Dissociation Constant Research Articles

Synchronized motion of interface residues for evaluating protein-RNA complex binding affinity: Application to aptamer-mediated inhibition of TDP-43 aggregates.

Investigating the binding between proteins and aptamers, such as peptides or RNA molecules, is of crucial importance both for understanding the molecular mechanisms that regulate cellular activities and for therapeutic applications in several pathologies. Here, a new computational procedure, employing mainly docking, clustering analysis, and molecular dynamics simulations, was designed to estimate the binding affinities between a protein and some RNA aptamers, through the investigation of the dynamical behavior of the predicted molecular complex. Using the state-of-the-art software catRAPID, we computationally designed a set of RNA aptamers interacting with the TAR DNA-binding protein 43 (TDP-43), a protein associated with several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). We thus devised a computational protocol to predict the RNA-protein molecular complex, so that the structural and dynamical behavior of such a complex can be investigated through extensive molecular dynamics simulation. We hypothesized that the coordinated and synchronized motion of the protein-binding residues, when in contact with RNA molecule, is a critical requisite in order to have a stable binding. Indeed, we calculated the motion covariance exhibited by the interface residues during molecular dynamics simulation: we tested the results against experimental measurements of binding affinity (in this case, the dissociation constant) for six RNA molecules, resulting in a linear correlation of about 0.9. Our findings suggest that the synchronized movement of interface residues plays a pivotal role in ensuring the stability within RNA-protein complexes, moreover providing insights into the contribution of each interface residue. This promising pipeline could thus contribute to the design of RNA aptamers interacting with proteins.

Competitive inhibition of family GH11 Aspergillus fumigatus endo-xylanase A by Oryza sativa xylanase inhibitor protein: Investigating key interface residues and non-covalent interactions

Glycoside hydrolase (GH) family 11 Aspergillus fumigatus endo-xylanase A (AfXylA11) was recombinantly expressed in Pichia pastoris X33 and secreted into culture medium. Hydrolysis of beechwood xylan by recombinant AfXylA11 (reAfXylA11) predominantly generated xylooligosaccharides (XOs), chiefly comprising xylotriose (X2) and xylotetraose (X3). These hydrolysates demonstrated significant antioxidant capabilities. Competitive inhibition of reAfXylA11 was observed in the presence of the Oryza sativa xylanase inhibitor protein (OsXIP), with an inhibition constant (Ki) of 120.98 nM. Molecular dynamics (MD) simulations and conformational analyses of the AfXylA11-OsXIP complex revealed that the extended loop (Lα4β5, K150-V158) of OsXIP penetrated the active groove of AfXylA11, thereby obstructing xylan from interacting with catalytic sites. The R153 at the bottom of the U-shaped loop, was found to form durable hydrogen bonds with E197 (acid/base catalyst) and Y97 of AfXylA11. Additionally, OsXIP established stable interactions with the “cord” and “thumb” regions of AfXylA11 during MD simulations. The binding free energy of the AfXylA11-OsXIP complex was determined to be -74.3 ± 7.6 kcal/mol, with electrostatic interactions and van der Waals forces being the predominant contributors to enzyme-inhibitor interaction. Further MD simulations demonstrated that the mutation of Y116A or S120A in the “cord” region of AfXylA11 significantly reduced its binding affinity to OsXIP by weakening interface residue interactions. Delving into the conformational dynamics of the AfXylA11-OsXIP complex yields insights into the molecular mechanisms dictating their competitive inhibition. This investigation offers useful basis for engineering mutant xylanases that resist to the inhibitory protein yet retain high catalytic efficacy.

Quassinoids from Eurycoma longifolia as Potential Dihydrofolate Reductase Inhibitors: A Computational Study.

