Search Results (464)

Atherosclerosis remains a leading cause of cardiovascular mortality despite advances in pharmacological and interventional therapies. Current treatment approaches face limitations including systemic side effects, inadequate local drug delivery, and restenosis following vascular interventions. Gel-based technologies offer unique advantages through tunable mechanical properties, controlled degradation kinetics, high drug-loading capacity, and potential for stimuli-responsive therapeutic release. This review examines gel platforms across multiple scales and applications in atherosclerosis research and intervention. First, gel-based in vitro models are discussed. These include hydrogel matrices simulating plaque microenvironments, three-dimensional cellular culture platforms, and microfluidic organ-on-chip devices. These devices incorporate physiological flow to investigate disease mechanisms under controlled conditions. Second, therapeutic strategies are addressed through macroscopic gels for localized treatment. These encompass natural polymer-based, synthetic polymer-based, and composite formulations. Applications include stent coatings, adventitial injections, and catheter-delivered depots. Natural polymers often possess intrinsic biological activities including anti-inflammatory and immunomodulatory properties that may contribute to therapeutic effects. Third, nano- and microgels for systemic delivery are examined. These include polymer-based nanogels with stimuli-responsive drug release responding to oxidative stress, pH changes, and enzymatic activity characteristic of atherosclerotic lesions. Inorganic–organic composite nanogels incorporating paramagnetic contrast agents enable theranostic applications by combining therapy with imaging-guided treatment monitoring. Current challenges include manufacturing consistency, mechanical stability under physiological flow, long-term safety assessment, and regulatory pathway definition. Future opportunities are discussed in multi-functional integration, artificial intelligence-guided design, personalized formulations, and biomimetic approaches. Gel technologies demonstrate substantial potential to advance atherosclerosis management through improved spatial and temporal control over therapeutic interventions. Full article

In this study, a strain of green microalga adapted to the extreme environmental conditions of the Tibetan Plateau was isolated from the Lalu Wetland. The isolate was identified and tentatively designated as Micractinium sp. LL-1. Following the inoculation of strain LL-1 into tannery wastewater, the ammonia nitrogen concentration was rapidly reduced, achieving a removal efficiency of 98.7%. The maximum accumulated biomass reached 1641.68 mg/L and 1461.28 mg/L. Integrated transcriptomic and label-free quantitative proteomic approaches were employed to systematically investigate the molecular response mechanisms of LL-1 under tannery wastewater stress. Transcriptomic analysis revealed that differentially expressed genes were enriched in pathways related to cell proliferation, morphogenesis, intracellular transport, protein synthesis, photosynthesis, and redox processes. Proteomic analysis indicated that LL-1 enhances cellular and enzymatic activities, strengthens regulatory capacity, modulates key metabolic pathways, and upregulates stress-responsive proteins. Under tannery wastewater stress, LL-1 exhibits dynamic adaptation involving signal perception and metabolic reconfiguration through the coordinated regulation of multiple pathways. Specifically, ribosomal translation and nucleic acid binding regulate biosynthetic capacity; the redistribution of energy metabolism boosts photosynthetic carbon fixation and ATP generation; and membrane transport coupled with antioxidant mechanisms mitigates stress-induced damage. Collectively, this study provides theoretical insights into microalgal adaptation to complex wastewater environments and offers potential targets for strain improvement and wastewater valorization. Full article

