Copper(I) . bleomycin. A structurally unique oxidation-reduction active complex

Cu(I) and Cu(II) form stable 1:1 complexes with bleomycin (BLM). The affinity of both metals for the drug is greater than that of Fe(II). Cu(I) . BLM A2 binds to calf thymus DNA with about the same affinity as Fe(II) . BLM, as judged by DNA-induced fluorescence quenching of the bithiazole moiety of BLM. Based on 1H NMR and potentiometric titration data, the Cu(I) complexes of BLM are shown to have geometries very different than those of other BLM . metal(II) complexes studied thus far. As Cu(I) . BLM is oxidation-reduction active, its geometry is of importance in defining the structural requirements for BLM activity.     

Redox potential of the active bleomycin-Fe(III) complex by cyclic voltammetry

The redox potential of the active Fe(III) complex of bleomycin (BLM), which is a DNA cleaving species, was measured by cyclic voltammetry at 25 °C under a hydrogen atmosphere. The cyclic voltammogram showed the reversible one-electron Fe(III)/Fe(II) coupled redox reaction at −0.225 V versus SCE. Under the same conditions the redox potentials of the iso-BLM—Fe(III) complex and the deglyco-BLM—Fe(III) complex were also observed, but the cyclic voltammogram for the inactive Fe(III) complex of BLM could not be obtained.     

Structural study of copper(I)-bleomycin

Previous NMR studies on Cu(I)-bleomycin have suggested that this adduct has a geometry distinct from Fe(II)BLM. The coordination chemistry of this bleomycin derivative has been investigated through the extension of the NMR data reported previously, and the use of molecular dynamics calculations. The data collected from the NMR experiments support the coordination to the metal center of the primary and secondary amines in beta-aminoalanine and the pyrimidine ring. The detection in the NMR spectra of the signal derived from the amide hydrogen in beta-hydroxyhistidine indicates that this amide is protonated in Cu(I)-bleomycin, precluding participation of the pyrimidinyl carboxamide nitrogen in the coordination of Cu(I), as previously reported. Three-dimensional solution structures compatible with the NMR data have been assayed for Cu(I)-bleomycin for the first time by way of molecular dynamics calculations, and two models showing four and five coordination have been found to be those that better fit the experimental data. In both models the primary amine in beta-aminoalanine is coordinated such that it is located on the same side, with respect to the coordination cage, as the peptide linker fragment. This result seems important for the favored models to be compatible with either their possible oxidation to become one of the reported structures for Cu(II)BLM, or their transformation into Fe(II) adducts able to cause DNA damage.     

Deglyco-peplomycin metal complexes on DNA fibers: a role of the sugar moiety for the stability and the orientation of the complexes

Binding structures of metal complexes of deglyco-peplomycin (dPEP) on DNA were investigated by comparing dPEP complexes with those of bleomycin (BLM) using DNA fiber EPR spectroscopy. A low spin species of Fe(III)dPEP observed in the DNA pellet changed irreversibly to several high spin species after the fabrication of the DNA fibers. The g values of the high spin species were different from those of Fe(III)BLM. The high spin species could not be nitrosylated reductively to ON-Fe(II)dPEP, suggesting that some nitrogen atoms coordinated to the Fe(III) were displaced on the DNA fibers. On the other hand, O(2)-Co(II)dPEP remained intact on the fibers similarly to O(2)-Co(II)BLM but with an increased randomness in the orientation on the DNA. In contrast to Cu(II)BLM, a considerable amount of Cu(II)dPEP bound almost randomly on B-form DNA fibers. These results indicated that the sugar moiety in peplomycin or bleomycin is playing an important role in enhancing the stability of the metal-binding domain and in the stereospecificity of the binding on DNA.     

Solution structure of Fe(II)–azide–bleomycin derived from NMR data: transition from Fe(II)–bleomycin to Fe(II)–azide–bleomycin as derived from NMR data and structural calculations

The coordination cage of the metal center in Fe(II)-bleomycin has been proposed to consist of the secondary amines in β-aminoalanine, the pyrimidinylpropionamide and imidazole rings, and the amide nitrogen in β-hydroxyhistidine as equatorial ligands, and the primary amine in β-aminoalanine and either the carbamoyl group in mannose or a solvent molecule occupying the axial sites. With the aim of supporting or not supporting coordination of a water molecule to the metal center in Fe(II)-bleomycin, the solution structure of Fe(II)-azide-bleomycin has been derived from NMR data. The structural changes that occur in Fe(II)-bleomycin upon azide binding have been monitored by comparing the experimental results with those obtained from the calculated structures for both bleomycin adducts. The results of this investigation strongly support a model of Fe(II)-bleomycin with six endogenous ligands as the most likely structure held in solution by this metallobleomycin in the absence of DNA.     

