The interaction of platinum II compounds with bacteriophages T7 and R17

The inactivation of the DNA-containing bacteriophage T7 and of the RNA-containing bacteriophage R17 by dichloro-ethylenediamine Pt II and by cis- and trans-dichloro-diammine Pt II has been studied under a variety of experimental conditions. It has been found that the mean lethal concentrations vary for T7 from 0.007 to 0.5 μg/ml and for R17 from 0.09 to 1.1 μg/ml depending upon which compound is used and the manner in which the experiment is performed. Experiments with the ¹⁴C-labelled ethylenediamine derivative have shown that inactivation is primarily related to the extent of reaction of the compound with the bacteriophage and that variations in inactivation observed under different experimental conditions simply reflect differences in the kinetics of the binding reactions. Quantitative comparisons have shown that at the mean lethal dose 1.5 molecules of platinum compound are bound to each R17 bacteriophage and 5 molecules to each T7.96% of the compound bound to R17 was bound to RNA and 76% of the compound bound to T7 was bound to the DNA.     

The kinetics of benzo(a)pyrene anti-7,8-dihydrodiol 9, 10-epoxide formation from benzo(a)pyrene and regulatory membrane effects

r-7,c-10,t-8,t-9-Tetrahydroxybenzo(a)pyrene (7,10/8,9-tetrol), which is the principal hydrolysis product of r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo(a)pyrene (anti-diol-epoxide), was resolved and measured by HPLC in organic extracts of incubations which contained induced rat liver microsomes and BP. Kinetic analyses showed that: (a) following a 5- to 7-min lag period, anti-diol-epoxide formation was linear, and (b) levels of anti-diol-epoxide formed were highly dependent upon the starting BP concentration. anti-Diol-epoxide production increased at starting BP concentrations of 0–12 μm and decreased in incubations containing 12–25 μm BP. However, between 25 and 100 μm BP, anti-diol-epoxide formation was stable at a level representing 65% of the peak production which occurred at a starting BP concentration of 12 μm. BP oxidation was competitively inhibited by (?)-trans-BP-7,8-dihydrodiol and about five times less effectively by the (+)-trans-BP-7,8-dihydrodiol. The inability of a severalfold excess of BP (25–100 μm) to totally inhibit BP-7,8-dihydrodiol oxidation was explained by the presence of a microsomal substrate compartment which was saturated at only 6–8 μm BP, the remaining BP present as aggregates in the aqueous compartment. Purification of microsomes by Sepharose 2B gel filtration after reaction with [³H]BP also indicated that BP-7,8-dihydrodiol was preferentially concentrated in the microsome compartment leading to a net increase in the ratio of BP-7,8-dihydrodiol to BP in the microsomal compartment, which favored BP-7,8-dihydrodiol oxidation to yield the biologically active anti-diol-epoxide.     

Stereoselective determination of R(−)- and S(+)-MK-571, a leukotriene D4 antagonist,in human plasma by chiral high-performance liquid chromatography

A stereoselective high-performance liquid chromatographic method that utilizes fluorescence detection was developed for the selective and sensitive quantification of R(−)- and S(+)-enantiomers of MK-571 (1), a potent and specific leukotriene D₄ antagonist, in human plasma. Racemic 1 was isolated from the acidified plasma using solid-phase extraction and the resulting residue was successfully reacted with isobutyl chloroformate and R(+)-1-(1-naphthyl)ethylamine in triethylamine—acetonitrile medium to form the diastereomer of each enantiomer. A structural analogue of 1 was used as internal standard. The derivatized sample was dissolved in 1,1,2-trichlorotrifluoroethane and an aliquot was chromatographed on a (R)-urea chiral column using a mobile phase containing 89% triethylamine—pentane (3:1000, v/v), 10% 2-propanol, and 1% acetonitrile at a flow-rate of 1.5 ml/min. The fluorescence response (excitation wavelength, 350 nm; emission wavelength, 410 nm) was linear (r²>0.999) for concentrations of enantiomers of 1 from 0.05 μg/ml, the lowest quantitation limit, up to 2.5 μg/ml. Intra-day coefficients of variation at 0.05 μg/ml were 2.4% for the R(−)-isomer and 2.0% for S(+)-isomer. The corresponding inter-day coefficients of variation for R(−)- and S(+)-1 were 2.6 and 3.6%, respectively. The utilit of the methodology was established by analysis of plasma samples from male volunteers receiving single intravenous and oral doses of racemic 1.     

