Simple oxidation of pyrimidinylhydrazones to triazolopyrimidines and their inhibition of Shiga toxin trafficking

The oxidative cyclisation of a range of benzothieno[2,3-d]pyrimidine hydrazones (7a–j) to the 1,2,4-triazolo[4,3-c]pyrimidines (8a–j) catalysed by lithium iodide or to the 1,2,4-triazolo[1,5-c]pyrimidines (10a–j) with sodium carbonate is presented. A complementary synthesis of the 1,2,4-triazolo[1,5-c]pyrimidines starting from the amino imine 11 is also reported. The effect of these compounds on Shiga toxin (STx) trafficking in HeLa cells and comparison to the previously reported Exo2 is also detailed

Absorption of pyrimidines, purines, and nucleosides by Co, Ni, Cu and Fe /III-montmorillonite /clay-organic studies XIII/

Absorption of pyrimidines, purines, and nucleosides by copper, nickel, cobalt, and iron montmorillonit

Mechanisms of base selection by human single-stranded selective monofunctional uracil-DNA glycosylase

hSMUG1 (human single-stranded selective monofunctional uracil-DNA glyscosylase) is one of three glycosylases encoded within a small region of human chromosome 12. Those three glycosylases, UNG (uracil-DNA glycosylase), TDG (thymine-DNA glyscosylase), and hSMUG1, have in common the capacity to remove uracil from DNA. However, these glycosylases also repair other lesions and have distinct substrate preferences, indicating that they have potentially redundant but not overlapping physiological roles. The mechanisms by which these glycosylases locate and selectively remove target lesions are not well understood. In addition to uracil, hSMUG1 has been shown to remove some oxidized pyrimidines, suggesting a role in the repair of DNA oxidation damage. In this paper, we describe experiments in which a series of oligonucleotides containing purine and pyrimidine analogs have been used to probe mechanisms by which hSMUG1 distinguishes potential substrates. Our results indicate that the preference of hSMUG1 for mispaired uracil over uracil paired with adenine is best explained by the reduced stability of a duplex containing a mispair, consistent with previous reports with Escherichia coli mispaired uracil-DNA glycosylase. We have also extended the substrate range of hSMUG1 to include 5-carboxyuracil, the last in the series of damage products from thymine methyl group oxidation. The properties used by hSMUG1 to select damaged pyrimidines include the size and free energy of solvation of the 5-substituent but not electronic inductive properties. The observed distinct mechanisms of base selection demonstrated for members of the uracil glycosylase family help explain how considerable diversity in chemical lesion repair can be achieved

Structure-based design and synthesis of antiparasitic pyrrolopyrimidines targeting pteridine reductase 1

The treatment of Human African Trypanosomiasis remains a major unmet health need in sub-Saharan Africa. Approaches involving new molecular targets are important and pteridine reductase 1 (PTR1), an enzyme that reduces dihydrobiopterin in Trypanosoma spp. has been identified as a candidate target and it has been shown previously that substituted pyrrolo[2,3-d]pyrimidines are inhibitors of PTR1 from T. brucei (J. Med. Chem. 2010, 53, 221-229). In this study, 61 new pyrrolo[2,3-d]pyrimidines have been prepared, designed with input from new crystal structures of 23 of these compounds complexed with PTR1, and evaluated in screens for enzyme inhibitory activity against PTR1 and in vitro antitrypanosomal activity. 8 compounds were sufficiently active in both screens to take forward to in vivo evaluation. Thus although evidence for trypanocidal activity in a stage I disease model in mice was obtained, the compounds were too toxic to mice for further development

