Search Results (217)

Background: Preeclampsia (PE) is a pregnancy-specific disease and hypertensive disorder with a multifactorial pathogenesis involving complex molecular regulatory networks. Recent studies highlight the critical role of non-coding RNAs, particularly miRNAs and lncRNAs, in PE development. This study investigates the molecular interaction between miR-7151-5p and the lncRNA KCNQ1OT1 and their functional contributions to PE pathogenesis. Methods: An integrative approach combining RNAhybrid-based bioinformatics, dual-luciferase reporter assays, qRT-PCR, Transwell migration and invasion assays, and RNA sequencing was employed to characterize the binding between miR-7151-5p and KCNQ1OT1 and assess their influence on trophoblast cell function and gene expression. Results: A bioinformatic analysis predicted a stable binding site between miR-7151-5p and KCNQ1OT1 (minimum free energy: –37.3 kcal/mol). The dual-luciferase reporter assay demonstrated that miR-7151-5p directly targets KCNQ1OT1, leading to suppressed transcriptional activity. In HTR8/SVneo cells, miR-7151-5p overexpression significantly downregulated both KCNQ1OT1 and Notch1 mRNA, whereas its inhibition showed no significant changes, suggesting additional regulatory mechanisms of Notch1 expression. Transwell assays indicated that miR-7151-5p overexpression suppressed trophoblast cell migration and invasion, whereas its inhibition enhanced these cellular behaviors. RNA-seq analysis further revealed that miR-7151-5p overexpression altered key signaling pathways, notably the TGF-β pathway, and significantly modulates PE-associated genes, including PLAC1, ANGPTL6, HIRA, GLA, HSF1, and BAG6. Conclusions: The regulatory effect of miR-7151-5p on KCNQ1OT1, along with its influence on trophoblast cell dynamics via Notch1 and TGF-β signaling pathways, highlights its role in PE pathogenesis and supports its potential as a biomarker in early PE screening. Full article

Leptin is an adipocyte-derived hormone that orchestrates different physiological processes, including energy balance, thermogenesis, immune regulation, reproduction, and tissue remodeling. These effects are mediated through interaction with the CRH2 domain of the leptin receptor (Ob-R). While the structural aspects of the interaction between leptin and Ob-R have been first studied in humans and mice, comparative analyses of stability across mammalian species under physiologically relevant microenvironmental conditions remain limited. We performed a bioinformatics-driven structural, stability, and thermodynamic characterization of the leptin–CRH2 complex. This included structural homology modeling using a full-length template, interface mapping, and binding energy estimation. Additionally, we analyzed the effect of pH, ionic strength, and temperature on complex formation to mimic physiological and pathological tissue conditions to enhance clarity in the structural features and stability of the complex. Our results show that the interaction is primarily enthalpy-driven and is sensitive to temperature, ionic strength, and pH changes for all heterodimers analyzed here. The predicted binding free energy (ΔG) ranged from −10.50 to −16.81 kcal/mol across species. The integrated bioinformatic analyses suggest that subtle sequence variations influence the stability and environmental responsiveness of the complex. This study provides a molecular framework for understanding how leptin–Ob-R binding adapts across species and tissue contexts. Full article

