Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.

Rational predictions on binding kinetics parameters of drugs to targets play significant roles in future drug designs. Full conformational samplings of targets are requisite for accurate predictions of binding kinetic parameters. In this review, we mainly focus on the applications of enhanced sampling technologies in calculations of binding kinetics parameters and residence time of drugs. The methods involved in molecular dynamics simulations are applied to not only probe conformational changes of targets but also reveal calculations of residence time that is significant for drug efficiency. For this review, special attention are paid to accelerated molecular dynamics (aMD) and Gaussian aMD (GaMD) simulations that have been adopted to predict the association or disassociation rate constant. We also expect that this review can provide useful information for future drug design.

Characterization of the enzyme kinetics of EMP and HMP pathway in Corynebacterium glutamicum: reference for modeling metabolic networks.

The model of intracellular metabolic network based on enzyme kinetics parameters plays an important role in understanding the intracellular metabolic process of Corynebacterium glutamicum, and constructing such a model requires a large number of enzymological parameters. In this work, the genes encoding the relevant enzymes of the EMP and HMP metabolic pathways from Corynebacterium glutamicum ATCC 13032 were cloned, and engineered strains for protein expression with E.coli BL21 and P.pastoris X33 as hosts were constructed. The twelve enzymes (GLK, GPI, TPI, GAPDH, PGK, PMGA, ENO, ZWF, RPI, RPE, TKT, and TAL) were successfully expressed and purified by Ni2+ chelate affinity chromatography in their active forms. In addition, the kinetic parameters (V max, K m, and K cat) of these enzymes were measured and calculated at the same pH and temperature. The kinetic parameters of enzymes associated with EMP and the HMP pathway were determined systematically and completely for the first time in C.glutamicum. These kinetic parameters enable the prediction of key enzymes and rate-limiting steps within the metabolic pathway, and support the construction of a metabolic network model for important metabolic pathways in C.glutamicum. Such analyses and models aid in understanding the metabolic behavior of the organism and can guide the efficient production of high-value chemicals using C.glutamicum as a host.

Formaldehyde Oxidation of Ce0.8Zr0.2O2 Nanocatalysts for Room Temperature: Kinetics and Effect of pH Value.

Ce0.8Zr0.2O2 catalysts were prepared via the co-precipitation method under different pH conditions. The catalysts were characterized via TEM, XRD, XPS, BET, Raman, and FTIR. The oxidation performance of formaldehyde was tested. Precipitation pH affects the physicochemical properties and performance of the Ce0.8Zr0.2O2 catalyst. By controlling the precipitation pH at 10.5, the Ce0.8Zr0.2O2 catalyst with the largest specific surface area, the smallest grain size with the best formaldehyde removal rate (98.85%), abundant oxygen vacancies, and the best oxidation performance were obtained. Meanwhile, the kinetic parameters of the catalyst were experimentally investigated and the calculated activation energy was 12.6 kJ/mol and the number of reaction steps was 1.4 and 1.2.

Identification and biotechnological characterisation of yeast microbiota involved in spontaneous fermented wholegrain sourdoughs.

BACKGROUND: New strategies in the cereal-based industry has brought about the elaboration of new sourdoughs with better microbial stability and safety as well as nutritional value such as those based on wholegrain flours. This has led to an increasing interest in the selection of adapted yeasts for using them as new starters. Therefore, this study aimed to isolate, identify, and characterise diverse yeast strains from wholegrain spontaneous sourdoughs. RESULTS: Three wholegrain sourdoughs (wheat, rye, and oat) were fermented and monitored for 96 h. Minimum pH values ranged from 3.1 to 3.5 while maximum yeast counts were reached at 72 h. A total of 76 yeast isolates were identified by polymerase chain reaction random amplification of polymorphic DNA (PCR-RAPD) and catalogued in six different species by sequencing the internal transcribed spacer (ITS) region. The major species were Candida glabrata, Saccharomyces cerevisiae, Kazachstania unispora, and Wickerhamomyces anomalus. The studied kinetic parameters of the growth curves (λ, G, ODmax , and µmax ) and the fermentation capacity allowed to ascertain that 12 and 5 strains, respectively, were better than baker's yeast control. The fibre assimilation ability (cellulose, xylose, and ß-glucan) was observed in the 27% of the strains and only four strains showed phytase activity. CONCLUSIONS: The yeast population in the three wholegrain sourdoughs were variable along the fermentation time. Genetic identification showed that strains and species presented a different trend for each sourdough although common species were determined (e.g., W. anomalus). Candida glabrata (4T1) and Saccharomyces cerevisiae (3A6) showed, respectively, better kinetics and impedance results than the positive control, while W. anomalus (C4) was notorious in fibre assimilation and phytase degradation. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The Control Strategy and Kinetics of VFAs Production in an ASBR Reactor Treating Low-Strength Mariculture Wastewater.

