Polycyclic nitrogen heterocycles as potential thymidine phosphorylase inhibitors: synthesis, biological evaluation, and molecular docking study

New polycyclic heterocycles were synthesised and evaluated as potential inhibitors of thymidine phosphorylase (TP). Inspired by the pharmacophoric pyrimidinedione core of the natural substrate, four series have been designed in order to interact with large empty pockets of the active site: pyrimidoquinoline-2,4-diones (series A), pyrimidinedione linked to a pyrroloquinoline-1,3-diones (series B and C), the polycyclic heterocycle has been replaced by a pyrimidopyridopyrrolidinetetraone (series D). In each series, the tricyclic nitrogen heterocyclic moiety has been synthesised by a one-pot multicomponent reaction. Compared to 7-DX used as control, 2d, 2l, 2p (series A), 28a (series D), and the open intermediate 30 showed modest to good activities. A kinetic study confirmed that the most active compounds 2d, 2p are competitive inhibitors. Molecular docking analysis confirmed the interaction of these new compounds at the active binding site of TP and highlighted a plausible specific interaction in a pocket that had not yet been explored.

Self-healing and reprocessable bromo butylrubber based on combined ionic cluster formation and hydrogen bonding

The properties of modified bromobutyl rubber are strongly influenced by competing interactions via hydrogen bridges and ionic cluster formation. Dynamic network formation enables self-healing and reprocessability of the material.

Synthesis of uracil nucleotide analogs with a modified, acyclic ribose moiety as P2Y(2) receptor antagonists

A series of new uracil nucleotide analogs (monophosphates, triphosphates, and phosphonates) was synthesized, in which the ribose moiety was replaced by acyclic chains, including branched or linear alkyl or dialkylether linkers. 1-omega-Bromoalkyluracil derivatives (2) were converted to the corresponding alcohols by treatment with sodium hydroxide and subsequently phosphorylated using phosphorus oxychloride followed by hydrolysis to yield the monophosphates, or by coupling with diphosphate to form the triphosphates. Reaction of 2 with triethyl phosphite followed by deprotection with trimethylsilyl bromide led to the omega-phosphonylalkyluracil derivatives. These products could be further phosphorylated by converting them into their imidazolides and subsequent treatment with diphosphate yielding the corresponding UTP analogs. Nucleoside analogs with an oxygen atom in the 2'-position, which are more similar to the natural ribosides, were synthesized from silylated uracil and trimethylsilyl iodide-treated 1,3-dioxolane, or 1,3-dioxane, respectively, and subsequently phosphorylated by standard procedures. The nucleotide analogs were investigated in a functional assay at NG108-15 cells, a neuroblastomaxglioma hybrid cell line which expresses the UTP- and ATP-activated nucleotide receptor subtype P2Y(2). The acyclic nucleotide analogs were generally weaker ligands than UTP, and-in contrast to UTP-they were antagonistic. The most potent compound was diphosphoric 5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)pentylphosphonic anhydride (5c) with an IC(50) value of 92microM showing that the replacement of the alpha-phosphate by phosphonate, which leads to enhanced stability, was well tolerated.

Effects of oligoDNA template length and sequence on binary self-assembly of a nucleotide bolaamphiphile

Templated self-assembly of nucleotide bolaamphiphile 1 (in which a 3'-phosphorylated thymidine moiety is connected to each end of a long oligomethylene chain) with a 10-, 20-, 30-, or 40-meric single-stranded oligoadenylic acid (2, 3, 4, or 5) led to the formation of right-handed helical nanofibers in 0.1x Tris/EDTA (TE) buffer solutions. The helical pitch increased as the length of the oligoadenylic acid template increased. DNA composed of oligoadenylic and oligocytidylic acid sequences (6, 7, and 8) also acted as templates to induce the formation of helical nanofiber structures. The diameter of the nanofibers remained constant (6-6.6 nm) irrespective of the template used. The binary self-assembly of 1 with 4 also produced higher-order, double-stranded nanofibers.

Stacking conformation of 9-[omega-(thymin-1-yl)alkyl]adenine in aqueous solution

An intramolecular stacking between adenine and thymine rings of 9-[omega-(thymin-1-yl)alkyl]adenine was investigated by means of NMR and UV spectroscopy. The stacking conformation was presumed on the basis of the temperature dependence on the chemical shifts of the adenine and thymine ring protons in the buffer solution at pD 7.0.

