Kinetic Analysis Research Articles

Numerical simulation method for the assessment of the effect of molar activity on the pharmacokinetics of radioligands in small animals

BackgroundIt is well recognized that the molar activity of a radioligand is an important pharmacokinetic parameter, especially in positron emission tomography (PET) of small animals. Occupation of a significant number of binding sites by radioligand molecules results in low radioligand accumulation in a target region (mass effect). Nevertheless, small-animal PET studies have often been performed without consideration of the molar activity or molar dose of radioligands. A simulation study would therefore help to assess the importance of the mass effect in small-animal PET. Here, we introduce a new compartmental model-based numerical method, which runs on commonly used spreadsheet software, to simulate the effect of molar activity or molar dose on the pharmacokinetics of radioligands.ResultsAssuming a two-tissue compartmental model, time-concentration curves of a radioligand were generated using four simulation methods and the well-known Runge–Kutta numerical method. The values were compared with theoretical values obtained under an ultra-high molar activity condition (pseudo-first-order binding kinetics), a steady-state condition and an equilibrium condition (second-order binding kinetics). For all conditions, the simulation method using the simplest calculation yielded values closest to the theoretical values and comparable with those obtained using the Runge–Kutta method. To satisfy a maximum occupancy less than 5%, simulations showed that a molar activity greater than 150 GBq/μmol is required for a model radioligand when 20 MBq is administered to a 250 g rat and when the concentration of binding sites in target regions is greater than 1.25 nM.ConclusionsThe simulation method used in this study is based on a very simple calculation and runs on widely used spreadsheet software. Therefore, simulation of radioligand pharmacokinetics using this method can be performed on a personal computer and help to assess the importance of the mass effect in small-animal PET. This simulation method also enables the generation of a model time-activity curve for the evaluation of kinetic analysis methods.

Effect of Translation-Enhancing Nascent SKIK Peptide on the Arrest Peptides Containing Consecutive Proline.

Ribosome arrest peptides (RAPs) such as the SecM arrest peptide (SecM AP: FSTPVWISQAQGIRAGP) and WPPP with consecutive Pro residues are known to induce translational stalling in Escherichia coli. We demonstrate that the translation-enhancing SKIK peptide tag, which consists of four amino acid residues Ser-Lys-Ile-Lys, effectively alleviates translational arrest caused by WPPP. Moreover, the proximity between SKIK and WPPP significantly influences the extent of this alleviation, observed in both PURE cell-free protein synthesis and in vivo protein production systems, resulting in a substantial increase in the yield of proteins containing such RAPs. Furthermore, we unveil that nascent SKIK peptide tag and translation elongation factor P (EF-P) alleviate ribosome stalling in consecutive-Pro-rich protein to synergistically promote translation. A kinetic analysis based on the generation of superfolder green fluorescent protein under in vitro translation reaction reveals that the ribosome turnover is enhanced by more than 10-fold when the SKIK peptide tag is positioned immediately upstream of the SecM AP sequence. Our findings provide valuable insights into optimizing protein production processes, which are essential for advancing synthetic biology applications.

Amorphous MoS3 Anchored within Hollow Carbon as a Cathode Material for Magnesium-Ion Batteries.

Magnesium-ion batteries are considered the next-generation promising large-scale energy storage devices owing to the low-cost and nondendritic features of metallic Mg anode. Nevertheless, such strong electrostatic interaction between bivalent Mg2+ and crystalline cathode materials will lead to low capacity and poor diffusion kinetics, which seriously hinders the further development of magnesium-ion batteries. Herein, amorphization and anion-rich strategies are employed to prepare well-designed cathode materials with MoS3 anchored on hollow carbon nanospheres (a-MoS3/HCS). The amorphous MoS3 provides unrestricted 3D diffusion access and effectively boosts the Mg2+ diffusion kinetics, while the anion-rich feature of MoS3 offers rich active sites for Mg2+ storage and finally contributes to a high discharge capacity driven by the anionic redox mechanism. Moreover, the effective modification of hollow carbon nanospheres buffers the volumetric changes of MoS3 and improves the electron transfer efficiency. Owing to the above-mentioned multiple advantages, a-MoS3/HCS exhibits an ultrahigh discharge capacity (489.2 mAh g-1 at 50 mA g-1) and high cyclic performance (200.1 mAh g-1 at 2 A g-1 for 300 cycles), distinctly superior to those of crystalline 1T/2H-MoS2/HCS and 2H-MoS2/HCS and surpassing almost all of the molybdenum sulfide-based cathodes. Furthermore, the high-performance a-MoS3/HCS-based pouch cell with the ability to drive various mini-type devices confirms the potential application values. The excellent magnesium storage properties of a-MoS3/HCS are further verified by the related kinetics analysis, DFT theoretical calculation, and reversible electrochemical reactions. The amorphous and redox-rich tactics of a-MoS3/HCS provide an innovative pathway to explore high-efficiency cathode materials for various multivalent-ion batteries.

