Mouse thymidylate synthase does not show the inactive conformation,observed for the human enzyme

Crystal structures of mouse thymidylate synthase (mTS) in complexes with (1) sulfate anion, (2) 2′-deoxyuridine 5′-monophosphate (dUMP) and (3) 5-fluoro-dUMP (FdUMP) and N ^5,10-methylenetetrahydrofolate (meTHF) have been determined and deposited in Protein Data Bank under the accession codes 3IHI, 4E5O and 5FCT, respectively. The structures show a strong overall similarity to the corresponding structures of rat and human thymidylate synthases (rTS and hTS, respectively). Unlike with hTS, whose unliganded and liganded forms assume different conformations (“inactive” and “active,” respectively) in the loop 181–197, in each of the three mTS structures, the loop 175–191, homologous to hTS loop 181–197, populates the active conformer, with catalytic Cys 189 buried in the active site and directed toward C(6) of the pyrimidine ring of dUMP/FdUMP, pointing to protein’s inability to adopt the inactive conformation. The binary structures of either dUMP- or sulfate-bound mTS, showing the enzyme with open active site and extended C-terminus, differ from the structure of the mTS–5-FdUMP–meTHF ternary complex, with the active site closed and C-terminus folded inward, thus covering the active site cleft. Another difference pertains to the conformation of the Arg44 side chain in the active site-flanking loop 41–47, forming strong hydrogen bonds with the dUMP/FdUMP phosphate moiety in each of the two liganded mTS structures, but turning away from the active site entrance and loosing the possibility of H-bonding with sulfate in the sulfate-bound mTS structure.     

Tyrosine nitration affects thymidylate synthase properties

Highly purified preparations of thymidylate synthase, isolated from calf thymus, and L1210 parental and FdUrd-resistant cells, were found to be nitrated, as indicated by a specific reaction with anti-nitro-tyrosine antibodies, suggesting this modification to appear endogenously in normal and tumor tissues. Each human, mouse and Ceanorhabditis elegans recombinant TS preparation, incubated in vitro in the presence of NaHCO(3), NaNO(2) and H(2)O(2) at pH 7.5, underwent tyrosine nitration, leading to a V(max)(app) 2-fold lower following nitration of 1 (with human or C. elegans TS) or 2 (with mouse TS) tyrosine residues per monomer. Enzyme interactions with dUMP, meTHF or 5-fluoro-dUMP were not distinctly influenced. Nitration under the same conditions of model tripeptides of a general formula H(2)N-Gly-X-Gly-COOH (X = Phe, Tyr, Trp, Lys, Arg, His, Ser, Thr, Cys, Gly), monitored by NMR spectroscopy, showed formation of nitro-species only for H-Gly-Tyr-Gly-OH and H-Gly-Phe-Gly-OH peptides, the chemical shifts for nitrated H-Gly-Tyr-Gly-OH peptide being in a very good agreement with the strongest peak found in (15)N-(1)H HMBC spectrum of nitrated protein. MS analysis of nitrated human and C. elegans proteins revealed several thymidylate synthase-derived peptides containing nitro-tyrosine (at positions 33, 65, 135, 213, 230, 258 and 301 in the human enzyme) and oxidized cysteine (human protein Cys(210), with catalytically critical Cys(195) remaining apparently unmodified) residues.     

Large blue-shift in the optical spectra of fluorinated polyphenylenevinylenes. A combined theoretical and experimental study

