6-Azauridine, a nucleoside with unusual ribose conformation. The molecular and crystal structure

The cytostatic analogue ribo-6-azauridine crystallizes in the orthorhombic space group P2₁2₁2₁ with eight molecules per unit cell of dimensions $\text{a = 20.230, b = 7.709, c = 12.863}\text{A}\text{?}$. A trial structure was obtained by direct methods. Least-squares refinement of co-ordinates and anisotropic thermal parameters based on 1998 reflections measured on a four-circle diffractometer led to a discrepancy index R = 4.0%. Like uridine, 6-azauridine has the anti conformation about the glycosidic bond and a C(3′)-endo sugar pucker. Unlike uridine, it exhibits a close approach of N(6) to C(2′) at only 2.814 and 2.844 Å in the two independent molecules, and a C(5′)(5′) bond that is gauche to C(4′)O(1′) but trans to C(4′)C(3′); this conformation about a C(4′)C(5′) bond has never been observed before for C(3′)-endo puckered riboses in the crystalline state. The crystal structure displays a pseudo-A face centering and very similar conformational parameters for the two independent molecules. Every OH and NH group in the structure serves as a proton donor in a hydrogen bond, including an unusual N(3)—H(3) … O(1′) link. Molecular orbital calculations by the extended Hückel method indicate that from uridine to 6-azauridine the net charge changes sign at ring positions 5 and 6 and disappears at 1.     

AMP deaminase: Stage-specific isozymes in differentiating chick muscle

The molecular basis of the developmental increase in AMP deaminase activity in chick muscle was investigated with a view toward determining whether isozymes of AMP deaminase exist in embryonic avian muscle and, if so, whether a stage-specific isozyme transition occurs during myogenesis in vivo and in vitro. Under specified conditions, AMP deaminase isozymes in adult chicken brain and muscle may be distinguished on the basis of differences in relative substrate specificities for 5′-dAMP and 5′-AMP (expressed as a ratio of the rates observed with these compounds; i.e., $\text{dAMP}\text{AMP}$ ratios), as well as by differential immunoinactivation by antibody directed against breast muscle AMP deaminase. It was found that the AMP deaminase(s) that is (are) present in 6-day embryos is (are) catalytically and immunologically similar to the enzyme in adult brain. With mixtures of known amounts of adult muscle and brain enzymes, values for the $\text{dAMP}\text{AMP}$ ratio (as well as the fraction of uninactivated AMP deaminase at antibody excess) were proportional to the fraction of muscle isozyme present. Standard curves constructed from these data were used to determine that the fraction of adult muscle-like AMP deaminase in developing muscle, as assessed by $\text{dAMP}\text{AMP}$ ratios (and differential immunoinactivation), on days 6, 8, 10, and 15 were 23 (28), 55 (65), 83 (85), and 93% (96), respectively, Thus, parallel results were obtained for the two techniques, and the isozyme transition is virtually complete by the 15th day of incubation. Primary muscle cultures were used to investigate the isozyme transition of AMP deaminase during myogenesis in vitro. Comparison of the data obtained from primary muscle cultures treated with bromodeoxyuridine, cytosine arabinoside, and fluorodeoxyuridine with data from control cultures showed that biochemical differentiation of AMP deaminase in vitro could be attributed to the muscle cell. Also, the isozyme composition changed from a small percentage of adult muscle-like isozyme at the time of plating, to approximately 100% by the 6th day of culture.     

Repair of deaminated cytosine residues of DNA: biological significance of the absence of uracil from DNA.

Uracil-DNA glycosylase of $\text{Bacillus}\text{subtilis}$ is involved in repair of deaminated cytosine residues of DNA. Survivals of SPO2 phage after treatment with bisulfite and weak alkali are considerably higher in wild type strains than in $\text{urg}$ mutants, which are deficient in the enzyme activity, whereas survivals of bisulfite/alkali-treated PBS1 phage in the two types of cells are essentially the same. The spontaneous mutation frequency of a $\text{urg}$ mutant is three fold higher than is that of a wild type strain.     