As an environment-friendly wastewater treatment process, the anaerobic fermentation process has been widely used for the pretreatment of high-strength wastewater. However, it is rarely applied to treat low-strength wastewater due to low methane recovery. In this study, anaerobic fermentation treating low-strength mariculture wastewater was studied in an anaerobic sequencing batch reactor (ASBR) with a COD removal rate of 75%. Anaerobic fermentation was successfully controlled at the acidification stage by increasing COD loading. As the greenhouse gas emission decreased, the residual organics were enough for biological nutrients' removal. Fluorescence in situ hybridization results showed that the dominant bacteria in the ASBR were acidogenic bacteria and methanogens, accounting for 39.7% and 46.5% of the total bacteria, respectively. Through the calculation processing of the experimental data, the order of the anaerobic fermentation reaction was a second-order reaction. The kinetic parameters of low-strength organic wastewater treatment were determined by using the Grau second-order substrate removal model, Stover-Kincannon model, Monod model and Haldane model. The maximum rate removal constant Umax, sludge yield coefficient Y and inhibition constant Ki were 1.157 g/(L·d), 0.153 mgVSS/mgCOD and 670 mg/L, respectively. It provided data support for the practical application of the anaerobic fermentation treating low-strength wastewater.

Air saturation methodology proposal for the analysis of wine oxygen consumption kinetics.

The great heterogeneity currently present when characterizing wine consumption kinetics means that a saturation method, as well as different parameters that allow comparison between wines, need to be established. The aim of this work was to establish a robust method for a wine saturation protocol and compare different fitting models to approximate the oxygen consumption kinetics. To differentiate wines, parameters extracted from the oxygen consumption curves were studied and proposed. 72 young commercial wines (red, white and rosé) from different Spanish appellations of origin, varieties and vintages were used. The results revealed that 5 min was enough to saturate wines up to the maximum level for each one at 35 °C. The inverse curve fitting model showed the best results for all wines. Oxygen at half consumption time (Omid) and time required to consume from 90% to 10% of the oxygen initially available (ΔtO_90_10) were the parameters that differentiated wines the most.

Removal of iron, zinc, and nickel-ions using nano bentonite and its applications on power station wastewater.

Removal of high concentrations of toxic heavy metals from wastewater is very important within the environmental field because heavy metals pollution a serious environmental problem due to them being nonbiodegradable. This study shed some light on the use of Nano bentonite as an adsorbent for the elimination of Iron, Zinc, and Nickel ions from wastewater, and the optimum conditions were evaluated to find out thermodynamic and kinetic parameters and equilibrium adsorption models have been applied. The results showed that adsorption percentage increases with increasing temperature, speed of rotation, and volume of solution, but decreases with adsorbent dose and initial concentration increase. The adsorption process has fit pseudo-second-order kinetic model Langmuir and Freundlich adsorption isotherm models were applied to analyze adsorption data and both were found to apply to these adsorption processes. Thermodynamic parameters e.g., ΔGo, ΔSo, and ΔHo of the adsorption process were found to be endothermic. Finally, the Nano bentonite was observed to be more powerful for the removal of Fe (III), Zn (II), and Ni (II) at the same experimental conditions.

Effective and Apparent Diffusion Coefficients of Chloride Ions and Chloride Binding Kinetics Parameters in Mortars: Non-Stationary Diffusion-Reaction Model and the Inverse Problem.

