Synthesis of Acyclic Nucleoside Analogs Related to Barbituric Acid

Abstract

The syntheses of the pyrimidine analogs 5,5-dihydroxymethyl-2,4,6-pyrimidineytrione I, 2-amino-5,5-dihydroxymethyl-4,6-pyrimidinedione II, 5,5-di(2-hydroxyethyl)-2,4,6-pyrimidinetrione III, and 2-amino-5,5-di(2-hydroxyethyl)-4,6-pyrimidinedione IV are described.     

Commentary: Metabolic Impediments to the use of Nucleotide Derivatives to Circumvent Resistance to Purine and Pyrimidine Analogs

Abstract

Many attempts have been made to design derivatives of analog nucleotides that might circumvent resistance due to deficiency of enzymes that convert analogs of purines, pyrimidines and nucleosides to nucleotides. None of these prodrugs that have been evaluated has been active against resistant tumor cells in vivo. The probable reason for this failure is that host cells, but not the resistant cells, have the capacity to form toxic nucleotides from bases or nucleosides resulting from degradation of the prodrugs. These considerations indicate that this strategy for circumvention of resistance will be successful only if the prodrug has some property, other than ability to enter the cell and be converted to toxic nucleotide, that will result in selective toxicity to resistant cells.     

Locked Nucleic Acids: Promising Nucleic Acid Analogs for Therapeutic Applications

Locked Nucleic Acid (LNA) is a unique nucleic‐acid modification possessing very high binding affinity and excellent specificity toward complementary RNA or DNA oligonucleotides. The remarkable properties exhibited by LNA oligonucleotides have been employed in different nucleic acid‐based therapeutic strategies both in vitro and in vivo. Herein, we highlight the applications of LNA nucleotides for controlling gene expression.     

Differential Sensitivity of Basal and Opioid-Stimulated Low Km GTPase to Guanine Nucleotide Analogs

In membranes derived from NG108-15 cells, the opioid peptide [D-Ala2,D-Leu5]enkephalin (DADLE) stimulates a low Km GTPase. The nucleotide analogs guanosine 5'-O-(2-thio)diphosphate (GDP beta S), guanosine 5'-(beta,gamma-imido)triphosphate [Gpp(NH)p] and guanosine 5'-O-(3-thio)-triphosphate (GTP gamma S) inhibit the basal enzymatic activity with the order of potency GTP gamma S greater than Gpp (NH)p greater than GDP beta S. In the presence of DADLE, the inhibition isotherms of GDP beta S and Gpp(NH)p are shifted to the right five- and fourfold, respectively, compared to the inhibition observed in the absence of DADLE. In contrast, the IC50 of GTP gamma S for inhibiting the enzyme is reduced by 55% in the presence of the opioid. Both Gpp(NH)p and GTP gamma S produce a concentration-dependent increase in the Km(app) of GTPase, without affecting its Vmax, indicating a competitive inhibition. However, the replots of Km(app) versus inhibitor concentration are hyperbolic, suggesting a partial type of inhibition. Both Gpp(NH)p and GTP gamma S, but not GTP, induce an increase in the EC50 of DADLE for stimulating GTPase. These findings indicate that the basal and the opioid-stimulated low Km GTPase differ in their respective sensitivities to inhibition by guanine nucleotide analogs.     

Structure-Activity Correlations with Compounds Related to Abscisic Acid

Inhibition of cell expansion of excised embryonic axes of Phaseolus vulgaris was used to evaluate the growth-inhibiting activity of abscisic acid and related compounds. None of the 13 compounds tested was as active as abscisic acid. 4-Hydroxyisophorone, a substance representative of the abscisic acid ring system was essentially inactive; cis, trans-3-methylsorbic acid, a compound resembling the side chain of abscisic acid, had low activity; and cis, trans-beta-ionylideneacetic acid was one-sixth as active. Loss of the ring double bond results in a drastic decrease in biological activity. Comparison of our results with those reported previously leads to the suggestion that the double bond of the cyclohexyl moiety may have an important function in determining the degree of activity of cis, trans-ionylideneacetic acids. Two modes of action are discussed. It seems possible that the ring double bond is involved in covalent bonding in binding of the abscisic acid analogue to macromolecules. This may require formation of an intermediate epoxide. It can also be argued that stereochemical differences between cyclohexane derivatives are important factors in determining the degree of biological activity.     

