Iron(II) bleomycin-mediated degradation of a DNA-RNA heteroduplex

The Interaction of the Metallo-Glycopeptide Anti-Tumour Drug Bleomycin with DNA

The cancer chemotherapeutic drug, bleomycin, is clinically used to treat several neoplasms including testicular and ovarian cancers. Bleomycin is a metallo-glycopeptide antibiotic that requires a transition metal ion, usually Fe(II), for activity. In this review, the properties of bleomycin are examined, especially the interaction of bleomycin with DNA. A Fe(II)-bleomycin complex is capable of DNA cleavage and this process is thought to be the major determinant for the cytotoxicity of bleomycin. The DNA sequence specificity of bleomycin cleavage is found to at 5′-GT* and 5′-GC* dinucleotides (where * indicates the cleaved nucleotide). Using next-generation DNA sequencing, over 200 million double-strand breaks were analysed, and an expanded bleomycin sequence specificity was found to be 5′-RTGT*AY (where R is G or A and Y is T or C) in cellular DNA and 5′-TGT*AT in purified DNA. The different environment of cellular DNA compared to purified DNA was proposed to be responsible for the difference. A number of bleomycin analogues have been examined and their interaction with DNA is also discussed. In particular, the production of bleomycin analogues via genetic manipulation of the modular non-ribosomal peptide synthetases and polyketide synthases in the bleomycin gene cluster is reviewed. The prospects for the synthesis of bleomycin analogues with increased effectiveness as cancer chemotherapeutic agents is also explored.

Reactivity of Nucleic Acid Radicals

Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.

Mechanism of inhibition of the human immunodeficiency virus type 1 by the oxygen radical generating agent bleomycin

Alternative targets of attack of the human immunodeficiency virus (HIV) are necessary in light of infection persistence due to onset of resistance after conventional reverse transcriptase and protease inhibitor therapy. We have recently shown that the cancer chemotherapeutic agent bleomycin (BLM) dose-dependently inhibits HIV-1 replication. The mechanism of this viral inhibition in vitro was investigated. Cell-free wild-type virions were affected directly by BLM in the presence of H2O2, as shown by a 38% decrease of viral infectivity. Viral inhibition by BLM did not proceed via NF-kappaB inhibition. The viral R/U5 DNA product was reduced by 70% without any effect on reverse transcriptase activity. In both a cell-free system as well as two-cell systems the antiviral dependence of BLM on iron and oxidant species was demonstrated. Bleomycin seems to inhibit HIV-1 replication through the same properties that make it a suitable anti-cancer agent. The results presented in this study describe a novel mechanism of HIV-1 inhibition with potential application in viral infections. The anti-HIV effects of BLM in patients receiving this drug in combination with HAART should be carefully monitored in order to evaluate the clinical significance of the findings described in this study.

Structure and function of "metalloantibiotics"

Although most antibiotics do not need metal ions for their biological activities, there are a number of antibiotics that require metal ions to function properly, such as bleomycin (BLM), streptonigrin (SN), and bacitracin. The coordinated metal ions in these antibiotics play an important role in maintaining proper structure and/or function of these antibiotics. Removal of the metal ions from these antibiotics can cause changes in structure and/or function of these antibiotics. Similar to the case of "metalloproteins," these antibiotics are dubbed "metalloantibiotics" which are the title subjects of this review. Metalloantibiotics can interact with several different kinds of biomolecules, including DNA, RNA, proteins, receptors, and lipids, rendering their unique and specific bioactivities. In addition to the microbial-originated metalloantibiotics, many metalloantibiotic derivatives and metal complexes of synthetic ligands also show antibacterial, antiviral, and anti-neoplastic activities which are also briefly discussed to provide a broad sense of the term "metalloantibiotics."

Protective mechanisms against the antitumor agent bleomycin: lessons from Saccharomyces cerevisiae

Bleomycin is a small glycopeptide antibiotic used in combination therapy for the treatment of a few types of human cancer. The antitumor effect of bleomycin is most likely caused by its ability to bind to DNA and induce the formation of toxic DNA lesions via a free radical reactive (Fe.bleomycin) complex. However, the chemotherapeutic potential of bleomycin is limited, as it causes pulmonary fibrosis and tumor resistance at high doses. The chemical structure and modes of action of bleomycin have been extensively studied and these provide a foundation towards improving the therapeutic value of the drug. This review provides a first account of the current state of knowledge of the cellular processes that can allow the yeast Saccharomyces cerevisiae to evade the lethal effects of bleomycin. This model organism is likely to provide rapid clues in our understanding of bleomycin resistance in tumor cells.

Anti-HIV effect of iron chelators: different mechanisms involved

BACKGROUND

Drugs for the treatment of AIDS have been directed to specific events in the human immunodeficiency virus (HIV-1) life cycle, aimed to stop viral replication by inhibition of reverse transcriptase or protease activity. Studies showing that oxidative stress and iron may be important in the activation of HIV-1 have focused attention on the potential therapeutic use of iron chelators.

OBJECTIVES

The goal of this review is to describe several possibilities as to how iron is involved in the replication of HIV and how iron chelation may interfere in this process.

STUDY DESIGN

First some physico-chemical properties of iron concerning solubility, oxidation-reduction potential, catalysis, and chelation will be discussed. In the second part, the role of iron in various biochemical systems is explained.

