An efficient mammalian transfer RNA target for bleomycin

The antitumor antibiotic bleomycin has long been believed to exert its therapeutic effects at the level of DNA cleavage. Recently, evidence has been presented to suggest that RNA cleavage may also be important and that one or more transfer RNAs may be involved. To define those tRNAs that may represent important loci for the action of bleomycin, we have fractionated chicken liver tRNAs and identified those isoacceptors most susceptible to oxidative cleavage by Fe(II).BLM. Two chicken liver tRNAs, tRNA3Lys and tRNAPhe, were found to be cleaved with exceptional facility by Fe(II).BLM, and both were cleaved predominantly at U66. The cleavage of tRNA3Lys was shown to be minimally affected by physiological concentrations of Mg2+. Chicken liver tRNA3Lys is identical in sequence with human tRNA3Lys. These findings support a possible role for a critical tRNA such as tRNA3Lys in the mechanism by which bleomycin mediates its antitumor activity.     

Resonance Raman studies of HOO-Co(III)bleomycin and Co(III)bleomycin: identification of two important vibrational modes, nu(Co-OOH) and nu(O-OH)

Bleomycin is an antitumor agent whose cytotoxicity is dependent on its ability to bind DNA in the nucleus and effect double-stranded DNA cleavage, which is difficult for the cell to repair. In order for this DNA cleavage to occur, bleomycin must, through a series of reactions, form a low-spin Fe(III) complex, the putative "activated" form of the drug, HOO-Fe(III)bleomycin. The relative strengths of the bonds in the Fe(III)-OOH linkage have not been determined due to the weakness of the hydroperoxo-to-iron(III) charge-transfer transition. The much more stable HOO-Co(III)bleomycin has often been studied as a structural analogue of HOO-Fe(III)bleomycin, and hence, an understanding of the relative bond strengths in the Co-OOH linkage may serve to enhance our understanding of the analogous Fe-OOH linkage. In this report, we present resonance Raman data that identify two important vibrational modes in the Co-OOH linkage, the stretching modes, nu(Co-OOH) and nu(O-OH). Both of these vibrational modes were found to be unperturbed by complexation of the drug with calf thymus DNA. Advantage was also taken of the isostructural realtionship between Fe-bleomycin and Co-bleomycin to analyze and assign the high-frequency modes for HOO-Co(III)bleomycin and Co(III)bleomycin (A(2) and B(2)). These data could be useful for future studies of photoactivated Co-bleomycin and Co-bleomycin analogues in an attempt to characterize oxygen-independent DNA damage pathways.     

Cryogenic photolysis of activated bleomycin to ferric bleomycin

Activated bleomycin (ABLM) is a drug--Fe(III)-hydroperoxide complex kinetically competent in DNA attack (via H4' abstraction). This intermediate is relatively stable, but its spontaneous conversion to ferric bleomycin (Fe(III).BLM) is poorly characterized because no observable intermediate product accumulates. Light was shown to trigger ABLM attack on DNA in liquid at -30 degrees C, so ABLM was irradiated (at its 350 nm ligand-to-metal charge-transfer transition) at 77 K to stabilize possible intermediates. ABLM photolysis (quantum yield, Phi = 0.005) generates two kinds of product: Fe(III).BLM (with no detectable intermediate) and one or more minor (1-2%) radical O-Fe-BLM byproduct, photostable at 77 K. Adding DNA, even without its target H4', increases the quantum yield of ABLM conversion >10-fold while suppressing the observed radical yield. Since cryogenic solid-phase reactions can entail only constrained local rearrangement, the reaction(s) converting ABLM to Fe(III).BLM must be similarly constrained.     

RNA cleavage and inhibition of protein synthesis by bleomycin

Bleomycin is a clinically used antitumor antibiotic long thought to function therapeutically at the level of DNA cleavage. Recently, it has become clear that bleomycin can also cleave selected members of all major classes of RNA. Using the computer program COMPARE to search the database established by the Anticancer Drug Screening Program of the National Cancer Institute, a possible mechanism-based correlation was found between onconase, an antitumor ribonuclease currently being evaluated in phase III clinical trials, and the chemotherapeutic agent bleomycin. Following these observations, experimentation revealed that bleomycin caused tRNA cleavage and DNA-independent protein synthesis inhibition in rabbit reticulocyte lysate and when microinjected into Xenopus oocytes. The correlation of protein synthesis inhibition to the previously reported site-specific RNA cleavage caused by bleomycin supports the thesis that RNA cleavage may constitute an important element of the mechanism of action of bleomycin.     

