RSC Advances

Numerous advances in quantum and computational chemistry over the last decades, well as the development of computer science, allowed utilisation of more precise and complex models, which can be now applied to much bigger systems than in the past. The authors used Gaussian, coupled with theoretical methods, to predict a new way of peptide bond formation, which could have taken place in prebiotic conditions. To better tackle this difficult task, the properties of substrates (glycine-derived radicals) were extensively analysed, using the aforementioned tool - Gaussian, paired with taking resonance and hybridisation into account, to better understand the stereochemistry and the very nature of processes taking place. The result is a series of reactions, which without any sophisticated catalysts and with relatively low energy thresholds ({inverted exclamation}20 kcal/mol) can lead to formation of dipeptides (and further, oligopeptides). The authors also hope, the other predicted properties of the investigated molecules can be of use to any researcher, who would like to utilise them in their experiments. Author summaryOur goal was to investigate a way first peptide bonds in prebiotic conditions could have been formed. This is an extremely important step in research into the beginning of life on Earth. We found a very promising series of reactions, which uses atomic hydrogen as its only catalyst and confirmed our expectations with theoretical calculations, using Gaussian. There are two radicals derived from glycine, which perform major roles in the process, so we investigated their properties with Gaussian and verified that the results are in agreement with our own theoretical considerations. This involved checking for possible geometric isomers and conformers and creating models which could explain their properties. We are well aware that such calculations have limitations and there is no model, which is 100% accurate, so our results should be further confirmed by empirical data in the future. However, we still to be as thorough as possible in how we approached the subject.

Chemotherapy treatment of colorectal cancers (CRC) using cisplatin (CDDP) encounters problems of drug resistance by the cancer cells and cytotoxicity to normal cells, highlighting the urgent need for joint therapeutical strategies. Selenium-enriched rapeseed extracts exhibit anti-cancer effects but the bioactive components and mechanisms remain unclear. Here, we applied different solvents to fractionate the extracts from Selenium-enriched rapeseed and found that the water extract (WE) fraction significantly enhanced the cytotoxic effect of CDDP on cancer cells but no damage on normal cells. HPLC-ICP-MS analysis revealed that methylselenocysteine (MSC) and selenocystine (SeCys2) were the main selenium speciation in WE. Through cell biology and integrative multi-omics analysis, we found a synergistic anti-CRC cell effect when combining CDDP with MSC, sulforaphane (SFN), celastrol (Cel), Indole-3-carbinol (I3C), -linolenic acid (ALA) or linoleic acid (LA). We propose that the CDDP-WE combination treatment holds the promise for improving curative efficacy for chemo-refractory CRC patients in the future.

Nile Red is widely used for the detection of microplastics because its fluorescence emission is sensitive to local polarity and can distinguish hydrophobic plastics from hydrophilic ones. The fluorescence of the molecular rotor, 9-(dicyanovinyl)-julolidine (DCVJ) is less sensitive to polarity but more to viscosity. DCVJ is less widely used for microplastic analysis, although it has been used to detect polystyrene nanobeads. Here, we compared these dyes with standard samples from the Hawaii Pacific University Polymer Kit 1.0 and confirmed that Nile Red, in general, was better for the detection and identification of microplastics. Fluorescence emission was analyzed using photography, as well as spectroscopy. The color and peak emission wavelength of some stained environmental microplastics were affected by additives. Raman spectroscopy was used to confirm the chemical identity of such samples. Although DCVJ emits green fluorescence on binding to some microplastics, a peak at 620 nm has been reported with polystyrene nanobeads, attributed to dimer/excimer formation. We confirmed this property and directly observed diffraction-limited spots using fluorescence microscopy, attributed to single or just a few nanobeads. Nile Red also stains polystyrene nanobeads and gave stronger signals than with DCVJ, but Nile Red was prone to false positives due to dye aggregation in aqueous solutions.

