Deoxyuridine Analogs Research Articles

Deoxyuridine analog nucleotides in deoxycytidine analog treatment: secondary active metabolites?

Deoxycytidine analogs (dCa's) are nucleosides widely used in anticancer and anti (retro) viral therapies. Intracellularly phosphorylated dCa anabolites are considered to be their main active metabolites. This article reviews the literature on the formation and pharmacological activity of deaminated dCa nucleotides. Most dCa's are rapidly deaminated into deoxyuridine analogs (dUa's) which are only slowly phosphorylated and therefore relatively inactive. dUa nucleotides are, however, also formed via deamination of dCa monophosphates by deoxycytidine monophosphate deaminase (dCMPD). dUa-monophosphates can interact with thymidylate synthase (TS), whereas dUa-triphosphates are incorporated into nucleic acids and interfere with polymerases. Administration of dCa's as monophosphate prodrugs or co-administration of the cytidine deaminase inhibitor tetrahydrouridine (THU) does not prevent dUa nucleotide formation which is, on the other hand, influenced by the dose and dCMPD activity. Taken together, these observations show that the formation of dUa nucleotides is a common phenomenon in treatment with dCa's and these compounds may play a role in treatment outcome. We conclude that more attention should be given to these relatively unknown, but potentially important metabolites.

β-Branched acyclic nucleoside analogues as inhibitors of Plasmodium falciparum dUTPase

We report a series of β-branched acyclic tritylated deoxyuridine analogues as inhibitors of Plasmodium falciparum deoxyuridine-5′-triphosphate nucleotidohydrolase ( PfdUTPase), an enzyme involved in nucleotide metabolism that acts as first line of defence against uracil incorporation into DNA. Compounds were assayed against both PfdUTPase and intact parasites showing a correlation between enzyme inhibition and cellular assays. β-Branched acyclic uridine analogues described here showed equal or slightly better potency and selectivity compared with previously reported analogues. The best inhibitor gave a K i of 0.5 μM against PfdUTPase with selectivity greater than 200-fold compared to the corresponding human enzyme and sub-micromolar growth inhibition of P. falciparum (EC 50 0.6 μM). A crystal structure of the complex of PfdUTPase with one of the inhibitors shows that this acyclic derivative binds to the active site in a similar manner to that previously reported for a tritylated cyclic deoxyuridine derivative.

Location, Location, Location

Location, Location, Location

Molecular combing in studies of the genome organization and DNA replication

Molecular combing (MC) yields preparations where individual DNA molecules are uniformly stretched and are parallel to each other. Fluorescence in situ hybridization on such preparations allows an exact mapping of DNA sequences, and pulsed inclusion of halogenated deoxyuridine analogs and their detection using fluorochrome-conjugated antibodies makes it possible to visualize replication. The MC technique was adapted for studying DNA replication in isolated Drosophila melanogaster organs, and it was checked whether a mutation of the Suppressor of UnderReplication (SuUR) gene directly affected the replication fork rate.

Role of Two Strictly Conserved Residues in Nucleotide Flipping and N-Glycosylic Bond Cleavage by Human Thymine DNA Glycosylase

Thymine DNA glycosylase (TDG) promotes genomic integrity by excising thymine from mutagenic G.T mismatches arising by deamination of 5-methylcytosine, and follow-on base excision repair enzymes restore a G.C pair. TDG cleaves the N-glycosylic bond of dT and some other nucleotides, including 5-substituted 2'-deoxyuridine analogs, once they have been flipped from the helix into its active site. We examined the role of two strictly conserved residues; Asn(140), implicated in the chemical step, and Arg(275), implicated in nucleotide flipping. The N140A variant binds substrate DNA with the same tight affinity as wild-type TDG, but it has no detectable base excision activity for a G.T substrate, and its excision rate is vastly diminished (by approximately 10(4.4)-fold) for G.U, G.FU, and G.BrU substrates. Thus, Asn(140) does not contribute substantially to substrate binding but is essential for the chemical step, where it stabilizes the transition state by approximately 6 kcal/mol (compared with 11.6 kcal/mol stabilization provided by TDG overall). Our recent crystal structure revealed that Arg(275) penetrates the DNA minor groove, filling the void created by nucleotide flipping. We found that the R275A and R275L substitutions weaken substrate binding and substantially decrease the base excision rate for G.T and G.BrU substrates. Our results indicate that Arg(275) promotes and/or stabilizes nucleotide flipping, a role that is most important for target nucleotides that are relatively large (dT and bromodeoxyuridine) and/or have a stable N-glycosylic bond (dT). Arg(275) does not contribute substantially to the binding of TDG to abasic DNA product, and it cannot account for the slow product release exhibited by TDG.