Quassinoids are degraded triterpene compounds that can be obtained from various species of the Simaroubaceae plant family, including Eurycoma longifolia. Quassinoids are the major compounds in E. longifolia, and they are known to have various medicinal potentials, such as anticancer and antimalarial properties. Dihydrofolate reductase (DHFR) was reported to be one of the important targets for certain anticancer and antimalarial drugs. Twelve quassinoids from E. longifolia were identified to have anticancer effects based on their IC50 values. This study aimed to evaluate the interactions of these twelve quassinoids with DHFR via Autodock 4.2 software and Biovia Discovery Studio Visualiser. Twelve quassinoids from E. longifolia and their interactions with DHFR were evaluated via Autodock 4.2 software and Biovia Discovery Studio Visualiser. Their drug-likeness and pharmacokinetic properties were also assessed using the ADMETlab 2.0 program. The molecular docking results showed that eleven quassinoids showed better docking scores than methotrexate, in which the binding energy (BE) of these quassinoids ranged from - 7.87 to -9.58 kcal/mol. Their inhibition constant (Ki) ranged from 0.095 to 1.71 μM. At the same time, the BE and Ki values for methotrexate were -7.80 kcal/mol and 1.64 μM, respectively. From the analysis, 6-dehydrolongilactone and eurycomalide B are among the twelve compounds that showed great potential as hit-to-lead compounds based on the docking score on DHFR, drug-likeness, and ADMET properties. These results suggest a great potential to pursue validation studies via in vitro and in vivo models.

Molecular Docking, Pharmacophore Mapping, and Virtual Screening of Novel Glucokinase Activators as Antidiabetic Agents

Background: A pivotal impetus has led to the development of numerous small molecules to develop therapeutic strategies for type 2 diabetes. Novel heterocyclic derivatives are now available with expansive pharmacological activity designed specifically to activate Glucokinase (GK) in the body. This target is of particular significance in antidiabetic drug design since it is a newly validated target. Individuals with type 2 diabetes are unable to maintain blood glucose homeostasis due to impaired glucokinase function. The novel approach to managing type 2 diabetes relies on utilizing heterocyclic derivatives to activate the GK enzyme, also known as a metabolic enzyme. Objective: In this research endeavor, the primary objective was to improve drug delivery while minimizing adverse effects by using molecules that activate glucokinase. Methods: There are 53,000 compounds included in Maybridge's online repository, which has been subjected to rigorous scrutiny. Eight two compounds that encompass the specific oxadiazole core were selectively extracted from this extensive collection. ChemBioDraw Ultra was used for structural drawing, and AutoDock Vina 1.5.6 was used to perform docking analysis. For the online prediction of log P, the SwissADME algorithm was employed. A PKCSM software program was used to predict toxicity for leading compounds. Results: Among all of the compounds, AD80 and AD27 displayed the highest affinity for GK receptors. These compounds, by adhering to Lipinski’s Rule of Five, exhibited good absorption and excretion profiles through the gastrointestinal (GI) tract. Lipinski’s Rule of Five refers to physicochemical properties that favor good oral bioavailability, and these specifications are zero to five hydrogen bond donors, zero to ten hydrogen bond acceptors, molecular weight below 500, and log P no more than five. These criteria ensure that the compounds of the invention have acceptable solubility and permeability, which are vital prerequisites when given orally, to be absorbed via the gastrointestinal wall, metabolized, and found in the urine. Therefore, the chance of drug candidates exhibiting favorable pharmacokinetic characteristics is increased, enhancing their chances of being developed for oral administration. In comparison with standard drugs Dorzagliatin as a glucokinase activator (GKA) and MRK (co-crystallized ligand), these compounds exhibit no skin sensitization, AMES toxicity, or hepatotoxicity. Conclusion: The recently designed lead molecules exhibit an improved pharmacokinetic profile, enhanced binding affinity, and minimal toxicity based on the computational study, potentially making them suitable candidates for further optimization as glucokinase activators.

Stabilizing Scaffold for Short Peptides Based on Knottins.

Bombesin (BBN) is a short peptide with a high affinity for receptors that are expressed on the surface of various types of cancer cells. However, a full length BBN molecule has low in vivo stability. In our study, we propose the use of peptide toxins, derived from animal and plant toxins, as scaffold molecules to enhance the bioavailability and stability of bombesin. These peptides possess a unique structure known as an inhibitory cystine knot. We synthesized structures in which short bombesin was incorporated into various domains of arthropod and plant toxins using solid-phase peptide synthesis. The stability under different conditions was assessed through high-performance liquid chromatography, and binding to cell cultures expressing the bombesin receptor was analyzed. Additionally, toxicity to cell cultures was evaluated using fluorescence microscopy. The data obtained demonstrated that placing the short peptide between the first and second cysteine residues in arachnid toxins results in increased in vitro stability and bioavailability, as well as low cytotoxicity. Arachnid toxins with an inhibitory cystine knot can be considered as a scaffold for increasing the stability of therapeutic peptides.

