Imidazole Ring Opening of 7-Methylguanosine at Physiological pH

Abstract

It is shown by carbon-13 NMR that the only product of the imidazole ring-opening of 7-methyl-guanosine at physiological pH is 2-amino-6-hydroxy-5-N-methylformamido-4-(N-β-ribofurano-sylamino)pyrimidine and that, contrary to previous results, the hydrolysis of the glycosylic bond at pH=7.2 is a much slower process than the ring opening. The ring opened formamidopyrimidine derivative is a very mobile molecule existing under different conformations depending on the solvent, and in water it is capable of giving different kinds of aggregates. Possible biochemical implications of these results are discussed.     

Nucleosides 137. Synthetic Modifications at the 2′Position of Pyrrolo[3,2-D]Pyrimidine and Thieno[3,2-D]Pyrimidine C-Nucleosides,Synthesis of “2′-Deoxy-9-Deazzadenosine” and of “9-Deaza ARA-A”

Abstract

The syntheses and preliminary biological evaluation of several novel pyrrolo[3,2-d]pyrimidine and thieno[3,2-d]pyrimidine C-nucleosides incorporating the arabinofuranosyl or 2′-deoxyribofuranosyl sugar moiety are described. The 2′-deoxy thieno[3,2-d]pyrimidine C-nucleosides (15 and 16) were obtained from 7-(β-D-ribofuranosyl)-4-oxo-3H-thieno[3,2-d]pyrimidine (3) and its 4-SMe derivative 8. “2”-Deoxy-9-deazaadenosine (31), “9-Deaza ara-A” (38) and the 2′-substituted arabinosyl pyrrolo[3,2-d]pyrimidine C-nucleosides (42 - 44) were synthesized from 4-amino-7-(2,3-O-isopropylidene-5-O-trityl-β-D-ribofuranosyl)-5H-pyrrolo[3,2-d]pyrimidine (21)     

Synthesis of C-6 Pyrimidine Acyclic Nucleoside Analogs as Potential Antiviral Agents

Abstract

A number of pyrimidine acyclic nucleosides in which the acyclic moiety is attached to the C-6 position rather than N-1 of the pyrimidine ring have been prepared. This was accomplished via treatment of lithiated 2,4-dimethoxy-5,6-dimethylpyrimidine, or, 2,4-dimethoxy-6-methylpyrirnidine with 1,3-bis-(benzyloxy)-2-propanone, benzyl chloromethyl ether or oxirane, respectively, to give the corresponding key intermediates 6-[3-benzyloxy-2-[(benzyloxy)methyl]-2-hydroxypropyl]-2,4-dimethoxy-5-methylpyrimidine (2a), 6-[3-Denzyloxy-2-[(benzyloxy)methyl]-2-hydroxypropyl]-2,4-dimethoxypyrimidine(2b), 6-(2-benzyloxyethyl)-2,4-dimethoxy-5-methylpyrimidine (3), and2,4-dunethoxy-6-(3-hydroxypropyl)-5-methylpyrimidine (4a). After acidic hydrolysis, followed by debenzylation with boron trichloride these key intermediates were converted to the target C-6 pyrimidine acyclic derivatives. Compounds 6–8b, 11–13, 15, 16, 20, 22, 26, and 29–32 were evaluated for activity against herpes viruses and human immunodeficiency virus. None of the compounds were active against the viruses nor were they cytotoxic at the highest concentration tested.     

Photo-Induced P-Methylbenzylation of 1,3-Dimethylthymine and 1, 3-Dimethyluracil in the Presence of Trifluoroacetic Acid

Abstract

Photolysis of a solution of a pyrimidine (i. e., 1, 3-dimethylthymine and 1, 3-dimethyluracil) in p-xylene in the presence of trifluoroacetic acid afforded mainly the 5, 6-dihydropyrimidine derivative together with the 5-p-methylbenzylated product and the 6-isomer as well. It is suggested that the first two products result from the C⁶-protonated pyrimidine electron adduct (III), while the 6-isomer is derived from the O⁴-protonated isomer (II).     

