Search Results (1,040)

In recent years, the pivotal role of the gut microbiota and its metabolites in host health and disease has garnered increasing attention. Dietary phosphatidylcholine and choline are metabolized by gut bacteria to generate trimethylamine (TMA). Upon entering the bloodstream, TMA is oxidized by host liver enzymes to trimethylamine N-oxide (TMAO), a known independent risk factor for various systemic diseases, including atherosclerosis, thrombosis, and chronic kidney disease. Within this complex “diet–gut–host” metabolic axis, the microbial choline TMA-lyase (CutC) acts as the key rate-limiting enzyme that catalyzes the cleavage of choline to produce TMA. This review systematically summarizes the discovery history, enzymatic structural characteristics, and catalytic mechanism of CutC, highlighting its potential as a microbial metabolic target for treating associated diseases. By specifically analyzing existing inhibitor strategies and interventions, this article emphasizes the extensive potential of specific targeting of the CutC enzyme in precisely regulating the functions of the microecology. Full article

The poly(A) tail has long been known to play a central role in mRNA stability, storage, and translational competence, making it a potential key regulator during hypometabolic states. During seasonal torpor, hibernating mammals must frequently enter these hypometabolic states to survive. In this study, we examined protein abundance changes in key enzymes involved in poly(A) tail synthesis, binding, and removal during torpor in the brown adipose tissue of the 13-lined ground squirrel, Ictidomys tridecemlineatus, using immunoblots. BAT during late torpor exhibited significantly reduced abundance of the catalytic cleavage enzyme CPSF73, but increased abundance of poly(A) polymerase PAPOLA. In contrast, poly(A)-binding proteins and major complex subunits of deadenylases, including CCR4-Not, exhibited no significant changes. Furthermore, despite unchanged levels of the translation initiation factor eIF4E, the phosphorylated variant of 4E-BP1, a potent inhibitor of the initiation factor when hypophosphorylated, was significantly reduced during late torpor. Overall, constrained mRNA maturation, preserved transcript stability, and reversible translational inhibition suggest that an important role exists for poly(A) tail regulatory machinery in hypometabolic survival throughout the torpid state. Full article

Histone deacetylase inhibitors (HDACi) are an emerging class of epigenetic anticancer drugs that exert their activity through coordination to the catalytic Zn²⁺ ion within the active site of histone deacetylases (HDACs). Due to the limited isoform-selectivity of hydroxamic acid-based inhibitors, benzamide-based HDACi (BBHDACi) have been developed as subtype-selective alternatives. Clinically relevant representatives include Chidamide, Entinostat, Mocetinostat, Zabadinostat, and Tacedinaline. Although these compounds share a conserved o-aminoanilide zinc-binding group (ZBG), they differ in linker and cap region structure, raising questions regarding their intrinsic Zn²⁺ affinity and coordination behavior. Herein, density functional theory (DFT) calculations were performed at the B3LYP/6-311++g(d,p) level of theory combined with the PCM solvation in methanol (ε = 33) and water (ε = 78). Geometry optimization confirmed that the trans (E) isomer of Chidamide is thermodynamically preferred. Coordination studies showed that the remaining BBHDACi adopt stable geometries, with the o-aminoanilide group preferentially forming tetracoordinated complexes that are more stable than hexacoordinated ones in polar media. Interestingly, calculated substitution free energies differed by less than ± 2 kcal.mol⁻¹, indicating nearly identical intrinsic Zn²⁺ affinities across the series. These results suggest that the ZBG contributes similarly to metal coordination across all BBHDACi, whereas the overall binding strength is mainly governed by interactions of the linker and cap regions rather than by the conserved zinc-binding group itself. Full article