Synthesis of α3 phage DNA in replication mutants of Escherichia coli

Host functions for DNA replication of bacteriophage α3, a representative of group A microvirid phages, were studied using dna and rep mutants of Escherichia coli. In dna⁺ cells, conversion of phage α3 single-stranded DNA (SS) into the double-stranded replicative form (RF) was insensitive to 30–150 μg/ml of chloramphenicol, 200 μg/ml of rifampicin, 50 μg/ml of nalidixic acid, or 200 μg/ml of novobiocin. At 43°C, synthesis of the parental RF was inhibited in dnaG and dnaZ mutants, but not in dnaE and rep strains. Replication of phage α3 progeny RF was prevented by 50 μg/ml of mitomycin C (in hcr⁺ bacteria), 50 μg/ml of nalidixic acid or 200 μg/ml of novoviocin, but neither by 30 μg/ml of chloramphenicol nor by 200 μg/ml of rifampicin. Besides dnaG and dnaZ gene products, dnaE and rep functions were essential for the progeny RF synthesis. Host factor dependence of α3 was relatively simple and, in contrast with phages øX174 and G4, α3 did not require dnaB and dnaC(D) activities.     

The electronic structure of and conformational energy barrier to rotation a round the C-N glycosidic linkage in adenosine-3',5'-cyclicmonophosphate (cyclic AMP) and its phosphonate analog

Extended Hückel molecular orbital calculations are reported on cyclic AMP and its phosphonate analog. A parallel Lennard-Jones potential and molecular orbital study on the barrier to rotation of the adenine base around the sugar phosphate moiety indicates a rather low barrier for both molecules studied (6.6 kcal/mole and less than 6 kcal/mole for the cyclic phosphate and cyclic phosphonate, respectively) with most favorable syn and anti forms possessing similar energies. According to the calculations this low barrier may be the most distinguishable property when compared to the molecule's precursor ATP and enzymically derived product 5′-AMP.     

Synthesis, characterization and structural analysis of isostructural dinuclear molybdenum and tungsten oxo-bis-μ-sulfido-benzenedithiolene complexes

Reactions of the molybdenum and tungsten precursors [MO₂S₂]²⁻ with equimolar amounts of benzenedithiol in acetonitrile give the title compounds [M₂O₂(μ-S)₂(bdt)₂]²⁻ with M = Mo, W and bdt = benzene-dithiolate. In case a tungsten to ligand ratio of 1:2 is used the dimer forms as well but only as a minor species whereas the monomer [WO(bdt)₂]²⁻ is the main product. In both dimeric compounds the syn-isomers are formed referring to the position of the apical oxo ligands with respect to the M₂S₂ plane. For the molybdenum compound this contrasts with a published crystal structure of the anti-isomer. Both complexes give highly symmetric isomorphous crystals but still show subtle differences in their bond lengths and angles around the central metal. The X-ray crystal structures of both are analyzed in detail and compared with each other and with the isomeric molybdenum compound. Differences and similarities between tungsten and both isomers of molybdenum complexes are shown to be more influenced by the conformation than by the central metal and a reason for the formation of syn- and anti-isomers based on the respective synthetic procedures is proposed.     

Conformations of cyclic 3',5'-nucleotides. Effect of the base on the synanti conformer distribution

The furanose and the phosphate rings of cyclic 3′,5′-nucleotides are locked in the ₄T³ and chair conformations respectively. The only variable which shows major conformational flexibility in these molecules is the rotation about the glycosyl bond which describes the orientation of the base relative to the sugar-phosphate bicyclic system. The glycosyl torsion angle has been analyzed for cyclic nucleotides with different purine and pyrimidine bases by use of conformational energy calculations. The results indicate that all the pyrimidine bases, U, T and C show a very strong energetic preference for the anti range of conformations. The calculations predict that among cyclic 3′,5′-purine nucleotides cyclic GMP and cyclic IMP favor the syn conformation to the anti by 95:5 and 70:30 respectively, while cyclic AMP shows a preference for the anti conformation to syn by 70:30. Thus the purines show a greater probability for the syn conformation than the pyrimidines in cyclic 3′,5′-nucleotides.     

