Search Results (1,193)

Neutrophil extracellular traps (NETs)—webs of DNA and granular proteins expelled by neutrophils—have been implicated in hepatocellular carcinoma (HCC) progression. NETs promote tumor angiogenesis, facilitate invasion/metastasis, and enable immune evasion. Recent data suggest that perioperative factors, including anesthetic techniques, may modulate NET formation (NETosis), thus potentially influencing oncologic outcomes. We conducted a literature review of experimental and clinical studies on NETosis pathophysiology and involvement in HCC and how anesthetic techniques may modulate NET formation and, implicitly, cancer outcomes. NET biomarkers such as citrullinated histone H3 (CitH3), cell-free DNA (cfDNA), and myeloperoxidase–DNA complexes (MPO-DNA) are elevated in HCC patients and correlate with tumor spread, showing diagnostic and prognostic potential. Perioperative anesthetic choices may influence NET activity and immune function. Regional anesthesia and local anesthetics (e.g., lidocaine infusion) attenuate the surgical stress response and preserve anti-tumor immunity. Notably, lidocaine may modulate NET formation and, in a few studies published so far, was shown to reduce postoperative NET markers and other pro-metastatic factors (MMP-9, VEGF) in cancer surgery. In conclusion, NETosis is a process that is strongly implicated in HCC biology. Data published so far suggest that the clinical significance of NETosis may lie in its potential as a marker for disease evaluation and progression, including during the perioperative period. Preliminary results suggest that lidocaine may have a role in decreasing NETosis. Future large randomized trials are needed to exactly quantify these effects. Targeting NETs may be another way to influence HCC outcomes. Full article

Colorectal cancer (CRC) remains a major cause of morbidity and mortality worldwide, with its incidence and biological behavior influenced by both genetic and environmental factors. Emerging evidence highlights notable sex differences in CRC, with men generally exhibiting higher incidence rates and poorer prognoses, while women often display stronger immune responses and distinct molecular profiles. Traditional screening tools, such as colonoscopy and fecal-based tests, have improved survival through early detection but are limited by invasiveness, cost, and adherence issues. In this context, biosensors have emerged as innovative diagnostic platforms capable of rapid, sensitive, and non-invasive detection of CRC-associated biomarkers, including genetic, epigenetic, and metabolic alterations. These technologies integrate biological recognition elements with nanomaterials, microfluidics, and digital systems, enabling the analysis of biomarkers such as proteins, nucleic acids, autoantibodies, epigenetic marks, and metabolic or VOC signatures from blood, stool, or breath and supporting point-of-care applications. Electrochemical, optical, piezoelectric, and FET platforms enable label-free or ultrasensitive multiplexed readouts and align with liquid biopsy workflows. Despite challenges related to standardization, robustness in complex matrices, and clinical validation, advances in nanotechnology, multi-analyte biosensing with artificial intelligence are enhancing biosensor performance. Integrating biosensor-based diagnostics with knowledge of sex-specific molecular and hormonal pathways may lead to more precise and equitable approaches in CRC detection, selection of therapeutic regimes and management. Full article

Surface Plasmon Resonance imaging (SPRi) is a powerful label-free technique for high-throughput biochemical analysis. Wavelength modulation is particularly suitable for SPRi due to its wide dynamic range and robustness to fabrication tolerances. However, conventional systems relying on tunable filters (e.g., AOTF, LCTF) suffer from high cost, complexity, and limited temporal resolution. To overcome these drawbacks, we developed a rapid wavelength-modulation SPRi system using a multi-LED source and an adaptive second-order fitting (ASF) algorithm. The system covers the 730–805 nm spectrum with five LEDs. The ASF algorithm first performs a coarse full-spectrum scan to locate the resonance wavelength, then dynamically selects an optimal three-LED subset for fast second-order fitting, enabling accurate reconstruction of resonance wavelength without mechanical scanning. This approach significantly reduces cost and complexity while achieving a scanning cycle of 105 ms, RI resolution of 5.54 × 10⁻⁶ RIU, dynamic range of 0.0241 RIU, and excellent multi-channel consistency. The system has been successfully applied to monitor multi-channel antibody–antigen interactions in real time. Furthermore, it was used to detect cartilage oligomeric matrix protein (COMP) in synovial fluid, where an elevated concentration in an osteoarthritis sample versus a control aligned with its role as a cartilage catabolism marker. This work validates a practical and reliable platform for early diagnosis of osteoarthritis. Full article

