Stability of 2'-deoxyxanthosine in DNA

The deamination of nucleobases in DNA occurs by a variety of mechanisms and results in the formation of hypoxanthine from adenine, uracil from cytosine, and xanthine and oxanine from guanine. 2′-Deoxyxanthosine (dX) has been assumed to be an unstable lesion in cells, yet no study has been performed under biological conditions. We now report that dX is a relatively stable lesion at pH 7, 37°C and 110 mM ionic strength, with a half-life (t_1/2) of 2.4 years in double-stranded DNA. The stability of dX as a 2′-deoxynucleoside (t_1/2 = 3.7 min at pH 2; 1104 h at pH 6) was increased substantially upon incorporation into a single-stranded oligodeoxynucleotide, in which the half-life of dX at different pH values was found to range from 7.7 h at pH 2 to 17 700 h at pH 7. Incorporation of dX into a double-stranded oligodeoxynucleotide resulted in a statistically insignificant increase in the half-life to 20 900 h at pH 7. Data for the pH dependence of the stability of dX in single-stranded DNA were used to determine the rate constants for the acid-catalyzed (2.6 × 10^–5 s^–1) and pH-independent (1.4 × 10^–8 s^–1) depurination reactions for dX as well as the dissociation constant for the N⁷ position of dX (6.1 × 10^–4 M). We conclude that dX is a relatively stable lesion that could play a role in deamination-induced mutagenesis.     

Highly stereoselective synthesis of C-vinyl furanosides through acid-catalyzed S(N)2 inversion at the C-3 position of 1,2-dideoxy-hept-1-enitols

A highly stereoselective synthesis of C-vinyl furanosides through the S_N2 inversion at the C-3 position of the 1,2-dideoxy-hept-1-enitols is disclosed. Treatment of the 1,2-dideoxy-hept-1-enitols with diphenylammonium trifluoromethanesulfonate as the acid catalyst produced the C-vinyl furanosides (3,6-anhydro-1,2-dideoxy-hept-1-enitol derivatives) via a subsequent S_N2 intramolecular debenzyloxyation-cycloetherification reaction at the C-3 position.     

Synthesis of N-phenyl-N-(3-(piperidin-1-yl)propyl)benzofuran-2-carboxamides as new selective ligands for sigma receptors

Novel benzofuran-2-carboxamide ligands, which are selective for sigma receptors, have been synthesized via a microwave-assisted Perkin rearrangement reaction and a modified Finkelstein halogen-exchange used to facilitate N-alkylation. The ligands synthesized are the 3-methyl-N-phenyl-N-(3-(piperidin-1-yl)propyl)benzofuran-2-carboxamides (KSCM-1, KSCM-5 and KSCM-11). The benzofuran-2-carboxamide structure was N-arylated and N-alkylated to include both N-phenyl and N-(3-(piperidin-1-yl)propyl substituents, respectively. These new carboxamides exhibit high affinity at the sigma-1 receptor with K_i values ranging from 7.8 to 34 nM. Ligand KSCM-1 with two methoxy substituents at C-5 and C-6 of the benzofuran ring, and K_i = 27.5 nM at sigma-1 was found to be more selective for sigma-1 over sigma-2.     

Design and synthesis of 1-(2-alkanamidoethyl)-6-methoxy-7-azaindole derivatives as potent melatonin agonists

A series of 7-azaindolic ligands bearing a methoxy group and a N-acetyl chain as melatoninergic pharmacophores were synthesized and their binding affinities towards MT₁ and MT₂ receptors were evaluated. Compounds 7a-c and 12 (cyclohexyl ring connected at C-2 and C-3 position) appears as important melatonin MT₂ and MT₁ receptors agonists. On the other hand, the presence of basic groups (amines) at position C-3 was detrimental to the melatoninergic affinities.     

