Efficient Binding Research Articles

Binding of a Tricationic meso-Substituted Porphyrin to poly(A)⋅poly(U): an Experimental Study.

The porphyrins are macrocyclic compounds widely used as photosensitizers in anticancer photodynamic therapy. The binding of a tricationic meso-tris(N-methylpyridinium)-porphyrin, TMPyP3+, to poly(A)⋅poly(U) polynucleotide has been studied in neutral buffered solution, pH6.9, of low and near-physiological ionic strength in a wide range of molar phosphate-to-dye ratios (P/D). Effective TMPyP3+ binding to the biopolymer was established using absorption spectroscopy, polarized fluorescence, fluorimetric titration and resonance light scattering. We propose a model in which TMPyP3+ binds to the polynucleotide in two competitive binding modes: at low P/D ratios (< 4) external binding of the porphyrin to polynucleotide backbone without self-stacking dominates, and at higher P/D (> 30) the partially stacked porphyrin J-dimers are embedded into the polymer groove. Enhancement of the porphyrin emission was observed upon binding in all P/D range, contrasting the binding of this porphyrin to poly(G)⋅poly(C) with significant quenching of the porphyrin fluorescence at low P/D ratios. This observation indicates that TMPyP3+ can discriminate between poly(A)⋅poly(U) and poly(G)⋅poly(C) polynucleotides at low P/D ratios. Formation of highly scattering extended porphyrin aggregates was observed near the stoichiometric in charge binding ratio, P/D = 3. It was revealed that the efficiency of the porphyrin external binding and aggregation is reduced in the solution of near-physiological ionic strength.

Structure‐Based Computational Approach in Search of the Potent Molecules Targeting Phosphoglycerate Dehydrogenase (PHGDH) Enzyme for Cancer Treatment

AbstractThis work aims to target phosphoglycerate dehydrogenase (PHGDH), a promising druggable target, that is overexpressed in various types of cancer. A structure‐based approach was employed to identify novel inhibitors against the enzyme. A common five‐feature pharmacophore model (RRHDA) was constructed using the active site co‐crystalized ligands. These chemical features were responsible for showing inhibition. The generated models were subsequently subjected to the validation method using a test set, receiver‐operator characteristic analysis, enrichment factor, and Güner–Henry studies. The validated models were subjected to the screening of a dataset of natural compounds. The screened unique natural compounds (1795) were further selected for the interaction analysis and study of ligand binding affinity considering the effect of the hydrogen bonding and desolvation and hydrophobic interactions contribution to the binding. The natural compounds which exhibited good ligand binding efficiency were selected and further subjected to pharmacokinetics and pharmacodynamic study. The natural compounds which exhibited good ligand binding efficiency were selected and further subjected to pharmacokinetics and pharmacodynamic study. The finalized complexes were selected for the simulation studies and MM/PBSA‐based binding free energy calculations. This study expands the possibilities for the development of shortlisted molecules as novel anti‐cancer compounds.

Targeted Delivery to Dying Cells Through P-Selectin–PSGL-1 Axis: A Promising Strategy for Enhanced Drug Efficacy in Liver Injury Models

To minimize off-target adverse effects and improve drug efficacy, various tissue-specific drug delivery systems have been developed. However, even in diseased organs, both normal and stressed, dying cells coexist, and a targeted delivery system specifically for dying cells has yet to be explored to mitigate off-target effects within the same organ. This study aimed to establish such a system. By examining the surfaces of dying cells in vitro, we identified P-selectin glycoprotein ligand-1 (PSGL-1) as a universal marker for dying cells, positioning it as a potential target for selective drug delivery. We demonstrated that liposomes conjugated with the PSGL-1 binding protein P-selectin had significantly greater binding efficiency to dying cells compared to control proteins such as E-selectin, L-selectin, galectin-1, and C-type lectin-like receptor 2. Using thioacetamide (TAA) to induce hepatitis and hepatocyte damage in mice, we assessed the effectiveness of our P-selectin-based delivery system. In vivo, P-selectin-conjugated liposomes effectively delivered fluorescent dye and the apoptosis inhibitor z-DEVD to TAA-damaged livers in wild-type mice, but not in PSGL-1 knockout mice. In TAA-treated wild-type mice, unconjugated liposomes required a 100-fold higher z-DEVD dose compared to P-selectin-conjugated liposomes to achieve a comparable, albeit less effective, therapeutic outcome in lowering plasma alanine transaminase levels and alleviating thrombocytopenia. This emphasizes that P-selectin conjugation enhances drug delivery efficiency by approximately 100-fold in mice. These results suggest that P-selectin-based liposomes could be a promising strategy for targeted drug delivery, enabling both diagnosis and treatment by specifically delivering cell-labeling agents and rescue agents to dying cells via the P-selectin–PSGL-1 axis at the individual cell level.

