Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine

The anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and agmatidine (agm2C), respectively, in the anticodon of tRNAIle to decipher AUA codon. L and agm2C contain long side chains with polar termini, but their functions remain elusive. Here we report the cryogenic electron microscopy structures of tRNAsIle recognizing the AUA codon on the ribosome. Both modifications interact with the third adenine of the codon via a unique C-A geometry. The side chains extend toward 3' direction of the mRNA, and the polar termini form hydrogen bonds with 2'-OH of the residue 3'-adjacent to the AUA codon. Biochemical analyses demonstrated that AUA decoding is facilitated by the additional interaction between the polar termini of the modified cytidines and 2'-OH of the fourth mRNA residue. We also visualized cyclic N6-threonylcarbamoyladenosine (ct6A), another tRNA modification, and revealed a molecular basis how ct6A contributes to efficient decoding.

Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance

The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 104 codons. In the universal genetic code, the AUN codon box specifies two amino acids, isoleucine and methionine. In bacteria and archaea, decoding specificity of the AUA and AUG codons relies on the wobble avoidance strategy that requires modification of C34 in the anticodon loop of isoleucine transfer RNAIleCAU (tRNAIleCAU). Bacterial tRNAIleCAU with 2-lysylcytidine (lysidine) at the wobble position deciphers AUA while avoiding AUG. Here we report cryo-electron microscopy structures of the Escherichia coli 70S ribosome complexed with elongation factor thermo unstable (EF-Tu) and isoleucine-tRNAIleLAU in the process of decoding AUA and AUG. Lysidine in tRNAIleLAU excludes AUG by promoting the formation of an unusual Hoogsteen purine-pyrimidine nucleobase geometry at the third position of the codon, weakening the interactions with the mRNA and destabilizing the EF-Tu ternary complex. Our findings elucidate the molecular mechanism by which tRNAIleLAU specifically decodes AUA over AUG.

Increased renal elimination of endogenous and synthetic pyrimidine nucleosides in concentrative nucleoside transporter 1 deficient mice

Concentrative nucleoside transporters (CNTs) are active nucleoside influx systems, but their in vivo roles are poorly defined. By generating CNT1 knockout (KO) mice, here we identify a role of CNT1 in the renal reabsorption of nucleosides. Deletion of CNT1 in mice increases the urinary excretion of endogenous pyrimidine nucleosides with compensatory alterations in purine nucleoside metabolism. In addition, CNT1 KO mice exhibits high urinary excretion of the nucleoside analog gemcitabine (dFdC), which results in poor tumor growth control in CNT1 KO mice harboring syngeneic pancreatic tumors. Interestingly, increasing the dFdC dose to attain an area under the concentration-time curve level equivalent to that achieved by wild-type (WT) mice rescues antitumor efficacy. The findings provide new insights into how CNT1 regulates reabsorption of endogenous and synthetic nucleosides in murine kidneys and suggest that the functional status of CNTs may account for the optimal action of pyrimidine nucleoside analog therapeutics in humans.

Carboxymethyl tethered poly(disubstituted)triazoles built on nucleoside skeletons: A unique class of ribonuclease A inhibitors designed using chemical logic

Molecular docking of N-1,4-disubstituted-1,2,3-triazole tethered carboxymethylated thymidine and uridine with ribonuclease A, indicated their possible binding with the P₁, B₁ and P₂ subsites with varied efficiencies. This theoretical study in combination of our earlier experimental observations was used as the guiding principles for designing a range of 1,4-disubstituted 1, 2, 3- triazole tethered carboxymethylated pyrimidine nucleosides. Triazoles are biologically important molecules and at the same time easily accessible through less complicated synthetic routes as reported about two decades back in the context of "click" reactions. Regioselective propargylation of the nucleosides under controlled conditions followed by the use of CuAAC strategy afforded mono-, bis-, tris- and tetratriazolyl pyrimidine nucleosides. Although the characteristics of nucleosides were lost in these densely functionalized polyheterocycles, the catalytic efficiency of ribonuclease A was significantly reduced by these molecules which were investigated experimentally and by docking studies. Triazoles as linkers helped one or more acidic groups to reach the P₁ subsite of ribonuclease A. Enzyme kinetics showed that the efficiency of inhibition reached the highest point with an optimum number of functional groups and were not linearly dependent on the number of triazole tethered carboxymethyl groups. The location of the triazole ring in the molecule affected the efficiency and nature of inhibition which were the result of the overall structure of the modified nucleosides. Thus, the tris-triazolylated thymidine derivative (T-3', 5', N-tris-CH₂TzCH₂COOH) as opposed to tetra-triazolylated uridine (U-2', 3', 5', N-tetrakis-CH₂TzCH₂COOH) emerged as the best inhibitor with an inhibition constant value of 2.3 ± 0.05 µM.