Activation of endo-β-N-acetylglucosaminidase from Arthrobacter protophormiae by various sugars

Endo-β-N-acetylglucosaminidase from Arthrobacter protophormiae was activated by the addition of glucose, mannose, N-acetylglucosamine, and β-allose. While the enzyme did not appear to be significantly affected by the addition of galactose or N-acetylgalactosamine. These results indicate that the C-4 and C-6 positions of the monosaccharide are the most important for enzyme activation. Moreover, the enzyme was activated by the addition of disaccharides such as cellobiose, gentiobiose, and di-N-acetylchitobiose, but not by polysaccharides such as starch and yeast mannan. In the presence of N-acetylglucosamine, the enzyme activation occurred well over pH 4.0 and the K_m value of the enzyme for (Man)₆(GlcNAc)₂-Asn-dansyl changes from 1.2 mM to 3.2 mM.     

Structure of 2-acetamido-3-amino-2,3-dideoxy-d-glucofuranurono-6,3-lactam

An X-ray crystallographic analysis of the title compound, an N-acetyl derivative of the 2,3-diamino-2,3-dideoxy-d-glucofuranurono-6,3-lactam found in the hydrolyzate of Pseudomonas aeruginosa P14 lipopolysaccharide, was performed. The crystals are monoclinic, space group P2₁, a = 11.704(2), b = 5.333(1), c = 7.399(2) Å, β = 91.63(2)°, and Z = 2. The structure was solved by direct methods and refined by the block-diagonal least-squares method to a final R value of 0.046 for 796 independent reflections. The dihedral angle between the mean plane through the furanose ring and that through the γ-lactam ring is 106.2(2)°, the furanose ring is ¹T₂, and the C-3, C-4, C-6, and N-3 atoms of the γ-lactam ring are nearly coplanar. The conformation in aqueous solution is discussed, based on the ¹H-n.m.r. data.     

Kinetics of the reaction of pentacyanonitrosylferrate(II) with aliphatic amines

The reactions of pentacyanonitrosylferrate(II) with ethyl-, n-propyl-, n-butyl-, cyclohexyl- and benzylamines were studied in dilute aqueous solution at 8.6–9.6 pH and 15–35 °C. Nitrosation, diazotation and deamination processes take place in the reactions resulting in alcohols and N₂ gas as final products. On the basis of spectrophotometric and gasvolumetric experiments the rate law was determined as follows.v = k[RNH₂][Fe(CN)₅NO^2?] The dependence on pH was interpreted by the protonation equilibria of the amines. From the function of the logarithm of rate constants vs. reciprocal temperature, relatively small activation enthalpies (15–70 kJ mol^?1) and extremely high negative activation entropies [(?80) ? (?240) J K^?1 mol^?1] were found. The mechanism was interpreted by the analogy with nitrous acid diazotation.A parallel trend was observed between the rate constants at 25 °C and the basicity constants of the amines.     

The influence of formaldehyde fixation time on the rate of nitrous acid deamination of erythrocytes and spinal cord proteins

Summary Alcohol fixed blood films and fresh blocks of spinal cord were immersed in phosphate buffered neutral 10% formol for graded intervals, the films for 10, 30 min, 1, 2, 4, 8, 24 hr; the blocks for 2, 4, 6, 24 hr at 3 and 24° C; 1, 3, 7, 14, 21, 28, 42, 56 da, 3 and 14 mo at 24–26°. Graded deaminations in 2 N NaNO₂/HAc at 3° C were applied: 1, 2, 5, 10, 20, 30 min; 1, 2, 4, 6, 8, 12, 18, 24, 36 hr. Blood films were stained at pH 6 and 6.5, tissue at pH 4.5 and 5.0, both in azure A eosin B. The point at which erythrocytes reached a slightly bluish green was taken as the end point, since no further color change occurred on further exposure and erythrocytes were the last of usually deamination susceptible tissue elements to lose their oxyphilia on deamination. Deamination of alcohol fixed blood films is completed in about 2 min, of sublimate fixed spinal cord in about 1 hr. Progressive formaldehyde exposure increased deamination time of blood films to 10–20 min in 1 hr, to 6–8 hr in 4 hr and to 12 hr in 24 hr. The tissue deamination showed similar progressive increase of deamination time, slower with 3° C fixation than with 24–26°, reaching 18–36 hr by about 3 days formol, and remaining about the same thereafter.Supported by National Cancer Institute Grant No. C-04816, National Institutes of Health.     

