Query generation to search for inhibitors of enzymatic reactions

A method for the generation of intermediates of enzyme-catalyzed reactions is presented. These intermediates can be used as three-dimensional structural queries for searching for inhibitors of enzymatic reactions. The intermediates can be considered as being structurally quite close to transition-state analogues. For this application, a database containing detailed chemical information on metabolic reactions is used. The likely three-dimensional structure of the intermediates of enzyme-catalyzed reactions can be generated from the information in the database. For three reactions catalyzed by the enzymes AMP deaminase (EC code 3.5.4.6), triose phosphate isomerase (EC code 5.3.1.1), and arginase II (EC code 3.5.3.1), we show how a 3D model of these intermediates can be superimposed onto known inhibitors of these enzymes by a program that uses a genetic algorithm. For this, we test different methods for the superimposition using information on the enzymatic binding site, using information on physicochemical properties calculated from the molecular structure, or without having any information in the superimposition process. We show that these inhibitors are most similar to the corresponding intermediates regarding the 3D structure.     

Off-line form of the Michaelis-Menten equation for studying the reaction kinetics in a polymer microchip integrated with enzyme microreactor

We firstly transformed the traditional Michaelis-Menten equation into an off-line form which can be used for evaluating the Michaelis-Menten constant after the enzymatic reaction. For experimental estimation of the kinetics of enzymatic reactions, we have developed a facile and effective method by integrating an enzyme microreactor into direct-printing polymer microchips. Strong nonspecific adsorption of proteins was utilized to effectively immobilize enzymes onto the microchannel wall, forming the integrated on-column enzyme microreactor in a microchip. The properties of the integrated enzyme microreactor were evaluated by using the enzymatic reaction of glucose oxidase (GOx) with its substrate glucose as a model system. The reaction product, hydrogen peroxide, was electrochemically (EC) analyzed using a Pt microelectrode. The data for enzyme kinetics using our off-line form of the Michaelis-Menten equation was obtained (K(m) = 2.64 mM), which is much smaller than that reported in solution (K(m) = 6.0 mM). Due to the hydrophobic property and the native mesoscopic structure of the poly(ethylene terephthalate) film, the immobilized enzyme in the microreactor shows good stability and bioactivity under the flowing conditions.     

Thermodynamic Feasibility of Enzymatic Reduction of Carbon Dioxide to Methanol

Production of valuable chemicals from CO₂ is highly desired for the purpose of controlling CO₂ emission. Toward that, enzymatic reduction of CO₂ for the production of methanol appeared to be especially promising. That has been achieved by reversing the biological metabolic reaction pathways. However, hitherto, there has been little discussion on the thermodynamic feasibility of reversing such biological pathways. The reported yields of methanol have been generally very low under regular reaction conditions preferred by naturally evolved enzymes. The current work examines the sequential enzymatic conversion of CO₂ into methanol from a thermodynamic point of view with a focus on factors that control the reaction equilibrium. Our analysis showed that the enzymatic conversion of carbon dioxide is highly sensitive to the pH value of the reaction solution and, by conducting the reactions at low pHs (such as pH 6 or 5) and ionic strength, it is possible to shift the biological methanol metabolic reaction equilibrium constants significantly (by a factor of several orders of magnitude) to favor the synthesis of methanol.     

Predictions of Enzymatic Parameters: A Mini-Review with Focus on Enzymes for Biofuel

Enzymatic reactions are very basic processes in biological systems, and parameters related to enzymatic reactions always provide good indicators for understanding of mechanisms underlined in enzymatic reactions, for better controlling of enzymatic reactions, and for comparison of different enzymes. In this mini-review: first, parameters in enzymatic reactions were briefly reviewed from three different standpoints; second, predictions of parameters in enzymatic reactions without information on enzyme structure were shortly reviewed from viewpoints of geometric approach, graphic approach and compartmental approach; third, predictions of parameters in enzymatic reaction with information on enzyme structure were reviewed from the points of view of modeling, with 19 currently available databases, and 17 software packages and web servers; fourth, the current state of prediction on parameters in enzymatic reaction in biofuel industry with respect to cellulolytic enzymes were reviewed; fifth, the pros and cons for future development were discussed; and finally, a worked example was given in the Appendix to describe the whole procedures of prediction of enzymatic parameters in reactions.     