Arabidopsis METHYLENETETRAHYDROFOLATE REDUCTASE 2 functions independently of PENETRATION 2 during primary immunity against rice blast.

Nonhost resistance (NHR) is the most durable and robust form of innate immunity, with a surge of interest in crop improvement. Of the NHR genes identified against rice blast, a devastating disease caused by Magnaporthe oryzae, Arabidopsis PEN2 is indispensable for pre-penetration resistance against M. oryzae, while a consortium of genes orchestrates post-penetration resistance via lesser-known mechanisms. We identified M. oryzae-susceptible mosA (mthfr2 pen2-3) from a randomly mutagenized Arabidopsis pen2-3 population using forward genetics. Analysis of T-DNA inserted mthfr2 lines and pen2-3 complemented mosA lines enunciated that MTHFR2-dependent resistance to M. oryzae is independent of PEN2. MTHFR2-defective plants exhibited higher ROS accumulation and expression of SA-dependent defense markers. MTHFR2-ligand docking revealed that A55V nonsynonymous substitution in mosA altered ligand binding efficiency. This further affected the metabolomic profile of mosA, effectively allowing in vitro germination and development of M. oryzae conidia. Moreover, the loss of function mutation in mthfr2 (involved in 1C metabolic pathway) potentiated mosA immunity against Pst DC3000. In conclusion, our findings assert MTHFR2 as a positive modulator of NHR against M. oryzae. This work documents another layer of conserved yet divergent metabolomic defense in Arabidopsis regulated by folate-mediated 1C metabolism that has the potential to revolutionize crop improvement.

Sonochemical synthesis of guar gum - Zirconium phosphate composite for efficient capture of uranium from water

The increasing presence of uranium as a radionuclide contaminant in water is a threat to human health and the environment. Sonication-assisted crosslinking of guar gum, a biopolymer, is carried out with zirconium phosphate to form an adsorbent (GG@ZrP) for the removal of uranium from water. The surface characteristics, functionalities, and thermal stability of the composite were established using various analytical and spectral tools. Langmuir, Freundlich, and Sips models were used to evaluate the batch adsorption parameters. The adsorbent exhibited an excellent Langmuir adsorption capacity of 500 mg g−1 towards adsorption of uranium at pH 6. The adsorption was endothermic (ΔH, 22.63 kJ mol−1) and followed pseudo-second order kinetics. The synergistic influence of hydroxyl-rich guar gum and phosphate moieties resulted in efficient binding of uranium. With a high selectivity towards interfering cations and anions and applicability over a good range of pH, this adsorbent is a promising candidate for uranium remediation from water.

Salvianolic acid B improves the microcirculation in a mouse model of sepsis through a mechanism involving the platelet receptor CD226.