Suppression of somatostatin levels in the hepatic portal and systemic plasma of the rat by synthetic human pancreatic polypeptide.

The 1:1 Cu(II), Co(II), Co(II)-O₂, Fe(II)-NO, and Fe(III) complexes of depBLM have been investigated by ESR spectroscopy and compared with the corresponding metal complexes of BLM. DepBLM which lacks the α-amino group of β-aminoalanine portion in BLM molecule, forms the metal complexes different from BLM with regard to the fifth axial donor. In addition, the formation of hydroxyl radical by the depBLM-Fe(II) complex is remarkably lower than that by the BLM-Fe(II) complex. This study indicates an important effect of fifth axial nitrogen on metal coordination and oxygen activation of BLM.     

Oxygen transfer from bleomycin-metal complexes

Both Fe(III) and Cu(II) complexes of bleomycin (BLM), but not N-acetyl BLM . Fe(III), mediated the transfer of oxygen from iodosobenzene to organic substrates. In analogy with results obtained using certain cytochrome P-450 analogs, cis-stilbene was converted cleanly to the respective oxide, while no more than traces of trans-stilbene oxide were formed from trans-stilbene under identical conditions. The possible relevance of these observations to the degradation of DNA by bleomycin was also studied. In both the presence and absence of O2, BLM . Cu(II) . C6H5IO effected DNA degradation, as judged by the release of [3H]thymine from radiolabeled Escherichia coli DNA. These findings provide a valuable new assay system for the study of bleomycin analogs and suggest the possibility that bleomycin may function as an "oxygen transferase" in its degradation of DNA in situ.     

Degradation of structurally modified DNAs by bleomycin group antibiotics

Bleomycin-mediated DNA strand scission has been shown to be diminished at certain sequences in proximity to 5-methylcytidines. We have investigated the molecular basis of this observed diminution using selective bleomycin (BLM) modifications at the C-terminus. Of the four different bleomycin congeners investigated, only bleomycin A2 and bleomycin BAPP were substantially affected by cytidine methylation. We have also examined the effect of other DNA modifications on bleomycin-mediated strand scission. Methylation at the N6 position of adenosine resulted in diminution of DNA cleavage by all four bleomycin congeners. The presence of bulky 5-(glucosyloxy)methyl groups in the major groove of T4 DNA had little effect on the efficiency of DNA strand scission mediated by bleomycin A2 or B2, suggesting the absence of important steric interactions between Fe(II).BLM and DNA in the major groove. In contrast, DNA cleavage mediated by bleomycin congeners was very sensitive to a major DNA conformational change, the B----Z transition. Salt and MgCl2 titrations of the DNA copolymers poly(dG-dC).poly(dG-dC) and poly(dG-MedC).poly(dG-MedC) demonstrated that bleomycin A2 and B2 did not cleave Z-DNA efficiently. In addition, circular dichroism titrations of these copolymers revealed that both bleomycin congeners increased the cation concentration necessary to induce the B----Z transition, implying that bleomycin preferentially binds to and stabilizes B-form DNA. These results are consistent with a model in which cytidine methylation at appropriate sequences of DNA is sufficient to induce subtle conformational changes that render the helix unreceptive to cleavage by some bleomycin congeners.     

Single-strand and double-strand deoxyribonucleic acid breaks produced by several bleomycin analogues

Production of single-strand breaks (ssb) and double-strand breaks (dsb) of PM2 phage DNA by several structurally related bleomycin (BLM) analogues was studied by gel electrophoresis. BLM A2 and BLM B2 produced a comparable extent of dsb. In various experiments, BLM A2 and BLM B2, at 22-41 ng/mL, degraded 50% of the form I DNA into 33-38% form II and 12-17% form III DNA. BLM B1' produced ssb and dsb at a ratio similar to that of BLM A2, but both at a rate less than half that of BLM A2. Phleomycin (PLM) D1 induced an equivalent amount of ssb but only one-eighth of dsb induced by BLM B2. The relatively lower extent dsb production for PLM D1 was observed either in borate buffer (pH 9.5) or in Tris-HCl buffer (pH 7.5) and in the presence or absence of exogenous Fe(II). Deamido-BLM A2 produced ssb to an extent approximately half that of BLM A2 and dsb to less than one-eighth that of BLM A2. The following conclusions were drawn. (1) BLM analogues produced ssb and dsb to different extents and ratios. (2) The ratio of dsb to ssb varied depending on the analogue, indicating a lack of a direct correlation between ssb and dsb. (3) The extent of ssb and dsb was affected by modifications on both the C- and N-terminal half-molecules of BLM: modification of either the N-terminal amide or the bithiazole greatly reduced dsb, whereas changes in structure or charge in the C-terminal amine affected ssb and dsb to a similar extent.     