Hydroxyl-Functionalized DNA: An Efficient Orthogonal Protecting Strategy and Duplex Stability

Tert-butyldiphenylsilyl (TBDPS) was found to be an effective orthogonal protecting strategy for the 5-substituted hydroxyl groups of de novo synthesized deoxyuridine analogues 1–3 and 7-(3-hydroxypropynyl)- of 8-aza-7-deazadeoxyadenosine 4 for their incorporation into oligodeoxynucleotides by phosphoramidite chemistry. It could be completely cleaved under normal and ultra-mild deprotection conditions applied to DNA synthesis, without extra cleaving operation. The new phosphoramidites were coupled as usual with high yields. The new modified oligodeoxynucleotides were characterized by MALDI-TOF and enzymatic cleavage analysis. The thermal stability and conformation of these hydroxyl-functionalized DNA duplexes were evaluated.

THE EFFECT OF 5-HALOGENATED DEOXYURIDINES ON THE FREQUENCY OF X-RAY-INDUCED CHROMOSOMAL ABERRATIONS IN VICIA FABA

The effects of 5-fluorodeoxyaridine (FUdR) and the thymidine analogs 5- chlorodeoxyuridine (CUdR), 5-bromodeoxyuridine (BUdR), and 5-iododeoxyuridine (IUdR) on the frequency of x-ray-induced chromatid aberrations in the root tips were studied. Pretreatments with CUdR, BUdR, and IUdR at concentrations of 100 mu M increased the effect of a given dose of x rays by factors of 1.3, 1.6, and 1.9, respectively. IUdR increased the frequency of x-rayinduced aberrations to the same extent whether the roots were irradiated under anaerobic or aerobic conditions. For maximum enhancement, it was necessary to treat the roots for at least 24 hr with the thymidine analogs. Posttreatment with IUdR did not influence radiosensitivity. When x irradiation was combined with a FUdR treatment, and the effect was scored in anaphase, the number of fragments was markedly increased and the number of bridges was decreased, in comparison with the x-ray control. The FUdR treatment was equally effective when given after as when given before and during irradiation. The results show that the frequency of x-ray-induced chromatid aberrations in the root tips of Vicia is influenced in the same way by these 5-halogenated deoxyaridines as is the killing effect of x rays on mammalian cells in tissue culture andmore » on bacteria. When the thynridine analogs were tested in equlmolar concentrations in Vicia IUdR was the most effective and CUdR the least effective. The difference in effectivity could be a result of a different incorporation of the analogs into DNA. The fact that a 4- hr pretreatment with IUdR resulted in an increased frequency of aberrations only when the roots were fixed between 9 and 15 hr after irradiation indicates that only those cells which were undergoing DNA synthesis when exposed to IUdR were sensitized. This is consistent with the idea that incorporation of thymidine and its analogs can reverse or prevent the chromosome damage produced by the deoxyuridine analog FUdR is consistent with the idea that the effect of FUdR on chromosome structure is a result of its inhibitory effect on the synthesis of thymidylic acid. The experiments have further shown that whereas FUdR-induced thymidine deficiency produces fragmentation of chromosomes, the incorporation of thymidine analogs, such as CUdR, BUdR, and IUdR, into chromosomal DNA does not itself, as a rue, cause chromosomal aberrations, but it makes the chromosomes more sensitive to the chromosome-breaking effect of x rays. It is concluded that the stability of the chromosome is dependent on the composition and state of its DNA, favoring a hypothesis of chromosome organization which allots to DNA an important fanction in keeping the chromosomes intact. (BBB)« less

Click‐iT™ assay with improved DNA distribution histograms

The Click-iT Assay developed and commercialized by Invitrogen is based on incorporation of a new 5-bromo-2'-deoxyuridine analog, 5-ethynyl-2'-deoxyuridine (EdU) into newly synthesized DNA and its recognition by azide dyes via a copper mediated "click" reaction. This relatively convenient and useful procedure depends on fixation of cells with paraformaldehyde and staining of the DNA with 7-aminoactinomycin-D (7-AAD). Both of these procedures result in DNA histograms with broad coefficients of variation (CV's). In this report, we have shown that after EdU incorporation, nuclei isolated by lysis can be incubated with the Click-iT Assay and stained with propidium iodide for generation of DNA histograms with low CV's. This modified procedure results in better DNA histograms by replacing 7-AAD with propidium iodide and also saves processing time by eliminating the fixation and permeabilization steps.

