 5 ¶-XGXWz (z = 3 F 1, W = A or T, X = any base but preferably a purine) and that robust sequence-selective blockade of transcription occurs at sites corresponding approximately to its DNA footprints.…”

“…DNA footprinting and in vitro transcription stop assay results suggest that it binds preferentially to the consensus motif 5 ¶-XGXWz (z = 3 F 1, W = A or T, X = any base but preferably a purine) and that robust sequence-selective blockade of transcription occurs at sites corresponding approximately to its DNA footprints. GWL-78 has also been shown to have good cellular/nuclear penetration properties, and a degree of correlation between cytotoxicity and DNA-binding affinity has been observed (18).…”

DNA sequence-selective C8-linked pyrrolobenzodiazepine–heterocyclic polyamide conjugates show anti-tubercular-specific activities

“…[21][22][23] The di-or tri-heterocyclic polyamide 80 chains of 1-12 are comprised of combinations of pyrrole (Py), imidazole (Im) and thiazole (Th) rings 81 known for their ability to modulate the ligands' DNA-binding affinity. 24 C8-linked PBD-polyamide 82 conjugates, unlike PBD dilactams, retain the ability to form covalent DNA-adducts, characteristic 83 responsible for their improved cancer cell cytotoxicity and antibacterial activities, 15 and have a more 84 favourable cytotoxicity profile compared to the PBD dimers.…”

Nuclear Localization and Gene Expression Modulation by a Fluorescent Sequence-Selective p-Anisyl-benzimidazolecarboxamido Imidazole-Pyrrole Polyamide

“…Our research groups have previously employed the topo IIa promoter as a model system for proof of principle of the ability of polyamides to modulate gene expression in cells (Tolner et al, 2001;Le et al, 2006;Wells et al, 2006;Hochhauser et al, 2007;Kotecha et al, 2008;Franks et al, 2010).…”