Search Results (3,185)

Background: Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), remain major causes of morbidity and mortality, yet no targeted pharmacological therapy is available. Excessive neutrophil and macrophage infiltration drives reactive oxygen species (ROS) production and cytokine release, leading to alveolar–capillary barrier disruption and fatal respiratory failure. Methods: We applied an integrative multi-omics strategy combining single-cell transcriptomics, peripheral blood proteomics, and lung tissue proteomics in a lipopolysaccharide (LPS, 10 mg/kg)-induced mouse ALI model to identify key signaling pathways. Harpagide, an iridoid glycoside identified from our natural compound screen, was evaluated in vivo (40 and 80 mg/kg) and in vitro (0.1–1 mg/mL). Histopathology, oxidative stress markers (SOD, GSH, and MDA), cytokine levels (IL-6 and IL-1β), and signaling proteins (HIF-1α, p-PI3K, p-AKT, Nrf2, and HO-1) were quantitatively assessed. Direct target engagement was probed using surface plasmon resonance (SPR), the cellular thermal shift assay (CETSA), and 100 ns molecular dynamics (MD) simulations. Results: Multi-omics profiling revealed robust activation of HIF-1, PI3K/AKT, and glutathione-metabolism pathways following the LPS challenge, with HIF-1α, VEGFA, and AKT as core regulators. Harpagide treatment significantly reduced lung injury scores by ~45% (p < 0.01), collagen deposition by ~50%, and ROS accumulation by >60% relative to LPS (n = 6). The pro-inflammatory cytokines IL-6 and IL-1β were reduced by 55–70% at the protein level (p < 0.01). Harpagide dose-dependently suppressed HIF-1α and p-AKT expression while enhancing Nrf2 and HO-1 levels (p < 0.05). SPR confirmed direct binding of Harpagide to HIF-1α (KD = 8.73 µM), and the CETSA demonstrated enhanced thermal stability of HIF-1α. MD simulations revealed a stable binding conformation within the inhibitory/C-TAD region after 50 ns. Conclusions: This study reveals convergent immune–microenvironmental regulatory mechanisms across cellular and tissue levels in ALI and demonstrates the protective effects of Harpagide through multi-pathway modulation. These findings offer new insights into the pathogenesis of ALI and support the development of “one-drug, multilayer co-regulation” strategies for systemic inflammatory diseases. Full article

Chicoric and chlorogenic acids (CRA and CGA), two caffeic acid derivatives found in a large variety of plants, particularly in Asteraceae, are known to modulate glucose-6-phosphatase (G6Pase) in hepatic and muscle cells. The aim of the present study is to use CRA/CGA to explore the modulation role and molecular mechanism of endocrine pancreatic beta-cells’ insulin secretion. The G6Pase enzyme activity influenced by caffeic and derivatives alone or in combination was assessed on microsomal fractions of INS1-beta-cells and hepatocytes. Overall, our results show inverse effects of CGA/CRA, allowing us to investigate the G6Pase activity modulation under low and high glucose concentrations. Our data strongly suggests the existence of two putative forms of the G6Pase enzyme. Based on these observations, we formulate the hypothesis of an adaptative bi-conformational model of G6Pase enzyme activity modulation depending on the level of the beta-cell glucose exposure. Full article

The inhibition mechanism and binding properties of four phenolic acids (ferulic acid (FA), p-coumaric acid (CA), gallic acid (GA), and protocatechuic acid (PA)) on xanthine oxidase (XOD) were investigated. All four phenolic acids acted via a mixed inhibition pattern, mainly influencing the hydrophobic regions and secondary conformation of XOD through hydrophobic bonding and hydrophobic association. Molecular dynamics simulations exhibited that the complexes of XOD with FA and CA revealed smaller radii of gyration (Rg) and solvent-accessible surface areas (SASA), along with lower variability in root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF), collectively indicating greater structural stability. FA, CA, and PA significantly reduced uric acid (UA) concentration in the 25–100 μM range. Although GA only reduced UA levels in cell models at 25 μM, this effect was likely due to its larger polar surface area, which limits cellular uptake. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) evaluation suggested that these phenolic acids have potential for development. Full article

