Mutagenicity of nitrophenanthrene derivatives for Salmonella typhimurium: effects of nitroreductase and acetyltransferase

Real time detection of live microbes using a highly sensitive bioluminescent nitroreductase probe

A highly sensitive and selective nitroreductase probe, showing a rapid and strong bioluminescence enhancement (>100-fold in 5 minutes), and its initial application in the real time detection of both Gram positive and Gram negative live bacteria and monitoring of their growth has been reported.

Electronic properties of environmental pollutants and their mutagenic activity: Nitro derivatives of azaphenanthrenes

The physico-chemical properties of nitroazaphenanthrene isomers: 4-nitro-9-azaphenanthrene (4-N-9-Aph), 5-nitro-9-azaphenanthrene (5-N-9-Aph), 6-nitro-4-azaphenanthrene (6-N-4-Aph), 8-nitro-1-azaphenanthrene (8-N-1-Aph), and 8-nitro-4-azaphenanthrene (8-N-4-Aph) have been investigated theoretically using Density Functional Theory (DFT) calculations. Equilibrium geometries, relative stability, ionization potentials, electron affinities, molecular electrostatic potentials, dipole moments, electric polarizabilities, and vibrational properties of these isomers are presented. Averaged O-N-C-C dihedral angle, dipole moment, polarizability, the summation of IR intensities (∑IIR) and the summation of Raman activities (∑ARaman) over all 3N-6 vibrational degrees of freedom are sensitive to the structure of isomers. A very good linear relationship between ∑ARaman values (R=1.00) and the Salmonella typhimurium strain TA98(-S9) mutagenic activity of the investigated nitroazaphenanthrene isomers (Tokiwa et al., 2003) reveals a very important role of inductive and dispersive forces on the mutagenic pathways of the investigated isomers.

Prediction of mutagenic activity of nitrophenanthrene and nitroanthracene isomers by simulated IR and Raman spectra

This paper expands upon our original work on nitroanthracenes in (Alparone, A., Librando, V., 2012. Spectrochim. Acta A 89, 129-136) on the series of nitrophenanthrene isomers. Geometries, electric properties, IR and Raman spectra of 1-, 2-, 3-, 4- and 9-nitrophenanthrene (1-NP, 2-NP, 3-NP, 4-NP and 9-NP) were obtained and analyzed using Density Functional Theory calculations. The balance between steric and π-conjugative interactions determines the order of stability 4-NP<1-NP~9-NP<2-NP∼3-NP. IR and Raman spectral zones between 1000 and 1600 cm(-1) show intense bands noticeably affected by the position of the substituent, being potentially useful to discriminate and monitor the investigated isomers. Dipole moments, summations of IR intensity (ΣI(IR)) and Raman activity (ΣA(Raman)) over the 3N-6 vibrational modes are sensitive to the structure, increasing steadily from the non-planar to the planar isomers. Good linear relationships between the ΣI(IR) (r=0.90) and ΣA(Raman) (r=0.99) against the Salmonella typhimurium strain TA98 mutagenic activity of nitrophenanthrenes and isomeric nitroanthracenes are found. On the basis of the structural and vibrational properties, 4-NP seems to have not mutagenic activity, while the unknown TA98 mutagenic potency of 1-nitroanthracene is predicted to be between that of 9-NP and 3-NP. Calculated ΣI(IR) and ΣA(Raman) values could be used as molecular descriptors for QSARs applications of series of isomers.

Comment on: "FT-IR, FT-Raman and UV spectral investigation; computed frequency estimation analysis and electronic structure calculations on 1-nitronaphthalene" by M. Govindarajan and M. Karabacak [Spectrochim. Acta A 85 (2012) 251-260]

The title paper [1] incorrectly establishes that, in gas phase the global minimum energy structure of 1-nitronaphthalene is planar (C(s) symmetry). By contrast, present calculations indicate that the planar C(s) form is an unstable structure on the potential energy surface, exhibiting an imaginary vibrational wavenumber value corresponding to the torsional mode of the nitro group around the C-N bond. At the B3LYP/6-311++G(d,p) level of calculation the global minimum energy structure of 1-nitronaphthalene in gas phase has a non-planar geometry, characterized by O-N-C-C dihedral angles of ca. 30° and lying 0.35 kcal/mol below the C(s) form.