Dissociation extraction: Theoretical foundations and applications

Dissociation extraction (DE) is a separation method that has been known for many decades but is not yet widely used in industry. However, there are a number of applications for which DE may be applied, for example, for new biorefinery separations. To facilitate future applications, we derived a new shortcut method for DE processes and demonstrated its application in the conceptual design of a separation process for acidic and basic organic mixtures. The new method allows for the calculation of the minimum energy requirement and a fast comparison of dissociation extraction with other separation methods. The shortcut method was validated using experimental data from the literature and is easy to implement because it is based only on the physical distribution coefficients and dissociation constants of the acids or bases to be separated.In the second part of this paper, we identify several areas that require effective separation techniques, where dissociation extraction can have an impact. These include biorefinery separation, polymer recycling, and fatty acid fractionation.In conclusion, we hope to promote DE as a known but less-used separation method for difficult separation problems in both fossil-based and bio-based sustainable chemical products.

A physiologically based toxicokinetic model for microplastics and nanoplastics in mice after oral exposure and its implications for human dietary exposure assessment

Evidence of microplastics (MPs) and nanoplastics (NPs) in foods and daily-use products, along with their frequent detection in the human body, has raised concerns regarding their potential impact on human health through dietary ingestion. However, there is a lack of quantitative tools to simulate their bioaccumulation and tissue distribution following environmental exposure. To address this gap, we developed the first physiologically based toxicokinetic (PBTK) model for predicting the biodistribution of MPs and NPs in mice following oral exposure under various exposure scenarios. This novel model incorporated key kinetic mass transport processes, such as membrane permeability, albumin binding, and cellular uptake. We identified that the absorption rate in the gastrointestinal tract and fecal excretion rate constant had significant impacts on organ dosimetry. Our regression analysis indicated that the size-dependent dissociation constant and urine clearance rate constant sharply increased by a factor of 3 as NPs particle size increased to 1µm. Finally, we developed a graphical user interface to enable interactive visualization and analysis for future applications, supporting human dietary exposure and risk assessment using available food consumption data and MPs/NPs residue data. The simulation results offer a mechanistic perspective, enhancing understanding of the internal organ dosimetry burden and health impacts from dietary exposure to MPs and NPs.

Preparation, characterization, and ex vivo evaluation of isoxanthohumol nanosuspension

This study assessed the equilibrium solubility, oil–water distribution coefficient, and dissociation constant of Isoxanthohumol (IXN), and formulated IXN nanoparticles (IXN-Nps) using a micro media grinding method. The research characterized the particle size, polydispersity index, zeta potential, morphology, and structure of the nanoparticles, and evaluated the optimal cryoprotectant. Additionally, the study examined the toxicity and in vitro and in vivo release of IXN on HT-29 cells. IXN is classified as a Biopharmaceutical Classification System (BCS) II class drug with weak acidity. The average particle size of IXN-Nps is 249.500 nm, with a polydispersity index (PDI) of 0.149 and a zeta potential of −25.210 mV. The research identified 5 % mannitol as the optimal cryoprotectant. Compared to IXN, the half-maximal inhibitory concentration of IXN-Nps decreased to one-third, demonstrating a significant inhibitory effect on HT-29 colon cancer cells. The in vitro cumulative release rate of IXN-Nps within 24 h was 3.5 times higher than that of the IXN solution. In vivo pharmacokinetic results revealed that the oral bioavailability of IXN-Nps increased significantly by 2.8 times compared to the IXN solution. The correlation coefficient (r = 0.9227) exceeded the critical value for significance at the 0.01 (r = 0.834) level, indicating a strong correlation between in vivo and in vitro results. Consequently, the nanosuspension overcame the low solubility limitation of IXN and proved to be an effective method for enhancing the oral bioavailability of IXN

Kinetic Features of Degradation of R-Loops by RNase H1 from Escherichia coli

R-loops can act as replication fork barriers, creating transcription–replication collisions and inducing replication stress by arresting DNA synthesis, thereby possibly causing aberrant processing and the formation of DNA strand breaks. RNase H1 (RH1) is one of the enzymes that participates in R-loop degradation by cleaving the RNA strand within a hybrid RNA–DNA duplex. In this study, the kinetic features of the interaction of RH1 from Escherichia coli with R-loops of various structures were investigated. It was found that the values of the dissociation constants Kd were minimal for complexes of RH1 with model R-loops containing a 10–11-nt RNA–DNA hybrid part, indicating effective binding. Analysis of the kinetics of RNA degradation in the R-loops by RH1 revealed that the rate-limiting step of the process was catalytic-complex formation. In the presence of RNA polymerase, the R-loops containing a ≤16-nt RNA–DNA hybrid part were efficiently protected from cleavage by RH1. In contrast, R-loops containing longer RNA–DNA hybrid parts, as a model of an abnormal transcription process, were not protected by RNA polymerase and were effectively digested by RH1.