A non-equilibrium diffusion-reaction model is proposed to describe chloride transport and binding in cementitious materials. A numerical solution for this non-linear transport with reaction problem is obtained using the finite element method. The effective chloride diffusion coefficients and parameters of the chloride binding are determined using the inverse method based on a diffusion-reaction model and experimentally measured chloride concentrations. The investigations are performed for two significantly different cements: ordinary Portland and blast furnace cements. The results are compared with the classical diffusion model and appropriate apparent diffusion coefficients. The role of chloride binding, with respect to the different binding isotherms applied, in the overall transport of chlorides is discussed, along with the applicability of the two models. The proposed work allows the determination of important parameters that influence the longevity of concrete structures. The developed methodology can be extended to include more ions, electrostatic interactions, and activity coefficients for even more accurate estimation of the longevity.

Oenological tannins to prevent Botrytis cinerea damage in grapes and musts: Kinetics and electrophoresis characterization of laccase.

Enzymatic parameters (KM and Vmax), residual activity, effect of bentonite and electrophoresis characterization of laccase in the presence of different oenological tannins (OT) were investigated in relation to B. cinerea negative effects in grapes and musts. Five OT were tested (gallotannin, ellagitannin, quebracho, grape-skin and grape-seed) in comparison with ascorbic acid (AA), sulfur dioxide (SO2) and bentonite. We added OT, AA, SO2 and bentonite to botrytized must obtained by inoculation of grapes with B. cinerea strain 213. Laccase activity was measured by the syringaldazine method at different concentrations of substrate. Enzymatic parameters were determined using Michaelis-Menten and Lineweaver-Burk plots. The B. cinerea strain was also grown in a liquid medium for laccase production. Molecular weight of laccases and effect of OT upon these laccases were studied by SDS-PAGE. Results confirm that bentonite, contrary to OT, did not permit to reduce laccase activity. Regardless the tannin considered, Vmax, KM and laccase activity were reduced and gallotannin, grape-skin and grape-seed tannin presented the greatest ability. Efficiency of grape-seed tannin addition in order to reduce the laccase activity, was comparable to that of AA or SO2 at the typical doses employed in oenology for each one. Oenological tannins appear to be excellent processing aids to prevent laccase effects and contribute to reduce the use of SO2 in grapes and musts.

Thermo-catalytic decomposition of polystyrene waste: Comparative analysis using different kinetic models.

Due to a huge increase in polymer production, a tremendous increase in municipal solid waste is observed. Every year the existing landfills for disposal of waste polymers decrease and the effective recycling techniques for waste polymers are getting more and more important. In this work pyrolysis of waste polystyrene was performed in the presence of a laboratory synthesized copper oxide. The samples were pyrolyzed at different heating rates that is, 5°Cmin-1, 10°Cmin-1, 15°Cmin-1 and 20°Cmin-1 in a thermogravimetric analyzer in inert atmosphere using nitrogen. Thermogravimetric data were interpreted using various model fitting (Coats-Redfern) and model free methods (Ozawa-Flynn-Wall, Kissinger-Akahira-Sunose and Friedman). Thermodynamic parameters for the reaction were also determined. The activation energy calculated applying Coats-Redfern, Ozawa-Flynn-Wall, Kissinger-Akahira-Sunose and Friedman models were found in the ranges 105-148.48 kJmol-1, 99.41-140.52 kJmol-1, 103.67-149.15 kJmol-1 and 99.93-141.25 kJmol-1, respectively. The lowest activation energy for polystyrene degradation in the presence of copper oxide indicates the suitability of catalyst for the decomposition reaction to take place at lower temperature. Moreover, the obtained kinetics and thermodynamic parameters would be very helpful in determining the reaction mechanism of the solid waste in a real system.

Oxytree Pruned Biomass Torrefaction: Process Kinetics.