Kinetic Modeling Enables Understanding of Off-Cycle Processes in Pd-Catalyzed Amination of Five-Membered Heteroaryl Halides.

The mechanism of Pd-catalyzed amination of five-membered heteroaryl halides was investigated by integrating experimental kinetic analysis with kinetic modeling through predictive testing and likelihood ratio analysis, revealing an atypical productive coupling pathway and multiple off-cycle events. The GPhos-supported Pd catalyst, along with the moderate-strength base NaOTMS, was previously found to promote efficient coupling between five-membered heteroaryl halides and secondary amines. However, slight deviations from the optimal concentration, temperature, and/or solvent resulted in significantly lower yields, contrary to typical reaction optimization trends. We found that the coupling of 4-bromothiazole with piperidine proceeds through an uncommon mechanism in which the NaOTMS base, rather than the amine, binds first to the oxidative addition complex; the resulting OTMS-bound Pd species is the resting state. Formation of the Pd-amido complex via base/amine exchange was identified as the turnover-limiting step, unlike other reported catalyst systems for which reductive elimination is turnover-limiting. We determined that the amine-bound Pd complex, usually an on-cycle intermediate, is instead a reversibly generated off-cycle species, and that base-mediated decomposition of 4-bromothiazole is the primary irreversible catalyst deactivation pathway. Predictive testing and kinetic modeling were key to the identification of these off-cycle processes, providing insight into minor mechanistic pathways that are difficult to observe experimentally. Collectively, this report reveals the unique enabling features of the Pd-GPhos/NaOTMS system, implementing mechanistic insights to improve the yields of particularly challenging coupling reactions. Moreover, these findings highlight the utility of applying predictive tests to kinetic models for the rapid evaluation of mechanistic possibilities in small-molecule catalytic systems.

Identification of a dengue 2 virus envelope protein receptor in Aedes aegypti critical for viral midgut infection

The establishment of a productive dengue virus (DENV) infection in the midgut epithelial cells of Aedes aegypti is critical for the viral transmission cycle. The hypothesis that DENV virions interact directly with specific mosquito midgut proteins was explored. We found that DENV serotype 2 (DENV2) pretreated with trypsin interacted with a single 31 kDa protein, identified as AAEL011180 by protein mass spectrometry. This putative receptor is a highly conserved protein and has orthologs in culicine and anopheline mosquitoes. We confirmed that impairing the expression of AAEL011180 in the midgut of Ae. aegypti females abolished the interaction with DENV2, and the virus also bound to immobilized recombinant purified receptor. Furthermore, recombinant DENV2 surface E glycoprotein bound to recombinant AAEL011180 with high affinity (38.2 nM) in binding kinetic analysis using surface plasmon resonance. The gene for this DENV2 E protein receptor (EPrRec) was disrupted, but since the gene is essential in Ae. aegypti, only heterozygote knockout (ΔEPrRec+/-) females could be recovered. Further reducing EPrRec mRNA expression in the midgut of ΔEPrRec+/- females by systemic dsRNA injection significantly reduced the prevalence of DENV2 midgut infection. EPrRec also interacts with heat shock protein 70 cognate 3 (Hsc70-3), and silencing Hsc70-3 expression in ΔEPrRec females also reduced the prevalence of DENV2 midgut infection.

Second-Sphere Histidine Catalytic Function in a Fungal Polysaccharide Monooxygenase.

