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.     

Enhanced Kinetic Isotope Effect of the Phosphate-Catalyzed Proton Exchange in N,N'-Dimethylurea

The concerted mechanism of phosphate-catalyzed proton exchange in N,N'-dimethylurea has been studied. Kinetic data were measured using the technigue of NMR line-shape analysis. A significant kinetic isotope effect was observed for the concerted proton transfer in N,N'-dimethylurea and is attributed to the tunnelling effect.     

A New 4.0-Generation Dendrimer Phosphorescence Labeling Reagent and Its Application to Determination of Trace Alkaline Phosphatase by Affinity Adsorption Solid Substrate-room Temperature Phosphorimetry

A Triton X-100-4.0G-D （4.0G-D refers to a 4.0-generation dendrimer） was brought forward as a new phosphorescence labeling reagent. Two types of specific affinity adsorption （AA） reactions （direct method and sandwich method） were carried out between the labeling product of Triton X-100-4：0G-D-Wheat germ agglutinin （WGA） and alkaline phosphatase （ALP）, the product of AA reaction preserved the good characteristics of room temperature phosphorescence （RTP） of 4.0G-D and △Ip of the product was proportional to the content of ALP. According to the fact stated above, a new method for the determination of trace ALP by affinity adsorption solid substrate-room temperature phosphorimetry （AA-SS-RTP） was established on the basis of WGA labeled with the Triton X-100-4.0G-D. The detection limits were 0.20 ag·spot^-1 （corresponding concentration： 5.0×10^-16 g·mL^-1, namely 5.0×10^-18 mol·L^-1） for a direct method and 0.14 ag·spot^-1 （corresponding concentration： 3.5×10^-16 g·mL^-1, namely 3.5×10^-18 mol·L^-1） for a sandwich method, respectively. For their high sensitivity, good repeatability and high accuracy, the direct method and sandwich method have been successfully appfied to determine the content of ALP in human serum, and the results were coincided with the clinical detection results of the enzyme-linked immunosorbent assay method by the Zhangzhou Hospital of Traditional Chinese Medicine. Meanwhile, the mechanism for the determination of trace ALP by AA-SS-RTP was discussed.     

Improving the properties of the proton exchange membranes by introducing α-methylstyrene in the pre-irradiation induced graft polymerization

New proton exchange membranes (PEMs) were prepared by pre-irradiation induced grafting of α-methylstyrene (AMS)/styrene (STY)/divinylbenzene (DVB) into the crosslinked polytetrafluoroethylene (RX-PTFE) films and successively sulfonated. The new PEMs showed the improved glass transition temperature and chemical stability as compared with the PEMs prepared by pre-irradiation induced grafting of STY/DVB. The balance of the cost, grafting kinetic, thermal properties and the properties of the resulted proton exchange membrane is the key point of this work.     

Study of Structures and Electronic Properties of Pdn–1Pb and Pdn （n≤8） Clusters

Geometric and electronic properties of Pdn–1Pb and Pdn (n≤8) clusters have been studied by using density functional theory with effective core potentials, focusing on the differences between mono- and bimetallic clusters. The average bond length of Pdn–1Pb (n≤8) bimetallic clusters is longer than that of pure palladium clusters except for n = 2 and 3. The most stable structure of Pdn–1Pb (n≤7) is the singlet where there is at least a Pd or Pb atom on its excited state. The energy gaps of Pd–Pb binary clusters are narrower than those of Pdn clusters, and then the chemical activity is strengthened when Pdn clusters are doped with Pb.     

流通池光度滴定法应用—络合反应中的质子释放数测定

用具有流通池的分光光度计作测定装置,建立了由平衡移动法测定络合反应中质子释放数的新方法。方法简单、快速,仅用一个标准溶液,适于在变更pH值范围内金属离子不发生水解和没有其他副反应的体系。     

The influence of cyclodextrin complexation on proton transfer in piperidinomethyl-2-naphthol

Summary Piperidinomethyl-2-naphthol forms inclusion complexes with -cyclodextrin with an equilibrium constant of 265M ^–1 in aqueous solution. The proton transfer equilibrium between the neutral and the zwitterionic form is strongly influenced by the association.

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Der Einfluß der Komplexierung mit -Cyclodextrin auf das Protontransfer-Gleichgewicht in Piperidino-2-naphthol (Kurze Mitt.)