Oxytree is a fast-growing energy crop with C4 photosynthesis. In this research, for the first time, the torrefaction kinetic parameters of pruned Oxytree biomass (Paulownia clon in Vitro 112) were determined. The influence of the Oxytree cultivation method and soil class on the kinetic parameters of the torrefaction was also investigated. Oxytree pruned biomass from a first-year plantation was subjected to torrefaction within temperature range from 200 to 300 °C and under anaerobic conditions in the laboratory-scale batch reactor. The mass loss was measured continuously during the process. The relative mass loss increased from 1.22% to 19.56% with the increase of the process temperature. The first-order constant rate reaction (k) values increased from 1.26 × 10-5 s-1 to 7.69 × 10-5 s-1 with the increase in temperature. The average activation energy for the pruned biomass of Oxytree torrefaction was 36.5 kJ∙mol-1. Statistical analysis showed no significant (p < 0.05) effect of the Oxytree cultivation method and soil class on the k value. The results of this research could be useful for the valorization of energy crops such as Oxytree and optimization of waste-to-carbon and waste-to-energy processes.

Comparative research on the metabolism of metoprolol by four CYP2D6 allelic variants in vitro with LC-MS/MS.

Specific study about the effect of cytochrome P450 2D6 (CYP2D6) polymorphisms on the metabolism of clinic drugs is of great significance for drug safety investigation. Here, the interaction between CYP2D6 variants (*1, *2, *10, *39) and metoprolol (MET) was intensively researched in vitro from the aspect of drug-enzyme kinetic study. To obtain quantitative data, α-hydroxymetoprolol (main metabolite of MET) was selected as an ideal analyte and an LC-MS/MS method was adopted for sample determination. Firstly, by selecting suitable internal standard and optimizing separation condition, the LC-MS/MS method was established and validated. Then, the drug-enzyme incubation system was optimized by two parameters: incubation time and amount of enzyme. Lastly, the interaction between CYP2D6 allelic variants and MET was characterized by Km, Vmax and CLint. As a result, four CYP2D6 enzymes displayed diverse Km or Vmax towards MET and the values of CLint showed a wide range from 8.91 to 100%. Relative to CYP2D6*1 (CLint*1 = 100%), CYP2D6*2 demonstrated the second high catalytic activity (CLint*2/*1 = 74.87%) while CYP2D6*39 (CLint*39/*1 = 29.65%) and CYP2D6*10 (CLint*10/*1 = 8.91%) showed minimal catalytic activity. This comprehensive in vitro data suggested the prominent influence of CYP2D6 polymorphisms on the metabolism of MET, which could offer valuable information for personalized administration of MET in clinic.

High efficiency removal of As(III) from waters using a new and friendly adsorbent based on sugarcane bagasse and corncob husk Fe-coated biochars.

Water contamination of As is a big issue in many areas around the globe. Therefore, cheap and efficient techniques are essential facing traditional treatment methods. Then, biochars (BC) emerged recently as material that can be used for As removal. However, research about efficiency of BC produced from local feedstock is still needed. The purpose of this study is to assess the efficiency of BC produced from sugarcane bagasse (SB) together with corncob husk (CH) with and without Fe(III) (BCFe) modification to be used for removal of As(III) from waters. The BC and BCFe produced at different pyrolysis temperatures were characterised using FTIR and SEM/EDS. Adsorption capacities of BC and BCFe were evaluated via batch adsorption, desorption and column tests and their performance was compared with adsorption using activated carbon. The results showed that Fe modification improve substantially the As(III) adsorption in a way that both BCFe-SB and BCFe-CH removed from 85% to 99.9% from 1000 µg/L As(III) solutions. Both materials fitted well in Langmuir model and the maximum adsorption capacity was 20 mg/g for BCFe-SB and 50 mg/g for BCFe-CH. The adsorption kinetics of BCFe was fast (≤ 30 min) and it had a better performance than activated carbon. The column tests showed that the process is efficient even at high As(III) concentrations. The fast removal process and good removal results make the BCFe-SB and BCFe-CH attractive for in situ and commercial (filters) use, since time and efficiency are required in new technologies.

Influence of the dissociation rate constant on the intra-tumor distribution of antibody-drug conjugate against tissue factor.