Fungal polysaccharide monooxygenases (PMOs) oxidatively degrade cellulose and other carbohydrate polymers via a mononuclear copper active site using either O2 or H2O2 as a cosubstrate. Cellulose-active fungal PMOs in the auxiliary activity 9 (AA9) family have a conserved second-sphere hydrogen-bonding network consisting of histidine, glutamine, and tyrosine residues. The second-sphere histidine has been hypothesized to play a role in proton transfer in the O2-dependent PMO reaction. Here the role of the second-sphere histidine (H157) in an AA9 PMO, MtPMO9E, was investigated. This PMO is active on soluble cello-oligosaccharides such as cellohexaose (Glc6), thus enabling kinetic analysis with the point variants H157A and H157Q. The variants appeared to fold similarly to the wild-type (WT) enzyme and yet exhibited weaker affinity toward Glc6 than WT (WT KD = 20 ± 3 μM). The variants had comparable oxidase (O2 reduction to H2O2) activity to WT at all pH values tested. Using O2 as a cosubstrate, the variants were less active for Glc6 hydroxylation than WT, with H157A being the least active. Similarly, H157Q was competent for Glc6 hydroxylation with H2O2, but H157A was less active. Comparison of the crystal structures of H157Q and WT MtPMO9E reveals that a terminal heteroatom of Q157 overlays with Nε of H157. Altogether, the data suggest that H157 is not important for proton transfer, but support a role for H157 as a hydrogen-bond donor to diatomic-oxygen intermediates, thus facilitating catalysis with either O2 or H2O2.

Accelerated Amyloid Aggregation Dynamics of Intrinsically Disordered Proteins in Heavy Water.

We explored the influence of D2O on the fibrillation kinetics and structural dynamics of amyloid intrinsically disordered proteins (IDPs), including α-synuclein, amyloid-β 1-42, and K18. Our findings revealed that fibrillation of IDPs was accelerated in D2O compared to that in H2O, exhibiting faster kinetics in contrast to the structured protein, insulin. Structural investigations using electrospray ionization ion mobility mass spectrometry and small-angle X-ray scattering combined with molecular dynamics simulations demonstrated that IDPs did not show significant structural changes that could influence accelerated fibrillation in D2O. Umbrella sampling of protein protofibrils verified that an increased level of hydrogen bonding of D2O and enhanced hydrophobic interactions stabilized β-sheet structured fibrils in D2O. These findings indicate that stabilizing β-sheet fibrils and a more hydrophobic microenvironment in D2O result in enhanced and faster fibrillation of IDPs. The study highlights the importance of considering D2O's differential impact on protein interactions when conducting structural and kinetic analyses, particularly for native peptides and proteins.

Engineering Heterointerface to Synergistically Regulate Kinetics and Stress of Copper-Cobalt Selenide toward Reversible Magnesium/Lithium Hybrid Batteries.

Metal chalcogenide-based cathodes are crucial for the development of rechargeable magnesium batteries, yet the strong electrostatic interactions of Mg2+ result in slow ion transport and high polarization. The Mg2+/Li+ hybrid battery holds promise for enhancing the energy storage capability. Herein, we establish a system that utilizes (Co,Cu)Se2/CoSex heterostructure grown on carbon cloth as the cathode and APC-LiCl as a dual-salt electrolyte to achieve high reversible capacity, enhanced cyclic stability, and impressive rate performance. First-principles calculations and kinetic analyses are employed to uncover that constructing the heterointerface stimulates the formation of an intrinsic electric field and high-density electron flows, thereby accelerating charge transfer and ion diffusion processes. Finite element simulations further demonstrate that the heterostructure effectively alleviates stresses associated with magnesiation/lithiation to enhance the structural integrity of the material. Moreover, the multistep reaction unveils a stepwise structural transformation pathway. This study initiates a new chapter in designing heterointerface strategies for advanced energy storage devices.

Balanced Miscibility and Crystallinity by 2D Acceptors Enabled Halogen-Free Solvent-Processed Organic Solar Cells to Achieve 19.28% Efficiency.

