On the Risks of Phylogeny-Based Strain Prioritization for Drug Discovery: Streptomyces lunaelactis as a Case Study.

Strain prioritization for drug discovery aims at excluding redundant strains of a collection in order to limit the repetitive identification of the same molecules. In this work, we wanted to estimate what can be unexploited in terms of the amount, diversity, and novelty of compounds if the search is focused on only one single representative strain of a species, taking Streptomyces lunaelactis as a model. For this purpose, we selected 18 S. lunaelactis strains taxonomically clustered with the archetype strain S. lunaelactis MM109T. Genome mining of all S. lunaelactis isolated from the same cave revealed that 54% of the 42 biosynthetic gene clusters (BGCs) are strain specific, and five BGCs are not present in the reference strain MM109T. In addition, even when a BGC is conserved in all strains such as the bag/fev cluster involved in bagremycin and ferroverdin production, the compounds produced highly differ between the strains and previously unreported compounds are not produced by the archetype MM109T. Moreover, metabolomic pattern analysis uncovered important profile heterogeneity, confirming that identical BGC predisposition between two strains does not automatically imply chemical uniformity. In conclusion, trying to avoid strain redundancy based on phylogeny and genome mining information alone can compromise the discovery of new natural products and might prevent the exploitation of the best naturally engineered producers of specific molecules.

Liquid chromatography/tandem mass spectrometry characterization of nitroso, nitrated and nitroxidized cardiolipin products.

Cardiolipins (CL) are anionic dimeric phospholipids bearing four fatty acids, found in inner mitochondrial membrane as structural components and are involved in several processes as oxidative phosphorylation or apoptotic signalling. As other phospholipids, CL can be modified by reactive oxygen species (ROS) and reactive nitrogen species (RNS), which can modulate various cellular functions. Modifications of CL by RNS remain largely unstudied although other nitrated lipids are emerging as bioactive molecules. In this work, we developed a C30-LC-HRMS/MS methodology to identify the nitrated and nitroxidized tetralinoleoyl-cardiolipin (TLCL), using a biomimetic model of nitration, and to disclose specific fragmentation pathways under HCD MS/MS. Using this lipidomics approach, we were able to separate and identify nitro, nitroso, nitronitroso, and nitroxidized TLCL derivatives, comprising 11 different nitrated compounds. These products were identified using accurate mass measurements and the fragmentation pattern acquired in higher-energy collision dissociation (HCD)-tandem MS/MS experiments. These spectra showed classifying fragmentation pathways, yielding phosphatidic acid (PA-), lysophosphatidic acid (LPA-), and carboxylate fragment ions with the modifying moiety. Remarkably, the typical neutral losses associated with the added moieties were not observed. In conclusion, this work has developed a new method for the identification of nitroso, nitrated and nitroxidized cardiolipin products by using a C30LC-MS platform method, potentially allowing their detection in biological samples.

Separation of rotamers of 5-nitrosopyrimidines and estimation of binding constants of their complexes with ß-cyclodextrin by capillary electrophoresis.

For the first time, capillary electrophoresis has been successfully employed for the fast and highly efficient separations of a novel type of stereoisomers - planar rotamers (planamers) of four newly synthesized 5-nitrosopyrimidine derivatives. These derivatives can form two rotamers differing in the orientation of nitroso group due to strong intramolecular hydrogen bonds. Partial separation of rotamers of two 5-nitrosopyrimidines was achieved in alkaline 50 mM sodium tetraborate, pH 9.3, and in acidic 18.5/42 mM Tris/phosphate, pH 2.3, background electrolytes (BGEs) free of stereoselectors. To improve the separation of these rotamers and to attain the baseline or better separation of rotamers of other two 5-nitrosopyrimidines, various BGEs and different cyclodextrins-based stereoselectors were tested. The most effective, i.e. the fastest and baseline or better separations of rotamers of all analyzed 5-nitrosopyrimidines were achieved within a short time, 3.7-9.3 min, in the above alkaline or acidic BGEs using ß-cyclodextrin (ß-CD) or carboxymethyl-ß-CD as stereoselectors. Moreover, since the experiments with ß-CD resulted in good separations of rotamers of all the investigated 5-nitrosopyrimidines, the apparent binding constants of their complexes with this selector were determined from the dependence of their effective mobilities on the ß-CD concentration in the BGEs. The examined complexes were found to be relatively weak, with the apparent binding constants in the range 11.3-153.0 L/mol.

Proteomic detection of nitroproteins as potential biomarkers for cardiovascular disease.