Modifications of the optical properties of poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] induced by fluorination of the vinylene units are investigated by means of time dependent density functional theory (TD-DFT) calculations and spectroscopic measurements in solution. The energy of the main absorption peak is blue-shifted by more than 0.8 eV in the fluorinated polymers. TD-DFT excitation energies for non-fluorinated and fluorinated oligomer structures of increasing number of monomers, employing fully relaxed geometries, are compared to the experimental absorption energies of the polymers. We found that the measured large blue-shift induced by the fluorination of the vinylene units is not caused by the electron-withdrawing effect of the fluorine substituents but it is related to a steric effect. The inter-monomer torsional angle of the fluorinated structures increases above 50 degrees , while in the non-fluorinated systems it is below 20 degrees . Further insight into the origin of the large blue-shift of the excitation energies is gained by a detailed analysis of the torsional potentials of non-fluorinated and fluorinated dihydroxystilbene. While for planar geometries the energy gap increases due to fluorination, it decreases for highly distorted geometries. In addition, we found that the torsional potential of dihydroxystilbene is rather flat, meaning that different isomers might, e.g., in the solid state, coexist.     

Synthesis of 2‐amino‐4‐oxo‐5‐substitutedbenzylthiopyrrolo[2,3‐d]‐pyrimidines as potential inhibitors of thymidylate synthase

A series of ten novel 2‐amino‐4‐oxo‐5‐[(substitutedbenzyl)thio]pyrrolo[2,3‐d]pyrimidines 2‐11 were synthesized as potential inhibitors of thymidylate synthase and as antitumor agents. The analogues contain various electron withdrawing and electron donating substituents on the benzylsulfanyl ring of the side chains and were synthesized from the key intermediate 2‐amino‐4‐oxo‐6‐methylpyrrolo[2,3‐d]pyrimidine, 14 . Appropriately substituted benzyl mercaptans were appended to the 5‐position of 14 via an oxidative addition reaction using iodine, ethanol and water. The compounds were evaluated against human, Escherichia coli and Toxoplasma gondii thymidylate synthase and against human, Escherichia coli and Toxoplasma gondii dihydrofolate reductase. The most potent inhibitor, ( 6 ) which has a 4′‐methoxy substituent on the side chain, has an IC₅₀=25 μM against human thymidylate synthase. Contrary to analogues of general structure 1 , electron donating or electron withdrawing substituents on the side chain of 2‐11 had little or no influence on the human thymidylate synthase inhibitory activity.     

Computational Analysis and Biological Activities of Oxyresveratrol Analogues,the Putative Cyclooxygenase-2 Inhibitors

Polyphenols are a large family of naturally occurring phytochemicals. Herein, oxyresveratrol was isolated from ethanolic crude extracts of Artocarpus lacucha Buch.-Ham., and chemically modified to derive its lipophilic analogues. Biological screening assays showed their inhibitory potency against cyclooxygenase-2 (COX-2) with very low cytotoxicity to the MRC-5 normal cell lines. At the catalytic site of COX-2, docking protocols with ChemPLP, GoldScore and AutoDock scoring functions were carried out to reveal hydrogen bonding interactions with key polar contacts and hydrophobic pi-interactions. For more accurate binding energetics, COX-2/ligand complexes at the binding region were computed in vacuo and implicit aqueous solvation using M06-2X density functional with 6-31G+(d,p) basis set. Our computational results confirmed that dihydrooxyresveratrol (4) is the putative inhibitor of human COX-2 with the highest inhibitory activity (IC₅₀ of 11.50 ± 1.54 µM) among studied non-fluorinated analogues for further lead optimization. Selective substitution of fluorine provides a stronger binding affinity; however, lowering the cytotoxicity of a fluorinated analogue to a normal cell is challenging. The consensus among biological activities, ChemPLP docking score and the binding energies computed at the quantum mechanical level is obviously helpful for identification of oxyresveratrol analogues as a putative anti-inflammatory agent.     