In silico structure-function analysis of E. cloacae nitroreductase

Reduction, catalyzed by the bacterial nitroreductases, is the quintessential first step in the biodegradation of a variety of nitroaromatic compounds from contaminated waters and soil. The Enterobacter cloacae nitroreductase (EcNR) enzyme is considered as a prospective biotechnological tool for bioremediation of hazardous nitroaromatic compounds. Using diverse computational methods, we obtain insights into the structural basis of activity and mechanism of its function. We have performed molecular dynamics simulation of EcNR in three different states (free EcNR in oxidized form, fully reduced EcNR with benzoate inhibitor and fully reduced EcNR with nitrobenzene) in explicit solvent and with full electrostatics. Principal Component Analysis (PCA) of the variance-covariance matrix showed that the complexed nitroreductase becomes more flexible overall upon complexation, particularly helix H6, in the vicinity of the binding site. A multiple sequence alignment was also constructed in order to examine positional constraints on substitution in EcNR. Five regions which are highly conserved within the flavin mononucleotide (FMN) binding site were identified. Obtained results and their implications for EcNR functioning are discussed, and new plausible mechanism has been proposed.

Effects of C60 on the Salmonella typhimurium TA100 transcriptome expression: Insights into C60 -mediated growth inhibition and mutagenicity

Rapid advances are being made in the creation and use of nanomaterials, but little is known about the impact these materials might have on key microbial functions if introduced into the environment. Previous studies have generated conflicting results with respect to the impact of fullerenes on microbial activity. In the present study, Salmonella typhimurium TA100 was selected as a model microbial system with which to investigate further the impact of C(60) aggregates on microbial growth, mutagenicity, and global transcript expression. Aggregates of C(60) predominantly less than 100 nm significantly impacted Salmonella growth at concentrations of ≥ 0.5 mg/L. In addition, C(60) aggregates also displayed mutagenic potential at concentrations ≥ 0.1 mg/L. Transcript expression analysis of S. typhimurium TA100 exposed to C(60) for 24 h indicated that 271 transcripts had significant differential expression relative to controls with twofold or more change. Of particular interest was the increased expression of transcripts coding for proteins involved in energy metabolism, amino acid biosynthesis, transcription, and DNA metabolism, and the decreased expression of transcripts coding for proteins involved in protein fate, transport, and binding and bacterial secretion systems. Collectively, these data indicate that C(60) interacts with the outer membrane of S. typhimurium TA100, resulting in delayed growth and mutagenicity, most likely by interfering with key transport functions and inducing a stress response, respectively.

Detection of DNA damage in fish Oreochromis mossambicus induced by co-exposure to phenanthrene and nitrite by ESI-MS/MS

BACKGROUND, AIM, AND SCOPE

Mutagenic nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) have been known to arise in the environment through direct emissions from combustion sources and nitration of PAHs, primarily in the atmosphere. In the marine environment, PAHs are one of the classic anthropogenic organic pollutants, while nitrite (NO(2)(-)) is produced naturally via various biological processes like imbalance in nitrification/denitrification or eutrophication and subsequent oxygen depletion from an oversupply of nutrients. In this paper, we report the formation of PAH-DNA adducts in fish contaminated with PAHs and exposed to NO(2)(-) in the ambient water. Electrospray ionization tandem mass spectrometric (ESI-MS/MS) analysis of the bile of the euryhaline fish Oreochromis mossambicus exposed simultaneously to field relevant sublethal concentrations of phenanthrene and NO(2)(-) and collision-induced dissociation of selected ions revealed the presence of DNA-PAH adducts. The present study indicates that, although several high sensitivity techniques have been developed for the analysis of PAH derived DNA adducts, MS/MS has emerged as a powerful tool in the detection and structure elucidation of DNA adducts.