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.     

A novel DNA hairpin substrate for bleomycin

A 16-nucleotide DNA hairpin containing 4-aminobenzo[g]quinazoline-2-one 2'-deoxyribose at position 15 has been prepared and found to lack significant fluorescence. When treated with Fe(II).BLM, the hairpin was found to undergo oxidative transformation selectively at position 15. The predominant fluorescent product was characterized and quantified. The pro-fluorescent DNA hairpin was used as a substrate for 15 bleomycin congeners, and the results were compared with those obtained following cleavage of a radiolabeled DNA duplex and PAGE analysis.     

Characterization of bleomycin cleavage sites in strongly bound hairpin DNAs

The first complete, systematic study of DNA degradation by bleomycin under conditions analogous to those likely in a therapeutic setting has been carried out. Hairpin DNAs selected for their ability to bind strongly to BLM A(5) were used to determine the relationship between high-affinity DNA binding sites and the cleavage efficiency and selectivity of BLM A(5) and deglycoBLM A(5) on these DNAs. Of the 10 hairpin DNAs examined, 8 contained at least one 5'-GC-3' or 5'-GT-3' cleavage site, which have traditionally been associated with strong cleavage by Fe·BLM. In the hairpin DNAs, these included the strongest cleavage sites for BLM A(5) and were generally among those for deglycoBLM A(5). However, numerous additional cleavages were noted, many at sequences not usually associated with (deglyco)BLM-mediated cleavage. The remaining DNAs lacked the preferred (5'-GC-3' or 5'-GT-3') BLM cleavage sequences; however, strong cleavage was nonetheless observed at a number of unusual cleavage sites. The most prominent cleavage sequences were 5'-AT-3', 5'-AA-3', 5'-GA-3', and 5'-TT-3'; treatment with Fe(II)·BLM A(5) or Fe(II)·deglycoBLM A(5) resulted in strong cleavage at these sequences. Additionally, in contrast with BLM A(5), which produced cleavage within the randomized and flanking invariant regions, deglycoBLM A(5) showed a preference for cleavage in the randomized region of the DNAs. Previous reports have established that deglycoBLM exhibits decreased DNA cleavage efficiency relative to BLM. This was also generally observed when comparing cleavage efficiencies for the strongly bound hairpin DNAs. However, some cleavage bands produced by Fe·deglycoBLM A(5) were stronger in intensity than those produced by BLM A(5) at concentrations optimal for both compounds. To investigate the chemistry of DNA degradation, selected hairpin DNAs were treated with n-butylamine following cleavage with Fe(II)·BLM A(5) or Fe(II)·deglycoBLM A(5) to explore the alkali labile pathway of DNA degradation by BLM. While all 10 DNAs showed evidence of alkali labile products, five DNA hairpins afforded some products formed solely via the alkali labile pathway.     

Solid-phase synthesis of bleomycin group antibiotics. Construction of a 108-member deglycobleomycin library

The bleomycins (BLMs) are structurally related glycopeptide antibiotics isolated from Streptomyces verticillus that mediate the sequence-selective oxidative damage of DNA and RNA. Deglycobleomycin, which lacks the carbohydrate moiety, cleaves DNA analogously to bleomycin itself, albeit less potently, and has been used successfully for analyzing the functional domains of bleomycin. Although structural modifications to bleomycin and deglycobleomycin have been reported, no bleomycin or deglycobleomycin analogue having enhanced DNA cleavage activity has yet been described. The successful synthesis of a deglycobleomycin on a solid support has permitted the facile solid-phase synthesis of 108 unique deglycobleomycin analogues through parallel solid-phase synthesis. Each of the deglycobleomycin analogues was synthesized efficiently; the purity of each crude product was greater than 60%, as determined by HPLC integration. The solid-phase synthesis of the deglycobleomycin library provided near-milligram to milligram quantities of each deglycobleomycin, thereby permitting characterization by (1)H NMR and high-resolution mass spectrometry. Each analogue demonstrated supercoiled plasmid DNA relaxation above background cleavage; the library included two analogues that mediated plasmid relaxation to a greater extent than the parent deglycobleomycin molecule.     