Synthesis and Anticancer and Antiviral Activities of C-2′-Branched Arabinonucleosides

d-Arabinofuranosyl-pyrimidine and -purine nucleoside analogues containing alkylthio-, acetylthio- or 1-thiosugar substituents at the C2’ position were prepared from the corresponding 3’,5’-O-silylene acetal-protected nucleoside 2’-exomethylenes by photoinitiated, radical-mediated hydrothiolation reactions. Although the stereochemical outcome of the hydrothiolation depended on the structure of both the thiol and the furanoside aglycone, in general, high d-arabino selectivity was obtained. The cytotoxic effect of the arabinonucleosides was studied on tumorous SCC (mouse squamous cell) and immortalized control HaCaT (human keratinocyte) cell lines by MTT assay. Three pyrimidine nucleosides containing C2’-butylsulfanylmethyl or -acetylthiomethyl groups showed promising cytotoxicity at low micromolar concentrations with good selectivity towards tumor cells. SAR analysis using a methyl β-d-arabinofuranoside reference compound showed that the silyl-protecting group, the nucleobase and the corresponding C2’ substituent are crucial for the cell growth inhibitory activity. The effects of the three most active nucleoside analogues on parameters indicative of cytotoxicity, such as cell size, division time and cell generation time, were investigated by near-infrared live cell imaging, which showed that the 2’-acetylthiomethyluridine derivative induced the most significant functional and morphological changes. Some nucleoside analogues also exerted anti-SARS-CoV-2 and/or anti-HCoV-229E activity with low micromolar EC₅₀ values; however, the antiviral activity was always accompanied by significant cytotoxicity.

FV-100 for the Treatment of Varicella-Virus (VZV) Infections: Quo Vadis?

The bicyclic nucleoside analogue (BCNA) Cf1743 and its orally bioavailable prodrug FV-100 have unique potential as varicella-zoster virus (VZV) inhibitors to treat herpes zoster (shingles) and the therewith associated pain, including post-herpetic neuralgia (PHN). The anti-VZV activity of Cf1743 depends on a specific phosphorylation by the VZV-encoded thymidine kinase (TK). The target of antiviral action is assumed to be the viral DNA polymerase (or DNA synthesis in the virus-infected cells).

Taylor-made production of pyrimidine nucleoside-5'-monophosphate analogues by highly stabilized mutant uracil phosphoribosyltransferase from Toxoplasma gondii

Nowadays, enzymatic synthesis of nucleotides is an efficient and sustainable alternative to chemical methodologies. In this regard, after the biochemical characterization of wild-type and mutant uracil phosphoribosyltransferases from Toxoplasma gondii (TgUPRT, TgUPRT_2, and TgUPRT₃), TgUPRT₂ was selected as the optimal candidate (69.5 IU mg^-1, UMP synthesis) for structure-guided immobilization onto Ni²⁺ chelate (M_NiUPRT₂) and onto glutaraldehyde-activated microparticles (M_GlUPRT₂). Among resulting derivatives, M_NiUPRT₂3 (6127 IU g^-1_biocat; 92% retained activity; 3-5 fold enhanced stability at 50-60 °C) and M_GlUPRT₂N (3711 IU g^-1_biocat; 27% retained activity; 8-20 fold enhanced stability at 50-60 °C) displayed the best operability. Moreover, the enzymatic synthesis of different pyrimidine NMPs was performed. Finally, the reusability of both derivatives in 5-FUMP synthesis (M_NiUPRT₂3, 80% retained activity after 7 cycles, 5 min; M_GlUPRT₂N, 70% retained activity after 10 cycles, 20 min) was carried out at short times.

HLB-MCX-Based Solid-Phase Extraction Combined with Liquid Chromatography-Tandem Mass Spectrometry for the Simultaneous Determination of Four Agricultural Antibiotics (Kasugamycin, Validamycin A, Ningnanmycin, and Polyoxin B) Residues in Plant-Origin Foods

An ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was established for the determination of four highly polar agricultural antibiotics kasugamycin, validamycin A, ningnanmycin, and polyoxin B in plant-derived foods. The samples were extracted with a 0.2% formic acid solution, purified by hydrophilic-lipophilic balance and mixed-mode cation-exchange solid-phase extraction, and then reconstituted for UPLC-MS/MS detection. The chromatographic analysis was performed on a BEH Amide column (100 mm × 2.1 mm, 1.7 μm) using gradient elution with a 0.1% formic acid solution and 0.1% formic acid acetonitrile as mobile phases. Method validation was performed on 15 matrices spiked at 0.02 (or 0.05), 0.5, and 2 mg/kg. The mean recovery rate ranged from 75 to 102% with relative standard deviations (RSD) was less than 20%. Good linearities (r > 0.99) in the range of 0.002-0.2 μg/mL were obtained. The limits of quantification (LOQs) were 0.02 and 0.05 mg/kg. Studies on the stability of the analytes in the stored kiwifruit samples showed that kasugamycin, validamycin A, and ningnanmycin were stable for at least 6 months, while polyoxin B was observed to be partially degraded (the degradation rate at 6 months was 31.3%). The method was demonstrated to be effective and reliable in real samples. In the kiwifruit samples treated after 7 days, no residues of ningnanmycin and polyoxin B were detected, while the residues of kasugamycin and validamycin A were 0.12 and 0.038 mg/kg, respectively.