MATERIALS AND METHODS

Juvenile O. mossambicus from a local estuarine fish farm were used with increasing frequency for carcinogenicity testing and comparative cancer research. The fish were exposed to the alkylating agent phenanthrene in the presence of NO(2)(-). Composite untreated bile samples after dilution with methanol: water (1:1; v/v) were analyzed by ESI-MS.

RESULTS

Several adducts could be evidenced in the bile by MS/MS. Deoxyadenosine/deoxyguanosine having a mass in the range of 450-650 amu is detected. In addition, a segment of modified dinucleotide with a mass that corresponds to a dimer consisting of a modified guanosine and a normal guanosine has also been identified in the bile.

DISCUSSION

The formation of certain types of DNA adducts is a crucial step in the induction of cancer and a primary stage in mutagenesis. Phenanthrene injected by i.p. route led to the transformation of phenanthrene to N-formyl amino phenanthrene-N(6)-deoxyadenosine adduct, whereas the fish co-exposed to phenanthrene and ambient nitrite metabolizes PAH to mono-, di- as well as trinitro derivatives, which then react with DNA leading to the formation of mainly modified guanosine and adenosine adducts. In the present investigation, dinitrophenanthrene diol epoxide (DNPDE) adduct with guanosine (m/z 587) seems to be the dominant adduct in the mixture, and its presence is shown first as a comparatively less stable adduct, which decomposes to give a more stable N(2) adduct (m/z 567).

CONCLUSIONS

MS/MS has proved to be useful in the rapid determination and discrimination of structurally different phenanthrene/derivatives DNA adducts in a complex mixture of fish bile co-exposed to phenanthrene and nitrite. However, the nature of metabolites formed is likely determined by the route of PAH administration, and there is a need to further define the early biochemical events of carcinogenesis in these species.

RECOMMENDATIONS AND PERSPECTIVES

DNA adduct analysis in fish bile offers a promising approach to study the risk of potentiation of anthropogenic chemicals into genotoxic compounds in the presence of nitrite in the marine environment. We believe this is the first report on the formation of DNA-phenanthrene adducts on co-exposure of the fish to PAH and nitrite.

Prediction of mutagenic activity of nitronaphthalene isomers by infrared and Raman spectroscopy

IR and Raman spectra of 1- and 2-nitronaphthalene isomers (1-NN and 2-NN) have been investigated to obtain more insight into the effect of the structure on mutagenic properties. To this purpose we have performed density functional theory calculations using B3LYP functional with cc-pVDZ basis set. The results have shown that IR and Raman spectra of nitronaphthalene isomers are somewhat similar to each other. A notable exception regards the symmetrical NO bonds stretching +CN bond stretching vibration (nusNO2+nuCN), which appears as very intense peak near 1350 cm(-1) in IR and Raman spectra of both isomers. Present calculations predict that for 2-NN isomer IR and Raman absorptions of this vibration are more intense by ca. 50 and 60%, respectively, than those of 1-NN isomer. The noticeably higher IR and Raman intensity values of the nusNO2+nuCN mode for 2-NN originate, respectively, from large dipole moment and polarizability changes with respect to the normal mode, suggesting that intermolecular interactions are especially favoured along this coordinate. These results are consistent with higher mutagenic activities of 2-NN in comparison to 1-NN isomer, supporting the binding to enzyme mechanism as a determining step in mutagenic pathways for this series of nitroaromatic compounds.

Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor

Nitroreductases (NTR) are enzymes that reduce hazardous nitroaromatic compounds and are of special interest due to their potential use in bioremediation and their activation of prodrugs in directed anticancer therapies. We elucidated the crystal structures of ydjA from Escherichia coli (Ec_ydjA), one of the smallest NTRs, in its flavin mononucleotide (FMN)-bound and cofactor-free forms. The alpha+beta mixed monomeric Ec_ydjA forms a homodimeric structure through the interactions of the long central helices and the extended regions at both termini. Two FMN molecules are bound at the dimeric interface. The absence of the 30 internal amino acids in Ec_ydjA, which forms two helices and restricts the cofactor and substrate binding in other NTR family members, creates a wider and more flexible active site. Unlike the bent FMN ring structures present in most NTR complexes currently known, the flavin system in the Ec_ydjA structure maintains a flat ring conformation, which is sandwiched between a Trp and a His residue from each monomer. The analysis of our Ec_ydjA structure explains its specificity for larger substrates and provides structural information for the rational design of novel prodrugs with the ability to reduce nitrogen-containing hazardous molecules.