Evaluating the insecticidal potential of alkaloids for the management of Thrips palmi: in vivo and in silico perspectives.

Insecticidal potential of seven commonly available alkaloids against melon thrips (Thrips palmi Karny) was investigated through in vivo experiments and the bioactivity was explained via in silico approaches. In vivo screening showed highest mortality of T. plami larvae for reserpine (43%), closely followed by tropinone (41%) after 24h of incubation. After 48h, tropinone surpassed reserpine with 83% mortality, indicating its prolonged insecticidal activity. A detailed bioassay of tropinone revealed its LC50 values as 1187.9 and 686.9µg mL-1 after 24 and 48h, respectively. While studying the molecular interactions between the alkaloids and four physiologically important target proteins of T. palmi, tropinone demonstrated the highest ligand efficiency and lowest predicted inhibitory constant, particularly when forming complexes with CathB protein. However, binding energy calculations of the docked complexes showed most favorable binding of reserpine with CathB. To clear the ambiguity, considering both binding energy and ligand efficiency as the evaluation parameters, a molecular dynamics study was carried out, which predicted higher stability of CathB-tropinone complex than CathB-reserpine complex in terms of the total energy of the system. These in silico findings aligned well with the in vivo results, confirming tropinone as a promising candidate for effective thrips management programs.

Novel Inhibitory Actions of Neuroactive Steroid [3α,5α]-3-Hydroxypregnan-20-One on Toll-like Receptor 4-Dependent Neuroimmune Signaling

The endogenous neurosteroid (3α,5α)-3-hydroxypregnan-20-one (3α,5α-THP) modulates inflammatory and neuroinflammatory signaling through toll-like receptors (TLRs) in human and mouse macrophages, human blood cells and alcohol-preferring (P) rat brains. Although it is recognized that 3α,5α-THP inhibits TLR4 activation by blocking interactions with MD2 and MyD88, the comprehensive molecular mechanisms remain to be elucidated. This study explores additional TLR4 activation sites, including TIRAP binding to MyD88, which is pivotal for MyD88 myddosome formation, as well as LPS interactions with the TLR4:MD2 complex. Both male and female P rats (n = 8/group) received intraperitoneal administration of 3α,5α-THP (15 mg/kg; 30 min) or a vehicle control, and their hippocampi were analyzed using immunoprecipitation and immunoblotting techniques. 3α,5α-THP significantly reduces the levels of inflammatory mediators IL-1β and HMGB1, confirming its anti-inflammatory actions. We found that MyD88 binds to TLR4, IRAK4, IRAK1, and TIRAP. Notably, 3α,5α-THP significantly reduces MyD88-TIRAP binding (Males: −31 ± 9%, t-test, p < 0.005; Females: −53 ± 15%, t-test, p < 0.005), without altering MyD88 interactions with IRAK4 or IRAK1, or the baseline expression of these proteins. Additionally, molecular docking and molecular dynamic analysis revealed 3α,5α-THP binding sites on the TLR4:MD2 complex, targeting a hydrophobic pocket of MD2 usually occupied by Lipid A of LPS. Surface plasmon resonance (SPR) assays validated that 3α,5α-THP disrupts MD2 binding of Lipid A (Kd = 4.36 ± 5.7 μM) with an inhibition constant (Ki) of 4.5 ± 1.65 nM. These findings indicate that 3α,5α-THP inhibition of inflammatory mediator production involves blocking critical protein-lipid and protein-protein interactions at key sites of TLR4 activation, shedding light on its mechanisms of action and underscoring its therapeutic potential against TLR4-driven inflammation.

Phage Display Against 2D Metal-Organic Nanosheets as a New Route to Highly Selective Biomolecular Recognition Surfaces.