Structural and Biochemical Studies on the Reaction Mechanism of Uridine-Cytidine Kinase

Uridine-cytidine kinase catalyzes phosphorylation of the pyrimidine nucleosides uridine and cytidine and plays an important role in nucleotide metabolism. However, the detailed molecular mechanism of these reactions remains to be elucidated. Here, we determined the structure of the ternary complex of Uridine-cytidine kinase from Thermus thermophilus HB8 with both cytidine and β,γ-methyleneadenosine 5'-triphosphate, a non-hydrolysable ATP analogue. Substrate binding is accompanied by substantial domain movement that allows the substrate-binding cleft to close. The terminal phosphodiester bond of the ATP analogue is in an ideal location for an inline attack of the 5'-hydroxyl group of cytidine. Asp40 is located near the 5'-hydroxyl group of cytidine. Mutation of this conserved residue to Asn or Ala resulted in a complete loss of enzyme activity, which is consistent with the notion that Asp40 acts as a general base that activates the 5'-hydroxyl group of cytidine. The pH profile of the activity showed an apparent pK a value of 7.4. Based on this structure, a likely mechanism of the catalytic step is discussed.

Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns

The ability of DNA polymerases (pols) to catalyze the template-directed synthesis of duplex oligonucleotides containing a nonstandard Watson-Crick base pair between a nucleotide bearing a 5-(2,4-diaminopyrimidine) heterocycle (d kappa) and a nucleotide bearing either deoxyxanthosine (dX) or N1-methyloxoformycin B (pi) has been investigated. The kappa-X and kappa-pi base pairs are jointed by a hydrogen bonding pattern different from and exclusive of those joining the AT and GC base pairs. Reverse transcriptase from human immunodeficiency virus type 1 (HIV-1) incorporates dXTP into an oligonucleotide opposite d kappa in a template with good fidelity. With lower efficiency and fidelity, HIV-1 reverse transcriptase also incorporates d kappa TP opposite dX in the template. With d pi in the template, no incorporation of d kappa TP was observed with HIV reverse transcriptase. The Klenow fragment of DNA pol I from Escherichia coli does not incorporate d kappa TP opposite dX in a template but does incorporate dXTP opposite d kappa. Bovine DNA pols alpha, beta, and epsilon accept neither dXTP opposite d kappa nor d kappa TP opposite d pi. DNA pols alpha and epsilon (but not beta) incorporate d kappa TP opposite dX in a template but discontinue elongation after incorporating a single additional base. These results are discussed in light of the crystal structure for pol beta and general considerations of how polymerases must interact with an incoming base pair to faithfully copy genetic information.

Formation of 2,5-diamino-4-hydroxy-6-(2'-deoxyribosyl)-formamidopyrimidine from 2'-deoxyguanosine in aqueous solution irradiated with 60Co gamma-rays

2'-Deoxyguanosine in aqueous solution (5 x 10(-4) mol/dm3) was irradiated with 60Co gamma-rays under N2O. Products were separated by gel chromatography (Cellulofine GC-15-m) and high performance liquid chromatography (Inertsil ODS-2). 2-Amino-4-hydroxy-5-formamido-6-(2'-deoxyribosyl)-aminopyrimidine was one of the main radiolytic products. The formation of 2,5-diamino-4- hydroxy-6-(2'-deoxyribosyl)-formamidopyrimidine was detected, this compound being verified by measuring its ultraviolet absorption spectrum and analyzing its trimethylsilylated derivative by gas chromato-mass spectrometry. Its yield in terms of 2-amino-4-hydroxy-5-formamido-6-(2'-deoxyribosyl)- aminopyrimidine was 1:3.

The synthesis of 5-C-(6-deoxy-1,2:3,4-di-O-isopropylidene-alpha-D-galactopyranos-6-yl)-2 ,3-O-isopropylidene-D-allo-pentofuranose [deaminotri-O-isopropylidene tunicamine]

Three approaches to the synthesis of deaminotunicamine and derivatives were developed. Tin tetrachloride condensation of 6-deoxy-1,2:3,4-di-O-isopropylidene-alpha-D-galacto-heptodialdo-1, 5-pyranose with 2-(trimethylsilyloxy)furan gave a mixture of stereoisomeric precursors. Condensation of 1,2:3,4-di-O-isopropylidene-alpha-D-galacto-hexodialdo-1,5-pyranos e with the phosphate carbanion obtained from diethyl (2-furyl)methoxymethyl phosphonate led to 6-deoxy-7-C-(2-furyl)-1,2:3,4-di-O-isopropylidene-L-glycero-alpha-D- galactoheptopyranose (13). This was converted, via the "delta 2"-butenolide route, to a mixture of stereoisomeric 5-C-(6-deoxy-alpha-D-galactopyranos-6-yl)-pentono-1,4-lacton es of the D-allo and D-talo configuration. In the third approach, 13 was transformed by the "enulose" approach to deamino-tri-(O-isopropylidene)tunicamine.