Mycosporine-like amino acids (MAAs) are among nature's most effective sunscreen compounds, capable of converting harmful ultraviolet radiation into harmless heat, and are widely distributed in marine organisms such as red macroalgae. Although decades of research have led to numerous discoveries, the rate of new MAA identifications has declined. To address this, we considerably expanded our previously developed combinatorial MAA database, increasing the number of covered structures tenfold. Following a comprehensive literature search for plausible but undescribed building blocks, the database now incorporates an extensive set of proteinogenic and non-proteinogenic amino acids, as well as other marine organic osmolytes, in combination with all (currently) known MAA scaffolds. This expanded resource was integrated into our identification platform, which combines UHPLC-VWD-HRMS2 analysis, feature-based molecular networking, and bioinformatics-driven annotation. Application of this updated workflow enabled the isolation and structural elucidation of a novel MAA, mycosporine-cysteinolic acid, from the red marine macroalga Vertebrata lanosa. Altogether, this study provides a valuable extension of the bioinformatics-based MAA screening pipeline, enhancing the annotation and discovery of novel MAAs in natural matrices.

Cancer is a serious public health problem, and is becoming more common, with a projected increase in deaths and more than 25 million new cases in coming decades. A number of molecular mechanisms are involved in the tumoral process, with one of them, never in mitosis A-related kinase 2 (NEK2), a serine/threonine protein kinase, being a frequent target of amplification in various malignancies that is responsible for chromosomal instability, aneuploidy and activation of several oncogenic pathways. Available kinase inhibitors are not yet optimized in terms of their pharmacokinetic properties for clinical use, and current therapies, such as chemotherapeutic agents or immunotherapies are often limited by their resistance. In silico methods represent an effective tool to search for novel potent inhibitors, before testing in animals, with time constraints and limited resources. To find new inhibitors of NEK2, we used E pharmacophore-based modeling and structure based virtual screening in this study. NEK2 was chosen as the target for therapeutic intervention and an energy optimized pharmacophore model was employed to screen the Enamine REAL library of millions of compounds. Pharmacodynamic and Pharmacokinetic properties of the Top hits were tested using ADMET profiling. These were further screened using molecular docking (standard precision and extra precision) and virtual screening to obtain three lead compounds 1, 2, and 3 which have docking score of -7.414, -8.037 and -7.562 respectively. MM-GBSA calculations were used to estimate the binding free energies for these complexes, which were determined to be -54.92, -54.18 and -49.23 kcal/mol. Lastly, 100 ns molecular dynamics simulations have been run to evaluate complex stability in dynamic situations. The overall results of the MD showed the overall stability of the NEK2-ligand complexes, and thus these three compounds are promising NEK2 inhibitor candidates and could be further validated in vitro and in vivo for clinical application. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/742111v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@14e9cfeorg.highwire.dtl.DTLVardef@24ec78org.highwire.dtl.DTLVardef@20be75org.highwire.dtl.DTLVardef@1b80c02_HPS_FORMAT_FIGEXP M_FIG C_FIG

Tissue regeneration using bioactive biomaterials has made great progress in the field of wound healing. Biopolymers play a cardinal role in regenerative medicine by providing safe, biocompatible and bioresorbable support. The electrospinning fabrication technique has been used in creating suitable wound care materials. PHBV and PLLA are FDA approved polymers having important applications in biomedical field. In this study, to increase the wound healing potential, PHBV was functionalized with -COOH group and electrospun nano-fibrous mat was produced using PHBV-COOH and PLLA blended solution. Antibiofilm peptide (IDR-1018) with immunomodulatory activity was incorporated into the blended solution to improve infected wound treatment by actively fighting against bacterial infections. Furthermore, in-vitro experiments including cell cytotoxicity assay and scratch wound healing assay were done to evaluate the potential of the synthesized bioactive nanofibrous mat as a potential wound management aid.