Control strategies for leishmaniasis increasingly target sand fly vectors through sugar feeding approaches containing bioactive compounds. This study investigated the behavioral and toxicological effects of the iridoids plumericin and isoplumericin, isolated from Himatanthus sucuuba, on Lutzomyia longipalpis by integrating computational and experimental approaches focused on gustatory system interactions. The iridoids were purified by column chromatography and characterized by GC-MS. The gustatory receptor A0A1B0CHD5 was structurally characterized through homology modeling, followed by molecular docking and 100 ns molecular dynamics simulations. Behavioral assays evaluated survival, repellency, and feeding preferences using sugar solutions supplemented with an iridoid mixture. Toxicity was assessed in Drosophila melanogaster as a non-target organism model. Molecular docking results revealed comparable binding affinities between sucrose (ChemPLP score 57.96) and the iridoids plumericin (49.08) and isoplumericin (47.75). Molecular dynamics simulations confirmed the stability of the ligand–receptor complexes and revealed distinct conformational changes. The iridoids did not affect L. longipalpis survival, showed no repellency, and did not reduce sugar feeding acceptance. Preference for the control diet was observed only after continuous exposure (48 h), suggesting involvement of post-ingestive sensory processing. No acute toxicity was observed in D. melanogaster (96% survival). These findings demonstrate that iridoids preserve vector feeding behavior and survival while exhibiting low toxicity to non-target organisms, supporting their potential use in gustatory modulation strategies in leishmaniasis vector control without compromising ecological safety. Full article

Gellan gum (Gellan), a versatile polysaccharide applied in gel formation and prebiotic formulations, is often processed to tailor its molecular properties. Previous studies employed gamma irradiation and chemical hydrolysis, though without addressing systematic scaling behavior. This study investigates the structural and conformational modifications of Gellan in dilute aqueous salt solutions using a safer and eco-friendly approach: atmospheric low-dose electron beam (e-beam) degradation coupled with viscosity analysis. Native and E-beam-treated Gellan samples (0.05 g/cm³ in 0.1 M KCl) were examined by relative viscosity at varying temperatures, with intrinsic viscosity and molar mass determined via Solomon–Ciuta and Mark–Houwink relations. Molar mass degradation followed first-order kinetics, yielding rate constants and degradation lifetimes. Structural parameters, including radius of gyration and second virial coefficient, produced scaling coefficients of 0.62 and 0.15, consistent with perturbed coil conformations in a good solvent. The shape factor confirmed preservation of an ideal random coil structure despite irradiation. Conformational flexibility was further analyzed using theoretical models. Transition state theory (TST) revealed that e-beam radiation lowered molar mass and activation energy but raised activation entropy, implying reduced flexibility alongside enhanced solvent interactions. The freely rotating chain (FRC) model estimated end-to-end distance (R_θ) and characteristic ratio (C_∞), while the worm-like chain (WLC) model quantified persistence length (l_p). Results indicated decreased R_θ, increased l_p, and largely unchanged C_∞, suggesting diminished chain flexibility without significant deviation from ideal coil behavior. Overall, this work provides new insights into Gellan’s scaling laws and flexibility under aerobic low-dose E-beam irradiation, with relevance for bioactive polysaccharide applications. Full article

Background/Objectives: Cancer progression is characterized by the suppression of apoptosis, activation of metastatic processes, and dysregulation of cell proliferation. The proper functioning of these mechanisms relies on critical signaling pathways, including Phosphoinositide 3-kinase/Protein kinase B/mammalian Target of Rapamycin (PI3K/Akt/mTOR), Mitogen-Activated Protein Kinase (MAPK), and Signal Transducer and Activator of Transcription 3 (STAT3). Although curcumin and resveratrol exhibit anticancer properties and affect these pathways, their pharmacokinetic limitations, including poor bioavailability and low solubility, restrict their clinical application. The aim of our study was to evaluate the synergistic anticancer potential of curcumin and resveratrol through hybrid molecules rationally designed from these compounds to mitigate their pharmacokinetic limitations. Furthermore, we analyzed the multi-target anticancer effects of these hybrids on the AKT serine/threonine kinase 1 (AKT1), MAPK, and STAT3 pathways using in silico molecular modeling approaches. Methods: Three hybrid molecules, including a long-chain (ELRC-LC) and a short-chain (ELRC-SC) hybrid, an ester-linked hybrid, and an ether-linked hybrid (EtLRC), were designed using the Avogadro software (v1.2.0), and their geometry optimization was carried out using Density Functional Theory (DFT). The electronic properties of the structures were characterized through Frontier Molecular Orbital (FMO), Molecular Electrostatic Potential (MEP), and Fourier Transform Infrared (FTIR) analyses. The binding energies of the hybrid molecules, curcumin, resveratrol, their analogs, and the reference inhibitor were calculated against the AKT1, MAPK, and STAT3 receptors using molecular docking. The stabilities of the best-fitting complexes were evaluated through 100 ns molecular dynamics (MD) simulations, and their binding free energies were estimated using the Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) method. Results: DFT analyses demonstrated stable electronic characteristics for the hybrids. Molecular docking analyses revealed that the hybrids exhibited stronger binding compared to curcumin and resveratrol. The binding energy of −11.4 kcal/mol obtained for the ELRC-LC hybrid against AKT1 was particularly remarkable. Analysis of 100 ns MD simulations confirmed the conformational stability of the hybrids. Conclusions: Hybrid molecules have been shown to exert multi-target mechanisms of action on the AKT1, MAPK, and STAT3 pathways, and to represent potential anticancer candidates capable of overcoming pharmacokinetic limitations. Our in silico-based study provides data that will guide future in vitro and in vivo studies. These rationally designed hybrid molecules, owing to their receptor affinity, may serve as de novo hybrid inhibitors. Full article

