Mapping Drug Interactions at the Covalent Topoisomerase II-DNA Complex by Bisantrene/Amsacrine Congeners

Abstract

To identify structural determinants for the sequencespecific recognition of covalent topoisomerase II-DNA complexes by anti-cancer drugs, we investigated a number of bisantrene congeners, including a 10-azabioisoster, bearing one or two 4,5-dihydro-1H-imidazol-2-yl hydrazone side chains at positions 1, 4, or 9 of the anthracene ring system. The studied bisantrene/amsacrine (m-AMSA) hybrid and bisantrene isomers were able to poison DNA topoisomerase II with an intermediate activity between those of bisantrene and m-AMSA. Moving the side chain from the central to a lateral ring (from C-9 to C-1/C-4) only slightly modified the drug DNA affinity, whereas it dramatically affected local base preferences of poison-stimulated DNA cleavage. In contrast, switching the planar aromatic systems of bisantrene and m-AMSA did not substantially alter the sequence specificity of drug action. A computer-assisted steric and electrostatic alignment analysis of the test compounds was in agreement with the experimental data, since a common pharmacophore was shared by bisantrene, m-AMSA, and 9-substituted analogs, whereas the 1-substituted isomer showed a radically changed pharmacophoric structure. Thus, the relative space occupancy and electron distribution of putative DNA binding (aromatic rings) and enzyme binding (side chains) moieties are fundamental in directing the specific action of topoisomerase II poisons and in determining the poison pharmacophore.The elucidation of structural determinants of the sequencespecific recognition of DNA by small molecules is fundamental for a rational design of gene-specific DNA binders that are effective in the therapy of human diseases. Several DNA-interactive compounds are known that may bind to the double helix in a site-selective manner; however, the degree and mechanisms of the specificity are very different among them (1-4). A wide variety of antitumor drugs, with and without the ability to bind to naked DNA, have been shown to poison DNA topoisomerases with a high sequence selectivity (2, 5-7). DNA topoisomerases are ubiquitous enzymes deputed to resolve topological problems that arise during various nuclear processes including transcription, recombination, and chromosome partitioning at cell division (8 -10). Type II enzymes make transient double-stranded breaks into one segment of DNA and pass an intact duplex through the broken DNA, before resealing the break (2, 8 -10). Anticancer agents able to poison the mammalian enzymes stabilize a key intermediate of the catalytic reaction wherein DNA strands are broken and covalently linked to the protein. Thus, the poisoning action results in increased DNA cleavage levels in living cells that eventually trigger a cell death process.Classical topoisomerase poisons stimulate DNA cleavage in a sequence-selective manner, yielding drug-specific cleavage intensity patterns in agarose as well as sequencing gels (2,5,6,11,12). Each pattern reflects the recognition of specific features of the enzyme-DNA covalent complex that are likely dictated by the n...

Molecular Analysis of Yeast and Human Type II Topoisomerases

“…4 and Table I), the human enzyme showed a clear preference for A ϩ1 (47 of 64 sites) and a complementary (although weaker) preference for T ϩ4 (28 of 64 sites), which conforms with earlier studies (29,33,34). The yeast protein also demonstrated a strong preference for A ϩ1 (29 of 61 sites) but an additional preference for T at position Ϫ1 (32 of 61 sites) as well as the complementary A at position ϩ5 (28 of 61 sites), which was not seen in the human enzyme.…”

“…The DNA sequence preference of drugs that target DNA top2 has been widely investigated (34). Early studies showed that topoisomerase-targeting drugs influence the sequence specificity of DNA cleavage by top2 compared with sites of DNA cleavage in the absence of drugs (28,29,39).…”

DNA Sequence Specificity for Topoisomerase II Poisoning by the Quinoxaline Anticancer Drugs XK469 and CQS

“…In general, drugs with similar shapes, and with shared pharmacophores and electronic structure, tend to have similar topoisomerase II-mediated DNA cleavage patterns, whereas topoisomerase II poisons of different chemical classes cause very different DNA cleavage patterns and/or cleavage intensity patterns (Capranico et al, 1993(Capranico et al, , 1994a(Capranico et al, , 1998Guano et al, 1999). However, there are exceptions to this rule.…”

Constrained bisantrene derivatives as G-quadruplex binders

“…18,19 Compounds were obtained by standard solution synthesis following the reported procedures, and the synthetic strategy is summarized in Scheme 1. Briefly, the procedure is based on a Friedel-Crafts acylation of the anthracene with acetyl chloride in the presence of AlCl 3 in dichloroethane.…”

“…We previously reported the synthetic procedure for compound Ant1,5. 18,19 Anthracene-1,5-diacetyl (2). A three-neck round bottom flask was charged with anthracene (10.00 g, 56 mmol) and AlCl 3 (23.00 g, 172 mmol) in 300.0 mL of dichloroethane.…”