Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Structural Basis for (2R,3R)-Taxifolin Binding and Reaction Products to the Bacterial Chalcone Isomerase of Eubacterium ramulus

The bacterial chalcone isomerase (CHI) from Eubacterium ramulus catalyses the first step in a flavanone-degradation pathway by a reverse Michael addition. The overall fold and the constitution of the active site of the enzyme completely differ from the well-characterised chalcone isomerase of plants. For (+)-taxifolin, CHI catalyses the intramolecular ring contraction to alphitonin. In this study, Fwe perform crystal structure analyses of CHI and its active site mutant His33Ala in the presence of the substrate taxifolin at 2.15 and 2.8 Å resolution, respectively. The inactive enzyme binds the substrate (+)-taxifolin as well defined, whereas the electron density maps of the native CHI show a superposition of substrate, product alphitonin, and most probably also the reaction intermediate taxifolin chalcone. Evidently, His33 mediates the stereospecific acid-base reaction by abstracting a proton from the flavonoid scaffold. The stereospecificity of the product is discussed.     

Computational Study of Mechanism and Enantioselectivity of Imine Reductase from Amycolatopsis orientalis

Imine reductases (IREDs) are NADPH-dependent enzymes (NADPH=nicotinamide adenine dinucleotide phosphate) that catalyze the reduction of imines to amines. They exhibit high enantioselectivity for a broad range of substrates, making them of interest for biocatalytic applications. In this work, we have employed density functional theory (DFT) calculations to elucidate the reaction mechanism and the origins of enantioselectivity of IRED from Amycolatopsis orientalis. Two substrates are considered, namely 1-methyl-3,4-dihydroisoquinoline and 2-propyl-piperideine. A model of the active site is built on the basis of the available crystal structure. For both substrates, different binding modes are first evaluated, followed by calculation of the hydride transfer transition states from each complex. We have also investigated the effect of mutations of certain important active site residues (Tyr179Ala and Asn241Ala) on the enantioselectivity. The calculated energies are consistent with the experimental observations and the analysis of transition states geometries provides insights into the origins of enantioselectivity of this enzyme.     

Synthesis and Bioactivity of New Chalcone Derivatives as Potential Tyrosinase Activator Based on the Click Chemistry

A new series of (E)‐1‐(4‐((1‐benzyl‐1H‐1,2,3‐triazol‐4‐yl)methoxy)phenyl)‐3‐phenylprop‐2‐en‐1‐one 1a (4‐((1‐benzyl‐1H‐1,2,3‐triazol‐4‐yl) methoxy)phenyl)‐1‐phenylprop‐2‐en‐1‐one 1b – 15b were designed, synthesized based on click chemistry, and biologically evaluated for their activity on tyrosinase. The result showed that most of prepared compounds 1a – 15a have potent activating effect on tyrosinase, especially for 3a , 8a – 10a and 14a – 15a . Among them, compounds 10a and 14a demonstrated the best activity with EC₅₀=1.71 and 5.60 µmol·L^?1 respectively, even better than the positive control 8‐MOP (EC₅₀=14.8 µmol·L^?1). Conversely, compounds 3b , 5b – 6b , 9b – 10b , and 15b induced enzymatic inhibition on tyrosinase.     

类球红杆菌羰基还原酶不对称催化还原性能与底物结构的关系

 将类球红杆菌 (Rhodobacter sphaeroides) 全细胞及其分离得到的羰基还原酶用于不对称催化还原多种潜手性酮类化合物, 通过比较产物的收率、ee 值、酶活力以及酶学动力学常数 Km, 探讨了类球红杆菌的催化还原性质与底物结构的关系. 结果表明, 对于类球红杆菌全细胞不对称催化还原苯乙酮衍生物, 产物 ee 值的变化遵循 Prelg 规则, 产物收率与底物苯环及侧链上取代基团的性质有关; 对于脂肪酮催化还原, 产物收率随底物链长的增加和分子量的增大而降低, 随支链数目的增加而升高, 产物 ee 值的变化也遵循 Prelg 规则. 利用羰基还原酶不对称催化还原潜手性酮类化合物发现, 对于芳香酮类化合物, 酶对 α 位为强电负性基团的底物专一性较强; 对于脂肪酮类化合物, 酶对五碳脂肪酮的专一性较高. 利用酶直接催化还原反应产物的 ee 值均为 99% 左右, 表明酶较全细胞有更高的立体选择性.     