Biochemical and biophysical properties of hyphomicrobium bacteriophage hyphi30

Hyphomicrobium bacteriophage Hy30 and its nucleic acid were studied to determine some of their biochemical and biophysical properties. The molecular weight of the phage is 55.4 × 10⁶, and its buoyant density is 1.508 g/ml. The nucleic acid of Hy30 is linear, double-stranded DNA with a molecular weight of 29.7 × 10⁶. The guanine-plus-cytosine content of the DNA was 62% as determined from its melting temperature and buoyant density.     

Separation of the glucuronides of entacapone and its (Z)-isomer in urine by micellar electrokinetic capillary chromatography

A micellar electrokinetic capillary chromatography (MECC) method was developed for the separation of the 3-O-glucuronides of entacapone and its (Z)-isomer, the two main urinary metabolites of entacapone in humans. Entacapone is a novel, potent inhibitor of catechol-O-methyltransferase (COMT) intended for use as an adjunct in the treatment of Parkinson’s disease. Urine samples spiked with synthetic 3-O-glucuronides were used to study the effects of running buffer pH, composition and applied voltage on separation of the closely migrating glucuronides. The 3-O-glucuronide of nitecapone, was used as internal standard. The greatest improvement in separation was achieved by increasing the running buffer ionic concentration. Changes in pH had little effect on the separation, whereas increase in sodium dodecyl sulfate (SDS) concentration slightly improved resolution. Baseline separation and good selectivity relative to urine components were achieved by using a phosphate (25 mM)–borate (50 mM)–SDS (20 mM) running buffer, pH 7.0, in a 75 μm×60/67 cm fused-silica capillary at 15 kV and a 335 nm cut-off filter in the UV detector. The limits of detection (LOD) at a signal-to-noise ratio of 3 were about 0.25 μg/ml (5.2·10 ⁻⁷M) (injection 0.5 p.s.i./8 s). The linear detection range was 2–100 μg/ml (r²>0.999). Good repeatability of injection and relative migration times were obtained.     

Tetrahydro-1H,5H-pyrazolo[1,2-a]pyrazole-1-carboxylates as inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase

The reactions between 5-substituted pyrazolidine-3-ones, aldehydes, and methyl methacrylate provided tetrahydropyrazolo[1,2-a]pyrazole-1-carboxylates as mixtures of syn- and anti-diastereomers. Testing for inhibition of dihydroorotate dehydrogenase of Plasmodium falciparum (PfDHODH) revealed high activity of some anti-isomers of the methyl esters, while the corresponding carboxylic acids and carboxamides were not active. The most active representative, methyl (1S*,3S*,5R*)-1,5-dimethyl-7-oxo-3-phenyltetrahydro-1H,5H-pyrazolo[1,2-a]pyrazole-1-carboxylate (IC₅₀ = 2.9 ± 0.3 μM), also exhibited very high selectivity of the parasite enzyme vs. the human enzyme, PfDHODH/HsDHODH > 350. According to the molecular docking score, this high activity is explainable by synergic interactions of the methyl, phenyl and the CO₂Me substituent with the hydrophobic pockets in the active site of the enzyme. The carboxylic acid and carboxamides derived from this compound did not inhibit PfDHODH.     

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales.     

Isolation and Characterization of a Bacteriophage Lytic for Desulfovibrio salexigens, a Salt-Requiring, Sulfate-Reducing Bacterium

A bacteriophage that lysed Desulfovibrio salexigens cells was isolated from marine sediments and preliminarily characterized by electron microscopy and electrophoretic analysis of structural proteins and genomic nucleic acid. The bacteriophage had an icosahedral head and a long flexible tail, and the buoyant density of the bacteriophage particles was 1.468 g/ml in cesium chloride. The particles consisted of a double-stranded DNA molecule about 33 kilobase pairs long and at least 11 structural proteins.     