Monophosphoric acid diesters of 7 beta-hydroxycholesterol and of pyrimidine nucleosides as potential antitumor agents: synthesis and preliminary evaluation of antitumor activity

7 beta-Hydroxycholesterol, which has been shown to be selectively cytotoxic toward tumor cells cultured in vitro, was converted into the corresponding water-soluble phosphoric acid ester and linked to a pyrimidine nucleoside such as 5-fluoro-2'-deoxyuridine or 2'-deoxyuridine. 2-Chlorophenyl phosphorodichloridate (3), without activation, was used directly to phosphorylate the protected oxygenated sterol. The intermediate phosphorylated the 5'-OH group of nucleoside selectively, leading to compounds 1a and 1b after deprotection. These compounds were screened for their antiproliferative activity toward EL-4 murine leukemia cells in vitro and for their antitumor activity against the mice bearing Krebs II ascitic carcinoma in vivo.

X-ray crystal structure of sangivamycin, a potent inhibitor of protein kinases

The X-ray crystal structure of sangivamycin, a potent nucleoside inhibitor of protein kinases, has been determined. Sangivamycin crystallizes from water with its purine ring in a conformation anti to its ribose sugar. Such an anti conformation has been detected in solution for sangivamycin and other potent protein kinase inhibitors and appears to correlate with inhibitor potency [(1990) Biochemistry (in press)]. An intramolecular hydrogen bond between purine ring substituents is detected in the X-ray structure and may be an important structural feature of sangivamycin related to its degree of inhibition of rhodopsin kinase and of protein kinases C and A.

Structural mimicry of adenosine by the antitumor agents 4-methoxy- and 4-amino-8-(beta-D-ribofuranosylamino)pyrimido[5,4-d]pyrimidine as viewed by a molecular modeling method

A rationale for the antitumor activity of 4-methoxy- and 4-amino-8-(beta-D-ribofuranosylamino)pyrimido-[5,4-d]pyrimidine (beta-MRPP and beta-ARPP, respectively) was studied by a molecular modeling method. Although these nucleoside analogues are structurally different from adenosine, they act as substrates for adenosine kinase. The molecular modeling method, which considered the three-dimensional structure and atom-based physicochemical properties of the nucleosides to quantify the molecular similarities, showed that certain low-energy conformations of the beta anomers of a series of nucleosides including beta-MRPP, beta-ARPP, and their 4-hydroxy, 4-amino-6-chloro, 4-methylthio-2,6-dichloro, 4,6-diamino, 4-dimethylamino, 4-methylamino, and 4-hydroxy-2,6-dichloro analogues have remarkable structural similarity to adenosine. The method also suggested that the selection of the reference compound adenosine in the structural comparison is of primary importance to gain insight into the observed antitumor activity. The success of the present method led to AM1 (Austin model 1) molecular orbital calculations and experimental studies indicating that the antitumor activity of the alpha anomer of ARPP is probably due to equilibration to the beta anomer. The AM1 calculation of the protonation energy of N5 of pyrimido[5,4-d]pyrimidines, which occupies the same position in space as the N1 of adenosine, gave a direct correlation between the basicity of the nitrogen with a lone pair of electrons and the observed antitumor activity.

Hydration of nucleosides in dilute aqueous solutions. Ultrasonic velocity and density measurements

The values of the concentration increments of the ultrasound velocity and their temperature slopes, apparent molar volumes, apparent molar expansibilities, apparent molar adiabatic compressibilities and their temperature gradients for 12 nucleosides and their analogs, as well as for ribose and deoxyribose, have been obtained using precision measurements of ultrasound velocity and density. The following hydration parameters for the atomic groups of the nucleosides, reflecting the state of water in the hydration shells of these groups, have been analyzed: (1) the contribution of ribose to the values of the concentration increment of ultrasound velocity A, the apparent molar volumes phi v and apparent molar adiabatic compressibilities phi ks of nucleosides; (2) contributions of the CH3, NH2 and O = ... -H groups of nucleic bases to the A, phi v and phi ks values of nucleosides and free nucleic bases; (3) contributions of the 2'-OH group of ribose to the values of A, phi v and phi ks nucleosides; (4) changes in the A values of nucleosides and free nucleic bases upon their protonation and deprotonation. Data have been obtained on the mutual influence of the atomic groups of nucleosides on their hydration. It is shown that the GC pairs of free deoxynucleosides undergo hydration more vigorously than the AT pairs, which contrasts with the relation of the degree of hydration of the GC and AT pairs of the double helix.