Background: Cancer cells exhibit metabolic reprogramming characterized by increased dependence on glutamine to sustain rapid proliferation and biosynthetic demands. Kidney-type glutaminase (KGA), which catalyzes the first and rate-limiting step of glutamine metabolism, represents a promising therapeutic target, particularly in triple-negative breast cancer (TNBC), an aggressive sub-type lacking effective targeted therapies. This study evaluated 2-amino-4-boronobutyric acid (ABBA), a boronic acid-containing glutamine analog, as a potential KGA inhibitor with anticancer activity. Methods: KGA inhibition was assessed using a fluorometric enzymatic assay. Cytotoxic effects were examined in multiple TNBC cell lines. Covalent docking and molecular simulation analysis were performed to characterize interactions between ABBA and the KGA active site. Results: ABBA potently inhibited KGA activity, with an IC₅₀ of approximately 1.0 μM, demonstrating greater efficacy than several non-proteinogenic amino acid analogs. ABBA induced dose-dependent cytotoxicity across multiple TNBC cell lines, with pronounced sensitivity observed in basal sub-type cells and cellular sensitivity correlated with KGA expression levels. Expression of γ-glutamyl transpeptidase 1 (GGT1) was negligible, and, excluding any off-target effects, the observed anticancer effects are primarily attributed to KGA inhibition. Docking analysis indicated that ABBA forms a reversible covalent adduct with the catalytic Ser286 residue of KGA in a boronate tetrahedral geometry resembling transition-state mimics, while molecular simulation demonstrated stabilization of the complex through hydrogen bonding and electrostatic interactions. Conclusions: ABBA is a potent boron-based glutaminase inhibitor with therapeutic potential for targeting glutamine metabolism in TNBC. Further structural optimization and in vivo evaluation are warranted to advance ABBA toward therapeutic development. Full article

Angiotensin-converting enzymes (ACE and ACE2) are key components of the renin–angiotensin–aldosterone system (RAAS) and are present in the gastrointestinal tract and intestinal content, preserving their catalytic activity, and may interact with the gut microbiota. The present study aimed to determine the origin of fecal ACE and ACE2 activity. Fecal pellets from germ-free, ACE and ACE2 knockout (KO) mice, and from the corresponding controls were analyzed using fluorimetric enzyme activity assays. ACE activity was assessed using Hippuryl-His-Leu and Z-Phe-His-Leu as substrates; ACE2 activity was assessed using Mca-APK (Dnp), with and without the ACE2 inhibitor MLN-4760. Germ-free mice showed increased fecal ACE and ACE2 activity compared to controls. ACE2-KO mice lacked fecal ACE2 activity, whereas ACE activity was unaffected. In ACE-KO mice, fecal ACE activity was reduced, but not abolished, while ACE2 activity remained similar to controls. In ACE C- and N-domain KO mice, ACE activity was similar to controls, and inhibition with captopril completely abolished fecal ACE activity using Hippuryl-His-Leu, but not Z-Phe-His-Leu, in those animals. These findings indicate that fecal ACE and ACE2 activity results from combined intestinal shedding and microbiota-related mechanisms, supporting a modulatory role of the gut environment on luminal RAAS activity. Full article

Endophytic fungi are promising sources of novel antiviral compounds, and the crude extract from Alternaria alternata PO4PR2 has previously shown anti-HIV-1 activity. This study evaluated its efficacy against integrase strand-transfer inhibitor (INSTI)-resistant HIV-1 and its mechanism of action. Key resistance mutations (Y143H, G118R, N155H, and R263K) were introduced into the HIV-1 pNL4.3 clone via site-directed mutagenesis and confirmed through Sanger sequencing. Viral infectivity was assessed in TZM-bl cells, while cytotoxicity was measured using an MTT assay. Antiviral activity was determined through a luciferase-based assay, and integration inhibition was evaluated using integrase activity assays and Alu-gag nested PCR. The extract demonstrated potent inhibition of resistant mutants, with low IC₅₀ values (0.02971–0.1652 μg/mL), and showed minimal cytotoxicity (CC₅₀ = 300 μg/mL), maintaining over 80% cell viability. It inhibited integrase activity by 67%, specifically targeting the strand-transfer step, and significantly reduced integrated viral DNA. Molecular docking of 14 compounds identified coumarin derivatives as key bioactive metabolites, exhibiting mutation-tolerant binding within the integrase catalytic pocket. Overall, these findings highlight PO4PR2 as a promising source of compounds for developing new therapies targeting drug-resistant HIV-1 integrase. Full article