This study aimed to identify novel angiotensin-converting enzyme (ACE)-inhibitory peptides from royal jelly proteins (RJPs) by integrating in silico digestion, virtual screening, and in vitro evaluation. Three major royal jelly proteins (MRJP1-3) were subjected to in silico digestion using 16 enzymatic systems, yielding 1411 unique peptides. Virtual screening based on predicted bioactivity, toxicity, water solubility, and ADMET profiles resulted in the selection of 27 candidate peptides. Molecular docking revealed strong binding affinities for these peptides compared with the positive control captopril, among which PYPDWSFAK and RPYPDWSF exhibited potent ACE-inhibitory activity, with IC₅₀ values of 110 ± 1.02 μmol/L and 204 ± 0.61 μmol/L, respectively. Kinetic analysis indicated that PYPDWSFAK acts as a mixed-type ACE inhibitor. Docking visualization demonstrated that PYPDWSFAK forms multiple hydrogen bonds with key residues in the ACE active pocket and directly coordinates with the catalytic Zn²⁺ ion. Cellular assays showed that PYPDWSFAK was non-cytotoxic, suppressed Ang II–induced endothelial cell migration, restored NO and ET-1 balance, and enhanced SOD and GSH-Px activities. Overall, this study enriches the repertoire of ACE-inhibitory peptides derived from royal jelly proteins. Furthermore, PYPDWSFAK is identified as a promising ACE-inhibitory peptide with potential for incorporation into natural antihypertensive ingredients or functional foods. Full article

Making advancements in Quantitative Structure-Activity Relationship (QSAR) modeling is crucial for predicting biological activities in new compounds. Traditional 2D-QSAR and 3D-QSAR methods often face challenges in terms of computational efficiency and predictive accuracy. This study introduces a machine learning approach using 3D Discrete Tchebichef Moments (3D-DTM) to address these issues. The 3D-DTM method offers efficient computation, robust descriptor generation, and improved interpretability, making it a promising alternative to conventional QSAR techniques. By capturing global 3D shape information, this method provides better representation of molecular interactions essential for biological activities. We applied the 3D-DTM model to a dataset of 46 molecules derived from the Dihydrophenanthrene scaffold, screened against the enzymatic activity of 3-chymotrypsin-like protease, a key antiviral target. Principal Component Analysis and k-means clustering refined descriptors, followed by stepwise Multiple Linear Regression (step-MLR), Partial Least Squares Regression (PLS-R), and Feed-Forward Neural Network (FFNN) techniques for 3DTMs-QSAR model development. The results showed high correlation and predictive accuracy, with significant validation from internal and external tests. The step-MLR model emerged as the optimal method due to its balance of predictive power and simplicity. Validation through y-Randomization and applicability domain analysis confirmed the model’s robustness. Virtual screening of 100 novel compounds identified 32 with improved pIC₅₀ values. This study highlights the potential of 3D-DTMs in QSAR modeling, providing a scalable and reliable tool for computational chemistry and drug discovery. A user-friendly software tool was also developed to facilitate 3D-DTM extraction from input 3D molecular images. Full article

Dermal papilla cells (DPCs) serve as the signaling hub regulating hair follicle (HF) development and cyclical growth. This study aims to investigate the biological function and molecular mechanisms of TGFBR1 (transforming growth factor β receptor 1), a differentially expressed gene identified through single-cell transcriptomic sequencing (scRNA-seq) in the DPCs from fine-wool sheep. Primary DPCs were isolated and purified using a combination of enzymatic digestion and mechanical dissociation, followed by immunofluorescence identification (α-SMA and SOX2-positive). Following successful transfection with constructed TGFBR1 overexpression plasmids and siRNA interference vectors, cell proliferation was assessed via EDU staining and CCK-8 assays. mRNA expression of key genes in Wnt/β-catenin, BMP, and Notch signaling pathways (PCNA, CCND1, CTNNB1, SFRP2, BMP2, NOTCH3, SMAD4, etc.) was validated by RT-qPCR. Single-cell transcriptomics revealed significant downregulation of TGFBR1 in DPCs from fine-wool sheep. Functional validation demonstrated that TGFBR1 overexpression markedly suppressed DPC proliferation, whereas knockdown of TGFBR1 expression promoted DPC proliferation. Molecular mechanism studies showed that TGFBR1 overexpression significantly downregulated PCNA, CCND1, CTNNB1, NOTCH3, and SMAD4 while upregulating SFRP2, BMP2, and TGFB1 expression. These findings demonstrate that TGFBR1 acts as a negative regulator of DPCs proliferation by modulating the activity of multiple signaling pathways, including Wnt/β-catenin, BMP, and Notch, thereby suppressing the proliferative capacity of DPCs. This study not only provides new theoretical support for elucidating the role of the TGF-β signaling pathway in H development but also offers theoretical reference for in-depth research on molecular breeding in ultra -fine-wool sheep and the molecular mechanisms underlying HF development. Full article