毛细管电泳序列分析技术用于在线酶分析研究进展

毛细管电泳技术具有操作简单、样品消耗量少、分离效率高和分析速度快等优势,不仅是一种高效的分离分析技术,而且已经发展成为在线酶分析和酶抑制研究的强有力工具。酶反应全程的实时在线监测,可以实现酶反应动力学过程的高时间分辨精确检测,以更准确地获得反应机制和反应速率常数,有助于更好地了解酶反应机制,从而更全面深入地认识酶在生物代谢中的功能。此外,准确、快速的在线酶抑制剂高通量筛选方法的发展,对加快酶抑制类药物的研发以及疾病的临床诊断亦具有重要意义。电泳媒介微分析法（EMMA）和固定化酶微反应器（IMER）是毛细管电泳酶分析技术中常用的在线分析方法。这两种在线酶分析法的进样方式通常为流体动力学进样和电动进样,无法实现酶反应过程中的无干扰序列进样分析。近年来,基于快速序列进样的毛细管电泳序列分析技术已经发展成为在线酶分析的另一种强有力手段,以实现高时间分辨和高通量的酶分析在线检测。该文从快速序列进样的角度,综述了近年来毛细管电泳序列分析技术在线酶分析的研究进展,并着重介绍了各种序列进样方法及其在酶反应和酶抑制反应中的应用,包括光快门进样、流动门进样、毛细管对接的二维扩散进样、流动注射进样、液滴微流控进样等。     

Enzymatic mechanisms of biological magnetic sensitivity: nuclear spin effects

Intracellular enzymatic reactions involving ion-radical states are shown to act as a universal mechanism of magnetically sensitive living organisms. Weak magnetic fields can affect the rate of intracellular enzymatic reactions. The main magnetically sensitive stage is the singlet-triplet conversion of ion-radical pairs in the active sites of enzymes induced by Zeeman and hyperfine interactions of electron and nuclear spins. The participation of a nuclear spin in the ion-radical process results in a strong dependence of the enzymatic reaction rate in weak magnetic fields comparable with the magnetic field of the Earth.     

Acoustic deposition with NIMS as a high-throughput enzyme activity assay

Mass spectrometry (MS)-based enzyme assay has been shown to be a useful tool for screening enzymatic activities from environmental samples. Recently, reported approaches for high-specificity multiplexed characterization of enzymatic activities allow for providing detailed information on the range of enzymatic products and monitoring multiple enzymatic reactions. However, the throughput has been limited by the slow liquid-liquid handling and manual analysis. This rapid communication demonstrates the integration of acoustic sample deposition with nanostructure initiator mass spectrometry (NIMS) imaging to provide reproducible measurements of multiple enzymatic reactions at a throughput that is tenfold to 100-fold faster than conventional MS-based enzyme assay. It also provides a simple means for the visualization of multiple reactions and reaction pathways.     

Chemistry and biology of biosynthetic Diels-Alder reactions

Nature's repertoire of biosynthetic transformations has recently been recognized to include the Diels-Alder cycloaddition reaction. Evidence now exists that there are enzymes that mediate the Diels-Alder reaction in secondary metabolic biosynthetic pathways. 2002 marked the 100th anniversary of Alder's birth and 75 years since the discovery of the Diels-Alder reaction. It would appear that living systems discovered and made use of this ubiquitously useful ring-forming reaction eons ago for the construction of complex natural products. In this Review an overview is given of all of the known classes of natural products (polyketides, isoprenoids, phenylpropanoids, alkaloids) that have been speculated to arise by a biological Diels-Alder reaction.     

