Homology modeling,docking and structure-based pharmacophore of inhibitors of DNA methyltransferase

DNA methyltransferase 1 (DNMT1) is an emerging epigenetic target for the treatment of cancer and other diseases. To date, several inhibitors from different structural classes have been published. In this work, we report a comprehensive molecular modeling study of 14 established DNTM1 inhibitors with a herein developed homology model of the catalytic domain of human DNTM1. The geometry of the homology model was in agreement with the proposed mechanism of DNA methylation. Docking results revealed that all inhibitors studied in this work have hydrogen bond interactions with a glutamic acid and arginine residues that play a central role in the mechanism of cytosine DNA methylation. The binding models of compounds such as curcumin and parthenolide suggest that these natural products are covalent blockers of the catalytic site. A pharmacophore model was also developed for all DNMT1 inhibitors considered in this work using the most favorable binding conformations and energetic terms of the docked poses. To the best of our knowledge, this is the first pharmacophore model proposed for compounds with inhibitory activity of DNMT1. The results presented in this work represent a conceptual advance for understanding the protein–ligand interactions and mechanism of action of DNMT1 inhibitors. The insights obtained in this work can be used for the structure-based design and virtual screening for novel inhibitors targeting DNMT1.     

Total Synthesis of Everninomicin 13,384-1-Part 1: Synthesis of the A(1)B(A)C Fragment

The powerful antibiotic everninomicin 13,384-1 (1, Ziracin) has been prepared for the first time through a total synthesis. The 1-->1'-disaccharide and the two orthoesters of this target molecule were introduced by new methodologies using a tin acetal and 1,2-phenylseleno migrations. The reaction sequence also relies on stereoselective glycosidations and subtle manipulations of protecting groups. In addition to the introduction of new synthetic methodologies, this total synthesis should allow the preparation of combinatorial libraries of semisynthetic analogues of this highly promising antibiotic for biological screening purposes.     

Influence of process parameters on the epoxidation of 2-buten-1-ol over titanium silicalite TS-1 catalyst

The influence of process parameters on the epoxidation of 2-buten-1-ol with 30 % hydrogen peroxide using the titanium silicalite TS-1 is presented. The studies were carried out under autogenic pressure (in autoclave). Methanol was used as a solvent in this process. The influence of temperature, 2-buten-1-ol to hydrogen peroxide mole ratio, amount of solvent used, TS-1 catalyst content, and reaction time on the reaction was studied. The major product of this reaction, 2,3-epoxybutan-1-ol (EB), has numerous applications in chemical industry.     

Paramagnetic 1H NMR spectrum of the cobalt(II) derivative of spinach plastocyanin

The native type 1 copper ion of spinach plastocyanin has been substituted with Co(II). The UV/vis spectrum of this derivative is similar to those for other Co(II)-substituted cupredoxins. The paramagnetic 1H NMR spectrum of Co(II) plastocyanin has been completely assigned. A number of similar studies on Co(II) cupredoxins have been published, but this is the first such analysis of a substituted plastocyanin that possesses the archetypal type 1 active site. A truly representative comparison of the available paramagnetic 1H NMR data for Co(II) cupredoxins is now possible. We demonstrate in this work that there is very little difference in the metal-ligand contacts between the Co(II) derivatives of cupredoxins possessing a type 1 axial site (plastocyanin) and those having perturbed (rhombic) spectroscopic features.     

间二氟苯溴化反应产物的气相色谱-质谱分析

采用气相色谱-质谱(GC/MS)法对间二氟苯溴化反应产物的组成与结构进行了分析,并对间二氟苯溴化反应的选择性及反应条件进行了初步探讨。结果表明:间二氟苯的溴化反应具有较强的选择性,其主要反应产物为1-溴-2,4-二氟苯,副产物为1-溴-2,6-二氟苯、1-溴-3,5二氟苯及二溴代间二氟苯等溴化物。该反应的反应条件对产物组成有较大影响。     

Biological deodorization of dimethyl sulfide using different fabrics as the carriers of microorganisms

Biological deodorization of dimethyl sulfide (DMS) was studied using nine unwoven fabrics as the carriers of microorganisms in a laboratory-scale deodorizing system. The activated carbon fabric FN-200CF-15 was the best packing material compared with other packing materials used, on the basis of removal rate. The maximum removal rate (Vm), evaluated by using Michaelis-Menten equation, was 2.28 g-Skg-dry fab.^-1 day^-1 in this fabric biofilter. The critical load of DMS in this fabric biofilter was dependent on space velocity (SV), determined as 0.78 and 0.66 g-Skg-dry fab.^-1 at SV 100 and 150 h^-1, respectively. Strain IM1 isolated from the carbon fabric FN-200CF-15 biofilter in modified Waksman (MW) medium successfully degraded DMS as well as hydrogen sulfide (H2S), methanethiol (MT), and dimethyl disulfide (DMDS) in batch test. The DMS removal rates (g-S cell^-1h-¹) by this strain measured in batch culture and calculated in FN-200CF-15 biofilter by the cell numbers appeared in MW medium were found almost equal, indicating that strain IM1 may be the dominant microorganism in this biofilter.     