Cyclin-dependent kinase 9 (CDK9) is a key regulator of transcriptional elongation and DNA repair, supporting cancer cell survival by sustaining the expression of oncogenes and anti-apoptotic proteins. Its overexpression in multiple malignancies makes it an attractive target for anticancer therapy. Here, we report a machine learning (ML) based approach to identify novel CDK9 inhibitors. Through systematic data collection and preprocessing, seventy predictive models were developed using five algorithms, two classification settings, and seven molecular representations. The best-performing model was employed to guide a virtual screening (VS) campaign, resulting in the identification of 14 compounds promising for their potential inhibitory effect. Upon enzymatic assays, two molecules with inhibitory activity in the low micromolar range were selected as promising candidates and further tested in three cancer cell lines with distinct genetic backgrounds. These experiments led to the identification of a novel compound exhibiting interesting therapeutic potential, both as a single agent and in combination with Camptothecin (CPT), revealing varying response profiles across the tested cell lines. These results illustrate the power of integrating ML within anticancer drug discovery pipelines and represent a valuable starting point for the development of novel CDK9 inhibitors. Full article

Traditional inducible systems typically induce the simultaneous expression of all genes controlled by similar promoters, thereby limiting their use. In this study, we used two metabolite-inducible systems, MarR from the Escherichia coli mar operon and TtgR from the Pseudomonas putida ttg operon, to assess their use as gene regulation platforms beyond reporter assays. Ligand-dependent transcription was validated using eGFP. The reporter was replaced with two flavonoid O-methyltransferases (OMTs), ROMT-9 and SOMT-2, under transcription factor (TF)-specific promoters. In E. coli, both systems enabled in using HPLC. TF-based expression did not impact enzyme activity. Induction with salicylic acid (MarR) produced stronger gains than that with 4′-hydroxyflavanone (TtgR), although the overall fold-changes in product levels were regulated by basal (leaky) expression. Thus, although transcriptional control was robust, enzymatic regulation was less stringent, highlighting the necessity for genetic engineering of components, including TFs, promoters, transcription factor binding sites, and ribosome binding sites, to reduce leakiness and expand the dynamic range. Overall, these orthogonal and modular TF-based systems offer a framework for independent and inducible control of multiple genes, with potential applications in biosensing, metabolic engineering, and programmable pathway design. Full article

Carbapenem-resistant Enterobacterales (CREs) pose a critical threat to global public health, largely driven by the enzymatic activity of Klebsiella pneumoniae carbapenemase-2 (KPC-2), a class A serine β-lactamase that hydrolyzes most β-lactam antibiotics. While β-lactamase inhibitors like avibactam offer temporary relief, emerging KPC variants demand novel, sustainable inhibitory scaffolds. This study aimed to identify and characterize potential natural inhibitors of KPC-2 from Pongamia pinnata, leveraging a comprehensive in silico workflow. A curated library of 86 phytochemicals was docked against the active site of KPC-2 (PDB ID: 3DW0). The top-performing ligands were subjected to ADMET profiling (pkCSM), and 100 ns molecular dynamics simulations (GROMACS) to evaluate structural stability and interaction persistence, using avibactam as control. Ponganone V exhibited the most favorable binding energy (−9.0 kcal/mol), engaging Ser70 via a hydrogen bond and forming π–π interactions with Trp105. Glabrachromene II demonstrated a broader interaction network but reduced long-term stability. ADMET analysis confirmed high intestinal absorption, non-mutagenicity, and absence of hERG inhibition for both ligands. Molecular dynamics simulations revealed that Ponganone V maintained compact structure and stable hydrogen bonding throughout the 100 ns trajectory, closely mirroring the behavior of avibactam, whereas Glabrachromene II displayed increased fluctuation and loss of compactness beyond 80 ns. Principal Component Analysis (PCA) further supported these findings, with Ponganone V showing restricted conformational motion and a single deep free energy basin, while avibactam and Glabrachromene II exhibited broader conformational sampling and multiple energy minima. The integrated computational findings highlight Ponganone V as a potent and pharmacologically viable natural KPC-2 inhibitor, with strong binding affinity, sustained structural stability, and minimal toxicity. This study underscores the untapped potential of Pongamia pinnata phytochemicals as future anti-resistance therapeutics and provides a rational basis for their experimental validation. Full article