Salvianolic acid B (SalB) demonstrates diverse clinical applications, particularly in cardiovascular and cerebral protection. This study primarily investigated the effects of SalB on sepsis. The model of sepsis via caecal ligation puncture (CLP) was established in male C57BL/6 mice. Therapeutic effects of SalB on hepatic and pulmonary injury, inflammatory responses and microcirculatory disturbances in sepsis were evaluated. Platelet aggregation and adhesion were measured via flow cytometry and an adhesion test. After overexpression of platelet-related activating molecules by 293T cells, the efficient binding of SalB and platelet CD226 molecules was further evaluated. Finally, neutralizing antibody experiments were used to assess the mechanism of SalB in alleviating the progression of sepsis. SalB mitigated hepatic and pulmonary impairments, reduced inflammatory cytokine levels and enhanced mesenteric microvascular blood flow in septic mice. SalB enhanced CLP-induced reduction of platelet count and platelet pressure cumulative volume. SalB reduced platelet adhesion to endothelial cells and platelet aggregation to leukocytes. A high binding efficiency was observed between SalB and the platelet adhesion molecule CD226. Ex vivo, interactions between SalB and platelets from CD226-knockout mice were markedly decreased. In vivo administration of CD226 neutralizing antibodies significantly delayed disease progression and enhanced mesenteric microcirculation in septic mice. In our murine model of sepsis, treatment with SalB improved the microcirculatory disturbance and hindered the progression of sepsis by inhibiting platelet CD226 function. Our results suggest SalB is a promising therapeutic approach to the treatment of sepsis.

Proteolytic Performance Is Dependent on Binding Efficiency, Processivity, and Turnover: Single Protease Insights

Proteolytic Performance Is Dependent on Binding Efficiency, Processivity, and Turnover: Single Protease Insights

Optimization and Investigation of Hemoglobin‐Loaded ZIF‐90 Metal–Organic Framework Nanoparticles as Artificial Oxygen Carriers

AbstractBlood transfusions are vital, yet limited shelf‐life and storage conditions of red blood cells (RBCs) hinder their use in emergencies. Hemoglobin‐based oxygen carriers (HBOCs) aim to address these challenges, but previous versions faced clinical setbacks due to safety concerns related to hemoglobin (Hb) extravasation. ZIF‐90, a novel metal–organic framework variant where imidazole‐2‐carboxaldehyde (2‐ICA) is bridged to Zn2+ ions, is explored. Optimizing Zn2+:2‐ICA ratios and Hb concentrations, Hb‐loaded ZIF‐90 nanoparticles (NPs) are synthesized in one‐step and under mild synthesis conditions. These NPs achieve a 25.1% yield, 7.0 mg mL−1 Hb concentration, 70.3% encapsulation efficiency (EE), and 96.4% drug loading. They exhibit a left‐shifted oxygen dissociation curve with p50 of ≈8 mmHg, indicating enhanced oxygen release at lower partial oxygen pressures as compared to native RBCs. This feature makes Hb‐loaded ZIF‐90 NPs suitable for certain medical applications including ischemia‐reperfusion injury management. Furthermore, the impact of two prominent capping agents: polyvinylpyrrolidone and polyethylene glycol (PEG) is assessed. PEG improves 2‐ICA incorporation and stabilizes the ZIF‐90 crystalline phase, albeit with reduced yield, Hb content, and EE. The findings underscore the potential of Hb‐loaded ZIF‐90 NPs as next‐generation HBOCs, offering enhanced uniformity, high Hb content, and efficient oxygen binding and release properties for medical applications.

ω‐Aminomethyl Longifolene Amide Derivatives: Synthesis, Crystal Structure, Hirshfeld Surface, DFT, Antimicrobial, and Molecular Docking Studies

AbstractTwelve novel ω‐aminomethyl longifolene amide derivatives (6 a–6 l) were synthesized and characterized. The intermolecular contacts and the relationship of structure‐property for the synthesized compounds were performed with the use of two‐dimensional fingerprint plots and Hirshfeld surface method. Moreover, the chemical reactivity and geometrical characteristics of target compounds were investigated using density functional theory (DFT) method. Molecular docking studies were performed to investigate the interactions between compounds 6 a–6 l and sortase A (SrtA) from S. aureus, the carboxy terminal domain of colicin E5 (E5‐CRD) and Serine/Threonine phosphatase Z1 (PPZ1) from C. albicans, respectively, and together with their biological activities. The docking results of the synthesized compounds 6 a–6 l showed different binding efficiencies and inhibitory effects on S. aureus, E. coli and C. albicans. Furthermore, preliminary antimicrobial activity assay showed that compounds 6 f, 6 i and 6 k exhibited comparable or superior antibacterial activity against S. aureus, B. subtilis and K. pneumoniae compared to rifampicin with minimum inhibitory concentration (MIC) values from 0.488 to 0.977 μg/mL. In addition, the absorption, distribution, metabolism and excretion (ADME) and drug‐likeness properties of the synthesized derivatives were evaluated as well.