Increased levels of reactive oxygen and nitrogen species are linked to many human diseases and can be formed as an indirect result of the disease process. The accumulation of specific nitroproteins which correlate with pathological processes suggests that nitration of protein tyrosine represents a dynamic and selective process, rather than a random event. Indeed, in numerous clinical disorders associated with an upregulation in oxidative stress, tyrosine nitration has been limited to certain cell types and to selective sites of injury. Additionally, proteomic studies show that only certain proteins are nitrated in selective tissue extracts. A growing list of nitrated proteins link the negative effects of protein nitration with their accumulation in a wide variety of diseases related to oxidation. Nitration of tyrosine has been demonstrated in diverse proteins such as cytochrome c, actin, histone, superoxide dismutase, α-synuclein, albumin, and angiotensin II. In vitro and in vivo aspects of redox-proteomics of specific nitroproteins that could be relevant to biomarker analysis and understanding of cardiovascular disease mechanism will be discussed within this review.

Exogenous vs. endogenous gamma-glutamyltransferase activity: Implications for the specific determination of S-nitrosoglutathione in biological samples.

The determination of S-nitrosoglutathione (GSNO) levels in biological fluids is controversial, partly due to the laborious sample handling and multiple pretreatment steps required by current techniques. GSNO decomposition can be effected by the enzyme gamma-glutamyltransferase (GGT), whose involvement in GSNO metabolism has been suggested. We have set up a novel analytical method for the selective determination and speciation of GSNO and its metabolite S-nitrosocysteinylglycine, based on liquid chromatography separation coupled to on-line enzymatic hydrolysis of GSNO by commercial GGT. In a post-column reaction coil, GGT allows the specific hydrolysis of the gamma-glutamyl moiety of GSNO, and the S-nitrosocysteinylglycine (GCNO) thus formed is decomposed by copper ions originating oxidized cysteinylglycine and nitric oxide (NO). NO immediately reacts with 4,5-diaminofluorescein (DAF-2) forming a triazole derivative, which is detected fluorimetrically. The limit of quantitation (LOQc) for GSNO and GCNO in plasma ultrafiltrate was 5 nM, with a precision (CV) of 1-6% within the 5-1500 nM dynamic linear range. The method was applied to evaluate the recovery of exogenous GSNO after addition of aliquots to human plasma samples presenting with different total GGT activities. By inhibiting GGT activity in a time dependent manner, it was thus observed that the recovery of GSNO is inversely correlated with plasmatic levels of endogenous GGT, which indicates the need for adequate inhibition of endogenous GGT activity for the reliable determination of endogenous GSNO.

Partial purification from hot dogs of N-nitroso compound precursors and their mutagenicity after nitrosation.

Hot dogs contain apparent N-nitroso compounds (ANC) and ANC precursors (ANCP). ANCP purification was followed by nitrosation, sulfamic acid treatment, and analysis for ANC. Aqueous hot dog extracts were adsorbed on silica gel, which was eluted with MeCN and MeOH. The MeOH eluate was adsorbed on cation exchange resin (H+ form) and eluted with NH4OH. Eluted ANCP traveled at moderate speeds in high-performance liquid chromatography (HPLC) on amino and Pb2+ columns. Gas chromatography-mass spectrometry (GC-MS) of trimethylsilyl (TMS) derivatives of crude water extract indicated the presence of glycerol, phosphate, lactic acid, and two monosaccharides. GC-MS of TMS derivatives of Pb2+ column HPLC eluates indicated that ANCP included 1-deoxy-N-1-glucosyl glycine. The nitrosated NH4OH eluate showed 4x background mutagenic activity for Salmonella typhimurium TA-100. Un-nitrosated fractions showed 2x background activity. Although tryptophan nitrosation gave 88% ANC yield, tryptophan is probably not a major ANCP in hot dogs. Hot dog patties prepared with or without sucrose or glucose showed similar ANC and ANCP levels. We discuss possible implications of these findings for the etiology of colon cancer.

Optimization of the aerobic biological treatment of thermophilically treated refractory wastewater.

