Search Results (12,655)

Structural insights into methyl-coenzyme M reductase from Methanobrevibacter ruminantium (M. ruminantium) has implications for methane mitigation strategies. Methanogenesis in ruminants is a major contributor to global greenhouse gas emissions, primarily driven by the rumen archaeon M. ruminantium. Central to this process is methyl-coenzyme M reductase (Mcr), an enzyme that catalyzes the final step of methane production. Despite its significance as a chemogenetic target for methane mitigation, the high-resolution structure of M. ruminantium Mcr has remained elusive. Here, we employed homology modeling and CDOCKER simulations within the CHARMM force field to elucidate the structural and functional features of the M. ruminantium Mcr/ligand complexes. We characterized two distinct states: the reduced Mcr_oxi-silent state bound to HS-CoM and CoB-SH, and the oxidized Mcr_silent state bound to the heterodisulfide CoM-S-S-CoB. Alanine-scanning mutagenesis identified 71 and 62 key residues per active site for each state, respectively, revealing the fundamental determinants of structural stability and substrate selectivity on the Ni-F₄₃₀ cofactor. Furthermore, structure-based pharmacophore modeling defined essential features (AAADDNNN and AAADDNN) that drive ligand binding. These findings provide a high-resolution molecular framework for the rational design of specific Mcr inhibitors, offering a robust starting point for developing broad-spectrum strategies to suppress enteric methane emissions. Full article

Isothiocyanates (ITCs) are well-known electrophilic agents with antioxidant and anticancer properties, largely attributed to their ability to activate the Nrf2/ARE pathway. Building on previous work with C1-ITC glycosyl derivatives, we designed and synthesized a new series of S-glycosyl isothiocyanates in which the ITC group was repositioned to the C6 carbon of the glucose scaffold. This structural rearrangement yielded stable and synthetically accessible derivatives with markedly enhanced biological profiles. Several compounds showed potent Nrf2 activation at non-cytotoxic concentrations, with CD values comparable to or exceeding those of natural ITCs. In parallel, the new C6-ITC derivatives displayed significant antiproliferative activity against leukemia and solid tumor cell lines. Among them, the phenylsulfone derivative 13 emerged as a particularly promising dual-action molecule, combining strong Nrf2 induction with low-micromolar cytotoxicity. Molecular docking was used as a hypothesis-generating approach and suggested a possible interaction with the STAT3 SH2 domain, although further studies are needed to validate this target. Overall, these results support glucose-based ITCs as a versatile platform for the development of multifunctional antioxidants with complementary anticancer properties. Full article

Intrinsically disordered regions enable transcription factors (TFs) to undergo structural changes upon ligand binding, facilitating the transduction of environmental signals into gene expression. In this study, we applied molecular modeling methods to explore the hypothesis that unstructured inter-domain and subdomain linkers in bacterial TFs can function as sensors for carbohydrate signaling molecules. We combined molecular dynamics simulations and carbohydrate docking to analyze six repressors with GntR-type DNA-binding domains, including UxuR, GntR and FarR from Escherichia coli, as well as AraR, NagR and YydK from Bacillus subtilis. Protein models obtained from different time points of the dynamic simulations were subjected to sequential carbohydrate docking. We found that the inter-domain linker of the UxuR monomer binds D-fructuronate, D-galacturonate, D-glucose, and D-glucuronate with an affinity comparable to nonspecific interactions. However, these ligands formed multimolecular clusters, a feature absent in the UxuR dimer, suggesting that protein dimerization may depend on linker occupancy by cellular carbohydrates. D-glucose interacted with linkers connecting subdomains of the LacI/GalR-type E-domains in GntR and AraR, forming hydrogen bonds that connected distant structural modules of the proteins, while in NagR, FarR and YydK, it bridged the inter-domain linkers and a β-sheet within the HutC-type E-domains. Hence, our results establish flexible linkers as pivotal metabolic sensors that directly integrate nutritional cues to alter gene expression in bacteria. Full article