Two highly crystalline 2D acceptors, ATIC-C11 and ATIC-BO, with acenaphthene-expanded quinoxaline central cores, have been demonstrated with very different characteristics in ternary organic solar cells (OSCs). The difference in side chains induces their distinctive molecular packing mode and unique crystal structure, in which ATIC-C11 displays a 3D structure with an elliptical framework, and ATIC-BO gives a rectangular framework. Their high crystallinity contributes to organized molecular packing in ternary devices, thus low energetic disorder and suppressed energy loss. Through the analysis of morphology and carrier kinetics, it is found that ATIC-BO's strong self-aggregation and immiscibility induce large aggregates and severely impede charge transfer (CT) and dissociation. Conversely, ATIC-C11's suitable crystallinity and compatibility positively regulate the crystalline kinetics during film formation, thus forming much-ordered molecular packing and favorable phase separation size in blend films. As a result, ATIC-C11-based ternary devices achieve a high efficiency of 19.28% with potential in scalability and stability, which is the top-ranking efficiency among nonhalogenated solvent-processed OSCs. This work not only displays highly efficient and stable halogen-free solvent-processed organic photovoltaics (OPVs), but also offers a new thought for material design and selection rule on the third component in highly efficient ternary OSCs.

Contrast Kinetics in CT Coronary Angiography

AbstractComputed tomography coronary angiography (CTCA) is a technically demanding radiological investigation that requires adequate opacification of coronary arteries at peak aortic enhancement phase, with minimal or no contrast in the superior vena cava and right-sided cardiac chambers to avoid streak artifacts of dense contrast. Therefore, it is prudent to know about contrast media, contrast kinetics, and contrast injection protocols. This article attempts to describe the essentials of various aspects of contrast media that should be considered for CTCA along with an in-depth analysis of contrast kinetics that every radiologist should know for obtaining adequate opacification of coronary arteries.

Investigating the Impact of Nano‐Metal Oxides (Copper and Iron) on the Thermal Decomposition Behavior of Advanced Propellants with Nitrocellulose/Polyurethane Binders

AbstractThis research delves into the combined effects of green nano metal oxides (copper and iron) and polyurethane (PU) modification on the thermal degradation kinetics of propellant based on solid ammonium nitrate composite modified simple base (CMSB). Surface modification of ammonium nitrate particles was achieved through repeated spray coating, ensuring effective catalyst binding. The formulated compositions of propellants underwent thorough thermal characterization, including thermogravimetric (TG) and differential scanning calorimetry (DSC) analyses. TG analysis revealed a significant decrease in the propellant's thermal degradation temperature, attributed to AN modification with nano metal oxides (nMOs) and the use of PU/NC as a binder. Isoconversional kinetic methods (It‐KAS, It‐FWO, and VYA/CE) were employed for further analysis, allowing prediction of kinetic parameters. Additionally, kinetic analysis results allowed calculation of the critical ignition temperature. The thermokinetic results underscore the substantial impact of nMOs particles and PU modification regarding the reactivity and catalytic performance of propellant containing ammonium nitrate, leading to a noteworthy reduction in activation energy and critical ignition temperature. Furthermore, modifying the binder with nitrocellulose and incorporating nanoparticles significantly reduces ignition delay and combustion duration while increasing flame intensity in CMDB solid propellants, enhancing overall combustion efficiency.

Diffusion and Viscosity in Mixed Protein Solutions.

The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately reproduced experimental trends across a wide range of protein concentrations, including highly crowded environments up to 300 g/L. Notably, viscosity increased with crowding but varied little between different crowder types, while diffusion rates were significantly reduced depending on protein-protein interaction strength. Analysis using the Stokes-Einstein relation indicated that the reduction in diffusion exceeded what was expected from viscosity changes alone, with the additional slow-down attributable to transient cluster formation driven by weakly attractive interactions. Contact kinetics analysis further revealed that longer-lived interactions contributed more significantly to reduced diffusion rates than short-lived interactions. This study also highlights the accuracy of current computational methodologies for capturing the dynamics of proteins in highly concentrated solutions and provides insights into the molecular mechanisms affecting protein mobility in crowded environments.

Enhancing the Non-Isothermal Crystallization Kinetics of Polylactic Acid by Incorporating a Novel Nucleating Agent.