Antibody-drug conjugates (ADCs) are currently considered to be promising agents for cancer therapy. However, especially in solid tumors, the uneven distribution of ADCs would decrease their efficacy in clinical studies. We suggest that in addition to optimizing ADC components, such as the linker structure and anticancer agent, it is necessary to consider the distribution of the ADC within tumor tissue. In this study, we established three kinds of anti-tissue factor (TF) ADCs: 1849ADC with a low kd, 444ADC with an intermediate kd, and 1084ADC with a high kd. All three of the anti-TF ADCs exhibited almost the same in vitro cytotoxicity and pharmacological and biochemical characteristics, although the binding kinetics parameters differed. In vivo, all ADCs exerted equivalent antitumor effects against small BxPC3 tumors. However, on larger BxPC3 tumors, 1084ADC (higher kd) exerted higher antitumor activity than 1849ADC (lower kd). Furthermore, immunofluorescence staining indicated that 1084ADC was distributed throughout the whole tumor, whereas 1849ADC was mainly localized close to tumor vessels. We conclude that the ADC with a higher kd increased the antitumor effect of because it penetrated and distributed evenly throughout the entire solid tumor. These findings highlight the importance of the kd of a mAb in ADC design.

Analytical Expressions for the Mixed-Order Kinetics Parameters of TL Glow Peaks Based on the two Heating Rates Method.

The two heating rates method (originally developed for first-order glow peaks) was used for the first time to evaluate the activation energy (E) from glow peaks obeying mixed-order (MO) kinetics. The derived expression for E has an insignificant additional term (on the scale of a few meV) when compared with the first-order case. Hence, the original expression for E using the two heating rates method can be used with excellent accuracy in the case of MO glow peaks. In addition, we derived a simple analytical expression for the MO parameter. The present procedure has the advantage that the MO parameter can now be evaluated using analytical expression instead of using the graphical representation between the geometrical factor and the MO parameter as given by the existing peak shape methods. The applicability of the derived expressions for real samples was demonstrated for the glow curve of Li2B4O7:Mn single crystal. The obtained parameters compare very well with those obtained by glow curve fitting and with the available published data.

Comparative study on the interaction between 3 CYP2C9 allelic isoforms and benzbromarone by using LC-MS/MS method.

Benzbromarone is a uricosuric drug metabolized predominantly by cytochrome P450 2C9 from in vitro findings. Human CYP2C9 exhibits extensive genetic polymorphism and numbers of clinic studies have demonstrated that CYP2C9 genetic polymorphism has a significant influence on the pharmacokinetics of benzbromarone. But in vitro study on the interaction between CYP2C9 allelic isoforms and benzbromarone was rare. Here, an LC-MS/MS method was established and validated to determine the concentration of benzbromarone in different CYP2C9 enzyme incubation systems for the drug-enzyme interaction study. By selecting appropriate internal standard and optimizing separation system, including mobile phase, sample solvent and gradient elution condition, this LC-MS/MS method was developed with fine linearity (r2≥0.996), good reproducibility (RSD≤6.6%), high stability (92.37-114.67%), efficient recovery (91.23-109.82%) and acceptable matrix effect (110.54-115.31%). Based on this method, the interaction between 3 CYP2C9 allelic isoforms and benzbromarone was researched by kinetics parameters (Km, Vmax, Clint). As a result, CYP2C9*1 displayed the highest metabolic activity towards benzbromarone, CYP2C9*2 showed a little lower catalytic activity than CYP2C9*1 (relative clearance/*1=85.86%), CYP2C9*3 showed the lowest catalytic activity (relative clearance/*1=21.57%). The result illustrated that various CYP2C9 allelic isoforms showed different enzymatic activities towards benzbromarone, which could offer effective consultation for personalized administration in clinic.

Effectiveness of Vegetated Drainage Ditches for Domestic Sewage Effluent Mitigation.

