Chemical Validation of Mycobacterium tuberculosis Phosphopantetheine Adenylyltransferase Using Fragment Linking and CRISPR Interference**

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused by Mycobacterium tuberculosis (Mtb). Seeking to identify inhibitors of Mtb phosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of the MtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a K_D <20 μM and on-target anti-Mtb activity, as demonstrated using CRISPR interference. This study represents a big step toward validating MtbPPAT as a potential drug target and designing a MtbPPAT-targeting anti-TB drug.     

Enzyme-regulated the changes of pH values for assembling a colorimetric and multistage interconnection logic network with multiple readouts

Based on enzymatic reactions-triggered changes of pH values and biocomputing, a novel and multistage interconnection biological network with multiple easy-detectable signal outputs has been developed. Compared with traditional chemical computing, the enzyme-based biological system could overcome the interference between reactions or the incompatibility of individual computing gates and offer a unique opportunity to assemble multicomponent/multifunctional logic circuitries. Our system included four enzyme inputs: β-galactosidase (β-gal), glucose oxidase (GOx), esterase (Est) and urease (Ur). With the assistance of two signal transducers (gold nanoparticles and acid–base indicators) or pH meter, the outputs of the biological network could be conveniently read by the naked eyes. In contrast to current methods, the approach present here could realize cost-effective, label-free and colorimetric logic operations without complicated instrument. By designing a series of Boolean logic operations, we could logically make judgment of the compositions of the samples on the basis of visual output signals. Our work offered a promising paradigm for future biological computing technology and might be highly useful in future intelligent diagnostics, prodrug activation, smart drug delivery, process control, and electronic applications.     

EPR Spectroscopic Studies of Lipoxygenases

Polyunsaturated fatty acids are sources of diverse natural, and chemically designed products. The enzyme lipoxygenase selectively oxidizes fatty acid acyl chains using controlled free radical chemistry; the products are regio‐ and stereo‐chemically unique hydroperoxides. A conserved structural fold of ≈600 amino acids harbors a long and narrow substrate channel and a well‐shielded catalytic iron. Oxygen, a co‐substrate, is blocked from the active site until a hydrogen atom is abstracted from substrate bis‐allylic carbon, in a non‐heme iron redox cycle. EPR spectroscopy of ferric intermediates in lipoxygenase catalysis reveals changes in the metal coordination and leads to a proposal on the nature of the reactive intermediate. Remarkably, free radicals are so well controlled in lipoxygenase chemistry that spin label technology can be applied as well. The current level of understanding of steps in lipoxygenase catalysis, from the EPR perspective, will be reviewed.     

Recent progress in two-photon small molecule fluorescent probes for enzymes

Enzymes are macromolecular biological catalysts which can accelerate chemical reactions in living organisms. Almost all the physiological metabolism activities in the cell need enzymes to sustain life via rapid catalysis. Currently, medical research has proved that abnormal enzyme activity is associated with numerous diseases, such as Parkinson’s disease (PD), Alzheimer's disease (AD) and cancers. On the other hand, early diagnosis of those diseases is of great significance to improve the survival rate and cure rate. In the current diagnostic tools, two-photon fluorescent probes (TPFPs) are developing rapidly due to their unique advantages, such as higher spatial resolution, deeper imaging depth, and lower biotoxicity. Therefore, the design and synthesis of two-photon (TP) small molecule enzymatic probes have broad prospects for early diagnosis and treatment of diseases. As of now, scientists have developed many TP small molecule enzymatic probes. This review aims to summarize the TP small molecule enzymatic probes and expound the reaction mechanism.     

Platform for Highly Sensitive Alkaline Phosphatase‐Based Immunosensors Using 1‐Naphthyl Phosphate and an Avidin‐Modified Indium Tin Oxide Electrode

We report a versatile platform for highly sensitive alkaline phosphatase (ALP)‐based electrochemical biosensors that uses an avidin‐modified indium tin oxide (ITO) electrode as a sensing electrode and 1‐naphthyl phosphate (NPP) as an ALP substrate. Almost no electrocatalytic activity of NPP and good electrocatalytic activity of 1‐naphthol (ALP product) on the ITO electrodes allow a high signal‐to‐background ratio. The effective surface covering of avidin on the ITO electrodes allows very low levels of nonspecific binding of proteins to the sensing electrodes. The platform technology is used to detect mouse IgG with a detection limit of 1.0 pg/mL.     