Multiple-drug resistant (MDR) Staphylococcus aureus strains (like methicillin-resistant S. aureus or MRSA) uses an arsenal of antioxidant enzymes to mitigate host-induced oxidative stress. Among them the non-canonical Staphylococcal glutathione peroxidase (SaGpx) plays a crucial role in bacterial redox homeostasis by reducing peroxides via thioredoxin-dependent pathways. Thus, enabling oxidative stress mitigation during host infection. Despite its importance in S. aureus, its role in bacterial pathogenesis remains unexplored. This study aimed to elucidate the possible role of SaGpx in Staphylococcal virulence. First, we determined the high-resolution crystal structure of SaGpx (at 1.65 [A] resolution) using X-ray crystallography. Guided by the catalytic cleft architecture of SaGpx, small-molecule based inhibitors were then rationally designed and synthesized. These inhibitors exhibited good binding affinity to SaGpx and complete enzymatic blockade. These inhibitors exhibited potent anti-S. aureus activity (MICs 6.25-31.25 M) along with no cytotoxicity in L929 fibroblast wound-healing assays. Furthermore, the in vivo antibacterial ability of these inhibitors was evaluated using S. aureus-infected skin wound mouse model, where these compounds show potent antibacterial and wound healing ability supported by subsequent histological as well as immunohistochemical analysis. These findings suggest SaGpx as a possible virulence determinant in S. aureus and position these synthesized inhibitors as promising antivirulence therapeutics. HighlightsO_LIThe high-resolution crystal structure of Staphylococcal glutathione peroxidase is solved. C_LIO_LIBased on the SaGpx catalytic site, ,{beta}-unsaturated ketoesters derivatives are synthesized. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives inhibit SaGpx activity and binds the protein at M range. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives show in vitro antibacterial activity against S. aureus at low M range. C_LIO_LISynthesized ,{beta}-unsaturated ketoesters derivatives show in vivo antibacterial and wound healing ability S. aureus-infected skin wound mouse model. C_LI

The tomato leafminer, Tuta absoluta, poses a severe global agricultural threat due to its rapid leaf-mining behavior and swift development of resistance to conventional chemical pesticides. While microbial chitinases are potent biopesticides, their field efficacy is limited by environmental degradation and the short exposure window before larvae penetrate leaf tissues. This study evaluates a stimuli-responsive, controlled-release nanobiopesticide system utilizing a novel chitinase from newly characterized Serratia marcescens GBS19. A 61.1 kDa chitinase (GBS19_ChiA) was heterologously expressed in Escherichia coli and purified to a specific activity of 215.01 U/mg. The enzyme was immobilized onto starch-coated silica nanoparticles designed for target-triggered release via host alpha-amylase. Genomic profiling and R-based kinetic modeling were integrated to evaluate the efficacy of purified and immobilized forms against T. absoluta. Immobilization enhanced thermal and pH stability, with the nanocarrier maintaining 85% activity over 10 weeks. In larval bioassays, immobilization increased mortality from 21.9% to 59.4% (5000 U/mL) by day 3, reaching 62.5% by day 6. Genomic analysis identified an expansive secretome and a Type VI Secretion System (T6SS), characterizing GBS19 as a multi-pronged pathogen. Kinetic modeling established that while immobilized enzymes are effective, the 2.5-hour exposure time on T. absoluta requires the synergistic action of chitinases (ChiA/B/C) to reach the lethal desiccation threshold before larvae establish protective mines. Starch-coated silica nanoparticles significantly improve chitinase stability and delivery. However, overcoming the rapid penetration of T. absoluta necessitates a whole-cell or multi-enzyme synergistic approach to outpace larval behavioural defences.

Production of recombinant proteins frequently yields inclusion bodies that must undergo refolding to yield active protein. Here, we optimized the refolding conditions for the recombinant leucyl aminopeptidase (rPepL) from Lactocaseibacillus casei expressed in inclusion bodies from E. coli. Several chemical additives were assessed for how well they facilitated an increase in refolding efficiency. The best, 0.5 M L-arginine, yielded 50.8% refolding. The addition of stabilizers, such as sucrose and glycerol, with L-arginine further increased yields to 85%. Urea at lower concentrations (0.25-0.5 M) also facilitated an increase in the refolding yield when co-added with L-arginine, whereas guanidinium chloride inhibited it. Sugars and polyols exhibited dose-dependent effects, with ranges for optima also defined. Fluorescence spectroscopy verified enhancements in the refolding under the optimized conditions. Molecular dynamics simulation under mixed solvent conditions provided atomic insights about stabilizing interactions that are likely to facilitate increased refolding. The results show that a series of aggregation suppressors and protein stabilizers can, in a collaborative way, increase the refolding efficiency for the recombinant proteins from the inclusion bodies. The protocol with the optimization using the additives L-arginine, sucrose, and glycerol is an efficient method for the production of active rPepL. This article outlines the best refolding method to recover recombinant leucyl aminopeptidase from inclusion bodies of E. coli using L-arginine combined with sucrose and glycerol. The combined experimental observations and computational simulations elucidate the molecular process of additive-induced stabilization, which elucidates how aggregation inhibition and hydrogen-bonded stabilization act synergistically. The results presented herein answer both mechanistic understanding and experimental guidance for improving protein refolding.