Synthesis and Biological Evaluation of New Enantiomers of 5-O-Carboranyl Pyrimidine Nucleosides

Abstract

The synthesis of new enantiomers of 5-o-carboranyl pyrimidine nucleosides is described. Some of these agents should be considered for boron neutron capture therapy.     

Pyrimidine Nucleotidases/Phosphotransferases from Human Erythrocyte

Abstract

Two cytoplasmic pyrimidine 5′-nucleotidase have been purified from human erythrocytes to homogeneity and partially characterized. The two enzymes, indicated as PN-I and PN-II, preferentially hydrolyse pyrimidine 5′-monophosphates and 3′-monophosphates, respectively. The kinetic analysis demonstrate that pyrimidine 5′-nucleotidases, in the presence of suitable nucleoside substrates, can operate as phosphotransferases by transferring phosphate to various nucleoside acceptors, including nucleoside analogues known as important drugs widely used in chemotherapy.     

Cytidine Kinase: A Novel Pyrimidine Ribonucleoside Phosphorylating Enzyme in Escherzchza Coli

Abstract

A previously undescribed pyrimidine ribonucleoside kinase that preferentially phosphorylates cytidine to yield its 5′-monophosphate form has been purified to near homogeneity from Escherichia coli.The enzyme was distinct from the known pyrimidine nucleoside kinase in the chromatographic profile, substrate specificity and molecular weight.

     

Crystal Structure of 04-Methyl Uridine: Stacking Induced Changes in the Geometry of the Pyrimidine Ring and Its Mutagenic Role

Abstract

The geometric properties of the pyrimidine ring of O⁴-methyl uridine more closely resemble those of cytidine than diketo uridine. Differences between the independent molecules of O⁴-methyl uridine are observed in the C(7)-O(4)-C(4)-C(5)-C(6) bond orders and the planarity of the pyrimidine rings. These differences are attributed to the monopole-induced dipole interactions between the ribose ring oxygen atom and a neighboring base of molecule A. A survey of the literature reveals that similar stacking-induced effects occur in other structures, involving both pyrimidine and purines. Finally, two base pairing schemes between O⁴-methyl uridine and guanosine, in which two hydrogen bonds can form, have been presented. Of these two the mispair with Watson-Crick geometry is favored.     

Hucleotide sequence of the Bos indicus α‐lactalbumin 5’ flanking region: Comparison with the 605 taurus sequence

Abstract

The 5’ flanking region of the α‐lactalbumin gene from Bos indicus (Brahman) and Bos taurus (Holstein) have been sequenced. The sequences were compared to detect potential sequence variations. The 538 bp of 5’ flanking region contained nine sequence variations between the two breeds. Seven of the variations occur in the 5’ flanking region of the α‐lactalbumin gene and two occur in the region encoding the 5’ untranslated region of the mRNA. Seven of the variations are conservative purine to purine or pyrimidine to pyrimidine variations, while two are purine to pyrimidine variations.     

Nucleosides and Nucleotides. 104. Radical and Palladium-Catalyzed Deoxygenation of the Allylic Alcohol Systems in the Sugar Moiety of Pyrimidine Nucleosides§,1

