From Gene to Whole Cell: Modeling, Visualization, and Analysis

Proteogenomics combines proteomic and genetic data to gain new insights in molecular mechanisms. Here, we extend this approach toward structural biology from a tool perspective. The chapter starts with tools which can be used to explore genetic information and then enrich those with proteomic data. Based on the corresponding identifiers, three-dimensional structures of proteins are identified and used to embed them in their molecular environment, here the surrounding membrane. This membrane is then mapped onto the surface of an interpretative three-dimensional cell model. Then, the embedded protein and the cell environment are associated with a metabolic pathway, again based on the identifiers provided by biomedical databases. Accompanying the different chapters, related work is discussed which can alternatively be used. Finally, an outlook toward immersive analytics is given.

Self-assembly of mixed-linkage glucan hydrogels formed following EG16 digestion

Mixed-linkage glucans are major components of grassy cell-walls and cereal endosperm. Recently identified plant endo-β-glucanase from the EG16 family cleaves MLGs with strong specificity towards regions with at least four sequential β(1,4)-linked glucose residues. This activity yields a low molecular-weight MLG with a repeating structure of β(1,3)-linked cellotriose that gels rapidly at concentrations as low as 1.0 % w/v. To understand the gelation mechanism, we investigated the structure and behavior using rheology, microscopy, X-ray scattering, and molecular dynamics simulations. Upon digestion, the material's rheological behavior changes from typical polymeric material to a fibrillar network behavior seen for e.g. cellulose nanofibrils. Scanning electron microscopy and confocal microscopy verifies these changes in micro- and nanostructure. Small-angle X-ray scattering shows in-solution self-assembly of MLG through ~10 nm elemental structures. Wide-angle X-ray scattering data indicate that the polymer association is similar to cellulose II, with dominant scattering at d-spacing of 0.43 nm. Simulations of two interacting glucan chains show that β(1,3)-linkages prevent the formation of tight helices that form between β(1,4)-linked d-glucan chains, leading to weaker interactions and less ordered inter-chain assembly. Overall, these data indicate that digestion drives gelation not by enhancement of interactions driving self-assembly, but by elimination of unproductive interactions hindering self-assembly.

β-Cyclodextrin-based geometrically frustrated amphiphiles as one-component, cell-specific and organ-specific nucleic acid delivery systems

We introduce an innovative β-cyclodextrin (βCD)-prototype for delivering nucleic acids: "geometrically frustrated amphiphiles (GFAs)." GFAs are designed with cationic centers evenly distributed across the primary O6 and secondary O2 positions of the βCD scaffold, while hydrophobic tails are anchored at the seven O3 positions. Such distribution of functional elements differs from Janus-type architectures and enlarges the capacity for accessing strictly monodisperse variants. Changes at the molecular level can then be correlated with preferred self-assembly and plasmid DNA (pDNA) co-assembly behaviors. Specifically, GFAs undergo pH-dependent transition between bilayered to monolayered vesicles or individual molecules. GFA-pDNA nanocomplexes exhibit topological and internal order characteristics that are also a function of the GFA molecular architecture. Notably, adjusting the pKa of the cationic heads and the hydrophilic-hydrophobic balance, pupa-like arrangements implying axial alignments of GFA units flanked by quasi-parallel pDNA segments are preferred. In vitro cell transfection studies revealed remarkable differences in relative performances, which corresponded to distinct organ targeting outcomes in vivo. This allowed for preferential delivery to the liver and lung, kidney or spleen. The results collectively highlight cyclodextrin-based GFAs as a promising class of molecular vectors capable of finely tuning cell and organ transfection selectivity.

Antimicrobial polymer-based zeolite imidazolate framework composite membranes for uranium extraction from wastewater and seawater

Extraction uranium (VI) (U(VI)) from wastewater and seawater is highly important for environmental protection and life safety, but it remains a great challenge. In this work, the growth of the zeolitic imidazolate framework-8 (ZIF-8) nanoparticles on the tannic acid (TA)-3-aminopropyltriethoxysilane (APTES) modified PVDF (TAP) membrane was designed to obtain an excellent U(VI) adsorbent. The zeolite imidazolate framework composite membrane (TAPP-ZIF-60) was prepared through polyethyleneimine (PEI) bridging strategy and temperature regulation strategy in solvothermal method. The coordination bond between PEI and ZIF-8 and the covalent bond between PEI and TAP are essential in forming stable composite membrane. TAPP-ZIF with different properties was synthesized through a temperature regulation process and the TAPP-ZIF prepared at 60 °C has the uniform morphology and good performance. The adsorption capacity of TAPP-ZIF-60 is 153.68 mg/g (C0 = 95.01 mg/L and pH = 8.0) and water permeability is 5459 L m-2 h-1 bar-1. After ten adsorption-desorption cycles, it is proved that TAPP-ZIF-60 has good repeatability and stability. In addition, the TAPP-ZIF-60 composites membrane has a good inhibitory effect on Staphylococcus aureus and Escherichia coli. X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) analysis reveal that the coordination between TAPP-ZIF-60 and uranyl ions is the primary factor contributing to the high adsorption capacity.

Tunable temperature-responsive photonic ionogels with dual signals output

Photonic ionogels with dual electrical and optical output have been intensively studied. However, tunable temperature-responsive photonic ionogel assembled by thermosensitive nanogels has not been studied yet. Herein, an innovative approach to fabricate photonic ionogels has been developed for smart wearable devices with tunable temperature sensitivity and structural color. Firstly, poly(isopropylacrylamide-r-phenylmaleanilic acid) P(NIPAm-r-NPMA) nanogels self-assemble into photonic crystals in 2-hydroxyethyl acrylate (HEA), water, and the ionic liquid of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate. And then robust photonic ionogels are developed through a polymerization of 2-hydroxyethyl acrylate crosslinked by poly(ethylene glycol) diacrylate (PEGDA). The incorporation of the ionic liquid, 1-ethyl-3-methylimidazolium trifluoromethanesulfonate, enhances the mechanical strength of photonic ionogels and tunes the temperature-sensitivity of the ionogels, making them adaptable to various environmental conditions. The findings demonstrate that these ionogels can serve dual functions in smart wearable devices, combining electrical and optical signal outputs due to the conductivity of the ionic liquid and structural color from the nanogel assembly. The resultant photonic ionogels exhibit exceptional substrate adhesion, mechanical stability, and fast resilience. More significantly, the nanogels within these ionogels serve as the building blocks of photonic crystals (PCs) endow with angle-independent coloration and enhance stretchability beyond 200 %, while the stretchability of the ionogles without the nanogels is only about 100 %. Our photonic ionogels with tunable temperature-sensitivity and dual outputs will open an avenue to the development of the innovative smart wearable devices.

Biomimetic androgen receptor-based AIE biosensor for detecting bisphenol analogues: An integrating in silico topological analysis, molecular docking, and experimental validation study

Bisphenol analogues are the typical class of endocrine disrupting chemicals (EDCs) that interfere with binding of endogenous hormones to androgen receptor (AR). With the expansion of industrial activities and the intensification of environmental pollution, an increasing array of bisphenol analogues is being released into the environment and food chain. This highlights the urgency to develop sensitive methods for the detection of bisphenol analogues. Here, we propose a biomimetic AR-based biosensor platform for detecting bisphenol analogues (BPF, TBBPA, and TBBPS) by binding with Aggregation-Induced Emission (AIE) probes. Following a comparison of the PROSS and ABACUS methods, biomimetic AR was designed using the ABACUS approach and subsequently expressed in vitro via the E. coli expression system. Through molecular docking and the observation of fluorescence changes upon binding with biomimetic AR, BS-46006 was selected as the AIE probe for the biosensor. The biomimetic AR-based biosensor showed sensitive detections of BPF, TBBPA, and TBBPS within a range of 0-50 mM. To further elucidate the multi-residue recognition mechanism, molecular orbitals, Electron Localization Function (ELF), and Localized Orbital Locator (LOL) were systematically calculated in this study. Lowest unoccupied molecular orbital and highest occupied molecular orbital indicated the energy gap of BPF, TBBPA, and TBBPS, which correspond to 0.12812, 0.19689, and 0.18711 eV, respectively. ELF and LOL offered clearer perspective through heat maps to visually represent the electron delocalization in BPF, TBBPA, and TBBPS. The matrix effect analysis suggested that the responses of bisphenol analogues in soil matrices could be effectively mitigated through sample pretreatment. The analysis of spiked soil samples showed the acceptable recoveries ranged from 91 % to 105 %. Additionally, the biomimetic AR-based AIE biosensor, which combines multi-residue detection with Tolerable Daily Intakes, shows great promise for the risk assessment of bisphenol analogues. This research may present a viable approach for the analysis of environmental pollutants.