Mutagenic activities and physicochemical properties of selected nitrobenzanthrones

Mutagenic activity of nine nitro derivatives of benzanthrone, namely 1-nitro-, 2-nitro-, 3-nitro-, 9-nitro-, 11-nitro-, 1,9-dinitro-, 3,9-dinitro-, 3,11-dinitro- and 3,9,11-trinitrobenzanthrone were tested with Salmonella strains TA98, TA100, YG1021 and YG1024 in both the presence and absence of an S9 mix. Each compound exhibited mutagenic activity with all the strains. Among these nine isomers, 3-nitrobenzantrone exhibited the most mutagenic activity with all the strains without the S9 mix. The mutagenic activities of the dinitro and trinitro derivatives of benzanthrone were lower than that of the 3-nitro derivative; this is evident from the mutagenic activity of nitrated polyaromatic hydrocarbons (PAH), which is generally enhanced with an increase in nitration. The physicochemical properties of nitrated benzanthrone (reduction potential, hydrophobicity and orientation of nitro groups to the aromatic ring) demonstrated that mononitrated benzanthrone exhibits a lower reduction potential than mononitroPAHs such as 1-nitropyrene and 3-nitrofluoranthene, but was almost equivalent to that of dinitroPAH. Moreover, the mutagenic activity of mononitrobenzanthrones clearly depend on the reduction potential of each compound; however, this tendency was not observed in polynitrobenzanthrones, probably because the reduction of the nitro groups to amino groups of polynitrated benzanthrone might be predominant without a sufficient formation of corresponding hydroxyamines. These results suggest that aromatic compounds that contain keto groups, when nitrated, may act as potentially powerful direct-acting mutagens.

Binding effect of polychlorinated compounds and environmental carcinogens on rice bran fiber

To accelerate the fecal excretion of polycyclic biphenyl (PCB), polychlorinated dibenzofurans (PCDFs), polychlorinated-p-dioxines (PCDDs) and various mutagens and carcinogens, their binding effect on rice bran fiber (RBF) was investigated for nine heterocyclic amines, six nitroarenes, 4-nitroquinoline-N-oxide, benzo[a]pyrene, furylfuramide, two kinds of flavonoid compounds and formaldehyde and ascorbic acid. PCBs, PCDFs and PCDDs suspended in nonane were incubated with RBF (10 mg/ml) at 37 degrees C and after centrifugation, unbound chemicals in the supernatant were analyzed by high-performance liquid chromatography (HPLC) and gas chromatography (GC). The binding effects on RBF were enhanced more than other dietary fibers (DFs), which were tested including corn, wheat bran, spinach, Hijiki (a kind of seaweed), sweet potatoes and burdock fibers. It was found that the binding effects were related to lignin contents. Binding of 3-amino-1(or 1,4)-dimethyl-5H-pyrido[4,3-b]indole (Trp-p-1 and Trp-p-2), food-derived carcinogens and 1-nitropyrene (1-NP), suspended in methanol, to RBF occurred within 10 min of incubation at 37 degrees C at pH 5-7, and decreased below pH 4; binding of food-derived carcinogens was pH dependent. The binding effects to RBF and pulp lignin were obtained at ratio of over 90%, while corn fiber and cellulose were at ratios of 4-30%. Polycyclic aromatic compounds were related to the number of rings, showing high binding effects to chemical structures with triple rings. Binding of 1-NP and PCB to RBF was not influenced in any aerobic and anaerobic bacterial cultures. It was also found that RBF was capable of binding even conjugates containing mutagens such as glucuronides and sulfates, as well as metabolites in urine. It was suggested, therefore, that mutagens and carcinogens were available for the fecal excretion of residual chemicals and their metabolites, and also for the fecal excretion of PCBs, PCDFs and related compound residues in patients of Yusho disease, who suffered food poisoning due to rice oil contaminated with PCB in Japan.

