Search Results (2,521)

Angiogenesis plays a pivotal role in the growth, survival, and metastasis of solid tumors, with Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) being overexpressed in many human solid tumors, making it an appealing target for anti-cancer therapies. This study aimed to identify potential lead compounds with azole moiety exhibiting VEGFR-2 inhibitory effects. A ligand-based pharmacophore model was constructed using the X-ray crystallographic structure of VEGFR-2 complexed with tivozanib (PDB ID: 4ASE) to screen the ZINC15 database. Following virtual screening, six compounds demonstrated promising docking scores and drug-likeness comparable to tivozanib. These hits underwent detailed pharmacokinetic analysis to assess their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Furthermore, Density Functional Theory (DFT) analysis was employed to investigate the molecular orbital properties of the top hits from molecular docking. Molecular dynamics (MD) simulations were conducted to evaluate the conformational stability of the complexes over a 100 ns run. Results indicated that the compounds (ZINC8914312, ZINC8739578, ZINC8927502, and ZINC17138581) exhibited the most promising lead requirements for inhibiting VEGFR-2 and suppressing angiogenesis in cancer therapy. This integrated approach, combining pharmacophore modeling, molecular docking, ADMET studies, DFT analysis, and MD simulations, provides valuable insights into the identification of potential anti-cancer agents targeting VEGFR-2. Full article

This study presents a molecular dynamics (MD) investigation of the evolution of local atomic environments (LAEs) in a Cu₆₆Zr₃₄ bulk metallic glass (BMG), both at rest and under constant shear deformation. LAEs were characterized using Voronoi polyhedra analysis. Even in the absence of external load, LAEs frequently transformed into one another due to short-ranged atomic position fluctuations. However, as expected, each transition from one polyhedra to another was balanced by the reverse transition, thereby preserving the proportions of the different polyhedra. Cu-centered icosahedral LAEs were observed to preferentially transform into and from <1,0,9,3,0>, <0,1,10,2,0>, and <0,2,8,2,0> LAEs. Upon applying pure shear, the simulation box was first deformed in one direction up to a strain of 25% and then in the opposite direction to the same strain level. Shear deformation induced large nonaffine atomic displacements in the directions parallel to the shear, which were concentrated in specific regions of the BMG, forming band-like regions. From the onset, shear deformation led to the destabilization of Cu-centered icosahedral LAEs, as indicated by more frequent transitions to and from other polyhedra. Unlike other Cu-centered LAEs, icosahedra were also found to be more sensitive to yielding. The destruction of Cu-centered icosahedra was primarily a result of net transformations into <1,0,9,3,0> and <0,2,8,2,0> LAEs in the BMG subjected to pure shear, with a minor contribution of transformations involving the <0,1,10,2,0> polyhedra. Full article

The increasing prevalence of metabolic diseases, including nonalcoholic fatty liver disease (NAFLD), obesity, and type 2 diabetes, poses significant global health challenges. Ketohexokinase (KHK), an enzyme crucial in fructose metabolism, is a potential therapeutic target due to its role in these conditions. This study focused on the discovery of selective KHK inhibitors using in silico methods. We employed structure-based drug design (SBDD) and ligand-based drug design (LBDD) approaches, beginning with molecular docking to identify promising compounds, followed by induced-fit docking (IFD), molecular mechanics generalized Born and surface area continuum solvation (MM-GBSA), and molecular dynamics (MD) simulations to validate binding affinities. Additionally, shape-based screening was conducted to assess structural similarities. The findings highlight several potential inhibitors with favorable ADMET profiles, offering promising candidates for further development in the treatment of fructose-related metabolic disorders. Full article

This study focuses on optimizing the storage capacity of an underground natural gas storage facility through numerical modeling and simulation techniques. The reservoir, characterized by an elongated dome structure, was discretized into approximately 16,000 cells. Simulations were conducted using key parameters such as permeability (10–70 mD) and porosity (12–26%) to assess the dynamics of gas injection and pressure distribution. The model incorporated core and petrophysical data to accurately represent the reservoir’s behavior. By integrating new wells in areas with storage deficits, the model demonstrated improvements in storage efficiency and pressure uniformity. The introduction of additional wells led to a significant increase in storage volume from 380 to 512 million Sm³ and optimized the injection process by reducing the storage period by 25%. The study concludes that reservoir performance can be enhanced with targeted well placement and customized flow rates, resulting in both increased storage capacity and economic benefits. Full article