Evaluation of Ruthenium(II) N-Heterocyclic Carbene Complexes as Antibacterial Agents and Inhibitors of Bacterial Thioredoxin Reductase

A series of ruthenium(II) complexes with N-heterocyclic carbene (NHC) ligands of the general type (arene)(NHC)Ru(II)X₂ (where X = halide) was prepared, characterized, and evaluated as antibacterial agents in comparison to the respective metal free benzimidazolium cations. The ruthenium(II) NHC complexes generally triggered stronger bacterial growth inhibition than the metal free benzimidazolium cations. The effects were much stronger against Gram-positive bacteria (Bacillus subtilis and Staphylococcus aureus) than against Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa), and all complexes were inactive against the fungus Candida albicans. Moderate inhibition of bacterial thioredoxin reductase was confirmed for selected complexes, indicating that inhibition of this enzyme might be a contributing factor to the antibacterial effects.     

Enzymatic synthesis of chiral heteroaryl alcohols using plant fragments as the only biocatalyst and reducing agent

Abstract

The enzymatic reduction of prochiral heterocyclic ketones by carrot (Daucus carota) root in water afforded the corresponding S-alcohols in accordance with the Prelog's rule. The reaction was performed under various conditions in order to optimize the procedure of bioreduction regarding reaction time, yield, and optimal mass of carrot. The optimized procedure was used to test the ability of other plants to carry out the reaction. In the latter experiment, it was observed that, with regard to stereospecificity, most vegetables tested were poorer reducing agents compared to D. carota.     

Enzymatic One-Step Reduction of Carboxylates to Aldehydes with Cell-Free Regeneration of ATP and NADPH

The direct generation of aldehydes from carboxylic acids is often a challenging synthetic task but undoubtedly attractive in view of abundant supply of such feedstocks from nature. Though long known, biocatalytic carboxylate reductions are at an early stage of development, presumably because of their co-factor requirement. To establish an alternative to whole-cell-based carboxylate reductions which are limited by side reactions, we developed an in vitro multi-enzyme system that allows for quantitative reductions of various carboxylic acids with full recycling of all cofactors and prevention of undesired over-reductions. Regeneration of adenosine 5′-triphosphate is achieved through the simultaneous action of polyphosphate kinases from Meiothermus ruber and Sinorhizobium meliloti and β-nicotinamide adenine dinucleotide 2′-phosphate is reduced by a glucose dehydrogenase. Under these conditions and in the presence of the carboxylate reductases from Neurospora crassa or Nocardia iowensis, various aromatic, heterocyclic and aliphatic carboxylic acids were quantitatively reduced to the respective aldehydes.     

Inhibition of Aldose Reductase by Ginsenoside Derivatives via a Specific Structure Activity Relationship with Kinetics Mechanism and Molecular Docking Study

This present work is designed to evaluate the anti-diabetic potential of 22 ginsenosides via the inhibition against rat lens aldose reductase (RLAR), and human recombinant aldose reductase (HRAR), using _DL-glyceraldehyde as a substrate. Among the ginsenosides tested, ginsenoside Rh2, (20S) ginsenoside Rg3, (20R) ginsenoside Rg3, and ginsenoside Rh1 inhibited RLAR significantly, with IC₅₀ values of 0.67, 1.25, 4.28, and 7.28 µM, respectively. Moreover, protopanaxadiol, protopanaxatriol, compound K, and ginsenoside Rh1 were potent inhibitors of HRAR, with IC₅₀ values of 0.36, 1.43, 2.23, and 4.66 µM, respectively. The relationship of structure–activity exposed that the existence of hydroxyl groups, linkages, and their stereo-structure, as well as the sugar moieties of the ginsenoside skeleton, represented a significant role in the inhibition of HRAR and RLAR. Additional, various modes of ginsenoside inhibition and molecular docking simulation indicated negative binding energies. It was also indicated that it has a strong capacity and high affinity to bind the active sites of enzymes. Further, active ginsenosides suppressed sorbitol accumulation in rat lenses under high-glucose conditions, demonstrating their potential to prevent sorbitol accumulation ex vivo. The findings of the present study suggest the potential of ginsenoside derivatives for use in the development of therapeutic or preventive agents for diabetic complications.     