Proper alignment of cells is crucial for functioning of various tissues such as skeletal muscle tissues, neural cells, adipose-derived stem cells, etc. Current in-vitro fabrication methods to replicate the cellular environment, e.g., photolithography and 3D printing, are not cost-effective and cannot capture the complexity of the surfaces to which these cells are exposed to. In this work, we used bio-mimicked leaf templates to closely resemble the in-vivo environment the muscle cells and cultured C2C12 cells, myoblast cell lines, on modified PDMS substrates fabricated using these leaf templates. Using image analysis software, we analyzed the degree of alignment of cells, aspect ratio and the area projected by individual cells cultured on these surfaces. The C2C12 cells cultured on the PDMS substrates formed utilizing the front and back sides of the leaves of Musaceae Banana were found to have an Aspect Ratio of 6.3 and 8.3, the highest among the surfaces studied in this paper. C2C12 cells cultured had the highest degree of alignment on the negative replica of the back side of Dracaena Sanderiana. Due to the availability of a wide range of leaf templates and bio-mimicked surface structures to measure cell response, it is difficult to find the optimal design. Hence, we have also tried to create a catalog using 15 different leaf surfaces and characterized these surfaces into various categories based on the grooves on the surfaces to provide a more comprehensive set of surface designs for studying cell behavior. To quantitatively analyze the groove pattern, 2D FFT analysis was also performed to find the dominant wavelength of the grooves. In surface characterization, hydrophobicity is also a parameter that needs to be considered; hence, the water contact angle of these surfaces was also measured. Our findings highlight the importance of surface topography and hydrophobicity in influencing cell alignment and can contribute to developing biomimetic surfaces for tissue engineering applications.

The ability of small molecules to cross the blood-brain barrier (BBB) remains a major bottleneck in neurotherapeutic development. While experimental assays and machine learning approaches provide approximate permeability estimates, they lack atomistic insight into the underlying transport mechanisms. Here, we employ all-atom molecular dynamics simulations of a compositionally realistic BBB lipid bilayer to characterize the passive permeation of two bioactive propolis-derived compounds, Caffeic Acid Phenethyl Ester (CAPE) and Artepillin-C (ARC). Using steered molecular dynamics and umbrella sampling, we computed free energy profiles, diffusion coefficients, and permeability metrics across the membrane. CAPE encounters a modest barrier at the lipid headgroup region but minimal resistance within the hydrophobic core, resulting in a low free energy barrier ([~]2-3 kcal/mol) and favorable permeability (logP_eff {approx} 0.28). In contrast, ARC exhibits a substantial energetic barrier within the membrane core, leading to high resistivity and strongly unfavorable permeability (logP_eff {approx} -10.91). The heterogeneous lipid model reproduces experimentally consistent membrane properties and reveals how lipid composition modulates transport energetics. These findings provide mechanistic insight into BBB permeability and demonstrate the utility of atomistic simulations for guiding the design of neuroactive therapeutics.

Human African trypanosomiasis, caused by a protozoan parasite Trypanosoma brucei, is a neglected tropical disease for which well-tolerated, conveniently administered, and highly efficacious medicines are still missing. Previously, T. brucei Phosphofructokinase was targeted by small-molecule inhibitor development efforts. This approach has shown promise both in vitro and in vivo. In this study, we have used these wet-lab results, evaluated the compounds already characterised by Molecular Dynamics simulations, found relationships between in silico and wet-lab data and used these observations to evaluate compounds that we selected through several different approaches of virtual screens. We observed that inhibitor-ATP interactions are highly predictive of the inhibitory activity. Several compounds selected through virtual screens have outperformed previously characterised compounds.