Tunable supramolecular self-assemblies based on cyclodextrin polymer as a loading platform for water-soluble drugs

Drug loading capacity is a crucial character of nano-scaled drug carriers to achieve high quality pharmaceutical preparations. However, efficient encapsulation of water-soluble small molecular drugs still faces large obstacles in many cases. Herein, we designed a novel supramolecular delivery system constructed by poly(β-cyclodextrin) containing benzoic acid groups (PCD-PA) and adamantyl terminated poly(ethylene glycol) (PEG-AD) to provide multiple intermolecular interactions for competent loading of water-soluble small-molecular drugs. PCD-PA had multiple host molecules, and PEG-AD could be inserted via host-guest interaction in different proportion to adjust the composition of supramolecular carrier. Meanwhile, π-π stacking and electrostatic interaction furnished by benzoic acid groups served as binding force for drug entrapment, which led to considerable loading capacity for several water-soluble drugs. Among the drugs with different chemical structures, mitoxantrone hydrochloride and doxorubicin hydrochloride bearing anthraquinone rings and several protonable amino groups acquired the highest loading content as about 14 % in PCD-PA3/PEG-AD supramolecular self-assemblies. Further computational simulations investigated the mechanism of drug loading based on the interactions between the carrier materials and the payloads. In addition, the weakly acidic environment obviously accelerated the release of certain drugs. All in all, this self-assembled supramolecular nano-system displayed great potentials as a delivery platform for diverse water-soluble drugs.

Starch/polyacrylamide hydrogels with flexibility, conductivity and sensitivity enhanced by two imidazolium-based ionic liquids for wearable electronics: Effect of anion structure

To meet the growing demands for sustainable and eco-friendly wearable electronics, biopolymer-based hydrogels have attracted much attention. As one of the most abundant sources of biopolymers, starch has the advantages of low-cost, renewability, biocompatibility and biodegradability. However, mechanical fragility, low conductivity and low sensitivity limited the application of starch-based hydrogels. Herein, two imidazolium-based ionic liquids with different anions (chloridion and acetate) were introduced into corn starch/polyacrylamide hydrogels. The mechanical properties (the maximum elongation: 515.4 %), conductivity (the maximum value: 3.1 S·m-1) and sensitivity (the maximum gauge factor value: 9.3) of the hydrogel were enhanced by the two ionic liquids and proved by the microcosmic characterizations and theoretical simulations (DFT). The two ionic liquids varied in their impacts on the above properties of the hydrogels due to the different anion structure. In mechanical properties, acetate was dominant over chloridion, while the opposite was true for conductivity. Based on the above properties of the starch-based hydrogels, wearable electronics were constructed for detecting human joint motions, subtle expressions, temperature and touch screen operations. This work not only provides novel starch-based hydrogels as candidates for the wearable electronics, but also lays a theoretical foundation for the application of ionic liquids in biopolymer-based materials.

Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures

JOURNAL/nrgr/04.03/01300535-202501000-00034/figure1/v/2024-05-14T021156Z/r/image-tiff Certain amino acids changes in the human Na+/K+-ATPase pump, ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1), cause Charcot-Marie-Tooth disease type 2 (CMT2) disease and refractory seizures. To develop in vivo models to study the role of Na+/K+-ATPase in these diseases, we modified the Drosophila gene homolog, Atpα, to mimic the human ATP1A1 gene mutations that cause CMT2. Mutations located within the helical linker region of human ATP1A1 (I592T, A597T, P600T, and D601F) were simultaneously introduced into endogenous DrosophilaAtpα by CRISPR/Cas9-mediated genome editing, generating the AtpαTTTF model. In addition, the same strategy was used to generate the corresponding single point mutations in flies (AtpαI571T, AtpαA576T, AtpαP579T, and AtpαD580F). Moreover, a deletion mutation (Atpαmut) that causes premature termination of translation was generated as a positive control. Of these alleles, we found two that could be maintained as homozygotes (AtpαI571T and AtpαP579T). Three alleles (AtpαA576T, AtpαP579 and AtpαD580F) can form heterozygotes with the Atpαmut allele. We found that the Atpα allele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila. Flies heterozygous for AtpαTTTF mutations have motor performance defects, a reduced lifespan, seizures, and an abnormal neuronal morphology. These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.

Cysteines in β-lactoglobulin affects its interfacial adsorption and protein film stabilization

HYPOTHESIS

Disulfide bonds in proteins are strong chemical bonds forming the secondary and tertiary structure like in the dairy protein β-lactoglobulin. We hypothesize that the partial or complete removal of disulfide bonds affects the structural rearrangement of proteins caused by intra- and intermolecular interactions that in turn define the interfacial activity of proteins at oil/water interfaces. The experimental and numerical investigations contribute to the mechanistic understanding of the structure-function relationship, especially for the interfacial adsorption behavior of proteins.

EXPERIMENTAL AND NUMERICAL

Systematically, the 5 cysteines of β-lactoglobulin were recombinantly exchanged by alanine. First, the protein structure of the variants in bulk was analyzed with Fourier-transform-infrared-spectroscopy and molecular dynamic simulations. Second, the structural changes after adsorption to the interface have been also analyzed by molecular dynamic simulations. The adsorption behavior was investigated by pendant drop analysis and the interfacial film properties by dilatational rheology.

FINDINGS

The structural flexibility of β-lactoglobulin with no cysteines encourages its unfolding at the interface, and accelerates the interfacial protein film formation that results in more visco-elastic films in comparison to the reference.

Hypotensive effect of potent angiotensin-I-converting enzyme inhibitory peptides from corn gluten meal hydrolysate: Gastrointestinal digestion and transepithelial transportation modifications

The study examined the antihypertensive effect of peptides derived from pepsin-hydrolyzed corn gluten meal, namely KQLLGY and PPYPW, and their in silico gastrointestinal tract digested fragments, KQL and PPY, respectively. KQLLGY and PPYPW showed higher angiotensin I-converting enzyme (ACE)-inhibitory activity and lower ACE inhibition constant (Ki) values when compared to KQL and PPY. Only KQL showed a mild antihypertensive effect in spontaneously hypertensive rats with -7.83 and - 5.71 mmHg systolic and diastolic blood pressure values, respectively, after 8 h oral administration. During passage through Caco-2 cells, KQL was further degraded to QL, which had reduced ACE inhibitory activity. In addition, molecular dynamics revealed that the QL-ACE complex was less stable compared to the KQL-ACE. This study reveals that structural transformation during peptide permeation plays a vital role in attenuating antihypertensive effect of the ACE inhibitor peptide.

Multifunctional near-infrared fluorescent probe for sensing of lysine and Cu2+/Fe3+ and relay detection of biothiols

Lysine (Lys), Cu2+ and Fe3+ ions and biothiols are essential to a myriad of biological and pathological pathways, and their dysregulation is implicated in a variety of diseases. Development of fluorescent probes capable of detecting multiple analytes may be of great significance for early and accurate diagnosis of diseases and remains a huge challenge. In this context, a novel coumarin-dicyanoisophorone-based probe, engineered for the concurrent sensing of Lys, Cu2+, Fe3+ and biothiols was developed. The probe exhibited turn-on response to Lys, colorimetric and turn-off response to Cu2+ by formation of the probe-Cu2+ complex, and ratiometric sensing of Fe3+. In addition, the probe-Cu2+ complex served colorimetric and fluorescence turn-on sensor for biothiols. The limit of detection (LOD) values for the analytes were in the range of 0.30-4.40 μM. Sensing mechanisms based on intramolecular charge transfer (ICT) and iron-mediated hydrolysis of Schiff base were proposed and substantiated through density functional theory (DFT) calculations. Application of the probe for living cell bioimaging was demonstrated.

Tailored polysaccharide entrapping metal-organic framework for RNAi therapeutics and diagnostics in atherosclerosis

Metal-organic frameworks (MOFs) hold promise as theranostic carriers for atherosclerosis. However, to further advance their therapeutic effects with higher complexity and functionality, integrating multiple components with complex synthesis procedures are usually involved. Here, we reported a facile and general strategy to prepare multifunctional anti-atherosclerosis theranostic platform in a single-step manner. A custom-designed multifunctional polymer, poly(butyl methacrylate-co-methacrylic acid) branched phosphorylated β-glucan (PBMMA-PG), can effectively entrap different MOFs via coordination, simultaneously endow the MOF with enhanced stability, lesional macrophages selectivity and enhanced endosome escape. Sequential ex situ characterization and computational studies elaborated the potential mechanism. This facile post-synthetic modification granted the administered nanoparticles atherosclerotic tropism by targeting Dectin-1+ macrophages, enhancing in situ MR signal intensity by 72 %. Delivery of siNLRP3 effectively mitigated NLRP3 inflammasomes activation, resulting a 43 % reduction of plaque area. Overall, the current study highlights a simple and general approach for fabricating a MOF-based theranostic platform towards atherosclerosis conditioning, which may also expand to other indications targeting the lesional macrophages.