Heme, a protoporphyrin IX iron complex, functions as an essential prosthetic group in hemoglobin and myoglobin, mediating oxygen storage and transport. Additionally, heme serves as a critical cofactor in various enzymes such as cytochrome c, enabling electron transfer within the mitochondrial respiratory chain. Unlike protein-bound heme, free or labile heme exhibits cytotoxic, pro-oxidant, and pro-inflammatory properties. Elevated levels of free heme are associated with various pathophysiological conditions, including hemolytic disorders such as sickle cell disease, malaria, and sepsis. In this review, we introduce the physiological roles of heme and its involvement in human health and disease. We also examine the mechanisms of heme sensing and regulation in bacterial cells. A variety of analytical methods have been developed to detect and quantify heme, enabling differentiation between protein-bound and free forms. These tools are discussed in the context of their applications in studying cellular heme regulation and their use in monitoring pathological conditions in humans. In particular, we describe examples of biosensors employing bacterial heme sensor proteins as recognition elements. Full article

Metallic biomaterials play essential roles in modern medical devices, but their long-term performance depends critically on protein adsorption and subsequent cellular responses at material interfaces. This review examines the molecular mechanisms governing these interactions and discusses surface modification strategies for controlling biocompatibility. The physicochemical properties of oxide layers formed on metal surfaces—including Lewis acid-base chemistry, surface charge, surface free energy, and permittivity—collectively determine protein adsorption behavior. Titanium surfaces promote stable protein adsorption through strong coordination bonds with carboxylate groups, while stainless steel surfaces show complex formation with proteins that can lead to metal ion release. Surface modification strategies can be systematically categorized based on two key parameters: effective ligand density (σ_eff) and effective mechanical response (E_eff). Direct control approaches include protein immobilization, self-assembled monolayers, and ionic modifications. The most promising strategies involve coupled control of both parameters through hierarchical surface architectures and three-dimensional modifications. Despite advances in understanding molecular-level interactions, substantial challenges remain in bridging the gap between surface chemistry and tissue-level biological performance. Future developments must address three-dimensional interfacial interactions and develop systems-level approaches integrating multiple scales of biological organization to enable rational design of next-generation metallic biomaterials. Full article

Sestrin2 (SESN2) is a highly conserved stress-inducible protein that serves as a central hub for integrating cellular responses to nutrient availability, oxidative stress, and endoplasmic reticulum (ER) stress. A key function of SESN2 is its role as a direct sensor for the branched-chain amino acid (BCAA) leucine, which modulates the activity of the mechanistic target of rapamycin complex 1 (mTORC1), a master regulator of cell growth and metabolism. While the functional link between leucine and SESN2 is well-established, the precise molecular determinants that confer its high specificity for leucine over other BCAAs, such as isoleucine and valine, remain poorly understood. This study employs an integrated computational approach, spanning atomic interactions to global protein dynamics, combining molecular docking, extensive all-atom molecular dynamics (MD) simulations, and binding free energy calculations, to elucidate the structural and dynamic basis of BCAA-SESN2 recognition. Our thermodynamic analysis reveals a distinct binding affinity hierarchy (Leucine > Isoleucine > Valine), which is primarily driven by superior van der Waals interactions and the shape complementarity of leucine’s isobutyl side chain within the protein’s hydrophobic pocket. Critically, a quantitative analysis of the conformational ensemble reveals that leucine induces a dramatic collapse of the protein’s structural heterogeneity. This “conformational locking” mechanism funnels the flexible, high-entropy unbound protein—which samples 35 distinct conformations—into a sharply restricted ensemble of just 9 stable states. This four-fold reduction in conformational freedom is accompanied by a kinetic trapping effect, which significantly lowers the rate of transitions between states. This process of conformational selection stabilizes a well-defined, signaling-competent structure, providing a comprehensive, atom-to-global-scale model of SESN2’s function. In the context of these findings, this work provides a critical framework for understanding SESN2’s complex role in disease and offers a clear rationale for the design of next-generation allosteric therapeutics. Full article