The majority of materials used for membrane-based separation of gas mixtures are non-renewable and non-biodegradable, and the assessment of alternative bio-based polymers requires expensive and time-consuming experimental campaigns. This effort can be reduced by adopting suitable modelling approaches. In this series of works, we propose various modelling approaches to assess the CO₂/CH₄ separation performance of eight different copolymers of 3-hydroxybutyrate and 3-hydroxyvalerate (PHBV) using a limited amount of experimental data for model calibration. In part 1, we adopted a fully atomistic approach based on Molecular Dynamics (MD), while, in this work, we propose a multiscale methodology where a molecular description of the polymers is bridged to a macroscopic prediction of its gas sorption behaviour. PHBV structures were simulated using MD to obtain pressure–volume–temperature data, which were used to parametrise the Sanchez–Lacombe Equation of State. This, in turn, allows for the evaluation of the CO₂ and CH₄ solubility in the copolymers at various pressures and compositions with little computational effort, enabling the estimate of the sorption-based selectivity. The gas separation performance obtained with this multiscale technique was compared to results obtained with a fully atomistic model and experimental data. The solubility–selectivity for the CO₂/CH₄ mixture is in reasonable agreement between the two models and the experimental data. The multiscale method presented is a time-efficient alternative to fully atomistic methods and detailed experimental campaigns and can accelerate the introduction of renewable materials in different applications. Full article

There are enormous differences in benzo[a]pyrene (BaP) acute toxicity tests on Daphnia magna, according to previous publications. The explanations of the reasons for this extreme variation are necessary. In this context, the acute toxicity tests of different experiment conditions (light/dark, culture medium, and solvent) were conducted on Daphnia magna with BaP as the toxicant of concern. Based on the experiments above, molecular dynamics (MD) simulations were employed to investigate the mechanisms of action. According to our results, the significant influence of light exposure on the acute toxicity test of BaP (p < 0.05) on D. magna was recorded. On the basis of the MD simulations, it was possible that BaP may not affect the normal operation of Superoxide Dismutase and Catalase directly, and it could be quickly transferred from the body through Glutathione S-transferase and Cytochromes P450. Therefore, when exposed to light, the oxidative stress process intensifies, causing damage to Daphnia magna. Apparently, the ecotoxicity tests based on inhibition for D. magna cannot adequately reflect the toxic effects of BaP. Full article

Amyloid β protein (Aβ) deposition has been implicated as the molecular driver of Alzheimer’s disease (AD) progression. The modulation of the formation of abnormal aggregates and their post-translational modification is strongly suggested as the most effective approach to anti-AD. Beta-site APP-cleaving enzyme 1 (BACE1) acts upstream in amyloidogenic processing to generate Aβ, which rapidly aggregates alone or in combination with acetylcholinesterase (AChE) to form fibrils. Accumulated Aβ promotes BACE1 activation via glycogen synthase kinase-3β (GSK-3β) and is post-translationally modified by glutaminyl cyclase (QC), resulting in increased neurotoxicity. A novel multi-target inhibitor as a potential AD agent was identified using an in silico approach and experimental validation. Magnolia officinalis, which showed the best anti-AD activity in our preliminary study, was subjected to analysis, and 82 compounds were studied. Among 23 compounds with drug-likeness, blood–brain barrier penetration, and safety, honokiol emerged as a lead structure for the inhibition of BACE1, AChE, QC, and GSK-3β in docking and molecular dynamics (MD) simulations. Furthermore, honokiol was found to be an excellent multi-target inhibitor of these enzymes with an IC₅₀ of 6–90 μM, even when compared to other natural single-target inhibitors. Taken together, the present study is the first to demonstrate that honokiol acts as a multiple enzyme inhibitor with an excellent pharmacokinetic and safety profile which may provide inhibitory effects in broad-range areas including the overproduction, aggregation, and post-translational modification of Aβ. It also provides insight into novel structural features for the design and discovery of multi-target inhibitors for anti-AD. Full article

The clean and efficient utilization of coal is a promising way to achieve carbon neutrality. Coking coal is a scarce resource and an important raw material in the steel industry. However, the presence of pyrite sulfur affects its clean utilization. Nonetheless, this pyrite could be removed using depressants during flotation. Commonly used organic depressants (sodium lignosulfonate (SL), calcium lignosulfonate (CL), and pyrogallol (PY)) and inorganic depressants (calcium oxide (CaO) and calcium hypochlorite (Ca(ClO)₂)) were chosen in this study. Their inhibition mechanism was discussed using FTIR, XPS, and molecular dynamics (MD) methods. The desulfurization ability of organic depressants was shown to be better than inorganic ones. Among the organic depressants, PY proved to be advantageous in terms of low dosage. Physical adsorption was identified as the main interaction form of SL, CL, and PY onto the surface of pyrite, as evidenced from FTIR and XPS analyses. Similarly, MD simulation results showed that hydrogen bonds played a proactive role in the interactions between PY and pyrite. The diffusion coefficient of water molecules on the pyrite surface was also observed to decrease when organic depressants were present, indicating an increase in the hydrophilicity of pyrite. This research is of great significance to utilize sulfur-containing coal and minerals. Full article