Pyrrolo[2,3-d]pyrimidine thymidylate synthase inhibitors: design and synthesis of one-carbon bridge derivatives

A series of novel pyrrolo[2,3-d]pyrimidine derivatives was designed and synthesized as thymidylate synthase (TS) inhibitors. Molecular design was performed on the human TS complex model built on the basis of the reported structure of TS-deoxyuridinemonophosphate (dUMP)-CB3717 ternary complex. From a docking study, we expected that a one-carbon bridge between pyrrolo[2,3-d]pyrimidine and an aromatic ring was suitable. Moreover, we found that the bridge carbon could be replaced with an alkyl group to fill out the unoccupied space. Based on this design, we synthesized five pyrrolo[2,3-d]pyrimidine derivatives with one-carbon bridge and evaluated their TS inhibitory activities. All synthesized compounds inhibited TS more potently than compound 2 (LY231514), and the C8-ethyl analogue (7) showed a remarkable inhibitory activity against TS (IC50=0.017 microM).     

Discriminative affinity labelling of opioid receptors by enkephalin and morphiceptin analogues containing 3-nitro-2-pyridinesulphenyl-activated thiol residues.

The thiol groups of leucinthiol, cysteamine and cysteine incorporated into opioid peptides enkephalin and morphiceptin were activated by the 3-nitro-2-pyridinesulphenyl (Npys) group to form mixed disulphides highly reactive to a free thiol. Enkephalin analogues containing Npys-leucinthiol or -cysteine at positions 4, 5 and 6 exhibited high affinities for both mu and delta receptors, while morphiceptin analogues containing Npys-cysteine at positions 4 and 5 showed relatively weak affinity only for mu receptors. When these S-activated opioid peptides were incubated with rat brain membrane preparations, it was found, by binding assay using radiolabelled and non-labelled [D-Ala2,MePhe4,Gly-ol5]enkephalin, that they label mu opioid receptors in a dose-dependent manner. The concentrations required to label half of the receptors were 0.2-2 microM for enkephalins and 10-30 microM for morphiceptins. These results suggested that the thiol group labelled by S-activated enkephalins and morphiceptins is present in the ligand binding site of receptor protein, but not in GTPase-binding protein.     

Synthesis and characterization of fluoronitroaryl azo diaminobenzene chromophores

The novel fluoronitroaryl azo diaminobenzene chromophores for potential NLO applications were synthesized and the effects of the position of the fluorine group on the properties of the chromophores were investigated. These chromophores exhibit high decomposition temperatures whilst keeping molecular hyperpolarizabilities similar to those of the non-fluorinated analogues. The chromophore 2,4-diamino-4′-fluoro-3′-nitroazobenzene (2R-4F-3N-DIAMINE) shows a significant UV blue shift and a combination of good transparency, high thermal stability and nonlinearity in comparison with 2,4-diamino-2′-fluoro-5′-nitroazobenzene (2R-2F-5N-DIAMINE) and its non-fluorinated analogue 2,4-diamino-3′-nitroazobenzene (2R-3N-DIAMINE).     

Time-dependent density functional theory calculations of the photoabsorption of fluorinated alkanes

Time-dependent density functional theory (TD-DFT) calculations of the transition energies and oscillator strengths of fluorinated alkanes have been performed. The TD-DFT method with the non-local B3LYP potential yields transition energies for the methanes, which are smaller by about 10% as compared to the experimental values. An empirical linear correlation was found between the calculated and experimental transition energies both at the B3LYP/DZ+Ryd(C, F) and B3LYP/cc-pVTZ+Ryd(C, F, H) levels for a total of 19 transitions of the fluorinated methanes with linear correlation coefficients of 0.987 for the former and 0.988 for the latter. This empirical correlation for fluorinated methane molecules is found to agree well with the previously obtained empirical correlations between calculated and experimental values for non-fluorinated molecules. The results show that a single empirical-correlation relationship can be used for both non-fluorinated and fluorinated molecules to predict transition energies. This linear relationship is then used to predict the photoabsorption spectra of ethane, propane, butane, and partially and fully fluorinated derivatives. A key result of these calculations is the dominance of Rydberg transitions in the spectral region of interest.     

