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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Bioorg Med Chem Lett. Author manuscript; available in PMC 2010 August 1.
Published in final edited form as:
PMCID: PMC2845530

On the Role of Topoisomerase I in Mediating the Cytotoxicity of 9-Aminoacridine-Based Anticancer Agents


The cytotoxicity and mechanism of action of a series of substituted 9-aminoacridines is evaluated using topoisomerase I and cancer cell growth inhibition assays. In previous work, compounds of this type were shown to catalytically inhibit topoisomerase II, leading to a G1-S phase arrest of the cell cycle and apoptosis in pancreatic cancer cells in vitro and in vivo. The present study expands the potential utility of these compounds in the development of cancer therapeutics by showing that these compounds inhibit proliferation of cell lines derived from the nine most common human cancers. Further results show that at least one of the compounds effectively stabilizes topoisomerase I-DNA adduct formation in intact cells. RNA interference experiments, however, indicate that this interaction does not contribute to the drug-induced killing of cancer cells indicating the compounds may be non-lethal poisons of topoisomerase I.

Keywords: topoisomerase, DNA, anticancer agents, siRNA, cytotoxicity, acridine, etoposide, doxorubicin, mechanism of action, cleavable complex, catalytic inhibitor

Topoisomerases I and II are well established targets in the development of anti-cancer agents.1-4 The roles of these enzymes in processes that involve changes in DNA topology, including replication, transcription and chromosome segregation, are well documented, as are the mechanisms of action of most, if not all, topoisomerase-targeted drugs. In general, topoisomerase inhibitors are divided into two main categories: poisons and catalytic inhibitors. Poisons, which include the most widely used drugs clinically for treating cancers, function by binding to the covalent DNA-topoisomerase enzyme complex (cleavable complex) and preventing DNA religation after DNA strand cleavage occurs. In susceptible cells, events triggered by this cleavable complex stabilization lead to apoptosis and cell death. Well established examples of poisons include doxorubicin, etoposide, mitoxantrone, and amsacrine, which primarily target topoisomerase II, and the camptothecins topotecan (TPT) and 7-ethyl-10-hydroxycamptothecin, which target topoisomerase I. Catalytic inhibitors are not as well defined mechanistically and can function through inhibiting any other step of the topoisomerase enzymatic cycles. Examples of catalytic inhibitors include the anthracycline aclarubicin, which blocks formation of DNA-enzyme complexes, and the bisdioxopiperazine ICRF-193, which stabilizes the close-clamped form of topoisomerase II.3,4

We have recently described a new series of potential anticancer agents that share a common structural core with amsacrine but function through a mechanism similar to that of aclarubicin.5-7 Detailed mechanistic studies have shown that the compounds in Figure 1 intercalate into DNA and inhibit the catalytic activity of topoisomerase II without poisoning it. The compounds have been also shown to induce a G1-S phase arrest followed by apoptotic cell death (a common consequence of topoisomerase II inhibition) in both SU86.86 and BXPC-3 pancreatic cancer cells in vitro.6,7 In vivo, the compounds were found to significantly reduce the proliferation of SU86.86 cells grown as xenografts in mice. The relative activity of the compounds against other cancers and potential function at related enzymatic targets (such as topoisomerase I), however, has not yet been determined.

Figure 1
Substituted 9-aminoacridines.

Given the utility of other topoisomerase-targeting agents (e.g., etoposide, doxorubicin or the camptothecins) in treating a variety of cancers, compounds 1-4 have now been further evaluated for activity against cell lines derived from the nine most common human cancers. In standard cytotoxicity assays (Table 1), the compounds exhibit relatively similar potency across all cancer cell lines, with some notable exceptions. The diethylamido tryptamine derivative 4, for example, shows a consistently higher potency across all nine cancer cell lines. It is interesting to note that this compound bears the weakest charge within the group, having only two protonatable nitrogens. The reduced charge or polarity of this compound may increase cellular uptake (through passive diffusion across the membrane) which may, in part, explain the general gain in potency noted. In terms of relative activity across the cell lines, the methylpiperizine 3 shows 3- to 4-fold greater potency against MEL melanoma and REH renal carcinoma cells, whereas compound 1 exhibits greater potency against SU86.86 pancreatic cancer cells. These cell line-specific differences are somewhat surprising because the only difference between 1 and 3 is the position of the amido substitution of the ring.

Table 1
Growth inhibition of 1-4 against lines derived from the 9 most common human cancers.a

Although a clear connection between topoisomerase II inhibition and the anticancer activity of the compounds has been established,6,7 it is unclear what role, if any, topoisomerase I inhibition plays in their cytotoxicity. It has previously been reported that acridine dyes and other intercalating agents can interfere with the catalytic activity of topoisomerase I. In particular, morpholinodoxorubicin and actinomycin D trap topoisomerase I-DNA covalent complexes;8,9 and pyrazoloacridine as well as doxorubicin inhibit topoisomerase I catalytic activity without trapping cleavable complexes.9-11 To assess the potential importance of topoisomerase I as a target of compounds 1-4, we have analyzed the effect of these agents on topoisomerase I catalytic activity under cell-free conditions and on topoisomerase I-DNA complexes in intact cells. In addition, we have utilized RNA interference to manipulate topoisomerase I levels and assess the impact on the antiproliferative effects of these compounds.

