Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications

Carefully designed molecules that are intimately related to the reaction mechanism of enzymes are often highly selective and potent inhibitors that serve as extremely useful chemical probes for understanding the reaction mechanism and structure of enzymes. This article describes the design, synthesis, and applications of specific inhibitors of two mechanistically distinct groups of enzymes, ATP-dependent amide ligases and Ser- and Thr-hydrolases. Our strategy is based on the premise that stable analogues of the transition state (transition-state analogues) are highly potent inhibitors that serve as good mechanistic probes, and that a key structure of a good inhibitor of one enzyme is also utilized for the inhibitors of other enzymes that share the same chemistry in their catalyzed reactions, irrespective of the degree of structural similarity and evolutionary link between the enzymes. According to these principles, we designed and synthesized a series of phosphinate- and sulfoximine-based transition-state analogue inhibitors of glutathione synthetase, gamma-glutamylcysteine synthetase and asparagine synthetase. For the second group of enzymes, we synthesized a gamma-monofluorophosphono glutamate analogue for mechanism-based affinity labeling of gamma-glutamyltranspeptidase and fluorescent phosphonic acid esters for the active-site titration of lipase. These inhibitors were used successfully as ligands for detailed kinetic analyses, X-ray crystallography, and mass analysis of the enzymes to identify the key amino acid residues responsible for catalysis and substrate recognition in the transition state.     

铝交联皂石的合成和表征及催化性能

用XRD、化学分析、IR、MASNMR、TPD等手段表征了合成皂石及其铝交联物的结构。结果表明:皂石的交联密度与四面体层电荷和交联条件(Al/土比)有关。在乙醇氨化反应中,交联皂石显示了较好的催化活性和选择性。皂石的交联密度与液相产物分布的关系表明层柱材料对此反应具有择形催化作用。醇氨化反应可能是在吸附态NH_3和气相醇分子间进行的。     

Terreinol--a novel metabolite from Aspergillus terreus: structure and C labeling

A novel metabolite from Aspergillus terreus, named terreinol, was isolated and its biosynthetic origin was determined by NMR based on the incorporation of [1-¹³C]-d-glucose. The labeling pattern indicated a predominant polyketide biosynthetic origin for this metabolite.     

不饱和链烃沸点的拓扑研究

基于邻接矩阵与边价 (fi)定义边价连接性指数 ( mF) ,其中的0 F ,1 F与 2 94种不饱和链烃 (包括烯烃、炔烃及烯炔烃 )的沸点 (Tb)关联 ,得到良好的数学模型 :ln( 70 0 -Tb) =6 5 2 3 3 1-0 0 0 4880 F2 -0 3 46771 F0 5(n =2 94,R =0 9979,R2 =0 995 8,F =3 490 4,S =5 12 ) ,该回归模型经Jackknife法检验具有总体稳健性 .可以预示 ,该指数将在定量构效关系研究中成为重要参数 .     

Potential of zero total charge of platinum single crystals: A local approach to stepped surfaces vicinal to Pt(111)

The electrochemical behavior of platinum single-crystal electrodes is revisited, with special emphasis on the determination of the potential of zero charge. We show that the measure of the charge displaced during CO adsorption allows the determination of the potential of zero total charge (PZTC). The estimation of the potential of zero free charge (PZFC) is discussed, with different degrees of approximation. The application of this methodology to the study of the PZTC of platinum stepped surfaces vicinal to Pt(111) reveals a marked decrease of the PZTC due to the introduction of surface steps. This effect is interpreted as the result of the existence of markedly smaller surface potentials localized on step sites. The importance of considering local aspects of the interface is emphasized with the use of N₂O reduction as a sensitive probe to the local structure of the surface. It is proposed that the different local maxima observed in the absolute value of the reduction current correspond to the local values of PZTC. It is shown that there is, in general, good agreement between the overall PZTC, obtained from the CO displacement, and that calculated from the local values inferred from the N₂O reduction. Further insight is obtained with the application of the laser-induced temperature jump method. This technique is useful to calculate the potential of maximum entropy of the double-layer formation. The resulting value of this potential for Pt(111) is discussed in the light of the PZFC value obtained from different approaches. For stepped surfaces vicinal to Pt(111), two local maxima in the entropy of the double layer are observed that are close to the local PZTC values estimated from the N₂O reduction. This result suggests the existence of cooperative effects in the organization of the water dipoles close to the electrode surface. Published in Russian in Elektrokhimiya, 2006, Vol. 42, No. 11, pp. 1275–1292. Based on the report delivered at the 8th International Frumkin Symposium “Kinetics of the Electrode Processes,” October 18–22, 2005, Moscow. The text was submitted by the authors in English.     