Elastin is the principal protein found in the elastic fibers of vertebrate tissues, and the water within these fibers plays a crucial role in preserving the structure and function of this hydrophobic protein. Soluble elastin was successfully obtained by repeatedly treating insoluble elastin, extracted from pig aorta, with oxalic acid. Solid-state NMR analysis was performed on the soluble elastin, focusing on conformation-dependent chemical shifts of alanine residues. This analysis revealed that cross-linked alanine residues exhibited both α-helix and random coil structures in the dry state. In contrast, the hydrated state favored random coil structures, with some distorted helices possibly present, indicating that the cross-linked configuration is relatively unstable. Similar conformational changes were observed in insoluble elastin, mirroring those found in the soluble form. Additionally, when the soluble elastin was re-cross-linked using 1,12-dodecanedicarboxylic acid and 4-hydroxyphenyl dimethylsulfonium methylsulfate, it retained a mixture of α-helix and random coil structures in the dry state. Remarkably, in the hydrated state, α-helix structures were more prominently preserved alongside random coils. These structural changes corresponded with increased stiffness of molecular chains in the hydrophobic regions compared to their state prior to re-cross-linking, even under hydrated conditions. Full article

Background/Objectives: Orofacial clefts (OFCs) are among the most common birth defects globally, sometimes exacerbated by adverse drug reactions (ADRs) from corticosteroids and antiepileptics. Comprehending the pharmacogenomic and pharmacogenetic elements that lead to ADRs is essential for enhancing precision medicine and clinical outcomes. This study examines rare genetic variants in drug-metabolizing and drug-transporting genes among Ghanaian and Nigerian families with a history of OFCs, intending to assess their pathogenicity and functional implications. Methods: We recruited 104 Ghanaian families and 26 Nigerian families, generating whole-genome sequencing (WGS) data from 390 individuals (130 case-parent trios). DNA isolated from saliva and buccal swab samples underwent WGS, and subsequent WGS data were analyzed through extensive bioinformatics analyses. Variants were called and annotated using the GATK workflow. The HOPE in silico modeling tool evaluated the structural impact of genetic variants on encoded proteins, while molecular docking using PyRx examined alterations in ligand binding affinity. Results: Our study revealed pathogenic variants in vital genes associated with drug metabolism and transport, specifically CYP1A2, CYP2C18, CYP27A1, CYP2B6, SLC6A2, and ABCC3. Structural modeling research demonstrated substantial size, charge, conformation, and hydrophobicity variations between wildtype and mutant proteins. Variants positioned near conserved regions or within functional domains were anticipated to be deleterious, potentially compromising protein function and ligand interactions. Molecular docking studies verified changes in binding affinities between wildtype and mutant proteins for common ligands. The identified variations were linked to the metabolism of frequently used pharmaceuticals in Africa, such as caffeine, ketoconazole, efavirenz, carbamazepine, and artemether. Conclusions: These findings highlight the need for pharmacogenetic screening to inform personalized medicine, diminish ADRs, and enhance the clinical care of OFCs in Sub-Saharan Africa. Full article