Peptides are important biomarkers for various diseases, however distinguishing specific amino-acid sequences using artificial receptors remains a major challenge in biomedical sensing. This study introduces a new approach for creating highly selective recognition surfaces using phage display biopanning against metal-organic nanosheets (MONs). Three MONs (ZIF-7, ZIF-7-NH2, and Hf-BTB-NH2) are added to a solution containing every possible combination of seven-residue peptides attached to bacteriophage hosts. The highest affinity peptides for each MON are isolated through successive bio-panning rounds. Comparison of the surface properties of the MONs and high-affinity peptides provide useful insights into the relative importance of electrostatic, hydrophobic, and co-ordination bonding interactions in each system, aiding the design of future MONs. Coating of the Hf-BTB-NH2 MONs onto a quartz crystal microbalance (QCM) produced a five-fold higher signal for phage with the on-target peptide sequence compared to those with generic sequences. Surface plasmon resonance (SPR) studies produce a 4600-fold higher equilibrium dissociation constant (KD) for on-target sequences and are comparable to those of antibodies (KD = 4 x 10-10m). It is anticipated that insights from the biopanning approach, combined with the highly tunable nature of MONs, will lead to a new generation of highly selective recognition surfaces for use in biomedical sensors.

Local depletion of large molecule drugs due to target binding in tissue interstitial space.

Drug-target binding determines a drug's pharmacodynamics but can also have a profound impact on a drug's pharmacokinetics, known as target-mediated drug disposition (TMDD). TMDD models describe the influence of drug-target binding and target turnover on unbound drug concentrations and are frequently used for biologics and drugs with nonlinear plasma pharmacokinetics. For drug targets expressed in tissues, the effect of TMDD may not be detected when analyzing plasma concentration curves, but it might still affect tissue concentrations and occupancy. This review aimed to investigate the likeliness of such a scenario by reviewing the literature for a typical range of TMDD parameter values and their impact on local drug concentrations and target occupancy in a whole-body PBPK model with TMDD. Our analysis demonstrated that tissue drug concentrations are impacted and significantly depleted in many physiological scenarios. In contrast, the effect on plasma concentrations is much lower, specifically for smaller organs with lower perfusion. Moreover, in scenarios with fast internalization of the drug-target complex, the distribution of large molecules from plasma to tissue interstitial space emerges as a rate-limiting step for the drug-target interaction. These factors may lead to overpredicting local drug concentrations when considering only plasma pharmacokinetics. A sensitivity analysis revealed the high and not always intuitive impact of drug-specific parameters, including the drug molecule hydrodynamic radius, dissociation constant (Kd), drug-target complex internalization rate constant (kint), and target dissociation rate constant (koff), on the drug's pharmacokinetics. Our analysis demonstrated that tissue TMDD needs to be considered even if plasma pharmacokinetics are linear.

Machine learning-based prediction of bioactivity in HIV-1 protease: insights from electron density analysis.

Aim: To develop a model for predicting the biological activity of compounds targeting the HIV-1 protease and to establish factors influencing enzyme inhibition.Materials & methods: Machine learning models were built based on a combination of Richard Bader's theory of Atoms in Molecules and topological analysis of electron density using experimental x-ray 'protein-ligand' complexes and inhibition constants data.Results & conclusion: Among all the models tested, logistic regression achieved the highest accuracy of 0.76 on the test set. The model's ability to differentiate between less active and highly active classes was relatively good, as indicated by an AUC-ROC score of 0.77. The analysis identified several critical factors affecting the biological activity of HIV-1 protease inhibitors, including the electron density contribution of hydrogen atoms, bond-critical points and particular amino acid residues. These findings provide new insights into how these molecular factors influence HIV-1 protease inhibition, emphasizing the importance of hydrogen bonding, glycine's flexibility and hydrophobic interactions in ligand binding.

The chemoreceptor controlling the Wsp-like transduction pathway in Halomonas titanicae KHS3 binds and responds to purine derivatives.

