Binding of 2-Azaanthraquinone Derivatives to DNA and Their Interference with the Activity of DNA Topoisomerases in Vitro

Abstract

We have investigated the binding ability to DNA of compounds belonging to the 2-azaanthraquinone-type structure and have examined the effect on the activity of DNA gyrase as well as on mammalian topoisomerases in vitro. Using different biophysical techniques it was found that one of these ligands, 9-((2-dimethylamino)ethyl)amino)-6-hydroxy-7-methoxy-5, 10-dihydroxybenzo[g]isoquinoline-5,10-dione (TPL-I), is an intercalating DNA binding agent, whereas the parent compound tolypocladin (TPL) and a derivative (TPL-II) showed almost no similar affinity to DNA. CD measurements demonstrated a significant and selective binding tendency of TPL-I to alternating purine/pyrimidine sequences with some preference for poly(dA-dT). poly(dA-dT). Tm values were increased of the ligand complex with the alternating AT-containing duplex polymer. The binding to various DNAs was characterized by CD and visible absorption spectral changes. From the latter, different binding constants of 6.2 x 10(5) and 1.5 x 10(5) M-1 were obtained for poly(dA-dT).poly(dA-dT) and poly(dA). poly(dT), respectively. Sedimentation measurements with supercoiled pBR322 plasmid DNA clearly indicated an intercalative binding mechanism associated with an unwinding angle of about 18 degrees. These results suggest that the intercalative binding of TPL-I is promoted by the 2-(dimethylamino)ethylamino group substituted on carbon 9 of the anthraquinone system. The cytotoxic compound TPL-I, but not TPL or TPL-II, effectively inhibited the DNA supercoiling reaction of DNA gyrase and the activity of mammalian topoisomerases I and II as measured by the relaxation assay. TPL-I affects the cleavage reaction of topoisomerases on a single site located in alternating purine-pyrimidine sequence regions. The inhibitory potency of TPL-I can be ascribed to a blocking of cleavage sites on the DNA substrate, which correlates with the sequence preference of the ligand.

Selective inhibition of DNA gyrase in vitro by a GC specific eight‐ring hairpin polyamide at nanomolar concentration

“…As evidenced earlier, minor groove binders may inhibit the gyrase mediated reaction of DNA supercoiling by influencing the binding of the enzyme at or around the cleavage and religation site [9,10]. The design of an eight‐ring hairpin polyamide, which can recognize six base pairs containing four contiguous GC pairs (GGCC) identical with a strong gyrase site prompted us to examine whether this type of minor groove binder offers a basis to enhance the potency and selectivity for an anti‐topoisomerase agent.…”

Investigation on the electrochemistry and cytotoxicity of the natural product marcanine A and its synthetic derivatives

“…7,8 In particular, azaanthraquinones were tested for their ability to bind DNA and interfere with DNA polymerase activity in vitro. 9 The mode of action of azaanthraquinones was determined to be intercalation into the DNA double strand and inhibition of DNA supercoiling. 9 It has been postulated that the cytotoxicity is mediated through semiquinone radical species, which are formed during the quinone to quinol conversion and vice versa.…”

Crystallization and preliminary X-ray diffraction studies of d(ACGTAGCTACGT)2:[actinomycin D, (echinomycin)2] and d(ACGTAGCTACGT)2:[actinomycin D, (triostin A)2] complexes

“…To extend the sequence speci®city, two or more binding agents were connected with tethers (for example, Khorlin et al, 1980;Gursky et al, 1983;Youngquist & Dervan, 1985;Lown et al, 1986Lown et al, , 1989Youngquist & Dervan, 1987;Grokhovsky & Zubarev, 1990;Singh et al, 1994;Mrksich et al, 1994;Nikolaev et al, 1996;Parks et al, 1996;White et al, 1997;Grokhovsky et al, 1998). Although most of these bis-and tri-linked polyamides did not bind to the speci®c DNA sequences, it has been reported that a few bis-linked netropsin derivatives inhibit selectively activities of topoisomerases I and II (Beerman et al, 1991;Burckhardt et al, 1997) and HIV-I reverse transcriptase (Filipowsky et al, 1996).…”