Synthesis and dopaminergic activity of a series of new 1-aryl tetrahydroisoquinolines and 2-substituted 1-aryl-3-tetrahydrobenzazepines

A series of new 1-aryl-6,7-dihydroxy tetrahydroisoquinolines with several substitution patterns in the 1-aryl group at C-1 were prepared in good yields. The influence of each substituent on the affinity and selectivity for D₁ and D₂ dopaminergic receptors was studied. Moreover, N-alkyl salts of these tetrahydroisoquinolines were used as starting material to synthesize a series of new 1-aryl-7,8-dihydroxy 3-tetrahydrobenzazepines derivatives with electron-withdrawing substituents at C-2 position by the diastereoselective Stevens rearrangement. The structure-activity relationship of these compounds was explored to evaluate the effect of the functional group at C-2 in benzazepines and the modification in the aryl group at the isoquinoline C-1 position towards the affinity and selectivity for the mentioned receptors. The 1-aryl-6,7-dihydroxy tetrahydroisoquinoline 4c shows significant affinity towards D₂ receptor, with K_i value of 31 nM. This significant affinity can be attributed to the presence of a thiomethyl group, and it is the most active 1-aryl-6,7-dihydroxy tetrahydroisoquinoline derivative reported to date.     

Properties of metal-ion coordinated imidazoles: nmr and C-2 H Exchange in Co(III) Complexes

The ¹H and ¹³C nmr spectra of Co(NH₃)₅ImH³⁺ and the ¹H nmr spectra of αCotrien(ImH)₂³⁺ and βCotrien(ImH)₂³⁺ are reported. The pK_a values determined from the dependence of the chemical shift on pH are 10.0, 9.6, and 10.1, respectively. The range of the chemical shift between the acid and base forms is unusually small in the ¹H nmr, 0.5–0.7 ppm for the C-2 H and about 0.25 ppm for the C-4 H and C-5 H. In the ¹³C nmr, C-2 and C-4 have large shifts to low field and C-5 a small shift to high field on deprotonation. The C-2 proton is not exchanged with solvent ²H under acidic or basic conditions, in marked contrast to the corresponding proton in both imidazole and 1-methylimidazole. These spectroscopic and chemical properties should be useful for the direct identification of metal-ion coordinated histidines in proteins.     

High-Resolution Denitrification Kinetics in Pasture Soils Link N2O Emissions to pH,and Denitrification to C Mineralization

Denitrification in pasture soils is mediated by microbial and physicochemical processes leading to nitrogen loss through the emission of N₂O and N₂. It is known that N₂O reduction to N₂ is impaired by low soil pH yet controversy remains as inconsistent use of soil pH measurement methods by researchers, and differences in analytical methods between studies, undermine direct comparison of results. In addition, the link between denitrification and N₂O emissions in response to carbon (C) mineralization and pH in different pasture soils is still not well described. We hypothesized that potential denitrification rate and aerobic respiration rate would be positively associated with soils. This relationship was predicted to be more robust when a high resolution analysis is performed as opposed to a single time point comparison. We tested this by characterizing 13 different temperate pasture soils from northern and southern hemispheres sites (Ireland and New Zealand) using a fully automated-high-resolution GC detection system that allowed us to detect a wide range of gas emissions simultaneously. We also compared the impact of using different extractants for determining pH on our conclusions. In all pH measurements, soil pH was strongly and negatively associated with both N₂O production index (IN₂O) and N₂O/(N₂O+N₂) product ratio. Furthermore, emission kinetics across all soils revealed that the denitrification rates under anoxic conditions (NO+N₂O+N₂ μmol N/h/vial) were significantly associated with C mineralization (CO₂ μmol/h/vial) measured both under oxic (r² = 0.62, p = 0.0015) and anoxic (r² = 0.89, p<0.0001) conditions.     