BackgroundMicrobial chain-elongation by Clostridium kluyveri using the products (acetate and ethanol) derived from the electrocatalytic CO2 reduction reaction (CO2RR) represents a unique sustainable strategy for producing C4-C6 chemicals from CO2. However, direct integration of electrocatalytic effluents with anaerobic bioprocesses is often impeded by the physiological incompatibility between electrocatalytic product streams and microbial metabolism. Specifically, CO2RR effluents commonly contain formate, which cannot be utilized by C. kluyveri for chain elongation and therefore reduces the overall carbon efficiency of CO2 conversion to C4-C6 chemicals. Moreover, both formate and the elevated phosphate concentrations typical of electrochemical reaction solutions may inhibit microbial growth. ResultsWe show that formate at concentrations of up to 50 mM did not inhibit the growth of or the chain elongation by C. kluyveri. Based on this finding, we developed a modular two-step bioprocess. In the first step, the acetogen Clostridium ljungdahlii converts formate in CO2RR product mixtures into acetate, thereby generating additional substrates for second-step C. kluyveri-driven chain elongation, thus increasing the CO2RR carbon-conversion efficiency to C- C6 chemicals. To address the issue of C. ljungdahliis inhibition by high phosphate concentrations in electrocatalytic solutions, we explored the use of C. ljungdahlii biofilms for the first, i.e. the formate-conversion, step. C. ljungdahlii biofilms exhibit tolerance to concentrated electrolytes, enabling the conversion of up to 50 mM formate in CO2RR solutions. ConclusionsThe demonstrated two-step process constitutes the basis for the development of a robust and carbon-efficient biological process for the scalable upgrading of C1-C2 CO2RR products into higher-value C4-C6 chemicals.

The extracellular matrix (ECM) is a complex network of ubiquitously present acellular material that plays a critical role in cell proliferation, migration, invasion, and tissue morphogenesis. Non-enzymatic glycation of ECM modifies the structure and function of ECM proteins and can support a pro-inflammatory milieu in the tumor microenvironment. However, the impact of glycated ECM on cancer cell growth remains underexplored despite its importance in facilitating disease progression. Here, we investigate the effect of ECM glycation on cancer cell morphology and migration behavior. We used methylglyoxal (MG) as a glycation agent and collagen as our ECM model protein. For in vitro growth analysis, breast cancer cells were seeded on growth surfaces coated with both non-glycated and glycated collagen. Cell behavior was monitored for 24 hours using a real-time holographic imaging system. Holographic image analysis revealed significant differences between non-glycated and glycated growth substrates in cell spreading area, eccentricity, perimeter length, optical thickness, and optical volume, as well as cell migration and motility, which directly influence cell adhesion and proliferation. These changes were found to be cell line biased. Overall, our findings suggest that ECM glycation has a significant effect on cell morphology, migration and cell growth. Holographic live cell imaging was determined to be an excellent method to monitor cells without the need for any labeling and with minimal perturbations.

Monitoring pH and extracellular acidification rate (ECA) in biological samples containing live mammalian cells can provide valuable information on the glycolytic activity and bioenergetic status of cells. Compared to pH electrodes, optochemical pH sensors look more advantageous, since they allow rapid, non-invasive parallel analysis of multiple samples with stable readout of pH. We have developed new fluorescent pH sensors based on hydrophobic protonable metal-free porphyrins,OEP and OEPK, embedded in a plasticized PVC matrix containing a proton transfer agent. These pH sensors provide internally-referenced calibration-free operation, both in ratiometric intensity and lifetime-based detection modes. Sensor development included optimization of the indicator dye and its photophysical characteristics, screening of different proton transfer agents to minimize sensor toxicity, tuning of the protonation range and pKa, long-term storage stability and response time studies. Optimised pH sensor coatings were then deposited on plastic substrates (96-well microplates) and used for real-time monitoring of Extracellular Acidification Rate (ECAR) for cultured cancer cells and 3D spheroid structures on standard laboratory equipment (multi-label plate reader and confocal FLIM microscope). The advanced pH sensors tailored for use with biological samples have high potential for cell analysis and related applications.