Interaction of bleomycin with deoxyribonucleic acid oligomer: proton nuclear magnetic resonance titration study using novel bleomycin complexes with Ni2+ and VO3+.

Two metal complexes of bleomycin (BLM), BLM-Ni2+ and BLM-VO3+ are used for studying interactions between BLM and deoxyribonucleic acid (DNA) by nuclear magnetic resonance. Although these BLMs do not mediate DNA strand scission under the usual conditions, they bind to DNA in the same manner as the active metal complexes of bleomycin (BLM-Fe2+ and BLM-Co3+). A self-complementary dodecanucleotide, d(CCCCAGCTGGGG), having a single site for cleavage was synthesized. d(CCCCAATTGGGG), which contains no -GpC- sequence, was also synthesized. The BLM-metal complexes were shown to bind specifically to the GpC site by circular dichroism and fluorescence titration studies. We assigned all the resonances for imino protons and phosphorus, and most of the nonexchangeable proton resonances of d(CCCCAGCTGGGG). No substantial change in the chemical shifts of these signals was observed upon titration with either BLM-Ni2+ or BLM-VO3+. This result is not consistent with a model of the strong intercalation of the BLMs between the base-pairs. The BLMs bind to DNA in a different manner, and DNA does not change its conformation upon binding with BLMs.     

Identification of strong DNA binding motifs for bleomycin

The bleomycins (BLMs) are clinically used antitumor antibiotics. Their mechanism of action is believed to involve oxidative cleavage of DNA and possibly also RNA degradation. DNA degradation has been studied extensively and shown to involve binding of an activated metallobleomycin to DNA, followed by abstraction of C4'-H from deoxyribose in the rate-limiting step for DNA degradation. It is interesting that while DNA and RNA degradation by activated Fe.BLM has been studied extensively, much less is known about the actual binding selectivity of BLM, that is, the obligatory step that precedes cleavage. Thus it is unclear whether cleavage specificity is defined by the binding event or whether cleavage occurs at a subset of preferred binding sites. With only a few exceptions, NMR binding studies have employed metalloBLMs such as Co.BLM and Zn.BLM whose therapeutic relevance is uncertain. A single biochemical study that compared DNA binding and cleavage directly also employed Co.BLM. It is logical to anticipate that preferred sites of DNA cleavage will occur at sites that are (a subset of) preferred DNA binding sites, but there are currently no data available relevant to this issue. Herein, we describe the development and implementation of a novel strategy to identify DNA motifs that bind BLM strongly.     

Metabolism of a novel antiangiogenic agent KR-31831 in rats using liquid chromatography-electrospray mass spectrometry

KR-31831 ((2S,3R,4S)-4-(((1H-imidazol-2-yl)methyl)(4-chlorophenyl)amino)-6-amino-2-(dimethoxymethyl)-2-methyl-3,4-dihydro-2H-chromen-3-ol) is a novel antiangiogenic agent. In vitro and in vivo metabolism of KR-31831 in rats has been investigated using LC-MS and LC-MS/MS analysis. Incubation of rat liver microsomes and hepatocytes with KR-31831 produced three metabolites (M1-M3). M1, M2, and M3 were identified as N-((1H-imidazol-2-yl)methyl)-4-chlorobenzenamine, (2R,3R,4S)-4-(((1H-imidazol-2-yl)methyl)(4-chlorophenyl) amino)-6-amino-2-(hydroxymethyl)-2-methyl-3,4-dihydro-2H-chromen-3-ol, and N-((2S,3R,4S)-4- (((1H-imidazol-2-yl)methyl)(4-chlorophenyl)amino)-2-(dimethoxymethyl)-3-hydroxy-2-methyl-3,4-dihydro-2H-chromen-6yl)acetamide, respectively, by co-chromatography with the authentic standards and by comparison with product ion spectra of the authentic standards. Those in vitro metabolites were also detected in bile, plasma, or urine samples after an intravenous administration of KR-31831 to rats. The metabolic routes for KR-31381 included the metabolism of acetal group to hydroxymethyl group (M2), N-dealkylation to M1, and N-acetylation at the 6-amino group (M3).     

