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.     

The role of radicals in enzymatic processes

Research on the mechanism of action of coenzyme B12, adenosylcobalamin, as a graduate student introduced the author to the field of organic free radicals in enzymology. Twenty years later, related work on S-adenosylmethionine (SAM) as a "poor man's coenzyme B12" was initiated in a detailed analysis of the mechanism of action of lysine 2,3-aminomutase (LAM). The interconversion of L-lysine and L-beta-lysine is catalyzed by LAM, which requires SAM, pyridoxal-5'-phosphate (PLP), and a [4Fe-4S] cluster as coenzymes. The mechanism of this reaction has been delineated as a radical isomerization, in which radical formation is initiated by the [4Fe-4S]-dependent cleavage of the SAM into methionine and the 5'-deoxyadenosyl radical. The mechanism of this process is discussed, together with the role of this radical in hydrogen abstraction from lysine to initiate the substrate radical isomerization. The chemistry underlying the functions of SAM, PLP, and [4Fe-4S] in the action of LAM is novel in all respects, except for the formation of a lysine-PLP aldimine at the active site. Of the four free radicals in the mechanism, three have been characterized by EPR spectroscopy. In the suicide inactivation of adenosylcobalamin-dependent dioldehydrase (DDH) by glycolaldehyde, the formation of cob(II)alamin and 5'-deoxyadenosine is accompanied by the conversion of glycolaldehyde to cis-ethanesemidione radical at the active site. The cis-ethanesemidione radical has been characterized by EPR spectroscopy. Its exceptional stability at the active site is the basis for the inactivation of DDH by glycolaldehyde.     

Thermodynamic molecular switch in sequence‐specific hydrophobic interactions

This communication will demonstrate the existence of a thermodynamic molecular switch in the pairwise, sequence‐specific hydrophobic interaction of Ile–Ile, Leu–Ile, Val–Leu, or Ala–Leu over the temperature range of 273–333 K reported by Nemethy and Scheraga in 1962. Based on Chun's development of the Planck–Benzinger methodology, the change in inherent chemical bond energy at 0 K, ΔH°(T₀), is 3.0 kcal mol^?1 for Ile–Ile, 2.4 for Leu–Ile, 1.8 for Val–Leu, and 1.2 kcal mol^?1 for Ala–Leu. The value of ΔH°(T₀) decreases as the length of the hydrophobic side chain decreases. It is clear that the strength and stability of the hydrophobic interaction is determined by the packing density of the side chains, with Ala–Leu being the most stable. At 〈T_m〉, the thermal agitation energy, $\int^{T}_{0}\Delta Cp^{\circ}(T)\,dT$, is about five times greater than ΔH°(T₀) in each case. Additionally, the thermal agitation energy for the same series, evaluated at 〈T_m〉, decreases in the same order, that is, as the length of the side chain decreases. This pairwise, sequence‐specific hydrophobic interaction is highly similar in its thermodynamic behavior to that of other biological systems, except that the negative Gibbs free energy change minimum at 〈T_s〉 occurs at a considerably higher temperature, 355 K compared to about 300 K. The melting temperature, 〈T_m〉, is also high, 470 K compared to 343 K in a biological system. The implication is that the negative Gibbs free energy minimum at a well‐defined 〈T_s〉 has it origin in the hydrophobic interactions, which are highly dependent on details of molecular structure. In addition to the four specific dipeptide interactions described, we have shown in our unpublished work the existence of a thermodynamic molecular switch in the interactions of 32 dipeptides wherein a change of sign in ΔCp°(T)_reaction leads to a true negative minimum in the Gibbs free energy of reaction, and hence, a maximum in the related K_eq. Indeed, all interacting biological systems that we have thus far examined using the Planck–Benzinger approach point to the universality of thermodynamic molecular switches. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Integrated Microanalytical System Coupling Permeation Liquid Membrane and Voltammetry for Trace Metal Speciation. Technical Description and Optimization

A new minicell coupling the liquid‐liquid extraction technique called permeation liquid membrane (PLM) with an integrated Ir‐based Hg‐plated microelectrode array for voltammetric detection has been developed for the speciation of heavy metals in natural waters. Lead and cadmium have been used as model compounds. The PLM consists of a carrier (0.1 M 22DD+0.1 M lauric acid) dissolved in 1 : 1 mixture of toluene/phenylhexane held in the small pores (30 nm) of a hydrophobic polypropylene membrane (Celgard 2500). One side of this membrane is in contact with a flowing source solution, containing the metal ions of interest. An acceptor or strip solution (pyrophosphate) is placed on the other side of the PLM with the microelectrode array placed at 480 μm of the PLM. The analyte is transported by the carrier from the source solution to the strip solution. The originality of the new minicell is that accumulation in the strip solution is voltammetrically followed by the integrated microelectrode array in real time, and at low concentration level, using square‐wave anodic stripping voltammetry (SWASV). In order to protect the Hg microelectrodes from the adsorption of the hydrophobic carrier, the microelectrodes are embedded in a thin gel layer (280 μm) of 1.5% LGL agarose gel containing 10% of hydrophobic silica particles C18. The choice of optimum conditions is discussed in details in this article. Due to the very small effective strip volume of the new cell (less than 1 μL), high enrichment factor can be obtained (e.g., 330 for Pb) after 2 hours of accumulation. No deaeration of the solutions is required for SWASV measurements. Detection limits under these conditions are 2 pM and 75 pM for Pb and Cd, respectively, using a voltammetric deposition time of 5 min. In addition, no fouling effects were observed with natural water samples.     