Rice husk (RH) is a widely available lignocellulosic residue for biohydrogen production but requires effective pretreatment to overcome lignin-related recalcitrance. This study investigates the kinetics of lignin removal from RH using 3% sodium hydroxide (NaOH) and water pretreatments at high temperatures between 100 and 129 °C (25 °C control) with short reaction times (15–60 min) in an autoclave system. Biomass composition, solid yield, delignification efficiency, and enzymatic hydrolysis for glucose production were evaluated. NaOH pretreatment achieved up to 72.72% lignin removal at 129 °C after 60 min, significantly outperforming water pretreatment, which reached a maximum delignification of 20.24% under the same conditions. Kinetic analysis revealed first-order reaction behavior, with the kinetic rate constants varying between 5.14 × 10⁻⁵ and 4.31 × 10⁻³ with water pretreatment and from 3.73 × 10⁻⁴ to 2.46 × 10⁻² with NaOH and activation energies of 42.61 kJ mol⁻¹ K⁻¹ and 39.31 kJ mol⁻¹ K⁻¹ for water and NaOH pretreatment, respectively. Enhanced lignin removal improved cellulose accessibility, resulting in glucose yields from enzymatic hydrolysis of up to 52.13 mg/g for NaOH-treated samples, double those obtained with water pretreatment (26.97 mg/g). While NaOH pretreatment achieved higher lignin removal efficiency and glucose yield, it exhibited significantly higher environmental impacts across multiple categories, including global warming potential and terrestrial ecotoxicity, based on the life cycle assessment (LCA). Even water-based pretreatment showed considerable burdens; thus, both pretreatment methods impose high life cycle impacts when applied to RH, which makes it an unsustainable feedstock for glucose production under the evaluated conditions. Alternative feedstocks or improved process integration strategies are required for environmentally viable biohydrogen production. Full article

The poly(ADP-ribose) polymerase (PARP) family constitutes a major group of proteins and enzymes essential for the maintenance of cellular homeostasis under physiological conditions and plays a pivotal role in the onset and progression of multiple pathological states. Members of the PARP family are classified into distinct subgroups based on their subcellular localization, structural organization, and ADP-ribosyltransferase activity. To date, the majority of studies have focused on DNA-dependent PARPs, owing to their well-established involvement in DNA repair mechanisms, cell cycle regulation, and diverse human pathologies. Nevertheless, over the past decade, a smaller subset of PARPs—limited in both abundance and enzymatic activity—has emerged as a critical regulator of numerous cellular processes, including embryonic development and disease progression. Within this subset, mono(ADP-ribosyl) transferases (MARTs) have gained growing attention as potential therapeutic targets in cancer, cardiovascular disorders, and neurodegenerative diseases. The ADP-ribose (ADPr) cycle, which comprises both branched poly(ADP-ribose) (PAR) polymers and mono-ADP-ribose moieties present either in free form or covalently bound to cellular substrates, is tightly regulated to ensure cellular homeostasis. This regulation relies on a finely tuned balance between ADP-ribosylation, DePARylation, and the subsequent recycling of mono-ADP-ribose. In this review, we provide a comprehensive overview of the biological roles of mono-ADP-ribosylation (MARylation) and DePARylation, with particular emphasis on their contribution to cancer-related processes. In addition, we discuss emerging evidence supporting their translational relevance and therapeutic potential. In conclusion, MARylation and DePARylation represent two increasingly recognized regulatory pathways whose expanding clinical significance highlights the need for deeper mechanistic understanding and further exploration in both basic and translational research. Full article