Abstract

New methods for the synthesis of 2′,3′-didehydro-2′,3′-dideoxy-2′ (and 3′)-methyl-5-methyluridines and 2′,3′-dideoxy-2′ (and 3′)-methylidene pyrimidine nucleosides have been developed from the corresponding 2′ (and 3′)-deoxy-2′ (and 3′)-methylidene pyrimidine nucleosides. Treatment of a 3′-deoxy-3′-methylidene-5-methyluridine derivative 8 with 1,1′-thiocarbonyldiimidazole gave the allylic rearranged 2′,3′-didehydro-2′,3′-dideoxy-3′-[(imidazol-1-yl)carbonylthiomethyl] derivative 24. On the other hand, reaction of 8 with methyloxalyl chloride afforded 2′-O-methyloxalyl ester 25. Radical deoxygenation of both 24 and 25 gave 26 exclusively. Palladium-catalyzed reduction of 2′,5′-di-O-acetyl-3′-deoxy-3′-methylidene-5-methyluridine (32) with triethylammonium formate as a hydride donor regioselectively afforded the 2′,3′-dideoxy-3′-methylidene derivative 35 and 2′,3′-didehydro-2′,3′-dideoxy-3′-methyl derivative 34 in a ratio of 95:5 in 78% yield. These reactions were used on the corresponding 2′-deoxy-2′-methylidene derivatives. An alternative synthesis of 2′,3′-dideoxy-2′-methylidene pyrimidine nucleosides (43, 52, and 54) was achieved from the corresponding 1-(3-deoxy-β-D-thero-pentofuranosyl)pyrimidines (44 and 45). The cytotoxicity against L1210 and KB cells and inhibitory activity of the pathogenicity of HIV-1 are also described     

Aminopyrimidines and Derivatives. 19 1. Reaction of 1, 6-Dihydro-4-Beta; D (2, 3, 4, 6-Tetra-0-Acetyl)Glucopyranosylamino-1-Methyl-Z-Methoxy-6-Oxo Pyrimidine with Choracetyl Chloride

Abstract

Reaction between 1, 6-dihydro-4-β-D(2, 3, 4, 6-tetra-O-acetyl) glucopyranosylamino-l-methyl-2-methoxy-6-oxo pyrimidine and chloracetyl chloride yields the corresponding 5-α-chloracetyl derivative and 2,6-di oxo-4-β -D (2,3,4,6-tetra-0-acetyl) glucopyranosylamino-l-methyl-1,2,3,6 tetrahdro pyrimidine. The first compund has been cyclized to the corresponding 7-β-D-glucopyranosyl-pyrrolo 2, 3-d pyrimidine and the second one to 3-βD-glucopyranosyl-vic-triazolo 4,5-d pyrimidine.     

Ring-Opening of 3-β-D-Ribofuranosyl-3,7,8,9-Tetrahydropyrimido [1,2-i]Purin-8-ol and Preparation of 2-Thio- and 2-aza-Adenosine Derivatives

The adduct 3-β-D-ribofuranosyl-3,7,8,9-tetrahydropyrimido[1,2-i]purin-8-ol (2), obtained from adenosine and epichlorohydrin, underwent ring fission at basic conditions. The initial ring-opening took place at C2 of the pyrimidine unit resulting in 2-(5-amino-1-β-D-ribofuranosyl-imidazol-4-yl)-1,4,5,6-tetrahydropyrimidin-5-ol (3). Also the tetrahydropyrimidine ring of 3 could be opened resulting in 5-amino-1-(β-D-ribofuranosyl)-imidazole-4-(N-3-amino-2-hydroxyl-propyl)-carboxamide (4). In hot acid conditions, 2 was both deglycosylated and ring-opened yielding 2-(5-amino-imidazol-4-yl)-1,4,5,6-tetrahydropyrimidin-5-ol (7) as the final product. When reacting 3 with CS₂ or HNO₂ ring-closure took place and 3-β-D-ribofuranosyl-3,4,7,8,9-pentahydropyrimido[1,2-i]purin-8-ol-5-thione (5), and 3-β-D-ribofuranosyl-imidazo[4,5-e]-3,7,8,9-tetrahydropyrimido[1,2-c][1,2,3]triazine-8-ol (6), respectively, were obtained. Also, the pyrimidine ring of the epichlorohydrin adduct with adenine, 10-imino-5,6-dihydro-4H,10H-pyrimido[1,2,3-cd]purin-5-ol (10), underwent ring fission and the product was identified as 3-hydroxy-1,2,3,4-tetrahydroimidazo[1,5-a]pyrimidine-8-carboximidamide (11).     