Incomplete factorial search for conditions leading to high quality crystals of Escherichia coli cytidine deaminase complexed to a transition state analog inhibitor

We have used an incomplete factorial design (Carter, C. W., and Carter, C. W., Jr. (1979) J. Biol. Chem. 254, 12219-12223) to find conditions for growing high quality crystals of Escherichia coli cytidine deaminase (EC 3.5.4.5). Crystals grow at pH 6.0 in hanging or sitting drops with either 1.6 M ammonium sulfate or 2.4-2.5 M sodium phosphate as precipitant. Both conditions produce crystals with identical morphologies and unit cell constants. The space group is P3(1)21 (or its enantiomorph P3(2)21), and the unit cell constants are a = b = 120.3 A, c = 78.4 A. The asymmetric unit is most reasonably one dimer of 66,000 Mr. The crystal size is very dependent on the supersaturation ratio, S = [initial protein concentration]/[equilibrium protein concentration], exhibiting a maximum at S = 7.7. The largest crystals diffract to at least 2.5 A and have a lifetime of 4 to 5 days in the x-ray beam at room temperature. The enzyme in these crystals is complexed with the transition state analog inhibitor 1-(beta-D-ribofuranosyl)-5-fluoropyrimidin-2-one (5-fluoropyrimidin-2-one riboside). We have collected data from parent crystals and from a heavy atom derivative in which the transition state analog is replaced by the active site directed inhibitor 5-(chloromercuri)cytidine.

Complex structural behavior of oligopurine-oligopyrimidine sequence cloned within the supercoiled plasmid

Synthetic sequence GATCC(AG)7ATCG(AT)4CG(AG)7 was cloned into plasmid and its structural behavior under the influence of supercoiling was analysed by chemical modification at variety of experimental conditions. It was found that this sequence adopts at least two different non-B conformations depending on -delta and pH values. Moreover, 12 nucleotide long non-pur.pyr spacer region separating two identical (AG)7 blocks does not provide a significant energy barrier protecting against unusual structures formation.

Formation of cyclopyrimidines via the direct effects of gamma radiation of pyrimidine nucleosides

Continuing our study of the direct effects of gamma radiation on DNA and its model compounds, we have isolated and characterized quantitatively an important lesion formed by irradiating pyrimidine 2'-deoxyribonucleosides in frozen aqueous solution. We report here the formation of 5',6-cyclo-5,6-dihydropyrimidine nucleosides via hydrogen abstraction at C5' of the osidic moiety with subsequent intramolecular attack at C6 of the base. We have so far managed to isolate six of the possible eight diastereomers of 5',6-cyclo-5,6-dihydrothymidine, and all four possible 5',6-cyclo-5,6-dihydro-2'-deoxyuridines formed by irradiation of 2'-deoxycytidine. Also presented is a detailed discussion of the configurational analysis of each isomer based on 1H NMR data.

Free radical generation by ultrasound in aqueous solutions of nucleic acid bases and nucleosides: an ESR and spin-trapping study

Direct evidence for the detection of intermediate radicals of nucleic acid constituents induced by ultrasound in argon-saturated aqueous solution is presented. The method of spin trapping with 3,5-dibromo-4-nitrosobenzene sulphonate, which is a water-soluble, non-volatile, aromatic nitroso spin trap, combined with ESR, was used for the detection of sonochemically induced radicals. Spin adducts were also generated by OH radicals produced by UV photolysis of aqueous solution containing H2O2. ESR spectra observed from these photolysis experiments were identical to those after sonolysis. The ESR spectra of the spin adducts suggest that the major spin-trapped radical of thymine and thymidine was the 5-yl radical, and that of cytosine, cytidine, uracil, and uridine was the 6-yl radical. To compare the radicals induced by sonolysis and photolysis, the decay of the ESR spectra of the thymine and thymidine spin adducts was investigated. The decay curves of thymine and thymidine after sonolysis indicated biphasic decay. However, after photolysis the spin adducts from both compounds showed very little decay. These results suggest that the observed spin adducts in the sonolysis of pyrimidine bases and nucleosides were formed by OH radical and H atom addition to the 5,6 double-bond.

Rate of incorporation of radiolabelled nucleosides does not necessarily reflect the metabolic state of cells in culture: effects of latent mycoplasma contamination

In response to cell-free conditioned medium derived from the human bladder carcinoma line T24 (T24 SN), we found greatly reduced incorporation of tritiated thymidine and uridine ([3H]TdR, [3H]UR) by the human carcinoma lines UCHNCu (small-cell lung carcinoma) and LS174T (colon carcinoma). The effect was not due to an excess of nucleosides or cytokines known to be present in T24 SN. Cell-cycle distribution, increase in cell numbers, and de novo nucleoside synthesis in the indicator cells were only slightly altered. This was in contrast to the gross reduction in [3H]TdR/[3H]UR incorporation and seemed to indicate selective downregulation of pyrimidine-salvage pathways, despite ongoing polynucleotide synthesis. Spontaneous [3H]TdR uptake remained low for several passages in vitro but was readily restored by pharmacological inhibition of de novo pathways with 5-fluoro-deoxy-uridine (5-FUdR). This suggested a stable but reversible regulatory effect of T24 SN on the pyrimidine metabolism of the indicator cells. Further investigation showed degradation of [3H]TdR by a particle-bound activity in T24 SN. Mycoplasma contamination of T24 had not been detectable using standard cultural and staining methods, but became apparent when T24-cell lysates were hybridized with a recently described DNA probe (Goebel & Stanbridge, 1984). We conclude that latent mycoplasma contamination can stimulate changes in cellular pyrimidine metabolism. Our results provide an example for latent mycoplasma infection mimicking metabolic changes in cultured cells by direct interference of a microbial enzyme with the assay system. We describe a rapid and simple bioassay to detect and distinguish particle-associated and soluble phosphorylase activity by [3H]TdR degradation. It may be a useful screening assay for mycoplasma contamination in tissue culture.