The importance of the long type 1 copper-binding loop of nitrite reductase for structure and function

The long 15-residue type 1 copper-binding loop of nitrite reductase has been replaced with that from the cupredoxin amicyanin (7 residues). This sizable loop contraction does not have a significant effect on the spectroscopy, and therefore, the structures of both the type 1 and type 2 Cu(II) sites. The crystal structure of this variant with Zn(II) at both the type 1 and type 2 sites has been determined. The coordination geometry of the type 2 site is almost identical to that found in the wild-type protein. However, the structure of the type 1 centre changes significantly upon metal substitution, which is an unusual feature for this class of site. The positions of most of the coordinating residues are altered of which the largest difference was observed for the coordinating His residue in the centre of the mutated loop. This ligand moves away from the active site, which results in a more open metal centre with a coordinating water molecule. Flexibility has been introduced into this region of the protein. The 200 mV increase in the reduction potential of the type 1 copper site indicates that structural changes upon reduction must stabilise the cuprous form. The resulting unfavourable driving force for electron transfer between the two copper sites, and an increased reorganisation energy for the type 1 centre, contribute to the loop variant having very little nitrite reductase activity. The extended type 1 copper-binding loop of this enzyme makes a number of interactions that are important for maintaining quaternary structure.     

Spectroscopic investigations and crystal structure from synchrotron powder data of the inclusion complex of beta-cyclodextrin with atenolol

Inclusion complexes of atenolol with beta-cyclodextrin (beta-CD) in aqueous solution have been investigated with (1)H NMR and UV-vis spectroscopy. The stoichiometry of this inclusion complex was established to be equimolar (1:1) and its stability constant was determined by UV-vis spectroscopy. The crystal structure of the beta-CD-atenolol (1:1) inclusion compound has been solved from synchrotron powder diffraction data using direct-space search techniques. The crystal structure model and (1)H NMR data are in good agreement and, with support of Hyperchem MM+ molecular dynamics results, suggest which protons are likely to be involved in the inclusion process that leads to the supramolecular architecture of this guest-host complex.     

卵磷脂反胶束体系中β-1，4葡萄糖苷酶的研究

测定了水、醋酸缓冲液和水杨苷醋酸 /醋酸钠缓冲液在水 /PC/庚烷 正丁醇反胶束体系中的饱和增溶量 ,利用UV、FT IR和NMR等技术考察了增溶到水 /PC/庚烷 正丁醇反胶束体系中的 β 1 ,4葡萄糖苷酶及水杨苷的结构变化 ,并研究了 β 1 ,4葡萄糖苷酶在水 /PC/庚烷 正丁醇反胶束中的活性 .发现了 β 1 ,4葡萄糖苷酶在水 /PC/庚烷 正丁醇反胶束中遵循米氏反应 ,最大反应速度vmax为 1 .475mg·min-1,是其在水中的 1 1 .8倍 ,米氏常数Km 为 0 .389mg·mL-1,是其在水中的 1 / 2 5 .β 1 ,4葡萄糖苷酶在水 /PC/庚烷 正丁醇反胶束中表现出的低底物浓度下的高催化速度 ,是微乳的界面发生的相互作用改变了 β 1 ,4葡萄糖苷酶的构象 ,增加了底物水杨苷的浓度 ,PC极性头部 -N (CH3 ) 3 正离子作用水杨苷糖苷键的氧有利于糖苷键的断裂等因素造成的 .     

Competitive potentiometric determination of binding constants between α-cyclodextrin and 1-alkanols

The binding constants of 1-alkanols with α-cyclodextrin (α-CD) were determined by indirect competitive potentiometry, although potentiometry is usually inapplicable to nonionic compounds. This novel method utilizes competitive binding of 1-alkanol and octyltrimethylammonium bromide (OTAB) to α-CD in aqueous media, where the concentration of free OTAB depending on the competitive binding is monitored with an OTAB-selective electrode. Therefore, the concentration of 1-alkanol is indirectly estimated from the observed electromotive force. The binding constants of 1-propapnol, 1-butanol, 1-hexanol, and 1-octanol with α-CD, obtained by this method, are close to the literature values. The implications and limitations of this indirect competitive potentiometry were discussed.     