Stability of Lactic Acid Bacteria to Freezing as Related to Their Fatty Acid Composition

The viability of Streptococcus lactis and Lactobacillus sp. A-12 after freezing at -17°C for 48 h was better preserved when the cells were grown in medium supplemented with oleic acid or Tween 80 (polyoxyethylene sorbitan monooleate). A pronounced change in the cellular fatty acid composition was noted when the bacteria were grown in the presence of Tween 80. In S. lactis the ratio of unsaturated to saturated fatty acids increased from 1.18 to 2.55 and in Lactobacillus sp. A-12 it increased from 0.85 to 1.67 when Tween 80 was added to the growth medium. The antibiotic cerulenin markedly inhibited the growth of lactic acid bacteria in tomato juice (TJ) medium but had almost no effect on the growth of the bacteria in TJ medium containing Tween 80 (or oleic acid). The antibiotic inhibited markedly the incorporation of [1-¹⁴C]acetate but had no inhibitory effect on the incorporation of exogenous [1-¹⁴C]oleate (or [1-¹⁴C]palmitate) into the lipid fractions of lactic acid bacteria. Thus, the fatty acid composition of lactic acid bacteria, inhibited by the antibiotic cerulenin, can be modulated by exogenously added oleic acid (or Tween 80) without the concurrent endogenous fatty acid synthesis from acetate. The data obtained suggest that cerulenin inhibits neither cyclopropane fatty acid synthesis nor elongation of fatty acid acyl intermediates. The radioactivity of cells grown in the presence of [1-¹⁴C]oleate and cerulenin was associated mainly with cyclopropane Δ19:0, 20:0 + 20:1, and 21:0 acids. As a consequence, cerulenin caused a decrease in the ratio of unsaturated to saturated fatty acids in lactic acid bacteria as compared with cells grown in TJ medium plus Tween 80 but without cerulenin. Cerulenin caused a decrease in the viability of S. lactis and Lactobacillus sp. A-12 after freezing at -17°C for 48 h only when Tween 80 was present in the growth medium. We conclude that the sensitivity of lactic acid bacteria to damage from freezing can be correlated with specific alterations in the cellular fatty acids.     

A Rapid Synthetic Route to Conformationally Restricted [5,5]-Bicyclic Nucleoside-Amino Acid Conjugates

A concise synthetic route to a novel class of conformationally rigid 3 ′,4 ′-cis-fused bicyclic nucleoside derivatives has been developed. The synthetic strategy and approach involves initial synthesis of a key [5,5]-bicyclic 6-aminofurofuran-2-one scaffold, employing an L-serine derived aminobutenolide as a strategically functionalized chiral template. Subsequent utilization of the carbonyl functionality of the above bicyclic lactone toward nucleobase incorporation, and linking of the resident amine functionality with appropriately protected amino acids completed the syntheses of the target bicyclic nucleoside-amino acid conjugates. Following the above route, and utilizing a combination of easily available nucleobases (4) and amino acids (4) as the two diversity elements, combinatorial synthesis of a 16-member demonstration library of the title amino acid-linked nucleosides has been accomplished.     

Synthesis of Oligosaccharides Structurally Related to Hyaluronic Acid Fragments

Russian Journal of Bioorganic Chemistry - Hyaluronic acid (HA) is a natural polysaccharide constructed from the alternating residues of β-D-glucuronic acid and N-acetyl-β-D-glucosamine....     

Quality by design (QbD) of amide isosteres: 5,5-Disubstituted isoxazolines as potent CRTh2 antagonists with favorable pharmacokinetic and drug-like properties

Isoxazoles are frequently used amide isosteres, as shown in the context of discovery of CRTh₂ antagonists from amide 1 to isoxazole 2. However, persistent agonism and poor solubility in isoxazole series presented challenges to its further development. Based on the concept of quality by design (QbD), 5,5-disubstituted isoxazolines 3 were introduced. The chirality at 5 position of isoxazolines controlled the switch between two modes of actions, which led to a novel series of pure antagonists. This non-planar motif also conferred a change of shape of these molecules, which avoided flat structures and improved their physical properties.     