In-situ synthesis of heteroatom-doped hard carbon for sodium-ion batteries: Dual benefits for green energy and environment

Heteroatom-doped carbon has been widely investigated as anode materials for sodium-ion batteries (SIBs). However, simplifying the preparation process and precisely controlling their microstructure to achieve excellent Na+ storage performance remain significant challenges. Therefore, in this study, high-performance N, P co-doped Na+ storage carbon anode electrode materials were prepared by one-step carbonization using N, P-rich Eichhornia crassipes (EC) as raw materials and systematically tested for their Na+ storage performance. The doping levels of N and P atoms as well as the spatial structure of the carbon material were adjusted by changing the carbonization temperature during the pyrolysis process. Among them, the anode material corresponding to 1300 °C (EC-PN1300) showed an excellent Na+ storage capacity of 336 ± 4 mAh g-1 (50 mA g-1) and excellent cycling stability (99.8 % retention after 2000 cycles). In addition, the Na+ storage mechanism of EC-PN1300 was systematically analyzed using galvanostatic intermittent titration (GITT), ex-situ XPS and in-situ Raman spectroscopy, providing accurate research directions for developing carbon anode electrode materials with superior electrochemical performance. This study not only provides some insights into the preparation of carbon anode materials in alkali metal batteries and the development of carbon materials in other fields, but also realizes the interaction between environmental protection and new energy development.

The Potential of Molecular Docking for Predictive Toxicology

Molecular modeling techniques are widely used in medicinal chemistry for the study of biological targets, the rational design of new drugs, or the investigation of their mechanism of action.They are also applied in toxicology to identify chemical potential harmful effects.Molecular docking is a computational technique to predict the ligand binding mode and evaluate the interaction energy with a biological target.This chapter describes a computational workflow to predict possible endocrine disruptors on peroxisome proliferator-activated receptor alpha (PPARα), a nuclear receptor involved in glucose and lipid metabolism. The analyzed compounds are food contact chemicals, natural or synthetic substances intentionally added to food or released from the package or during production or technological processes.

PK-PD relationship of poorly absorbable active ingredients from traditional Chinese medicines explaining by metabolic enzyme of gut microbiota: A case study of Dehydrocorydaline

Many active ingredients in traditional Chinese medicines generally have the characteristic of poor oral absorption but definite efficacy. It is necessary to establish a comprehensive technical system to explain the "PK-PD relationship" of them. Dehydrocorydaline (DHC), the quality control component in the Chinese patent drug "Kedaling Tablets", has poor oral absorption but clear efficacy for coronary heart disease. Using DHC as a model drug, the changes in absorption and pharmacological effects of DHC in rats before and after inhibiting nitroreductase (NR) from gut microbiota were studied. The results showed that after inhibiting of NR activity, the plasma concentration of DHC in rats was decreased, the serum level of total cholesterol, triglyceride and low-density lipoprotein cholesterol were significantly increased. The levels of tumor necrosis factor-α, interleukin-1β, hypersensitive C-reactive protein, intercellular cell adhesion molecule-1 and Monocyte chemoattractant protein-1 were significantly increased, and pathological sections also showed that the efficacy of DHC decreased after inhibiting the activity of NR. We further investigated the drug metabolism of DHC under NR and found that DHC was metabolized into a hydrogenated metabolite, which may have stronger membrane permeability. In summary, NR may mediate the absorption degree and efficacy of DHC in vivo by metabolizing DHC into absorbable metabolite.

Inclusion complexes of novel formyl chromone Schiff bases with β-Cyclodextrin: Synthesis, characterization, DNA binding studies and in-vitro release study

The present study involved the synthesis of five novel Schiff bases (SB1-SB5) of formyl chromone and their inclusion complexes with β-cyclodextrin through kneading approach to enhance the solubility and stability of SBs. Characterization was conducted using FTIR, NMR, SEM, TEM, p-XRD, and Mass Spectrometry. UV fluorescence and pH stability studies confirmed the formation of the inclusion complex. Structural validation of complexes was conducted via molecular docking (PDB ID: 1BFN) and 50 ns MD simulation study. DFT studies were performed on SBs using B3LYP/6-31 + G(d,p) basis set. All SBs exhibited favorable ADME properties and high binding interactions were observed in molecular docking with ctDNA (PDB Id: 1BNA). Further, in-vitro UV absorption and fluorescence experiments demonstrated strong ctDNA interactions for all Schiff bases, with binding constants in the order of 105 M-1, indicating groove binding mode. Among the SBs, SB4 exhibited the highest affinity for DNA grooves, with a binding constant (Kb) of 1.7 × 106 M-1. However, the SB4/β-Cyd inclusion complex also interacted with DNA but with low binding constants compared to SB4. An in-vitro release study of SB4/β-Cyd, revealed 78.92 % dissolution of the inclusion complex, highlighting its potential for enhanced solubility and stability in biological systems.

Ozonolysis of ketoprofen in polluted water: Reaction pathways, kinetics, removal efficiency, and health effects

Ketoprofen (KET), as a non-steroidal anti-inflammatory drug frequently detected in aqueous environments, is a threat to human health due to its accumulation and low biodegradability, which requires the transformation and degradation of KET in aqueous environments. In this paper, the reaction process of ozone-initiated KET degradation in water was investigated using density functional theory (DFT) method at the M06-2X/6-311++g(3df,2p)//M06-2X/6-31+g(d,p) level. The detailed reaction path of KET ozonation is proposed. The thermodynamic results show that ozone-initiated KET degradation is feasible. Under ultraviolet irradiation, the reaction of ozone with water can also produce OH radicals (HO·) that can react with KET. The degradation reaction of KET caused by HO· was further studied. The kinetic calculation illustrates that the reaction rate (1.99 × 10-1 (mol/L)-1 sec-1) of KET ozonation is relatively slow, but the reaction rate of HO· reaction is relatively high, which can further improve the degradation efficiency. On this basis, the effects of pollutant concentration, ozone concentration, natural organic matter, and pH value on degradation efficiency under UV/O3 process were analyzed. The ozonolysis reaction of KET is not sensitive to pH and is basically unaffected. Finally, the toxicity prediction of oxidation compounds produced by degradation reaction indicates that most of the degradation products are harmless, and a few products containing benzene rings are still toxic and have to be concerned. This study serves as a theoretical basis for analyzing the migration and transformation process of anti-inflammatory compounds in the water environment.

Elucidating charge transfer process and enhancing electrochemical performance of laser-induced graphene via surface engineering with sustainable hydrogel membranes: An electrochemist's perspective

Laser-induced graphene (LIG) has emerged as a promising solvent-free strategy for producing highly porous, 3D graphene structures, particularly for electrochemical applications. However, the unique character of LIG and hydrogel membrane (HM) coated LIG requires accounting for the specific conditions of its charge transfer process. This study investigates electron transfer kinetics and the electroactive surface area of LIG electrodes, finding efficient kinetics for the [Fe(CN)6]3-/4- redox process, with a high rate constant of 4.89 x 10-3 cm/s. The impact of polysaccharide HM coatings (cationic chitosan, neutral agarose and anionic sodium alginate) on LIG's charge transfer behavior is elucidated, considering factors like ohmic drop across porous LIG and Coulombic interactions/permeability affecting diffusion coefficient (D), estimated from amperometry.It was found that D of redox species is lower for HM-coated LIGs, and is the lowest for chitosan HM. Chitosan coating results in increased capacitive share in the total current while does not apparently reduce Faradaic current. Experimental findings are supported by ab-initio calculations showing an electrostatic potential map's negative charge distribution upon chitosan chain protonation, having an effect in over a two-fold redox current increase upon switching the pH from 7.48 to 1.73. This feature is absent for other studied HMs. It was also revealed that the chitosan's band gap was reduced to 3.07 eV upon acetylation, due to the introduction of a new LUMO state. This study summarizes the operating conditions enhanced by HM presence, impacting redox process kinetics and presenting unique challenges for prospective LIG/HM systems' electrochemical applications.

Mechanism investigation of Forsythoside A against esophageal squamous cell carcinoma in vitro and in vivo

CONTEXT

Forsythoside A (FSA) was extracted from Forsythia suspensa, a traditional Chinese medicine, which has been demonstrated to exert anti-inflammatory, antibacterial, and other pharmacological effects. However, the anticancer effect of FSA in esophageal squamous cell carcinoma (ESCC) has not been documented.

OBJECTIVE

The present study aimed to elucidate the mechanism of FSA against ESCC.

MATERIALS AND METHODS

Network pharmacology and molecular docking were employed to predict the mechanism. FSA was utilized to treat ESCC cell lines KYSE450 and KYSE30, followed by CCK-8 assay, cell cloning formation assay, flow cytometry, Western blot, RNA-seq analysis, and subsequent in vivo experiments.

