On the role of the bithiazole moiety in sequence-selective DNA cleavage by Fe.bleomycin

Design and synthesis of an anthranyl bridged optically active dinuclear iron(II)-ligand and evaluation of DNA-cleaving activity

It is necessary to design a ligand that is compatible with the target molecule to optimally use the DNA-cleaving ability of metal complexes. In this study, we synthesized an optically active dinuclear ligand, (1R,1'R,2R,2'R)-N¹,N^1'-(anthracene-1,8-diylbis(methylene))bis(N²,N²-bis(pyridin-2-ylmethyl)cyclohexane-1,2-diamine) (R-ABDC, 4a) and its enantiomer (S-ABDC, 4b). We then prepared their Fe(II) complexes by mixing the ligand with FeSO₄·7H₂O in situ and investigated DNA-cleaving activities using plasmid DNA in the presence of excess sodium ascorbate at atmospheric conditions. The Fe(II) complexes efficiently cleaved DNA and selectively recognized two consecutive A and/or T sequences.

The C-terminal part of microcin B is crucial for DNA gyrase inhibition and antibiotic uptake by sensitive cells

Microcin B (McB) is a ribosomally synthesized antibacterial peptide. It contains up to nine oxazole and thiazole heterocycles that are introduced posttranslationally and are required for activity. McB inhibits the DNA gyrase, a validated drug target. Previous structure-activity analyses indicated that two fused heterocycles located in the central part of McB are important for antibacterial action and gyrase inhibition. Here, we used site-specific mutagenesis of the McB precursor gene to assess the functional significance of the C-terminal part of McB that is located past the second fused heterocycle and contains two single heterocycles as well as an unmodified four-amino-acid C-terminal tail. We found that removal of unmodified C-terminal amino acids of McB, while having no effect on fused heterocycles, has a very strong negative effect on activity in vivo and in vitro. In fact, even nonconservative point substitutions in the last McB amino acid have a very strong effect by simultaneously decreasing uptake and ability to inhibit the gyrase. The results highlight the importance of unmodified McB amino acids for function and open the way for creation of recombinant McB derivatives with an altered or expanded spectrum of antibacterial action.

Total syntheses of (-)-pyrimidoblamic acid and P-3A

Total syntheses of (-)-pyrimidoblamic acid and P-3A are disclosed. Central to the convergent approach is a powerful inverse electron demand Diels-Alder reaction between substituted electron-deficient 1,2,3-triazines and a highly functionalized and chiral primary amidine, which forms the pyrimidine cores and introduces all necessary stereochemistry in a single step. Intrinsic in the convergent approach is the potential it provides for the late stage divergent synthesis of modified analogs bearing deep-seated changes in either the pyrimidine cores or the highly functionalized C2 side chain common to both natural products. The examination of the key cycloaddition reaction revealed that the inherent 1,2,3-triazine mode of cycloaddition (C4/N1 vs C5/N2) as well as the amidine regioselectivity were unaffected by introduction of two electron-withdrawing groups (-CO2R) at C4 and C6 of the 1,2,3-triazine even if C5 is unsubstituted (Me or H), highlighting the synthetic potential of the powerful pyrimidine synthesis.

Effect of thiol compounds on bleomycin-induced DNA and chromosome damage in human cells

Non-protein thiols are considered radioprotectors, preventing DNA damage by ionizing radiation. As bleomycin (BLM) is a radiomimetic agent it was proposed that thiols may prevent DNA damage produced by this antibiotic. However, results obtained with thiols and BLM-combined treatments in living cells are contradictory. The goal of this work was to assess the influence of five non-protein thiols of different electrical charge and chemical composition, on the DNA damage, DNA repair, chromosomal aberrations and cell killing induced by BLM. We found that, at the chromosomal level and cell killing, Glutathione, β-Mercaptoethanol and cysteine showed a protective effect, while ditiothreitol and cysteamine increased them, whereas at the DNA level all thiols potentiated the DNA damage induced by BLM, most probably due to a reactivation of the BLM complex.