Vanadium (V) is a potential insulinomimetic that can modulate carbohydrate metabolism, but its biological effects are sensitive to chemical form, concentration, and sex. Chelation of vanadium with organic ligands, in particular citrate, allows to increase its bioavailability and optimize pharmacokinetic properties. The aim of the study was to evaluate tissue-, dose-, and sex-dependent changes in physiological parameters and activity of the key glycolytic enzyme - lactate dehydrogenase (LDH) - under the influence of vanadium citrate. The study was conducted on 6-week-old Wistar rats of both sexes. The animals received vanadium citrate orally for 36-38 days at doses of 3, 12.5, and 50 g VCit/kg body weight. LDH activity in skeletal muscle, liver, kidney, and pancreas was investigated. No pronounced toxic effect on physiological parameters was detected: body weight dynamics corresponded to age norms, no behavioral changes were observed. LDH activity demonstrated pronounced sexual dimorphism and depended on the dose received. It was established that the optimal dose, which provides a modulating effect without signs of metabolic stress, for females is 12.5 g VCit/kg, while for males - 3 g VCit/kg. The most significant changes in LDH activity were recorded in the pancreas at a dose of 50 g V/kg, where the indicators decreased from 0.81 to 0.31 mol/(min x mg protein) in females and from 1.02 to 0.28 mol/(min x mg protein) in males. The effect of vanadium citrate on carbohydrate metabolism, as well as its dose-, tissue- and sex-specific nature, is likely determined by a dual action: the insulin-like effect of vanadium (redirecting pyruvate to oxidation) and the allosteric inhibition of glycolysis by the citrate ligand (substrate limitation for LDH). The obtained results emphasize the importance of considering sex and dose in the research and development of metabolically active compounds.

BackgroundCaspase-3 and -7 are key effector caspases in the apoptotic pathway, a form of programmed cell death, and their activities serve as a well-established biomarker for evaluating environmental chemical toxicity and informing chemical risk assessment. Loss of mitochondrial membrane potential is a key event in the activation of Caspase-3/7 signaling and the subsequent induction of apoptosis. Therefore, simultaneous assessment of mitochondrial membrane potential and Caspase-3/7 activity enables elucidation of the mechanisms and pathways through which apoptosis is initiated.. Rapid and accurate assessment of the potential toxicity of environmental chemicals and drugs remains a major challenge. Quantitative Structure-Activity Relationship (QSAR) modeling have been widely used for toxicity prediction. Graph-based approaches encode compounds directly as molecular graphs, allowing structure-activity relationships to be learnt from molecular topology without the information loss in binary fingerprints. While advanced graph models such as graph transformers (GTs) have shown outstanding performance in many domains, they have not been fully leveraged in QSAR modeling on Caspase and mitochondrial toxicity. MethodsWe propose a QSAR modeling pipeline that encompasses assay data preprocessing, feature representations (fingerprints and molecular graphs), and benchmarking machine learning (ML) models, including classic ML models, graph neural networks (GNNs), GTs, and their consensus ensembles. Based on in vitro Caspase and mitochondrial assays in PubChem, we applied the pipeline to predict Caspase-3/7 activation and mitochondrial membrane potential (MMP). Beyond in vitro assays, we also built in vivo QSAR modeling for FDA Drug-Induced Liver Injury (DILI) gold standard on human hepatotoxicity. Moreover, mechanistic analysis on Caspase-3/7 activation was conducted by comparing with MMP disruption to identify chemical substructures that may be responsible for dual activations. We also investigated cell-line-specific responses by identifying structural motifs that selectively induce Caspase-3/7 activation in individual cell lines. ResultsExperimental evaluations show that GTs and GNNs outperformed classic ML models when the number of active compounds is large, such as MMP disruption, while classic ML models and GTs performed good for highly imbalance data with limited active compounds, such as Caspase-3/7 activation. For DILI prediction, the full consensus model achieved the highest AUC 0.69 and Graphormer had the highest F1 score 0.79, both surpassing the previous best model with AUC 0.63 and F1 0.65 with a large margin. Our mechanistic analysis shows that phenolic compounds bearing a para-hydroxyphenyl motif, as well as members of the lipophilic chain family with long alkyl chains can trigger the collapse of MMP, leading to the activation of caspases-3 and -7. Human embryonic kidney (HEK293) was the only cell line with a distinct structural motif: 1,1-dichloroethane and chlorobenzene. Human neuroblastoma (SK-N-SH) is uniquely impacted by an epoxide fragment and rat hepatoma (H-4-II-E) is uniquely impacted by a tetramethylcyclohexene motif and an acetaldehyde fragment. ConclusionsThe proposed pipeline for QSAR modeling, including data preprocessing, feature representations, and incorporation of advanced graph ML approaches, is highly effective in predicting not only on Caspase-3/7 activation and membrane potential collapse, but also on FDA DILI human hetatotoxicity. As future research directions, we will leverage extra information, e.g., biological activity and findings in existing toxicity literature, and recent advances in large language models and agentic AI to further improve the predictive performance and enable a sensitive and specific framework for assessing human hepatotoxicity of environmental compounds.