RESULTS

Network pharmacology and molecular docking predicted that the therapeutic effect of FSA in ESCC is mediated through proteins such as BCL2 and BAX, influencing KEGG pathways associated with apoptosis. In vitro experiments showed that FSA inhibited cell proliferation and plate clone formation, promoted cell apoptosis and impacted the cell cycle distribution of G2/M phase by regulating BCL2, BAX, and p21. Further RNA-seq in KYSE450 cells showed that FSA regulated the expression of 223 genes, specifically affecting the biological process of epidermal development. In vivo experiments showed that gastric administration of FSA resulted in notable reductions in both tumor volume and weight by regulating BCL2, BAX, and p21. 16S rRNA sequencing showed that FSA led to significant changes of beta diversity. Abundance of 11 specific bacterial taxa were considerably changed following administration of FSA.

CONCLUSIONS

This study presents a novel candidate drug against ESCC and establishes a foundation for future clinical application.

Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics

Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.

In silico vaccine design for Yersinia enterocolitica: A comprehensive approach to enhanced immunogenicity, efficacy and protection

Yersinia enterocolitica, a foodborne pathogen, has emerged as a significant public health concern due to its increased prevalence and multidrug resistance. This study employed reverse vaccinology to identify novel vaccine candidates against Y. enterocolitica through comprehensive in silico analyses. The core genome's conserved protein translocase subunit SecY was selected as the target, and potential B-cell, MHC class I, and MHC class II epitopes were mapped. 3B-cell epitopes, 3 MHCI and 11 MHCII epitopes were acquired. A multi-epitope vaccine construct was designed by incorporating the identified epitopes, TLR4 Agonist was used as adjuvants to enhance the immunogenic response. EAAAK, CPGPG and AYY linkers were used to form a vaccine construct, followed by extensive computational evaluations. The vaccine exhibited desirable physicochemical properties, stable secondary and tertiary structures as evaluated by PDBSum and trRosetta. Moreover, favorable interactions with the human Toll-like receptor 4 (TLR4) was observed by ClusPro. Population coverage analysis estimated the vaccine's applicability across 99.74 % in diverse populations. In addition, molecular dynamics simulations and normal mode analysis confirmed the vaccine's structural stability and dynamics in a simulated biological environment. Furthermore, codon optimization and in silico cloning facilitated the evaluation of the vaccine's expression potential in E. coli and pET-28a was used a recombinant plasmid. This study provides a promising foundation for the development of an efficacious vaccine against Y. enterocolitica infections.

Deciphering the genetic impact of signal peptide missense CTLA-4 polymorphism with rheumatoid arthritis in the Indian population: A case-control and in silico studies

Cytoplasmic T Lymphocyte Antigen-4 (CTLA-4) gene encodes for a glycoprotein, expressed on activated T-cells to transfer an inhibitory signal to control T-cell activation and proliferation. Techniques coupled with Real-time Polymerase Chain Reaction (PCR) and High-Resolution Melting Analysis (HRMA) were used to screen a missense signal peptide polymorphism (CTLA-4 + 49 A/G rs231775) in the Indian population to detect its association with Rheumatoid Arthritis (RA). Further, the resulting outcome was confirmed by Sanger's sequencing technique, and genotype frequencies were calculated. In eukaryotic cells, the M domain of the Signal Recognition Particle (SRP-54) recognizes the N-terminal region of the Signal Peptide (SP) sequence. SP directs the polypeptide chain into the Sec-61 translocon of the Endoplasmic Reticulum (ER) for further protein modification. As the Single Nucleotide Polymorphism (SNP) rs231775 lies in the signal peptide region of CTLA-4, an in-silico study was also performed to predict the mRNA stability and SP-SRP protein interaction. From the study, it was observed that the genotype frequency of rs231775 SNP G/G homozygous dominant was significantly higher in RA patients than G/A heterozygous dominant and A/A homozygous recessive conditions (Odd Ratio (OR) = 2.0862; 95 % Confidence Interval (C.I) = 1.2584 to 3.4584; Relative Risk (RR) = 1.8507; p = 0.0044). Moreover, the rs231775 SNP G allele frequency was higher in RA than the control group G = 0.407 (40.7 %) vs 0.32 (32 %). In silico approaches of Protein-Protein docking and Molecular Dynamics (MD) simulation reveal CTLA-4 rs231775 SNP (G allele) has destabilized the SP-SRP protein complex, which may affect the translocation of CTLA-4 nascent polypeptide chains into the ER via activating Regulation of Aberrant Protein Production (RAPP) pathway.

A ratiometric fluorescence method for the detection of diquat by a large Stokes shift fluorescent probe

Pesticide residues are currently a prominent concern for food safety, and the development of a rapid, convenient, and accurate method for detecting pesticide residues is crucial to ensure the quality of agricultural products. In this study, a small molecule fluorescent probe based on biphenyl disulfonic acid (BDSA) was designed and prepared, and a sensitive, specific, and rapid detection method for diquat (DQ) and paraquat (PQ) was developed. The fluorescent molecule (BDSA-NDA) was synthesized through amide reaction between BDSA and 1,8-naphthalic anhydride, which exhibited cyan fluorescence (480 nm) when excited at 305 nm in aqueous solution with a large Stokes shift (>150 nm). Diquat and paraquat were found to quench the fluorescence of the probe through internal filtration effect (IFE) and photoelectron transfer (PET). Moreover, diquat possessed a large conjugated structure that emitted fluorescence at 340 nm which was assembled into a pair of ratio fluorescence with BDSA-NDA. Under optimized experimental conditions, the developed method achieved detection limits of 0.003 mg/L for diquat and 0.202 mg/L for paraquat. Furthermore, it could identify paraquat doped in diquat formulations. Additionally, when applied to environmental water samples as well as rice and urine, this detection method demonstrated good recovery rates (water: 96.2-100.6 %, rice: 93.5-101.9 %, urine: 96-103.7 %), meeting actual sample detection requirements effectively. This work presents a novel approach for rapidly detecting diquat and paraquat residues which holds practical application value in areas such as pesticide residue analysis in foods, environmental or clinical samples.

Molecular modeling study to unravel complexation of daclatasvir and its enantiomer by β-cyclodextrins. Computational analysis using quantum mechanics and molecular dynamics

A computational study was performed to unravel mechanisms underlying capillary electrophoresis enantioseparations of daclatasvir and its (R,R,R,R)-enantiomer with native and methylated β-cyclodextrins (β-CDs) as chiral selectors. Considering the enantioseparation results as benchmark, the structures of β-CD and seven methylated β-CDs were optimized by quantum mechanics, and their topography and computed molecular properties were compared. Furthermore, the electron charge density distribution of the macrocycles was also evaluated by calculating the molecular electrostatic potential of pivotal regions of native and methylated β-CDs. The function of hydrogen bonds in the complexation process of daclatasvir and the CDs was derived from quantum mechanics analysis and confirmed by molecular dynamics, as orthogonal computational techniques. The presence of a round-shaped cavity in the CDs used as chiral selector appeared as a necessary requirement for the enantioseparation of daclatasvir and its (R,R,R,R)-enantiomer. In this regard, it was confirmed that the round shape of the CDs is sustained by hydrogen bonds formed between adjacent glucopyranose units and blocking rotation of the linking glycosidic bonds. The presence of hydroxy groups at the 6-position of the glucopyranose units and the concurrent absence of hydroxy groups at the 2-position were evidenced as important factors for enantioseparation of daclatasvir and its enantiomer by methylated β-CDs.

The third-order nonlinear optical responses of zinc porphyrin oligomers: Cycles vs linear chains

Porphyrins are widely used as potential nonlinear optical (NLO) materials because of their highly delocalized π electrons and feasible synthesis and functionalization with broad biological applications. A variety of linear and cyclic porphyrin derivatives have been synthesized, and the correlation between their structures and NLO properties awaits being disclosed. In this work, the electronic structures and third-order NLO properties of linear and cyclic butadiyne-linked zinc porphyrin oligomers have been studied by quantum chemical methods and sum-over-states model. The static second hyperpolarizability (<γ0>) increases exponentially with the number of zinc porphyrin units ([<γ0>n] = 0.67[<γ0>1]n2.63, n = 2 ∼ 6) in linear π-conjugated oligomers, and the <γ0> of the linear hexamer is about 74 times that of the monomer. Such enhancement of <γ0> in linear oligomers originates from closely-lying frontier molecular orbitals available for low energy electron excitations and strong charge transfer-based excitations across porphyrins. The <γ0>s of cyclic porphyrins are lower than that of the linear hexamer, though the interaction between the ring and the ligand enhances the <γ0> of some cyclic zinc porphyrin complexes. The large two-photon absorption cross sections confer on these zinc porphyrin derivatives excellent candidates for two-photon absorption applications.