Catalytic mechanism of bleomycin N-acetyltransferase proposed on the basis of its crystal structure

Bleomycin (Bm) N-acetyltransferase, BAT, is a self-resistance determinant in Bm-producing Streptomyces verticillus ATCC15003. In our present study, we crystallized BAT under both a terrestrial and a microgravity environment in the International Space Station. In addition to substrate-free BAT, the crystal structures of BAT in a binary complex with CoA and in a ternary complex with Bm and CoA were determined. BAT forms a dimer structure via interaction of its C-terminal domains in the monomers. However, each N-terminal domain in the dimer is positioned without mutual interaction. The tunnel observed in the N-terminal domain of BAT has two entrances: one that adopts a wide funnel-like structure necessary to accommodate the metal-binding domain of Bm, and another narrow entrance that accommodates acetyl-CoA (AcCoA). A groove formed on the dimer interface of two BAT C-terminal domains accommodates the DNA-binding domain of Bm. In a ternary complex of BAT, BmA(2), and CoA, a thiol group of CoA is positioned near the primary amine of Bm at the midpoint of the tunnel. This proximity ensures efficient transfer of an acetyl group from AcCoA to the primary amine of Bm. Based on the BAT crystal structure and the enzymatic kinetic study, we propose that the catalytic mode of BAT takes an ordered-like mechanism.

Synthesis of 2,2'-Bis(3,6,9-triazanonyl)-4,4'-bithiazole and related compounds as new DNA cleavage agents

Two new bithiazole derivatives, 2,2'-bis(3,6,9-triazanonyl)- and 2,2'-bis(3,7,11-triazaundecyl)-4,4'-bithiazoles (3a, b), were readily synthesized in six steps using the corresponding dialkylenetriamine as starting materials. Under physiological conditions, 5.0 microM 3a exhibited significant DNA cleavage activity in the presence of Co(II), whereas even at 50 micriM, 3b exhibited no DNA cleavage activity. Furthermore, it was demonstrated that 3a forms a 1 : 2 complex with Co(II) ions, whereas 3b does not. These conclusions were based on measurements of stoichiometries of the bithiazole-cobalt complexes obtained by the Job continuous variation method. In contrast, 3a, which contains diethylenetriamine moieties, showed decreased affinity for Calf Thymus (CT) DNA compared with that of 3b, which contains dipropylenetriamine moieties. These findings indicate that the structure of the two aminoalkyl side chains attached at the 2- and 2'-positions of the 4,4'-bithiazole ring significantly influence the formation of cobalt complexes, and affects the compound's ability to cleave DNA as well as its affinity for double-stranded DNA.

Biochemical evaluation of a 108-member deglycobleomycin library: viability of a selection strategy for identifying bleomycin analogues with altered properties

The bleomycins (BLMs) are clinically used glycopeptide antitumor antibiotics that have been shown to mediate the sequence-selective oxidative damage of both DNA and RNA. Previously, we described the solid-phase synthesis of a library of 108 unique analogues of deglycoBLM A6, a congener that cleaves DNA analogously to BLM itself. Each member of the library was assayed for its ability to effect single- and double-strand nicking of duplex DNA, sequence-selective DNA cleavage, and RNA cleavage in the presence and absence of a metal ion cofactor. All of the analogues tested were found to mediate concentration-dependent plasmid DNA relaxation to some extent, and a number exhibited double-strand cleavage with an efficiency comparable to or greater than deglycoBLM A6. Further, some analogues having altered linker and metal-binding domains mediated altered sequence-selective cleavage, and a few were found to cleave a tRNA3Lys transcript both in the presence and in the absence of a metal cofactor. The results provide insights into structural elements within BLM that control DNA and RNA cleavage. The present study also permits inferences to be drawn regarding the practicality of a selection strategy for the solid-phase construction and evaluation of large libraries of BLM analogues having altered properties.

Kinetic studies of the interaction between antitumor antibiotics and DNA using quartz crystal microbalance

OBJECTIVE

Kinetic studies of the interaction process between antitumor antibiotics, Mitomycin C (MMC) and Bleomycin (BLM), and DNA were performed with a novel analytical method, piezoelectric quartz crystal (PQC) impedance analysis.

DESIGN AND METHODS

DNA was directly immobilized on the Au-electrode surface of a piezoelectric quartz crystal by adsorption. The DNA-modified piezoelectric sensor was in contact with Mitomycin C and Bleomycin solution, respectively.

RESULTS

The experimental results demonstrated that antitumor antibiotics concentration had an effect on the interaction. A pseudo-first-order kinetic model for the interaction between antitumor antibiotics and DNA was derived to describe the process. All fitted results were well in agreement with the corresponding experimental results. The kinetic parameters, the interaction rate constants (k(MMC) and k(BLM)), were determined by fitting experimental data to the model. At 37 +/- 0.5 degrees C, the k(MMC) and k(BLM) values obtained were 4.56 (+/-0.02) x 10(-3) and 9.11 (+/-0.02) mM(-1) s(-1), respectively.

CONCLUSION

Piezoelectric quartz crystal impedance (PQCI) analysis is a very powerful method to study the kinetic process of antitumor drugs and DNA interaction.