In the present research, metal–organic framework-5 (MOF-5) was synthesized and loaded with zerumbone (ZER@MOF-5), followed by the evaluation of its anticancer, antibacterial, antifungal, DNA-binding, and free radical scavenging potentials. The synthesized nanoparticles were characterized using X-ray diffraction, ultraviolet–visible spectroscopy, Fourier-transform infrared spectroscopy, energy-dispersive X-ray spectroscopy, and scanning electron microscopy. The in vitro anticancer activity of ZER@MOF-5 was studied in a human breast cancer cell line (MCF-7) using the CCK-8 assay. The interaction of ZER@MOF-5 with pBR322 plasmid DNA was assessed by gel electrophoresis. The antimicrobial effect of ZER@MOF-5 was examined in gram-positive and gram-negative bacterial strains and yeast strains using the microdilution method. The free radical scavenging activity was assessed using the DPPH assay. Cytotoxicity assay revealed a notable enhancement in the anticancer activity of zerumbone upon its encapsulation into MOF-5. The IC₅₀ value for ZER@MOF-5 was found to be 57.33 µg/mL, which was lower than that of free zerumbone (IC₅₀: 89.58 µg/mL). The results of the DNA-binding experiment indicate that ZER@MOF-5 can bind to target DNA and cause a conformational change in DNA. The results of the antibacterial activity experiment showed that the antibacterial ability of ZER@MOF-5 was limited compared to free zerumbone. The results of the DPPH assay demonstrated that the antioxidant activity of free zerumbone was higher than that of ZER@MOF-5. MOFs encapsulate compounds within their porous crystalline structure, which leads to prolonged circulation time compared to single ligands. Although the unique structure of MOFs may limit their antibacterial and antioxidant activity in the short term, it may increase therapeutic efficacy in the long term. However, to fully understand the long-term antibacterial and antioxidant effects of the ZER@MOF-5, further comprehensive in vitro and in vivo experiments are necessary. This finding indicates that the MOF-5 could potentially be an impressive carrier for the oral administration of zerumbone. Full article

The production of solid biofuels from torrefied biomass holds significant potential for renewable energy applications. Durable pellet formation from severely torrefied biomass is hindered by the loss of natural binding properties, yet studies on mild torrefaction that preserves sufficient binding capacity for pellet production without external binders or changes to die conditions remain scarce. This paper investigated the production of fuel pellets from torrefied biomass without using external binders or adjusting pelletization parameters. Experiments were conducted using a mild torrefaction temperature (230 °C and 250 °C) and shorter residence time (10, 15, and 30 min). The torrefied materials were then subjected to pelletization using a single-pellet press; and the influence of torrefaction on the mechanical durability, hydrophobicity, and fuel characteristics of the pellets was examined. Results indicated that the mass loss ranging from 10 to 20% among the mild torrefaction treatments was less than the typical extent of mass loss due to severe torrefaction. Pellets made from torrefied biomass (torrefied pellets) had improvement in the hydrophobicity (moisture resistance) when compared to pellets made from untreated biomass (untreated pellets). Improved hydrophobicity is important for storage and transportation of pellets that are exposed to humid environmental conditions, as it reduces the risk of pellet degradation and spoilage. Thermogravimetric analysis of the pyrolysis and combustion behaviour of torrefied pellets indicated the improvement of fuel characteristics in terms of a much higher comprehensive pyrolysis index and greater thermal stability compared to untreated pellets, as evidenced by the prolonged burnout time and reduced combustion characteristics index. Residence time had a more significant impact on pellet durability than temperature, but the durability of the torrefied pellets was lower than that of the untreated pellets. Further research is required to explore the feasibility of producing binder-free durable pellets under mild torrefaction conditions. Overall, the study demonstrated that mild torrefaction could enhance the fuel quality and moisture resistance of biomass pellets, offering promising advantages for energy applications, despite some trade-offs in mechanical durability. Full article