RESULTS

Nuclear factor kappa B (NF-kappaB) activation, regulating proviral transcription, can be influenced by iron through the production of reactive oxygen species. A second route by which iron chelation could influence HIV replication, is by inhibition of DNA synthesis through inactivation of iron-dependent ribonucleotide reductase. Another strategy which can be employed in targeting iron chelators against HIV-1, is direct oxidative viral RNA/DNA attack. This could be achieved by bleomycin, a cytostatic agent with the ability to form a complex with DNA and RNA.

CONCLUSION

Chelation may withhold iron from viral metabolism but on the other hand may also favor catalysis of reactive oxygen species directed to viral constituents. In combination with existing antivirals, iron chelation could add to improve the treatment of HIV-disease.

Bleomycin: new perspectives on the mechanism of action

The bleomycin group antitumor antibiotics have long been of interest as a consequence of their efficacy in the treatment of certain tumors, not to mention their unique structures and properties in mediating dioxygen activation and sequence selective degradation of DNA. At a chemical level, the structure originally assigned to bleomycin was subsequently reassigned and the new structure has been confirmed by total synthesis. Through the elaboration of structurally modified bleomycin congeners and fragments, synthetic efforts have also facilitated an understanding of the contribution of individual structural domains in bleomycin to sequence selective DNA binding and cleavage, and have also provided insights into the nature of the chemical processes by which DNA degradation takes place. Within the last several years, it has also become apparent that bleomycin can mediate the oxidative degradation of all major classes of cellular RNAs; it seems entirely plausible that RNA may also represent an important locus of action for this class of antitumor agent. In parallel with ongoing synthetic and mechanistic efforts using classical methods, the study of bleomycins attached to solid supports has been shown to provide important mechanistic insights, and the actual elaboration of modified bleomycins by solid phase synthesis constitutes a logical extension of such efforts.

On the chemistry of RNA degradation by Fe.bleomycin

The chemistry of RNA degradation by Fe.bleomycin was studied using two RNA substrates that are modified efficiently at a small number of sites by the antitumor antibiotic. Cleavage of tRNAHis precursor transcript by Fe(II).BLM A2 was shown to require O2; cleavage was also observed when the same substrate was treated with Fe(III).BLM A2 + H2O2. Consistent with earlier observations made for DNA, the extent of tRNAHis precursor cleavage was greater for Fe(II).BLM A5 than for Fe(II).BLM A2; the least cleavage was obtained using Fe(II).BLM demethyl A2. By the use of 32P end labeled tRNAHis precursor transcript that was also 3H labeled within the uracil moieties, it was shown that release of uracil was nearly stoichiometric with tRNA strand scission by Fe(II).BLM A2. Nonetheless, treatment of the tRNAHis with hydrazine following BLM-mediated cleavage indicated formation of a new product that must have derived from a BLM-induced lesion. Also employed for characterization of BLM cleavage of RNA were the octanucleotides CGCTAGCG, C3-ribo-CGCTAGCG and C3-ara-CGCTAGCG. Analysis of the products of cleavage indicates that Fe.BLM is capable of mediating cleavage by abstraction of a H atom either from C-4' H or c-1' H of the chimeric oligonucleotides.

Mechanistic analyses of site-specific degradation in DNA-RNA hybrids by prototypic DNA cleavers

Bleomycin (BLM) binding and chemistry are apparently sensitive to differences in nucleic acid conformation and could conceivably be developed as a probe for sequence-dependent elements of conformation. We report on the development of a new methodology to synthesize heterogeneous DNA-RNA hybrids of defined sequence and present the results of our comparative studies on the cleavage of DNA and DNA-RNA hybrids by four drugs: BLM, neocarzinostatin and esperamicins A1 and C. In the case of BLM with duplex DNA, purine-pyrimidine steps such as GT and GC, are consistently hit, as previously observed. However, in heterogeneous sequence hybrids, not all GC sites are recognized by the drug, although all GT sites are. Suppressed GC sites are consistently flanked by pyrimidines on both the 3' and 5' sides, suggesting that the BLM binding site in hybrids spans at least four bases. Kinetic isotope studies with specifically deuterated substrates (kH/kD = 1.2-4.0) and the effect of oxygen on the product profile are presented in support of a mechanism consistent with 4'-hydrogen abstraction in hybrids. The powerful double-labeled probe technique was extended to study the mechanism of action of other DNA degrading drugs on DNA-RNA hybrids. For neocarzinostatin, the sequence specificity lies in the AT-rich region for hybrids and is similar to that of DNA, however, the overall cleavage pattern for the hybrid is significantly different from that for the same sequence of DNA. In the hybrid, a stretch of AT residues is essential and the A sites are damaged to a greater extent than they are in DNA. However, no kinetic isotope effects are observed and, based on the product profile, the mechanism of degradation of the DNA strand of hybrids seems to be limited to abstraction of the 5'-hydrogen. For esperamicin A1, damage on the DNA strand of hybrids occurs exclusively via 5'-hydrogen abstraction in a non-rate determining step and primarily at A and T sites. Esperamicin C behaves similarly, exhibiting no isotope effects at 1', 4' and 5' positions. Overall, the differences observed in site-specific cleavage between the two substrates is proposed to be a result of conformational differences between the DNA strand of duplex DNA and DNA-RNA hybrids.

Fe.bleomycin as a probe of RNA conformation

Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.