A pilot scale conventional activated sludge was operated for over 600 days to study its effectiveness at further remediating the effluent of an existing industrial site's thermophilic biological treatment stage. During the course of the study, the activated sludge was able to further biodegrade the contaminants in the incoming industrial wastewater in terms of both BOD and nitrogen reductions at varying hydraulic and solids retention times, despite elevated concentrations of soluble copper being present. A limiting hydraulic retention time (HRT) for BOD removal of 1.5 days was observed as well as the loss of nitrification occurred at a solids retention time (SRT) of approximately 6 days. Biokinetic coefficients were determined with the maximum rate of substrate utilization per unit mass of microorganisms, k, of 0.14 mgVSS/(mgsBOD-d) and the Monod half velocity constant, K(s), of 9.4 mgsBOD/L. Simultaneous nitrification and denitrification (SND) of the nitrogenous compounds found in this wastewater was observed throughout the majority of the experimentation while the bulk DO in the system was greater than 1 mg/L. The activated sludge was estimated to contain soluble copper on the order of 1 mg/L throughout the course of operation with no apparent detriment to nitrification. Additionally, the activated sludge was able to biologically remove the main solvents found in the influent wastewater. The removals of trace levels of N-nitrosodimethylamine (NDMA) were also observed.

Isolation of a Se-nitrososelenol: a new class of reactive nitrogen species relevant to protein Se-nitrosation.

Nitric oxide (NO) is a messenger molecule implicated in a number of physiological processes. Nitrosation of selenoproteins has been suggested as playing an important role in NO-mediated cellular functions such as the inactivation of glutathione peroxidase (GPx), but no chemical information about Se-nitrosated species has been available to date. Here a stable Se-nitrososelenol (RSeNO), a new class of NO derivative, was synthesized and fully characterized by X-ray crystallography and spectroscopic methods. This Se-nitrososelenol can be formed by direct transnitrosation from an S-nitrosothiol to a selenol, as is the case in the proposed mechanism for the NO-mediated inactivation of GPx.

Purity of different preparations of sodium 3,5-dibromo-4-nitrosobenzenesulphonate and their applicability for EPR spin trapping.

During the preparation of sodium 3,5-dibromo-4-nitrosobenzenesulphonate (DBNBS) of high purity for electron paramagnetic resonance (EPR) spin-trapping purposes, it was found that the material synthesised as part of the present study differed significantly from some commercially available samples of DBNBS. A thorough chemical characterisation of the contents of the various samples led to the conclusion that the preparations synthesised in the present study, as well as one of four commercially available samples, contained essentially pure DBNBS and had efficient spin-trapping activity. In contrast, the remaining three commercially available samples contained almost exclusively sodium 3,5-dibromo-4-nitrobenzenesulphonate, i.e. a one-oxygen oxidation product of DBNBS, and had little spin-trapping activity. The two compounds were readily separated by reverse-phase high performance liquid chromatography (HPLC). It was further found that the quality of DBNBS preparations may be determined by NMR spectrometry, IR spectrometry, fast atom bombardment-mass spectrometry (FAB-MS) and EPR spectrometry. In particular, UV-Visible spectroscopy may be used to determine A308/A280, which should be greater than 1.8 for a high purity DBNBS preparation.

Synthesis and biological evaluation of enantiopure thionitrites: the solid-phase synthesis and nitrosation of D-glutathione as a molecular probe.

The D-isomer of the naturally-occurring tripeptide glutathione (gamma-L-Glu-L-Cys-Gly, L-GSH) has been synthesised using the Fmoc solid phase peptide synthesis strategy. The D-GSH obtained has been nitrosated to give the D-isomer of the bioactive thionitrite, S-nitroso-L-glutathione. The biological activity of both enantiomers of S-nitrosoglutathione has been studied and compared to the activity of the D- and L-isomers of N-acetyl-S-nitrosopenicillamine (SNAP) and S-nitrosocysteine (CysNO).

Ferroverdins, inhibitors of cholesteryl ester transfer protein produced by Streptomyces sp. WK-5344. I. Production, isolation and biological properties.

Streptomyces sp. WK-5344, a soil isolate, was found to produce structurally related inhibitors of cholesteryl ester transfer protein (CETP). New active compounds, designated ferroverdins B and C, were isolated along with known ferroverdin A from the fermentation broth by solvent extraction, ODS column chromatography and silica gel column chromatography. All ferroverdins showed a dose-dependent inhibitory activity against human CETP. The IC50 values were 21, 0.62 and 2.2 microM for ferroverdins A, B and C, respectively, indicating that ferroverdin B is one of the most potent CETP inhibitors of microbial origin.

Nitritocobalamin and nitrosocobalamin may be confused with sulfitocobalamin using cation-exchange chromatography.