High-performance cellulose/thermoplastic polyurethane composites enabled by interaction-modulated cellulose regeneration

Strong interfacial adhesion between cellulose and other polymers is critical to achieve the properties required for specific applications in composite materials. Here, we developed a method for the simultaneous homogeneous dissolution of cellulose and thermoplastic polyurethane (TPU) in 1,8-diazabicyclo (5.4.0) undec-7-ene levulinate/dimethyl sulfoxide ([DBUH]Lev/DMSO) solvent. This process is essential for preparing cellulose/TPU composite films and fibers through interaction-modulated cellulose regeneration. Both cellulose and TPU can be easily dissolved together in [DBUH]Lev/DMSO solvent under mild conditions. The resulting cellulose/TPU solutions exhibited strong temperature sensitivity, shear-thinning behavior and viscoelasticity, making them suitable for cast films and continuous spinning. More importantly, research findings, including density functional theory calculations and experimental characterization, confirmed the high compatibility and interaction modulability of cellulose and TPU in the composite films. The representative C90T10 sample (cellulose/TPU, 90/10) showed high transparency (90 % at 800 nm) and excellent mechanical properties (tensile strength: 176 MPa; elongation at break: 8.1 %). Additionally, the maximum tensile strength and elongation at the break of the composite fiber from C90T10 were 214 MPa and 48.1 %, respectively. This method may provide a feasible approach to design and produce homogeneous environmentally friendly composites of cellulose and other polymers at the molecular level.

Spatial organization of the ions at the free surface of imidazolium-based ionic liquids

HYPOTHESIS

Experimental information on the molecular scale structure of ionic liquid interfaces is controversial, giving rise to two competing scenarios, namely the double layer-like and "chessboard"-like structures. This issue can be resolved by computer simulation methods, at least for the underlying molecular model. Systematically changing the anion type can elucidate the relative roles of electrostatic interactions, hydrophobic (or, strictly speaking, apolar) effects and steric restrictions on the interfacial properties.

SIMULATIONS

Molecular dynamics simulation is combined with intrinsic analysis methods both at the molecular and atomic levels, supplemented by Voronoi analysis of self-association.

FINDINGS

We see no evidence for the existence of a double-layer-type arrangement of the ions, or for their self-association at the surface of the liquid. Instead, our results show that cation chains associate into apolar domains that protrude into the vapour phase, while charged groups form domains that are embedded in this apolar environment at the surface. However, the apolar chains largely obscure the cation groups, to which they are bound, while the smaller and more mobile anions can more easily access the free surface, leading to a somewhat counterintuitive net excess of negative charge at the interface. Importantly, this excess charge could only be identified by applying intrinsic analysis.

Dissolution of denim waste in N-methyl morpholine-N-oxide monohydrate for fabrication of regenerated cellulosic film: Experimental and simulation study

Despite the significant amount of denim waste and its potential as a cellulose source, its use has been neglected. This study uses N-methyl morpholine-N-oxide, an eco-friendly solvent, to dissolve denim (including 100 % cotton) and create a denim film. Achieving a 10 % denim record solubility, a cellulosic film was also fabricated for comparison. Characterisation techniques were applied, and molecular dynamics simulations explored intramolecular interactions and the influence of indigo dye on dissolution process. FTIR spectra indicated no chemical reactions during dissolution and regeneration, though a shift in OH stretching suggested a change in crystallinity, confirmed by XRD results showing decreased crystallinity and a structural shift from cellulose I to cellulose II. 13C NMR analysis revealed disruptions in interchain hydrogen bonds after regeneration. TGA results showed lower decomposition temperatures for both films compared to the powders. Testing mechanical properties showed the denim film had higher elongation at break but lower tensile strength than the cellulose film. MD simulations indicated indigo dye did not significantly affect fundamental interactions but decreased denim solubility by reducing the diffusion coefficient. Rheological tests supported the simulation results, showing higher viscosity and molecular weight for the denim solution compared to cellulose.

Elucidation of the hydration pattern of trifluoroacetic acid in dilute solutions: FTIR and computational study

The atmospheric partitioning of trifluoroacetic acid (TFA) in aerosol is a complex function of the size of suspended water droplets and their pH value. The unraveling of the affinity of TFA towards basic but not acidic conditions may be accomplished by providing an insight into the hydration pattern of undissociated TFA. Owing to rather scarce details on very dilute aqueous solutions of trifluoroacetic acid (TFA), we examined CF3COOD and CF3COONa solutions in D2O in the concentration range 0.001-0.1 mol dm-3 using transmission FTIR spectroscopy and computational methods. Besides detecting the signals originated from undissociated species in both CF3COOD (1787 cm-1 and 1766 cm-1 at c0 = 0.1 mol dm-3) and CF3COONa (1807 cm-1 at c0 = 0.1 mol dm-3) D2O solutions, through computational techniques we identified different TFA hydrates that contribute to the complexity of the spectral appearance. The combination of experimental and computational data suggested the concentration dependence of the predominant hydrogen bonding pattern of TFA. The results obtained in this work should help in understanding the partitioning of TFA into micron-size water droplets in the atmosphere in molecular and structural terms, i.e. the eventual stability of a hydrated complex for a particular TFA conformer.

Multiple pathways for lanthanide sensitization in self-assembled aqueous complexes

Lanthanide photoluminescence (PL) emission has attracted much attention for technological and bioimaging applications because of its particularly interesting features, such as narrow emission bands and very long PL lifetimes. However, this emission process necessitates a preceding step of energy transfer from suitable antennas. While biocompatible applications require luminophores that are stable in aqueous media, most lanthanide-based emitters are quenched by water molecules. Previously, we described a small luminophore, 8-methoxy-2-oxo-1,2,4,5-tetrahydrocyclopenta[de]quinoline-3-phosphonic acid (PAnt), which is capable of dynamically coordinating with Tb(III) and Eu(III), and its exchangeable behavior improved their performance in PL lifetime imaging microscopy (PLIM) compared with conventional lanthanide cryptate imaging agents. Herein, we report an in-depth photophysical and time-dependent density functional theory (TD-DFT) computational study that reveals different sensitization mechanisms for Eu(III) and Tb(III) in stable complexes formed in water. Understanding this unique behavior in aqueous media enables the exploration of different applications in bioimaging or novel emitting materials.

DFT studies on N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl)

In this work, molecular descriptors of N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl) halogenated benzamides (1a-h) have been computed using a quantum chemical technique through DFT. Prior work involved the synthesis of compounds (1a-h) and the assessment of their anticancer activity on breast, colon, and liver tumors: MCF-7, HCT-116, and HepG-2 cell lines respectively. Since 1a, 1b, and 1d showed the most potential anticancer impact, their ability to inhibit EGFRWT was investigated. Based on the biological data, 1b inhibited EGFRWT the most. According to the docking evaluation, an H-bond with the threonine residue was one of the main non-covalent contacts between 1b and the EGFRWT active site residues. PES, MESP, HOMOs, LUMOs, energy band gap, global reactivity indices [electron affinity (A), ionization energies (I), electrophilicity index (ω), nucleophilicity index (ε), chemical potential (μ), electronegativity (χ), hardness (η), and softness (S)], condensed Fukui functions, NBO, and NCIs are the molecular descriptors of 1a-h that were computed using DFT technique. According to the theoretical investigation results, compounds (1a-h) might have anticancer effects; these findings are consistent with the biological findings from our previous research. Compound 1b had the lowest binding energy, according to an assessment of the binding energies between the threonine and the three most active compounds (1a, 1b, and 1d). This is consistent with the outcomes of the docking study and the biological examination of the influence of 1a, 1b, and 1d on EGFRWT.

Antioxidant activity of Zuccagnia-type propolis: A combined approach based on LC-HRMS analysis of bioanalytical-guided fractions and computational investigation

This study reports a combined approach to assess the antioxidant activity of Zuccagnia-type propolis. Fractions exhibiting the highest antioxidant activities evidenced by DPPH, a β-carotene bleaching and superoxide radical scavenging activity-non-enzymatic assays, were processed by LC-HRMS/MS to characterize the relevant chemical compounds. A computational protocol based on the DFT calculations was used to rationalize the main outcomes. Among the 28 identified flavonoids, caffeic acids derivatives were in the fraction exhibiting the highest antioxidant activity, with 1-methyl-3-(4'-hydroxyphenyl)-propyl caffeic acid ester and 1-methyl-3-(3',4'-dihydroxyphenyl)-propyl caffeic acid ester as major components. Results clearly showed roles of specific chemical motifs, which can be supported by the computational analysis. This is the first report ascribing the antioxidant ability of Zuccagnia-type propolis to its content in specific caffeic acid derivatives, a potential source of radical scavenging phytochemicals. The proposed protocol can be extended to the study of other plant-products to address the most interesting bioactive compounds.