The chemosensory pathway HtChe2 from the marine bacterium Halomonas titanicae KHS3 controls the activity of a diguanylate cyclase. Constitutive activation of this pathway results in colony morphology alterations and an increased ability to form biofilm. Such characteristics resemble the behavior of the Wsp pathway of Pseudomonas. In this work, we investigate the specificity of Htc10, the only chemoreceptor coded within the HtChe2 gene cluster. The purine derivatives guanine and hypoxanthine were identified as ligands of the recombinantly produced Htc10 ligand-binding domain, with dissociation constants in the micromolar range, and its structure was solved by X-ray protein crystallography. The sensor domain of Htc10 adopts a double Cache folding, with ligands bound to the membrane-distal pocket. A high-resolution structure of the occupied guanine-binding pocketallowed the identification of residues involved in ligand recognition. Such residues were validated by site-directed mutagenesis and isothermal titration calorimetry analyses of the protein variants. Moreover, heterologous expression of Htc10 in a Pseudomonas putida mutant lacking the native Wsp chemoreceptor promoted biofilm formation, a phenotype that was further enhanced by Htc10-specific ligands. To our knowledge, this is the first description of binding specificity of a chemoreceptor that controls the activity of an associated diguanylate cyclase, opening the way for dynamic studies of the signaling behavior of this kind of sensory complex.

Therapeutic potential of mackerel-derived peptides and the synthetic tetrapeptide TVGF for sleep disorders in a light-induced anxiety zebrafish model

IntroductionAnxiety-like insomnia is a known risk factor for the onset and worsening of certain neurological diseases, including Alzheimer’s disease. Due to the adverse effects of current anti-insomnia medications, such as drug dependence and limited safety, researchers are actively exploring natural bioactive compounds to mitigate anxiety-like insomnia with fewer side effects. Mackerel (Pneumatophorus japonicus), a traditional Chinese medicine, is known for its tonic effects and is commonly used to treat neurasthenia. The use of mackerel protein extract has been shown to effectively improve symptoms of light-induced anxiety-like insomnia in a zebrafish model.MethodsThis study examines the effects of mackerel bone peptides (MW < 1 kDa, MBP1) and the synthetic peptide Thr-Val-Gly-Phe (TVGF) on light-induced anxiety-like insomnia in zebrafish. The evaluation is conducted through behavioral observation, biochemical marker analysis, and gene transcriptome profiling.ResultsMBP1 significantly alleviated abnormal hyperactivity and restored neurotransmitter levels (dopamine and γ-aminobutyric acid) to normal. Moreover, it mitigated oxidative stress by reducing reactive oxygen species production and malonaldehyde levels, while enhancing antioxidant enzyme activities (superoxide dismutase and catalase). This was further attributed to the regulation of lipid accumulation and protein homeostasis. Furthermore, MBP1 ameliorated sleep disturbances primarily by restoring normal expression levels of genes involved in circadian rhythm (per2 and sik1) and visual function (opn1mw2, zgc:73075, and arr3b). Molecular docking analysis indicated that TVGF exhibited good affinity for receptors linked to sleep disturbances, including IL6, HTR1A, and MAOA. TVGF exhibited sedative effects in behavioral assays, mainly mediated by regulating the normal expression of genes associated with circadian rhythm (cry1bb, cry1ba, per2, per1b and sik1), visual function (opn1mw1, gnb3b, arr3b, gnat2), purine metabolism (pnp5a), and stress recovery (fkbp5).DiscussionThese findings suggest that MBP1 and TVGF could be promising therapies for light-induced anxiety-like insomnia in humans, offering safer alternatives to current medications. Additionally, the regulation of genes related to circadian rhythm and visual perception may be a key mechanism by which MBP1 and TVGF effectively relieve anxiety-like insomnia.

High Compression in Palladium Alloy Metal Foil Pumps

Metal foil pumps (MFPs) are key components in the direct internal recycling inner fuel cycle loop for the recovery of hydrogen isotopes from deuterium-tritium fusion exhaust. Operating under vacuum conditions, they utilize superthermal hydrogen as the feed gas in a process called superpermeation. A notable feature of MFPs is their ability to pump against a pressure gradient. This study examines the compression capabilities of PdAg and PdCu MFPs at low temperatures with a constant feed pressure of 10 Pa. At 75°C, compression ratios exceeding 200 were readily achieved, with downstream pressures exceeding 4500 Pa using PdCu. For both alloys, net fluxes decreased by only ~15% at downstream pressures of 1000 Pa, which offers potential simplifications for the downstream pump train. Performance declined markedly when the temperature was elevated to 200°C. Pump curves were constructed and advocated as the most appropriate manner to assess MFP performance. Separate pressure-driven-permeation experiments at relevant conditions were conducted, providing a direct measurement of the hydrogen dissociation constant k d , which was found to be in good agreement with the previous literature. These measurements were used to predict pump curves and maximum compression ratios by balancing superpermeation with pressure-driven permeation, achieving excellent agreement with experiment. Last, experiments using asymmetric MFPs revealed the detrimental impact that surface impurities have on performance in this system.

