Antitumor activity of sequence-specific alkylating agents: pyrolle-imidazole CBI conjugates with indole linker

Abstract

DNA-targeting agents, including cisplatin, bleomycin and mitomycin C, are used routinely in cancer treatments. However, these drugs are extremely toxic, attacking normal cells and causing severe side effects. One important question to consider in designing anticancer agents is whether the introduction of sequence selectivity to DNA-targeting agents can improve their efficacy as anticancer agents. In the present study, the growth inhibition activities of an indole-seco 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) (1) and five conjugates with hairpin pyrrole-imidazole polyamides (2-6), which have different sequence specificities for DNA alkylation, were compared using 10 different cell lines. The average values of -log GI50 (50% growth inhibition concentration) for compounds 1-6 against the 10 cell lines were 8.33, 8.56, 8.29, 8.04, 8.23 and 8.83, showing that all of these compounds strongly inhibit cell growth. Interestingly, each alkylating agent caused significantly different growth inhibition patterns with each cell line. In particular, the correlation coefficients between the -log GI50 of compound 1 and its conjugates 2-6 showed extremely low values (R<0). These results suggest that differences in the sequence specificity of DNA alkylation lead to marked differences in biological activity. Comparison of the correlation coefficients between compounds 6 and 7, with the same sequence specificity as 6, and MS-247, with sequence specificity different from 6, when used against a panel of 37 human cancer cell lines further confirmed the above hypothesis.

Figure 1

Mechanism of the formation of 1,2,9,9a‐tetrahydrocyclopropa[1,2‐c]benz[1,2‐e]indol‐4‐one (CBI) from seco‐CBI and DNA alkylation by CBI derivatives.

Figure 2

(a) Structures of compound 1 and conjugates 2–6. (b) Thermally induced strand cleavage of 5′‐Texas Red‐labeled DNA fragments of the green fluorescent protein (GFP) gene alkylated by compound 1. Lanes 1–4: 250, 100, 50, 25 nM of compound 1. Lane 5: DNA control. Lanes G, C, T, and A contain Sanger‐sequencing products.

Figure 3

(a) Schematic representation of DNA alkylation by compounds 1–6. Open circles, filled circles and ellipses indicate pyrroles, imidazoles and indoles, respectively. W indicates A or T. Arrows indicate the site of alkylation. (b) Graphs of the mean 50% growth inhibition concentrations (GI₅₀) for compounds 1–6 against a panel of 10 cell lines. The –log GI₅₀ for each cell line is shown. Columns extending to the right are more sensitive; columns extending to the left are resistant. One unit represents one logarithm difference. (c) The correlation coefficients for the mean GI₅₀ values of compounds 1–6.

Figure 4

The energy‐minimized structures of the (a) 1‐d(GCGTATACGC)/d(GCGTATACGC) and (b) 6‐d(GCTGTCCAGC)/d(GCTGGACAGC) complexes. Minimization was carried out in the presence of 18 sodium cations and a 10‐Å layer of H₂O using the consistent force field force field. For simplicity, the sodium ions and water molecules are not represented. Each strand of DNA is drawn in line, pyrrole (Py) and imidazole (Im) are drawn in the CPK color scheme, the indole linker is drawn in purple and the 1,2,9,9a‐tetrahydrocyclopropa[1,2‐c]benz[1,2‐e]indol‐4‐one (CBI) moiety is drawn in green. The colour scheme is based on the colors of the popular plastic space‐filling models that were developed by Corey and Pauling and later improved by Kultun (CPK)

Figure 5

(a) Graphs of the mean 50% growth inhibition concentrations (GI₅₀) for compounds 6, 7 and MS‐247 against a panel of 37 human cancer cell lines. Columns extending to the right are more sensitive; columns extending to the left are resistant. One unit represents one logarithm difference. The correlation coefficients for the mean GI₅₀ values of compounds 6, 7 and MS‐247. (b) Chemical structures of compound 7 and MS‐247.