Reactions of 5-bromo substituted pyrimidine nucleosides with aqueous alkalies: kinetics and mechanisms

Kinetics for the parallel and consecutive steps of the reactions of 5-bromocytidine, 5-bromouridine and its 5'-O-methyl and 2',3'-O-isopropylidene derivatives with aqueous alkalies were studied by LC. The mechanisms of the partial reactions involved are discussed.

Bagougeramines A and B, new nucleoside antibiotics produced by a strain of Bacillus circulans. II. Physico-chemical properties and structure determination

Bagougeramines A and B obtained as sulfates were soluble in water and positive to Sakaguchi, chlorine-tolidine and ninhydrin color reactions. Their structures were determined by acid hydrolysis and spectroscopic analysis. Structurally they were closely related to gougerotin and they contained the guanidino-D-alanine instead of the serine residue in gougerotin. Bagougeramine B had the spermidine instead of the 6'-NH2 in structure of bagougeramine A.

New adducts of chloroethylene oxide and chloroacetaldehyde with pyrimidine nucleosides

Pyrimidine nucleosides were treated with chloroethylene oxide (CEO) and 2-chloroacetaldehyde (CAA) in methanol and, following trimethylsilylation, the products were analysed by combined gas chromatography-mass spectrometry (GC-MS). Reaction of CEO with 2'-deoxycytidine gave 3,N4-etheno-2'-deoxycytidine and diadduct isomers in which a 1-hydroxy-2-chloroethyl group was substituted for hydrogen on either deoxyribose hydroxyl group. When the N-3-position of 2'-deoxycytidine was blocked by a methyl group, CEO or CAA added a 2-chlorovinyl group at the exocyclic N4 amino nitrogen, as evidenced by a pair of cis/trans isomers. Reaction of 3-methylcytidine and CEO also gave the cis/trans 2-chlorovinyl base adducts, as well as six isomers with a 1-hydroxy-2-chloroethyl group attached to ribose and nine isomeric diadducts, which are possibly positional and optical isomers. Although CEO and CAA were less reactive towards uracil in 3-methyluridine than to cytosine in 3-methyl(deoxy)-cytidine, both electrophiles were able to alkylate 3-methyluridine on ribose, yielding 1-hydroxy-2-chloroethyl derivatives. These data suggest that CEO and CAA may also yield non-cyclic adducts with cytosine in double-stranded DNA where the N-3 position is of low accessibility. Such adducts are of interest in view of their potential promutagenic properties. The data also imply a new mechanism of reaction of CEO with nucleophiles.

Inhibitors of the biosynthesis and processing of N-linked oligosaccharides

A number of glycoproteins have oligosaccharides linked to protein in a GlcNAc----asparagine bond. These oligosaccharides may be either of the complex, the high-mannose or the hybrid structure. Each type of oligosaccharides is initially biosynthesized via lipid-linked oligosaccharides to form a Glc3Man9GlcNAc2-pyrophosphoryl-dolichol and transfer of this oligosaccharide to protein. The oligosaccharide portion is then processed, first of all by removal of all three glucose residues to give a Man9GlcNAc2-protein. This structure may be the immediate precursor to the high-mannose structure or it may be further processed by the removal of a number of mannose residues. Initially four alpha 1,2-linked mannoses are removed to give a Man5 - GlcNAc2 -protein which is then lengthened by the addition of a GlcNAc residue. This new structure, the GlcNAc- Man5 - GlcNAc2 -protein, is the substrate for mannosidase II which removes the alpha 1,3- and alpha 1,6-linked mannoses . Then the other sugars, GlcNAc, galactose, and sialic acid, are added sequentially to give the complex types of glycoproteins. A number of inhibitors have been identified that interfere with glycoprotein biosynthesis, processing, or transport. Some of these inhibitors have been valuable tools to study the reaction pathways while others have been extremely useful for examining the role of carbohydrate in glycoprotein function. For example, tunicamycin and its analogs prevent protein glycosylation by inhibiting the first step in the lipid-linked pathway, i.e., the formation of Glc NAc-pyrophosphoryl-dolichol. These antibiotics have been widely used in a number of functional studies. Another antibiotic that inhibits the lipid-linked saccharide pathway is amphomycin, which blocks the formation of dolichyl-phosphoryl-mannose. In vitro, this antibiotic gives rise to a Man5GlcNAc2 -pyrophosphoryl-dolichol from GDP-[14C]mannose, indicating that the first five mannose residues come directly from GDP-mannose rather than from dolichyl-phosphoryl-mannose. Other antibodies that have been shown to act at the lipid-level are diumycin , tsushimycin , tridecaptin, and flavomycin. In addition to these types of compounds, a number of sugar analogs such as 2-deoxyglucose, fluoroglucose , glucosamine, etc. have been utilized in some interesting experiments. Several compounds have been shown to inhibit glycoprotein processing. One of these, the alkaloid swainsonine , inhibits mannosidase II that removes alpha-1,3 and alpha-1,6 mannose residues from the GlcNAc- Man5GlcNAc2 -peptide. Thus, in cultured cells or in enveloped viruses, swainsonine causes the formation of a hybrid structure.(ABSTRACT TRUNCATED AT 400 WORDS)