Structural activity relationship between Salmonella-mutagenicity and nitro-orientation of nitroazaphenanthrenes

Nitroazaphenanthrenes (NAphs) and their N-oxides (NAphOs) were synthesized as derivatives with nitrogen atoms in the 1, 4, and 9 positions of phenanthrene rings, and as nitrated derivatives substituted at the 1, 2, 3, 4, 5, 6, 7, and 8 positions of phenanthrene rings. To determine the structure activity relationship of these derivatives, all 19 isomers were bioassayed with Salmonella tester strains. NAphs substituted at the 4, 6, 7 and 8 positions were mutagenic for TA98, and 1-, 2-, and 3-N-9-AphOs, 6-N-1-AphO and 6-N-4-AphO were mutagenic for TA98 and TA100 without the S9 mix, while 5-N-1-AphO and 5-N-9-AphO were non- or weakly mutagenic. Nitrated derivatives, 6-N-4-Aph, 6-N-9-Aph, 6-N-1-AphO, and 6-N-4-AphO, were powerful mutagens for TA98 and TA100. Mutagenicity was enhanced by mutant strains producing nitroreductase, such as YG1021 and 1026, and by those producing O-acetyltransferase, such as YG1024 and 1029. Nitro derivatives substituted at positions 4 and 5 in the phenanthrene rings were perpendicular, while those at positions 2, 3, 6 and 7 were coplanar to the phenanthrene rings. NAphs substituted at the 1 and 8 positions were noncoplanar due to steric hindrance of the aromatic proton at the peri position. On the other hand, 1,5- and 1,8-dinitro-4-azaphenanthrenes showed high mutagenicity for strains TA98 and TA100 in the absence of the S9 mix, and were strongly enhanced by nitroreductase and O-acetyltransferase, over-producing mutants. Therefore, it was found that the mutagenic potency of NAphs and NAphOs was closely associated with the chemical properties and orientation of nitro substitution of aromatic rings.

Structures of nitroreductase in three states: effects of inhibitor binding and reduction

The crystal structure of the nitroreductase enzyme from Enterobacter cloacae has been determined for the oxidized form in separate complexes with benzoate and acetate inhibitors and for the two-electron reduced form. Nitroreductase is a member of a group of enzymes that reduce a broad range of nitroaromatic compounds and has potential uses in chemotherapy and bioremediation. The monomers of the nitroreductase dimer adopt an alpha+beta fold and together bind two flavin mononucleotide prosthetic groups at the dimer interface. In the oxidized enzyme, the flavin ring system adopts a strongly bent (16 degrees ) conformation, and the bend increases (25 degrees ) in the reduced form of the enzyme, roughly the conformation predicted for reduced flavin free in solution. Because free oxidized flavin is planar, the induced bend in the oxidized enzyme may favor reduction, and it may also account for the characteristic inability of the enzyme to stabilize the one electron-reduced semiquinone flavin, which is also planar. Both inhibitors bind over the pyrimidine and central rings of the flavin in partially overlapping sites. Comparison of the two inhibitor complexes shows that a portion of helix H6 can flex to accommodate the differently sized inhibitors suggesting a mechanism for accommodating varied substrates.

From mutagenic to non-mutagenic nitroarenes: effect of bulky alkyl substituents on the mutagenic activity of 4-nitrobiphenyl in Salmonella typhimurium. Part I. Substituents ortho to the nitro group and in 2'-position