The emergence of multidrug-resistant Staphylococcus aureus underscores the urgent need for novel therapeutic agents targeting essential bacterial pathways. The lipoteichoic acid synthase (LtaS) is crucial for the synthesis of lipoteichoic acid in the cell wall of Gram-positive bacteria and represents a promising and vulnerable target for antimicrobial drug development. This study employed a comprehensive computational pipeline to identify potent inhibitors of the LtaS enzyme. A library of natural compounds was retrieved from the COCONUT database and screened against the crystal structure of the extracellular domain of LtaS (eLtaS) (PDB ID: 2W5R, obtained from the Protein Data Bank) through a multi-stage molecular docking strategy. This process started with High-Throughput Virtual Screening (HTVS), followed by Standard Precision (SP) docking, and culminated in Extra Precision (XP) docking to refine the selection of hits. The top-ranking compounds from XP docking were subsequently subjected to MM-GBSA binding free energy calculations for further filtration. The stability and dynamic behavior of the resulting candidate complexes were then evaluated using 100 ns molecular dynamics (MD) simulations, which confirmed the structural integrity and binding stability of the ligands. Density Functional Theory calculations revealed that screened ligands exhibit improved electronic stabilization and charge-transfer characteristics compared to a reference compound, suggesting enhanced reactivity and stability relevant for hit identification. Finally, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiling was conducted to assess the drug-likeness and pharmacokinetic safety of the lead compounds. These findings support them as promising orally active leads for further optimization. Our integrated approach shortlisted eight initial hits (A–H) that showed interesting scaffold diversity and finally identified two compounds, herein referred to as Compound A and Compound B, which demonstrated stable binding, favorable free energy, and an acceptable Absorption, Distribution, Metabolism, and Excretion, and Toxicity (ADMET) profile. These candidates emerge as promising starting points for developing novel anti-staphylococcal agents targeting the LtaS enzyme that cand be further proved by experimental validation. Full article

The aim of this study was to investigate the molecular interactions of heparin, diclofenac, and their supramolecular complexes with cyclooxygenase enzymes (COX-1 and COX-2) using computational docking techniques. Diclofenac is a widely used nonsteroidal anti-inflammatory drug (NSAID) that inhibits COX isoforms, whereas heparin is a polyanionic glycosaminoglycan with established anticoagulant and emerging anti-inflammatory properties. Supramolecular association between these agents may modulate their physicochemical behavior and target engagement. Molecular modeling, dual-drug docking, and molecular dynamics (MD) simulations were employed to characterize the interactions of heparin, diclofenac, and pre-formed heparin–diclofenac complexes with COX-1 and COX-2. Geometry optimization and lipophilicity (logP) estimates were obtained using HyperChem, while protein–ligand docking was performed in HEX using crystallographic COX structures from the Protein Data Bank. Docking poses were analyzed in Chimera, and selected complexes were refined through short MD simulations. Pre-formed heparin–diclofenac assemblies exhibited markedly enhanced docking scores toward both COX isoforms compared with single ligands. Binding orientation strongly influenced affinity: for COX-1, the heparin–diclofenac configuration yielded the most favorable interaction, whereas for COX-2 the diclofenac–heparin configuration was preferred. Both assemblies adopted binding modes distinct from free diclofenac, suggesting cooperative electrostatic and hydrophobic contacts at the enzyme surface. Supramolecular complexation also altered calculated logP values relative to the individual compounds. MD simulations supported the relative stability of the top-ranked complex–COX assemblies. These findings indicate that heparin–diclofenac assemblies may enhance and reorganize predicted COX interactions in a configuration-dependent manner and illustrate the utility of dual-drug docking for modeling potential synergistic effects. Such insights may inform the design of localized or topical formulations, potentially incorporating non-anticoagulant heparin derivatives, to achieve effective COX inhibition with reduced systemic exposure. However, the results rely on simplified heparin fragments, legacy docking tools, and short MD simulations, and should therefore be interpreted qualitatively. Experimental studies will be essential to confirm whether such supramolecular assemblies form under physiological conditions and whether they influence COX inhibition in vivo. Full article

