A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects.This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing.The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.     

A generalization of the Rouse-Zimm model

The idea of consistently averaging the hydrodynamic interaction and its various consequences for Hookean dumbbells are reviewed. For long chains this idea can be used to generalize the Rouse-Zimm model for polymer solutions. Unlike the usual Rouse-Zimm model, the new model for steady shear flow predicts a nonzero second normal stress coefficient and shear rate dependent material functions. In the limit of long chains, the viscosity and the normal stress coefficients are universal functions of the reduced shear rate.This paper was presented at the Frühjahrstagung des Fachausschusses Polymerphysik der Deutschen Physikalischen Gesellschaft at Kaiserslautern (West Germany), March 12–14, 1986.     

DNA光复活作用机理研究中的模型化合物

用模型化合物模拟光解酶诱导的DNA光复活作用，能深入认识其作用机理。介 绍了用于DNA光复活机理研究的各种模型化合物的合成，并综述了由模型化合物研 究得到的光复活机理，以及底物嘧啶二聚体的修复效率受外界因素的影响。     

Solvent effect on heats of protonation of some amines

The heats of protonation of n-pentylamine, dipentylamine, tributylamine and heats for the first protonation step of 1,8-diamino-3,6-dioxaoctan, diazacrownether 22 and cryptand 222 in pure acetonitril and propylene carbonate and of diazacrownether 22 and dibenzosubstituted ligand 22BB in water + acetonitrile mixtures have been measured at 298.15 K using calorimetric titrations. The values of the reaction enthalpies in the solvents as well as the data in aqueous and methanol solutions reported in literature are analysed in terms of the simple electrostatic model and thermodynamic parameters of transfer (solvation) of the reactants. Estimation of the electrostatic and covalent contributions to standard enthalpy of transfer of the reactions from water to non-aqueous and mixed solvents has been made.     

Preparation and characterization of fused-silica capillary columns coated with <Emphasis Type="Italic">m</Emphasis>-carborane–siloxane copolymers for gas chromatography

The carborane–siloxane copolymers Dexsil 300, a 34.5% bis(dimethylsilyl)-m-carborane–65.5% dimethylsiloxane copolymer, and Dexsil 400, a 24.9% bis(dimethylsilyl)-m-carborane–50.8% dimethyl, 24.3% methylphenylsiloxane copolymer, were coated on fused silica capillary columns and their gas chromatographic properties were evaluated. Their selectivity was evaluated using both Rohrschneider–McReynolds constants and triacylglycerol indices. The bis(dimethylsilyl)-m-carborane unit turned out to be equivalent to two dimethylsiloxy units and one half of a diphenylsiloxy unit. The m-carborane unit was found to cause a 15–25 K shift in the elution temperature between 120 and 360 °C. The working range was from 20 and 0 °C to 380 °C for Dexsil 300 and Dexsil 400, respectively. The column bleeding levels at 380 °C were below 20 and 15 pA for Dexsil 300 and Dexsil 400, respectively.     

黄素酶的模拟

本综述介绍模拟黄素酶的进展, 涉及两条途径: 半合成黄素酶和黄素酶模型化合物。     

Structure and properties of the dinuclear complex [Co2(μ-OAc)2(OAc)2(μ-H2O)(phen)2]

The dinuclear complex [Co₂(μ-OAc)₂(OAc)₂(μ-H₂O)(phen)₂] has been prepared and its structure was determined. The compound crystallizes in the monoclinic space group P2(1)/c. The Co–Co distance is 3.574 Å and is similar to the Fe–Fe distance in the reduced methane monooxygenase hydroxylase. The electronic and IR spectra of the complex confirm octahedral coordination of the cobalt atoms and formation of strong O–HO hydrogen bonds in the solid state. The dependence of the magnetic susceptibility of the complex on temperature indicates an antiferromagnetic interaction, the value of the isotropic exchange parameter J was estimated to be −2.1 cm⁻¹. The ¹H NMR spectra show that in organic solvents the structure of compound is the same as in the solid state, however, in water solution the complex dissociates giving compounds with different Co:phen ratios.     

Kinetics of adsorption and desorption of Pb(II) in aqueous solution on activated carbon by two-site adsorption model

The adsorption and desorption equilibrium and kinetics of lead ions from aqueous solutions on a granular activated carbon (GAC) were examined. Rapid increase followed by slow increase in Pb(II) amount on the GAC was observed as a function of time for the adsorption, while rapid decrease and consecutive very slow decrease was observed in desorption. Based on the experimental results, a two-site adsorption model was proposed for the adsorption and the desorption of Pb(II) under the study conditions. The Pb(II) adsorption on the GAC was estimated to have simultaneously occurred on the strong and the weak adsorption sites. Conventional Langmuir-type kinetic equations were introduced to quantitatively predict the adsorption and desorption with the two-site model by optimizing the parameters to fit the equilibrium and the kinetic experimental results. The equilibrium and kinetic experimental results could be represented by the equations by using one set of the common Langmuir parameters. Resultant kinetic parameters revealed that the adsorption equilibrium constant was two orders of magnitude greater for strong adsorption site than for weak adsorption site, though the maximum number of weak adsorption site was 1.5 times as great as that of strong adsorption site. The strong adsorption equilibrium constant resulted from a small desorption rate constant for the site. The equations were demonstrated to be applicable for predicting other desorption performances as well.     

Modeling research in low-medium temperature geothermal field, Tianjin

The geothermal reservoir in Tianjin can be divided into two parts: the upper one is theporous medium reservoir in the Tertiary system; the lower one includes the basement reservoir inLower Paleozoic and Middle-Upper Proterozoic. Hot springs are exposed in the northern mountainand confined geothermal water is imbedded in the southern plain. The geothermal reservoir is in-cised by several fractures. In recent years, TDS of the geothermal water have gone up along withthe production rate increasing, along the eastern fracture zone (Cangdong Fracture and West Bai-tangkou Fracture). This means that the northern fracture system is the main seepage channel ofthe deep circulation geothermal water, and the reservoir has good connection in a certain area anddefinite direction. The isotopic research about hydrogen and carbon chronology indicates that themain recharge period of geothermal water is the Holocene Epoch, the pluvial and chilly period of20 kaBP. The karst conduits in weathered carbonate rocks of the Proterozoic and Lower Paleozoicand the northeast regional fracture system are the main feeding channels of Tianjin geothermalwater. Since the Holocene epoch, the geothermal water stayed at a sealed warm period. Thetracer test in WR45 doublet system shows that the tracer test is a very effective measure forunderstanding the reservoir's transport nature and predicting the cooling time and transportvelocity during the reinjection. 3-D numerical simulation shows that if the reinjection well keeps asuitable distance from the production well, reinjection will be a highly effective measure to extractmore thermal energy from the rock matrix. The cooling of the production well will not be a problem.