Polylactic acid (PLA) is a widely recognized biodegradable polymer. However, the slow crystallization rate of PLA restricts its practical applications. In this study, camphor leaf biochar decorated with multi-walled carbon nanotubes (C@MWCNTs) was prepared using the strong adhesive properties of polydopamine, and PLA/C@MWCNTs composites were fabricated via the casting solution method. The influence of C@MWCNTs as a novel nucleating agent on the melt behavior and non-isothermal crystallization behavior of PLA was investigated using differential scanning calorimetry (DSC). The crystallization kinetic parameters were obtained through the Jeziorny, Ozawa, and Mo methods, and the crystallization activation energy of the PLA/C@MWCNTs composites was calculated by the Kissinger method. The results show that the PLA/C@MWCNTs composites exhibit higher crystallinity and crystallization temperatures than those of PLA. Non-isothermal crystallization kinetic analysis reveals that the Mo method better describes the non-isothermal crystallization kinetics of both PLA and PLA/C@MWCNTs composites. In addition, it was found that C@MWCNTs, despite increasing the crystallization activation energy, can act as an efficient nucleating agent to increase the crystallization rate of PLA. These experimental results provide valuable insights for enhancing the slow crystallization rates associated with PLA.

Anomaly Detection Utilizing One-Class Classification—A Machine Learning Approach for the Analysis of Plant Fast Fluorescence Kinetics

The analysis of fast fluorescence kinetics, specifically through the JIP test, is a valuable tool for identifying and characterizing plant stress. However, interpreting OJIP data requires a comprehensive understanding of their underlying theory. This study proposes a Machine Learning-based approach using a One-Class Support Vector Machine anomaly detection model to effectively categorize OJIP measurements into “normal”, representing healthy plants, and “anomalies”. This approach was validated using a previously published dataset. A subgroup of the identified “anomalies” was clearly linked to stress-induced reductions in photosynthesis. Furthermore, the percentage of these “anomalies” showed a meaningful correlation with both the progression and severity of stress. The results highlight the still largely unexploited potential of Machine Learning in OJIP analysis.

Proton Relays in Molecular Catalysis for Hydrogen Evolution and Oxidation: Lessons From the Mimicry of Hydrogenases and Electrochemical Kinetic Analyses

AbstractThe active sites of metalloenzymes involved in small molecules activation often contain pendant bases that act as proton relay promoting proton‐coupled electron‐transfer processes. Here we focus on hydrogenases and on the reactions they catalyze, i. e. the hydrogen evolution and oxidation reactions. After a short description of these enzymes, we review some of the various biomimetic and bioinspired molecular systems that contain proton relays. We then provide the formal electrochemical framework required to decipher the key role of such proton relay to enhance catalysis in a single direction and discuss the few systems active for H2 evolution for which quantitative kinetic data are available. We finally highlight key parameters required to reach bidirectional catalysis (both hydrogen evolution and hydrogen oxidation catalyzed) and then transition to reversible catalysis (both reactions catalyzed in a narrow potential range) as well as illustrate these features on few systems from the literature.

Proton Relays in Molecular Catalysis for Hydrogen Evolution and Oxidation: Lessons From the Mimicry of Hydrogenases and Electrochemical Kinetic Analyses

AbstractThe active sites of metalloenzymes involved in small molecules activation often contain pendant bases that act as proton relay promoting proton‐coupled electron‐transfer processes. Here we focus on hydrogenases and on the reactions they catalyze, i. e. the hydrogen evolution and oxidation reactions. After a short description of these enzymes, we review some of the various biomimetic and bioinspired molecular systems that contain proton relays. We then provide the formal electrochemical framework required to decipher the key role of such proton relay to enhance catalysis in a single direction and discuss the few systems active for H2 evolution for which quantitative kinetic data are available. We finally highlight key parameters required to reach bidirectional catalysis (both hydrogen evolution and hydrogen oxidation catalyzed) and then transition to reversible catalysis (both reactions catalyzed in a narrow potential range) as well as illustrate these features on few systems from the literature.

Catalytic Asymmetric Cycloaddition of Olefins with In Situ Generated N-Boc-Formaldimine.