Synthesis and Antiviral Activities of 1,3-Oxathiolanyl Nucleosides with 5-Hydroxymethyl Substituent

Abstract

Novel 1,3-oxathiolanyl pyrimidine nucleosides with 5-hydroxymethyl substituent were synthesized starting from _d-mannose and evaluated for antiviral activities against HIV-1, HSV type 1,2 and HCMV.     

Synthesis and Binding Properties of a Homopyrimidine 2′,5′-Linked Xylose Nucleic Acid (2′,5′-XNA)

Abstract

The synthesis and hybridization properties of pyrimidine 2′,5′-RNA and 2′,5′-Xylose Nucleic Acid (2′,5′-XNA) are described.     

The effects of recessive lethal Notch mutations of Drosophila melanogaster on flavoprotein enzyme activities whose inhibitions cause Notch-like phenocopies

The biochemical action of the Notch locus whose mutants cause morphological aberrations in flies, viz., notches of wings and bristle multiplication, has been analyzed (1) by the addition to the food medium of enzyme inhibitors causing phenocopies of Notch and (2) by comparison of enzyme activity patterns of Notch mutants with different degrees of phenotypic expression. Notch phenocopies were induced by inhibitors of enzyme activities in two biochemical pathways: (1) the de novo pyrimidine synthesis by 5-methylorotate (inhibitor of dihydroorotate dehydrogenase) and (2) the choline shunt by amobarbital (inhibits choline dehydrogenase) and methoxyacetate (inhibits sarcosine dehydrogenase). The inhibition of de novo pyrimidine synthesis prevents the production of deoxyuridine-5-phosphate, the substrate for the synthesis of thymidine-5-phosphate via thymidylate synthase, whereas the inhibition of the choline shunt prevents the production of HCHO groups and glycine, both of which are involved in the synthesis of 5,10-methylenetetrahydrofolate, which is a cofactor of thymidylate synthase. It was already known that the inhibition of the latter enzyme in vivo induces Notch phenocopies. Notch mutants with a strong morphological expression show low enzyme activities for dihydroorotate dehydrogenase and choline dehydrogenase. Both are flavoprotein enzymes linked to the respiratory chain. The correspondence between the low enzyme activities in Notch mutants with a strong morphological expression and the phenocopying effect of antimetabolites on these enzymes in the two biochemical pathways involved strongly suggests that the morphological effects of Notch on flies are a consequence of lowered activities of choline dehydrogenase and dihydroorotate dehydrogenase.     

DNA Triple Helix Formation by N-Alkylphosphoramidate α-Oligonucleosides

Abstract

Triplex formation of pyrimidine N-alkylphosphoramidate α-oligonucleosides (12-mer) containing either dC or 5-Me-dC with their phosphodiester oligonucleoside homopurine target was evaluated by UV melting experiments.     

Triazole pyrimidine nucleosides as inhibitors of Ribonuclease A. Synthesis,biochemical, and structural evaluation

Five ribofuranosyl pyrimidine nucleosides and their corresponding 1,2,3-triazole derivatives have been synthesized and characterized. Their inhibitory action to Ribonuclease A has been studied by biochemical analysis and X-ray crystallography. These compounds are potent competitive inhibitors of RNase A with low μM inhibition constant (K_i) values with the ones having a triazolo linker being more potent than the ones without. The most potent of these is 1-[(β-d-ribofuranosyl)-1,2,3-triazol-4-yl]uracil being with K_i = 1.6 μM. The high resolution X-ray crystal structures of the RNase A in complex with three most potent inhibitors of these inhibitors have shown that they bind at the enzyme catalytic cleft with the pyrimidine nucleobase at the B₁ subsite while the triazole moiety binds at the main subsite P₁, where P-O5′ bond cleavage occurs, and the ribose at the interface between subsites P₁ and P₀ exploiting interactions with residues from both subsites. The effect of a susbsituent group at the 5-pyrimidine position at the inhibitory potency has been also examined and results show that any addition at this position leads to a less efficient inhibitor. Comparative structural analysis of these RNase A complexes with other similar RNase A—ligand complexes reveals that the triazole moiety interactions with the protein form the structural basis of their increased potency. The insertion of a triazole linker between the pyrimidine base and the ribose forms the starting point for further improvement of these inhibitors in the quest for potent ribonucleolytic inhibitors with pharmaceutical potential.     

