Synthesis of poly-L-glutamates containing 5-substituted uracil moieties

The polymer reaction of cyclic derivatives of uracil and 5-bromouracil with polyacrylic and polymethacrylic acids, and poly-L-glutamic acid was studied in dimethylformamide solution. A similar reaction of cyclic derivatives of uridine with the polymeric acids was also made. Alkaline hydrolysis was further carried out on the polymers obtained.     

Incorporation of 5-substituted uracil derivatives into nucleic acids. Part IV.The synthesis of 5-ethynyluracil.

5-Acetyluracil (I) has been treated with POCI3 to give 5-(1-chlorovinyl)-2,4-dichloropyrimidine (II). Treatment of II with KOEt gave a mixture of 2-ethoxy-5-ethynyl-4 (3H)-pyrimidinone (IIIA) and 4-ethoxy-5-ethynyl-2 (1H)-pyrimidinone (IIIB). IIIA and IIIB were isolated and characterised. The mixture of IIIA and IIIB upon treatment with HCI gave 5(1-chlorovinyl)uracil (IV). Reaction of IV with KOEt gave 5-ethynyluracil (V). 5-Ethynyluracil was more easily obtained by the treatment of II with KOH in aqueous dioxan.     

Conformational analysis of TOAC-labelled alamethicin F50/5 analogues

In the preceding paper in this issue, we reported the total syntheses in solution of a set of four TOAC-containing analogues of the [L-Glu(OMe)(7,18,19)] F50/5 component of alamethicin, the prototype of peptaibol antibiotics forming channels in the biological membranes. In this article, we have expanded this work to the examination of their preferred conformation in solution by use of a combination of CD, FT-IR absorption, and NMR spectroscopies. The results are strongly in favor of the view that replacement of the Aib residues at positions 1, 8, and 16 with TOAC (both are members of the helicogenic sub-class of C(alpha)-tetrasubstituted alpha-amino acids) does not significantly affect the overwhelmingly populated alpha-helical 3D structure of alamethicin. The X-ray diffraction crystal structure of the N(alpha)-protected, C-terminal, hexapeptide amide segment Z-L-Pro-L-Val-(Aib)(2)-[L-Glu(OMe)](2)-Fol lends further support to our conformational conclusions.     

Incorporation of 5-substituted uracil derivatives into nucleic acids. The isolation and gamma-radiation-sensitivity of bacteriophage T3 containing the thymine analogue 5-vinyluracil.

A compound with properties identical with the glucose-containing dolichyl diphosphate oligosaccharide present in animal tissues was detected in alfalfa roots incubated with [14C]glucose. The products of mild acid hydrolysis behaved the same on paper chromatography, on treatment with specific glucosidases and on N-deacetylation.     

Synthesis and anticancer evaluation of certain alpha-methylene-gamma-(4-substituted phenyl)-gamma-butyrolactone bearing thymine, uracil, and 5-bromouracil

Certain alpha-methylene-gamma-(4-substituted phenyl)-gamma-butyrolactone bearing thymine, uracil, and 5-bromouracil were synthesized and evaluated for their anticancer activity. These compounds demonstrated a strong growth inhibitory activity against leukemia cell lines. The anticancer potency for the substituents of the lactone C(gamma)-phenyl is in an order of 4-Ph > 4-Cl, 4-Br > 4-Me, 4-NO2 > 4-F. For the pyrimidine portion, 5-bromouracil is more potent than uracil and thymine.     