One-step conversion of cellulose to fructose using coimmobilized cellulase, β-glucosidase,and glucose isomerase

Glucose isomerase was immobilized by itself and coimmobilized with cellulase and β-glucosidase using a polyurethane foam (Hypol® FHP 2002). Approximately 50% of the enzyme added was immobilized. The immobilized enzyme was active at pH values as low as 6.8. When immobilized alone, the K_m for Mg²⁺ increased by 5.5fold and the K_m for fructose increased 62%. The half-life of the immobilized glucose isomerase was approximately 160 h of continuous hydrolysis, with a substantial (about 35–40%) amount of activity remaining even after 1000 h. When all three enzymes were immobilized together, the system was found capable of functioning at pH 7.0 to produce fructose from both soluble and insoluble cellulose substrates. At this pH, the glucose:fructose ratio was 70:30. The advantageous properties of the foam as a support for enzyme immobilization and the efficiency of the one-step conversion process outlined combine to make this system appear valuable for use in high fructose syrup production.     

Validation of a High-Performance Liquid Chromatography with Photodiode Array Detection Method for the Separation and Quantification of Antioxidant and Skin Anti-Aging Flavonoids from Nelumbo nucifera Gaertn. Stamen Extract

Nelumbo nucifera Gaertn., or the so-called sacred lotus, is a useful aquatic plant in the Nelumbonaceae family that has long been used to prepare teas, traditional medicines as well as foods. Many studies reported on the phytochemicals and biological activities of its leaves and seeds. However, to date, only few studies were conducted on its stamen, which is the most important ingredient for herbal medicines, teas and other phytopharmaceutical products. Thus, this present study focuses on the following: (1) the application of high-performance liquid chromatography with photodiode array detection for a validated separation and quantification of flavonoids from stamen; (2) the Nelumbo nucifera stamen’s in vitro and in cellulo antioxidant activities; as well as (3) its potential regarding the inhibition of skin aging enzymes for cosmetic applications. The optimal separation of the main flavonoids from the stamen ethanolic extract was effectively achieved using a core-shell column. The results indicated that stamen ethanolic extract has higher concentration of in vitro and in cellulo antioxidant flavonoids than other floral components. Stamen ethanolic extract showed the highest protective effect against reactive oxygen/nitrogen species formation, as confirmed by cellular antioxidant assay using a yeast model. The evaluation of potential skin anti-aging action showed that the stamen extract has higher potential to inhibit tyrosinase and collagenase compared with its whole flower. These current findings are the first report to suggest the possibility to employ N. nucifera stamen ethanolic extract as a tyrosinase and collagenase inhibitor in cosmetic applications, as well as the utility of the current separation method.     

Improving the Enzymatic Cascade of Reactions for the Reduction of CO2 to CH3OH in Water: From Enzymes Immobilization Strategies to Cofactor Regeneration and Cofactor Suppression

The need to decrease the concentration of CO₂ in the atmosphere has led to the search for strategies to reuse such molecule as a building block for chemicals and materials or a source of carbon for fuels. The enzymatic cascade of reactions that produce the reduction of CO₂ to methanol seems to be a very attractive way of reusing CO₂; however, it is still far away from a potential industrial application. In this review, a summary was made of all the advances that have been made in research on such a process, particularly on two salient points: enzyme immobilization and cofactor regeneration. A brief overview of the process is initially given, with a focus on the enzymes and the cofactor, followed by a discussion of all the advances that have been made in research, on the two salient points reported above. In particular, the enzymatic regeneration of NADH is compared to the chemical, electrochemical, and photochemical conversion of NAD⁺ into NADH. The enzymatic regeneration, while being the most used, has several drawbacks in the cost and life of enzymes that suggest attempting alternative solutions. The reduction in the amount of NADH used (by converting CO₂ electrochemically into formate) or even the substitution of NADH with less expensive mimetic molecules is discussed in the text. Such an approach is part of the attempt made to take stock of the situation and identify the points on which work still needs to be conducted to reach an exploitation level of the entire process.