Hydrogen-bond-like M···H–C interactions in square-planar d⁸ metal complexes have recently gained attention as structure-directing elements and design motifs in asymmetric catalysis. In this study, we explore these weak interactions not as static features, but as key modulators of molecular motion. We synthesized four cis-[N,N′-pentamethylenebis(iminomethylazolato)]M(II) (M = Pt, Pd), including iminomethyl-2-imidazole, iminomethyl-5-imidazole, and iminomethylpyrrolato Pt(II) complexes and an iminomethylpyrrolato Pd(II) analog. All complexes display reversible flipping of the alkylene bridge across the coordination plane, with the M···H–C interaction alternately engaging from above or below. This dynamic motion was characterized by variable-temperature ¹H NMR spectroscopy, revealing activation parameters for the flipping process. X-ray crystallography confirmed geometries consistent with hydrogen-bond-like interactions, while NBO analysis based on DFT calculations provided insight into their electronic nature. Interestingly, although Pt and Pd display comparable M···H–C distances, solvent effects dominate the flipping kinetics over metal identity. These findings highlight the role of hydrogen-bond-like M···H–C interactions not only in structural stabilization, but also in regulating conformational dynamics. Full article

An extensive study on the interactions between O-phosphorylethanolamine (PEA) and O-phosphorylcholine (PPC), Cu²⁺ and Zn²⁺, is thoroughly described. The formation constants were determined at different temperatures (15 ≤ t/°C ≤ 37) and ionic strengths (0.15 ≤ I/mol L⁻¹ ≤ 0.97) by potentiometric titrations. For the Zn²⁺-PEA/-PPC systems, speciation models were also confirmed by ¹H NMR titrations at t = 25 °C and I = 0.15 mol L⁻¹ in NaCl. Sequestering abilities were calculated under different temperatures and physiological conditions. Density Functional Theory (DFT) calculations along with enhanced sampling of the conformational space were performed aimed to better elucidate the Cu²⁺-, Zn²⁺- PEA/PPC molecular interactions and their relative stabilities. Overall, both experiments and computer simulations showed that the complex species involved in the Cu²⁺–PEA system exhibited a significant and selective stability, particularly in conditions simulating cerebrospinal fluid. While the binding molecular mechanisms were elucidated via DFT supplemented by automized conformational search, the computational binding energies trend qualitatively follows the experimental logK behavior across the Cu²⁺-, Zn²⁺- PEA/PPC complexes. These results highlight the potential physiological role of PEA in modulating free copper levels and regulating its redox activity in pathological conditions, such as Wilson’s Disease (WD). Full article

RNA polymerases are essential enzymes that catalyze DNA transcription into RNA, vital for protein synthesis, gene expression regulation, and cellular responses. Non-template-dependent RNA polymerases, which synthesize RNA without a template, are valuable in biological research due to their flexibility in producing RNA without predefined sequences. However, their substrate polymerization mechanisms are not well understood. This study examines Poly (A) polymerase (PAP), a nucleotide transferase superfamily member, to explore its substrate selectivity using computational methods. Previous research shows PAP’s polymerization efficiency for nucleoside triphosphates (NTPs) ranks ATP > GTP > CTP > UTP, though the reasons remain unclear. Using 500 ns Gaussian accelerated molecular dynamics simulations, stability analysis, secondary structure analysis, MM-PBSA calculations, and Markov state modeling, we investigate PAP’s differential polymerization efficiencies. Results show that ATP binding enhances PAP’s structural flexibility and increases solvent-accessible surface area, likely strengthening protein–substrate or protein–solvent interactions and affinity. In contrast, polymerization of other NTPs leads to a more open conformation of PAP’s two domains, facilitating substrate dissociation from the active site. Additionally, ATP binding induces a conformational shift in residues 225–230 of the active site from a loop to an α-helix, enhancing regional rigidity and protein stability. Both ATP and GTP form additional π–π stacking interactions with PAP, further stabilizing the protein structure. This theoretical study of PAP polymerase’s substrate selectivity mechanisms aims to clarify the molecular basis of substrate recognition and selectivity in its catalytic reactions. These findings offer valuable insights for the targeted engineering and optimization of polymerases and provide robust theoretical support for developing novel polymerases for applications in drug discovery and related fields. Full article