Introduction: Magnetic nanoparticles are widely investigated as multifunctional platforms for drug delivery and theranostic applications, yet their biomedical implementation is hindered by aggregation, limited colloidal stability, and insufficient biocompatibility. Hybrid biopolymer coatings can mitigate these issues while supporting drug incorporation. Aim: This study aimed to develop casein–pullulan-coated Fe₃O₄ nanocomposites loaded with xanthohumol, enhancing stability and enabling controlled release for potential theranostic use. Methods: Fe₃O₄ nanoparticles were synthesized through co-precipitation and incorporated into a casein–pullulan matrix formed via polymer complexation and glutaraldehyde crosslinking. A 3² full factorial design evaluated the influence of casein:pullulan ratio and crosslinker concentration on physicochemical performance. Nanocomposites were characterized for size, zeta potential, morphology, composition, and stability, while drug loading, encapsulation efficiency, and release profiles were determined spectrophotometrically. Molecular docking was performed to examine casein–pullulan interactions. Results: Uncoated Fe₃O₄ nanoparticles aggregated extensively, displaying mean sizes of ~292 nm, zeta potential of +80.95 mV and high polydispersity (PDI above 0.2). Incorporation into the biopolymer matrix improved colloidal stability, yielding particles of ~185 nm with zeta potentials near –35 mV. TEM and SEM confirmed spherical morphology and uniform magnetic core incorporation. The optimal formulation, consisting of a 1:1 casein:pullulan ratio with 1% glutaraldehyde, achieved 5.7% drug loading, 68% encapsulation efficiency, and sustained release of xanthohumol up to 84% over 120 h, fitting Fickian diffusion (Korsmeyer–Peppas R² = 0.9877, n = 0.43). Conclusions: Casein–pullulan hybrid coatings significantly enhance Fe₃O₄ nanoparticle stability and enable controlled release of xanthohumol, presenting a promising platform for future targeted drug delivery and theranostic applications. Full article

Mothers face high depression risks during pregnancy, and untreated depression can harm both mother and baby. Vortioxetine is a novel antidepressant with a multimodal mechanism, unlike traditional ones. However, little is known about its safety and effectiveness in pregnancy due to limited preclinical and clinical data. This study investigated how maternal vortioxetine exposure during pregnancy affects DNA methylation in the brain tissue of mother and offspring rats. It also explored putative structural interactions of vortioxetine through molecular docking with key epigenetic enzymes to provide a hypothesis-generating context. Fifty female Sprague-Dawley rats were screened using a repeated forced-swim paradigm to characterize a passive stress-coping phenotype. They were then mated and randomly assigned to five groups (n = 10 each): vortioxetine at 0.5, 1.0, 2.0 mg/kg/day orally, saline control, and escitalopram (2.6 mg/kg/day orally) as a comparison. Treatments were given throughout pregnancy. On the day of cesarean section (G20), brain tissue was collected from both the mother and fetus. Global 5-mC levels were measured with ELISA (three replicates). The binding affinities and interaction motifs of vortioxetine and escitalopram with TET2, DNMT3A, and DNMT3B were analyzed via molecular docking. Global 5-mC levels in brain tissue did not differ between groups. However, a significant decrease in overall methylation was observed in offspring given the highest dose of vortioxetine (2.0 mg/kg/day). Docking analyses revealed that vortioxetine and escitalopram could bind strongly to TET2 and DNMT3A/3B; the observed reduction in global 5-mC was compatible with the hypothesis of altered de novo methylation pathways. The results show a specific dose threshold for the fetus. Low to moderate maternal exposures were not associated with detectable differences in global 5-mC under the current assay conditions, whereas high exposure was associated with hypomethylation in offspring. These findings underscore the importance of careful dose selection and mechanism validation for vortioxetine. Full article