Ultrafiltration-light absorption spectrophotometric determination of silicon in blood

An ultrafiltration-light absorption spectrometric method for soluble molybdate-reactive silicon was assessed and applied to bovine and ovine blood plasma and sera, giving precise analytical results. Interfering protein above molecular weight 10,000–25,000 was removed by ultrafiltration, and silicon in ultrafiltrates was quantitated by measuring light absorption at 810 nm of the 1,2,4-aminonaphthol sulfonic acid/ascorbic acid-reduced silicomolybdate. Chemical interferences on the color-forming reaction of remaining blood components were tested by measuring recoveries of silicon added to real blood plasma samples and to synthetic blood plasma solutions, the latter containing typical levels of the major ions Na⁺, K⁺, Ca²⁺, HCO₃^?, and Cl^?, together with varying quantities of the potential interferants (amount per analytical reaction): phosphate (0–0.5 mg P), ferric ion (0–3 mg), fluoride (0–1.25 mg), vanadate (0–0.5 mg V), arsenate (0–10 μg As), and germanate (0–0.5 μg Ge). The mean recovery of added 0.8–9 μg silicon/g of bovine and ovine plasma was 97.7% (SE = 1.0, n = 17); the mean recovery of 1 and 5 μg silicon from synthetic blood plasma solutions with interferant levels up to 50-fold that in normal plasma was 99.2% (SE = 0.3, n = 47). Silicon concentrations found in bovine and ovine blood plasma and sera were typically around 7 μg/ml with procedural reagent blanks consistently low at a mean of 0.12 μg/test (SD = 0.011, n = 20). The silicon level in Center for Disease Control bovine serum (reference specimen Lot R-2274) was found to be (mean ± SE, n = 10) 1.147 ± 0.013 μg/g or 1.172 ± 0.013 μg/ml (25°C). The method detectivity (detection limit) was estimated at 0.03 μg.     

Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer

Modified thrombin-binding aptamers carrying 2′-deoxyguanine (dG) residues with locked North- or South-bicyclo[3.1.0]hexane pseudosugars were synthesized. Individual 2′-deoxyguanosines at positions dG5, dG10, dG14 and dG15 of the aptamer were replaced by these analogues where the North/anti and South/syn conformational states were confined. It was found that the global structure of the DNA aptamer was, for the most part, very accommodating. The substitution at positions 5, 10 and 14 with a locked South/syn-dG nucleoside produced aptamers with the same stability and global structure as the innate, unmodified one. Replacing position 15 with the same South/syn-dG nucleoside induced a strong destabilization of the aptamer, while the antipodal North/anti-dG nucleoside was less destabilizing. Remarkably, the insertion of a North/anti-dG nucleoside at position 14, where both pseudosugar conformation and glycosyl torsion angle are opposite with respect to the native structure, led to the complete disruption of the G-tetraplex structure as detected by NMR and confirmed by extensive molecular dynamics simulations. We conclude that conformationally locked bicyclo[3.1.0]hexane nucleosides appear to be excellent tools for studying the role of key conformational parameters that are critical for the formation of a stable, antiparallel G-tetrad DNA structures.     

Investigation of the mechanisms of photo-induced formation of cyclobutane dimers of cytosine and 2,4-diaminopyrimidine

The mechanisms of the formation of cyclobutane dimers (CBD) of cytosine and 2,4-diaminopyrimidine were studied at the CC2 theoretical level and cc-pVDZ basis functions. Four orientations of the two monomers are explored: cys-syn, cis-anti, trans-syn, and trans-anti. The research revealed that in all cases the cyclobutane structures are formed along the ¹ππ* excited-state reaction paths of the stacked aggregates. We localized the S₁/S₀ conical intersections mediating those transformations. The results obtained agree well with the previously reported investigations on the cis-syn cyclodimer formations of other pyrimidines.     

Synthesis of 3-aza[4.4.3]propellanes with high σ1 receptor affinity

In order to obtain rigid σ₁ receptor ligands with defined orientation of pharmacophoric elements, the azapropellane scaffold was chosen. Schmidt rearrangement of propellan-8-ones 6 and 10 provided 3-azapropellan-4-ones 7 and 11. Benzylation of the secondary lactams 7 and 11 followed by LiAlH₄ reduction furnished the azapropellanes 4a and 4c, respectively. A second hydrophobic element was introduced by transformation of the alcohols 4a into carbamates 4b. The σ₁ affinity of the azapropellanes 4 is strongly dependent on the stereochemistry and the substitution pattern in 12-position. anti-configured azapropellanes anti-4a and anti-4b show higher σ₁ affinity than their syn-configured counterparts syn-4a and syn-4b. Conversion of the alcohol anti-4a into the carbamate anti-4b led to increased σ₁ affinity, but complete removal of the 12-substituent resulted in the highest σ₁ affinity (K_i(4c)?=?17?nM). It can be concluded that the propellane scaffold alone is able to form strong lipophilic interactions and stabilize the ligand–σ₁ receptor complex as does usually the primary hydrophobic region.     