The use of proton beam therapy (PBT), as a more precision-targeted radiotherapy technique, is increasing in the treatment of head and neck squamous cell carcinoma (HNSCC). PBT benefits from the precise delivery of the radiation dose to the tumour via the Bragg peak. However, challenges still remain in the treatment of HNSCC with radiotherapy, particularly with tumour radioresistance and recurrence, requiring strategies leading to radiosensitisation. There are added complexities with the use of PBT given the increase in linear energy transfer (LET) at and around the Bragg peak, which can cause an altered cellular response compared to low-LET radiation. Nevertheless, targeting the cellular DNA damage response is considered an important strategy to enhance tumour cell killing caused by radiotherapy. Therefore, using specific inhibitors against the protein kinases ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3-related (ATR) and the DNA-dependent protein kinase catalytic subunit (DNA-Pkcs), we investigated their impact in radiosensitising HPV-negative HNSCC cells to PBT of increasing LET. We demonstrate that inhibitors against ATR (AZD6738), and particularly ATM (AZD1390) and DNA-Pkcs (AZD7648), could significantly decrease clonogenic survival of HNSCC cell lines following PBT at both low and relatively high LET (~2 keV/µm and ~8 keV/µm, respectively). We confirmed that the inhibitors in combination with PBT led to DSB persistence through neutral comet assays and monitoring γH2AX/53BP1 foci. We also show that this strategy can enhance the sensitivity of patient-derived organoids of HNSCC to PBT of both low and high LET, highlighting this as a strategy which should be exploited further. Full article

A novel series of hybrid tetrahydro-β-carboline (THβC)-imidazolium (IM) salts incorporating a fused diketopiperazine scaffold was designed, synthesized, and evaluated as cholinesterase inhibitors for potential application in Alzheimer’s disease. The molecular design integrates a π-conjugated THβC core with a cationic IM moiety to promote dual-site interactions within the acetylcholinesterase (AChE) active-site gorge. All compounds exhibited micromolar inhibitory activity against AChE and butyrylcholinesterase (BChE), with a pronounced preference for AChE. The most active derivative, 12d, showed an IC₅₀ value of 0.72 μM toward AChE, while compound 12c demonstrated the highest selectivity (SI = 8.4). Structure–activity relationship studies revealed that both stereochemistry and N-alkyl chain length are critical determinants of activity, with S,S-configured derivatives consistently outperforming their R,R-configured analogs. In silico ADMET analysis indicated favorable physicochemical properties and predicted central nervous system permeability, although potential hepatotoxicity highlights the need for further optimization. Molecular docking studies suggested that the most promising compound adopts a dual-binding mode, interacting with both the peripheral anionic site and catalytic active site of AChE. These results identify THβC-IM hybrids as a structurally novel and promising scaffold for the development of selective cholinesterase inhibitors, providing a basis for further optimization toward multifunctional anti-Alzheimer agents. Full article

Phosphatidylinositol-3-kinases (PI3Ks) are heterodimers of catalytic and regulatory subunits that regulate cell metabolism, activation, and survival. PI3K, particularly the p110α catalytic isoform, is frequently mutated in cancer, and highly specific inhibitors such as alpelisib are currently used in oncology and in PIK3CA-related overgrowth disorders. Given the relevance of macrophages in anti-tumor immunity, we examined the impact of alpelisib on murine monocytes’ intracellular signaling and on in vitro differentiation, polarization, and effector functions of macrophages. Real-time qPCR (RT-qPCR) showed comparable relative expression of PI3K isoforms (p110α, p110β, p110δ, p110γ and p85) in bone marrow monocytes and in macrophages differentiated with macrophage colony-stimulating factor (M-CSF) or granulocyte-macrophage colony-stimulating factor (GM-CSF). However, alpelisib increased p110α, p110β, and p85 relative gene expression (2–3-fold) during M-CSF-dependent differentiation. Functionally, alpelisib-treated M-CSF macrophages displayed enhanced interleukin (IL)-6 and tumor necrosis factor alpha (TNF-α) secretion and reduced IL-10 production after lipopolysaccharide (LPS) plus interferon gamma (IFN-γ) or LPS stimulation. In contrast, GM-CSF macrophages differentiated with alpelisib secreted lower levels of IL-6 and TNF-α and reduced inducible nitric oxide synthase (iNOS) and arginase-1 (Arg-1) gene expression. Additionally, cytokine profiles (IL-2, IL-6, IFN-γ and IL-10) were altered when alpelisib-treated macrophages were cocultured with CD4⁺ T cells under either antigen-specific or polyclonal activation conditions, indicating that the inhibitor modifies both differentiation and subsequent effector interactions of the macrophages. Thus, alpelisib induces lasting effects on macrophage differentiation and function, with potential implications in tumor-associated macrophages that develop under M-CSF or GM-CSF-rich cancer microenvironments. Full article