Synthesis of 5‐(1,2,3‐Triazol‐4‐yl)‐2′‐deoxyuridines by a Click Chemistry Approach: Stacking of Triazoles in the Major Groove Gives Increased Nucleic Acid Duplex Stability

A general protocol for converting alkyl and aryl halides into azides and for converting these in situ into 1,4-disubstituted triazoles was applied with 5-ethynyl-2'-deoxyuridine. This afforded three modified 2'-deoxyuridine analogues with either unsubstituted or 1-phenyl-/1-benzyl-substituted triazoles in their 5-positions. Modelling demonstrates coplanarity of the two heteroaromatic rings, and UV spectroscopy showed the uracil pK(a) values to be almost unchanged. The three nucleosides were introduced into nonamer oligonucleotides by phosphoramidite chemistry. The heteroaromatic triazoles became positioned in the major grooves of the short dsDNA and DNA-RNA duplexes. While single modifications led to decreased duplex stability, the stacking of four consecutive modifications led to enhanced duplex stability, especially for DNA-RNA duplexes. The duplex structures were studied by CD spectroscopy and molecular dynamics simulations, which supported the conjecture that the duplex stabilizing effect is due to efficient stacking of the heteroaromatic triazoles.

Selective Phosphorylation of Antiviral Drugs by Vaccinia Virus Thymidine Kinase

The antiviral activity of a new series of thymidine analogs was determined against vaccinia virus (VV), cowpox virus (CV), herpes simplex virus, and varicella-zoster virus. Several compounds were identified that had good activity against each of the viruses, including a set of novel 5-substituted deoxyuridine analogs. To investigate the possibility that these drugs might be phosphorylated preferentially by the viral thymidine kinase (TK) homologs, the antiviral activities of these compounds were also assessed using TK-deficient strains of some of these viruses. Some of these compounds were shown to be much less effective in the absence of a functional TK gene in CV, which was unexpected given the high degree of amino acid identity between this enzyme and its cellular homolog. This unanticipated result suggested that the CV TK was important in the mechanism of action of these compounds and also that it might phosphorylate a wider variety of substrates than other type II enzymes. To confirm these data, we expressed the VV TK and human TK1 in bacteria and isolated the purified enzymes. Enzymatic assays demonstrated that the viral TK could efficiently phosphorylate many of these compounds, whereas most of the compounds were very poor substrates for the cellular kinase, TK1. Thus, the specific phosphorylation of these compounds by the viral kinase may be sufficient to explain the TK dependence. This unexpected result suggests that selective phosphorylation by the viral kinase may be a promising new approach in the discovery of highly selective inhibitors of orthopoxvirus replication.

Characterization of the rat Na+/nucleoside cotransporter 2 and transport of nucleoside-derived drugs using electrophysiological methods

The Na(+)-dependent nucleoside transporter 2 (CNT2) mediates active transport of purine nucleosides and uridine as well as therapeutic nucleoside analogs. We used the two-electrode voltage-clamp technique to investigate rat CNT2 (rCNT2) transport mechanism and study the interaction of nucleoside-derived drugs with the transporter expressed in Xenopus laevis oocytes. The kinetic parameters for sodium, natural nucleosides, and nucleoside derivatives were obtained as a function of membrane potential. For natural substrates, apparent affinity (K(0.5)) was in the low micromolar range (12-34) and was voltage independent for hyperpolarizing membrane potentials, whereas maximal current (I(max)) was voltage dependent. Uridine and 2'-deoxyuridine analogs modified at the 5-position were substrates of rCNT2. Lack of the 2'-hydroxyl group decreased affinity but increased I(max). Increase in the size and decrease in the electronegativity of the residue at the 5-position affected the interaction with the transporter by decreasing both affinity and I(max). Fludarabine and formycin B were also transported with higher I(max) than uridine and moderate affinity (102 +/- 10 and 66 +/- 6 microM, respectively). Analysis of the pre-steady-state currents revealed a half-maximal activation voltage of about -39 mV and a valence of about -0.8. K(0.5) for Na(+) was 2.3 mM at -50 mV and decreased at hyperpolarizing membrane potentials. The Hill coefficient was 1 at all voltages. Direct measurements of radiolabeled nucleoside fluxes with the charge associated showed a ratio of two positive inward charges per nucleoside, suggesting a stoichiometry of two Na(+) per nucleoside. This discrepancy in the number of Na(+) molecules that bind rCNT2 may indicate a low degree of cooperativity between the Na(+) binding sites.