Nonclassical 5-substituted tetrahydroquinazolines as potential inhibitors of thymidylate synthase

Classical inhibitors of thymidylate synthase such as N^l0-propargyl-5,8-dideazafolic acid (1), N-(5-[N-(3,4-dihydro-2-methyl-4-oxoquinazolin-6-ylmethyl)-N-methylamino]-2-thenoyl)-L-glutamic acid (ZD1694, 2) and N-[2-amino-4-oxo-3,4-dihydro(pyrrolo[2,3-d]pyrintidin-5-yl)ethylbenzoyl]-L-glutamic acid (LY231514, 3) while potent, suffer from a number of potential disadvantages, such as impaired uptake due to an alteration of the active transport system required for their cellular uptake, as well as formation of long acting, non-effluxing polyglutamates via the action of folylpolyglutamate synthetase, which are responsible for toxicity. To overcome some of the disadvantages of classical inhibitors, there has been considerable interest in the synthesis and evaluation of nonclassical thymidylate synthase inhibitors, which could enter cells via passive diffusion. In an attempt to elucidate the role of saturation of the B-ring of non-classical, quinazoline antifolate inhibitors of thymidylate synthase, analogues 7-17 were designed. Analogues 13-17 which contain a methyl group at the 7-position, were synthesized in an attempt to align the methyl group in an orientation which allows interaction with tryptophan-80 in the active site of thymidylate synthase. The synthesis of these analogues was achieved via the reaction of guanidine with the appropriately substituted cyclohexanone-ketoester. These ketoesters were in turn synthesized via a Michael addition of the appropriate thiophenol with 2-carbethoxycyclohexen-1-one or 5-methyl-2-carbethoxycyclo-hexen-1-one to afford a mixture of diastereomers. The most inhibitory compound was the 3,4-dichloro, 7-methyl derivative 17 which inhibited the Escherichia coli and Pneumocystis carinii thymidylate syntheses 50% at 5 × 10⁵ M. Our results confirm the importance of the 7-CH₃ group and electron withdrawing groups on the aromatic side chain for thymidylate synthase inhibition.     

Fluorine-19 nuclear magnetic resonance and biochemical characterization of fluorotyrosine-labeled-thymidylate-synthetase

Fluorotyrosine has been incorporated into thymidylate synthetase from Lactobacillus casei by growth of the bacterium in media containing 3-fluorotyrosine. The enzyme exhibited a specific activity 70% of that of the normal enzyme and formed a covalent binary complex with pyrimidine nucleotides, as well as a covalent ternary complex with 5-fluorodeoxyuridylate and 5,10-methylenetetrahydrofolate. ¹⁹F nuclear magnetic resonance spectroscopy has been used to follow the formation of these complexes. 5-Fluorodeoxyuridylate, dUMP, dTMP and dCMP produced identical conformational changes in the enzyme as monitored by the fluorotyrosyl resonances. Ternary complex formation of the fluorotyrosine-containing enzyme with 5-fluorodeoxyuridylate and 5,10-methylenetetrahydrofolate resulted in further spectral changes.     

NMR studies on 4‐thio‐5‐furan‐modified and 4‐thio‐5‐thiophene‐modified nucleosides

Systematic NMR characterization of 4‐thio‐5‐furan‐pyrimidine nucleosides or 4‐thio‐5‐thiophene‐pyrimidine nucleosides (ribonucleosides and 2′‐deoxynucleosides) was performed. All proton and carbon signals of 4‐thio‐5‐thiophene‐ribouridine and related analogues were unambiguously assigned. The orientations of the base (4‐thiouridine or its deoxy analogue) relative to the ring (furan or thiophene) are explored by a NMR approach and further supported by X‐ray crystallographic studies. The procedures presented here would be applicable to other modified nucleosides and nucleotides. Copyright © 2016 John Wiley & Sons, Ltd.     