Synchronous Modulation of H-bond Interaction and Steric Hindrance via Bio-molecular Additive Screening in Zn Batteries.

In addressing challenges such as side reaction and dendrite formation, electrolyte modification with bio-molecule sugar species has emerged as a promising avenue for Zn anode stabilization. Nevertheless, considering the structural variability of sugar, a comprehensive screening strategy is meaningful yet remains elusive. Herein, we report the usage of sugar additives as a representative of bio-molecules to develop a screening descriptor based on the modulation of the hydrogen bond component and electron transfer kinetics. It is found that xylo-oligosaccharide (Xos) with the highest H-bond acceptor ratio enables efficient water binding, affording stable Zn/electrolyte interphase to alleviate hydrogen evolution. Meanwhile, sluggish reduction originated from the steric hindrance of Xos contributes to optimized Zn deposition. With such a selected additive in hand, the Zn||ZnVO full cells demonstrate durable operation. This study is anticipated to provide a rational guidance in sugar additive selection for aqueous Zn batteries.

Broadly therapeutic antibody provides cross-serotype protection against enteroviruses via Fc effector functions and by mimicking SCARB2.

Enteroviruses contain multiple serotypes and can cause severe neurological complications. The intricate life cycle of enteroviruses involving dynamic virus-receptor interaction hampers the development of broad therapeutics and vaccines. Here, using function-based screening, we identify a broadly therapeutic antibody h1A6.2 that potently protects mice in lethal models of infection with both enterovirus A71 and coxsackievirus A16 through multiple mechanisms, including inhibition of the virion-SCARB2 interactions and monocyte/macrophage-dependent Fc effector functions. h1A6.2 mitigates inflammation and improves intramuscular mechanics, which are associated with diminished innate immune signalling and preserved tissue repair. Moreover, cryogenic electron microscopy structures delineate an adaptive binding of h1A6.2 to the flexible and dynamic nature of the VP2 EF loop with a binding angle mimicking the SCARB2 receptor. The coordinated binding mode results in efficient binding of h1A6.2 to all viral particle types and facilitates broad neutralization of enterovirus, therefore informing a promising target for the structure-guided design of pan-enterovirus vaccine.

"Pseudosubstrate Envelope"/Free Energy Perturbation-Guided Design and Mechanistic Investigations of Benzothiazole HIV Capsid Modulators with High Ligand Efficiency.

Based on our proposed "pseudosubstrate envelope" concept, 25 benzothiazole-bearing HIV capsid protein (CA) modulators were designed and synthesized under the guidance of free energy perturbation technology. The most potent compound, IC-1k, exhibited an EC50 of 2.69 nM against HIV-1, being 393 times more potent than the positive control PF74. Notably, IC-1k emerged as the highest ligand efficiency (LE = 0.32) HIV CA modulator, surpassing that of the approved drug lenacapavir (LE = 0.21). Surface plasmon resonance assay and crystallographic analysis confirmed that IC-1k targeted HIV-1 CA within the chemical space of the "pseudosubstrate envelope". Further mechanistic studies revealed a dual-stage inhibition profile: IC-1k disrupted early-stage capsid-host-factor interactions and promoted late-stage capsid misassembly. Preliminary pharmacokinetic evaluations demonstrated significantly improved metabolic stability in human liver microsomes for IC-1k (T1/2 = 91.3 min) compared to PF74 (T1/2 = 0.7 min), alongside a favorable safety profile. Overall, IC-1k presents a promising lead compound for further optimization.