Activation of the DNA-dependent protein kinase by drug-induced and radiation-induced DNA strand breaks

The DNA-dependent protein kinase (DNA-PK) is a DNA-end activated protein kinase that is required for efficient repair of DNA double-strand breaks (DSBs) and for normal resistance to ionizing radiation. DNA-PK is composed of a DNA-binding subunit, Ku, and a catalytic subunit, DNA-PKcs (PRKDC). We have previously shown that PRKDC is activated when the enzyme interacts with the terminal nucleotides of a DSB. These nucleotides are often damaged when DSBs are introduced by anticancer agents and could therefore prevent recognition by DNA-PK. To determine whether DNA-PK could recognize DNA strand breaks generated by agents used in the treatment of cancer, we damaged plasmid DNA with anticancer drugs and ionizing radiation. The DNA breaks were tested for the ability to activate purified DNA-PK. The data indicate that DSBs produced by bleomycin, calicheamicin and two types of ionizing radiation ((137)Cs gamma rays and N(7+) ions: high and low linear energy transfer, respectively) activate DNA-PK to levels matching the kinase activation obtained with simple restriction endonuclease-induced DSBs. In contrast, the protein-linked DSBs produced by etoposide and topoisomerase II failed to bind and activate DNA-PK. Our findings indicate that DNA-PK recognizes DSBs regardless of chemical complexity but cannot recognize the protein-linked DSBs produced by etoposide and topoisomerase II.

Conformationally constrained analogues of bleomycin A5

The bleomycin (BLM) group antitumor antibiotics are glycopeptide-derived natural products shown to cause sequence selective lesions in DNA. Prior studies have indicated that the linker region, composed of the methylvalerate and threonine residues, may be responsible for a conformational bend in the agent required for efficient DNA cleavage. We have synthesized a number of conformationally constrained methylvalerate analogues and incorporated them into deglycobleomycin A(5) congeners using our recently reported procedure for the solid phase construction of (deglyco)bleomycin and its analogues. These analogues were designed to probe the effects of conformational constraint of the native valerate moiety. Initial experiments indicated that the constrained molecules, none of which mimic the conformation proposed for the natural valerate linker, possessed DNA cleavage activity, albeit with potencies less than that of (deglyco)BLM and lacking sequence selectivity. Further experiments demonstrated that these analogues failed to produce alkali-labile lesions in DNA or sequence selective oxidative damage in RNA. However, two of the conformationally constrained deglycoBLM analogues were shown to mediate RNA cleavage in the absence of added Fe(2+). The ability of the analogues to mediate the oxygenation of small molecules was also assayed, and it was shown that they were as competent in the transfer of oxygen to low molecular weight substrates as the parent compound.

Structures of HO(2)-Co(III)bleomycin A(2) bound to d(GAGCTC)(2) and d(GGAAGCTTCC)(2): structure-reactivity relationships of Co and Fe bleomycins

HO(2)-Co(III)bleomycin is a model for HO(2)-Fe(III)bleomycin, which initiates single and double strand cleavage of DNA. In order to enlarge the understanding of its structure and reactivity, three-dimensional structures of HO(2)-Co(III)bleomycin bound to two DNA oligomers, d(GAGCTC)(2) (I) and d(GGAAGCTTCC)(2) (II), that have 5'-GC-3' binding sites, have been determined by nuclear magnetic resonance (NMR) methods. Besides previously recognized determinants of binding selectivity, a probable hydrogen bond was detected between the pyrimidinyl acetamido NH(2) and the carbonyl of cytosine base paired to G at the recognition site. Another hydrogen bond between the NH of the dimethylsulfonium R group and N7 of guanine opposite cytosine at the GC site may contribute to specification of the pyrimidine. Substitution of G with inosine shifted HO(2)-Co(III)Blm A(2)[bond]I and Fe(III)Blm[bond]I into fast exchange on the NMR time scale, supporting the role of the 2-amino group in site specification for each molecule. The conformationally stable metal-domain linker established a close-packed adduct with the minor groove in which the hydroperoxide ligand occupies a sterically constrained pocket that is isolated from the solvent. The hydroperoxide group is directed toward one of the two cytosine H4' hydrogens but is sterically blocked from access to the other by the drug. These findings enlarge the structural understanding of selective binding of Co(III)/Fe(III)Blm species at G-pyrimidine sites. They also rationalize the instability of a number of ligands bound to Co(III)/Fe(III)Blm at specific binding sequences and the relative unreactivity of Fe(III)Blm[bond]I with ascorbate as well as its lack of interaction with spin labels.

