Bisintercalating Threading Diacridines:  Relationships between DNA Binding, Cytotoxicity, and Cell Cycle Arrest

Abstract

We have synthesized a series of bis(9-aminoacridine-4-carboxamides) linked via the 9-position with neutral flexible alkyl chains, charged flexible polyamine chains, and a semirigid charged piperazine-containing chain. The carboxamide side chains comprise N,N-dimethylaminoethyl and ethylmorpholino groups. The compounds are designed to bisintercalate into DNA by a threading mode, in which the side chains are intended to form hydrogen-bonding contacts with the O6/N7 atoms of guanine in the major groove, and the linkers are intended to lie in the minor groove. By this means, we anticipate that they will dissociate slowly from DNA, and be cytotoxic as a consequence of template inhibition of transcription. The dimers remove and reverse the supercoiling of closed circular DNA with helix unwinding angles ranging from 26 degrees to 46 degrees, confirming bifunctional intercalation in all cases, and the DNA complexes of representative members dissociate many orders of magnitude more slowly than simple aminoacridines. Cytotoxicity for human leukemic CCRF-CEM cells was determined, the most active agents having IC(50) values of 35-50 nM in a range extending over 20-fold, with neither the dimethylaminoethyl nor the ethylmorpholino series being intrinsically more toxic. In common with established transcription inhibitors, the morpholino series, with one exception, have no effect on cell cycle distribution in randomly dividing CCRF-CEM populations. By contrast, the dimethylaminoethyl series, with two exceptions, cause G2/M arrest in the manner of topoisomerase poisons, consistent with possible involvement of topoisomerases in their mode of action. Thus, the cellular response to these bisintercalating threading agents is complex and appears to be determined by both their side chain and linker structures. There are no simple relationships between structure, cytotoxicity, and cell cycle arrest, and the origins of this complexity are unclear given that the compounds bind to DNA by a common mechanism.

Novel fluorinated benzimidazole-based scaffolds and their anticancer activity in vitro

“…Subsequently, we investigated the preparation of linked benzimidazole derivative 5 [28] (Scheme 2) as a nucleophilic partner to add to pentafluoropyridine to form tethered heterocyclic scaffolds, as linked compounds [29] were of interest due to their potential for acting as bis-intercalating [30,31] and cross linking agents [32,33,34] for DNA binding. The bis-benzimidazole 5 (Scheme 2) (X-ray structure shown in Figure 2), with a four-methylene spacer chain, reacted readily with excess pentafluoropyridine 2, in the presence of sodium hydride, to form 6.…”

Considerations for Treatment Development in Rhabdomyosarcoma: In Vitro Assessment of Novel DNA Binding Drugs

“…In doing so it was our intention to identify agents with the potential to expand treatment options for RMS patients and further improve the efficacy of chemotherapy protocols that utilize general cytotoxic agents. Each of the novel compounds assessed in this study contain tricyclic carboxamide moieties that act as DNA intercalating chromophores and have previously been shown to be cytotoxic in leukaemia and/or solid tumour cell lines (Wakelin et al, 2003;Baguley et al, 1995;Atwell et al, 1984). One group of novel transcription inhibitors ( Figure 1A) contain dual intercalating chromophores that are joined via their 9-amino groups by linker chains of various structures and contain N,N-dimethylaminoethyl (DMAE) active side chains.…”

“…One group of novel transcription inhibitors ( Figure 1A) contain dual intercalating chromophores that are joined via their 9-amino groups by linker chains of various structures and contain N,N-dimethylaminoethyl (DMAE) active side chains. These agents bind to DNA in a bisintercalating threading fashion inspired by the binding mechanism of nogalamycin (Wakelin et al, 2003). In this design the carboxamide sidechains spear the DNA helix and make bonding interactions with guanine bases in the major groove to promote transcription inhibition by enhancing DNA residence time without increasing binding affinity.…”

“…In this design the carboxamide sidechains spear the DNA helix and make bonding interactions with guanine bases in the major groove to promote transcription inhibition by enhancing DNA residence time without increasing binding affinity. This is a desirable characteristic for activity in solid tumours where tumour penetration correlates inversely with DNA binding affinity (Wakelin et al, 2003). Differences in these compounds are found in their linker chains with flexibility, charge and length all varying.…”

“…Differences in these compounds are found in their linker chains with flexibility, charge and length all varying. With the linker chains laying in the minor groove of the DNA helix they play a crucial role in the overall activity of the compound by placing a physical block in the path of DNA tracking enzymes (Wakelin et al, 2003). The second class of transcription inhibitors ( Figure 1B,C) contain representatives of phenazine-1-carboxamide dimers bridged via their side chains with alkylamino linkers of various structures (Spicer et al, 2000).…”