The previously reported ability of SP-Sephadex C25 column chromatography for partitioning biologically important cobalamins has been modified to include analytical separation of nitritocobalamin (NO2-Cbl) and nitrosocobalamin (NO-Cbl). Gel column dimensions (1.5 x 11.0 cm), a low eluent flow-rate (125 microliters/min), collection of small eluate fractions (160 microliters) plus maintenance of He saturated mobile and gel phases all combined to eliminate ordinarily confusing proximal elution of NO2-Cbl and NO-Cb1 with sulfitocobalamin (SO3-Cbl) and cyanocobalamin. Cobalamin elution profiles from the gel column were monitored by direct radiometric analysis of 57Co-labelled cobalamin standards or competitive intrinsic factor radioassays for cobalamin sample sizes up to 10.0 ng. Failure to implement the chromatographic conditions detailed here totally obscured analysis of NO2-Cbl coexisting with SO3-Cbl in brain tissues for chicks exposed to dietary sulfites and caused oversight of NO-Cb1 normally coexisting in prepared NO2-Cbl standards.

Synthesis, characterization and mutagenicity of 2-nitroso-6,7-dimethoxytetrahydroisoquinoline.

The compound 6,7-dimethoxytetrahydroisoquinoline (Scheme 2, (ii] reacts with nitrous acid at ambient temperature and pH approximately 3.0 to give, in high yield the expected 2-nitroso-6,7-dimethoxytetrahydroisoquinoline (Scheme 2, (iii)). An unequivocal chemical structure of this nitroso derivative was established by high resolution mass spectrometry and 1H NMR spectrometry. Unlike many N-nitroso compounds, (iii) crystallizes in a single rotational isomer which spontaneously forms, in dimethylsulfoxide (DMSO) solution, an equilibrium mixture of the two E/Z isomeric forms with a t1/2 approximately 53 h. The compound is mutagenic to Salmonella tester strains TA98, TA100, TA1538, TA1535, and TA1537 but only in the presence of induced rat liver microsomes. The highest mutagenic activity of approximately 10 net revertants/nM was obtained with TA100 at a dose of 10 micrograms/plate. The compound (ii) is a close structural analog to the tetrahydroisoquinolines formed by endogenous condensation/cyclization reactions that can occur, between acetaldehyde and dopamine or norepinephrine, when alcohol is consumed.

Preparation, toxicity and mutagenicity of 1-methyl-2-nitrosoimidazole. A toxic 2-nitroimidazole reduction product.

1-Methyl-2-nitrosoimidazole (INO), the 2-electron reduction product of 1-methyl-2-nitroimidazole (INO2), was prepared by electrochemical reduction of INO2 to 2-hydroxylamino-1-methyl-imidazole (INHOH), followed by back oxidation with iodine. Although stable in crystalline form, INO reacted in water, phosphate-buffered saline, and mammalian cell growth medium. Half-lives for decay were determined by UV-visible spectroscopy. INO was found to be highly toxic towards Chinese hamster ovary (CHO) cells, concentrations of 10-60 microM producing significant cytotoxicity. The rate of INO decay was found to be increased in the presence of CHO cells. INO was also toxic and mutagenic towards Salmonella typhimurium TA-100. When compared on a molar basis to the parent nitro compound INO2, and the 4- and 6-electron reduction products INHOH and 2-amino-1-methylimidazole (INH2), INO was by far (two orders of magnitude) the most toxic under aerobic conditions. These results suggest that the nitroso reduction product of 2-nitroimidazoles may be the reduced species responsible for hypoxic cell selective toxicity of 2-nitroimidazoles.

Attempts to isolate N-nitroso compounds from Chinese-style salted fish.

Various types of salted fish have been collected from Hong Kong and analyzed for volatile nitrosamines and bacterial mutagenicity. Both of these parameters were low in the samples as collected. Exposure of these samples to nitrite yields substantial quantities of nitrosamines and mutagenic activity.

N-nitrosamines and nitrosatable compounds in rubber nipples and pacifiers.

Rubber nipples and pacifiers were analysed for volatile N-nitrosamines using gas chromatography-thermal energy analysis after extraction with 'artificial saliva'. All of the 17 samples tested were found to contain at least two of the following: N-nitrosodimethylamine, N-nitrosodiethylamine, N-nitrosodibutylamine and N-nitrosopiperidine. Total volatile N-nitrosamine levels up to 19.7 micrograms/kg rubber were found, with a mean content of 7.3 micrograms/kg. Nitrosatable compounds, measured as N-nitrosamines after nitrosation, were detected in 15 of the 17 samples to total levels up to 13.7 mg/kg, the mean being 5.0 mg/kg.