The 1.6-A crystal structure of the copper(II)-bound bleomycin complexed with the bleomycin-binding protein from bleomycin-producing Streptomyces verticillus

Bleomycin (Bm) in the culture broth of Streptomyces verticillus is complexed with Cu(2+) (Cu(II)). In the present study, we determined the x-ray crystal structures of the Cu(II)-bound and the metal-free types of Bm at a high resolution of 1.6 and 1.8 A, respectively, which are complexed with a Bm resistance determinant from Bm-producing S. verticillus, designated BLMA. In the current model of Cu(II).Bm complexed with BLMA, two Cu(II).Bm molecules bind to the BLMA dimer. The electron density map shows that the copper ion is clearly defined in the metal-binding domain of the Bm molecule. The metal ion is penta-coordinated by a tetragonal monopyramidal cage of nitrogens and binds to the primary amine of the beta-aminoalanine moiety of Bm. The binding experiment between Bm and BLMA showed that each of the two Bm-binding pockets has a different dissociation constant (K(d)(1) and K(d)(2)). The K(d)(1) value of 630 nm for the first Bm binding is larger than the K(d)(2) value of 120 nm, indicating that the first Bm binding gives rise to a cooperative binding of the second Bm to the other pocket.

Structure-activity analysis of the potentiation by aminothiols of the chromosome-damaging effect of bleomycin in G0 human lymphocytes

The radioprotective aminothiols 2-[(aminopropyl)amino] ethanethiol (WR-1065) and cysteamine (CSM) potentiate the induction of chromosomal damage by the radiomimetic compound bleomycin (BLM) in G0 human lymphocytes. To investigate the mechanism of potentiation, we measured the clastogenic activity of BLM in the cytokinesis-block micronucleus assay in the presence and absence of amines, thiols, and aminothiols. The hydroxy analog of WR-1065, 2-(3-aminopropylamino) ethanol (WR-OH), potentiates BLM only slightly, indicating the critical nature of the thiol group. As thiols, WR-1065 and CSM may donate electrons for the activation of Fe(+2)-BLM or for the regeneration of Fe(+2)-BLM from inactive Fe(+3)-BLM. The amines putrescine, spermidine, and spermine all potentiate BLM, but they are weaker potentiators than the aminothiols, and they are effective only at high concentrations. Their activity, like that of WR-OH, is probably a consequence of conformational alteration of DNA. Dithioerythritol (DTE) and 2-mercaptoethanol (2-ME), thiols lacking an amino group, are less effective potentiators of BLM than are the aminothiols. The thiol group of WR-1065 and CSM is therefore essential, but insufficient, for explaining the strong enhancement of BLM activity. The cationic nature of CSM and WR-1065, conferred by the amino groups, evidently concentrates the active thiol function at the site of BLM action on DNA. As expected on this basis, the diamine WR-1065 is a more effective potentiator of BLM than is the monoamine CSM, whereas cysteine and N-acetylcysteine (NAC), which lack a net positive charge, potentiate BLM only weakly. These studies suggest that potentiation of the clastogenic action of BLM by aminothiols can be explained by the combination of a thiol-mediated redox mechanism and an amine-mediated targeting of the thiol function to DNA.

Solid-phase synthesis of bleomycin group antibiotics. Elaboration of deglycobleomycin A(5)

The solid-phase syntheses of two deglycobleomycin A(5) analogues were achieved using a commercially available polystyrene resin containing triphenylmethyl-linked spermidine. The final products were deblocked and released from the resin, analyzed, and purified by C(18) reversed phase HPLC and characterized by high-field (1)H NMR spectroscopy and mass spectrometry. The purified products relaxed supercoiled plasmid DNA in a concentration-dependent fashion and to the same extent as authentic material derived from natural BLM A(5).

Synthesis, hydroxyl radical production and cytotoxicity of analogues of bleomycin

Two pyridine analogues of the metal complexing region of the anticancer drug bleomycin and two related but deactivated prodrugs have been linked to a 2,6-diphenylpyridine derivative as a DNA binding unit. The 2,6-diphenylpyridine system is structurally related to known amplifiers of the cytotoxicity of bleomycin. The conjugates were found to bind to DNA more strongly than bleomycin-A2 and were more cytotoxic than the corresponding compounds lacking the DNA binding unit. On exposure of a mixture of cells and prodrugs to hypoxia and then air, the prodrug containing the nitrohistidine unit was not bioreductively activated but the prodrug having an N-oxide group was bioreductively activated. This result represents a novel approach to the improvement of the therapeutic ratio of bleomycin analogues.