Synthesis and biological evaluation of N-difluoromethyl-1,2-dihydropyrid-2-one acetic acid regioisomers: Dual Inhibitors of cyclooxygenases and 5-lipoxygenase

A new group of acetic acid (7a–c, R¹ = H), and propionic acid (7d–f, R¹ = Me), regioisomers wherein a N-difluoromethyl-1,2-dihydropyrid-2-one moiety is attached via its C-3, C-4, and C-5 position was synthesized. This group of compounds exhibited a more potent inhibition, and hence selectivity, for the cyclooxygenase-2 (COX-2) relative to the COX-1 isozyme. Attachment of the N-difluoromethyl-1,2-dihydropyrid-2-one ring system to an acetic acid, or propionic acid, moiety confers potent 5-LOX inhibitory activity, that is, absent in traditional arylacetic acid NSAIDs. 2-(1-Difluoromethyl-2-oxo-1,2-dihydropyridin-5-yl)acetic acid (7c) exhibited the best combination of dual COX-2 and 5-LOX inhibitory activities. Molecular modeling (docking) studies showed that the highly electronegative CHF₂ substituent present in 7c, that showed a modest selectivity for the COX-2 isozyme, is oriented within the secondary pocket (Val523) present in COX-2 similar to the sulfonamide (SO₂NH₂) COX-2 pharmacophore present in celecoxib, and that the N-difluoromethyl-1,2-dihydropyrid-2-one pharmacophore is oriented close to the region containing the LOX enzyme catalytic iron (His361, His366, and His545). Accordingly, the N-difluoromethyl-1,2-dihyrdopyrid-2-one moiety possesses properties suitable for the design of dual COX-2/5-LOX inhibitory drugs.     

Transition state stabilization by deaminases: Rates of nonenzymatic hydrolysis of adenosine and cytidine

Nonenzymatic rates of hydrolytic deamination of adenosine and cytidine by acids and bases analogous to side chains of naturally occurring amino acids are compared with the rates of uncatalyzed deamination in water and with the rates of the hydroxide- and hydrogen ion-catalyzed reactions. For adenosine, hydroxide ion is an effective catalyst, with a second-order rate constant of 7.5 × 10⁻⁶ m⁻¹ s⁻¹ at 85°C and an energy of activation of 19.9 kcal/mol. Acid-catalyzed deamination of adenine proceeds with a second-order rate constant of 1.5 × 10⁻⁶ m⁻¹ s⁻¹ at 85°C. At concentrations of 1 m and at pH values corresponding to their respective pK_a values, dimethylamine, acetate, selenide, imidazole, phosphate, and zinc(II) do not enhance the rate of deamination of adenosine beyond that observed in water, and 2-mercaptoethanol produces only a modest rate enhancement. The uncatalyzed rate of adenosine deamination in water is 8.6 × 10⁻⁹ s⁻¹ at 85°C: extrapolation to 37°C and comparison with k_cat for rat hepatoma adenosine deaminase yield a rate enhancement by the enzyme of approximately 2 × 10¹²-fold. 1,6-Dimethyladenosine, the conjugate acid of which has a pK_a value much higher than that of adenosine, is not readily deaminated, suggesting that the uncatalyzed deamination of adenosine does not proceed by hydroxide ion attack on the rare protonated form of adenosine, but rather by attack on the neutral species. Deamination of cytidine is catalyzed most effectively by hydroxide ion, with a second-order rate constant of 4.5 × 10⁻⁴ m⁻¹ s⁻¹ at 85°C and an energy of activation of 28.5 kcal/mol. The uncatalyzed rate of deamination of cytidine in water, which also exhibits an energy of activation of 28.5 kcal/mol, is 8.8 × 10⁻⁸ s⁻¹ at 85°C. Comparison of the rate extrapolated to 25°C with k_cat for bacterial cytidine deaminase gives a rate enhancement for the enzyme of 4 × 10¹¹-fold. The C-5 proton of the pyrimidine ring of cytidine does not exchange with solvent during alkaline hydrolysis, suggesting that deamination under these conditions does not involve prior addition of water across the 5,6 double bond.     

Synthesis of 5-beta-D-ribofuranosylcytosine (pseudo-cytidine) and its alpha isomer

The dilithio derivative of 2,4-di-O,N-trimethylsilylcytosine was condensed with 2,4:3,5-di-O-benzylidene-D-ribose to give a mixture of the protected, epimer at C-1′ pentitols 5 and 6; in addition, a compound substituted at N-3 or N-4, whose structure was not elucidated, was also obtained. The epimers were treated with acid to give 4-amino-2-hydroxy-5-(β-and α-D-ribofuranosyl)pyrimidine (10 and 12). The n.m.r. spectrum of 10 corresponds predominantly to the C-2′ endo structure. On the other hand, the n.m.r. spectrum of 12 presents couplings identical with those of the “α pseudo-uridine”. On nitric deamination, each isomer gave in a highly preponderant yield the corresponding pseudo-uridine at C-1′.     