Effect of ethylene oxide groups on calcite wettability reversal by nonionic surfactants: An experimental and molecular dynamics simulation investigation

HYPOTHESIS

Ethoxylated nonionic surfactants are promising candidates for enhanced oil recovery (EOR) from oil-wet carbonate reservoirs due to their ability to reverse the mineral wettability. The wettability-reversal efficiency increases with the number of the ethoxy (EO) groups in the surfactant molecule.

METHODOLOGY

Contact angle measurements, scanning electron microscopy (SEM) and molecular dynamics (MD) simulations were combined to investigate the wettability reversal of an oil-wet calcite by three ethoxylated nonionic surfactants with 1, 4 and 8 EO groups, respectively, to directly probe the role of the EO groups and to uncover the molecular mechanism responsible for the wettability reversal.

FINDINGS

Both experiments and simulations consistently show a clear correlation between the number of EO groups and the wettability reversal efficiency of the surfactants, whereby the higher number of EO groups results in greater degree of wettability reversal. This is due to 1) the more hydrophilic surfactant headgroup weakening the carboxylate interactions with the surface by expanding the surface-adjacent water layer, and 2) the physically larger surfactant molecule attracting the carboxylates more strongly, thus aiding in their removal from the surface.

Defect-mediated Fermi level modulation boosting photo-activity of spatially-ordered S-scheme heterojunction

Spatially-ordered S-scheme photocatalysts are intriguing due to their enhanced light harvesting, spatially isolated redox sites, and strong redox abilities. Nonetheless, heightening the performance of S-scheme photocatalysts via controllable defect engineering is still challenging to now. In this work, multi-armed MoSe2/CdS S-scheme heterojunction with intimate Mo-S bond coupling and adjustable Se vacancies (VSe) and Mo5+ concentrations was constructed, which consisted of few- or even single-layered MoSe2 growing on the {11-20} facets of wurtzite CdS arms. The S-scheme charge transmission mechanism of MoSe2/CdS heterojunction was validated by density functional theory calculation combined with in situ photo-irradiated X-ray photoelectron spectroscopy, surface photovoltage, and radical measurements. Moreover, the Fermi level gap between CdS and MoSe2 was enlarged by regulating the contents of donor (VSe) and acceptor (Mo5+) impurities with synthesis temperature, which strengthens the built-in electric field and carriers transfer driving force of MoSe2/CdS composites, contributing to an outstanding H2 evolution activity of 52.62 mmol·g-1·h-1 (corresponding to an apparent quantum efficiency of 34.8 % at 400 nm) under visible-light irradiation (λ > 400 nm), 25.8 times that of Pt-loaded CdS counterpart and a substantial amount of reported CdS-containing photocatalysts. Our study results are anticipated to facilitate the rational design of advanced semiconductor nanostructures for efficient solar conversion and utilization.

Boosting electrocatalytic nitrate-to-ammonia of single Fe active sites via coordination engineering: From theory to experiments

Atomically dispersed iron-nitrogen-carbon (Fe-N4-C) catalysts show great promises for the electrocatalytic nitrate (NO3-) reduction to ammonia (NH3). Nevertheless, the microenvironmental engineering of the single Fe active sites for further optimizing the catalytic performance remains a challenge. Herein, we proposed to regulate the coordination environment of single Fe active sites to boost its intrinsic electrocatalytic activity for NO3- -to-NH3 conversion by the incorporation of new heteroatoms, including B, C, O, Si, P, and S. Our results revealed that most of the candidates possess low formation energies, showing great potential for experimental synthesis. Moreover, incorporating heteroatoms effectively modulates the charge redistribution and the d-band center of single Fe active sites, enabling the regulation of the binding strength of nitrogenous intermediates. As a result, the N and C coordinated Fe active site (Fe-N3C) exhibits superior catalytic performance for NO3- electroreduction with a relatively low limiting potential (-0.13 V) due to its optimal adsorption strength with nitrogenous intermediates induced by its moderate charge and d-band center. Importantly, our experimental measures confirmed such theoretical prediction: a maximum NH3 yield rate of 21.07 mg h-1 mgcat.-1 and 95.74 % Faradaic efficiency were achieved for NO3- electroreduction on Fe-N3C catalyst. These findings not only suggest a highly efficient catalyst for nitrate reduction but also provide insight into how to design and prepare electrocatalysts with enhanced catalytic performance.

A magnetic carboxyl-functionalized covalent organic framework for the efficient enrichment of foodborne heterocyclic aromatic amines prior to UPLC-MS analysis

Foodborne heterocyclic aromatic amines (HAAs) are potent mutagens and carcinogens, posing significant health risks. Existing enrichment methods for HAAs need better adsorption selectivity and capacity for daily exposure assessment. This study hypothesized that introducing carboxylic groups into magnetic covalent organic frameworks (m-COFs) would improve HAAs adsorption by providing additional binding sites. Hence, we prepared a novel magnetic adsorbent, termed as Fe3O4@DOPA-TpPa-(COOH)2 capable of enhancing the HAAs detection through magnetic solid-phase extraction (MSPE) coupled with UPLC-MS. This sorbent demonstrated a large specific surface area (130.7 m2/g), high magnetic responsivity (21.05 emu/g), and robust stability, with an adsorption capacity (Qm[cal]: 81.82 mg/g) driven by electrostatic, LP - π/C-H - π interactions, and hydrogen bonding. Optimal MSPE conditions provided sensitive detection with a broad linear range (5-500 ng/mL), low limits of detection (0.01-7.01 ng/g), and excellent repeatability. Application to Cantonese mooncake samples showed satisfactory recoveries (62.12%-126.86%). This method offers a more accurate tool for detecting HAAs.

Graphene-supported MN4 single-atom catalysts for multifunctional electrocatalysis enabled by axial Fe tetramer coordination

Multifunctional electrocatalysts for oxygen reduction reaction (ORR), oxygen evolution reaction (OER), and hydrogen evolution reaction (HER) are crucial for development of the key electrochemical energy storage and conversion devices, for which single-atom catalyst (SAC) has present great promises. Very recently, some experimental works showed that structurally well-defined ultra-small transition-metal clusters (such as Fe and Co tetramers, denoted as Fe4 and Co4, respectively), can efficiently modulate the catalytic behavior of SACs by axial coordination. Herein, taking the graphene-supported MN4 SACs as representatives, we theoretically explored the feasibility of realizing multifunctional SACs for ORR, OER and HER by this novel axial coordination engineering. Through extensive first-principles calculations, from 23 candidates, IrN4 decorated with Fe4 (IrN4/Fe4) is identified as the promising trifunctional catalyst with the theoretical overpotential of 0.43, 0.51 and 0.30 V for OER, ORR and HER, respectively. RhN4/Fe4 and CoN4/Fe4 are recognized as potential OER and ORR bifunctional catalysts. In addition, NiN4/Fe4 exhibits the best ORR activity with an overpotential of 0.30 V, far superior to the pristine NiN4 SAC (0.88 V). Electronic structure analyses reveal that the significantly enhanced ORR/OER activity can be ascribed to the orbital and charge redistribution of Ni/Ir active center, resulting from its electronic interaction with Fe4 cluster. This work could stimulate and guide the rational design of graphene-based multifunctional SACs realized by axial coordination of small TM clusters, and provide insights into the modulation mechanism.

An Eu (III)-functionalized covalent organic framework fluorescent probe for specific detection of Flumequine based on pore restriction and antenna effect

The overuse of quinolone antibiotics has led to a series of health and environmental issues. Herein, we combine the distinct luminescence properties of Eu3+ with the unique structure of covalent organic frameworks (COFs) to develop a precise and sensitive fluorescent probe for detecting Flumequine (Flu) in water. Eu3+ is thoroughly anchored into the channels of COFs as recognition sites, while the synthesized probe material still maintains its intact framework structure. The unique structure of COFs provides excellent support and protection for Eu3+. Therefore, COF-Eu can rapidly bind with Flu which can transfer the absorbed energy to Eu3+ through an "antenna effect", resulting in red fluorescence. Moreover, there is a good linear relationship between Flu concentration in the range of 0-30 µM, with a detection limit of 41 nM. Simultaneously, the material maintains remarkable reproducibility, with its performance remaining almost unchanged after five cycles of use. Remarkably, the probe demonstrates excellent Flu recovery rates in real samples. This study provides a viable approach for the recognition of flumequine in the environment through a customized fluorescence detection method.