Ground-based full-physical experiments for space rendezvous and docking serve as a critical step in verifying the reliability of docking technology. The high-precision active attitude setting of spacecraft simulators represents a key technology for ground-based full-physical experiments. In order to satisfy the requirement for high-precision attitude control in these experiments, this paper proposes an enhanced method based on auto disturbance rejection control (ADRC). This paper addresses the limitations of traditional deadband–hysteresis relay controllers, which exhibit low steady-state accuracy and insufficient disturbance rejection capability. This approach employs a nonlinear extended state observer (NESO) to estimate and compensate for total system disturbances in real time. Concurrently, it incorporates an adaptive mechanism for deadband and hysteresis parameters, dynamically adjusting controller parameters based on disturbance estimates and attitude errors. This overcomes the trade-off between accuracy and power consumption that is inherent in fixed-parameter controllers. Furthermore, the method incorporates a nonlinear tracking differentiator (NTD) to schedule transitions, enabling rapid attitude settling without overshoot. The stability analysis demonstrates that the proposed controller achieves local asymptotic stability and global uniformly bounded convergence. The simulation results demonstrate that under three typical operating conditions (conventional attitude setting, pre-separation connector stabilisation, and docking initial condition establishment), the steady-state attitude error remains within ±0.01°, with convergence times under 3 s and no overshoot. These results closely match ground test data. This approach has been demonstrated to enhance the engineering applicability of the control system while ensuring high precision and robust performance. Full article

Patulin (PAT) is a fatal mycotoxin that exerts serious threats to human and animal health. Biodegradation of PAT is considered to be one of the promising ways for controlling its contamination. In this study, Lactiplantibacillus plantarum 6076 (LP 6076) with reliable removal efficiency on PAT was screened out from three lactic acid bacteria (LAB) strains. It was found that the PAT was eliminated through degradation by LP 6076, and the intracellular proteins played a crucial role in PAT degradation with the induction of PAT. The proteomic analysis showed that the response of LP 6076 to PAT was by a concerted effort to repair DNA damage, in parallel to adaptive changes in cell wall biosynthesis and central metabolism. Eleven differentially expressed proteins with high fold changes were picked out and identified as PAT degradation candidate enzymes. The 3D structures of the candidate enzymes were predicted, and molecular docking between the enzymes and PAT was performed. Five enzymes, including Acetoin utilization AcuB protein (AU), GHKL domain-containing protein (GHLK), Dihydroneopterin aldolase (DA), YdeI/OmpD-associated family protein (YDEL), and Transcription regulator protein (TR), could dock with PAT with lower affinity and shorter distance. Through molecular docking analysis, DA was ultimately identified as a potential key degrading enzyme. The choice of DA was substantiated by its superior combination of strong binding affinity and a productive binding pose with PAT. VAL84 and GLN51 residues of DA were likely the active sites, forming four hydrogen bonds with PAT. Our study could accelerate the commercial application of biodegradation toward PAT decontamination. Full article

A synthetically accessible library of N-acyl sulfonamides was constructed using a combination of copper(I)-catalyzed azide–alkyne cycloaddition (CuAAC) and N-acylation of primary sulfonamides. The proposed two-step reaction sequence had a high experimentally confirmed synthetic success rate (up to 85%) and gave reasonable product yields (up to 61%). As a result of the validation process, a 262-member compound library (out of >70K accessible combinations) was prepared. Biological profiling of the synthesized library by differential scanning fluorimetry and enzymatic assays identified several low micromolar inhibitors of human carbonic anhydrase. The interaction of the discovered hits with the biological target was studied by docking and molecular dynamics. Full article

Contrast-induced acute kidney injury (CIAKI) has emerged as the third most prevalent etiology of clinically acquired acute kidney injury, with a lack of specific preventive and therapeutic strategies. Rubia Cordifolia L. (madder root), a medicinal herb with a long-standing history and extensive clinical application, exhibits multiple pharmacological activities. This study aimed to clarify the renal protective effect of Rubia cordifolia L. dichloromethane extract (RCDE) on CIAKI modeling rats and investigate potential anti-apoptotic and autophagy-inducing effects molecular mechanisms. In this study, RCDE constituents were identified by UPLC-Q-TOF-MS. A CIAKI rat model was established to evaluate the nephroprotective effect of RCDE. The results showed that RCDE high-dose group significantly decreased serum SCr and BUN levels, attenuated renal histopathological damage, and modulated oxidative stress markers by decreasing MDA and CAT while increasing SOD, compared with the model group. It downregulated the expressions of Bcl-2, caspase-3 and p62, upregulated the expressions of Bax, Beclin1 and reduced the LC3B-II/LC3B-I ratio in renal tissues. Molecular docking indicates that anthraquinone compounds are probably the principal active constituents of RCDE. This study provides experimental evidence for the intervention efficacy of RCDE against CIAKI. Full article