Umami is a fundamental taste sensation, often described as a delicious and pleasant flavor perception. To enhance or complement the original flavor and meet the tastes of diverse regions, umami dipeptides have been extensively utilized in global food manufacturing. Currently, the application and purification techniques of dipeptides are relatively mature, while their umami mechanisms and molecular modification are both scarce. In this work, the 3D structure of the umami dipeptide target T1R1/T1R3 was first obtained through sequence alignment and homology modeling, then followed by the successful construction of a database containing 400 samples of dipeptides. Subsequently, the complex models of T1R1/T1R3, respectively, with DG (Asp-Gly) and EK (Glu-Lys) (i.e., T1R1_DG/T1R3, T1R1/T1R3_DG, T1R1_EK/T1R3, and T1R1/T1R3_EK) were obtained via molecular docking and virtual screening. Finally, based on comparative molecular dynamics (MD) simulation trajectories, the binding free energy was calculated to investigate receptor–ligand recognition and conformational changes, providing some implications for potential modifications of umami dipeptides. T1R1 tends to bind relatively small umami dipeptides, whereas T1R3 does the opposite, both of which favor the recognition of acidic and hydrophilic dipeptides. By comparing strategies such as hydroxyl introduction and chain length alteration, electrostatic effects may be more important than non-polar effects in molecular design. This work not only explores the recognition mechanism of umami dipeptides with the receptor T1R1/T1R3 showing certain theoretical significance, but also provides feasible suggestions for dipeptide screening and modification having certain application value. Full article

KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS allostery remain poorly understood. In this study, we employ microsecond molecular dynamics simulations, mutational scanning, and binding free energy calculations together with dynamic network modeling to dissect how engineered DARPin proteins K27, K55, K13, and K19 engage KRAS through diverse molecular mechanisms ranging from effector mimicry to conformational restriction and allosteric modulation. Mutational scanning across all four DARPin systems identifies a core set of evolutionarily constrained residues that function as universal hotspots in KRAS recognition. KRAS residues I36, Y40, M67, and H95 consistently emerge as critical contributors to binding stability. Binding free energy computations show that, despite similar binding modes, K27 relies heavily on electrostatic contributions from major binding hotspots while K55 exploits a dense hydrophobic cluster enhancing its effector-mimetic signature. The allosteric binders K13 and K19, by contrast, stabilize a KRAS-specific pocket in the α3–loop–α4 motif, introducing new hinges and bottlenecks that rewire the communication architecture of KRAS without full immobilization. Network-based analysis reveals a strikingly consistent theme: despite their distinct mechanisms of recognition, all systems engage a unifying allosteric architecture that spans multiple functional motifs. This architecture is not only preserved across complexes but also mirrors the intrinsic communication framework of KRAS itself, where specific residues function as central hubs transmitting conformational changes across the protein. By integrating dynamic profiling, energetic mapping, and network modeling, our study provides a multi-scale mechanistic roadmap for targeting KRAS, revealing how engineered proteins can exploit both conserved motifs and isoform-specific features to enable precision modulation of KRAS signaling in oncogenic contexts. Full article

SPR biosensors operate on the principle of evanescent wave propagation at metal–dielectric interfaces in total internal reflection conditions, with consequent photonic energy attenuation. This plasmonic excitation occurs in specific conditions of incident light wavelength, angle, and the dielectric refractive index. This principle has been the basis for SPR-based biosensor setups wherein mass/concentration-induced changes in the refractive indices of dielectric media reflect as plasmonic resonance condition changes quantitatively reported as arbitrary response units. SPR biosensors operating on this conceptual framework have been designed to study biomolecular interactions with real-time readout and in label-free setups, providing key kinetic characterization that has been valuable in various applications. SPR biosensors often feature antibodies as target affinity probes. Notably, the operational challenges encountered with antibodies have led to the development of aptamers—oligonucleotide biomolecules rationally designed to adopt tertiary structures, enabling high affinity and specific binding to a wide range of targets. Aptamers have been extensively adopted in SPR biosensor setups with promising clinical and industrial prospects. In this paper, we explore the growing literature on SPR setups featuring aptamers, specifically providing expert commentary on the current state and future implications of these SPR aptasensors for drug discovery as well as disease diagnosis and monitoring. Full article