Synthesis of 5-Tethered Carborane-Containing Pyrimidine Nucleosides as Potential Agents for DNA Incorporation

Abstract

Several 5-substituted-2′-deoxyuridines have been prepared in which the carborane moiety is attached at the terminus of a flexible hydrocarbon chain containing an ester linkage. These boron moieties as the B-10 enriched compounds have potentiality for use in the treatment of cancer by means of boron neutron capture therapy. A convenient synthetic route, in high yield, has been developed for the preparation of these 5-tethered carborane-containing pyrimidine nucleosides.     

Synthesis,Antiproliferative, and Antiviral Evaluation of Certain Acyclic 6-Substituted Pyrrolo[2,3-D]-pyrimidine Nucleoside Analogs Related to Sangivamycin and Toyocamycin

Abstract

A number of 6-substituted 7-[(2-hydroxyethoxy)methyl]pyrrolo[2,3-d]pyrimidine and 7-[(1,3-dihydroxy-2-propoxy)methyl]pyrrolo[2,3-d]pyrimidine derivatives related to the nucleoside antibiotics toyocamycin and sangivamycin were prepared and tested for their biological activity. Treatment of 2-amino-5-bromo-3,4-dicyanopyrrole (2) with triethylorthoformate, followed by alkylation via the sodium salt method with either 2-(acetoxyethoxy)methyl bromide or (1,3-diacetoxy-2-propoxy)methyl bromide, furnished the corresponding N-substituted pyrroles 3a and 3b. These compounds were then smoothly converted to the requisite deprotected 4-amino-6-bromopyrrolo[2,3-d]-pyrimidine-5-carbonitriles 5a and 5b (toyocamycin analogs) by methanolic ammonia. The 6-amino-derivatives were obtained by a displacement of the bromo group with liquid ammonia. Conventional functional group transformations involving the 5-cyano group furnished the 5-carboxamide (sangivamycin) and 5-thioamide analogs. Compounds substituted at the 7-position with a ribosyl moiety were active against human cytomegalovirus (HCMV) at micromolar concentrations, but the apparent activity was not selective. The 7-ribosyl compounds also had no activity against human immunodeficiency virus (HIV), though they were all cytotoxic. The new compounds were also evaluated against HCMV, herpes simplex virus type I (HSV-1), HIV, and also for their ability to inhibit the growth of L1210 murine leukemic cells in vitro. None of these compounds with (2-hydroxyethoxy)methyl substituents or 7-(1,3-dihydroxy-2-propoxy)methyl substituent at N-7 showed significant cytotoxicity toward L1210, or toward uninfected human foreskin fibroblasts (HFF cells), and KB cells. Nor were they cytotoxic in human lines CEM or MT2. Only compound 4a was found to be active against HCMV, having an IC₅₀ of 32 μM.     

Studies on the Synthesis of S 5′,6-Methano-5′-Thiourldines

Abstract

Two approaches to the synthesis of the title compounds are described. In the first route, a reactive 5-oxo-6-methylene pyrimidine intermediate that is generated by treating the bis-acetylated or bis-benzoylated nucleosides 10 and 11 with sodium hydroxide undergoes intramolecular attack by the 5′-thiol group to afford the 5-hydroxy cyclonucleoside 12. In the second and higher yielding approach, the S_5′,6-methano linkage is established by an internal allylic displacement reaction that occurs when the 5-bromo-6-methyl nucleoside 24 is treated with base. The conformational properties of S_5′,6-methano-5′-thiouridine (3) and certain long-range spin-spin couplings observed in the NMR spectra of the intermediate nucleosides are discussed.