Oxidative damage, bleomycin, and gamma radiation induce different types of DNA strand breaks in normal lymphocytes and thymocytes. A comet assay study

Most anticancer treatments such as chemo- and radiotherapy induce DNA damage and apoptosis in normal cells. The aim of this study was to assess the induction of single and double DNA strand breaks (ssb and dsb, respectively) and apoptosis in normal human lymphocytes and rat thymocytes subjected to the action of H2O2, bleomycin and ionizing radiation. Normal human peripheral thymocytes and young rat thymocytes were subjected to the following treatments: a) H2O2; b) bleomycin, and c) gamma-radiation, all with various doses. DNA strand breaks were studied with the alkaline and neutral comet assay for detection of ssb and dsb. Apoptosis was quantified morphologically and with DNA agarose gel electrophoresis. After H2O2 treatment, a dose-dependent increase of ssb was observed. Bleomycin treatment produced a moderate increase of ssb at lower concentrations and a striking increase of dsb at higher concentrations that coincided with the presence of apoptosis and DNA ladders. Gamma radiation initially induced the formation of ssb, and after three hours an increase of dsb in a dose-dependent manner. Apoptosis and DNA laddering appeared only 3 hours post-irradiation. The biomonitoring of DNA damage inflicted by antineoplastic agents can be easily performed with the comet assay and could be useful to monitor and modulate chemo- and radiotherapeutic regimes in cancer patients.

New Robust Bleomycin Analogues: Synthesis, Spectroscopy, and Crystal Structures of the Copper(II) Complexes

Two new bleomycin analogues, 2-[((2-(4-imidazolyl)ethyl)amino)carbonyl]-6-[((2-amino-2-methylpropyl)amino)methyl]pyridine = L(3)() and 2-[((2-(4-imidazolyl)ethyl)amino)carbonyl]-6-[((2-amino-1,1,2-trimethylpropyl)amino)methyl]pyridine = L(4)(), were synthesized in order to create air-stable ligands of their Cu(I) (and Fe(II)) complexes. The protonation constants (log K(n)()) of the ligands at 25 degrees C and I = 0.1 M NaNO(3) were 9.9, 6.9, and 5.2 for L(3)() and 10.0, 6.7, and 3.9 for L(4)(). The complexation of the triprotonated L(3)() and L(4)() with Cu(II) started at pH < 5 to yield 4-coordinate [Cu(II)(H(-)(1)L).H(+)](2+) complexes, 4 and 6, respectively, followed by formation of square-pyramidal [Cu(II)(H(-)(1)L)](+) complexes, 5 and 7, with pK(a) values of 5.6 for 5 and 5.9 for 7. The complexation constants, log K(Cu)()II(H)()-1(L), were 8.9 for [Cu(II)(H(-)(1)L(3))](+), 5, and 8.6 for [Cu(II)(H(-)(1)L(4))](+), 7, respectively. The structures of [Cu(II)(H(-)(1)L(3))]ClO(4) (5.ClO(4)) and [Cu(II)(H(-)(1)L(4))]BF(4) (7.BF(4)) were determined by X-ray crystallography. Crystal data for 5.ClO(4): monoclinic, space group P2(1)/n (No. 14), a = 13.978(6) Å, b = 8.103(3) Å, c = 18.037(5) Å, beta = 98.61(3) degrees, V = 2019(1) Å(3), Z = 4, R = 0.053, and R(w) = 0.044 for 2996 [I > 3sigma(I)] reflections. Crystal data for 7.BF(4): monoclinic, space group P2(1)/n (No. 14), a = 16.092 (4) Å, b = 7.974(4) Å, c = 16.819(2) Å, beta = 99.64(1) degrees, V = 2127(1) Å(3), Z = 4, R = 0.040, and R(w) = 0.025 for 1633 [I > 4sigma(I)] reflections. The coordination geometry around the copper was a distorted square-pyramid in 5, while that of 7 was the intermediate between a trigonal-bipyramid and a square-pyramid. The distortion is influenced strongly by the number of the methyl group. The EPR spectral data for both copper(II) complexes were consistent with the retention of the solid-state structure in frozen DMF/MeOH (1:1) solution at 77 K. The visible absorption spectra of 10% DMF/aqueous solutions (pH 9.5) of 5 and 7 at I = 0.1 M NaNO(3) showed absorption maxima at 646 nm with a shoulder at ca. 900 nm for 5 and at 658 and 888 nm for 7. The red-shift of 7 by ca. 12 nm relative to 5 reflects the distortion toward the trigonal-bipyramidal geometry of 7 in solution. Both complexes displayed irreversible redox behavior in DMF at I = 0.1 M tetra(n-butyl)ammonium tetrafluoroborate. The anodic and cathodic peak potentials obtained by cyclic voltammetry for 5 and 7 were -0.14 and -0.76 V for 5 and -0.17 and -0.80 for 7 vs Ag/AgCl. The cathodic potentials of copper(II) complexes were shifted toward the anodic direction by ca. 20-60 mV compared to the nonsubstituted 5-coordinate, [Cu(II)(H(-)(1)L(1))](+) complex, 16 (-0.82 V vs Ag/AgCl). The Cu(I) complexes (9and 10) are air-oxidized to the corresponding Cu(II) complexes, 5 and 7, respectively.