To investigate the microscopic mechanism of aging-induced “dewetting” at the matrix/filler interface in Nitrate Ester Plasticized Polyether (NEPE) propellant, this study decoupled the aging process into two factors: crosslinking density evolution and nitrate ester decomposition. Molecular dynamics (MD) simulations were employed to construct all-component matrix models and matrix/filler interface models with varying aging extents. Key parameters including crosslinking density, mechanical properties, free volume fraction, diffusion coefficients of the matrix, as well as interfacial binding energy and radial distribution function (RDF) were calculated to analyze the effects of both aging factors on “debonding”. The results indicate the following: 1. Increased crosslinking density enhances matrix rigidity, suppresses molecular mobility, and causes interfacial binding energy to initially rise then decline, peaking at 40% crosslinking degree. 2. Progressive nitrate ester decomposition expands free volume within the matrix, improves binder system mobility, and weakens nitrate ester-induced interfacial damage, thereby strengthening hydrogen bonding and van der Waals interactions at the interface. 3. The addition of a small amount of bonding agent improved the interfacial bonding energy but did not change the trend of the bonding energy with aging. Full article

OT has gained attention for its high polyphenol content and therapeutic potential. To elucidate this further, this study investigated the electron-shuttling bioactive compounds of OT and evaluated their effect on dysregulated breast cancer (BC) genes. OT extracts were obtained via solvent extraction (SE) and supercritical fluid extraction (SFE), followed by in vitro assays. Phytochemical analysis revealed that ethanol-extracted OT (OTL-E) had the highest polyphenol, flavonoid, and tannin contents, correlating with strong antioxidant activity, while water-extracted OT (OTL-W) exhibited greater bioelectricity-stimulating properties in microbial fuel cells (MFC), confirmed by cyclic voltammetry (CV). Based on phytochemical analyses, SE displayed a better extraction technique for isolating OT bioactive compounds compared to SFE. In silico approaches through network pharmacology, molecular docking and dynamics simulations revealed that polyphenols with ortho- or para-dihydroxyl groups targeted dysregulated BC proteins involved in kinase signaling, apoptosis, and hormone receptor pathways. Luteolin exhibited the highest binding affinities to MAPK1 and PIK3CA with free energy (ΔG) of −9.1 and −8.4 kcal/mol, respectively. Trajectory-based analyses confirmed enthalpy-favored ligand-induced conformational changes to these oncoproteins, altering their function in BC development. These findings suggest the potential of OT as a bioelectricity-stimulating and chemopreventive agent, warranting further in vitro and in vivo validation. Full article

The SARS-CoV-2 spike receptor-binding motif is crucial for viral entry via interaction with the human ACE2 receptor. Mutations N501Y and E484K, found in several variants of concern, impact viral transmissibility and immune escape, but experimental data on their binding effects remain inconsistent. Using isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations, we analyzed the thermodynamic and structural effects of these mutations. ITC confirmed that N501Y increases ACE2 affinity by 2.2-fold, while E484K enhances binding by 5.8-fold. The Beta/Gamma variant (carrying both mutations) showed the strongest affinity, with a 15-fold increase. E484K was enthalpy-driven, while N501Y introduced entropy-driven effects, suggesting hydrophobic interactions and conformational changes. MD simulations revealed distinct binding poses, with Beta/Gamma peptides interacting with a secondary ACE2 site. A strong correlation was found between entropy contributions and hydrophobic contacts. Additionally, a convolutional neural network was used to estimate the free binding energy of these complexes. Our findings confirm that N501Y and E484K enhance ACE2 binding, with the greatest effect when combined, providing insights into SARS-CoV-2 variant evolution and potential therapeutic strategies. Full article