Iron-bleomycin-deoxyribonucleic acid system. Evidence of deoxyribonucleic acid interaction with the alpha-amino group of the beta-aminoalanine moiety

The Fe(III) complex of bleomycin (BLM) is, at pH 4, in the high-spin form. At pH 7, the coordination of the alpha-amino group of the beta-aminoalanine moiety of BLM converts it to a low-spin species: BLM X Fe(III) X alpha NH2. The conversion of the high-spin species to the low-spin one can also take place at pH 4 (i) by addition of ligands L such as N3-, S2O3(2-), and SCN- or (ii) through interaction with DNA. Moreover, the addition, at pH 7, of DNA to BLM X Fe(III) that has been previously complexed with one of these ligands L displaces this latter from its position. These results suggest that (i) the ligand L occupies the same site of coordination as the alpha-amino group and (ii) an interaction occurs between the beta-aminoalanine moiety of BLM and DNA that lowers the pKd of the alpha-amino group, promoting its coordination to iron.     

The anticancer drug bleomycin investigated by density functional theory

Activated bleomycin (ABLM) is an oxygenated iron drug complex which embodies the drug's DNA-cleaving activity. This activity is exercised on DNA, if present, but if DNA is absent, the drug itself is inactivated. We have employed quantum density functional theory (DFT)-based methods to investigate (i) the structure of the Fe(II)BLM complex that is first formed in the human body after drug's administration, and (ii) the activation mechanism of the O–O bond present in the ABLM. We have identified the controversial second axial ligand as the endogenous oxygen atom of the carbamoyl group. Our first principles molecular dynamics (MD) simulations indicate a homolytic cleavage as the mechanism of the O–O bond activation in the ABLM complex.     

Copper(I)-bleomycin: structurally unique complex that mediates oxidative DNA strand scission

Copper(I)-bleomycin [Cu(I) X BLM] was characterized in detail by 13C and 1H NMR. Unequivocal chemical shift assignments for Cu(I) X BLM and Cu(I) X BLM X CO were made by two-dimensional 1H-13C correlated spectroscopy and by utilizing the observation that Cu(I) X BLM was in rapid equilibrium with Cu(I) and metal-free bleomycin, such that individual resonances in the spectra of BLM and Cu(I) X BLM could be correlated. The binding of Cu(I) by bleomycin involves the beta-aminoalaninamide and pyrimidinyl moieties, and possibly the imidazole, but not N alpha of beta-hydroxyhistidine. Although no DNA strand scission by Cu(II) X BLM could be demonstrated in the absence of dithiothreitol, in the presence of this reducing agent substantial degradation of [3H]DNA was observed, as was strand scission of cccDNA. DNA degradation by Cu(I) X BLM was shown not to depend on contaminating Fe(II) and not to result in the formation of thymine propenal; the probable reason(s) for the lack of observed DNA degradation in earlier studies employing Cu(II) X BLM and dithiothreitol was (were) also identified. DNA strand scission was also noted under anaerobic conditions when Cu(II) X BLM and iodosobenzene were employed. If it is assumed that the mechanism of DNA degradation in this case is the same as that under aerobic conditions (i.e., with Cu(I) X BLM + O2 in the presence of dithiothreitol), then Cu X BLM must be capable of functioning as a monooxygenase in its degradation of DNA.     

The Cys-Xaa-His metal-binding motif: {<Emphasis Type="Italic">N</Emphasis>} versus {<Emphasis Type="Italic">S</Emphasis>} coordination and nickel-mediated formation of cysteinyl sulfinic acid