The sinus tarsi, a small osseoligamentous recess of the subtalar joint, contains multiple soft-tissue structures with a complex sensory network. However, the detailed neural architecture and clinical significance of its innervation remain incompletely defined. The aim of this study was to conduct a comprehensive review of histological and immunohistochemical studies on the neural structures of the sinus tarsi. Histological staining and validated immunohistochemical markers (S100, p75, PGP9.5, neurofilament, myelin basic protein) were the methods used in these studies to analyze human sinus tarsi tissue. Across all investigations, free nerve endings predominated, while Ruffini, Pacinian and Golgi-like corpuscles were variably identified, mainly near ligament insertions. The sinus tarsi exhibits a dense and heterogeneous neural network that likely contributes to both pain perception and sensorimotor control. Further standardized and quantitative research is warranted to clarify the neurofunctional role of this region. Full article

Background: Congenital disorders of glycosylation (CDG) are rare inborn errors of metabolism with multisystemic manifestations. SSR4-CDG is an ultra-rare X-linked subtype caused by pathogenic variants in SSR4, a component of the translocon-associated protein (TRAP) complex essential for protein translocation and N-glycosylation. Case presentation: We report a two-year-old Malaysian male presenting with global developmental delay, central hypotonia, microcephaly with complete agenesis of the corpus callosum, recurrent infections, bilateral vesicoureteral reflux, and failure to thrive. Growth parameters (weight, length, and head circumference) were persistently below the expected percentiles, indicating postnatal growth restriction. Initial metabolic and biochemical investigations for global developmental delay were unremarkable, apart from mild hyperammonemia. Transferrin isoform analysis demonstrated a type I CDG pattern, raising suspicion of a glycosylation defect. Results: Transferrin glycopeptide LC–MS/MS showed impaired N-glycan occupancy at both glycosylation sites (Asn432 and Asn630), with reduced fully sialylated glycoforms and increased non-glycosylated peptides. Targeted metabolomics using triple quadrupole LC–MS/MS revealed systemic abnormalities, including elevated arginine and phenylalanine, reduced glutamate, increased lysophosphatidylcholine (C24:0-LPC), and generalized depletion of free and acylcarnitines. Whole-exome sequencing identified a novel hemizygous SSR4 variant (c.98del; p.Pro33LeufsTer23) on the X chromosome, predicted to produce a truncated, nonfunctional protein. Conclusions: This is the first Malaysian patient with SSR4-CDG, comprehensively characterized using a multi-omics diagnostic workflow. The integration of glycoproteomics, metabolomics, and exome sequencing provided a detailed biochemical fingerprint that expands the clinical, genetic, and metabolic spectrum of SSR4-CDG and demonstrates the diagnostic and translational value of multi-omics approaches in inborn errors of metabolism. Full article