Conformational transitions of uracil transporter UraA from Escherichia coli: a molecular simulation study

The Escherichia coli uracil/H + symporter UraA, known as the representative nucleobase/cation symporter 2(NCS2) protein, gets involved in several crucial physiological processes for most living organisms on Earth, such as the uptake of nucleobases and transport of vitamin C. Some experiments proposed a working model to explain proton-coupling and uracil transporting process of UraA on the basis of the crystal structure of NCS2 protein, but the details of conformational changes remained unknown. Thus, in order to make clear conformational changes caused by the protonation and deprotonation process of some conserved proton-coupled residues, the molecular dynamics simulation was used to study the conformation of UraA complexes in different protonation states. The results demonstrated that the protonation of residue Glu241 and Glu290 resulted in the whole conformational transition from the inward-open to the outward-open state. It can be concluded that Glu290 was crucial in a network of hydrogen-bonds in the middle of the core domain involving another essential residue, mainly including tyr288 in TM8, Tyr342, Ser338 in TM12, and the network of hydrogen-bonds was the key to maintain the stability of conformation. Protonation of Glu290 affects the stability of network of H-bond and changed the domains TM3 TM10 TM12. Thus, Glu290 may play a vital role as a ‘proton trigger’ that affects spatial structural of amino and residues near substrate binding side leading to an outward-open conformation transition.     

Dynamics of uracil and 5-fluorouracil in DNA

The prodrug 5-fluorouracil (5-FU), after activation into 5-F-dUMP, is an extensively used anticancer agent that inhibits thymidylate synthase and leads to increases in dUTP and 5-F-dUTP levels in cells. One mechanism for 5-FU action involves DNA polymerase mediated incorporation of dUTP and 5-F-dUTP into genomic DNA leading to U/A, 5-FU/A, or 5-FU/G base pairs. These uracil-containing lesions are recognized and excised by several human uracil excision repair glycosylases (hUNG2, hSMUG2, and hTDG) leading to toxic abasic sites in DNA that may precipitate cell death. Each of these enzymes uses an extrahelical base recognition mechanism, and previous studies with UNG have shown that extrahelical recognition is facilitated by destabilized base pairs possessing kinetically enhanced base pair opening rates. Thus, the dynamic properties of base pairs containing 5-FU and U are an important unknown in understanding the role of these enzymes in damage recognition and prodrug activation. The pH dependence of the (19)F NMR chemical shift of 5-FU imbedded in a model trinucleotide was used to obtain a pK(a) = 8.1 for its imino proton (10 °C). This is about 1.5 units lower than the imino protons of uracil or thymine and indicates that at neutral pH 5-FU exists significantly as an ionized tautomer that can mispair with guanine during DNA replication. NMR imino proton exchange measurements show that U/A and 5-FU/A base pairs open with rate constants (k(op)) that are 6- and 13-fold faster than a T/A base pair in the same sequence context. In contrast, these same base pairs have apparent opening equilibrium constants (αK(op)) that differ by less than a factor of 2, indicating that the closing rates (k(cl)) are enhanced by nearly equal amounts as k(op). These dynamic measurements are consistent with the previously proposed kinetic trapping model for extrahelical recognition by UNG. In this model, the enhanced intrinsic opening rates of destabilized base pairs allow the bound glycosylase to sample dynamic extrahelical excursions of thymidine and uracil bases as the first step in recognition.     

Conformational analysis of xyloglucans

Xyloglucan isolated from the elongating regions of pea stems was examined using X-ray diffraction and energy calculations. The X-ray fibre pattern suggested that the backbone (1----4)-beta-D-glucan takes an extended two-fold helix similar to common cellulose. In order to study side chains (xylosyl or fucosyl-galactosyl-xylosyl residues) of the polysaccharide, energetically preferable conformations were searched by calculation of interactions between non-bonded atom pairs. A stepwise calculation for the conformation of fucosyl-galactosyl-xylosyl residue gave 10 allowed area (phi-psi) maps which are useful to deduce xyloglucan conformations of both monocotyledons and dicotyledons in the walls of growing plant cells.     

Conformational analysis of poly-N-methyl-L-alanine

Sterically allowed forms of the poly-N-methyl-L -alanine chain were found by calculation of conformational energies as a function of the rotation angles of its chain bonds. The lowest energy form seems to be a right-handed, approximately threefold helix.     