Synthesis, crystal structure, Hirshfeld surface analysis, DFT computations and protein binding efficiency of a 1-D Ni(II) chain derived from a tridentate Schiff base ligand

A new Ni(II)-azido 1-D coordination polymer, [Ni2L2(μ1,1-N3)(μ1,3-N3)]n, was obtained through reaction of 1-[(3-dimethylamino-propylimino)-methyl]-naphthalen-2-ol (HL) and the perchlorate salt of nickel(II) in the presence of pseudohalide azide. X-ray crystallography and spectroscopic experiments (IR and UV-Vis) were used to describe this coordination polymer (CP). Single crystal X-ray studies revealed that the CP is a one-dimensional chain of Ni(II) in which the neighboring dimeric units (triply bridged by di-μ2-phenoxidoand µ1,1-N3) are further connected by μ1,3-azido bridges in a zig-zag fashion. The cooperative participation of N···H hydrogen bonding, π···π stacking and C-H···π interactions occur during crystal packing. A 2-D supramolecular architecture with star-shaped voids results from additional C–H···π stacking interactions. Hirshfeld surface analysis was used to look at the intermolecular interactions. DFT studies were carried out to calculate the HOMO-LUMO band gap of the ligand as well as the coordination polymer. Interaction of the CP with bovine serum albumin (BSA) protein was investigated spectroscopically by absorption and fluorescence titration methods. The result showed that the CP could quench the intrinsic fluorescence of BSA. Fluorescence resonance energy transfer (FRET) studies revealed that energy transfer takes place from BSA to the CP. Cyclic voltammetry of the CP indicated an irreversible cathodic redox couple assigned to Ni(II)/Ni(I).

Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations.

Carbohydrates are key biological mediators of molecular recognition and signaling processes. In this case study, we explore the ability of absolute binding free energy (ABFE) calculations to predict the affinities of a set of five related carbohydrate ligands for the lectin protein, concanavalin A, ranging from 27-atom monosaccharides to a 120-atom complex-type N-linked glycan core pentasaccharide. ABFE calculations quantitatively rank and estimate the affinity of the ligands in relation to microcalorimetry, with a mean signed error in the binding free energy of -0.63 ± 0.04 kcal/mol. Consequently, the diminished binding efficiencies of the larger carbohydrate ligands are closely reproduced: the ligand efficiency values from isothermal titration calorimetry for the glycan core pentasaccharide and its constituent trisaccharide and monosaccharide compounds are respectively -0.14, -0.22, and -0.41 kcal/mol per heavy atom. ABFE calculations predict these ligand efficiencies to be -0.14 ± 0.02, -0.24 ± 0.03, and -0.46 ± 0.06 kcal/mol per heavy atom, respectively. Consequently, the ABFE method correctly identifies the high affinity of the key anchoring mannose residue and the negligible contribution to binding of both β-GlcNAc arms of the pentasaccharide. While challenges remain in sampling the conformation and interactions of these polar, flexible, and weakly bound ligands, we nevertheless find that the ABFE method performs well for this lectin system. The approach shows promise as a quantitative tool for predicting and deconvoluting carbohydrate-protein interactions, with potential application to design of therapeutics, vaccines, and diagnostics.

Enhancing preventive and therapeutic cancer vaccine efficacy through biotherapeutic ligand-associated extracellular vesicles

Extracellular vesicles (EVs), secreted by almost all living cells, have gained significant attention for their role in intercellular communication and their potential as versatile carriers for biotherapeutics. However, the clinical translation of EV-based therapies faces significant challenges, primarily due to the lack of efficient methods for loading biotherapeutic agents into EVs. This study introduces a simple, reproducible strategy for the simultaneous incorporation of various biotherapeutics within EVs. The process is gentle and preserves the essential physicochemical and biological characteristics of EVs, thereby protecting labile ligands from premature degradation and elimination. The binding and uptake efficiency of EVs by target cells reached approximately 97 % within 24 h of incubation. Administration of EVs loaded with oligodeoxynucleotides (ODN) resulted in a 4-fold increase in IFNγ+ CD4+ T cells and a 5-fold increase in IFNγ+ CD8+ T cells in the spleens and lymph nodes. Additionally, the co-administration of EVs with ODN and ovalbumin (OVA) induced elevated Th1-biased antibody responses and antigen-specific cytotoxic T-cell responses, providing long-lasting complete protection in 60 % of mice against T-cell thymoma challenge. Furthermore, EVs associated with three different ligands (OVA, CpG-ODN, and α-GalCer) effectively regressed established murine melanoma and significantly improved survival rates in mice. This study presents a powerful and promising approach to overcoming the limitations of EV-based cancer vaccines, advancing the development of effective cancer immunotherapies. SummaryImmunization with EVs that are co-associated with antigen and biotherapeutic cargo through a lyophilization-based technique elicits potent anti-cancer immunity.

