Thiol-dependent DNA cleavage by 3H-1,2-benzodithiol-3-one 1,1-dioxide

Noncovalent DNA binding drives DNA alkylation by leinamycin: evidence that the Z,E-5-(thiazol-4-yl)-penta-2,4-dienone moiety of the natural product serves as an atypical DNA intercalator

Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif, such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 10(3) M(-1). Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allow construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA.

Characterization of DNA damage induced by a natural product antitumor antibiotic leinamycin in human cancer cells

Leinamycin is a structurally novel Streptomyces-derived natural product that displays very potent activity against various human cancer cell lines (IC(50) values in the low nanomolar range). Previous in vitro biochemical studies have revealed that leinamycin alkylates DNA, generates apurinic (AP) sites and reactive oxygen species (ROS), and causes DNA strand breaks. However, it is not clear whether these events occur inside cells. In the present study, we have determined the endogenous amount of AP sites and DNA strand breaks in genomic DNA and the amount of oxidative stress in a human pancreatic carcinoma cell line, MiaPaCa, treated with leinamycin by utilizing the aldehyde-reactive probe assay, the comet assay, and fluorescent probes, respectively. We demonstrated that AP sites are formed rapidly following exposure to leinamycin, and the number of AP sites was increased up to seven-fold in a dose-dependent manner. However, only 25-50% of these sites remain 2 h after media containing drug molecules were aspirated and replaced with fresh media. We also observed leinamycin-induced ROS generation and a concomitant increase in apoptosis of MiaPaCa cells. Because both AP sites and ROS have the potential to generate strand breaks in cellular DNA, the comet assay was utilized to detect damage to nuclear DNA in leinamycin-treated MiaPaCa cell cultures. Both alkaline and neutral electrophoretic analysis revealed that leinamycin produces both single- and double-stranded DNA damage in drug-treated cells in a dose-dependent manner. Taken together, the results suggest that rapid conversion of leinamycin-guanine (N7) adducts into AP sites to produce DNA strand breaks, in synergy with leinamycin-derived ROS, accounts for the exceedingly potent biological activity of this natural product.

Thiol-dependent DNA cleavage by aminomethylated Beaucage's reagent

Aminomethylated Beaucage's reagent 1 was found to be more potent than 3H-1,2-benzodithiol-3-one 1,1-dioxide (Beaucage's reagent) in causing DNA cleavage. The current study demonstrated the importance of the amino functionality in enhancing DNA-cleaving activities, and such findings may facilitate development of novel sulfur-containing DNA-cleaving molecules in cancer therapy.

DNA cleavage promoted by 2,9-dimethyl-4,7-diazadecane-2,9-dithiol (DDD) derivatives

Three piperidine derivatives of 2,9-dimethyl-4,7-diazadecane-2,9-dithiol (DDD), NEPDDD, NEMPDDD, and NEMMPDDD, were synthesized and used as catalysts in DNA cleavage. Under physiological conditions, a series of experiments have been done. The effects of DNA cleavage with three ligands were studied under different concentrations, cleavage time, and pH values. The results strongly suggested that the plasmid DNA (pUC 19) can be cleaved efficiently by these ligands. For the cleavage reaction catalyzed by NEMPDDD, Form I DNA could convert to Form II completely, and the DNA-cleavage mechanism involved an oxidative pathway.

Synthesis and Cytotoxicity of Leinamycin Antibiotic Analogues

A simple synthesis of 1,2-dithiolan-3-ones from alpha,beta-unsaturated thiophenyl esters is reported. Introduction of the biologically active 1,2-dithiolan-3-one-1-oxide moiety of leinamycin into aldehydo-d-arabinose 11, the uridine derivative 16, and the deoxythymidine 21 was established. An extended bioactive part of leinamycin carrying a carbon-carbon triple bond was also synthesized. All of these analogues of leinamycin showed cytotoxic activity against HeLa3 tumor cells. Interestingly, the lipophilic, silyl group-containing derivatives proved to be more active than the hydrophilic counterparts.

Chemical properties of the leinamycin-guanine adduct in DNA

The reaction of the antitumor agent leinamycin with thiols converts this natural product into an episulfonium ion that alkylates the N7-position of guanine residues in double-stranded DNA. It is reported here that depurination of this adduct is unusually facile, occurring with a half-life of about 3.5 h at pH 7 and 37 degrees C in duplex DNA. This is one of the most rapid depurination reactions ever observed for an N7-alkylguanine residue. The rate constant for the depurination reaction was measured at several temperatures, and the activation parameters were calculated from the data. The energy of activation (E(a)) for this reaction is 24.6 kcal/mol, and the Arrhenius A value is 1.2 x 10(13) s(-1). These values correspond to a DeltaH(++) = 24.0 kcal/mol and DeltaS(++) = -0.78 eu and are consistent with the expected unimolecular (D(N) + A(N)) mechanism for the depurination reaction. Changes in ionic strength (0-500 mM NaCl) or pH (3-8) do not significantly alter the rate of depurination, and the base excision repair protein Aag, which removes a variety of N7-alkylguanine residues from duplex DNA, does not excise the leinamycin-guanine adduct. Possible biological implications of this rapid depurination process are considered. Finally, during the course of these studies, the release of hydrolyzed leinamycin (4; Scheme 1) from leinamycin-modified DNA was observed. This result suggests that leinamycin may be a reversible DNA alkylating agent.

Photoinduced cleavage of DNA by bromofluoroacetophenone-pyrrolecarboxamide conjugates

Bromofluoroacetophenone derivatives which produce fluorine substituted phenyl radicals that cleave DNA upon excitation were investigated as a novel photonuclease. Pyrrolecarboxamide-conjugated bromofluoroacetophenones; 4'-bromo-2'-fluoroacetophenone and 2'-bromo-4'-fluoroacetophenone were synthesized and their DNA cleaving activities and sequence selectivities were determined. Bromofluoroacetophenone-pyrrolecarboxamide conjugates were found to be effective DNA cleaving agents upon irradiation in concentration dependent manner based on plasma relaxation assay. The DNA cleaving activities of 2'-bromo-4'-fluoroacetophenone derivatives were larger than those of 4'-bromo-2'-fluoroacetophenone derivatives.

Reaction of thiols with 7-methylbenzopentathiepin

Polysulfides typically react readily with thiols, thus, reactions of endogenous cellular thiols with the polysulfide linkage in naturally-occuring pentathiepin cytotoxins are likely to be an important aspect of their biological chemistry. Here, it is reported that the reaction of thiols with the pentathiepin ring system initially produces a complex mixture of polysulfides that further decomposes in the presence of excess thiol to yield the corresponding 1,2-benzenedithiol with concomitant production of H(2)S and dimerized thiol. In this reaction, a single molecule of the pentathiepin consumes approximately six equivalents of thiol. The reaction of thiols with the pentathiepin ring system is faster than the analogous reaction involving typical di- and trisulfides.

Benzotrithiole 2-oxide: a new family of thiol-activated DNA-cleaving functionalities

It was demonstrated in our studies that benzotrithiole 2-oxide was capable of causing efficient DNA cleavage in the presence of 2-mercaptoethanol or glutathione and exhibited potent cytotoxic properties against certain cancer cell lines.