A series of peptide ligands containing the sequence -Cys-Xaa-His- (CXH; Xaa=Gly or Lys) has been prepared and the coordination chemistry of these peptides with nickel(II) investigated. Selective protection of either the N-terminal cysteine thiol or amine group gave complexes with amino or thiolato coordination, respectively, to nickel(II). Insertion of CGH into a pentapeptide, N-acetyl-Ala-Cys-Gly-His-Ala-CONH₂, allowed the formation of a square-planar thiolato Cys-Gly-His complex with nickel(II) in an internal position of the peptide. Inclusion of an N-terminal cysteine residue with a free amino terminus gave rise to pH- and dioxygen-dependent coordination behavior. Solutions of CGH-CONH₂ with nickel(II) at neutral pH yielded a red nickel-thiolate complex, but at higher pH (8.5 or above) or with exposure to dioxygen, yellow nickel complexes with N-terminal amino coordination were observed. The disulfide-bridged dimers formed from Ni(CGH-CONH₂) in the presence of air were characterized and found to have the typical coordination found in the amino-terminal binding motif of the serum albumins. Nickel(II) coordination and thiol reactivity were also studied by determination of rates of thiol alkylation and by monitoring air oxidation in the presence of various metals. Zinc(II) effectively inhibits thiol alkylation and oxidation (disulfide formation) in all the peptides studied. Nickel(II) inhibits aerobic oxidation and alkylation of N-terminal protected peptides such as N-acetyl-Cys-Gly-His, but does not inhibit air oxidation of free amino terminal peptides such as Cys-Gly-His. Instead, nickel(II) mediates the formation an additional product under aerobic conditions, a cysteinesulfinic acid.Electronic Supplementary Material Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.Abbreviations CGH cysteinylglycylhistidine - GGH glycylglycylhistidine - Xaa any amino acid     

Molecular crystals: the crystal field effect on molecular electronic structure

The effect of crystal packing on the electronic structure of organic molecules was modeled by incorporation of the external electrostatic potential into the semiempirical Hamiltonian of the molecule. An empirical correction procedure was devised in order to compensate for systematic errors in the charge distribution typical of semiempirical methods. The model was applied to 79 crystal structures belonging to various syngonies and space groups. The effect of the crystal field is subject to wide variations depending on the crystal packing motif. The difference between the effect of the crystal field on the molecular electronic structure and the solvent effect modeled with COSMO is highlighted. The effect of intermolecular hydrogen bonds on the molecular electronic structure and electronic spectra was modeled with this approach, and it does not predominate over the effect of long-range electrostatic interactions. INDO/S calculations employing the crystal electrostatic potential give an insight into the origin of crystallochromy, in particular, they properly predict color difference for several groups of polymorphs. Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.Electronic Supplementary Material Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction

Some sulfate-reducing and microaerophilic bacteria rely on the enzyme superoxide reductase (SOR) to eliminate the toxic superoxide anion radical (O2*-). SOR catalyses the one-electron reduction of O2*- to hydrogen peroxide at a nonheme ferrous iron center. The structures of Desulfoarculus baarsii SOR (mutant E47A) alone and in complex with ferrocyanide were solved to 1.15 and 1.7 A resolution, respectively. The latter structure, the first ever reported of a complex between ferrocyanide and a protein, reveals that this organo-metallic compound entirely plugs the SOR active site, coordinating the active iron through a bent cyano bridge. The subtle structural differences between the mixed-valence and the fully reduced SOR-ferrocyanide adducts were investigated by taking advantage of the photoelectrons induced by X-rays. The results reveal that photo-reduction from Fe(III) to Fe(II) of the iron center, a very rapid process under a powerful synchrotron beam, induces an expansion of the SOR active site.     

Selective strand scission by intercalating drugs at DNA bulges

A bulge is an extra, unpaired nucleotide on one strand of a DNA double helix. This paper describes bulge-specific strand scission by the DNA intercalating/cleaving drugs neocarzinostatin chromophore (NCS-C), bleomycin (BLM), and methidiumpropyl-EDTA (MPE). For this study we have constructed a series of 5'-32P end labeled oligonucleotide duplexes that are identical except for the location of a bulge. In each successive duplex of the series, a bulge has been shifted stepwise up (from 5' to 3') one strand of the duplex. Similarly, in each successive duplex of the series, sites of bulge-specific scission and protection were observed to shift in a stepwise manner. The results show that throughout the series of bulged duplexes NCS-C causes specific scission at a site near a bulge, BLM causes specific scission at a site near a bulge, and MPE-Fe(II) causes specific scission centered around the bulge. In some sequences, NCS-C and BLM each cause bulge-specific scission at second sites. Further, bulged DNA shows sites of protection from NCS-C and BLM scission. The results are consistent with a model of bulged DNA with (1) a high-stability intercalation site at the bulge, (2) in some sequences, a second high-stability intercalation site adjacent to the first site, and (3) two sites of relatively unstable intercalation that flank the two stable intercalation sites. On the basis of our results, we propose a new model of the BLM/DNA complex with the site of intercalation on the 3' side (not in the center) of the dinucleotide that determines BLM binding specificity.(ABSTRACT TRUNCATED AT 250 WORDS)     

Iron-bleomycin interactions with oxygen and oxygen analogues. Effects on spectra and drug activity.