The transition to renewable carbon resources has positioned lignocellulosic biomass as a key feedstock for sustainable fuel and chemical production; however, its intrinsic recalcitrance limits efficient conversion. Dilute acid pretreatment functions as a homogeneous Brønsted acid catalytic system that selectively depolymerizes hemicellulose and disrupts lignin–carbohydrate complexes, while competing with consecutive sugar dehydration reactions, thereby enhancing downstream processing. This review presents a feedstock-specific analysis of acid catalyzed biomass deconstruction across agricultural residues, woody biomass, and energy crops, with xylose yield employed as a kinetically and mechanistically relevant descriptor of catalytic performance. By correlating proton activity, reaction severity, diffusion constraints, lignin chemistry, and mineral interference with observed conversion behavior, the work establishes a structure–reactivity–performance framework for biomass dependent hydrolysis. Particular attention is given to competing dehydration and condensation pathways that reduce pentose selectivity and generate fermentation inhibitors. The analysis identifies optimal severity windows for maximizing catalytic efficiency while suppressing degradation reactions and provides guidance for feedstock-tailored pretreatment and next-generation acid catalytic systems and reactor configurations in integrated biorefineries. Full article

Background/Objectives: Selective inhibition of JAK1 remains a major challenge in cytokine-signaling therapeutics due to the high structural similarity of the JAK family. Here, we present an integrated computational framework that combines large-scale binding-site conformational analysis, ensemble docking, and protein–ligand interaction fingerprinting (PLIF) to elucidate the structural determinants of JAK1 selectivity and prioritize JAK1-biased scaffolds. Methods: A curated set of JAK1 and JAK2 catalytic-domain structures was clustered to capture binding-site diversity, and representative conformers were evaluated using >2300 annotated ligands. Docking performance was assessed via AUC, early enrichment metrics, and structural pose validation against experimentally resolved complexes. The workflow was subsequently applied to a library of ~6000 drug-like compounds to prioritize candidates with predicted JAK1 preference. Results: Across the ensemble, the most predictive features reliably separated active from inactive ligands (AUC = 0.78–0.82) and captured subtle, systematic rank shifts supporting the reported JAK1 bias. Interaction fingerprint analysis revealed a conserved hinge-binding motif required for potency, alongside a JAK1-enriched hotspot adjacent to Glu aD.55 that contributes to isoform discrimination. Applied to a library of ~6000 drug-like molecules, the workflow yielded 174 candidates predicted to exhibit preferential JAK1 recognition and reduced JAK2 engagement. Conclusions: These findings define the structural and physicochemical features underlying JAK1 selectivity and illustrate how ensemble-based modeling can guide the discovery of next-generation selective kinase inhibitors. Full article

Background/Objectives: SHP2 (PTPN11) is a key regulator of RAS/MAPK signaling and a well-validated target in cancer and developmental disorders. Designing ligands for its catalytic site is challenging due to the pocket’s intrinsic flexibility and the presence of conserved structural water molecules critical for ligand recognition, which limits traditional discovery approaches. This study aimed to systematically identify and prioritize novel SHP2-binding candidates using a computational strategy that accounts for these challenges. Methods: An integrative computational workflow was applied, combining water-aware docking, large-scale virtual screening of 714,409 compounds, MM/GBSA binding free-energy analysis, AI-driven chemical space modeling using ChemBERTa, and microsecond-scale molecular dynamics (MD) simulations. The high-resolution catalytic PTP domain of SHP2 structure was analyzed to identify conserved water molecules (W711, W716, W726, W776) essential for reproducing the crystallographic binding mode of the reference ligand 3LU. Candidates were prioritized based on docking scores, physicochemical criteria, structural inspection, MM/GBSA energetic profiles, and occupancy of distinct chemical space regions. Results: Seven compounds were selected. SwissADME analysis confirmed favorable drug-likeness and GI absorption, with no BBB permeation. ChemBERTa embeddings revealed substantial structural novelty relative to known SHP2 inhibitors. 1 μs molecular dynamics simulations suggested stable binding of compound 4 (2-(3-methyl-2,6-dioxopurin-7-yl)acetate) and persistent interactions with the conserved water network. MM/GBSA evaluation subsequently highlighted its energetically coherent profile. Conclusions: The workflow prioritizes compound 4 as a promising and structurally innovative SHP2-binding candidate. This integrative strategy provides a generalizable approach for targeting proteins with flexible pockets, critical water networks, and limited scaffold diversity, offering a roadmap for challenging computational ligand-prioritization projects. Full article