Nucleoside phosphorylase activity of Octopus vulgaris hepatopancreas

From a research on partially purified extracts of Octopus vulgaris hepatopancreas a number of properties of the nucleosidase present in such extracts have been defined, such as enzyme affinity towards different purine and pyrimidine ribo- and deoxyribo-nucleosides. The phosphorolytic mechanism of action of the Octopus enzyme system is similar to the mechanism already known for many nucleosidases from animal tissues. The possibility is envisaged of two different nucleosidases being present, one specific for ribonucleosides, with an acid optimum pH, and the other one for deoxyribonucleosides, with an alkaline pH optimum. Adenosine deaminase also appears to be a component of Octopus hepatopancreas.

Tunicamycins, streptovirudins, and corynetoxins, a special subclass of nucleoside antibiotics

Tunicamycins, streptovirudins, and very recently, corynetoxins have been determined to be structurally related nucleoside antibiotics. Because of their special biological activity as inhibitors of protein glycosylation and their relatively complicated chemical structures, which differ from the common nucleoside antibiotics, they can be grouped together as a special subclass. A general specification system based on structural characteristics is included. The complete separation of the natural complex is still problematical, but seems to be necessary because differences in the biological activities of the individual components were observed.

Effects of streptovirudin on influenza viruses type A and B: inhibition of the lipid-linked oligosaccharide synthesis of fowl plague virus

Antibiotics of the streptovirudin complex (SV) inhibited the growth of influenza A and B viruses such as influenza A/fowl plague virus (FPV), strain Weybridge (Hav1 Neq1), influenza A/England 42/72 (H3N2), influenza A/Port Chalmers 1/73 (H3N2), influenza B/Leningrad 235/74, influenza B/Tokyo 7/66, and influenza B/Jamagata in chick embryo cell (CEC) cultures, in permanent canine kidney cells (MDCK), and in suspended fragments of chick embryo chorioallantoic membranes (CAM). As revealed by spectrophotometric turbidity measurements, SV completely inhibited the FPV-induced cytopathic effect (CPE). A 99.99% reduction of infectious virus yield was obtained in one-step growth cycle experiments and in the plaque reduction test. The haemagglutination inhibition titres of influenza viruses in suspended CAM fragment cultures in the presence of SV drugs were also substantially reduced. The incorporation assays indicated that SV exhibited no effect on virus-induced RNA synthesis, but influenced virus maturation by inhibition of lipid-linked oligosaccharide synthesis. A partial protection from infection was found in influenza virus A/England infected mice.

Correlation between glycosyl torsion angle and sugar ring pucker does not always exist

A survey of the conformational parameters of deoxypyrimidine nucleosides and nucleotides shows that the correlation between glycosyl torsion angle and sugar pucker, which has often been considered to be well-established, does not always exist. This may be of significance when interactions between DNA and other molecules are considered.

[Induction of immune interferon by erythrogenic toxins A and B from Streptococcus pyogenes]

By interaction of streptococcal erythrogenic toxins A and B with chick embryo fibroblasts and human amnion (FL) cells an antiviral interferon-like factor was secreted. It inhibited the replication of vesicular stomatitis, vaccinia and Mengo viruses. The streptococcal toxin type B was 50 times more cytotoxic for both cell cultures in comparison with streptococcal toxin A. The maximum tolerated doses of the two types of streptococcal toxins induced approximately the same antiviral protection effect. The production curve of the antiviral factor showed a maximum at the 12th hour after incubation at 37 degrees C with graduate decrease up to the 24th hour using a 6 hours induction time. The interferons induced by the streptococcal erythrogenic toxins A and B were thermostable at 56 degrees C for 30 min and were partially destroyed at pH 2 as tested against Mengo virus in FL cells. The antiviral effect could be reversed by addition of streptococcal erythrogenic toxin A at the maximum tolerated dose simultaneously with the glycosylating inhibitors streptovirudin and D-glucosamine by 90 and 100 per cent, respectively.