Enhanced enzymatic activity exerted by a packed assembly of a single type of enzyme

In contrast to the dilute conditions employed for in vitro biochemical studies, enzymes are spatially organized at high density in cellular micro-compartments. In spite of being crucial for cellular functions, enzymatic reactions in such highly packed states have not been fully addressed. Here, we applied a protein adaptor to assemble a single type of monomeric enzyme on a DNA scaffold in the packed or dispersed states for carbonic anhydrase. The enzymatic reactions proceeded faster in the packed than in the dispersed state. Acceleration of the reaction in the packed assembly was more prominent for substrates with higher hydrophobicity. In addition, carbonic anhydrase is more tolerant of inhibitors in the packed assembly. Such an acceleration of the reaction in the packed state over the dispersed state was also observed for xylose reductase. We propose that the entropic force of water increases local substrate or cofactor concentration within the domain confined between enzyme surfaces, thus accelerating the reaction. Our system provides a reasonable model of enzymes in a packed state; this would help in engineering artificial metabolic systems.

The enzymatic reactions proceeded faster in the packed than in the dispersed state.     

Better understanding of the ring-cleavage process of cyanocyclopropyl anionic derivatives. A theoretical study based on the electron localization function

[reaction: see text] Theoretical calculations at the B3LYP/6-31+G(d), MP2/6-31+G(d), and G3(MP2) levels have been carried out to understand the alternative reaction pathways (the cyclopropyl ring cleavage (RC) and the retrocycloaddition reaction (rCA)) of a constrained tricyanocyclopropyl anionic derivative. The more energetically favorable path is found to be the RC process, a formally "forbidden" rearrangement (Leiviers, M.; Tam, I.; Groves, K.; Leung, D.; Xie, Y.; Breslow, R. Org. Lett. 2003, 5, 19, 3407) yielding an allylic anion system via a concerted transition structure, in agreement with experimental outcomes. rCA is more energetically favorable along a two-stage mechanism, via an intermediate, than a synchronous concerted process. By using isodesmic reactions, we have found that B3LYP presents limitations when it calculates carbon-carbon bond-breaking processes along the present rCA reaction. A detailed analysis of the nature of the topology of the reactive potential energy surface for the RC process points out the presence of a valley-ridge inflection point in the uphill part. An explanation for the low-energy barrier associated with RC is furnished on the analysis of the evolution of the twisting (dis-/conrotatory) motions of cyano substituents in the cyclopropyl ring as well as on the number and type of electron pairs provided by the electron localization function (ELF).     

Elucidating organ-specific metabolic toxicity chemistry from electrochemiluminescent enzyme/DNA arrays and bioreactor bead-LC-MS/MS

Human toxic responses are very often related to metabolism. Liver metabolism is traditionally studied, but other organs also convert chemicals and drugs to reactive metabolites leading to toxicity. When DNA damage is found, the effects are termed genotoxic. Here we describe a comprehensive new approach to evaluate chemical genotoxicity pathways from metabolites formed in situ by a broad spectrum of liver, lung, kidney and intestinal enzymes. DNA damage rates are measured with a microfluidic array featuring a 64-nanowell chip to facilitate fabrication of films of DNA, electrochemiluminescent (ECL) detection polymer [Ru(bpy)₂(PVP)₁₀]²⁺ {(PVP = poly(4-vinylpyridine))} and metabolic enzymes. First, multiple enzyme reactions are run on test compounds using the array, then ECL light related to the resulting DNA damage is measured. A companion method next facilitates reaction of target compounds with DNA/enzyme-coated magnetic beads in 96 well plates, after which DNA is hydrolyzed and nucleobase-metabolite adducts are detected by LC-MS/MS. The same organ enzymes are used as in the arrays. Outcomes revealed nucleobase adducts from DNA damage, enzymes responsible for reactive metabolites (e.g. cyt P450s), influence of bioconjugation, relative dynamics of enzymes suites from different organs, and pathways of possible genotoxic chemistry. Correlations between DNA damage rates from the cell-free array and organ-specific cell-based DNA damage were found. Results illustrate the power of the combined DNA/enzyme microarray/LC-MS/MS approach to efficiently explore a broad spectrum of organ-specific metabolic genotoxic pathways for drugs and environmental chemicals.     