Sensing mechanism of the benzo-bodipy based fluorescent probe for Hypochlorous acid detection: Invalidity of photoinduced electron transfer

In vivo real-time detection of hypochlorous acid (HClO) in biological systems plays a crucial role in diagnosing immune-related diseases. Experimentally, a benzo-bodipy probe based on the photo-induced electron transfer (PeT) sensing mechanism has been developed for live fluorescence imaging. However, there have been no theoretical studies conducted to substantiate the precision of the sensing mechanism. This paper employs density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods to investigate the fluorescence detection mechanism of benzo-bodipy derivatives (BBy-T and BBy-TO), proposing a detection approach based on dark nπ* state quenching. The study reveals that the fluorescence quenching mechanism of BBy-T is primarily regulated by a thiomorpholine moiety, involving a dark nπ* state transition non-radiatively. Furthermore, this paper explains the fluorescence enhancement observed in BBy-TO. Theoretical investigations demonstrate, based on frontier molecular orbitals (FMOs) and hole-electron analysis, that the fluorescence enhancement for BBy-TO is not governed by the previously proposed intramolecular charge transfer (ICT) mechanism in experiments but rather follows a locally excited (LE) ππ* pattern. This work offers new insights for the design of novel fluorescence probes based on bodipy and benzo derivatives, expanding the understanding of their fluorescence properties.

Cellulose-based fluorescent chemosensor with controllable sensitivity for Fe3+ detection

Polymer-based sensors, particularly those derived from renewable polymers, are gaining attention for their superior properties compared to organic small molecules. However, their complex preparation and poor, uncontrollable sensitivity have hindered further development. Herein, cellulose-based polymer photoluminescence (PL) chemosensors were fabricated using a straightforward and adjustable strategy. Specifically, water-soluble cellulose acetoacetate (CAA) was used as the substance for the in-situ synthesis of 1,4-dihydropyridine (DHPs) fluorescent rings on cellulose chains via a catalyst-free, room-temperature Hantzsch reaction. Benefiting from the synergetic through-space conjugation of DHPs rings and semi-rigid cellulose chains with heteroatoms, the sensors exhibit bright and stable PL properties. Based on this performance, the cellulose-based sensor excels in the specific recognition of Fe3+ in aqueous systems, showing exceptional selectivity, stability, and anti-interference performance due to the synergy between the inner filter effect (IFE) and intramolecular charge transfer (ICT). Theoretical calculations confirm the role of the extended π-conjugated structure at the DHPs-4 position in modulating the sensor sensitivity, achieving a low limit of detection (LOD) of 0.48 μM. Furthermore, the versatility of the Hantzsch reaction shows the potential of this strategy for developing a new generation of biomass-based polymer portable sensors for real-time and on-site detection.

Mechanistic insights into ASO-RNA complexation: Advancing antisense oligonucleotide design strategies

Oligonucleotide drugs, an emerging modulator class, hold promise for targeting previously undruggable biomacromolecules. To date, only 18 oligonucleotide drugs, including sought-after antisense oligonucleotides (ASOs) and splice-switching oligonucleotides, have approval from the U.S. Food and Drug Administration. These agents effectively bind mRNA, inducing degradation or modulating splicing. Current oligonucleotide drug design strategies prioritize full Watson-Crick base pair (bp) complementarity, overlooking mRNA target three-dimensional shapes. Given that mRNA conformational diversity can impact hybridization, incorporating mRNA key structural properties into the design may expedite ASO lead discovery. Using atomistic molecular dynamics simulations inspired by experimental data, we demonstrate the advantages of incorporating common triple bps into the design of ASOs targeting RNA hairpin motifs, which are highly accessible regions for interactions. By using an RNA pseudoknot modified into an ASO-hairpin complex, we investigate the effects of ASO length and hairpin loop mutations. Our findings suggest that ASO-mRNA complex stability is influenced by ASO length, number of common triple bps, and the dynamic accessibility of bases in the hairpin loop. Our study offers new mechanistic insights into ASO-mRNA complexation and underscores the value of pseudoknots in constructing training datasets for machine learning models aimed at designing novel ASO leads.

Interaction of plant phenol vanillin with human hemoglobin: A spectroscopic and molecular docking study

Vanillin is a phenolic aldehyde widely used as a flavouring agent in the food industry. Vanillin has many health benefits and has gained attention in pharmacological industries also, due to its antioxidant properties and non-toxic nature. The interaction of vanillin with human hemoglobin (hHb), an abundant tetrameric heme protein, was investigated by several spectroscopic techniques and molecular modeling methods. UV-visible spectra showed that the binding of vanillin to hHb induces structural changes due to alterations in the micro-environment of hHb. Vanillin quenches the intrinsic fluorescence of hHb by the dynamic mechanism, which was confirmed by both temperature dependent and time resolved fluorescence studies. Vanillin binds spontaneously to hHb at a single site and the binding is stabilized by hydrogen bonds and hydrophobic interactions. The circular dichroism spectra showed that the binding of vanillin altered the secondary structure of hHb due to change in its alpha-helical content. Molecular docking identified the amino acids of hHb involved in binding to vanillin and also that the free energy change of the binding reaction is -5.5 kcal/mol. Thus, our results indicate that vanillin binds spontaneously to hHb at a single site and alters its secondary structure. This will help in understanding the potential use of vanillin and related antioxidants as therapeutic agents in various hematological disorders.

Theoretical study on optimizing dipeptidomimetic isocyanonaphthalene chemosensor and the fluorescence mechanism for detecting Hg2

The excited (S1) state charge distribution characteristics and fluorescence mechanism of fluorescence probes benzyl (6-cyano-2-naphthoyl)-L-valinate (NPI) and benzyl (6-amino-2-naphthoyl)-L-valinate (NPA) have been discussed using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). Further analysis by constructing a torsional potential energy curve (PEC) shows that a well-defined minimum energy conformation is observed when the C-C single bond between the valine benzyl ester and naphthalene ring in NPI rotates. For NPA, the most stable conformation is the naphthalene ring conformation with dihedral angle N2C1C2C3 of -30.60°, whose total energy is 0.17 kcal/mol lower than that of the second most stable conformer. The frontier molecular orbitals (FMOs) demonstrate that NPI exhibits a low degree of charge coupling, and the oscillator intensity is close to zero, indicating that it is not conducive to luminescence. However, in the S1 state, the oscillator strength of NPA is 1.2044, which is a bright state, resulting in the strong emitting. Additionally, fluorescence imaging is favored as a visual observation technique, and Stokes shift is an important physical parameter to measure fluorescence. According to the idea that changing the number and position of functional groups can affect the photophysical properties of fluorescent dyes, o-NPDI, p-NPDI and m-NPDI dyes were newly designed and o-NPDA, p-NPDA, m-NPDA produced after recognition of Hg2+. The spectral performance results show that the newly designed fluorescent dye (p-NPDA) can not only emit in the near infrared region after recognizing Hg2+, but also has a large Stokes shift (236 nm). This indirectly reflects that para-substitution is more conducive to Stokes shift, and has become one of the strategies for fluorescent dye design.

Utilizing artificial intelligence for precision exploration of N protein targeting phenanthridine sars-cov-2 inhibitors: A novel approach

The persistent mutation of the novel coronavirus presents a continual threat of infections and associated illnesses. While considerable research efforts have concentrated on the functional proteins of SARS-CoV-2 in the development of anti-COVID-19 therapeutics, the structural proteins, particularly the N protein, have received comparatively less attention. This study focuses on the N protein, a critical structural component of the virus, and employs advanced deep learning models, including EMPIRE and DeepFrag, to optimize the structures of phenanthridine-based compounds. More than 10,000 small molecules, derived through deep learning, underwent high-throughput virtual screening, resulting in the synthesis of 44 compounds. Compound 38 showed a binding potential energy of -8.2 kcal/mol in molecular docking. Surface Plasmon Resonance (SPR) and Microscale Thermophoresis (MST) validation yielded dissociation constants of 353 nM and 726 nM, confirming strong binding to the N protein. Compound 38 demonstrated antiviral activity in vitro and exhibited anti-COVID-19 effects by interfering with the binding of N proteins to RNA. This research underscores the potential of targeting the SARS-CoV-2 N protein for therapeutic intervention and illustrates the efficacy of deep learning model in the design of lead compounds. The application of these deep learning models represents a promising approach for accelerating the discovery and development of antiviral agents.

Uncovering the sensing mechanism of a zinc ion sensor: Fluorescence enhancement induced by the elimination of the TICT state

Precise detection of zinc ion is of fundamental importance in the fields of environment protection and food safety. A comprehensive understanding of the sensing mechanism will help to the design of such sensors. The detailed photophysical process of a zinc ion sensor as well as the sensing mechanism are uncovered with the aid of density functional theory (DFT) and time-dependent density functional theory (TDDFT). Both the ground state and first excited state potential energy surfaces (PES) of the sensor are carefully explored to reveal the photo-physical process of the sensor. Excited state intramolecular proton transfer (ESIPT) is observed on the S1 state PES. Then, the twist motion of C=N double bond is triggered after the ESIPT process, which leads to a twisted intramolecular charge transfer (TICT) state. This TICT state is found to make the sensor non-emissive. With the addition of Zn2+, the TICT state is eliminated which greatly enhances the fluorescence of the sensor and achieves zinc ion detection. The interaction of the sensor with Cd2+ and Hg2+ are also explored, which well explains the good selectivity of the sensor.