Zusammenfassung Piperidinomethyl-2-naphthol bildet Einschlußkomplexe mit -Cyclodextrin mit einer Gleichgewichtskonstante von 265M ^–1. Das Protontransfer-Gleichgewicht zwischen neutraler Form und zwitterionischer Struktur wird durch diese Assoziation stark beeinflußt.

     

The measurement of high proton affinities for a variety of metallic compounds: a new approach by flame-ion mass spectrometry

A small amount (≤ 10⁻⁶ mol fraction) of four alkaline earth metals, tin and yttrium were introduced into five, premixed, fuel-rich, H₂–O₂–N₂ flames at atmospheric pressure in the temperature range 1820–2400 K. Aqueous salt solutions of the metals were sprayed into the premixed flame gas as an aerosol using an atomizer technique. Ions in a flame were observed by sampling flame gas through a nozzle into a mass spectrometer. The concentrations of the major neutral metallic species present in the flame were calculated from thermodynamic data currently available. The principal metallic ions observed were AOH⁺ (A = Mg, Ca, Sr, Ba, Sn) and A(OH)₂⁺ (A = Y), formed initially by proton transfer to AO and OAOH from H₃O⁺, a natural flame ion. Except for Mg, the ions were also produced by chemi-ionization processes. By adjusting the concentration(s) of the salt solution in the atomizer, it was found that a pair of ions could be brought into equilibrium within the time scale of the flame; the pairs included H₃O⁺ with a metal ion or two metallic ions. Because water is a major product of combustion, a very large difference in proton affinity PA⁰(AO) − PA⁰(H₂O) ≤ 490 kJ mol⁻¹ (117 kcal mol⁻¹) could be attempted for the proton transfer equilibrium. Using PA⁰(H₂O) = 691.0 kJ mol⁻¹ (165.2 kcal mol⁻¹) as a reference base to anchor the proton affinity scale, ion ratio measurements led to proton affinity PA⁰ values of 766, 912, 1004, 1184, 1201, and 1222 kJ mol⁻¹ (183, 218, 240, 283, 287, and 292 kcal mol⁻¹) corrected to 298 K for OYOH, SnO, MgO, CaO, SrO, and BaO, respectively; of these, only the value for OYOH has not been reported previously. If it is assumed that the neutral thermodynamic data are correct (although some appear to be in error), the uncertainties in the PA results reported here are ± 21 kJ mol⁻¹ (5 kcal mol⁻¹). The realization that these equilibria can be achieved in flames provides a new approach to consolidate and build the high end of the proton affinity ladder, primarily of metallic species which are not accessible at lower temperatures.     

A role of non-hydrogen framework vibrational modes in formation of ferroelectric properties of H-bonded K3H(SO4)2-like materials

An effect of molecular vibrational modes within the dimers [O₃AO–(H/D)OAO₃]³⁻ on behavior of H-bond protons or deuterons is studied theoretically for H-bonded antiferroelectrics and quantum paraelectrics of the M₃(H/D)(AO₄)₂ family (M=alkali metal, A=S, Se). The ‘heavy’ reorganization modes in D-species of this family and both reorganization and promoting modes in corresponding H-analogues are examined. It is shown that the analysis with due regard for the reorganization modes results in insignificant decreasing of the effective tunneling frequency of light nuclei. Hence the reasonable estimations of the critical temperature of the low-temperature phase transition in M₃D(AO₄)₂ materials are available only with additional corrections related to potential profiles of a deuteron. It is noted that in the limits of the proposed model the promoting mode in the case of H-species can favor, in principle, the increasing as well as the decreasing of effective proton level splitting.     

Shape of the proton potential in an intramolecular hydrogen-bonded system. Part II

The crystals of 5,5′-dibromo-3-diethylaminomethyl-2,2′-biphenol N-oxide were studied by X-ray and FT-IR spectroscopy. Within this molecule two short OHO intramolecular hydrogen bonds are formed. The NO?H⁺?O⁻ bond between the OH and the N-oxide groups is very strong, of 2.419(7) Å between the oxygen atoms. The proton potential of this hydrogen bond is flat, broad and has probably no barrier—consequently it could not be located from X-ray diffraction data. The other hydrogen bond formed between two hydroxyl groups appears asymmetrical from FT-IR spectra, and shows also relatively limited proton polarizability. The molecular conformation is non-planar, due to strong overcrowding effect between the oxygen atoms involved in the hydrogen bonds.