Multicoordinate driven method for approximating enzymatic reaction paths: automatic definition of the reaction coordinate using a subset of chemical coordinates

We present a generalization of the reaction coordinate driven method to find reaction paths and transition states for complicated chemical processes, especially enzymatic reactions. The method is based on the definition of a subset of chemical coordinates; it is simple, robust, and suitable to calculate one or more alternative pathways, intermediate minima, and transition-state geometries. Though the results are approximate and the computational cost is relatively high, the method works for large systems, where others often fail. It also works when a certain reaction path competes with others having a lower energy barrier. Accordingly, the procedure is appropriate to test hypothetical reaction mechanisms for complicated systems and provides good initial guesses for more accurate methods. We present tests on a number of simple reactions and on several complicated chemical transformations and compare the results with those obtained by other methods. Calculation of the reaction path for the enzymatic hydrolysis of the substrate by dUTPase for an active-site model with 85 atoms, including several loosely bound water molecules, indicates that the method is feasible for the study of enzyme mechanisms.     

Biohydrogenation from biomass sugar mediated by in vitro synthetic enzymatic pathways

Different from NAD(P)H regeneration approaches mediated by a single enzyme or a whole-cell microorganism, we demonstrate high-yield generation of NAD(P)H from a renewable biomass sugar--cellobiose through in vitro synthetic enzymatic pathways consisting of 12 purified enzymes and coenzymes. When the NAD(P)H generation system was coupled with its consumption reaction mediated by xylose reductase, the NADPH yield was as high as 11.4 mol NADPH per cellobiose (i.e., 95% of theoretical yield--12 NADPH per glucose unit) in a batch reaction. Consolidation of endothermic reactions and exothermic reactions in one pot results in a very high energy-retaining efficiency of 99.6% from xylose and cellobiose to xylitol. The combination of this high-yield and projected low-cost biohydrogenation and aqueous phase reforming may be important for the production of sulfur-free liquid jet fuel in the future.     

Designing for sustainability with biocatalytic and chemoenzymatic cascade processes

Cascade reactions have been widely recognized to cut costs, decrease solvent usage, and reduce cycle times in chemical processes. Recently, biocatalytic cascades have altered how we design synthetic routes to complex molecules to achieve sustainable commercial processes for pharmaceutical, agricultural, and fine chemical industries. With advancements in protein engineering and an increase in the number of enzyme classes available to chemists, industrial and academic groups alike have endeavored to expand the scope of biocatalysis from single reactions to multi-enzyme cascades to rapidly build complex molecular structures. Recent reports have drawn inspiration from biosynthetic pathways and have applied engineered enzymes to in vitro enzymatic cascades. Furthermore, combining transition-metal catalysis and enzymes in one-pot chemoenzymatic cascades likewise serves to broaden the scope of biocatalysis, enabling traditional chemical reactions to be performed under mild aqueous conditions. In this article, we review recent biocatalytic and chemoenzymatic cascades from 2019 to 2021.     

How Small Heterocycles Make a Reaction Network of Amino Acids and Nucleotides Efficient in Water

Organisms use enzymes to ensure a flow of substrates through biosynthetic pathways. How the earliest form of life established biosynthetic networks and prevented hydrolysis of intermediates without enzymes is unclear. Organocatalysts may have played the role of enzymes. Quantitative analysis of reactions of adenosine 5’‐monophosphate and glycine that produce peptides, pyrophosphates, and RNA chains reveals that organocapture by heterocycles gives hydrolytically stabilized intermediates with balanced reactivity. We determined rate constants for 20 reactions in aqueous solutions containing a carbodiimide and measured product formation with cyanamide as a condensing agent. Organocapture favors reactions that are kinetically slow but productive, and networks, over single transformations. Heterocycles can increase the metabolic efficiency more than two‐fold, with up to 0.6 useful bonds per fuel molecule spent, boosting the efficiency of life‐like reaction systems in the absence of enzymes.     

Two general methods for the isolation of enzyme activities by colony filter screening

We describe two general methodologies, based on filter-sandwich assays, for isolating enzymatic activities from a large repertoire of protein variants expressed in the cytoplasm of E. coli cells. The enzymes are released by the freezing and thawing of bacterial colonies grown on a porous master filter and diffuse to a second "reaction" filter that closely contacts the master filter. Reaction substrates can be immobilized either on the filter or on the enzyme itself (which is then, in turn, captured on the reaction filter). The resulting products are detected with suitable affinity reagents. We used biotin ligase as a model enzyme to assess the performance of the two methodologies. Active enzymes were released by the bacteria, locally biotinylated the immobilized target substrate peptide, and allowed the sensitive and specific detection of individual catalytically active colonies.     