Epoxide hydrolases (EHs) constitute a conserved enzyme family that catalyzes the hydrolysis of epoxides into less reactive diols. Beyond their canonical roles in xenobiotic detoxification, EHs have emerged as critical regulators of lipid metabolism, redox balance, and inflammatory signaling. Accumulating evidence implicates EH family members, particularly Ephx1 (microsomal EH) and Ephx2 (soluble EH), in cardiovascular diseases, cancer, neurodegeneration, metabolic disorders, and other pathological conditions. More recently, studies have uncovered specialized functions of Ephx3 and Ephx4, broadening our understanding of EH biology and highlighting their tissue-specific roles in skin homeostasis and lipid signaling. Here, we systematically review the structural features, catalytic mechanisms, and physiological functions of EHs, with an emphasis on their regulatory networks in human diseases. We further discuss advances in genetic, epigenetic, and translational studies that connect EHs to disease susceptibility and progression. Finally, we evaluate the therapeutic potential and challenges of targeting EHs, particularly soluble EH inhibitors, and propose future research directions to bridge basic discoveries with clinical translation. This review aims to provide a comprehensive framework for understanding the multifaceted roles of EHs and to inspire novel strategies for precision medicine. Full article

Pancreatic lipase (PL) plays a central role in dietary lipid digestion and is a promising target for food-derived inhibitors. In this study, pea protein hydrolysates (PPHs) with PL inhibitory activity were prepared by enzymatic hydrolysis and characterized for their functional and peptidomic properties. Compared with pea protein isolate, PPH showed lower surface hydrophobicity, and moderate antioxidant activity. Peptidomic analysis identified 1740 peptides in the active hydrolysate. Combined in silico screening and in vitro validation further identified three peptides, GFSL, WFE, and FGF, as effective PL inhibitors, with IC₅₀ values of 337.81 ± 17.32, 473.32 ± 19.61, and 689.45 ± 39.32 μM, respectively. Molecular simulations indicated that these peptides interact with the catalytic pocket of PL mainly through hydrophobic interactions, van der Waals forces, and hydrogen bonding, with Ile79 serving as a key residue for peptide recognition. Overall, these findings indicate the potential of pea-derived peptides as natural PL inhibitors and support their application as functional food ingredients for modulating lipid digestion. Full article

Background/Objectives: The rapid emergence of antimicrobial resistance (AMR) is driven not only by antibiotic selective pressure but also by bacterial adaptive responses that enhance genetic diversification under stress. The SOS response, regulated by the RecA-LexA axis, plays a central role in coordinating DNA repair, mutagenesis, and phenotypic adaptation. Targeting this pathway represents a promising strategy to limit bacterial adaptability without directly affecting viability. This study aimed to evaluate benzoxaborole-based compounds as potential inhibitors of the LexA regulatory pathway. Methods: A drug repurposing approach was employed to investigate the benzoxaborole scaffold and the clinically approved derivatives tavaborole and crisaborole. Biochemical assays were used to assess LexA autocleavage in a RecA-dependent co-protease system. Molecular docking analyses were performed to evaluate compound binding within the LexA catalytic site. Microbiological assays were conducted to examine the effects on antibiotic-induced filamentation and biofilm formation under different growth conditions. Results: Selected benzoxaboroles inhibited LexA autocleavage, with tavaborole showing the strongest inhibitory profile in the biochemical assay. Docking analyses supported these findings, indicating stable binding within the LexA catalytic site near the catalytic serine residue. At the cellular level, tavaborole and benzoxaborole significantly reduced levofloxacin-induced filamentation at sub-inhibitory concentrations. Both compounds also decreased biofilm formation under nutrient-limited conditions, while no significant effects were observed on preformed biofilms. Crisaborole showed limited cellular activity despite measurable biochemical effects. Conclusions: These findings identify benzoxaboroles as modulators of the LexA-dependent SOS response and support the potential repurposing of clinically approved compounds as adjuvants to limit bacterial adaptive responses associated with antimicrobial resistance. Full article