Orotic Aciduria

Orotic acid is an intermediate found in the pathway for pyrimidine synthesis. The mitochondrial enzyme dihydroorotate dehydrogenase (DHODH) catalyzes the production of orotic acid by the conversion of the compound dihydroorotate to orotic acid. Orotic acid is commonly produced by this reaction in erythrocytes, hepatocytes, and kidney cells. Chemical modification of orotic acid in the pyrimidine pathway will generate nucleotides involved in DNA and RNA synthesis. Orotic aciduria can occur as a secondary manifestation due to a defect in an enzyme or transporter within the urea cycle, due to competitive inhibition by anti-cancer drugs such as allopurinol and 6-azauridine, or due to diseases such as Reye’s syndrome and mitochondrial disorders. The primary cause of orotic aciduria is a rare, autosomal recessive disorder in the family of inborn errors in metabolism, and can be categorized into three groups. Type I, II, and III orotic aciduria occur due to a genetic defect in the bifunctional enzyme uridine monophosphate synthase (UMPS). Neonatal patients diagnosed with this disorder commonly exemplify symptoms such as lethargy, difficulty feeding, and low birth weight and height. Neural and developmental deficits, megaloblastic anemia, and crystalluria may also occur. Laboratory findings typically include extremely high urinary orotic acid levels, megaloblastic anemia, and very low UMPS activity. Since early treatment with Xuriden may cause remission of symptoms, future studies should focus on improving early detection screening methods. Early diagnosis and treatment is clinically significant because impaired pyrimidine synthesis can lead to severe symptoms such as mental retardation, coma, or death

Electronic Spectroscopy of Isolated DNA Polyanions

In solution, UV-vis spectroscopy is often used to investigate structural changes in biomolecules (i.e., nucleic acids), owing to changes in the environment of their chromophores (i.e., the nucleobases). Here we address whether action spectroscopy could achieve the same for gas-phase ions, while taking the advantage of additional spectrometric separation of complex mixtures. We therefore systematically studied the action spectroscopy of homo-base 6-mer DNA strands (dG6, dA6, dC6, dT6) and discuss the results in light of gas-phase structures validated by ion mobility spectrometry and infrared ion spectroscopy, of electron binding energies measured by photoelectron spectroscopy, and of calculated electronic photo-absorption spectra. When UV photons interact with oligonucleotide polyanions, two main actions may take place: (1) fragmentation and (2) electron detachment. The action spectra reconstructed from fragmentation follow the absorption spectra well, and result from multiple cycles of absorption and internal conversion. The action spectra reconstructed from the electron photodetachment (ePD

Diversity oriented synthesis : substitution at C5 in unreactive pyrimidines by Claisen rearrangement and reactivity in nucleophilic substitution at C2 and C4 in pteridines and pyrido[2,3-d]pyrimidines

Diversity oriented synthesis of fused pyrimidines leads to scaffolds with many biological activities. In the case of the preparation of pyrido[2,3-d]pyrimidines from 2-alkylthiopyrimidines, the formation of a new carbon-carbon bond at C5 is required, a reaction that is very limited in scope. However Claisen type rearrangement of simple 4-allylic ethers affords C5 substituted pyrimidines readily; in cases with an ester substituent, rearrangement occurs at room temperature. Subsequent cyclisation to afford 6-methylpyrido[2,3-d]pyrimidin-7(8H)-ones was achieved in high yield. Using allylic ethers derived from 3-chloromethyl-4-arylbut-3-en-2-ones as substrates, a new titanium[IV]chloride catalysed reaction affording 6-arylmethyl-7-methylpyrido[2,3-d]pyrimidines was discovered. In contrast, 2-alkylthiopteridines are readily available. In both cases, substitution at C2 and C4 to generate diversity has been carried out and the reactivity compared; yields of substitution products were generally higher with pteridine substrates. In biological assays unexpected hits were found for activity against the Gram positive bacterium, Nocardia farcinia, and against the parasite Trypanosoma brucei brucei, illustrating the value of diversity oriented synthesis in the discovery of biologically active compound

A Growth model for DNA evolution

A simple growth model for DNA evolution is introduced which is analytically solvable and reproduces the observed statistical behavior of real sequences.Comment: To be published in Europhysics Letter