Cyclopenta(f)isoquinoline derivatives designed to bind specifically to native deoxyribonucleic acid. 3. Interaction of 6-carbamylmethyl-8-methyl-7H-cyclopenta(f)isoquinolin-3(2H)-one with deoxyribonucleic acids and polydeoxyribonucleotides

By the use of space-filling models, a novel compound, 6-carbamylmethyl-8-methyl-7$\text{H}$-cyclopenta[f]isoquinolin-3(2$\text{H}$)-one ($\text{1}$) was devised which would be expected to hydrogen bond specifically to GC pairs in the major groove of the double helix such that (i) the amino group of the cytosine molecule donates a hydrogen bond to the C-3 carbonyl of the isoquinoline moiety and (ii) the amide proton of the side chain donates a hydrogen bond to the N-7 of guanine. From difference spectra studies it was found that $\text{1}$ binds to native calf thymus DNA better than to denatured DNA; $\text{1}$ inhibited RNA synthesis by a DNA-dependent RNA polymerase; and equilibrium dialysis experiments revealed that $\text{1}$ binds to poly(dG).poly(dC), whereas no such binding to poly(dA).poly(dT) was observed.     

THE EFFECT OF CYTOSINE ARABINOSIDE IN VITRO ON AGAR COLONY FORMING CELLS AND SPLEEN COLONY FORMING CELLS OF C57BL MOUSE BONE MARROW

This study reports the effect of cytosine arabinoside in culture on two classes of bone marrow progenitor cells in C57BL mice, agar colony forming cells (ACU) and spleen colony forming cells (CFU). Both normal cells and rapidly proliferating cells were studied. The results show that in normal mice, 23 % of ACU but only 7 % of CFU are killed following 1 hr incubation with the drug. With longer periods of incubation, the survival of ACU in the controls is poor, and the results for the drug-treated cultures suggest that the cells are held up in cycle. In continuously irradiated mice, the proportion of ACU and CFU killed after 1 hr incubation with drug is increased to 43–54%, confirming previous results that these cells are proliferating more rapidly than in normal mice. In mice treated with myerlan, 54 % of ACU are killed by 1 hr in vitro exposure to cytosine arabinoside, again confirming that ACU are rapidly proliferating. However, the proportion of CFU killed is lower (23 %). These results are compared with other studies of the effect of cytosine arabinoside in vivo and also with thymidine suicide in the same strain of mice. The results show that cytosine arabinoside has the same effect as tritiated thymidine, and also that the proportion of CFU killed by these agents in vitro is lower than when the agents are injected in vivo. It is suggested that the conditions in culture have an adverse effect on CFU, which cease DNA synthesis, and are protected from the killing effect of cytosine arabinoside and tritiated thymidine. Since cytosine arabinoside in vitro has an effect similar to tritiated thymidine in vitro on bone marrow progenitor cells in C57BL mice, in vitro incubation with cytosine arabinoside could be an alternative method to thymidine suicide for measuring differences in cell proliferation rate.     

Photodynamic alteration of cornea endothelium: Relation to bicarbonate fluxes and oxygen concentration

Corneas were mounted in flux chambers and endothelial bicarbonate fluxes were determined following sensitization of endothelial cells with 5 · 10^?6 M rose bengal and exposure to light. Corneas exposed to light demonstrated an increased passive bicarbonate flux compared to corneas not photosensitized. Active bicarbonate flux was reduced after 5 min of light exposure, but not after 1 min of light exposure. The increase in passive bicarbonate flux was prevented by the addition of 200 μg/ml catalase to the bathing solution; however, catalase had no effect on the photodynamic alteration of active flux. Neither 10 mM ascorbic acid nor 1.012 g/l glutathione prevented the photodynamically induced increase in passive flux. Perfusion of corneas with 5 · 10^?6 M rose bengal dissolved in a sucrose-substituted Krebs-Ringer bicarbonate solution with a $\text{p}{}_{\mathrm{<mtext>o</mtext>}}{}_2$ of $\text{124 ± 4.0}\text{mmHg}$ and exposed to light swelled at rates more rapid than corneas treated in a similar fashion but perfused with a solution with a $\text{P}{}_{\mathrm{<mtext>o</mtext>}}{}_2$ of $\text{20 ± 4.6}\text{mmHg}$. This study demonstrates that photodynamically induced corneal endothelial cell alteration results in increased passive bicarbonate flux, a time-dependent decrease in active bicarbonate flux, is oxygen dependent, and is at least in part secondary to H₂O₂ produced by the dismutation reaction of the superoxide free radical.     

2H-1,3-Oxazine-2,6(3H)-dione,a new pyrimidine antimetabolite

2H-1,3-Oxazine-2,6(3H)-dione inhibits the growth of $\text{Escherichia}\text{coli}$ B, the inhibition being complete at a concentration of 10^?4M. It may be relieved with uridine, cytidine and partly with uracil. Orotic acid, cytosine, purine bases and purine ribonucleosides show no effect. At a molar ratio of uridine to the inhibitor of 1:2 the inhibition is completely suppressed. 2H-1,3-Oxazine-2,6(3H)-dione is thus a novel inhibitor of the biosynthesis of pyrimidine precursors of nucleic acids.     