Effect of geometric isomerism on the anticancer property of new platinum complexes with glycine derivatives as asymmetric N, O donate ligands against human cancer

In this project, to fallow the anticancer ability of new Pt drugs, several new Pt complexes were synthesized with the asymmetric bidentate glycine derivatives, as named propyl- and hexyl glycine (L), in the general formula: [Pt(NH3)2(L)]NO3, and cis- and trans-[Pt(L)2]. The structure of two cis- and trans-[Pt(propylgly)2] complexes was proved by single crystallography analysis. However, all complex structures were characterized by various methods of 1H NMR, 13C NMR, 195Pt NMR, FTIR, LC-Mass, and Raman spectroscopy. To study the passage of water-soluble complexes of [Pt(NH3)2(L)]NO3 via cell membrane, their solubility, and lipophilicity were analyzed. In addition, the cytotoxic properties of these complexes were evaluated against normal and malignant cell lines (skin, breast, and lung cancer cells). The results indicated that they were either comparable to cisplatin or less damaging than carboplatin and oxaliplatin. It was expected that due to less steric effect, and the presence of length aliphatic hydrocarbon chain in the complex structure, trans-[Pt(hexylgly)2] is more toxic on cancerous cell lines than trans-[Pt(propylgly)2]. Cellular accumulation of all complexes was evaluated on A549 and MCF7 cell lines, and the amount of platinum metal (ng) was measured by the ICP method. Results showed that trans-[Pt(hexylgly)2] complex has the highest accumulation inside both mentioned cell lines and [Pt(NH3)2(L)]NO3 complexes behave like clinical Pt-drugs. Ultimately, the interaction patterns of DNA were examined using spectroscopic methods and molecular docking simulations for all substances.

Integrating serum pharmacochemistry, network pharmacology and untargeted metabolomics strategies to reveal the material basis and mechanism of action of Feining keli in the treatment of chronic bronchitis

ETHNOPHARMACOLOGICAL RELEVANCE

Feining keli (FNKL) is herbal preparation mainly made from Senecio cannabifolius Less., In recent years, more and more studies have found that FNKL has excellent therapeutic effects on chronic bronchitis (CB). Nevertheless, its pharmacodynamic material basis and mechanism of action are still unknown.

AIM OF THE STUDY

This study aimed to explore the pharmacodynamic material basis and mechanism of action of FNKL in treating CB.

MATERIALS AND METHODS

The CB rat model was induced using nasal drops of lipopolysaccharide (LPS) in combination with smoking. Various assessments including behavioral and body mass examination, lung index measurement, enzyme linked immunosorbent assay (ELISA), as well as histological analyses using hematoxylin and eosin (H&E) and Masson staining were conducted to validate the reliability of the CB model. The serum components of FNKL in CB rats were identified using ultra-high-performance liquid chromatography Orbitrap Exploris mass spectrometer (UHPLC-OE-MS). Network pharmacology was used to predict the network of action of the active ingredients in FNKL based on these serum components. Signaling pathways were enriched and analyzed, and molecular docking was conducted for key targets. Molecular dynamics simulations were performed using GROMACS software. The mechanism was confirmed through a series of experiments including Western blot (WB), immunofluorescence (IF), and reverse transcription (RT)-PCR. Additionally, untargeted metabolomics was employed to identify biomarkers and relevant metabolic pathways associated with the treatment of CB with FNKL.

RESULTS

In CB rats, FNKL improved body mass, lung index, and pathological damage of lung tissues. It also decreased interleukin (IL)-6, tumor necrosis factor-alpha (TNF-α), malonaldehyde (MDA) levels, and percentage of lung collagen fiber area. Furthermore, FNKL increased IL-10 and superoxide dismutase (SOD) levels, which helped alleviate bronchial inflammation in the lungs. A total of 70 FNKL chemical components were identified in CB rat serum. Through network pharmacology analysis, 5 targets, such as PI3K, AKT, NF-κB, HIF-1α, and MYD88, were identified as key targets of FNKL in the treatment of CB. Additionally, the key signaling pathways identified were PI3K/AKT pathway、NF-κB/MyD88 pathway、HIF-1α pathway. WB, IF, and RT-PCR experiments were conducted to confirm the findings. Molecular docking studies demonstrated successful docking of 16 potential active components with 5 key targets. Additionally, molecular dynamics simulations indicated the stability of quercetin-3-galactoside and HIF-1α. Metabolomics analysis revealed that FNKL primarily regulated pathways related to alpha-linolenic acid metabolism, primary bile acid biosynthesis, bile secretion, arachidonic acid metabolism, neuroactive ligand-receptor interaction, and folate biosynthesis. Furthermore, the expression levels of traumatic acid, traumatin, alpha linolenic acid, cholic acid, 2-arachidonoylglycerol, deoxycholic acid, 7,8-dihydroneopterin, and other metabolites were found to be regulated.

CONCLUSION

FNKL exhibits positive therapeutic effects on CB, with quercetin-3-galactoside identified as a key active component. The mechanism of FNKL's therapeutic action on CB involves reducing inflammatory response, oxidative stress, and regulating metabolism, and its molecular mechanism was better elucidated in a holistic manner. This study serves as a reference for understanding the pharmacodynamic material basis and mechanism of action of FNKL in treating CB, and provides avenues for exploring the effects of compounded herbal medicines on CB.

Design and synthesis of pyrano[2,3-c]pyrazole-4-aminoquinoline hybrids as effective antimalarial compounds

In this work, a series of nineteen novel pyrano[2,3-c]pyrazole-4-aminoquinoline hybrids were synthesized as potent antimalarial agents by covalently linking the scaffolds of 4-aminoquinoline and pyrano[2,3-c]pyrazoles via an ethyl linker and characterized using Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy (NMR). Molecular docking was used to test each hybrid's and standard chloroquine's ability to bind to Plasmodium falciparum lactate dehydrogenase enzyme (PfLDH), an important enzyme in the parasite's glycolytic pathway. The hybrid compounds had a stronger binding affinity than the standard chloroquine (CQ). The schizontical antimalarial test of pyrano[2,3-c]pyrazole-4-aminoquinoline hybrid compound shows that all nineteen hybrid compounds were potent with the IC50 values ranging from 0.0151 to 0.301 μM against the CQ-sensitive 3D7 P. falciparum strain, and were active against the CQ-resistant K1 P. falciparum strain with the IC50 values ranging from 0.01895 to 2.746 μM. All the tested hybrid compounds were less potent than the standard drug chloroquine dipaspate (CQDP) against the CQ-sensitive 3D7 strain. In contrast, nine of the nineteen hybrids (16d, 16g, 16h, 16i, 16l, 16n, 16o, 16r, and 16s) displayed superior antimalarial activity than the CQDP against the CQ-resistant K1 P. falciparum strain. Among all the tested hybrids, 16c against the 3D7 strain and 16h against the K1 strain were the most promising antimalarial agents with 0.0151 and 0.01895 μM of IC50 values, respectively. In addition, the compounds were selective, showing moderate to low cytotoxic activity against a human normal liver WRL68 cell line. The synthesis of pyrano[2,3-c]pyrazole-4-aminoquinoline hybrids introduces new chemical entities that have the potential to exhibit potent antimalarial activity. It could address the ongoing challenge of drug resistance in malaria treatment.

Discovery of novel substituted pyridine carboxamide derivatives as potent allosteric SHP2 inhibitors

Src homology-2-containing protein tyrosine phosphatase 2 (SHP2), a critical regulator of proliferation pathways and immune checkpoint signaling in various cancers, is an attractive target for cancer therapy. Here, we report the discovery of a novel series of substituted pyridine carboxamide derivatives as potent allosteric SHP2 inhibitors. Among them, compound C6 showed excellent inhibitory activity against SHP2 and antiproliferative effect on MV-4-11 cell line with IC50 values of 0.13 and 3.5 nM, respectively. Importantly, orally administered C6 displayed robust in vivo antitumor efficacy in the MV-4-11 xenograft mouse model (TGI = 69.5 %, 30 mg/kg). Subsequent H&E and Ki67 staining showed that C6 significantly suppressed the proliferation of tumor cells. Notably, flow cytometry, ELISA and immunofluorescence experiments showed that C6 remarkably decreased the population of CD206+/Ly6C+ M2-like tumor-associated macrophages (TAMs), the expression level of interleukin-10 (IL-10), and the number of F4/80+/CD206+ M2-like TAMs, suggesting that C6 could effectively alleviate the activation and infiltration of M2-like TAMs. Taken together, these results illustrate that C6 is a promising SHP2 inhibitor worthy of further development.