Synthesis of novel chiral compounds of purine and pyrimidine bases

The physiologically active groups such as purine and pyrimidine bases are introduced to the asymmetric ynthesis. The optically pure compounds bearing purine and pyrimidine bases (5a—5e) were prepared via the asymetric Michael addition reaction of purines and pyrimidines as Michael donators with the chiral source 5-(R)-[(1R, 2S, 5R)-menthyloxy]-2(5H)-furanone (3a), which was prepared from the natural chiral auxiliary (-)-menthol. The synthetic method was studied in detail and the new compounds were identified on the basis of their analytical data and spectroscopic data, such as [α]_D~(20), IR, UV, ~1H NMR, ~(13)C NMR and MS. The absolute configuration of 5a was established by X-ray crystallography. The results provided an efficient synthetic route to chiral purines and pyrimidine analogues, and offered chiral sources for further research on the physiologically active compounds of chiral nucleotides.     

基于2,4-二丙稀酰胺嘧啶的氢键复合物的稳定性和光谱

氢键对含有以嘧啶为基的衍生物的生命体具有重要作用。用AM1 和 DFT 方法对2,4-二丙稀酰胺嘧啶(2,4-BAAP) 衍生物与1-取代的脲嘧啶形成的氢键复合物电子结构进行理论研究。用INDO/SCI 和 B3LYP/6-31G(d)方法分别计算了复合物的UV和NMR光谱。结果表明,由于结合能为负值,两单体能通过三重氢键形成复合物,取代基存在时结合能变小。这种削弱效应取决于电子效应和空间效应的协同作用。当2,4-BAAP上哌啶基存在时,由于异构复合物的形成,复合物的结合能变小。供电基存在时复合物的能隙变小。共轭体系的扩展使复合物易于注入电子和空穴。复合物电子光谱的第一吸收峰与母体相比发生红移由于其具有较小的LUMO-HOMO能隙。在13C NMR谱中,复合物C=O键上的C原子的化学位移向低场移动。     

Direct observation of the participation of flavin in product formation by thyX-encoded thymidylate synthase

The synthesis of thymine for DNA is catalyzed by the enzyme thymidylate synthase (TS). A family of flavin-dependent TSs encoded by the thyX gene has been discovered recently. These newly discovered TSs require a reducing substrate in addition to 2'-deoxyuridine monophosphate (dUMP) and 5,10-methylenetetrahydrofolate (CH2THF), suggesting that the enzyme-bound flavin is a redox intermediary in catalysis. The oxidation of the reduced flavin of the TS from Campylobacter jejuni has been observed directly upon mixing with dUMP and CH2THF under anaerobic conditions, thus providing the first direct demonstration of its redox role in catalysis. Product analysis showed that the one mole of 2'-deoxythymidine monophosphate is formed along with one mole of tetrahydrofolate for each mole of reduced enzyme-bound flavin. The classic TS inactivator 5-fluoro-2'-deoxyuridine monophosphate (FdUMP) was able to bind to the reduced enzyme but was unable to oxidize the flavin, even in the presence of CH2THF. Furthermore, the nucleotide binding site of the enzyme treated with FdUMP and CH2THF was irreversibly blocked, suggesting the formation of a stable substrate adduct analogous to that formed by the well-studied thyA-encoded TS. The formation of inactivated enzyme without flavin oxidation indicates that methylene transfer from the folate to the nucleotide occurs prior to flavin redox chemistry.     

Sinularia属珊瑚中嘧啶类化合物的分离与鉴定

分离和鉴定了采自中国南海硇州岛软珊瑚Sinularia Bassica样本中新的嘧啶类化合物。样本用工业酒精提取,提取物溶液经乙酸乙酯萃取后,萃取物经硅胶柱层析,以极性不断增大的溶剂体系(石油醚-乙酸乙酯、氯仿-甲醇)梯度洗脱,再经过HPLC分离,得到2,4(1H,3H)-嘧啶二酮、5-甲基-2,4(1H,3H)-嘧啶二酮、1,3-二甲基-2,4(1H,3H)-嘧啶二酮和5-甲氧基-1,3-二甲基-2,4(1H,3H)-嘧啶二酮4种新的嘧啶类化合物,其结构通过红外光谱、1HNMR和13C NMR等光谱数据分析确定。     