Formation of 2'-deoxyoxanosine from 2'-deoxyguanosine and nitrous acid: mechanism and intermediates

The reaction mechanism for the formation of 2′-deoxyoxanosine from 2′-deoxyguanosine by nitrous acid was explored using methyl derivatives of guanosine and an isolated intermediate of the reaction. When 1-methylguanosine was incubated with NaNO₂ under acidic conditions, N⁵-methyloxanosine and 1-methylxanthosine were generated, whereas the same treatment of N²,N²-dimethylguanosine generated no product. In a similar experiment without NO₂^–, participation of a Dimroth rearrangement was ruled out. In the guanosine–HNO₂ reaction system, an intermediate with a half-life of 5.6 min (pH 7.0, 20°C) was isolated and tentatively identified as a diazoate derivative of guanosine. The diazoate intermediate was converted into oxanosine and xanthosine at a molar ratio (oxanosine:xanthosine) of 0.26 at pH 7.0 and 20°C. The ratio was not affected by the incubation pH between 2 and 10, but increased linearly with temperature from 0.22 (0°C) to 0.32 (50°C). The addition of acetone also increased the ratio up to 0.85 (98% acetone). Based on these results, a con-ceivable pathway for the formation of 2′-deoxyoxanosine from 2′-deoxyguanosine by HNO₂ is proposed.     

Design,synthesis, and pharmacological evaluation of N-(4-mono and 4,5-disubstituted thiazol-2-yl)-2-aryl-3-(tetrahydro-2H-pyran-4-yl)propanamides as glucokinase activators

A series of N-thiazole substituted arylacetamides were designed on the basis of metabolic mechanism of the aminothiazole fragment as glucokinase (GK) activators for the treatment of type 2 diabetes. Instead of introducing a substituent to block the metabolic sensitive C-5 position on the thiazole core directly, a wide variety of C-4 or both C-4 and C-5 substitutions were explored. Compound R-9k bearing an iso-propyl group as the C-4 substituent was found possessing the highest GK activation potency with an EC₅₀ of 0.026 μM. This compound significantly increased both glucose uptake and glycogen synthesis in rat primary cultured hepatocytes. Moreover, single oral administration of compound R-9k exerted significant reduction of blood glucose levels in both ICR and ob/ob mice. These promising results indicated that compound R-9k is a potent orally active GK activator, and is warranted for further investigation as a new anti-diabetic treatment.     

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

Cryoturbated peat circles (that is, bare surface soil mixed by frost action; pH 3–4) in the Russian discontinuous permafrost tundra are nitrate-rich ‘hotspots'' of nitrous oxide (N₂O) emissions in arctic ecosystems, whereas adjacent unturbated peat areas are not. N₂O was produced and subsequently consumed at pH 4 in unsupplemented anoxic microcosms with cryoturbated but not in those with unturbated peat soil. Nitrate, nitrite and acetylene stimulated net N₂O production of both soils in anoxic microcosms, indicating denitrification as the source of N₂O. Up to 500 and 10 μ nitrate stimulated denitrification in cryoturbated and unturbated peat soils, respectively. Apparent maximal reaction velocities of nitrite-dependent denitrification were 28 and 18 nmol N₂O g_DW⁻¹ h⁻¹, for cryoturbated and unturbated peat soils, respectively. Barcoded amplicon pyrosequencing of narG, nirK/nirS and nosZ (encoding nitrate, nitrite and N₂O reductases, respectively) yielded ≈49 000 quality-filtered sequences with an average sequence length of 444 bp. Up to 19 species-level operational taxonomic units were detected per soil and gene, many of which were distantly related to cultured denitrifiers or environmental sequences. Denitrification-associated gene diversity in cryoturbated and in unturbated peat soils differed. Quantitative PCR (inhibition-corrected per DNA extract) revealed higher copy numbers of narG in cryoturbated than in unturbated peat soil. Copy numbers of nirS were up to 1000 × higher than those of nirK in both soils, and nirS nirK⁻¹ copy number ratios in cryoturbated and unturbated peat soils differed. The collective data indicate that the contrasting N₂O emission patterns of cryoturbated and unturbated peat soils are associated with contrasting denitrifier communities.     