Plant species have an important role in eco-ditches; however, the Michaelis-Menten kinetic parameters of nutrient uptake, growth rate and purification efficiency of ditch plants and their influences on domestic sewage treatment efficiency are still unclear. Growth rates of all nine species, but especially Lemna gibba, Cladophora and Myriophyllum verticillatum were best in undiluted domestic sewage as opposed to a mixture of domestic sewage. Performance of species to accumulate nutrients was not only species-specific, but was also affected by both sewage treatments. Removal efficiency of nutrients was dependent on both plant species and treatment. Uptake kinetic parameters were significantly affected by both nutrient form and plant species. The maximum uptake rate (Vmax) of NH4-N was higher than NO3-N. Similarly, Km values for NH4-N were greater than NO3-N. These results could be used to identify plants for sewage treatment efficiency and enhance water quality in eco-ditch treatment systems.

Characterization and Low-Resolution Structure of an Extremely Thermostable Esterase of Potential Biotechnological Interest from Pyrococcus furiosus.

Enzymes isolated from extremophiles often exhibit superior performance and potential industrial applications. There are several advantages performing biocatalysis at elevated temperatures, including enhanced reaction rates, increased substrate solubility and decreased risks of contamination. Furthermore, thermophilic enzymes usually exhibit high resistance against many organic solvents and detergents, and are also more resistant to proteolytic attack. In this study, we subcloned and characterized an esterase from the hyperthermophilic archaeon Pyrococcus furiosus (Pf_Est) that exhibits optimal activity around 80 °C using naphthol-derived substrates and p-nitrophenyl palmitate (pNPP). According to the circular dichroism spectra, the secondary structure of P. furiosus esterase, which is predominantly formed by a ß-sheet structure, is very stable, even after incubation at 120°C. We performed SAXS to determine the low-resolution structure of Pf_Est, which is monomeric in solution at 80 °C and has a molecular weight of 28 kDa. The Km and V max values for this esterase acting on pNPP were 0.53 mmol/L and 6.5 × 10-3 U, respectively. Pf_Est was most active in the immiscible solvents and retained more than 50 % in miscible solvents. Moreover, Pf_Est possesses transesterification capacity, presenting better results when isobutanol was used as an acyl acceptor (2.69 ± 0.14 × 10-2 µmol/min mg) and the highest hydrolytic activity toward olive oil among different types of oils testes in this study. Collectively, these biophysical and catalytic properties are of interest for several biotechnological applications that require harsh conditions, including high temperature and the presence of organic solvents.

Kinetic parameters of red pepper waste as biomass to solid biofuel.

This work aimed to study the kinetic of thermal degradation of red pepper waste as solid biofuel to bioenergy production. The thermal degradation experiments were conducted at three heating rates, 5°C/min, 7.5°C/min and 10°C/min in a thermogravimetric analyzer and oxidative atmosphere. The kinetic analysis was carried out applying the isoconversional model of Ozawa-Flynn-Wall. The activation energy was considerate low and varied 29.49-147.25k J/mol. The enthalpies revealed the energy difference between the reagent and the activated complex agreed with activation energies, the values of the pre-exponential factor indicated empirical first order reactions, Gibbs free energy varied from 71.77 kJ/mol to 207.03 kJ/mol and the changes of entropies had negative values, indicating that the degree of disorder of products formed through bond dissociations was lower than initial reactants. The calorific value was 19.5 MJ/kg, considered a relevant result for bioenergy production.

Microbial kinetics of Clostridium termitidis on cellobiose and glucose for biohydrogen production.

OBJECTIVE: To determine Monod kinetics parameters (µmax, Ks, kd and YX/S) of the mesophilic H2 producer Clostridium termitidis grown on glucose and cellobiose by modeling in MATLAB. RESULTS: Maximum specific growth rates (µmax) were 0.22 and 0.24 h(-1) for glucose and cellobiose respectively; saturation constants (Ks) were 0.17 and 0.38 g l(-1) respectively and the biomass yields (YX/S) were 0.26 and 0.257 g dry wt g(-1) substrate. H2 yields of 1.99 and 1.11 mol H2 mol(-1) hexose equivalent were also determined for glucose and cellobiose respectively. CONCLUSION: The microbial kinetics of this model microorganism will enhance engineering biofuel production applications.