Chiral 1,3-amino alcohols are ubiquitous structural motifs in natural products and active pharmaceutical ingredients. We present a highly enantioselective, inverse-electron-demand hetero-Diels-Alder reaction of olefins with in situ generated N-Boc-formaldimine catalyzed by strong and confined Bro̷nsted acids. This transformation provides direct access to valuable 1,3-amino alcohols from styrenes and 1,1-disubtituted alkenes. Isotope labeling studies and kinetic analysis reveal an unusual mechanism involving an oxazinium intermediate and a catalyst order greater than one.

Efficient CO2 adsorption by deoiled flaxseed hydrochar

This study optimizes CO2 adsorption using hydrochar from de-oiled flaxseed (FDOP), a waste byproduct of the oil extraction industry, through hydrothermal carbonization (HTC). The aim is to enhance CO2 capture sustainably and cost-effectively. Using Response Surface Methodology (RSM), in optimal conditions achieved 1153.26 mg/g CO2 adsorption capacity under 215.15 °C synthesis temperature, 3.05 h synthesis time, 0.99 M acid concentration, 8.997 bar pressure, and 25.07 °C adsorption temperature. Statistical analysis (F-value: 44.48, R²: 0.9705) confirmed strong model reliability. Kinetic analysis showed both physical and chemical adsorption, while thermodynamic analysis revealed exothermic behavior (ΔH° values: -46.697 kJ/mol for M-225, -40.230 kJ/mol for MA-203). After 10 regeneration cycles, the adsorption capacity was reduced by only 2.8% and 3.1%, indicating excellent recyclability. This study highlights FDOP-derived hydrochar as a highly efficient, low-cost adsorbent, offering industrial applications for carbon capture and waste management.

The Trajectory of Damaged-Base Eversion into the Active Site of Apurinic/Apyrimidinic Endonuclease APE1 Regulates This Enzyme's Substrate Specificity.

Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for the hydrolysis of the phosphodiester bond on the 5' side of an apurinic/apyrimidinic site during base excision repair. Moreover, in DNA, this enzyme can recognize nucleotides containing such damaged bases as 5,6-dihydro-2'-deoxyuridine (DHU), 2'-deoxyuridine (dU), alpha-2'-deoxyadenosine (αA), and 1,N6-ethenoadenosine (εA). Previously, by pulsed electron-electron double resonance spectroscopy and pre-steady-state kinetic analysis, we have revealed multistep DNA rearrangements during the formation of the catalytic complex. In the present study, the modeling of the eversion trajectory of nucleotides with various damaged bases was performed by directed molecular dynamics simulations. It was found that each damaged base at the beginning of the eversion interacts with protein loop Val196-Arg201, which should be moved to enable further nucleotide eversion. This movement involves a shift in loop Val196-Arg201 away from loop Asn253-Thr257 and requires the disruption of contacts between these loops. The Glu260Ala substitution facilitates the separation of the two loops. Moreover, conformational changes in the Asn253-Thr257 loop should occur in the second half of the lesion eversion trajectory. All these perturbations within the protein globule tend to reduce steric interactions of each damaged base with the protein during the eversion of the nucleotide from DNA and movement to the active site. These perturbations are important determinants of substrate specificity of endonuclease APE1.

Rate-Controlled Washing of Surface-Modified Nanoparticles Using Rationally Designed Supercritical CO2 Media.

In practical applications of surface-modified nanoparticles (NPs), the washing stage has a number of challenges, such as insufficient washing, long treatment time, and various waste liquors. Cosolvent-enhanced supercritical CO2 (scCO2) is an appealing solvent system for complete, rapid, and eco-friendly washing owing to its high diffusivity and recyclability. In this paper, we report a rapid washing guideline for surface-modified NPs using ethanol-enhanced scCO2. Kinetic analysis was performed on the washing behavior of oleic acid-modified NPs mixed with various modifiers (C10 to C18 fatty acids) at 40 °C and 20.0 MPa while designing scCO2 media based on rationally estimated modifier solubilities. Notably, the scCO2 medium showed superior washing rates to that of ethanol for various modifiers with a wide range of solubilities in scCO2. The washing rate was dependent on solubility and could be organized into two regions, with a threshold value of 0.016 mol kg-1: solubility/diffusivity-controlled and diffusivity-controlled washing. These findings provide valuable guidelines for designing cosolvent-enhanced scCO2 media for the rapid washing of surface-modified NPs.