Synthesis and Evaluation of an Intercalator–Polyamide Hairpin Designed to Target the Inverted CCAAT Box 2 in the Topoisomerase IIα Promoter

Abstract

The synthesis and DNA-binding properties of a novel naphthalimide-polyamide hairpin (3) designed to target the inverted CCAAT box 2 (ICB2) site on the topoisomerase IIalpha (topoIIalpha) promoter are described. The polyamide component of 3 was derived from the minor-groove binder, 2, and tailored to bind to the 5'-TTGGT sequence found in and flanking ICB2. The propensity of mitonafide 4 to intercalate between G-C base pairs was exploited by the incorporation of a naphthalimide moiety at the N terminus of 2. Hybrid 3 targeted 5'-CGATTGGT and covered eight contiguous base pairs, which included the underlined ICB2 site. DNase I footprinting analysis with the topoIIalpha promoter sequence demonstrated that 3 bound selectively to the ICB2 and ICB3 sites. Thermal-denaturation studies confirmed these results, and the highest degree of stabilization was found for ICB2 and -3 in preference to ICB1 (4.1, 4.6, and 0.6 degrees C, respectively). CD studies confirmed minor-groove binding and suggested a 1:1 binding stoichiometry. Emission-titration experiments established intercalative binding. Surface plasmon resonance results showed strong binding to ICB2 (2.5x10(7) M(-1)) with no observable binding to ICB1. Furthermore, the binding constant of 3 to ICB2 was larger than that of the parent polyamide 2. The increased binding affinity was primarily due to a reduction in the dissociation-rate constant of the polyamide-DNA complex, which can be attributed to the N-terminal naphthalimide moiety. In addition, the binding site of 3 was larger than that of 2, which innately improved sequence selectivity. We conclude that the polyamide-naphthalimide 3 selectively binds to the ICB2 site by simultaneous intercalation and minor-groove binding, and warrants further investigation as a model compound for the regulation of topoIIalpha gene expression.

Recent advances in the development of 1,8-naphthalimide based DNA targeting binders, anticancer and fluorescent cellular imaging agents

“…Another example is that of Lee et al 88 who combined the intercalation effect of the 1, Another example of the use of chromophores conjugated to peptidyl chains with the view of achieving sequence selective recognition of DNA is that of by Iverson et al 89 who developed the peptide 73 (and many other related structures) as a DNA bis-intercalator. While the scope of this review is not to explore the field of these related naphthalimide structures, we end this review on this particular naphthalene diimide example, giving its close relation to the topic herein.…”

Naphthalimides and Azonafides as Promising Anti-Cancer Agents

“…In view of these interesting results, Braña et al in 1995 synthesized a series of 5-amino-8-nitronaphthalimides to combine the electron withdrawing effects of the nitro group and the electron donating aspects of the amino group [6]. These compounds (59)(60)(61)(62)(63)(64)(65) were tested for their in vitro cytotoxicity against human CX-1 colon and LX-1 lung carcinomas ( Table 3) and showed higher activity than amonafide and mitonafide [3]. Two of them also showed promising in vivo activity in the L1210 leukemia and Fig.…”

“…Bailly et al [61] reported observations which strengthened the case for elinafide binding via the major groove of the double helix, in contrast to nearly all common intercalating drugs, which could be important in explaining the unique biological selectivity of bis-naphthalimides. Flores et al [62] have reported the synthesis of a novel naphthalimide-polyamide hairpin, designed to target the inverted CCAAT box 2 (ICB2) site on the topo II promoter. The compound appears to selectively bind to the ICB2 site by simultaneous intercalation and minor-groove binding.…”

Novel N-(3-carboxyl-9-benzyl-β-carboline-1-yl)ethylamino acids: Synthesis, anti-tumor evaluation, intercalating determination, 3D QSAR analysis and docking investigation

“…The synthesis and anticancer activities of a numerous compounds that intercalate into DNA have been reported recently [7][8][9][10][11][12][13]. Some b-carboline alkaloids such as harmine and its derivatives, are highly cytotoxic against human tumor cell lines [14][15][16][17][18][19].…”