Synthesis of Novel Plant Growth Inhibitors Structurally Related to Abscisic Acid

When paraffin wax is dispersed in medium as emulsion, some kinds of bacteria and yeasts readily grow on it. This paper presents a study on microbial cell production from solid paraffin. In this study a paraffin wax which contains 91% of normal paraffins ranging from C₂₅ to C₃₇ with the melting point of 62.5°C was used as a substate, but no solvent was used for the dispersion of the wax.

As a result of this study, the following have been found out. (1) Many strains of liquid normal paraffin assimilating bacteria and yeasts can assimilate paraffin wax. (2) Dried cell yields on added hydrocarbons of Corynebacterium hydrocarboclastus S-12-B2 and Candida tropicalis S-315-Y1 are 70% and 56% respectively, when they are cultured by wax emulsion of 0.6% concentration. (3) When nonion surface-active agent (Plysurf A210G) was added as an emulsifing agent, highly concentrated wax emulsion was obtained, but the growth of microorganisms on it was slower. Further investigation is needed to obtain better strains of bacteria and yeasts and also to find out optimum culture conditions.     

Catabolism of Pyrimidines in Yeast: A Tool to Understand Degradation of Anticancer Drugs

The pyrimidine catabolic pathway is of crucial importance in cancer patients because it is involved in degradation of several chemotherapeutic drugs, such as 5-fluorouracil; it also is important in plants, unicellular eukaryotes, and bacteria for the degradation of pyrimidine-based biocides/antibiotics. During the last decade we have developed a yeast species, Saccharomyces kluyveri, as a model and tool to study the genes and enzymes of the pyrimidine catabolic pathway. In this report, we studied degradation of uracil and its putative degradation products in 38 yeasts and showed that this pathway was present in the ancient yeasts but was lost approximately 100 million years ago in the S. cerevisiae lineage.     

Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition

Although strand-biased gene distribution(SGD) was described some two decades ago,the underlying molecular mechanisms and their relationship remain elusive.Its facets include,but are not limited to,the degree of biases,the strand-preference of genes,and the influence of background nucleotide composition variations.Using a dataset composed of 364 non-redundant bacterial genomes,we sought to illustrate our current understanding of SGD.First,when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy,the SGD of the polC group stood out more significantly than that of the non-polC group.Second,when examining horizontal gene transfer,coupled with gene functional conservation(essentiality) and expressivity(level of expression),we realized that they all contributed to SGD.Third,we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance(both G and A) on the leading strand of the polC group.We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands,and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.     

Common Single Nucleotide Polymorphisms in Genes Related to Immune Function and Risk of Papillary Thyroid Cancer

Accumulating evidence suggests that alterations in immune function may be important in the etiology of papillary thyroid cancer (PTC). To identify genetic markers in immune-related pathways, we evaluated 3,985 tag single nucleotide polymorphisms (SNPs) in 230 candidate gene regions (adhesion-extravasation-migration, arachidonic acid metabolism/eicosanoid signaling, complement and coagulation cascade, cytokine signaling, innate pathogen detection and antimicrobials, leukocyte signaling, TNF/NF-kB pathway or other) in a case-control study of 344 PTC cases and 452 controls. We used logistic regression models to estimate odds ratios (OR) and calculate one degree of freedom P values of linear trend (P_SNP-trend) for the association between genotype (common homozygous, heterozygous, variant homozygous) and risk of PTC. To correct for multiple comparisons, we applied the false discovery rate method (FDR). Gene region- and pathway-level associations (P_Region and P_Pathway) were assessed by combining individual P_SNP-trend values using the adaptive rank truncated product method. Two SNPs (rs6115, rs6112) in the SERPINA5 gene were significantly associated with risk of PTC (P_SNP-FDR/P_SNP-trend = 0.02/6×10⁻⁶ and P_SNP-FDR/P_SNP-trend = 0.04/2×10⁻⁵, respectively). These associations were independent of a history of autoimmune thyroiditis (OR = 6.4; 95% confidence interval: 3.0–13.4). At the gene region level, SERPINA5 was suggestively associated with risk of PTC (P_Region-FDR/P_Region =0.07/0.0003). Overall, the complement and coagulation cascade pathway was the most significant pathway (P_Pathway = 0.02) associated with PTC risk largely due to the strong effect of SERPINA5. Our results require replication but suggest that the SERPINA5 gene, which codes for the protein C inhibitor involved in many biological processes including inflammation, may be a new susceptibility locus for PTC.     