Synthesis and antiherpesviral activity of 5-C-substituted uracil nucleosides

Reaction of 2'-deoxy-5-hydroxyuridine with some Wittig reagents gave 5-alkoxycarbonylmethyl-, 5-carbamoylmethyl-, 5-cyanomethyl-and 5-acetonyl-2'-deoxyuridines. The corresponding 1-beta-D-arabinofuranosyl derivatives were prepared from 1-beta-D-arabinofuranosyl-5-hydroxymethyluracil. The latter was also converted to 1-beta-D-arabinofuranosyl-5-vinyluracil via triphenylphosphonium salt, and then to 5-(2-halogenovinyl)derivatives. Some of these compounds showed marked antiherpesviral activity in vitro.     

Conformational energy analysis of melanostatin

Conformational energy calculations were carried out on the hypothalamic hormone melanostatin, a tripeptide with the primary structure H-L-Pro-L-Leu-Gly-NH2. The calculated lowest energy conformation was a type II beta bend, very similar to that reported in an X-ray crystal study. This conformation, however, was only one of 109 low-energy structures (less than or equal to 3 kcal/mol above the global minimum), indicating that the molecule in solution exists as an ensemble of conformations and is very flexible, in agreement with relaxation data from n.m.r. measurements. A statistical analysis yielded an average end-to-end distance of 6.8 A and a bend probability of 0.62, suggesting that, in nonpolar solvents, bend structures predominate within the statistical ensemble. The statistical analysis, however, also yielded a probability of only 0.11 for the occurrence of a 4 leads to 1 hydrogen bond. Hence, the calculations show that, although bend conformations predominate, bends would be difficult to observe in solution if the experiments were designed only to detect 4 leads to 1 hydrogen bonds.     

Conformational analysis of methyl 5-O-methyl septanosides: effect of glycosylation on conformer populations

Methyl 5-O-methyl-alpha-d-glycero-d-idoseptanoside (3) and methyl 5-O-methyl-beta-d-glycero-d-guloseptanoside (4) were investigated as (1-->5)-linked di-/oligoseptanoside mimetics. Here we report the synthesis of 3 and 4 and describe their preferred solution conformations through a combination of ab initio/DFT calculations and (1)H (3)J(H,H) NMR coupling constant analysis. The conformations of 3 and 4 observed in this study are discussed in comparison to those of the parent (C5 hydroxy) compounds 1 and 2. The results indicate that methyl 5-O-methyl-alpha-septanoside 3 is relatively rigid and adopts the same (3,4)TC(5,6) conformation as 1. Methyl 5-O-methyl-beta-septanoside 4 is somewhat less rigid than its parent septanoside (2). In addition to the (6,O)TC(4,5) conformation adopted by 2, beta-septanoside 4 also populates the adjacent (3,4)TC(5,6) conformation. Glycosylation at C5 on beta-septanoside 4 therefore increases its overall flexibility and allows access to alternative ring conformations.     

Conformational analysis of substituted pyrrolidones

Consistent force-field calculations were performed on a series of methyl substituted pyrrolidones. Methyl substitution enhances the non-planarity of the pyrrolidone ring in a way wich varies with the position of the substituent. The effect of ring distortion is to produce skeletal contributions to the rotatory strength of the nπ* transition of the amide group. Depending on position of substitution, these reinforce or oppose the substituent contribution to optical activity. There is favorable agreement between the conformational calculations and the quadrant rule for the optical activity of the nπ* transition of the peptide chromophore.     

Conformational analysis of peracetylated hexononitriles

The conformations of six peracetylated hexononitriles in solution have been investigated by Fourier-transform, proton n.m.r. spectroscopy at 90 MHz, with iterative analysis and simulation of many of the spectra. The conformation of tetra-O-acetyl-L-arabinononitrile has been re-examined by the same methods. A shift reagent [Eu(fod)₃-d₃₀] and spectra at 220 MHz were used to improve spectral dispersion, where necessary. For practically all of the derivatives studied, the vicinal, proton-proton coupling-constants are consistent with a zigzag conformation in which the cyano group lies in the plane of the other carbon atoms of the chain, unless this conformation contains a parallel 1,3-interaction of substituents. Other conformers that are also consistent with the coupling constants observed are discussed, including rotamers about chain-terminal, carbon-carbon bonds.