Kinetics and regioselectivity of peptide-to-heterocycle conversions by microcin B17 synthetase

BACKGROUND

The Escherichia coli peptide antibiotic microcin B17 (MccB17) contains four oxazole and four thiazole rings introduced post-translationally in the 69 amino acid McbA gene product, an MccB17 precursor, by the microcin B,C,D enzyme complex. Both monocyclic and 4,2-bis-heterocyclic moieties are generated. The enzymatic cyclization involves 14 of the last 43 amino acids of McbA and requires the presence of the first 26 amino acids that function as a specificity-conferring propeptide.

RESULTS

We have constructed maltose-binding protein (MBP)-McbA1-46 fusion proteins and have mutagenized the Gly39-Ser40-Cys41 (GSC) wild-type sequence to assess the regioselectivity and chemoselectivity of MccB17-synthetase-mediated heterocycle formation at the first two loci, residues 40 and 41 of McbA. Four single-site and four double-site substrates showed substantial differences in turnover as assessed by western assays, UV-visible spectroscopy and mass spectrometry. Cysteine-derived thiazoles form at a greater rate than serine-derived oxazoles. Formation of bis-heterocycles is sensitive both to composition and sequence context.

CONCLUSIONS

The E. coli McbB,C,D MccB17 synthetase is the first peptide heterocyclization enzyme to be characterized. This study reveals substantial regioselectivity and chemoselectivity (thiazole > oxazole) at the most amino-terminal bis-heterocyclization site of McbA. The heterocyclization of GSS and GCC mutants of McbA1-46 by MccB17 synthetase demonstrates that the complex can efficiently generate tandem bis-oxazoles and bis-thiazoles, moieties not found in MccB17 but present in natural products such as hennoxazole and bleomycin. The observations suggest a common enzymatic mechanism for the formation of peptide-derived heterocyclic natural products.

N-methyl threonine analogues of deglycobleomycin A2: synthesis and evaluation

The synthesis of 5 and its D-allo-threonine epimer 6 and the comparison of their DNA cleavage efficiency and selectivity with that of deglycobleomycin A2 (3) are detailed. The studies illustrate that N-methylation of the L-threonine subunit within deglycobleomycin A2 dramatically reduces the DNA cleavage efficiency (10-15-fold), weakens and nearly abolishes the inherent DNA cleavage selectivity, but has little effect on the inherent oxidation capabilities of the activated Fe(III) complexes. The results are consistent with a previously unrecognized prominent role for the threonine NH and the potential importance of a hydrogen bond to the Fe(III) hydroperoxide complex of bleomycin or a subsequent activated complex implicated in recent structural models.

Mapping of the cleavage-associated bleomycin binding site on DNA with a new method based on site-specific blockage of the minor groove with N2-isobutyrylguanine

Although the binding of various forms of bleomycin to DNA has been studied extensively, the transient nature of the activated bleomycin species which ultimately attacks DNA has largely precluded direct examination of its physical interactions with DNA. In an attempt to map the minimum binding site required for this species to effect DNA cleavage, several oligonucleotide duplexes were synthesized, each of which contained a single N2-isobutyrylguanine moiety at a specific position in the sequence. These duplexes were end-labeled, and sequence-specific bleomycin-induced cleavage was assessed in each strand of each duplex. Isobutyrylguanine substitution immediately 5' to a primary bleomycin target site suppressed bleomycin-induced cleavage by more than 10-fold. Substitution two bases 5' to a target site suppressed cleavage by about 4-fold, and substitution directly opposite the target site suppressed cleavage by 7-fold. Substitution immediately 3' to the target site, or at other more distant positions 3' or 5', had little or no effect. In cases where cleavage at a primary site was strongly suppressed, cleavage at the corresponding secondary site (the putative site of the second break in a bleomycin-induced double-strand break) was also inhibited, even when the secondary site was several bases away from the isobutyrylguanine substitution. The results suggest that the binding site required for bleomycin-induced DNA cleavage spans a region of approximately 2 or 3 bp in the minor groove, including the base associated with the sugar attacked and one or two bases to its 5' side. Computer-based molecular modeling indicated that these results are consistent with the predictions of recently proposed models in which the bithiazole is intercalated immediately 3' to the cleavage site, and the iron coordination site binds in the minor groove immediately 5' to the cleavage site. Both the empirical data and the modeling studies suggest that N2-isobutyrylguanine substitution effectively blocks the minor groove, but without significantly disturbing DNA secondary structure. Thus, it is proposed that site-specific incorporation of N2-isobutyrylguanine may provide a general method for mapping binding sites of minor groove-binding ligands on DNA.