Synthesis of Some 2-Alkylated-5-Aminoimidazoles Related to Intermediates in Purine Nucleotide de novo and Thiamine Biosynthesis

Abstract

Routes to 2-alkylated-5-aminoimidazole nucleosides have been investigated in which the 2-substituent has up to 3 carbon atoms and capable of being interconverted into suitable oxy and 0x0 alkyl derivatives for use in enzyme inhibition and biochemical incorporation studies involving both purine nucleotide de novo and thiamine biosynthesis.     

Functional Study of One Nucleotide Mutation in Pri-MiR-125a Coding Region which Related to Recurrent Pregnancy Loss

MicroRNAs (miRNAs) are short non-coding RNAs which modulate gene expression by binding to complementary segments present in the 3′UTR of the mRNAs of protein coding genes. MiRNAs play very important roles in maintaining normal human body physiology conditions, meanwhile, abnormal miRNA expressions have been found related to many human diseases spanning from psychiatric disorders to malignant cancers. Recently, emerging reports have indicated that disturbed miRNAs expression contributed to the pathogenesis of recurrent pregnancy loss (RPL). In this study, we identified a new mutation site (+29A>G, position relative to pre-miR-125a) by scanning pri-miR-125a coding region in 389 Chinese Han RPL patients. This site was co-existed with two polymorphisms (rs12976445 and rs41275794) in patients heterogeneously and changed the predicted secondary structures of pri-miR-125a. Subsequent in vitro analysis indicated that the A>G mutation reduced mature miR-125a expression, and further led to less efficient inhibition of verified target genes. Functional analysis showed that mutant pri-mir-125a can enhance endometrial stromal cells (ESCs) invasive capacity and increase the sensitivity of ESCs cells to mifepristone. Moreover, we further analyzed the possible molecular mechanism by RIP-chip assay and found that mutant pri-mir-125a disturbed the expression of miR-125a targetome, the functions of which includes embryonic development, cell proliferation, migration and invasion. These data suggest that A>G mutation in pri-miR-125a coding region contributes to the genetic predisposition to RPL by disordering the production of miR-125a, which consequently meddled in gene regulatory network between mir-125a and mRNA.     

Nucleic Acid Related Compounds: A Convenient Synthesis of 3-Deazauridine Analogues

Abstract

A novel synthesis of 3-deazapyrimidine glycosides utilizing pyridine-2(1H)-ones or their sodium salts and α-halomonosugars namely D-glucose or D-galactose as starting components is described.     

Synthesis of Photoreactive Tryptophan Analogs: Enzymatic Conversion of Azidoindoles to Azidotryptophans

Four photoreactive azidoindoles, 4, 5, 6, and 7 azidoindole, were synthesized and converted to the corresponding azidotryptophans by a crude enzyme preparation of tryptophan synthetase from Neurospora crassa.     

Analogs of the Antituberculous Agent Pyrazinamide Are Competitive Inhibitors of NADPH Binding to M. tuberculosis Fatty Acid Synthase I

Analogs of pyrazinamide (=pyrazine‐2‐carboxamide; PZA), an essential component of short‐course antituberculous chemotherapy, such as 5‐chloropyrazinamide (5‐Cl‐PZA) act as competitive inhibitors of NADPH binding to purified mycobacterial fatty acid synthase I (FAS I) as shown by Saturation Transfer Difference (STD) NMR studies. In addition, pyrazinoic acid esters (POE) and 5‐Cl‐POE reversibly bind to FAS I with the relatively greater affinity of longer‐chain esters for FAS I, clear from the STD amplification factors. The competitive binding of PZA and 5‐Cl‐PZA clearly illustrates that both agents bind FAS. In contrast to PZA, at low NADPH concentrations 5‐Cl‐PZA is a cooperative inhibitor of NADPH binding.