Kinetics of deamination and Cu(II)/H2O2/Ascorbate-induced formation of 5-methylcytosine glycol at CpG sites in duplex DNA

Mutation in p53 tumor suppressor gene is a hallmark of human cancers. Six major mutational hotspots in p53 contain methylated CpG (mCpG) sites, and C →T transition is the most common mutation at these sites. It was hypothesized that the formation of 5-methylcytosine glycol induced by reactive oxygen species, its spontaneous deamination to thymine glycol and the miscoding property of the latter may account, in part, for the ubiquitous C →T mutation at CpG site. Here, we assessed the kinetics of deamination for two diastereomers of 5-methylcytosine glycol in duplex DNA. Our results revealed that the half-lives for the deamination of the (5S,6S) and (5R,6R) diastereomers of 5-methylcytosine glycol in duplex DNA at 37°C were 37.4 ± 1.6 and 27.4 ± 1.0 h, respectively. The deamination rates were only slightly lower than those for the two diastereomers in mononucleosides. Next, we assessed the formation of 5-methyl-2′-deoxycytidine glycol in the form of its deaminated product, namely, thymidine glycol (Tg), in methyl-CpG-bearing duplex DNA treated with Cu(II)/H₂O₂/ascorbate. LC-MS/MS quantification results showed that the yield of Tg is similar as that of 5-(hydroxymethyl)-2′-deoxycytidine. Together, our data support that the formation and deamination of 5-methylcytosine glycol may contribute significantly to the C →T transition mutation at mCpG dinucleotide site.     

Synthesis of 1-(methanesulfonyl- and aminosulfonylphenyl)acetylenes that possess a 2-(N-difluoromethyl-1,2-dihydropyridin-2-one) pharmacophore: Evaluation as dual inhibitors of cyclooxygenases and 5-lipoxygenase with anti-inflammatory activity

A hitherto unknown class of linear acetylene regioisomers were designed such that a SO₂Me or SO₂NH₂ group was located at the ortho-, meta- or para-position of the acetylene C-1 phenyl ring, and a N-difluoromethyl-1,2-dihydropyridin-2-one moiety was attached via its C-5 position to the C-2 position on an acetylene template (scaffold). All three SO₂Me regioisomers, and the 4-SO₂NH₂ analog, were potent inhibitors of 5-lipoxygenase (5-LOX IC₅₀ = 3.2–3.5 μM range) relative to the reference drug caffeic acid (IC₅₀ = 4.0 μM). The SO₂Me regioisomers exhibited weak cyclooxygenease-1 (COX-1) and -2 (COX-2) inhibitory activity with a modest COX-2 selectivity index. The most potent 3-SO₂Me, 4-SO₂Me and 4-SO₂NH₂ compounds, with respective ED₅₀ values of 66.1, 68.5 and 86.5 mg/kg po, exhibited comparable oral anti-inflammatory (AI) activity to that of the reference drug ibuprofen (ED₅₀ = 67.4 mg/kg po). The N-difluoromethyl-1,2-dihydropyridin-2-one moiety provides a novel pharmacophore for the design of cyclic hydroxamic mimetics capable of inhibiting 5-LOX for exploitation in the development of 5-LOX inhibitory AI drugs.     

Effect of Glucose and CO(2) on Nitrate Uptake and Coupled OH Flux in Ankistrodesmus braunii

In Ankistrodesmus braunii, in the absence of CO₂, i.e. in CO₂-free air or N₂, photosynthetic nitrate uptake and nitrate reduction were inhibited, especially at low pH. Under such conditions, glucose stimulated nitrate uptake and reduction to almost the same level in the pH range between 6 and 8.5. CO₂ at 0.03% effected an intermediate pH dependence of nitrate uptake; saturating CO₂ concentration (more than 1%) eliminated the pH dependence, as did glucose, but the rates were enhanced compared with glucose. Glucose and, even more, CO₂, drastically reduced the release of nitrite and ammonia to the medium, the stoichiometry between alkalinization of the medium and nitrate uptake (OH⁻/NO₃⁻) approached 1.