Dimethyl fumarate (DMF) has established a significant position among therapies for multiple sclerosis and psoriasis and is now being investigated for repurposing to many other non-malignant diseases. Despite decades of preclinical research, some issues about its pharmacology remain unresolved, with ongoing debate over which of the methyl esters of fumarate, whether DMF or monomethyl fumarate (MMF), is the active ingredient. It is generally accepted that DMF undergoes enzymatic hydrolysis to MMF and methanol. However, there is disagreement regarding its exact site, its extent, and the responsible enzyme(s). The enzymatic mechanisms, particularly the roles of carboxylesterases-1 and 2, vary across tissues and species, complicating the translation of in vitro and in vivo preclinical findings into clinical practice. In addition, the impact of DMF and MMF is often not clearly distinguishable and sometimes overlaps, making the true molecular mediators of therapeutic and side effects unclear. Thus, the interpretation of some results obtained in studies is inconsistent because of interchanging of in vitro and in vivo observed features of fumarate esters: while DMF demonstrates rapid and strong effects in cell culture studies, including nuclear factor erythroid 2-related factor 2 (NRF2) function activation and glutathione depletion, these observations may not exactly reflect systemic pharmacology and physiology dominated by MMF. Moreover, methanol, the co-product of DMF metabolism, may contribute to the observed DMF effects through increased production of reactive oxygen species, which could result in activation of NRF2-dependent mechanisms. This review highlights specific unresolved issues in DMF metabolism, which are sometimes overlooked. Full article

Background: Antimicrobial resistance is a growing global health threat, with beta-lactamases playing a central role in resistance to beta-lactam antibiotics. Building on our previous survey of 2340 putative beta-lactamases, we conducted an in-depth analysis of 129 prioritized candidates (70–98.5% amino acid identity to characterized enzymes) detected in 102 bacterial genera across 13 phylogenetic classes from environmental, animal, and human sources worldwide. Methods: We applied a motif-centric assessment of class-defining catalytic residues, evaluated the genomic context using a heuristic Index of Proximal Mobility (IPM) derived from the two immediately adjacent open reading frames, and examined the phylogenetic placement. AI-based substrate predictions were generated at a restricted scope as exploratory evidence. Results: Candidates spanned all Ambler classes (A–D); preservation of catalytic motifs was common and consistent with potential catalytic activity. Twelve of 129 (9.3%) loci had nearby mobile-element types (e.g., insertion sequences, integrases, transposases) and scored High IPM, indicating genomic contexts compatible with horizontal gene transfer. We also observed near-identical class A enzymes across multiple genera and continents, frequently adjacent to mobilization proteins. Conclusions: We propose a reproducible, bias-aware, early warning framework that prioritizes candidates based on motif integrity and mobility context. The framework complements existing surveillance (GLASS/EARS-Net) and aligns with a One Health approach integrating human, animal, and environmental reservoirs. Identity thresholds and IPM are used for inclusion and contextual prioritization, rather than as proof of function or mobility; AI-based predictions serve as hypothesis-generating tools. Experimental studies will be essential to confirm enzymatic activity, mobility, and clinical relevance. Full article