Immune checkpoint inhibitors (ICIs) for cancer therapy may induce immune-related adverse events including myocarditis, which occurs infrequently but carries a high mortality rate. Crocins are the active constituents derived from Crocus sativus L. (saffron), and have demonstrated various bioactivities including anti-tumor, anti-inflammation, antioxidation, anti-ischemia, anti-aging, and neuroprotective effects. This study established a subcutaneous xenotransplanted tumor model of human liver cancer in nude mice to better mimic ICI-related myocarditis. Animal experimental results revealed that crocins improved cardiac function, relieved myocardial damage and autoimmune response, and suppressed oxidative stress and inflammatory reaction. Quantitative proteomics and Western blotting verification confirmed that crocins ameliorated experimental ICI-related myocarditis by targeting the Hpx/Nrf2/HO-1 pathway. Molecular docking revealed that the best docking activities were demonstrated by crocin I–HO-1, crocin II–Hpx, and crocin III–Nrf2. These findings shed new light on the development of therapeutic strategies for treating ICI-related myocarditis and provided the fundamental basis for expanding the clinical application of crocins. Full article

Glycosylation serves as an effective strategy to enhance the solubility, bioavailability, and pharmacological activity of polyhydroxyphenols. In this study, we explored the glycosylation of natural and natural-inspired phenolic compounds using the glycosyltransferase AbCGT and evaluated the anti-renal fibrotic potential of the resulting glycosides. Among them, 1,3,5,8-tetrahydroxyxanthone 5-O-β-D-glucopyranoside (2-1a), synthesized via the regioselective 5-O-glycosylation of demethylbellidifolin, demonstrated significant anti-renal fibrotic activity. In contrast, its homologous glycosyltransferase, UGT73AE1, predominantly glycosylated demethylbellidifolin at the 3-OH position. Molecular docking studies revealed the structural basis for this regioselectivity difference. To enhance the production of 2-1a, we established a UDP-glucose (UDPG) recycling system by coupling AbCGT with Glycine max sucrose synthase (GmSuSy) and subsequently optimized the reaction conditions. Furthermore, targeted mutagenesis of AbCGT informed by molecular docking analysis identified a F138A mutant that enhanced glycosylation yield by 2.3-fold. This work develops a novel glycosyltransferase-based catalytic system and identifies a new compound with potential anti-renal fibrotic activity. Full article

This study examined whether co-fermentation with Lactobacillus casei CGMCC 15956 and Lactobacillus delbrueckii CGMCC 21287 could enhance the bioactivity of peptides derived from pecan nut cake (PNC) and clarify the underlying mechanisms. The fermented hydrolysate (PNCH) was compared with an unfermented control. PNCH showed higher antioxidant and α-glucosidase inhibitory activities. Total antioxidant capacity increased from 3.17 to 4.81 mM Trolox, and DPPH radical scavenging activity increased from 62.69% to 84.12%. In addition, the IC₅₀ value for α-glucosidase inhibition decreased from 7.549 to 4.509 mg/mL. In a mouse model of acute alcohol-induced liver injury, PNCH significantly alleviated liver damage through the synergistic enhancement of antioxidant and α-glucosidase inhibitory activities. Peptidomic analysis identified two representative bioactive peptides, FAGDDAPR (from actin) and LAGNPDDEFRPQ (from cupin domain–containing protein 1), both of which exhibited antioxidant and α-glucosidase inhibitory activities. Additionally, these peptides alleviated H₂O₂-induced oxidative stress in Caco-2 cells, significantly improving GSH and MDA levels, as well as SOD activity. Molecular docking suggested potential interactions of these peptides with superoxide dismutase, Keap1, and α-glucosidase. These findings support the high-value utilization of PNC and the development of functional peptide-based ingredients. Full article