Crystal structure of an inhibitor and a model for inhibition of replicative DNA synthesis

6-(p-Hydroxyphenylhydrazino)-uracil is an antimicrobial agent that selectively blocks replicative DNA synthesis in Bacillus subtilis by inhibiting DNA polymerase III. The drug crystallizes as a monoclinic monohydrate, space group $\text{C2}\text{c}$, with $\text{a = 23.920(6)}\text{A}\text{̊}\text{, b = 5.587(3)}\text{A}\text{̊}\text{, c = 17.466(5)}\text{A}\text{̊}\text{, β = 101.45(8) °}$, and eight hydrated molecules per cell. Three-dimensional X-ray diffraction data were collected. The structure was solved by Patterson methods and refined to an R value of 6.8% for the 1651 data. The geometry of the uracil ring is unusual. The bond distances suggest that a resonance form involving a positively charged hydrazino nitrogen and a negatively charged carbonyl oxygen, O(4), makes a large contribution to the valence bond structure of this compound. The exocyclic C(6)N bond is short (1.335 Å), the C(6)C(5) bond distance is 1.371 Å, which is longer than in uracil, and the C(5)C(4) distance (1.396 Å) is short. The uracil ring, the linked hydrazino nitrogen, and the hydrogen on this nitrogen are in the same plane. Each uracil group is hydrogen bonded to a nearly coplanar uracil across a center of symmetry. The water molecule is also near the plane of these paired bases and forms a hydrogen bond with the uracil-linked hydrazino NH group. This paired base arrangement and the restricted rotation about the exocyclic C(6)N link that constrains the hydrazino NH group to lie near the uracil plane suggest a model for the interaction of the drug with template-primer DNA. The drug acts when cytosine is the base to be copied in the template strand, and the drug is competitive with dGTP. Both cytosine and guanine can be accommodated with little distortion of the crystal structure geometry in a manner compatible with the known geometry of DNA. The structural and biochemical aspects of the model for drug action are discussed.     

In vivo chain elongation of hepatic DNA: 1-beta-D-arabinofuranosyl cytosine sensitive steps.

The $\text{in vivo}$ chain elongation of rat liver DNA following partial hepatectomy was studied using alkaline sucrose gradients. DNA made in 5 min was less than 4 × 10⁷ daltons and that made in 30 min was heterodisperse and by 4 hr 75% of the DNA became larger than 1 × 10⁹ daltons. Administration of 1-β-D-arabinofuranosyl cytosine (ara-C) 5 min after thymidine-³H injection inhibited the chain elongation, whereas if given 30 minutes after thymidine-³H pulse did not inhibit the chain elongation. Thus the $\text{in vivo}$ chain elongation of rat liver DNA consists of at least two steps 1) a step sensitive to ara-C involving nucleotides addition and 2) the other insensitive to ara-C and probably involving ligation of polynucleotide chains.     

The crystal and molecular structure of cytosine-glycyl-glycine-copper(II) complex,a biologically important ternary coordination complex

The title compound was prepared and studied to gain some insight into the structural basis for the protein-nucleic acid-metal ion interaction. The crystal structure has been determined from three-dimensional diffractometer X-ray data using Cu Kα radiation. The crystals are monoclinic, space group $\text{P2}{}_1\text{c}$, with cell dimension; a=10.642(1)Å, b=8.081(1)Å, c=17.792(1)Å, β=124.29(1)^o, z=4. Amino and amide nitrogen, carboxyl O(8) of glycylglycine, N(3) of cytosine and O(2) of adjacent cytosine molecule coordinate to the central copper ion to form a square pyramid. An additional weak interaction in complex molecule between copper and O(2) of cytosine is also observed. The complex molecules are held together by hydrogen- and coordination-bonds in crystalline state.     

Non-covalently bound adenine nucleotides in adenosine triphosphatase of Escherichia coli.

The term, xeroderma pigmentosum variants designates patients who suffer from the clinical manifestations of the disease, but whose cells have normal rates of excision repair of UV-induced lesions in DNA. In contrast to normal human fibroblasts, if cells from such variants are maintained in medium containing caffeine from immediately following exposure to UV until the survivors have undergone three doublings, the cytotoxic and mutagenic effect of UV light is dramatically increased. In the presence of 0.7mM caffeine, the slope of the UV survival curve increases $\text{ca.}$ 3-fold. Similarly, the slope of the curve describing the frequency of mutations to azaguanine resistance induced by UV as a function of dose is $\text{ca.}$ 3-fold steeper.     