Copper interconnect technology faces limitations due to the electron’s mean free path and electromigration, driving the adoption of cobalt alternatives. This study proposes a novel mechanism to achieve superfilling by tuning the adsorption energy of additive molecules on cobalt surfaces. The adsorption energies of additives are tailored by changing molecular structures with different functional groups. Computational results reveal that carbon–carbon triple bonds critically strengthen adsorption, while ether bonds further enhance binding on distinct cobalt crystallographic planes. Specifically, 1,4-bis(2-hydroxyethoxy)-2-butyne (BEO) containing both triple bonds and ether groups exhibits the highest adsorption energy (−22.62 eV). Replacing ether with hydroxyl groups in 2-butyne-1,4-diol (BOZ) reduces the adsorption energy to −10.39 eV, while eliminating triple bonds in 1,4-butanediol diglycidyl ether (BDE) further decreases it to −8.43 eV. Experimental studies demonstrate that BOZ and BEO preferentially adsorb on the (101) and (110) planes of hexagonal close-packed cobalt (HCP-Co) due to their differential adsorption energies. This selective suppression promotes preferential growth along the densely packed (002) orientation. This leads to a trench-filling process dominated by the most densely packed plane, resulting in better electrical performance. Superfilling is achieved when molecular adsorption energies are in the range of 5–8 eV. The work establishes a functional group design strategy to regulate additive adsorption, enabling crystallographic control for advanced cobalt electrodeposition processes. Full article

Dietary and environmental exposure to aflatoxins via contaminated food items can pose major health challenges to both humans and animals. Studies have reported the coexistence of aflatoxins and other environmental toxins. This emphasizes the urgent need for efficient and effective mitigation strategies for aflatoxins. Previous reports from our laboratory have demonstrated the potency of the green-engineered clays (GECs) on ochratoxin and other toxic chemicals. Therefore, this study sought to investigate the binding and detoxification potential of chlorophyll (CMCH and SMCH) and chlorophyllin (CMCHin and SMCHin)-amended montmorillonite clays for aflatoxin B1 (AFB1). In addition to analyzing binding metrics including affinity, capacity, free energy, and enthalpy, the sorption mechanisms of AFB1 onto the surfaces of engineered clays were also investigated. Computational and experimental studies were performed to validate the efficacy and safety of the clays. CMCH showed the highest binding capacity (Qmax) of 0.43 mol/kg compared to the parent clays CM (0.34 mol/kg) and SM (0.32 mol/kg). Interestingly, there were no significant changes in the binding capacity of the clays at pH2 and pH6, suggesting that the clays can bind to AFB1 throughout the gastrointestinal track. In silico investigations employing molecular dynamics simulations also demonstrated that CMCH enhanced AFB1 binding as compared to parent clay and predicted hydrophobic interactions as the main mode of interaction between the AFB1 and CMCH. This was corroborated by the kinetic results which indicated that the interaction was best defined by chemosorption with favorable thermodynamics and Gibbs free energy (∆G) being negative. In vitro experiments in Hep G2 cells showed that clay treatment mitigated AFB1-induced cytotoxicity, with the exception of 0.5% (w/v) SMCH. Finally, the in vivo results validated the protection of all the clays against AFB1-induced toxicities in Hydra vulgaris. This study showed that these clays significantly detoxified AFB1 (86% to 100%) and provided complete protection at levels as low as 0.1%, suggesting that they may be used as AFB1 binders in feed and food. Full article

The mineralocorticoid receptor (MR) is a steroid hormone receptor that plays a key role in regulating sodium and water homeostasis and blood pressure. MR antagonists are a guideline recommended for therapy for the treatment of hypertension and cardiovascular disease but can cause hyperkalaemia. Modelling was performed for binding of the endogenous ligands aldosterone and cortisol and MR antagonist spironolactone to the ligand binding domain (LBD) of the MR. A molecular docking screen of compounds that were structurally similar to known antagonists was performed, leading to the identification of two novel compounds, C79 and E67. Molecular dynamics (MD) assessed the dynamic interactions with C79, E76, endogenous ligands, and spironolactone with the MR ligand binding domain (LBD). Analysis of the protein backbone showed modest changes in the overall structure of the MR LBD in response to binding of antagonists, with movement in helix 12 consistent with previous observations. All ligands tested maintained stable binding within the MR LBD throughout the simulations. Hydrogen bond formation played a more prominent role in the binding of endogenous ligands compared to antagonists. MM-PBSA binding free energy calculations showed that all ligands had similar binding affinities, with binding facilitated by key residues within the binding site. The novel antagonists demonstrated similar binding properties to spironolactone, warranting further evaluation. This study provides insights into the molecular mechanisms of MR activation and inhibition, which can aid in the development of novel therapeutic strategies for cardiovascular diseases. Full article