Synthesis and photochemistry of 1-iodocyclohexene: influence of ultrasound on ionic vs. radical behaviour

Simultaneous application of UV light and ultrasonic irradiation to a reaction mixture containing 1-iodocyclohexene is reported. The irradiation of 1-iodocyclohexene in methanol was carried out with or without addition of zinc. The effect of ultrasound or mechanical stirring on this solid-liquid system was also compared. The irradiation of 1-iodocyclohexene in methanol in the presence of zinc increases the yield of the nucleophilic trapping product, compared with the yield after irradiation in the absence of zinc. The photodegradation of 1-iodocyclohexene was slightly accelerated after addition of zinc. A rapid formation of radical product was accompanied by substantial decrease of 1-iodocyclohexene after application of ultrasound and irradiation without the zinc. The ultrasound significantly affects the photobehaviour of this reaction, predominantly its radical route. The joint application of ultrasound and zinc contributes positively to the production of radical and ionic products. The sonochemical stirring is more effective than mechanical stirring.     

Synthesis of labeled 1-amino-2-methylenecyclopropane-1-carboxylic acid, an inactivator of 1-aminocyclopropane-1-carboxylate deaminase

1-Amino-2-methylenecyclopropane-1-carboxylic acid (2-methylene-ACC) is an irreversible inhibitor for a bacterial enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which catalyzes the conversion of ACC to alpha-ketobutyrate and ammonia. The inactivation has been proposed to proceed with the ring scission induced by an addition of an enzyme nucleophile, resulting in the formation of a reactive turnover product that then traps an active-site residue. To gain further insight into this unique enzymatic reaction, the tritiated 2-methylene-ACC was prepared and incubated with ACC deaminase to locate and identify the entrapped amino acid residue. The synthesis of this radiolabeled compound and the results of its incubation with ACC deaminase are reported in this paper.     

Effect of pH on the self-exchange reactivity of the plant plastocyanin from parsley

The self-exchange rate constant (25 degrees C) for parsley plastocyanin is 5.0 x 10(4) M-1 s-1 at pH* 7.5 (I = 0.10 M). This value is quite large for a higher plant plastocyanin and can be attributed to a diminished upper acidic patch in this protein. The self-exchange rate constant is almost independent of pH* in the range 7.5-5.6, with a value (25 degrees C) of 5.6 x 10(4) M-1 s-1 at pH* 5.6 (I = 0.10 M). At this pH*, the ligand His87 is protonated in approximately 50% of the reduced protein molecules (pKa* 5.6), and this would be expected to hinder electron transfer between the two oxidation states. However, this effect is counterbalanced by the enhanced association of two parsley plastocyanins at lower pH* due to the partial protonation of the acidic patch.     

The fluorescence mechanism of 5-methyl-2-pyrimidinone: an ab initio study of a fluorescent pyrimidine analog

The photophysically important potential energy surfaces of the fluorescent pyrimidine analog 5-methyl-2-pyrimidinone have been explored using multireference configuration-interaction ab initio methods at three levels of dynamical correlation, all of which support a fluorescence mechanism. At vertical excitation S1 (dark, n(N)pi*) and S2 (bright, pipi*) are almost degenerate at 4.4 eV, with S3 (dark, n(O)pi*) at 5.1 eV. The excited system can follow the S1-S2 seam of conical intersections, accessible from the Franck-Condon region, to its minimum and then evolve from this conical intersection on the S1 (pipi*) surface to a global minimum. At lower levels of correlation, the S1 surface shows two minima separated by a barrier of up to 0.18 eV. The secondary minimum found at the lower levels of correlation becomes the global minimum with higher correlation. The S1 population at this minimum can be trapped from accessing the lowest energy S0-S1 (pipi*/gs) conical intersection by an energy gap at least 0.3-0.4 eV higher than the S1 minimum. The calculated emission energy from this minimum is 2.80 eV. Gradient pathways connecting important S1 geometries are presented, as well as other excited state conical intersections.     