FORMULATION OF SELF-NANO EMULSIFYING SYSTEM (SNES) CONTAINING SNAKEHEAD FISH EXTRACT PROTEIN INCORPORATED INTO CORN OIL BY HYDROPHOBIC ION PAIRING METHOD

Objective: The purpose of this study was to determine whether the protein complexation of snakehead fish extract using the hydrophobic ion pairing method with Sodium Dodecyl Sulfate (SDS) as a complexing ligand could be loaded into the corn oil component of the SNES and to explore the ratio of oil, surfactant, and cosurfactant in the Self-Nanoemulsifying System (SNES) formula that can produce good SNES characteristics. Methods: Snakehead fish proteins were extracted using pressurized hot water and then complexed with SDS at acidic pH. The SDS-protein complex was loaded into the oil component of the SNES and then combined with the surfactant component (Tween 80) and cosurfactant (propylene glycol) in a ratio of 1:9:1, which, based on the preliminary miscibility screening, has the best miscibility among other screening results. Results: The results of the study were as follows. The binding efficiency of the SDS-protein-complex was 31.74% and the loading efficiency into SNES was 83.17%. The nanoemulsion formed had visible light transmittance of 100.4%, particle size 72.7 nm, zeta potential-53.03 mV, and emulsification time 71.67 seconds. The nanoemulsion was stable at storage and 100 and 1000 times dilution challenges using aqueous media, Simulated Gastric Fluid (SGF), and Simulated Intestinal Fluid (SIF). Conclusion: The hydrophobic ion-pair complexation of snakehead fish protein extract with SDS as the complexing ligand was able to load the protein into the oil component of SNES and the ratio of oil, surfactant, and cosurfactant in the SNES formula that produce good SNES characteristics was corn oil, Tween 80, and propylene glycol at a ratio of 1:9:1

Chitosan-Based Charge-Controllable Supramolecular Carrier for Universal Immobilization of Enzymes with Different Isoelectric Points.

Electrostatic adsorption is an enzyme immobilization method that effectively maintains enzyme activity and exhibits considerable binding efficiency. However, enzymes carry different charges at their respective reaction pH levels, which prevents the use of the same carrier to immobilize enzymes with different charges. In this study, we employed a template-mediated polysaccharide-enzyme coupling self-assembly strategy to develop a charge-controllable supramolecular immobilization carrier by regulating the charge properties of carboxymethyl chitosan, enabling the universal immobilization of enzymes with different charge levels across a range of reaction pH values. By using silica nanoparticles of certain sizes as templates, the size of the carrier can be precisely controlled and the hollow network structure formed after removing the template can effectively reduce mass transfer resistance. Trypsin and papain are used as model enzymes, and the experimental results show that the supramolecular self-assembly immobilization strategy does not disrupt the secondary structure of the enzyme molecules. After 2 h of reaction, the enzyme activities of immobilized papain and immobilized trypsin are 13.2% and 7.7% higher than those of the free enzymes, respectively. After 10 consecutive reactions, the enzyme activities of immobilized papain and immobilized trypsin retained 56.3% and 64.3% of their initial values, respectively.

Bioinspired Glycopeptide Hydrogel Reestablishing Bone Homeostasis through Mediating Osteoclasts and Osteogenesis in Periodontitis Treatment.