The liver plays a crucial role in maintaining lipid homeostasis by converting toxic free fatty acids into VLDL, which the body uses for energy. Even minor changes in VLDL formation and secretion can result in serious health conditions such as atherosclerosis and non-alcoholic fatty liver disease. Despite the importance of VLDL, the proteins and signaling pathways involved in its regulation remain largely unknown. This study aims to develop a novel methodology to study intracellular VLDL transport events and explore the role of liver fatty acid-binding protein (LFABP) in VLDL transport and secretion. Current methods to study VLDL are often tedious, time-consuming, and expensive, underscoring the need for an alternative approach. We designed a new immunofluorescence-based assay to track the formation and secretion of VLDL in cells over time using fluorescently tagged TopFluor oleic acid. Confocal microscopy confirmed that TopFluor oleic acid enters hepatocytes and colocalizes with the ER, Golgi, and plasma membrane. Additionally, the collection of cell culture media revealed that TopFluor was incorporated into VLDL particles, as confirmed by fluorescence readings and ApoB100 immunoblots. This novel assay provides a valuable tool for further research into the mechanisms of VLDL regulation and the development of potential therapeutic targets for related diseases. Utilizing this assay, we identified LFABP as a key regulatory protein in post-Golgi VLDL trafficking. Our data suggest that LFABP plays a crucial role in this process, and its functional impairment leads to reduced VLDL secretion. Full article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continually undergoes mutation, leading to variants with altered pathogenicity and transmissibility. The Omicron variant (B.1.1.529), first identified in South Africa in 2021, has become the dominant strain worldwide. It harbors approximately 50 mutations compared to the original strain, with 15 located in the receptor-binding domain (RBD) of the spike protein that facilitates viral entry via binding to the human angiotensin-converting enzyme 2 (ACE2) receptor. How do these mutated residues modulate the intermolecular interactions and binding affinity between the RBD and ACE2? This is a question of great theoretical importance and practical implication. In this study, we employed quantum chemical calculations at the B2PLYP-D3/def2-TZVP level of theory to investigate the molecular determinants governing Omicron’s ACE2 interaction. Comparative analysis of the Omicron and wild-type RBD–ACE2 interfaces revealed that mutations including S477N, Q493R, Q498R, and N501Y enhance binding through the formation of bifurcated hydrogen bonds, π–π stacking, and cation–π interactions. These favorable interactions counterbalance such destabilizing mutations as K417N, G446S, G496S, and Y505H, which disrupt salt bridges and hydrogen bonds. Additionally, allosteric effects improve the contributions of non-mutated residues (notably A475, Y453, and F486) via structural realignment and novel hydrogen bonding with ACE2 residues such as S19, leading to an overall increase in the electrostatic and π-system interaction energy. In conclusion, our findings provide a mechanistic basis for Omicron’s increased infectivity and offer valuable insights for the development of targeted antiviral therapies. Moreover, from a methodological perspective, we directly calculated mutation-induced binding energy changes at the residue level using advanced quantum chemical methods rather than relying on the indirect decomposition schemes typical of molecular dynamics-based free energy analyses. The strong correlation between calculated energy differences and experimental deep mutational scanning (DMS) data underscores the robustness of the theoretical framework in predicting the effects of RBD mutations on ACE2 binding affinity. This demonstrates the potential of quantum chemical methods as predictive tools for studying mutation-induced changes in protein–protein interactions and guiding rational therapeutic design. Full article