Design and synthesis of novel dinucleotide analogs

Syntheses of dinucleotide analogs, (S,R) cis-(4-((4-amino-2-oxopyrimidin-1(2H)-yl)methyl)-1,3-dioxolan-2-yl)methyl (2R,3R,5R)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-tetrahydrofuran-3-yl hydrogen phosphate (5a) and (S,R) cis-(5-((4-amino-2-oxopyrimidin-1(2H)-yl)methyl)-1,3-oxathiolan-2-yl)methyl (2R,3R,5R)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-tetrahydrofuran-3-yl hydrogen phosphate (5b), were accomplished by the use of a new strategy. The use of phenyldichlorophosphate (Method A) as the coupling reagent was shown to possess superiority relative to the reported use of di(1H-benzo[d][1,2,3]triazol-1-yl)phenyl phosphonate (Method B).     

Synthesis of a new Pt(II) complex containing valganciclovir drug and calf-thymus DNA interaction study using multispectroscopic methods

A new complex, [Pt(valcyte)(DMSO)Cl]Cl, in which valcyte (trade name) served as valganciclovir hydrochloride drug ([2-[(2-amino-6-oxo-3H-purin-9-yl)methoxy]-3-hydroxypropyl](2S)-2-amino-3-methylbutanoate), was synthesized and characterized by different physicochemical methods. Binding interaction of this complex with calf-thymus DNA (ct-DNA) has been investigated by multispectroscopic techniques. The complex displays significant binding properties with ct-DNA. The results of fluorescence and UV–vis absorption spectroscopy indicated that this complex interacted with ct-DNA in a groove-binding mode, and the binding constant was 3.8 × 10⁴ M^?1. Furthermore, the complex induced detectable changes in the CD spectrum of ct-DNA and slightly changed its viscosity which verified the groove-binding mode. Finally, all results indicated that Pt(II) complex interact with DNA via groove-binding mode.     

Orientation of iron bleomycin and porphyrin complexes on DNA fibers

Bleomycin (Blm) is an antitumor agent that requires iron and oxygen for strand cleavage of DNA. In this study, ferric bleomycin, Fe(III)Blm, or the nitric oxide adduct of ferrous bleomycin, ON-Fe(II)Blm, were bound to one-dimensionally oriented DNA fibers. Reductive nitrosylation of Fe(III) complexes took place in situ on B-form DNA fibers. Electron paramagnetic resonance (EPR) spectra were obtained as a function of the angle phi between the magnetic field B and the fiber axis Zf. For comparison, EPR spectra were acquired for ON-Fe(II)TMpyP and ON-Fe(II)TMpyP-Im on oriented DNA fibers, where TMpyP is 5,10,15,20-tetrakis(1-methyl-4-pyridino)porphyrin and Im is imidazole. EPR spectra showed both low-spin Fe(III)Blm and ON-Fe(II)Blm bound to B-form DNA in two slightly different binding orientations in the ratio of 1:0.2. With A-form DNA, a fraction of bound Fe(III)Blm was high spin. Specifically, the angle beta between the fiber axis Zf and the g axis, gz, perpendicular to or nearly perpendicular to the equatorial plane of the iron complex was estimated as 20 degrees and 25 degrees for ON-Fe(II)Blm and 30 degrees and 25 degrees for Fe(III)Blm, respectively. The angle gamma that determines the orientation of gx and gy axes was estimated as 90 degrees for the two ON-Fe(II)Blm species and 10 degrees for the two Fe(III)Blm species, respectively. The NO was held rigidly in place as the temperature increased from 123 K to room temperature for ON-Fe(II)Blm but not for ON-Fe(II)TMpyP or ON-Fe(II)TMpyP-Im. It is hypothesized that the NO is structurally oriented by hydrogen bonding like the peroxide is held in HO2(-)-Co(III)Blm (Wu et al. J. Am. Chem. Soc. 1996, 118, 1281-1294). The EPR parameters are consistent with a six-coordinate complex for ON-Fe(II)Blm, although the superhyperfine structure from the trans nitrogen was not detected. The increase in g value anisotropy upon binding ON-Fe(II)Blm to DNA fiber may be caused by an increase in the overlap of d pi and 2p pi* orbitals induced by an interaction of NO with DNA and/or by a perturbation of d orbitals due to the pyrimidine-guanine interaction. It is concluded that the EPR parameters of ON-Fe(II)Blm and Fe(III)Blm bound to oriented DNA support the hypothesis that FeBlm species bind to DNA with adduct structures similar to those formed by related CoBlm species and DNA.     