The effects of compounds 1-4 on the catalytic activity of topoisomerase I are shown in Figure 2A. In contrast to pyrazoloacridine, which completely suppressed the ability of topoisomerase I to relax supercoiled DNA at a concentration of 8 μM (Figure 2A, lanes 1-3), compounds 1-4 failed to significantly inhibit relaxation of supercoiled DNA even at concentrations as high as 100 μM. Because topoisomerase I poisons such as camptothecin are poor inhibitors of topoisomerase I catalytic activity,12 the compounds were also assayed for the ability to stabilize covalent topoisomerase I-DNA adducts under cell-free conditions. Like the camptothecin derivative topotecan (TPT, Figure 2B, lane 3), compound 2 stabilized these adducts, as indicated by the appearance of nicked plasmid in the presence of topoisomerase I (Figure 2B, lane 7). To further evaluate this result, the ability of these compounds to stabilize topoisomerase I cleavable complexes in intact cells was assessed using the more sensitive ICE assay. Examination of CsCl2-purified DNA fractions for the presence of topoisomerase I (Figure 2C) demonstrated that compound 2, like topotecan, stabilized topoisomerase I-DNA adducts in intact cells. To a smaller and more variable extent, compounds 1 and 4 also stabilized small numbers of topoisomerase I-DNA adducts.

Figure 2
Effects of compounds 1, 2, 3, and 4 on topoisomerase I catalytic activity (A), formation of covalent topoisomerase I-DNA complexes (B) and ICE assay (C)

While the data indicate that compound 2 (and to a lesser extent 1 and 4) can trap topoisomerase I-DNA adducts in vitro and in intact cells, these observations do not establish whether the stabilization of these complexes is critical for inhibition of cancer cell growth. To address this question, HeLa cells treated with control or topoisomerase I-directed siRNA were exposed to compound 2 for 24 h, washed, and assayed for the ability to form colonies. Consistent with previous results in gene-targeted yeast13,14 and siRNA-treated mammalian cells,16 topoisomerase I siRNA diminished the cytotoxicity of camptothecin (Figure 3A). In contrast, the cytotoxicity of compound 2 was relatively unaffected (Figure 3B), indicating that stabilization of topoisomerase I-DNA complexes is not the major mechanism by which compound 2 kills cells. These results are consistent with the previous conclusion that compounds 1-4 act predominantly as topoisomerase II inhibitors.7

Figure 3
Effect of topoisomerase I siRNA on drug sensitivity

Collectively, these results provide important new insight into the cytotoxic action of compounds 1-4. Our previous work has suggested that these compounds function by intercalating DNA through a threading mechanism that sterically hinders interactions with both the major and minor grooves of DNA. Given that this mechanism is typically considered to be non-specific, the finding that only one of the compounds binds to and strongly stabilizes the topoisomerase I-DNA complex is surprising. Furthermore, all four compounds failed to show catalytic inhibition of topoisomerase I activity. This suggests that the binding and stabilization of topoisomerase I-DNA complexes by the 9-aminoacridines may, in fact, be structure-based which points to the existence of a specific binding site within the enzyme-DNA complex. A similar conclusion was reached in prior work evaluating the topoisomerase II activity of a larger library of substituted acridines.6 It is important to point out, however, that this trapping of the complex by 2 does not appear to lead to cytotoxicity. Unlike camptothecin, which becomes less toxic when topoisomerase I is downregulated (Fig. 3A), compound 2 shows little sensitivity to the siRNA knockdown (Fig. 3B). One explanation for this apparent lack of sensitivity is that compound 2 effectively diminishes DNA synthesis. Prior work has shown that active DNA synthesis is required to convert topoisomerase I cleavage complexes into lethal damage.16,17 Based on the effects of other intercalating agents, it is possible that decreased DNA synthesis in the presence of compound 2 reflects inhibition of helicases or polymerases that are critical for DNA replication, thereby antagonizing any effect of stabilizing topoisomerase I cleavable complexes. Alternatively, the failure of topoisomerase I downregulation to affect the cytotoxicity of compound 2 may simply reflect the fact that catalytic inhibition of topoisomerase II (as previously postulated) rather than trapping of topoisomerase I is the primary mechanism of action of cell killing at the concentrations used in the clonogenic assays shown in Fig. 3. In either case, compound 2 appears to be a non-lethal poison of topoisomerase I. Non-productive binding of this type can have a significant impact on efficacy (as well as toxicity and the development of resistance), underscoring the importance of verifying the mechanism of action in the design and development of cytotoxic drugs.

Supplementary Material


This work was supported by a Faculty Research Development grant from the University of Minnesota Academic Health Center (D.M.F and H.H.) and by the National Institutes of Health, R01 CA73709 (S.H.K.)


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