Cross-linking chemistry and biology: development of multifunctional photoaffinity probes

An efficient method of photoaffinity labeling has been developed based on rationally designed multifunctional photoprobes. Photoaffinity techniques have been used to elucidate the protein structure at the interface of biomolecules by the photochemical labeling of interacting sites. However, the identification of labeled sites within target proteins is often difficult. Novel biotinyl bioprobes bearing a diazirine photophore have contributed significantly to the rapid elucidation of ligand binding sites within proteins, thereby extending conventional photoaffinity methods. This article discusses the synthesis and applications of various photoprobes bearing a biotin, including strategies using cleavable linkages between photophores. The combination of photoaffinity methods with chip technology is also described as a novel entry to rapid affinity-based screening of inhibitors. This review focuses on a rapid and reliable photoaffinity method utilizing diazirine-based multifunctional photoprobes with numerous potential applications in functional proteomics of biomolecular interactions.     

Cp/mas 13c nmr and Electron Diffraction Study of Bacterial Cellulose Structure Affected by Cell Wall Polysaccharides

Acetobacter xylinum was cultured in Schramm–Hestrin medium containing pectin (pectin medium), xylan (xylan medium), or glucomannan (mannan medium). X-ray diffractometry revealed that xylan and glucomannan affected the size of the cellulose crystals and their d-spacing values. Solid-state cross polarization magic angle spinning carbon-13 nuclear magnetic resonance spectroscopy indicated that the ratio of cellulose I was reduced by the addition of polysaccharides. These effects were more remarkable on the cellulose in the mannan medium than that in the xylan medium, and were scarcely observed in the pectin medium. Electron diffraction analysis revealed that these effects on hemicelluloses along cellulose microfibrils are continuous in the mannan medium and discontinuous in the xylan medium. These findings suggest that the uronic acid in the polysaccharides prevents interactions with cellulose leading to alterations of the structure of the cellulose crystal.     

Actin-binding marine macrolides: total synthesis and biological importance

Marine organisms produce a fascinating range of structurally diverse secondary metabolites, which often possess unusual and sometimes unexpected biological activities. This structural diversity makes these marine natural products excellent molecular probes for the investigation of biochemical pathways. Recently, a number of novel and stereochemically complex macrolides, having a large macrolactone (22- to 44-membered) ring, that interact with the actin cycloskeleton have been isolated from different marine sources. Actin, like tubulin, is a major component of the cytoskeleton and has important cellular functions. Although the details of these interactions are still under investigation, these marine macrolides are becoming increasingly important as novel molecular probes to help elucidate the cellular functions of actin. Owing to their potent antitumor activities, these compounds, for example the aplyronines, also have potential for preclinical development in cancer chemotherapy. Their appealing molecular structures, with an abundance of stereochemistry, and biological significance, coupled with the extremely limited availability from the marine sources, have stimulated enormous interest in the synthesis of these compounds. This review summarizes the biological properties of these unusual marine natural products and features the recently completed total syntheses of swinholide A, scytophycin C, aplyronine A, mycalolide A--all of these being potent cytotoxic agents that target actin--and a diastereoisomer of ulapualide A. Rather than detailing each individual step of these multistep total syntheses, the different synthetic strategies, key reactions, and methods adopted for controlling the stereochemistry are compared.     

过渡金属羰基簇合物的键价计算和分析

本文运用原子簇化合物键价计算公式 ,对过渡金属羰基簇合物成键情况进行了分析 ,利用金属键轨道数 ,价非键轨道数和金属配体成键轨道数计算簇合物价轨道总数 .计算结果表明 :簇合物价轨道总数与金属键轨道数成线性关系 ,BT=9N -Bn.对于一般簇合物其价轨道总数与Lauher的EHMO计算结果 ,与唐敖庆的结构拓扑规则一致 ,对于反常的高核簇合物其价轨道总数与按化学式计算的 1/ 2VE相吻合     

Effects of Total Thermal Balance on the Thermal Energy Absorbed or Released by a High-Temperature Phase Change Material

Front tracking and enthalpy methods used to study phase change processes are based on a local thermal energy balance at the liquid–solid interface where mass accommodation methods are also used to account for the density change during the phase transition. Recently, it has been shown that a local thermal balance at the interface does not reproduce the thermodynamic equilibrium in adiabatic systems. Total thermal balance through the entire liquid–solid system can predict the correct thermodynamic equilibrium values of melted (solidified) mass, system size, and interface position. In this work, total thermal balance is applied to systems with isothermal–adiabatic boundary conditions to estimate the sensible and latent heat stored (released) by KNO3 and KNO3/NaNO3 salts which are used as high-temperature phase change materials. Relative percent differences between the solutions obtained with a local thermal balance at the interface and a total thermal balance for the thermal energy absorbed or released by high-temperature phase change materials are obtained. According to the total thermal balance proposed, a correction to the liquid–solid interface dynamics is introduced, which accounts for an extra amount of energy absorbed or released during the phase transition. It is shown that melting or solidification rates are modified by using a total thermal balance through the entire system. Finally, the numerical and semi-analytical methods illustrate that volume changes and the fraction of melted (solidified) solid (liquid) estimated through a local thermal balance at the interface are not invariant in adiabatic systems. The invariance of numerical and semi-analytical solutions in adiabatic systems is significantly improved through the proposed model.