Accurate evaluation of extracellular matrix (ECM) mineralization at the nano-scale is essential for establishing relevant in vitro bone models. This is particularly important with the development and increased application of three-dimensional (3D) cell models for biological research. Transmission electron microscopy (TEM) allows to perform ultra-structural analysis of cells and ECM organization, but its application in in vitro bone models remains limited, due to the potential alteration or loss of the mineral phase during sample preparation. In this study, we compared two TEM sample preparation methods - the conventional chemical fixation and the anhydrous methods - to evaluate their ability to preserve the mineralized ECM in MC3T3-E1 cells cultured as monolayers and as alginate-encapsulated bone spheroids. Chemical fixation preserved cellular ultra-structure and collagen organization, allowing for detailed assessment of cells and ECM organization. Although mineral deposits were detected and their needle-like morphology assessed, characterization of more immature deposits was partially limited by the effects of uranyl acetate and the overall sample preparation process, which could lead to alteration or loss of less stable mineral phases. The anhydrous preparation method resulted in limited preservation of cellular and ECM morphology and did not allow reliable identification of mineral deposits. When applied to spheroids, the chemical fixation method preserved the 3D architecture, collagen-rich ECM and inner mineral deposits, confirming spheroids as a relevant model for bone studies. Overall, these results highlight the need for optimized sample preparation strategies that preserve both ultra-structure and mineral components for accurate nano-scale characterization of bone mineralization.

Electrophysiological interfacing remains difficult in three-dimensional in vitro models, when using planar microelectrode arrays or optical methods. This challenge limits experimental progress using such models, despite their promise of better physiological relevance than monolayer cell culture. Mesh MEAs which can integrate conformally on or even within tissue offer a possible solution but are not yet widely accessible. Here, we present a mesh MEA device, designed as a simple, manufacturable platform for spheroid electrophysiology. In neural spheroids, the device enabled longitudinal electrophysiological recordings and pharmacological modulation of spontaneous electrical activity. On native polyimide meshes, spheroids maintained their shape while cells enveloped the mesh, embedding electrodes to a depth of 100 {micro}m after 2 weeks. In contrast, laminin biofunctionalization of the mesh promoted outgrowth and migration of cells. This device and associated methods should be adaptable to organoids, ex vivo tissue, or bioengineered in vitro models.

A priori assessment of target proteins' druggability remains an unsolved problem in the field of drug development. The empirical approaches widely used to solve this problem demonstrate low efficiency. In this work, we investigated the factor of hydration of a representative set of 65 evolutionarily and structurally unrelated human enzymes in a water environment. This factor depends only on the structure of the proteins, and not on the physical and chemical properties of any potential ligands. The results show that, unlike the widely used approaches based on calculations of the accessible surface area (ASA), the content of low-entropy water molecules (LEW) in the active sites of human enzymes is systematically higher than that in other areas of their surface, including inactive cavities. Optimal criteria and a step-by-step procedure for identifying protein ligand binding sites are proposed. The proposed approach, based on the calculation of the LEW content in the first hydration layer of potentially interesting target proteins, makes it possible to evaluate their medicinal suitability even before the development of any ligands. The article also presents the results of a comparative analysis of experimental Raman spectroscopy data and the results of molecular dynamics simulations of water hydrogen bonds using three widely used water models (TIP3P, OPC3, and TIP5P) and standard algorithms for calculating hydrogen bond networks.