DNA damage and mutagenesis by radiomimetic DNA-cleaving agents: bleomycin, neocarzinostatin and other enediynes

Bleomycin and the enediyne antibiotics effect concerted, simultaneous site-specific free radical attack on sugar moieties in both strands of DNA, resulting in double-strand breaks of defined geometry and chemical structure, as well as abasic sites with closely opposed strand breaks. The hypersensitivity of several mammalian double-strand break repair-deficient mutants to these agents confirms the role of these double-strand breaks in mediating cytotoxicity. In bacteria, mutagenesis by both bleomycin and neocarzinostatin appears to result from replicative bypass of abasic sites, the repair of which is blocked by the presence of closely opposed strand breaks. However, in mammalian cells, such abasic sites decompose to form double-strand breaks, and mutagenesis consists primarily of small deletions, large deletions, and gene rearrangements, all of which probably result from errors in double-strand break repair by a nonhomologous end-joining mechanism. Studies with the radiomimetic antibiotics emphasize the importance of this end-joining repair pathway, and these agents provide useful probes of its mechanistic details, particularly the effects of chemically modified DNA termini on repair.

Photoinduced DNA Cleavage Reactions by Designed Analogues of Co(III)-Bleomycin: The Metalated Core Is the Primary Determinant of Sequence Specificity

A 2,4'-bithiazole group has been covalently attached to the Co(III) complex of a designed ligand PMAH that mimics the metal-binding locus of the antitumor drug bleomycin (BLM). The deprotonated PMA(-) ligand binds Co(III) via five nitrogens located in primary and secondary amines, a pyrimidine and an imidazole ring, and a peptide moiety. The 2,4'-bithiazole group is tethered to the [Co(PMA)](2+) unit via an imidazole that is connected to the bithiazole moiety with a (CH(2))(3) spacer. The structure of this hybrid analogue, namely, [Co(PMA)(Bit)]Cl(2) (7, Bit = 2'-methyl-2,4'-bithiazole-4-carboxamido-N'-(3-propyl)imidazole) has been established by spectroscopic techniques. 7 promotes photocleavage of DNA at micromolar concentrations. Unlike simpler analogues like [Co(PMA)(H(2)O)](2+) and [Co(PMA)Cl)](+) which induce random DNA cleavage upon UV illumination, 7 exhibits sequence specificity in the DNA photocleavage reaction. Intriguing is to note that 7 exhibits the same 5'GG-N3' sequence preference as another hybrid analogue [Co(PMA)(Int-A)]Cl(2) (6, Int-A = acridine-9-carboxamido-N'-(3-propyl)imidazole) that contains an acridine moiety as the DNA-binding group. The observed sequence specificity of 6 and 7 therefore does not reflect the sequence preferences of the DNA-binding groups (acridine and bithiazole). The results indicate that the metalated core of the hybrid analogues, i.e., the [Co(PMA)](2+) unit is the key factor in determining their sequence specificity.

Synthesis and evaluation of deglycobleomycin A2 analogues containing a tertiary N-methyl amide and simple ester replacement for the L-histidine secondary amide: direct functional characterization of the requirement for secondary amide metal complexation

The synthesis and comparative examination of 3-5, analogues of deglycobleomycin A2 (2) which address the inferred importance of the L-histidine secondary amide directly, are detailed. The agent 3 lacks only the L-histidine beta-hydroxy group of deglycobleomycin A2 and the corresponding agents 4 and 5 incorporate a tertiary N-methyl amide and simple ester in place of the L-histidine secondary amide. The DNA cleavage properties of 3 proved essentially indistinguishable from those of deglycobleomycin A2 (2) confirming that the distinctions between bleomycin A2 (1) and deglycobleomycin (2) are due to the removal of the disaccharide and not the introduction of the L-histidine free beta-hydroxy group. The agents 4 and 5 containing a tertiary N-methyl amide and ester in place of the L-histidine secondary amide were found to cleave duplex DNA but to do so in a nonsequence selective fashion with a substantially reduced efficiency and a diminished double to single strand cleavage ratio that are only slightly greater than that of free iron itself. These latter observations establish the functional requirement for the L-histidine secondary amide and are consistent with the proposals that the L-histidine deprotonated secondary amide is required for functional metal chelation and activity.