A novel electrochemical approach to the characterization of oxidoreductase reactions

Electrochemical methods based on enzyme-electrochemical reactions have been developed for studying oxidoreductase reactions. The methods measure a current resulting from an oxidoreductase reaction with an electrode serving as a final electron acceptor (or donor) in the reaction. A theoretical equation for the enzyme-electrochemical reaction, called bioelectrocatalysis, is derived, which enables kinetic analysis of the reaction. In combination with spectrophotometry, the electrochemical method provides a method for determining the redox potentials of proteins and enzymes. An alternative method based on bulk electrolysis in a quartz cell for UV-vis spectroscopy has been developed for the measurements of protein redox potentials on a conventional spectrophotometer. The electrochemical methods are applied to kinetic and thermodynamic analyses for the reactions of a variety of enzymes including a newly discovered enzyme, quinohemoprotein amine dehydrogenase (QH-AmDH), and bilirubin oxidase (BOD) [EC 1.3.3.5, from Myrothecium verrucaria], a copper-containing enzyme useful for bioelectrocatalytic O(2) reduction in biofuel cells. The electrochemical method for kinetic analysis has been successfully applied to the analysis of oxidoreductase reactions in vivo, as demonstrated by the reaction of glucose dehydrogenase in Escherichia coli. The advantages of the electrochemical methods are discussed.     

Real‐Time Monitoring of Mass‐Transport‐Related Enzymatic Reaction Kinetics in a Nanochannel‐Array Reactor

To understand the fundamentals of enzymatic reactions confined in micro‐/nanosystems, the construction of a small enzyme reactor coupled with an integrated real‐time detection system for monitoring the kinetic information is a significant challenge. Nano‐enzyme array reactors were fabricated by covalently linking enzymes to the inner channels of a porous anodic alumina (PAA) membrane. The mechanical stability of this nanodevice enables us to integrate an electrochemical detector for the real‐time monitoring of the formation of the enzyme reaction product by sputtering a thin Pt film on one side of the PAA membrane. Because the enzymatic reaction is confined in a limited nanospace, the mass transport of the substrate would influence the reaction kinetics considerably. Therefore, the oxidation of glucose by dissolved oxygen catalyzed by immobilized glucose oxidase was used as a model to investigate the mass‐transport‐related enzymatic reaction kinetics in confined nanospaces. The activity and stability of the enzyme immobilized in the nanochannels was enhanced. In this nano‐enzyme reactor, the enzymatic reaction was controlled by mass transport if the flux was low. With an increase in the flux (e.g., >50 μL min^?1), the enzymatic reaction kinetics became the rate‐determining step. This change resulted in the decrease in the conversion efficiency of the nano‐enzyme reactor and the apparent Michaelis–Menten constant with an increase in substrate flux. This nanodevice integrated with an electrochemical detector could help to understand the fundamentals of enzymatic reactions confined in nanospaces and provide a platform for the design of highly efficient enzyme reactors. In addition, we believe that such nanodevices will find widespread applications in biosensing, drug screening, and biochemical synthesis.     

A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate

We present a new computational strategy for the design and evaluation of novel enzymatic pathways for the biosynthesis of fuels and chemicals. The approach combines the use of the Biochemical Network Integrated Computational Explorer (BNICE) framework and a structure-based screening method for rapid generation and evaluation of novel enzymatic reactions and pathways. The strategy is applied to a case study of 1-butanol production from pyruvate, which yielded nine novel biosynthetic pathways. Using screening criteria based on pathway length, thermodynamic feasibility, and metabolic flux analysis, all nine novel pathways were deemed to be attractive candidates. To further assess their feasibility of implementation, we introduced a new screening criterion based on structural complementarity using molecular docking methods. We show that this approach correctly reproduces the native binding poses for a wide range of enzymes in key classes related to 1-butanol production and provides qualitative agreement with experimental measures of catalytic activity for different substrates. In addition, we show that the structure-based methods can be used to select specific proteins that may be promising candidates to catalyze novel reactions.