Poly(carboxybetaine methacrylate)s (PCBMA) belongs to a class of zwitterionic polymers that offer promising alternatives to polyethylene glycol (PEG) in biomedical applications. This review highlights how the unique zwitterionic structure of PCBMA dictates its strong antifouling behavior, low immunogenicity, and sensitivity to environmental stimuli such as pH and ionic strength. These features make PCBMA promising for designing advanced systems suited for complex biological environments. This review describes PCBMA-based materials—ranging from hydrogels, nanogels, and surface coatings to drug carriers and protein conjugates—and critically evaluates their performance in drug delivery, tissue engineering, diagnostics, and implantable devices. Comparative studies demonstrated that PCBMA consistently outperformed other zwitterionic polymers and PEG in resisting protein adsorption, maintaining bioactivity of conjugated molecules, and ensuring long circulation times in vivo. Molecular dynamics simulations provide additional information into the hydration shells and conformational behaviors of PCBMA in aqueous dispersions. These insights underscore PCBMA’s broad potential as a promising high-performance material for next generation healthcare technologies. Full article

Peach gum polysaccharide (PGP), a natural biopolymer extracted from the resin of the peach tree, holds significant potential for applications in food, cosmetics, and pharmaceutical industries. However, detailed analysis and exploration of its physical and chemical properties remain limited. This study investigates the physicochemical properties, rheological behavior and emulsion stability of PGPs extracted using thermal (TPGP) and enzymatic (EPGP) methods. The results indicate that both polysaccharide fractions exhibit similar arabinogalactan (AG) structures, with high contents of arabinose and xylose, as evidenced by FTIR spectra and monosaccharide composition. However, high-performance size-exclusion chromatography (HPSEC) revealed differences in molecular weights and chain conformations, leading to distinct rheological behaviors. PGP solutions exhibited pseudoplastic flow behavior, with TPGP demonstrating higher viscosity due to its larger molecular weight (1.295 × 10⁷ g mol⁻¹). As the PGP concentration increased, gel strength and emulsion stability improved significantly. This study provides more insight into the rheological and emulsifying characteristics of PGPs extracted by varied methods, facilitating their potential applications in food industries. Full article

Oxidative stress, caused by excessive free radicals, leads to cellular damage and various diseases. Antioxidant peptides from natural proteins offer potential in alleviating this stress. In this study, antioxidant peptides were identified from deer antler proteins using in silico enzymatic hydrolysis and machine learning. Peptides with high prediction scores and non-toxic profiles were selected for evaluation. The antioxidant activities of top candidates, PHPAPTL and VPHGL, were confirmed by radical scavenging assays and their protective effects in HepG2 cells. Molecular dynamics simulations revealed stable binding of these peptides to Keap1, enhancing system stability and reducing residue fluctuations at the ligand-binding interface. Key interactions involved Arg415, Arg483, Arg380, and Ser555. Secondary structure analysis showed peptide binding induced local conformational transitions, notably increasing parallel β-sheet formation near active sites. These findings provide mechanistic insight into their antioxidant effects and support their potential application in functional food development. Full article

Lignin, the most abundant aromatic biopolymer, represents a key renewable feedstock for sustainable biorefineries, yet its structural complexity poses a formidable challenge for enzymatic degradation. While ligninolytic enzymes such as laccases (LACs), lignin peroxidases (LiPs), and manganese peroxidases (MnPs) exhibit remarkable catalytic versatility, the molecular mechanisms underlying their ability to balance substrate specificity and structural flexibility remain unresolved. Here, we employed all-atom molecular dynamics (MD) simulations and virtual mutagenesis to dissect the dynamic interactions between these enzymes and lignin model compound (β-O-4-linked H-type dimers). Our simulations revealed a dual recognition mechanism in which polar residues (such as Asp, Glu, Arg and His) formed hydrogen bonds with hydroxyl and keto groups near catalytic cleavage sites, ensuring precise alignment for bond scission, while aromatic residues stabilized diverse lignin conformations via hydrophobic interactions with conserved aromatic rings. Conformational dynamics of active-site residues enabled adaptive adjustments to substrate heterogeneity, reconciling enzymatic specificity with structural promiscuity. Virtual mutation experiments further demonstrated that aromatic residues were indispensable for binding stability, whereas polar residues dictated cleavage-site selectivity. These findings provide atomic-scale insights into the catalytic mechanism of ligninolytic enzymes, with implications in the rational design of superior biocatalyst for lignin biorefineries. Full article