Synthesis and evaluation of potential N pi and N sigma metal chelation sites within the beta-hydroxy-L-histidine subunit of bleomycin A2: functional characterization of imidazole N pi metal complexation

The synthesis and evaluation of 4 and 5, fully functionalized deglycobleomycin A2 (2) analogues incorporating an oxazole and a pyrrole in place of the beta-hydroxy-L-histidine imidazole, are detailed. The oxazole agent is only capable of Npi metal complexation through a form related to the N1-H imidazole tautomer of bleomycin A2 (1) while the pyrrole agent may potentially mimic the Nsigma metal complexation capabilities of the imidazole N3-H tautomer. Metal complexes (Fe-II, Fe-III) of 4 and 5 were found to cleave duplex DNA in the presence of O2 (Fe-II) or H2O2 (Fe-III). The oxazole agent 4 which is incapable of Nsigma metal chelation was found to behave analogous to, albeit slightly less effectively than, deglycobleomycin A2 resulting in the characteristic 5'-GC/5'-GT sequence selective cleavage of duplex DNA directly confirming that imidazole/oxazole Npi metal chelation is sufficient for functional reactivity. Importantly, the effective substitution of the oxazole O-1 for the histidine N-1 further illustrates that this group does not require deprotonation upon metal complexation, oxygen activation, or the ensuing oxidation reactions, that the functional bleomycin A2 tautomer is the imidazole N'-H tautomer, and that the imidazole N'-H functionality is not contributing to the polynucleotide recognition through H-bonding to the phosphate backbone or nucleotide bases. In contrast, the pyrrole agent 5 which is incapable of Npi metal chelation, but possesses the capabilities of functioning as a Nsigma metal donor was also found to cleave duplex DNA, but does so in a nonsequence selective fashion with a significantly reduced efficiency and a diminished double to single strand cleavage ratio both only slightly above that of background iron itself. These observations are analogous to those made with 3 which lacks the imidazole altogether and further support the observations that Nsigma coordination, not Npi coordination, of the imidazole is required for the functional activity of bleomycin A2.

Synthesis of key analogs of bleomycin A2 that permit a systematic evaluation of the linker region: identification of an exceptionally prominent role for the L-threonine substituent

The synthesis of a full series of analogs 2b-k of deglycobleomycin A2 (2a) containing systematic variations in the linker domain of bleomycin A2 (1) is described. The agents 2b-k, which are not accessible through structural modification of 1 or 2a, constitute key substructure analogs incorporating deep-seated structural modifications in the linker domain capable of delineating the contribution of the individual backbone substituents to the DNA cleavage efficiency, characteristic DNA cleavage selectivity, and double strand to single strand DNA cleavage ratio. The comparative examination of the DNA cleavage properties of the Fe(II) and Fe(III) complexes of 2a-k upon activation by O2-thiol or H2O2, respectively, revealed several characteristic features and trends. First, none of the substituents affect the characteristic 5'-GC, 5'-GT > 5'-GA DNA cleavage selectivity of bleomycin A2. In contrast, an exceptionally prominent role for the L-threonine substituent and an important role for the C4-methyl substituent of the (2S,3S,4R)-4-amino-3-hydroxy-2-methylpentanoic acid subunit were observed on the DNA cleavage efficiency of the agents. Similarly, the L-threonine substituent was found to substantially increase the ratio of double strand to single strand DNA cleavage events (2-3 times). In a w794 DNA cleavage assay, shortening the linker region by two carbons resulted in an exceptionally large reduction in DNA cleavage efficiency (125 times) and provided an agent that was only 1.3 times more effective than Fe(III) indicating that this deep-seated modification essentially destroys the DNA cleavage capabilities of the agent. The L-threonine substituent contributes in an exceptional manner, and its removal resulted in a 25 times reduction in DNA cleavage efficiency. A substantial contribution was observed for the C4-methyl group on the 4-aminobutanoic acid subunit and its removal resulted in a 7 times reduction in DNA cleavage efficiency. Little effect for the C3-hydroxyl and C2-methyl substituents on the 4- aminobutanoic acid subunit was observed (0-2.5 times) and even their inversion of stereochemistry had little impact on DNA cleavage efficiency or selectivity. Notably, the magnitude of the previously unappreciated L-threonine substituent contribution to the DNA cleavage efficiency and on the ratio of double to single strand DNA cleavage events is the largest effect observed to date including the well recognized disaccharide potentiation (6 times) of the DNA cleavage properties. Consequently, the past role and relative importance of the L-threonine subunit and substituent has been underestimated. Moreover, the cumulative effect of the two important linker chain substituents clearly illustrate that the functional role of this domain is much more important than its simply serving as a linker.