Background/Objectives: Monkeypox is endemic to the African continent and has recently garnered global attention due to reported outbreaks in non-endemic nations. No approved drug is available for non-severe cases, and some isolates gained resistance to approved antivirals. In this study, we employed a drug repositioning strategy to evaluate the efficacy of existing FDA-approved antiviral drugs if repurposed for use against emerging Monkeypox, representing a cost-effective method for identifying novel therapeutic interventions. Methods: Methodology including Egyptian virus strain isolation, propagation and titration followed by in vitro studies, molecular docking and molecular dynamics simulations combined with binding free energy were carried out. Twenty-three FDA-approved drugs, including Abacavir, Acyclovir, Amantadine, Chloroquine, Daclatasvir, Dolutegravir, Entecavir, Favipiravir, Hydroxychloroquine, Lamivudine, Molnupiravir, Nevirapine, Oseltamivir, Penciclovir, Remdesivir, Ribavirin, Sofosbuvir, Tenofovir, Valaciclovir, Valganciclovir, Velpatasvir, Zanamivir, and Zidovudine, were screened for potential anti-monkeypox activity in vitro. In silico studies were carried out against three monkeypox proteins, Thymidylate Kinase, A42R Profilin-Like Protein, and VACV D13, to identify their potential targets. Results: In vitro testing showed that two antiviral drugs are positive. The employed computational methods indicate that remdesivir demonstrated superior binding patterns with elevated scores and stable complexes throughout the simulation. Conclusions: Our findings showed that Remdesivir therapeutic compound is potent against the tested strain of MPXV, and exhibited a robust binding affinity for Thymidylate Kinase, A42R Profilin-Like Protein, and VACV D13 enzymes, and thus may potentially be utilized as antiviral for the treatment of monkeypox virus. Full article

A novel heavy metal-resistant bacterium with significant bioremediation capabilities, Sinirhodobacter sp. 1C5-22 was isolated from moderately polluted Shenzhen Futian mangrove rhizosphere sediments. This strain showed exceptional tolerance (MIC ≥ 600 mg/L for Cu/Zn; > 500 mg/L for Ni). Analyses revealed distinct metal-specific distribution strategies: Cd and Ni were predominantly bound extracellularly (>80%); Cu was bound intracellularly (~60%); and Zn exhibited balanced partitioning. Integrated omics analysis identified a molecular defense mechanism coordinated by the CreB transcriptional regulator. This Adsorption–Sequestration–Efflux (ASE) system integrates extracellular polymer binding, periplasmic sequestration via stable metal-binding proteins, and efflux pump activity, resolving the apparent adsorption-tolerance paradox at elevated concentrations. For bioremediation applications, we developed a polyvinyl alcohol–sodium alginate immobilized consortium (PVA-SA 1C5-22). The engineered agent displayed significantly enhanced biosorption capacity compared to free cells and effectively mitigated heavy metal-induced oxidative damage, evidenced by stabilized malondialdehyde levels. It demonstrated robust reusability, maintaining high metal enrichment across five adsorption–desorption cycles in multi-metal wastewater with efficient HCl-driven desorption (55–70%). Critically, it achieved stable nickel removal performance (~20% adsorption, >50% desorption) from authentic electroplating wastewater (1850 mg/L Ni²⁺) through successive multiple cycles. Our integrated approach bridges microbial ecology and environmental biotechnology, establishing this immobilized system as a highly sustainable strategy for complex industrial effluent remediation. Full article

Background/Objectives: GuaB, which is known as inosine 5′-phosphate dehydrogenase (IMPDH), is an enzymatic target involved in the de novo guanine biosynthetic pathway of the multidrug-resistant (MDR) Acinetobacter baumannii. GuaB has emerged as a potential therapeutic target to cope with increasing antibiotic resistance. Here, we used machine learning-based virtual screening as a verification technique to find potential inhibitors possessing different chemical scaffolds, using structure-based drug design as a discovery platform. Methods: Four machine learning models, built based on chemical fingerprint data, were trained, and the best models were used for virtual screening of the ChEMBL library, which covers 153 active molecules. Molecular dynamics (MD) simulations of 200 ns were carried out for all three compounds in order to explain conformational changes, evaluate stability, and provide validation of the docking results. Post-simulation analyses include principal component analysis (PCA), bond analysis, free-energy landscape (FEL), dynamic cross-correlation matrix (DCCM), radial distribution function (RDF), salt-bridge identification, and secondary-structure profiling, etc. Results: For molecular docking, the screened compounds were used against the GuaB protein to achieve proper docked conformation. Upon visual examination of the best-docked compounds, three leads (lead-1, lead-2, and lead-3) were found to have better interaction with the GuaB protein in comparison to the control. The mean RMSD scores between the three leads and the control were between 2.54 and 2.89 Å. In addition, the three leads as well as the control were characterized for pharmacokinetic features. All three leads met Lipinski’s Rule 5 and were thus drug-like. PCA and FEL analyses showed that lead-2 exhibited improved conformational stability, identified as deeper energy minima, whereas RDF and DCCM analyses revealed that lead-2 and lead-3 exhibited strong local structuring and concerted dynamics. In addition, lead-2 displayed a very rich hydrogen-bonding network with a total of 460 frames possessing such interactions, which is the highest among the complexes investigated here. Based on entropy calculations and the maximum entropy method of gamma–gram, lead-1 proved to be the most stable one with the lowest binding free-energy. Conclusions: This study provides an integrated machine learning-based virtual screening pipeline for the identification of new scaffolds to moderate infections associated with AMR; however, in vitro validation is still required to assess the efficacy of such compounds. Full article