Irreversible alveolar bone resorption is one of the important clinical manifestations of periodontitis, which is initiated by a plaque biofilm and exacerbated by the imbalance of osteoclast activity and osteogenesis, affecting a patient's masticatory function and resulting in a high recurrence rate of periodontitis. Herein, to reestablish bone homeostasis in periodontitis, a minocycline hydrochloride (MH)-loaded glycopeptide hydrogel (MH/GRWgel) is fabricated to mediate alveolar bone absorption through sequential antibacterial and RANKL-blocking activities. GRWgel shows an ECM-like fibrous and porous microstructure serving as a scaffold for cell proliferation and differentiation and holds the merits including injectability, self-healing properties, and good biocompatibility. After injection in situ, MH is released rapidly from the hydrogel in the early stage, demonstrating a potent antimicrobial effect to combat the biofilm in the deep periodontal pocket. Moreover, MH/GRWgel exhibits a high specific binding efficiency with RANKL to suppress osteoclast maturation by shielding the RANKL/RANK interaction and enhancing osteogenic differentiation, thereby synergistically regulating bone homeostasis. In the rat periodontitis model, MH/GRWgel significantly curtails periodontitis progression through antimicrobial activity, inhibition of alveolar bone resorption, and promotion of bone regeneration, which is superior to the treatment of a commercial gel. These findings suggest that MH/GRWgel with superiority in regulating bone homeostasis provides a promising therapeutic strategy for periodontitis.

Deciphering the toxicological and computational assessment of Verbascum yemenese.: Integrating phytochemistry and bioinformatics tools

This study explores the phytochemical composition and biological activities of Verbascum yemenense, a plant known for its medicinal properties. The plant extract revealed a rich presence of bioactive compounds that exhibited significant antioxidant properties against free radicals. The enzyme inhibition potential was particularly notable against cholinesterases (AChE: 2.56 mg GALAE/g; BChE: 1.98 mg GALAE/g), and tyrosinase (87.94 mg KAE/g), α-glucosidase suggesting potential therapeutic applications in neurodegenerative diseases, skin disorders and diabetes. Molecular docking studies and Molecular Dynamics simulations, providing insights into the interaction mechanisms of the identified compounds with the target proteins. Molecular docking studies revealed high binding affinities of the phytoconstituents, with compounds like VY4 and phyllanthusol-A (VY15) showing substantial docking scores against AChE (−9.840 kcal/mol) and BChE (−9.853 kcal/mol), respectively. For instance, the RMSD values during the MD simulations for compound VY17 in the AML complex showed a stable conformation, fluctuating within a range of 0.75 Å to 1.75 Å, indicating a strong and consistent interaction with the enzyme. MESP studies highlighted VY17's distinctive electrostatic features, notably a pronounced electronegative region, which might contribute to its binding efficiency. These findings suggest that V. yemenense is a promising candidate for developing novel therapeutic agents.

Truncated M13 phage for smart detection of E. coli under dark field

BackgroundThe urgent need for affordable and rapid detection methodologies for foodborne pathogens, particularly Escherichia coli (E. coli), highlights the importance of developing efficient and widely accessible diagnostic systems. Dark field microscopy, although effective, requires specific isolation of the target bacteria which can be hindered by the high cost of producing specialized antibodies. Alternatively, M13 bacteriophage, which naturally targets E. coli, offers a cost-efficient option with well-established techniques for its display and modification. Nevertheless, its filamentous structure with a large length-diameter ratio contributes to nonspecific binding and low separation efficiency, posing significant challenges. Consequently, refining M13 phage methodologies and their integration with advanced microscopy techniques stands as a critical pathway to improve detection specificity and efficiency in food safety diagnostics.MethodsWe employed a dual-plasmid strategy to generate a truncated M13 phage (tM13). This engineered tM13 incorporates two key genetic modifications: a partial mutation at the N-terminus of pIII and biotinylation at the hydrophobic end of pVIII. These alterations enable efficient attachment of tM13 to diverse E. coli strains, facilitating rapid magnetic separation. For detection, we additionally implemented a convolutional neural network (CNN)-based algorithm for precise identification and quantification of bacterial cells using dark field microscopy.ResultsThe results obtained from spike-in and clinical sample analyses demonstrated the accuracy, high sensitivity (with a detection limit of 10 CFU/μL), and time-saving nature (30 min) of our tM13-based immunomagnetic enrichment approach combined with AI-enabled analytics, thereby supporting its potential to facilitate the identification of diverse E. coli strains in complex samples.ConclusionThe study established a rapid and accurate detection strategy for E. coli utilizing truncated M13 phages as capture probes, along with a dark field microscopy detection platform that integrates an image processing model and convolutional neural network.Graphical