Thigmomorphogenesis denotes a suite of anatomical, physiological, biochemical, biophysical, and molecular responses of plants to mechanical stimulation. This phenomenon is evolutionarily conserved among diverse plant lineages; however, the magnitude and character of the response are strongly determined by both the frequency and intensity of the applied stimulus. In angiosperms, thigmomorphogenetic reactions typically occur gradually, reflecting a complex interplay of morphological alterations, biochemical adjustments, and genetic reprogramming. In dicotyledonous plants, thigmomorphogenesis is commonly expressed as a reduction in leaf blade surface area, shortening of petioles, decreased plant height, radial thickening of stems, and modifications in root system architecture. In monocotyledons, in turn, mechanical stress frequently results in stem rupture below the inflorescence, with concomitant shortening and increased flexibility of younger internodes. These specific traits can be explained by structural features of monocot secondary walls as well as by the absence of vascular cambium and lateral meristems. Mechanical stimulation has been shown to initiate a cascade of responses across multiple levels of plant organization. The earliest events involve activation of mechanoresponsive genes (e.g., TCH family), followed by enzymatic activation, biochemical shifts, and downstream physiological and molecular adjustments. Importantly, recent findings indicate that prolonged mechanical stress may significantly suppress auxin biosynthesis, while leaving auxin transport processes unaffected. Moreover, strong interdependencies have been identified between thigmostimulation, gibberellin biosynthesis, and flowering intensity, as well as between mechanical stress and signaling pathways of other phytohormones, including abscisic acid, jasmonic acid, and ethylene. At the molecular scale, studies have demonstrated a robust correlation between the expression of specific calmodulin isoforms and the GH3.1 gene, suggesting a mechanistic link between mechanosensing, hormone homeostasis, and regulatory feedback loops. The present study consolidates current knowledge and integrates novel findings, emphasizing both morphological and cellular dimensions of thigmomorphogenesis. In particular, it provides evidence that mechanical stress constitutes a critical modulator of hormonal balance, thereby shaping plant growth, development, and adaptive potential. Full article

Astragalus species are characterized by rich active compounds, mainly polysaccharides, saponins, and polyphenols, with various important bioactivities, such as antioxidant, antitumor, anti-diabetes, antiviral, etc. In this study, the chemical profiles of ethanol, ethyl acetate, and dichloromethane extracts from different parts (leaves, flowers, and roots) of two endemic Astragalus species growing in Türkiye, i.e., A. strictispinus and A. macrocephalus subsp. finitimus were determined, along with their antioxidant, anti-enzymatic, and antibacterial properties. According to the results, naringenin and apigenin were identified as two common phenolic compounds of both Astragalus species, while only ethanol extracts of the roots and leaves and ethyl acetate extracts of flowers of A. strictispinis exhibited a low level of antioxidant activity (5–16%). Moreover, AChE and BChE inhibitory activities were higher in the ethyl acetate extract of A. macrocephalus subsp. finitimus leaves, while all leaf extracts of the analyzed Astragalus species, except dichloromethane extract of A. strictispinus, exhibited antibacterial activity against S. aureus. In conclusion, this study provides detailed information that may serve as the scientific basis for the use of Astragalus species as sources of bioactive compounds with multiple functions in the nutraceutical, cosmetic, and pharmaceutical industries. Full article

Wine is one of the oldest alcoholic beverages, produced from the fermentation of the grape Vitis vinifera. Currently, the wine industry is exploited worldwide in multiple regions, generating significant amounts of agro-industrial waste at different stages of the production chain. These wastes represent a source of environmental contamination due to the toxic nature of some of their compounds. From a biotechnological perspective, the by-products of the wine industry are an attractive source of bioactive compounds with potential applications in various fields, including food, pharmaceuticals, and cosmetics. The extraction of these compounds can be carried out using fermentation techniques that utilize microorganisms to facilitate the release and biotransformation of the desired metabolites through their enzymatic tools. This work provides a review of the history of the wine industry and its current activities, describes the wine production process, and outlines the waste generated during this process. The fermentation process is described as a biotechnological alternative for the valorization of these residues. This purpose enables their reintegration into the production chain through the extraction of high-value bioactive compounds with potential use as drugs in pharmacology. Full article