Evaluation of Bacillus anthracis thymidine kinase as a potential target for the development of antibacterial nucleoside analogs

Bacillus anthracis, which causes anthrax, has attracted attention because of its potential use as a biological weapon. The risk of multidrug resistance against B. anthracis increases the need for antibiotics with new molecular targets. Nucleoside analogs are well-known antiviral and anticancer prodrugs, and thymidine kinase catalyzes the rate-limiting step in the activation of pyrimidine nucleoside analogs used in chemotherapy. The thymidine kinase gene from B. anthracis Sterne strain (34F2) (Ba-TK) was cloned and expressed in E. coli, and the product was purified and characterized regarding its substrate specificity. Ba-TK phosphorylated pyrimidine nucleosides and all natural nucleoside triphosphates served as phosphate donors. Size exclusion chromatography indicated a dimeric form of Ba-TK, regardless of the presence of ATP. Thymidine was the most efficient substrate with a low K(m) value (0.6 microM) and a V(max) of 3.3 micromol dTMP mg(-1) min(-1), but deoxyuridine (K(m)=4.2 microM, V(max)=4.1 micromol dUMP mg(-1) min(-1)) was also a good substrate. Several pyrimidine analogs were also tested and analogs with 5-position modifications showed higher activities compared to analogs with 3'- and N3-position modifications. Deoxyuridine analogs were the most potent inhibitors of B. anthracis growth in vitro. These results may be used to guide future development of nucleoside analogs against B. anthracis.

The Crystal Structure of Mismatch-specific Uracil-DNA Glycosylase (MUG) from Deinococcus radiodurans Reveals a Novel Catalytic Residue and Broad Substrate Specificity

Deinococcus radiodurans is extremely resistant to the effects of ionizing radiation. The source of the radiation resistance is not known, but an expansion of specific protein families related to stress response and damage control has been observed. DNA repair enzymes are among the expanded protein families in D. radiodurans, and genes encoding five different uracil-DNA glycosylases are identified in the genome. Here we report the three-dimensional structure of the mismatch-specific uracil-DNA glycosylase (MUG) from D. radiodurans (drMUG) to a resolution of 1.75 angstroms. Structural analyses suggest that drMUG possesses a novel catalytic residue, Asp-93. Activity measurements show that drMUG has a modified and broadened substrate specificity compared with Escherichia coli MUG. The importance of Asp-93 for activity was confirmed by structural analysis and abolished activity for the mutant drMUGD93A. Two other microorganisms, Bradyrhizobium japonicum and Rhodopseudomonas palustris, possess genes that encode MUGs with the highest sequence identity to drMUG among all of the bacterial MUGs examined. A phylogenetic analysis indicates that these three MUGs form a new MUG/thymidine-DNA glycosylase subfamily, here called the MUG2 family. We suggest that the novel catalytic residue (Asp-93) has evolved to provide drMUG with broad substrate specificity to increase the DNA repair repertoire of D. radiodurans.

Proton affinity ladder for uridine and analogs: influence of the hydroxyl group on the sugar ring conformation

A ladder of relative proton affinities (PA) for a series of modified uridines (e.g. araU, ddU, 5BrU, 5BrdU and 5IU) was established from competitive dissociations of proton-bound heterodimers using Cooks and co-workers' kinetic method. The studied heterodimers are constituted of a modified nucleoside and either an amino acid or a nucleoside with known PA value. These non-covalent heterodimers were prepared under electrospray conditions to be selected and dissociated into the ion-trap analyzer. These results allowed our PA ladder of uridine and deoxyuridine analogs substituted at the C-5 position in the uracil ring to be extended. From this scale, it was showed that the substitution of hydrogen atom at the C-2' position in the sugar ring by a hydroxyl group involves a decrease of about 7 kJ mol(-1). The experimental values for U, 5MeU, dU, 5MedU, ddU and araU are consistent with those obtained by DFT calculations (B3P86/6-31+G//B3LYP/6-31G(.)). Several neutral and protonated conformations of these compounds were considered, in particular the ring conformation of furanose and the orientation of the base with respect to the sugar ring. These calculated results showed the influence of sugar substituent on the conformation of the neutral form of theses nucleosides. However, the most stable protonated structure is the same for all the studied nucleosides except for araU, where the position of the anti 2'-OH group imposes a specific conformation.