On the Temperature–Pressure Free‐Energy Landscape of Proteins

We studied the thermodynamic stability of a small monomeric protein, staphylococcal nuclease (Snase), as a function of both temperature and pressure, and expressed it as a 3D free‐energy surface on the p,T‐plane using a second‐order Taylor expansion of the Gibbs free‐energy change ΔG upon unfolding. We took advantage of a series of different techniques (small‐angle Xray scattering, Fourier‐transform infrared spectroscopy, differential thermal analysis, pressure perturbation calorimetry and densitometry) in the evaluation of the conformation of the protein and in evaluating the changes in the thermodynamic parameters upon unfolding, such as the heat capacity, enthalpy, entropy, volume, isothermal compressibility and expansivity. The calculated results of the free‐energy landscape of the protein are in good agreement with experimental data of the p,T‐stability diagram of the protein over a temperature range from 200 to 400 K and at pressures from ambient pressure to 4000 bar. The results demonstrate that combined temperature–pressure‐dependent studies can help delineate the free‐energy landscape of proteins and hence help elucidate which features and thermodynamic parameters are essential in determining the stability of the native conformational state of proteins. The approach presented may also be used for studying other systems with so‐called re‐entrant or Tamman loop‐shaped phase diagrams.     

K3MnH5, das erste salzartige Manganhydrid

K₃MnH₅, the First Salt-like Manganese Hydride K₃MnH₅ and K₃MnD₅ were synthesized by the reaction of potassium hydride (deuteride) with manganese powder under a hydrogen pressure above 3000 bar at 875 K. X-ray investigations on powdered samples and elastic neutron diffraction experiments on the deuterated compound at the time-of-flight spectrometer LAD in the temperature range 5–600 K led to the complete structure determination. The atomic arrangement is isotypic with that of Cs₃[CoCl₄]Cl (space group: 14/mcm, Z = 4). The structure of K₃MnH₅ contains isolated [MnH₄]^2?-tetrahedra and additional hydrogen ions which are exclusively coordinated by potassium cations. The magnetic susceptibilities show Curie-Weiss behaviour. At temperatures below 50 K there are obviously antiferromagnetic interactions.     

How can the Cross-Link Adducts Formed by Novel Trans Platinum Drug be Influenced by Hydrogen Bond

A systematic quantum chemical characterization of intrinsic structure, energies and spectral properties of all the studied cross-link adducts formed by the novel trans platinum with thiazole ligand has been carried out at B3LYP/6-31G^＊ level of theory with the Lanl2dz pseudo potential basis set for the Pt atom. Special attention has been paid to the relative stability of these complexes and the factors that probably alter the order of the relative stability. The important influence of hydrogen bond on the structures, the energies and the spectral property was revealed. Other factors that contribute to relative stability including solvation effect, entropy and electronic delocalization energy were taken into account. The stability energy of the whole complex, and the interaction energy between two purine bases and the [Pt-（NH3）thiazole]^2＋ group were adopted to study the interplay among subsystems and their contribution to relative stability of all the studied cross-link model. Finally, basic spectral properties of these complexes including H（8） chemical shifts of all the studied complexes and the VCD （vibrational circular dichroism） spectra of two pairs of GG chelate enantiomers, were provided in order to define the structure of the most possible duplex bearing novel trans platinum drug lesions.     

Quantum chemical calculations of the isomer shift in iron(II) complexes of 1,2,4-triazoles with a 1 A 1 ⇔ 5 T 2 spin transition

DFT calculations have been performed to determine the isomer shift for a series of iron(II) clusters with nitrogen-containing ligands which serve as models of coordination units in Fe(II) complexes with 1,2,4-triazoles possessing a ¹ A ₁ ? ⁵ T ₂ spin transition. Good agreement has been found between the theoretical and experimental values of the isomer shift for both low-and high-spin phases. Our calculations confirmed the hypothesis about relationship between the experimentally observed differences in the isomer shift for the low-spin phases of the complexes and variations of the Fe-N mean bond length.     

Solar Photocatalytic Degradation of 4‐Chlorophenol in Kaolinite Catalysts

This research applies semiconductor photocatalysts, which are formed by metal ion exchange on the surface of kaolinite catalyst with cations, to the study of photocatalytic degradation of 4‐chlorophenol. The analysis results of catalyst properties shows that, after sintering at 400 °C, kaolinite catalyst has a particle size of between 10–100 nm indicating the nano level of synthesized catalysts. Under the same condition, kaolinite‐Ag/Zn catalyst works better in degradation efficiency than single kaolinite‐Ag and kaolinite‐Zn catalysts. Kaolinite‐Zn catalyst declines in degradation efficacy after 150 minutes and performs poorer than the other three types of kaolinite catalysts. In the experiments of different amounts of catalysts, when the concentration exceeds 0.1 wt%, utilization of light energy and degradation efficiency will be reduced due to shielding effect. When at different pH values, the higher the pH value, the more OH‐will be released and that is beneficial for reaction with substances and the increase of reaction rate. Finally multivariate analysis proves that there is one determining factor that influences the photocatalytic degradation of 4‐chlorophenol in kaolinite catalysts, named as “the factor with intermediates competition degree,” the one affecting the 4‐CP degradation at different weight percentages that is referred to as the “shielding effect factor.”     

L-卡尼丁分子压印聚合物作为手性分离色谱固定相的研究

以L－卡尼丁为模板分子，分别以α－甲基丙烯酸和丙烯酰胺为功能单体，乙二醇二甲基丙烯酸酯为 剂，采用分子压印技术合成了对L－卡尼丁具有高选择性的分子压印聚合物。将所得聚合物用作高效液相色谱固定相，研究了它们对外消旋卡尼丁盐酸盐的拆分能力，分析结果表明，α－甲基丙烯酸作为功能单体所得聚合物对外消旋卡尼丁盐酸盐具有良好的拆分作用，其分离因子α为1．89。