Pyrimidine ribonucleoside phosphorylase activity vs 5- and/or 6-substituted uracil and uridine analogues, including conformational aspects

The pyrimidine ribonucleoside phosphorylase from Salmonella typhimurium phosphorylyses 6-methyluridine, a uridine analogue sterically constrained to the syn conformation about the glycosylic bond, as effectively as uridine itself. In conjunction with the observation that 3-methyluridine is a very poor substrate compared to 5-methyluridine and 5,6-dimethyluridine, it follows that the phosphorolysis reaction involves the initial conversion of uridine, and other 5-substituted uridines (including 5-fluorouridine), to the syn conformation during interaction with the enzyme. Furthermore, and consistent with the foregoing, the enzyme recognizes as substrates, to varying degrees, the N(3)-ribosides of xanthine and uric acid, and will also catalyze the formation of these ribosides from the corresponding purines, which may be considered formally as 5,6-disubstituted uracils. Similar observations are reported for the synthetic 5,6-trimethyleneuridine. The enzyme does not, however, recognize 6-methyluracil and 5,6-tetramethyleneuridine in the reverse, synthetic, reaction. The conformational aspects of these reactions are discussed. Since it was previously shown that 6-methyluridine is an equally effective substrate for the pyrimidine phosphorylase of primary rabbit kidney cells, at least some of these conformational requirements apply to the enzyme from mammalian sources, and are consequently of relevance in the design of chemotherapeutic agents, for which some examples are cited.

Reactions of the hydroxyl radical

Free radicals produced by the reactions of OH radicals with ribose phosphates, pyrimidine nucleosides and nucleotides in aqueous solutions have been investigated by e.s.r. and spin-trapping techniques. OH radicals were generated by U.V. -photolysis of hydrogen peroxide and short-lived free radicals of the samples were spin-trapped by t-nitrosobutane and identified by e.s.r. spectroscopy. For ribose-5'-phosphate and 2' -deoxyribose-5' -phosphate, e.s.r. spectra observed consisted mainly of singles due to -C(5')H2 radicals which were initiated by H-abstraction from the sugar at the C-4' position and formed by the radical transfer to the C-5' position. It has also been shown that OH radicals abstract a hydrogen atom from the sugar at C-1' and C-5' positions. For cytidine, deoxycytidine, 5'-CMP, 3' -CMP and 5' -dCMP, four radicals have been observed and for uridine, deoxyuridine, 5' -UMP, 3' -UMP and 5' -dUMP, the existence of at least three radical species have been established. In contrast to the case of ribose phosphates, no signals due to -C(5')H2 radicals were detected for pyrimidine nucleosides and nucleotides. The results are discussed in relation to a recent mechanism which described OH-induced strand breaks of DNA.

Biological activities of isolated tunicamycin and streptovirudin fractions

The nucleoside antibiotics tunicamycin and streptovirudin were separated by high-performance liquid chromatography into a series of 256-nm-absorbing peaks. Most of the streptovirudin peaks eluted from a Biosil ODS column earlier than those of tunicamycin, indicating that they were less hydrophobic. With the exception of the first peak, 17 other tunicamycin peaks were potent inhibitors of the formation of dolichylpyrophosphoryl-N-acetylglucosamine with 50% inhibition of the solubilized GlcNAc-1-P transferase requiring about 10 ng of antibiotic per mL. These fractions also inhibited the synthesis of dolichylphosphorylglucose, but in these cases about 500 ng/mL was necessary to achieve 50% inhibition. In MDCK cells in culture, the four major tunicamycin peaks inhibited the incorporation of [2-(3)H]mannose into protein by 50% at about 0.2-0.5 microgram/mL, but [3H]leucine incorporation into protein was unaffected, except at high levels of antibiotic (5-10 microgram/mL). Essentially the same results were observed with the streptovirudin fractions except that they were somewhat less active and some inhibition of protein synthesis was observed with several of these peaks.

Gold complexes of purine and pyrimidine nucleosides

the reactions of chloroauric acid (HAuCl4) with inosine=ino, guanosine=guo, triacetylinosine=trino, triacetylguanosine=trguo, and cytidine=cyd were studied. Complexes of AU(III) and AU(I) with these nucleosides have been isolated from the reactions at different pH values in aqueous and in methanolic solutions. The Au(I) complexes were obtained by reducing Au(III) with 1-ascorbic acid in aqueous solutions. All the isolated complexes were characterized by elemental analyses, conductivity measurements, IR, 1H nmr, and esr spectra. The Au(III) complexes correspond to the general formulae [Au(nucl)2Cl2]Cl, Au(nucl)Cl3, and Au(nucl-H+Cl2, while the Au(I)complexes are of the au(nucl)2Cl type, where nucl represents the above nucleosides. In the complex with the composition (AucydCl2]2 that was isolated from aqueous solutions, the Au atom is believed to be in the (II) oxidation state. Possible structures for all the isolated complexes based on the experimental data are proposed and discussed.

Complex formation between spin-labeled polyuridylic acid and pyrimidine nucleosides

Complex formation between poly (U) and pyrimidine nucleosides, uridine and cytidine, was observed using spin labeling technique. The binding of these nucleosides with poly (U) takes place within a narrow range of their concentration and is characterized by a relatively strong cooperativity. It is shown, that both hydrogen bonding and stacking interaction contribute to the complex stability. Some thermodynamic parameters of the process were obtained from the binding isotherms. At 21 degrees C the equilibrium constants for nucleation were found to be 0.23 M-1 and 0.42 M-1, and those for chain growth 2.63 M-1 and 2.19 M-1 for uridine and cytidine respectively. Complex formation of poly (U) with adenosine was also studied by spin labeling method.