Synthesis and Properties of Oligonucleotides Containing 5‐Substituted Pyrimidine Nucleoside

AbstractFor Abstract see ChemInform Abstract in Full Text.

Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 2'-deoxyuridines and their application in DNA triplex formation

The incorporation of C5-amino-modified 2′-deoxyuridine analogues into DNA have found application in nucleic acid labelling, the stabilization of nucleic acid structures, functionalization of nucleic acid aptamers and catalysts, and the investigation of sequence-specific DNA bending. In this study, we describe the physicochemical properties of four different C5-amino-modified 2′-deoxyuridines in which the amino group is tethered to the base via a 3-carbon alkyl, Z- or E-alkenyl or alkynyl linker. Conformational parameters of the nucleosides and their pKa values were deduced using 1H NMR. All of them display the expected anti-conformation of the nucleoside with 2′-endo sugar puckers for the deoxyribose ring. A preference for the cisoid conformation for the Z-alkenyl analogue is found, while the E-alkenyl analogue exists exclusively as its transoid conformation. The pKa values range from 10.0 for the analogue with an aliphatic propyl linker to 8.5 for the propargylamino analogue. The analogues have been used for the synthesis of triple-helix forming oligonucleotides (TFOs) in which they replace thymidine in the natural sequence. Oligonucleotides containing the propargylamino analogue display the highest stability especially at low pH, while those containing analogues with propyl and especially Z-alkenyl linkers are destabilized to a great extent. TFOs containing the analogue with the E-alkenyl linker have stability similar to the unmodified structures. The chemical synthesis of TFOs containing the analogue, 5-(3-hydroxyprop-1-ynyl)-2′-deoxyuridine that possesses a neutral but polar side chain show a remarkable stability, which is higher than that of all TFOs containing the alkylamino or alkenylamino analogues and only slightly lower than that of TFOs containing the propargylamino analogue. Both the hydroxyl and propargylamino substitutions impart enhanced triple-helix stability relative to the analogous sequences containing C5-propynyl-2′-deoxyuridine. Furthermore, a similar dependence of stability on pH is found between TFOs containing the hydroxypropynyl modifications and those containing the propargylamino side chains. This suggests that the major factor responsible for stabilizing such triple helices is due to the presence of the alkyne with an attached electronegative group.

Synthesis of a technetium-99m-labeled thymidine analog: a potential HSV1-TK substrate for non-invasive reporter gene expression imaging

{2-[5-(2′-Fluoro-2′-deoxyuridin-5-yl)pent-4( E)-enyl] [2-(2-mercaptoethyl)aminoethyl]aminoethanethiolato(3)- N,N′ ,S,S′}oxo-[ 99mTc]technetium(V), a potential viral thymidine kinase substrate, was synthesized by coupling 2′-fluoro-2′-deoxyuridine analog with a N2S2 radiometal chelator, followed by [Tc-99m]technetium conjugation. The chemical structure of the radioactive probe was characterized by 1H NMR and high resolution MS using Re-188 conjugated mimics. The radiochemical purity and yield were identified as 98% and 42%, respectively.

First Regioselective Enzymatic Alkoxycarbonylation of Primary Amines. Synthesis of Novel 5′‐ and 3′‐Carbamates of Pyrimidine 3′,5′‐Diaminonucleoside Derivatives Including BVDU Analogues.

AbstractFor Abstract see ChemInform Abstract in Full Text.

First regioselective enzymatic alkoxycarbonylation of primary amines. Synthesis of novel 5'- and 3'-carbamates of pyrimidine 3',5'-diaminonucleoside derivatives including BVDU analogues.

The first regioselective enzymatic alkoxycarbonylation of primary amino groups has been achieved in pyrimidine 3',5'-diaminonucleoside derivatives. Thus, Candida antarctica lipase B (CAL-B) catalyzed this reaction with nonactivated homocarbonates allowing the selective synthesis of several N-5' carbamates, including (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) analogues, with moderate-high yields, whereas immobilized Pseudomonas cepacia lipase (PSL-C) afforded mixtures of alkoxycarbonylated regioisomers. To obtain N-3' carbamates selectively, a short and efficient chemoenzymatic route was used employing some of the N-5'-protected derivatives previously synthesized.

Commercial‐Scale Synthesis of Protected 2′‐Deoxycytidine and Cytidine Nucleosides

AbstractFor Abstract see ChemInform Abstract in Full Text.