Studies on the activity of brown adipose tissue in suckling,pre-obese, obob mice

The properties and activity of brown adipose tissue have been investigated in suckling, pre-obese, $\text{ob}\text{ob}$ mice in order to determine whether decreased thermogenesis in the tissue precedes the development of obesity in this mutant. At 14 days of age there was no difference between the $\text{ob}\text{ob}$ and normal animals in the total amount of interscapular brown adipose tissue, and the DNA content, protein content, and cytochrome oxidase activity of the tissue were similar in the two groups of mice. Respiration rates of brown adipose tissue mitochondria in the presence of albumin were, however, greater in the normal than the $\text{ob}\text{ob}$ animals, although after the addition of GDP to recouple the mitochondria there was no difference between the two groups. The mitochondrial membrane potential, measured with [³H]methyltriphenylphosphonium, was less affected by exogenous GDP in $\text{ob}\text{ob}$ mice than in normal animals. GDP binding to brown adipose tissue mitochondria, an index of the proton conductance pathway, was much greater in normal than in $\text{ob}\text{ob}$ mice at both 10 and 14 days of age; the decreased GDP binding in the mutant animals was found to result from a reduction in the number of binding sites. It is concluded that brown adipose tissue mitochondria of pre-obese $\text{ob}\text{ob}$ mice are more tightly coupled than those of normal siblings, and that the activity of the ‘thermogenic’ proton conductance pathway is lower in the mutant animals. A decrease in thermogenesis in brown adipose tissue is therefore an early event in the development of the $\text{ob}\text{ob}$ mouse and precedes the appearance of obesity.     

Demethylation of O6-methylguanine in a synthetic DNA polymer by an inducible activity in Escherichiacoli

$\text{O}$⁶-Methyl[8-³H]deoxyguanosine in a synthetic DNA polymer, poly(dC, dG, m⁶dG), is demethylated by cell-free extracts of $\text{Escherichia}\text{coli}\text{B}\text{r}$ adapted by exposure to $\text{N}$-methyl-$\text{N}$′-nitro-$\text{N}$-nitrosoguanidine, as shown by the appearance of ³H-labeled deoxyguanosine in hydrolysates of the recovered DNA. The demethylating activity could not be detected in extracts of nonadapted $\text{E}\text{.}\text{coli}$. These results provide direct evidence that a previously described inducible repair activity in $\text{E}\text{.}\text{coli}$ acts by demethylating $\text{O}$⁶-methylguanine at the DNA level.     

Controlled alkaline hydrolysis of steroidal α-bromoketones: New conditions and synthesis of 2α-hydroxy-3-ones

Controlled alkaline hydrolysis of 16α-bromo-17-keto steroids $\text{1}$, $\text{5}$ and $\text{7}$ with potassium carbonate and tetra-n-butylammonium hydroxide (n-Bu₄NOH) and synthesis of 2α-hydroxy-3-ones $\text{11}$, $\text{13}$ and $\text{16}$ by the controlled hydrolysis of the corresponding 2α-bromo-3-ones $\text{9}$, $\text{12}$ and $\text{15}$ are described. Treatm carbonate in aqueous acetone or with n-Bu₄NOH in aqueous dimethylformamide (DMF) gave 16α-hydroxy-17-ones $\text{3}$, $\text{6}$ and $\text{8}$ in 85–90% yield, respectively. 2α-Hydroxy-3-ones $\text{11}$, $\text{13}$ and $\text{16}$ were obtained by hydrolysis of the corresponding bromoketones $\text{9}$, $\text{12}$ and $\text{15}$ in high yields using the above conditions or sodium hydroxide in pyridine or DMF, respectively. Deuterium labeling experiments suggested that equilibration between the 2α-bromoketone $\text{9}$ and the 2β-bromo isomer $\text{10}$ precedes the formation of the ketol $\text{11}$ in which the true intermediate might be the 2β-isomer $\text{10}$. However, rearranged androstane derivatives, 3β-hydroxy-2-ones $\text{18}$ and $\text{20}$, were stereoselectively obtained by treatment of the bromoketones $\text{12}$ and $\text{15}$ with an excess amount of sodium hydroxide.     

Cellular binding of benzo(a)pyrene to DNA characterized by low temperature fluorescence

A new approach has been developed to detect ultra low concentrations of benzo(a)pyrene products bound to nucleic acids $\text{in}\text{vivo}$. The binding to DNA of hamster embryo cell cultures was characterized by low temperature fluorescence spectroscopy. The method can detect less than one polycyclic hydrocarbon residue per 50,000 nucleotides. The fluorescence spectra indicate that the benzo(a)pyrene derivative bound to DNA has a pyrene-like chromophore and resembles that obtained when DNA is reacted $\text{in}\text{vitro}$ with the 7,8-diol-9,10-oxide of benzo(a)pyrene. This confirms that metabolism of the 7,8,9,10 ring on benzo(a)pyrene precedes reaction with DNA. The method should be useful for detecting and characterizing the $\text{in}\text{vivo}$ binding of other fluorescent carcinogens to nucleic acids.     