Despite extensive structural dissimilarities, iron . bleomycin complexes and heme-containing oxygenases display remarkable similarities in binding oxygen antagonists and in spectral properties deriving from bound iron. Fe(II)-bleomycin reversibly forms a complex with either CO or isocyanide (lambda max = 384 and 497 nm, respectively), either of which interfere with its oxygen-dependent cleavage of DNA. A similar but paramagnetic complex forms with NO (lambda max = 470 nm; AN = 24 G). In contrast, cyanide enhances bleomycin activity against DNA. Complexes of bleomycin and FE(III), formed either by direct association or by autoxidation of the Fe(II) . bleomycin complex, exhibit indistinguishable EPR and visible spectra, which change characteristically with pH. At neutral pH, Fe(III) . bleomycin is a low spin complex (g = 2.45, 2.18, 1.89; lambda max = 365, 384 nm) and, at low pH, it is a high spin rhombic complex (geff = 9.4, 4.3; lambda max = 430 nm). These complexes are interconvertible (pK 4.3). Fe(II) . bleomycin oxidation, although reversible by spectral criteria, is accompanied by drug inactivation unless DNA is present.     

A role for ferrous ion and oxygen in the degradation of DNA by bleomycin.

An interaction between bleomycin and low concentrations of Fe(II) in the degradation of DNA is reported. Complete conversion of simian virus 40 DNA to acid-soluble products occurs at approximately equimolar levels of Fe(II), bleomycin, and DNA; Fe(III) does not substitute for Fe(II) in this reaction. Anaerobiosis inhibits the observed DNA degradation by bleomycin and Fe(II). Optical spectral studies reveal that an oxygen-labile complex is formed between bleomycin and Fe(II).     

Reaction of DNA-bound Co(II)bleomycin with dioxygen.

The aerobic oxidation of Co(II)bleomycin bound to calf thymus DNA has been investigated in relation to the mechanism of reaction in solution in the absence of DNA. Kinetics of dioxygenation of the Co(II) complex were followed by spectrophotometric and electron spin resonance spectroscopy as well as dioxygen analysis. The reaction is slower than when carried out in solution; its rate is inversely related to the ratio of DNA base pairs to Co(II)bleomycin. The subsequent oxidation reaction, observed spectrophotometrically and by dioxygen analysis, is second order in cobalt complex. The calculated second order rate constant is also inversely related to the base pair to metal complex ratio. Once this ratio exceeds three, the reaction rate slows significantly with each additional increment of DNA added to the starting reaction mixture. Taking advantage of the high stability of O(2)-Co(II)bleomycin bound to greater than a 3-fold excess of DNA base pairs, it could be demonstrated that the rate constant for oxidation of two O(2)-Co(II)bleomycin molecules is much slower than that for O(2)-Co(II)bleomycin plus Co(II)bleomycin. With the same technique it was observed that the metal centers of O(2)-Co(II)bleomycin and Fe(II)bleomycin also undergo oxidation. The binding to DNA of both solution products of the oxidation of Co(II)bleomycin by O2 was examined by 1H NMR spectroscopy. Peroxy-Co(III)bleomycin, Form I, binds with higher affinity than Co(III)bleomycin, Form II. At lower ionic strength, the size of the DNA binding site for each form is about 2 base pairs/molecule of drug.     

Deglyco-bleomycin. Degradation of DNA and formation of a structurally unique Fe(II) . CO complex

In analogy with bleomycin, deglyco-bleomycin B2 has been found to form a stable, diamagnetic complex with Fe(II) and CO. Although the stoichiometry of this complex appeared to be the same as that formed with bleomycin, the geometry of the deglyco-bleomycin complex was fundamentally different, especially as regards orientation of the beta-aminoalanine moiety. In the presence of Fe(II) and O2, deglyco-bleomycin A2 and deglyco-bleomycin B2 were found to release [3H]thymine from radiolabeled PM-2 DNA; when employed at limiting concentrations, deglyco-bleomycin A2 and B2 gave about half as much [3H]thymine release as the respective bleomycins. In view of the spectral evidence (Burger, R. M., Horwitz, S. B., Peisach, J., and Wittenberg, J. B. (1979) J. Biol. Chem. 254, 12299-12302) that Fe(II) . bleomycin . CO has the same geometry as the complex formed by initial association of bleomycin, Fe(II), and O2, the accumulated data suggest strongly that all metal complexes of bleomycin (derivatives) capable of DNA degradation need not have the same geometry.