氨基酸卟啉锌配合物对氨基酸酯的分子识别研究(英文)

用紫外可见吸收光谱滴定方法研究了一种新型的苏氨酸卟啉锌配合物(主体)对氨基酸酯(客体)的分子识别.这种锌卟啉可以与氨基酸酯形成 1:1和 1:2的两种加合物.氨基酸酯的氨基首先与氨基酸残基的羧基作用形成 1:1的加合物,然后与锌卟啉的中央锌原子配位形成 1:2的加合物,客体分子与主体分子上的氨基酸残基之间的排斥作用以及主客体之间的色散力作用是主体分子能识别客体分子的另外两种作用。     

土卫六大气中H2和N+反应的动力学研究

依据Titan大气的压强和温度条件计算了N++H2→NH++H反应的热化学函数. 结果发现, 该反应是一个吸热反应, 在Titan的低温环境中不具有反应自发性. 运用量子化学理论计算研究了反应的动力学性质, 发现该反应在300 K温度下的反应速率k=4.16×10−10 cm3•mol−1•s−1, 在实验室温度下(298.15 K)的反应势垒是109.847 kJ•mol−1. 依据Titan电离层气压温度条件计算了90 Pa压强条件下1 K到5000 K温度范围内(极低温度和极高温度)的 反应活化能和反应速率, 研究发现低温下该反应的反应速率非常低, 而且, 随着温度的降低, 反应速率急剧降低. 理论计算值和文献中的实验值也符合得较好, 理论计算数据可以为星际分子的模拟实验提供一定的参考.     

Binding free energy of several sterols to the N-terminal domain of Niemann-Pick C1-like 1 protein due to mutation: Molecular dynamics study

The membrane protein Niemann-Pick type C1-like 1 (NPC1L1) plays a central role in the absorption of cholesterol in the small intestine. Other sterols, notably vitamin E and vitamin K1 also utilize NPC1L1 as a membrane transporter even though other absorption paths exist. Many NPC1L1 mutations causing the disease due to poor transport of cholesterol are known. It is not clear at this moment if the same mutation can lead to reduced transport behavior with these vitamins. In this study, we have obtained the binding free energies of these two sterols using molecular dynamics simulation and compared these values with the cholesterol-binding free energy. The N-terminal domain (NTD) of the wild as well as the disease-causing two mutations, T61M and L110F, are used for this purpose. The result indicates that the mutations show reduced binding affinity compared to the wild except for the vitamin K1 in the T61M mutant, which has increased binding free energy. Also, we found the similarity of the key amino acids responsible for the change of free energy by mutation between T61M and L110F. At the same time, non-negligible differences exist also.     

Electronic energy levels in all-trans long linear polyenes: the case of the 3,20-di(tert-butyl)-2,2,21,21-tetramethyl-all-trans-3,5,7,9,11,13,15,17,19-docosanonaen (ttbp9) conforming to Kasha's rule

The absorption, fluorescence and fluorescence excitation spectra for 3,20-di(tert-butyl)-2,2,21,21-tetramethyl-all-trans-3,5,7,9,11,13,15,17,19-docosanonaen (ttbP9) in dilute solutions of 2-methylbutane were recorded at temperatures over the range 120-280 K. The high photostability of this nonaene allows us to assert that it exhibits a single fluorescence and that this can be unequivocally assigned to emission from its 1(1)B(u) excited state, it being the first excited electronic state. Available photophysical data for this polyene and the wealth of information reported for shorter all-trans polyenes allow us to conclude that if the first excited electronic state for the chromophore possessed 2(1)A(g) symmetry, then the energy of such a state might have been so close to that of the 1(1)B(u) state that: 1) the radiationless internal conversion mechanism would preclude the observation of the emission from the 1(1)B(u) state reported in this work and 2) the 2(1)A(g) state reached through internal conversion would be vibrationally coupled to 1(1)B(u) and would facilitate the detection of the emission from 2(1)A(g), which was not observed in any of the solvents used in this work. The spectroscopic and photochemical implications of these findings for other polyenes are discussed.     

Ring-chain tautomerism of 1-hydroxyphthalans. An examination of structural effects

1,3-Dihydro-1-isobenzofuranol,(1-hydroxyphtha1an) and 2-(hydroxymethyl)-benzaldehyde exist in a tautomeric equilibrium. The effects of molecular structure on this equilibrium was examined using various derivatives of dihydroisobenzofuranol. Two effects of this molecular modification were identified: (i) 1-arylmethyl substituents favored the ring-opened tautomer if steric effects arose in the ring closed form and (ii) extending the conjugated system of the dihydroisobenzofuran ring (i.e. dihydronaphtho[2,3-c] furan also favored the ring-opened form. These effects are discussed.