Chloroquine susceptibility in malaria: dependence on exposure of parasites to the drug.

Chloroquine-resistant $\text{P.}$$\text{berghei}$ is as susceptible to chloroquine as chloroquine-susceptible $\text{P.}$$\text{berghei}$ when adequately exposed for short periods of time (1 hour) $\text{in}$$\text{vitro}$. In both cases 3.1 mM chloroquine causes a significant decrease in infectivity of the parasites whereas 0.31 mM chloroquine is without effect. Since there is no evidence that chloroquine has a peculiar mechanism of action $\text{in}$$\text{vitro}$, these results support the hypothesis of inadequate exposure of intracellular parasites as the cause of chloroquine resistance.     

Quantitative turbidimetric assay for potency evaluation of colchicine-like drugs.

A modified Shelanski method has been applied to quantitatively compare cochicine-like drugs with regard to their inhibition of the rate of rat brain tubulin polymerisation $\text{in vitro}$. The potency of six known microtubule-disrupting drugs was in increasing order: griseofulvin < colchicine < podophyllotoxin < rotenone < vinblastine < vincristine. Two other drugs which have been claimed to interfere with microtubules, melatonin and isopropyl-n-phenylcarbamate were inactive. Methyl benzimidazol-2-yl-carbamate showed only a marginal effect. The usefulness of the method in screening colchicine-like drugs is discussed.     

4-Nitro-L-histidine as a substrate for histidine ammonia-lyase: the role of beta-hydrogen acidity in the rate-limiting step.

The K_m for the interaction of 4-nitro-L-histidine with histidine ammonia-lyase (reduced enzyme, pH 8.0) is comparable to that for L-histidine, while V_max is $\text{1}\text{8}$ that for the natural substrate. With the analog, addition of Cd⁺² effects a small decrease in K_m but fails to alter V_max; the normal deuterium isotope effect for removal of the β-hydrogen (1.5–2.0) is eliminated; and enzyme-catalyzed incorporation of solvent tritium into substrate occurs to a much greater extent than into histidine. Thus, the nitro group increases the acidity of the β-hydrogen and the stability of the conjugate carbanion to such a degree that CH bond cleavage now precedes rate-limiting CN bond cleavage.     

The enzyme "aldehyde oxidase" is an iminium oxidase. Reaction with nicotine delta 1'(5') iminium ion.

The second of the two reaction steps involved in the metabolic transformation of (?)-nicotine to (?)-cotinine $\text{(}\text{3}\text{) (}\text{i.}\text{e.}$, the oxidation of the intermediate $\text{2}\text{)}$ is mediated mainly, if not solely, by the enzyme aldehyde oxidase (EC 1.2.3.1). Of the molecular species that constitute $\text{2}$, nicotine Δ^1′(5′) iminium ion $\text{(}\text{2a}\text{)}$ appears to serve as the substrate. The enzyme has a strong affinity for $\text{2a}$, as shown in a study on the inhibition of the oxidation of 3-(aminocarbonyl)-1-methylpyridinium chloride. This study gave a value of K_i = 6 μM; K_m = 2 μM (pH 7.4). Mainly in view of this finding, “iminium oxidase” seems to be a more adequate name than “aldehyde oxidase” for this enzyme.     

Prostaglandin synthesis in rat embryo tissue: The effect of non-steroidal anti-inflammatory drug in vivo and ex vivo

Aspirin and salicylate are well-known but poorly understood teratogens in laboratory animals. Because aspirin inhibits PG synthesis, we systematically examined PG synthesis in rat embryo homogenates, the inhibition of PG synthesis $\text{in vivo}$ and $\text{ex vivo}$ by various non-steroidal anti-inflammatory drugs, and tested the hypothesis that the inhibition of PG synthesis is responsible for aspirin-induced limb defects in rats. We report that embryonic rat homogenates synthesis 6-keto-PGF_1α, PGE, and PGF in large amounts from endogenous substrate, that aspirin and other non-steroidal anti-inflammatory drugs inhibit PG synthesis $\text{in vitro}$ but not necessarily $\text{in vivo}$, and that contrary to our original hypothesis, the inhibition of PG synthesis is likely not responsible for aspirin-induced limb defects in rats.