Control of sensitivity in metal oxide electrolyte gated field-effect transistor-based glucose sensor by electronegativity modulation

In this study, the sensitivity of electrolyte-gated field-effect transistor-based glucose sensors using oxide semiconductor materials was controlled via electronegativity modulation. By controlling the enzymatic reaction between glucose and glucose oxidase, which is affected by the surface potential, the sensitivity of the glucose sensor can be effectively adjusted. To evaluate the sensitivity characteristics of the glucose sensor according to electronegativity control, devices were fabricated based on InO through Ga and Zn doping. The results confirmed that the specific sensitivity range could be adjusted by increasing the electronegativity. In addition, density functional theory calculations, confirmed that the attachment energy of the surface-functionalized material and the enzyme binding energy in the surface-functionalized thin film can be modulated depending on the electronegativity difference. The dissociation constant was controlled in both directions by doping with metal cations with larger(Ga, 1.81) or smaller(Zn, 1.65) electronegativities in InO(In, 1.78). We expect that this study will provide a simple method for the gradual and bidirectional control of the glucose sensitivity region.

Immunoinformatics investigation on pathogenic Escherichia coli proteome to develop an epitope-based peptide vaccine candidate.

Escherichia coli (E. coli), a gram-negative bacterium, quickly colonizes in the human gastrointestinal tract after birth and typically sustains a long-term, symbiotic relationship with the host. However, certain virulent strains of E. coli can cause diseases such as urinary tract infections, meningitis, and enteric disorders. The rising antibiotic resistance among these strains has heightened the urgency for an effective vaccine. This study employs immunoinformatics and a reverse vaccinology technique to identify prospective antigens and create an efficient vaccine construct. In this study, we reported the "Attaching and Effacing Protein" a novel outer-membrane protein conserved in all pathogenic E. coli strains, based on proteome screening. We developed an in silico multi-epitope vaccine that includes helper T lymphocyte (HTL), cytotoxic T lymphocyte (CTL), B cell lymphocyte (BCL), and pan HLA DR-binding reactive epitope (PADRE) sequences, along with appropriate linkers and adjuvants. Machine Learning algorithms were used to evaluate antigenicity, solubility, stability, and non-allergenicity of the vaccine construct. Additionally, molecular docking analysis revealed that vaccine construct has a strong predicted binding affinity for human toll-like receptors on the cell surface. In this context, laboratory validations are necessary to demonstrate the effectiveness of the possible vaccine design that showed encouraging findings through computational validation.

Sunflower Trypsin Monocyclic Inhibitor Selected for the Main Protease of SARS-CoV-2 by Phage Display.

Main protease (Mpro), also known as 3-chymotrypsin-like protease (3CLpro), is a nonstructural protein (NSP5) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the cleavage of virus polyproteins during viral replication at 11 sites, which generates 12 functional proteins. Mpro is a cysteine protease that presents specificity for the amino acid residue glutamine (Gln) at the P1 position of the substrate. Due to its essential role in processing the viral polyprotein for viral particle formation (assembly), Mpro inhibition has become an important tool to control coronavirus disease 2019 (COVID-19), since Mpro inhibitors act as antivirals. In this work, we proposed to identify specific inhibitors of the Mpro of SARS-CoV-2 using a monocyclic peptide (sunflower trypsin inhibitor (SFTI)) phage display library. Initially, we expressed, purified and activated recombinant Mpro. The screening of the mutant SFTI phage display library using recombinant Mpro as a receptor resulted in the five most frequent SFTI mutant sequences. Synthetized mutant SFTIs did not inhibit Mpro protease using the fluorogenic substrate. However, the mutant SFTI 4 efficiently decreased the cleavage of recombinant human prothrombin as a substrate by Mpro, as confirmed by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE). Additionally, SFTI 4 presented a dissociation constant (KD) of 21.66 ± 6.66 µM for Mpro by surface plasmon resonance. Finally, 0.1 µM SFTI 4 reduced VERO cell infection by SARS-CoV-2 wt after 24 and 48 h. In conclusion, we successfully screened a monocyclic peptide library using phage display for the Mpro of SARS-CoV-2, suggesting that this methodology can be useful in identifying new inhibitors of viral enzymes.