Internucleobase-interaction-directed self-assembly of nanofibers from homo- and heteroditopic 1,omega-nucleobase bolaamphiphiles

The complementary 1,omega-thymine, 1,omega-adenine, and 1,omega-(thymine, adenine) bolaamphiphiles, [N,N'-bis[3-(2,4-dihydroxy-5-methylpyrimidine-1-yl)propionyl]1,n-diaminoalkane [T-n-T (n = 10, 11, 12)], N, N'-bis[3-(6-aminopurine-9-yl)propionyl]1,n-diaminoalkane [A-n-A (n = 10, 11, 12)], and N-[3-(2,4-dihydroxy-5-methylpyrimidine-1-yl)propionyl], N'-[3-(6-aminopurine-9-yl)propionyl]1,n-diaminoalkane [T-n-A (n = 10, 11, 12)], respectively] have been synthesized. The spontaneous homo- and heteroassembly of these nucleobase-based bolaamphiphiles has been studied by light microscopy, energy-filtering transmission electron microscopy, FT-IR, and powder X-ray diffraction analyses. The achiral T-10-T bolaamphiphile produced in 10% ethanolic/aqueous solutions unprecedented double-helical ropes of 1-2 microm in widths and several hundred micrometers in length, whereas the complementary homologue A-10-A gave only microcrystalline solids of 1-10 microm in size. In contrast, an equimolar mixture of T-10-T and A-10-A yielded supramolecular fibers of 15-30 nm in width. (1)H NMR, CD, and UV studies of solution photoreactions of T-10-T suggested that under natural light the chiral rope formation is triggered by photodimerization of trace amounts of the thymine moieties in the T-10-T assemblies. Complementary hydrogen bond formation between the thymine-adenine heterobase pairs was found to prevent such a photoreaction and resulted in no chiral rope formation. The heteroditopic T-12-A bolaamphiphile self-assembled to form supramolecular fibers. Multilamellar organization was proposed for the homo- and heteroassemblies made of T-n-T and A-n-A.

Conformational effects on photophysical characteristics of C5-C5'-linked dihydrothymine dimers in solution

Photophysical characteristics of N-substituted C5-C5'-linked dihydrothymine dimers (1a,b[meso], meso compounds of [5R,5'S]-bi-5,6-dihydrothymines; 1a,b[rac], racemic compounds of [5R,5'R]-bi-5,6-dihydrothymines and [5S,5'S]-bi-5,6-dihydrothymines) in aqueous solution with varying contents of less-polar aprotic solvent such as tetrahydrofuran or dioxane have been investigated by UV-absorption, and steady-state and time-resolved fluorescence spectroscopies. Among the C5-C5'-linked dimers, (5R,5'S)-bi-5,6-dihydro-1-methylthymine (1a[meso]) showed a red-shifted weak UV-absorption band at 270-350 nm and excimer fluorescence emission at lambda max = 370 nm with a quantum yield (phi F) of approximately 0.1 in phosphate buffer (pH < 10) at 293 K. Racemic compound of 5,6-dihydro-1-methylthymine dimer (1a[rac]), meso and racemic compounds of 5,6-dihydro-1,3-dimethylthymine dimers (1b[meso] and 1b[rac]) in phosphate buffer were nonfluorescent under similar conditions. The UV-absorption and fluorescence spectral characteristics of 1a[meso] in aqueous solution were interpreted in terms of intramolecular stacking interactions between the dihydropyrimidine chromophores leading to a preferential "closed-shell" conformation both in the ground state and the excited singlet state. In basic solutions at pH > pKa = 11.7, the fluorescence quantum yield of 1a[meso] decreased due to a dominant "open-shell" conformation resulting from the electrostatic repulsion between the deprotonated dihydrothymine chromophores of 1a[meso] in a dianion form.

Design, synthesis, and enzymatic evaluation of multisubstrate analogue inhibitors of Escherichia coli thymidine phosphorylase

A series of acyclic phosphonate derivatives of thymine has been synthesized and tested as multisubstrate analogue inhibitors of Escherichia coli thymidine phosphorylase. The compounds synthesized include 1-(phosphonoalkyl)thymines with six to nine methylenes (1-4, respectively); 1-[(Z)-4-phosphonomethoxy-2-butenyl]thymine (5) and its butyl and 2,3-cis-dihydroxybutyl derivatives (6 and 7, respectively); 1-[(Z)-(4-(phosphonomethoxy)methoxy)-2-butenyl]thymine (8) and also its butyl and 2,3-cis-dihydroxybutyl analogues (9 and 10); and 1-[((Z)-4-(phosphonomethoxy)-2-butenoxy)methyl]thymine (11). Evaluation of these compounds against E. coli revealed significant enzymatic inhibition by 2, 3, 4, 6, and 8 at a concentration of 1000 microM, 3 and 4 being the most potent. Replacement of the thymine base in 3 by 6-amino-5-bromouracil and 7-deazaxanthine afforded compounds 12 and 13, which showed a pronounced improvement of TPase inhibition, comparable to 7-deazaxanthine. When inorganic phosphate was used as a variable substrate, compounds 12 and 13 displayed competitive kinetics with respect to phosphate, indicating a direct interaction of these compounds with the phosphate binding site. Also compounds 12 and 13 were found to be competitive inhibitors of TPase against thymidine as a variable substrate. These results are consistent with the compounds being multisubstrate analogue inhibitors of E. coli TPase, and they represent the first example of such TPase inhibitors.