Lipotoxicity and oxidative stress are key pathogenic drivers in the development of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD). The underlying mechanisms of MASLD are not fully understood, and approved pharmacotherapies remain elusive. Thus, exploring therapeutic targets and potential drugs for MASLD is still a major challenge. In our previous study, a new cuspidatyl ferulate (2,3-dihydroxy-4-carboxylic butyl (E)-4-[3-(4-hydroxy-3-methoxyphenyl)-2-propenoate], CuF) was first isolated and identified from Hyssopus cuspidatus Boriss (H. cuspidatus). Here, we investigated the effects of this novel phenolic acid on free fatty acid (FFA)-induced oxidative stress and lipid accumulation in HepG2 cells. Exposure to FFA significantly increased intracellular reactive oxygen species (ROS) levels and lipid accumulation. Notably, CuF treatment effectively reversed FFA-induced suppression of key antioxidant enzymes, including superoxide dismutase (SOD) and catalase (CAT), and attenuated lipid accumulation, as evidenced by reduced total cholesterol (TC) and triglyceride (TG) levels. Mechanistically, molecular docking and capillary electrophoresis analyses revealed that CuF directly interacts with Kelch-like ECH-associated protein 1 (Keap1), disrupting the Keap1-Nrf2 protein complex, thereby promoting nuclear translocation of Nrf2 and activating the antioxidant response pathway. In summary, our findings demonstrate that this novel phenolic acid exhibits strong antioxidant and anti-lipotoxic activities in vitro, offering a potential natural product-based drug candidate for MASLD therapy. Full article

Plant–microbe interactions exert a significant influence on host stress responses; however, the molecular mechanisms underlying these effects remain inadequately understood. In this study, we characterize FaMAN8, an α-mannosidase from Fragaria × ananassa, to explore its role in adaptation to heat waves and water deficit, as well as its modulation by fungal endophytes. Transcriptomic analysis identified FaMAN8 as the sole α-mannosidase isoform highly conserved across reported sequences, with root-specific induction under conditions of heat stress, deficient irrigation, and endophytic colonization. Structural modeling revealed that FaMAN8 exhibits the canonical domain organization of glycoside hydrolase family 38 (GH38) enzymes, featuring a conserved catalytic architecture and metal-binding site. Molecular docking and dynamics simulations with the Man₃GlcNAc₂ ligand indicated a stable binding pocket involving key catalytic residues and strong electrostatic complementarity. MM-GBSA and free energy landscape analyses further supported the thermodynamic stability of the protein–ligand complex. Cavity analysis revealed a larger active site in FaMAN8 compared to its homolog JbMAN, suggesting broader substrate accommodation. Collectively, these findings identify FaMAN8 as a stress-responsive glycosidase potentially involved in glycan remodeling during beneficial root–fungus interactions. This work provides molecular insights into plant–microbe symbiosis and lays the groundwork for microbiome-informed strategies to enhance crop stress resilience. Full article