Vapour phase chemistry of oxovanadium iv β-diketonates

A series of fluorinated and one non-fluorinated β-diketonate complexes of oxovanadium IV have been prepared, their gas phase IR spectra examined, vapour pressures determined and their vapour phase thermal decomposition investigated. Decomposition of the fluorinated complexes occurred according to the overall reaction scheme VO(β-diket)₂»VOF₂ + Furanone. The furanones C₅HF₅O₂, C₅H₄F₂O₂ and C₈H₁₀F₂O₂ were isolated and identified. The non-fluorinated complex gave the parent diketone and a vanadium oxide as its principal products.     

5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies

Summary We applied the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) approach to evaluate relative stability of the extended (flat) and C-shaped (bent) solution conformational forms of the 5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) molecule in aqueous solution. Calculations indicated that both forms have similar free energies in aqueous solution but detailed energy components are different. The bent solution form has lower intramolecular electrostatic and van der Waals interaction energies. The flat form has more favorable solvation free energy and lower contribution from the bond, angle and torsion angle molecular mechanical internal energies. We exploit these results and combine them with known crystallographic data to provide a model for the progressive binding of the mTHF molecule, a natural cofactor of thymidylate synthase (TS), to the complex forming in the TS-catalyzed reaction. We propose that at the time of initial weak binding in the open enzyme the cofactor molecule remains in a close balance between the flat and bent solution conformations, with neither form clearly favored. Later, thymidylate synthase undergoes conformational change leading to the closure of the active site and the mTHF molecule is withdrawn from the solvent. That effect shifts the thermodynamic equilibrium of the mTHF molecule toward the bent solution form. At the same time, burying the cofactor molecule in the closed active site produces numerous contacts between mTHF and protein that render change in the shape of the mTHF molecule. As a result, the bent solution conformer is converted to more strained L-shaped bent enzyme conformer of the mTHF molecule. The strain in the bent enzyme conformation allows for the tight binding of the cofactor molecule to the productive ternary complex that forms in the closed active site, and facilitates the protonation of the imidazolidine N10 atom, which promotes further reaction. *To whom correspondence should be addressed. Fax: +4822-822-5342; E-mail: a.jarmula@nencki.gov.pl     

Chemical modelling of the thymidylate synthase reaction: evidence for the formation of an exocyclic methylene intermediate from analogues of the covalent ternary complex formed by intramolecular thiol addition to C(6) of 5-aminomethyluracil derivatives.

The intramolecular thiol addition to C(6) in 1-(3-mercaptopropyl)-5-aminomethyluracil derivatives in protic media leads to the formation of bicyclic; 5,6-dihydrouracil derivatives, which maybe regarded as models of the covalent ternary complex in the thymidylate synthase reaction. Evidence is presented for the formation of an exocyclic methylene intermediate from these model compounds.     

Separation of fluorinated amino acids and oligopeptides from their non-fluorinated counterparts using high-performance liquid chromatography

Chromatographic conditions for the separation of fluorinated amino acids and oligopeptides from their non-fluorinated counterparts were explored. The separation of six pairs of analytes, including both aromatic and aliphatic fluorocarbons, was investigated at various temperatures using both hydrocarbon and fluorocarbon columns and eluents. Our results show that when hydrocarbon eluents are used, fluorocarbon column provides better separation of fluorinated amino acids or oligopeptides from their non-fluorinated counterparts; when fluorocarbon eluents are used, hydrocarbon column provides better separation of fluorinated amino acids or oligopeptides from their non-fluorinated counterparts. These chromatographic behaviors reflect the fluorophilicity possessed by fluorinated amino acids and oligopeptides.