Independent generation and study of 5,6-Dihydro-2'-deoxyuridin-6-yl,a member of the major family of reactive intermediates formed in DNA from the effects of gamma-radiolysis

Nucleobase radicals are the major family of reactive intermediates formed when nucleic acids are exposed to gamma-radiolysis. Elucidation of their reactivity is complicated by the formation of multiple species randomly throughout the biopolymers. 5,6-Dihydro-2'-deoxyuridin-6-yl (1) was generated upon photolysis (350 nm) of the respective tert-butyl ketone (2). The radical abstracts hydrogen atoms from beta-mercaptoethanol (k = 8.8 +/- 0.5 x 10(6) M(-)(1) s(-)(1)) and 2,5-dimethyltetrahydrofuran (k = 31 +/- 2.5 M(-)(1) s(-)(1)). The latter was used as a model for the 2-deoxyribose component of DNA. The major product formed in the presence of O(2) was 6-hydroxy-5,6-dihydro-2'-deoxyuridine (11), which is believed to be formed directly from the peroxy precursor and not via elimination of superoxide. Small amounts of 2-deoxyribonolactone (13) were also formed under aerobic conditions. This product is believed to result from intramolecular hydrogen atom abstraction by the C6-peroxyl radical (14) and suggests that gamma-radiolysis may indirectly result in oxidation of the C1'-position of nucleotides, despite the inaccessibility of this hydrogen in duplex DNA.     

Aminoalkyl derivatives of 2,4′-bithiazole-4-carboxylic acid,the intercalating part of bleomycin

The synthesis of three 2,4′-bithiazole derivatives related to the antibiotic antitumor bleomycin is reported. These compounds substituted by aminoalkyl chains on 2′ and/or 4-positions were prepared by the Hantzs synthesis between new thioamides and methyl 2-(2-bromoacetyl)thiazole-4-carboxylate and will be useful for the study of the intercalative moiety of bleomycin.     

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.     

Alteration of the selectivity of DNA cleavage by a deglycobleomycin analogue containing a trithiazole moiety

The bleomycin (BLM) group of antitumor antibiotics effects DNA cleavage in a sequence-selective manner. Previous studies have indicated that the metal-binding and bithiazole moieties of BLM are both involved in the binding of BLM to DNA. The metal-binding domain is normally the predominant structural element in determining the sequence selectivity of DNA binding, but it has been shown that replacement of the bithiazole moiety with a strong DNA binder can alter the sequence selectivity of DNA binding and cleavage. To further explore the mechanism by which BLM and DNA interact, a trithiazole-containing deglycoBLM analogue was synthesized and tested for its ability to relax supercoiled DNA and cleave linear duplex DNA in a sequence-selective fashion. Also studied was cleavage of a novel RNA substrate. Solid-phase synthesis of the trithiazole deglycoBLM A(5) analogue was achieved using a TentaGel resin containing a Dde linker and elaborated from five key intermediates. The ability of the resulting BLM analogue to relax supercoiled DNA was largely unaffected by introduction of the additional thiazole moiety. Remarkably, while no new sites of DNA cleavage were observed for this analogue, there was a strong preference for cleavage at two 5'-GT-3' sites when a 5'-(32)P end-labeled DNA duplex was used as a substrate. The alteration of sequence selectivity of cleavage was accompanied by some decrease in the potency of DNA cleavage, albeit without a dramatic diminution. In common with BLM, the trithiazole analogue of deglycoBLM A(5) effected both hydrolytic cleavage of RNA in the absence of added metal ion and oxidative cleavage in the presence of Fe(2+) and O(2). In comparison with BLM A(5), the relative efficiencies of hydrolytic cleavage at individual sites were altered.     

An eco-compatible multicomponent strategy for the synthesis of new 2-amino-6-(1H-indol-3-yl)-4-arylpyridine-3,5-dicarbonitriles in aqueous micellar medium promoted by thiamine-hydrochloride

A thiamine hydrochloride (VB₁) accelerated, one-pot synthesis of 2-amino-6-(1H-indol-3-yl)-4-arylpyridine-3,5-dicarbonitriles was achieved via four-component reaction of 3-cyanoacetyl indole, aromatic aldehydes, ammonium acetate, and malononitrile in aqueous micellar conditions by a Knoevenagel condensation reaction followed by Michael-addition, which upon cyclization and dehydration yielded the corresponding product in excellent proportion.