Background/Objectives: The high volatility of volatile drugs significantly restricts their clinical applicability. Although excipients capable of strong interactions can reduce volatilization, conventional screening methods rely on empirical trial-and-error, resulting in low efficiency and high resource consumption. To address this limitation, this study introduces an artificial intelligence (AI)-driven strategy for screening drug–excipient interactions. Using d-borneol as a model drug, this approach aims to efficiently identify strongly interacting excipients and develop stable nano-formulations. Methods: High-throughput simulations were performed using the Protenix structure prediction model to evaluate interactions between d-borneol and 472 FDA-approved excipients. The top 50 candidate excipients were selected based on these simu-lations. Molecular docking and stability experiments were conducted to validate the predictions. Results: Molecular docking and stability experiments confirmed the consistency between predicted and experimental results, validating the model’s reliability. Among the candidates, soybean phospholipid (PC) was identified as the optimal excipient. A lyophilized liposomal formulation prepared with PC significantly suppressed the volatilization of d-borneol and improved both thermal and storage stability. Mechanistic investigations indicated that d-borneol stably incorporates into the hydro-phobic region of phospholipids, enhancing membrane ordering via hydrophobic interactions without disturbing the polar headgroups. Conclusions: This study represents the first application of a structure prediction model to excipient screening for volatile drugs. It successfully addresses the stability challenges associated with d-borneol and offers a new paradigm for developing nano-formulations for volatile pharmaceuticals. Full article

Background/Objectives: Osteoporosis is a multifactorial skeletal disorder in which chronic inflammation, dysregulated cytokine signaling, and metabolic imbalance contribute to excessive bone resorption and impaired bone formation. Asiatic acid has demonstrated bone-protective effects, but its molecular mechanisms in osteoporosis remain incompletely understood. This study aimed to investigate the anti-osteoporotic mechanisms of asiatic acid using an integrative in silico strategy. Methods: Network pharmacology analysis was performed to identify osteoporosis-related molecular targets of asiatic acid. Molecular docking was used to predict the binding modes and affinities between asiatic acid and its target proteins. Molecular dynamics simulation was used to assess the structural stability and interaction persistence of the asiatic acid–protein complex. Results: Network pharmacology identified 135 overlapping targets between asiatic acid and osteoporosis, with IL-6, STAT3, PPARG, and NFKB1 emerging as key hubs. KEGG analysis indicated the PPAR signaling pathway as a potential mechanism underlying the anti-osteoporotic effect. Molecular docking showed strong binding energies of asiatic acid with all predicted target proteins, with the highest affinity observed for IL-6, involving key residues ASN61, LEU62, GLU172, LYS66, and ARG168. Consistently, molecular dynamics simulation confirmed stable binding of asiatic acid to IL-6, with persistent interactions with ASN61, LYS66, LEU62, LEU64, and GLN154 mediated by hydrogen bonds, water bridges, and hydrophobic interactions. Conclusions: This integrative in silico study provides mechanistic insight into the potential anti-osteoporotic actions of asiatic acid, implicating IL-6 as a plausible upstream molecular target. These results establish a robust mechanistic framework for future translational studies exploring asiatic acid as a natural therapeutic candidate for osteoporosis. Full article

Over the past two decades, pharmaceutical peptides have emerged as a powerful alternative to traditional small molecules, offering high potency, specificity, and low toxicity. However, most computational drug discovery tools remain optimized for small molecules and need to be entirely adapted to peptide-based compounds. Molecular docking algorithms, commonly employed to rank drug candidates in early-stage drug discovery, often fail to accurately predict peptide binding poses due to their high conformational flexibility and scoring functions not being tailored to peptides. To address these limitations, we present PepScorer::RMSD, a novel machine learning-based scoring function specifically designed for pose selection and enhancement of docking power (DP) in virtual screening campaigns targeting peptide libraries. The model predicts the root-mean-squared deviation (RMSD) of a peptide pose relative to its native conformation using a curated dataset of protein–peptide complexes (3–10 amino acids). PepScorer::RMSD outperformed conventional, ML-based, and peptide-specific scoring functions, achieving a Pearson correlation of 0.70, a mean absolute error of 1.77 Å, and top-1 DP values of 92% on the evaluation set and 81% on an external test set. Our PLANTS-based workflow was benchmarked against AlphaFold-Multimer predictions, confirming its robustness for virtual screening. PepScorer::RMSD and the curated dataset are freely available in Zenodo Full article