Strategy for Low Background‐Current Levels in the Electrochemical Biosensors Using Horse‐Radish Peroxidase Labels

This article describes an electrochemical strategy to achieve low background‐current levels in horse‐radish peroxidase (HRP)‐based electrochemical immunosensors. The strategy consists of (i) the use of an HRP substrate/product redox couple whose formal potential is high and (ii) the use of an electrode that shows moderate electrocatalytic activity for the redox couple. The strategy is proved by a model biosensor using a catechol/o‐benzoquinone redox couple and an indium tin oxide (ITO) electrode. The combined effect of high formal potential and moderate electrocatalytic activity allows o‐benzoquinone electroreduction with minimal catechol electrooxidation and H₂O₂ electroreduction. The detection limit for mouse‐IgG is 100 pg/mL.     

Cleavage of Menger’s aliphatic amide: A model for peptidase enzyme solely explained by proximity orientation in intramolecular proton transfer

Ab initio HF/6-31G and DFT B3LYP/6-31G (d,p) calculations for the cleavage of Menger’s aliphatic amide 3 (a peptidase model) under physiological conditions, indicate that the rate limiting step in the cleavage process is a proton transfer from one of the carboxyl groups onto the amidic carbonyl oxygen. The acceleration in rates is mainly due to proximity orientation, and the effect of pseudoallylic strain relief on the rates is negligible. Moreover, the calculations reveal that the mode and the mechanism of the amide cleavage are largely dependent on the pH of the reaction. These results explain the findings that peptidase enzymes are reactive around neutral pH while their activities vanish under basic medium.     

Thermosonication as a potential quality enhancement technique of apple juice

Enzymatic browning and microbial growth lead to quality losses in apple products. In the present study, fresh apple juice was thermosonicated using ultrasound in-bath (25 kHz, 30 min, 0.06 W cm⁻³) and ultrasound with-probe sonicator (20 kHz, 5 and 10 min, 0.30 W cm⁻³) at 20, 40 and 60 °C for inactivation of enzymes (polyphenolase, peroxidase and pectinmethylesterase) and microflora (total plate count, yeast and mold). Additionally, ascorbic acid, total phenolics, flavonoids, flavonols, pH, titratable acidity, ^°Brix and color values influenced by thermosonication were investigated. The highest inactivation of enzymes was obtained in ultrasound with-probe at 60 °C for 10 min, and the microbial population was completely inactivated at 60 °C. The retention of ascorbic acid, total phenolics, flavonoids and flavonols were significantly higher in ultrasound with-probe than ultrasound in-bath at 60 °C. These results indicated the usefulness of thermosonication for apple juice processing at low temperature, for enhanced inactivation of enzymes and microorganisms.     

Combined of ultrasound irradiation with high hydrostatic pressure (US/HHP) as a new method to improve immobilization of dextranase onto alginate gel

In this research work, dextranase was immobilized onto calcium alginate beads by the combination of ultrasonic irradiation and high hydrostatic pressure (US/HHP) treatments. Effects of US/HHP treatments on loading efficiency and immobilization yield of dextranase enzyme onto calcium alginate beads were investigated. Furthermore, the activities of immobilized enzymes prepared with and without US/HHP treatments and that prepared with ultrasonic irradiation (US) and high hydrostatic pressure (HHP), as a function of pH, temperature, recyclability and enzyme kinetic parameters, were compared with that for free enzyme. The maximum loading efficiency and the immobilization yield were observed when the immobilized dextranase was prepared with US (40 W at 25 kHz for 15 min) combined with HHP (400 MPa for 15 min), under which the loading efficiency and the immobilization yield increased by 88.92% and 80.86%, respectively, compared to immobilized enzymes prepared without US/HHP treatment. On the other hand, immobilized enzyme prepared with US/HHP treatment showed V_max, K_M, catalytic and specificity constants values higher than that for the immobilized enzyme prepared with HHP treatment, indicated that, this new US/HHP method improved the catalytic kinetics activity of immobilized dextranase at all the reaction conditions studied. Compared to immobilized enzyme prepared either with US or HHP, the immobilized enzymes prepared with US/HHP method exhibited a higher: pH optimum, optimal reaction temperature, thermal stability and recyclability, and lower activation energy, which, illustrating the effectiveness of the US/HHP method. These results indicated that, the combination of US and HHP treatments could be an effective method for improving the immobilization of enzymes in polymers.     

Studies on the formation of porphyrinogens from monopyrroles in presence of the enzymes PBG deaminase and/or Uro’gen III synthase

The substrate-specificities of two enzymes in the biosynthetic pathway to vitamin B₁₂, PBG deaminase and Uro’gen III synthase, which are involved in the formation of Uro’gen III from the pyrrole PBG, are investigated for the preparation of Uroporphyrin analogs. Both enzymes display strong substrate-specificity. However, tetramerization of pyrroles with carboxylate β-substituents in mildly basic buffer represents the best and most rapid route to a family of Uro I analogs for enzymatic activity studies.