Eleven alkyl substituted derivatives of 4-nitrobiphenyl (4NBp) and two corresponding nitroso compounds were synthesised and tested for mutagenic potency in strains TA98 and TA100 of Salmonella typhimurium. The mutagenicity of compounds substituted ortho to the nitro group (3-methyl-, 3-ethyl-, 3-isopropyl-, 3-tertbutyl-, 3, 5-diethyl-, 3,5-diisopropyl-, and 3,5-ditertbutyl-4NBp) decreased with growing steric demand of the alkyl substituents in both tester strains. The most sterically hindered compounds were non-mutagenic even at highest concentrations. This reduction of mutagenicity is correlated with deviations from the coplanar orientation of the nitro group relative to the aromatic plane. Since a comparable decrease of mutagenicity for the nitroso compounds (4NOBp and 3-tertbutyl-4NOBp) was not observed, the first reduction step of non-planar nitro groups must be inhibited. Alkyl groups in the 2'-position of 4NBp (2'-methyl-, 2'-ethyl-, 2'-isopropyl-, and 2',4', 6'-trimethyl-4NBp) also reduced mutagenic activity with increasing size and removed it completely for the most sterically hindered species (2'-isopropyl-, 2',4',6'-trimethyl-4NBp). In this case, the co-planarity of the nitro group is not affected but the twisting of the two aromatic rings, which is associated with a less effective charge delocalisation of the nitrenium ion. The experimental mutagenicities of all nitro compounds were compared to predicted values, that are based on recently developed empirical equations. While there was reasonable correspondence for the parent compound (4NBp), its ortho methylated derivative (3-methyl-4NBp) and two highly hydrophobic dialkylated species (3,5-diisopropyl- and 3, 5-ditertbutyl-4NBp), predictions for all other alkyl substituted compounds were too high. Thus, steric parameters should be included to improve the general validity of predictions by means of quantitative structure-activity relationships (QSAR).

Steady-state kinetic mechanism, stereospecificity, substrate and inhibitor specificity of Enterobacter cloacae nitroreductase

Enterobacter cloacae nitroreductase (NR) is a flavoprotein which catalyzes the pyridine nucleotide-dependent reduction of nitroaromatics. Initial velocity and inhibition studies have been performed which establish unambiguously a ping-pong kinetic mechanism. NADH oxidation proceeds stereospecifically with the transfer of the pro-R hydrogen to the enzyme and the amide moiety of the nicotinamide appears to be the principal mediator of the interaction between NR and NADH. 2,4-Dinitrotoluene is the most efficient oxidizing substrate examined, with a kcat/KM an order of magnitude higher than those of p-nitrobenzoate, FMN, FAD or riboflavin. Dicoumarol is a potent inhibitor competitive vs. NADH with a Ki of 62 nM. Several compounds containing a carboxyl group are also competitive inhibitors vs. NADH. Yonetani-Theorell analysis of dicoumarol and acetate inhibition indicates that their binding is mutually exclusive, which suggests that the two inhibitors bind to the same site on the enzyme. NAD+ does not exhibit product inhibition and in the absence of an electron acceptor, no isotope exchange between NADH and 32P-NAD+ could be detected. NR catalyzes the 4-electron reduction of nitrobenzene to hydroxylaminobenzene with no optically detectable net formation of the putative two-electron intermediate nitrosobenzene.

Overexpression, isotopic labeling, and spectral characterization of Enterobacter cloacae nitroreductase

Bacterial nitroreductases have generated much interest recently due to their central roles in both nitroaromatic bioremediation and nitroaromatic toxicity, mutagenicity, and carcinogenicity. Enterobacter cloacae nitroreductase (NR) has been subcloned into the pET overexpression system and purified to homogeneity via a four-step procedure resulting in a final yield of 65.7 mg per liter. Overexpression in minimal media containing 15NH4Cl as the sole source of nitrogen yielded 37.6 mg per liter of homogenous NR containing > 99 atom % 15N. A series of melting curves generated under a variety of solvent conditions established the optimal conditions for NR stability as pH 7.5, low ionic strength phosphate buffer. A two-dimensional 1H-15N heteronuclear single quantum coherence nuclear magnetic resonance spectrum demonstrates this enzyme to be amenable to study by high-resolution multidimensional NMR in combination with amino-acid-specific isotopic labeling. Optical spectra of the purified enzyme suggest that the noncovalently bound flavin mononucleotide cofactor binds in a hydrophobic environment and is in the neutral and anionic protonation states in the oxidized and two-electron reduced oxidation states, respectively. NR exhibits a novel visible region circular dichroism spectrum which has a small distinct negative band at 366 nm and a large positive ellipticity at 454 nm with a shoulder centered at 480 nm.