Regio- and enantioselective bioreduction of methyleneketoesters using both polymeric resin and cellulose matrix

Methyleneketoesters were prepared in >90% yield by performing an IBX oxidation of Morita–Baylis–Hillman adducts. A methodology was developed to achieve methyl 3-aryl-3-keto-2-methylenepropanoate reduction using a screening of yeast strains in three different reaction procedures to obtain products with both high yield and diastereoselectivity. The reactions conducted in water provided inferior yields (50%) for substrates 2b–c. Employing Amberlite^® XAD7HP which was a substrate reservoir that also immediately extracted the products from the reaction medium after their formation, syn-4a–c and anti-4a–c were isolated in 60–70% yield, with high stereoselectivity (98–99% ee). The best results were obtained using substrates adsorbed on filter paper which provided products yields above 70%, a 99% ee and a diastereomoeric ratio (syn-4: anti-4) 9:1. Cellulose matrix has excellent potential to be successfully employed in general biocatalytic reactions.     

Determination of non-protein bound phenylbutazone in bovine plasma using ultrafiltration and liquid chromatography with ultraviolet detection

A liquid chromatographic procedure using UV detection was coupled with ultrafiltration for the quantitation of free phenylbutazone in bovine plasma, in the range of 20 ng/ml to 2.0 μg/ml. Whole plasma samples (0.5 to 1 ml) were placed in a 2-ml centrifugal concentrator with a molecular-mass cut-off membrane of 10 000 and centrifuged at 4500 g for 2 h at 4°C using a fixed angle rotor. The ultrafiltrate was transferred to an LC vial with a 200-μl insert and 100 μl was injected into an LC system. The chromatographic system used a C₁₈ reversed-phase column connected to a UV detector set at 264 nm. The mobile phase was 0.2 M sodium phosphate buffer (pH 7)–methanol (1:1). Recoveries of phenylbutazone from protein-free plasma water fortified at levels of 20 ng/ml to 2 μg/ml ranged from 91 to 93%, with relative standard deviations (R.S.D.s) ranging from 1 to 4%. The concentration of incurred non-protein bound phenylbutazone obtained from a cow intravenously dosed twice with 2 g phenylbutazone, 8 h apart, was 111, 26 and 11 ng/ml for 2, 72 and 104 h post first phenylbutazone dose, respectively.     

Ion-pair high-performance liquid chromatographic assay method for the assessment of clarithromycin stability in aqueous solution and in gastric juice

A simple and selective ion-pair HPLC method has been developed for the analysis of clarithromycin in aqueous solutions and in gastric juice. A Hypersil ODS 5-μm (150 × 4.6 mm I.D.) column was used with a mobile phase consisting of acetonitrile-aqueous 0.05 M phosphate buffer (pH 4.6) containing 5 mM 1-octanesulphonic acid (50:50, v/v). The column temperature was 50°C and detection was by UV absorption (210 nm). The limits of detection of 50-μl samples were 0.4 μg/ml (aqueous) and 0.78 μg/ml (0.5 ml gastric juice) or better. The assay was linear in the range of 1.56 to 100 μg/ml with r² values greater than 0.99. The recovery from the gastric juice samples was 98.5±2.9%. The method was applied successfully to determine the stability of clarithromycin in 0.01 M HCl and gastric juice.     

Ficin-catalyzed asymmetric aldol reactions of heterocyclic ketones with aldehydes

Ficin from fig tree latex displayed a promiscuous activity to catalyze the direct asymmetric aldol reactions of heterocyclic ketones with aromatic aldehydes. Ficin showed good substrate adaptability to different heterocyclic ketones containing nitrogen, oxygen or sulfur. The enantioselectivities up to 81% ee and diastereoselectivities up to 86:14 (anti/syn) were achieved under the optimized reaction conditions.