This study characterized the binding mechanisms of the lectin cMoL (from Moringa oleifera seeds) to carbohydrates using spectroscopy and molecular dynamics (MD). The interaction with carbohydrates was studied by evaluating lectin fluorescence emission after titration with glucose or galactose (2.0–11 mM). The Stern–Volmer constant (Ksv), binding constant (Ka), Gibbs free energy (∆G), and Hill coefficient were calculated. After the urea-induced denaturation of cMoL, evaluations were performed using fluorescence spectroscopy, circular dichroism (CD), and hemagglutinating activity (HA) evaluations. The MD simulations were performed using the Amber 20 package. The decrease in Ksv revealed that cMoL interacts with carbohydrates via a static mechanism. The cMoL bound carbohydrates spontaneously (ΔG < 0) and presented a Ka on the order of 10², with high selectivity for glucose. Protein–ligand complexes were stabilized by hydrogen bonds and hydrophobic interactions. The Hill parameter (h~2) indicated that the binding occurs through the cMoL dimer. The loss of HA at urea concentrations at which the fluorescence and CD spectra indicated protein monomerization confirmed these results. The MD simulations revealed that glucose bound to the large cavity formed between the monomers. In conclusion, the biotechnological application of cMoL lectin requires specific methods or media to improve its dimeric protein structure. Full article

PHOTH-graphene is a newly predicted 2D carbon material with a low-energy structure. However, its mechanical stability and fracture properties are still elusive. The mechanical stability, elastic, and fracture properties of PHOTH-graphene were investigated using classical molecular dynamics (MD) simulations equipped with REBO potential in this study. The influence of orientation and temperature on mechanical properties was evaluated. Specifically, the Young’s modulus, toughness, and ultimate stress and strain varied by −26.14%, 36.46%, 29.04%, and 25.12%, respectively, when comparing the armchair direction to the zigzag direction. The percentage reduction in ultimate stress, ultimate strain, and toughness of the material in both directions after a temperature increase of 1000 K (from 200 K to 1200 K) ranged from 56.69% to 91.80%, and the Young’s modulus was reduced by 13.63% and 7.25% in both directions, respectively, with Young’s modulus showing lower sensitivity. Defects usually weaken the material’s strength, but adding random point defects in the range of 3% to 5% significantly increases the ultimate strain of the material. Furthermore, hydrogen atom adsorption induces crack expansion to occur earlier, and the crack tip without hydrogen atom adsorption just began to expand when the strain was 0.135, while the crack tip with hydrogen atom adsorption had already undergone significant expansion. This study provides a reference for the possible future practical application of PHOTH-graphene in terms of mechanical properties and fracture failure. Full article

Dengue (DENV) and Zika (ZIKV) virus continue to pose significant challenges globally due to their widespread prevalence and severe health implications. Given the absence of effective vaccines and specific therapeutics, targeting the highly conserved NS5 RNA-dependent RNA polymerase (RdRp) domain has emerged as a promising strategy. However, limited efforts have been made to develop inhibitors for this crucial target. In this study, we employed an integrated in silico approach utilizing combinatorial chemistry, docking, molecular dynamics simulations, MM/GBSA, and ADMET studies to target the allosteric N-pocket of DENV3-RdRp and ZIKV-RdRp. Using this methodology, we designed lycorine analogs with natural S-enantiomers (LYCS) and R-enantiomers (LYCR) as potential inhibitors of non-structural protein 5 (NS5) in DENV3 and ZIKV. Notably, 12 lycorine analogs displayed a robust binding free energy (<−9.00 kcal/mol), surpassing that of RdRp-ribavirin (<−7.00 kcal/mol) along with promising ADMET score predictions (<4.00), of which (LYCR728-210, LYCS728-210, LYCR728-212, LYCS505-214) displayed binding properties to both DENV3 and ZIKV targets. Our research highlights the potential of non-nucleoside lycorine-based analogs with different enantiomers that may present different or even completely opposite metabolic, toxicological, and pharmacological profiles as promising candidates for inhibiting NS5-RdRp in ZIKV and DENV3, paving the way for further exploration for the development of effective antiviral agents. Full article

This work employs a multiscale simulation framework to systematically explore the spallation behavior of ductile tantalum (Ta) subjected to high strain rate impacts. The approach integrates macroscopic simulations, utilizing both the Lagrangian mesh and Smoothed Particle Hydrodynamics (SPH) methods, with microscopic molecular dynamics (MD) simulations to dissect the dynamic failure processes of tantalum. The macroscopic simulations, validated against experimental data, demonstrate the effectiveness of the SPH method in accurately capturing the spallation process. An exponential correlation between spallation strength and tensile strain rate has been established. An in-depth analysis of the free surface velocity profile indicates that the pullback signal is associated with microvoid nucleation, where the velocity drop signifies the initiation conditions for microvoid development. Additionally, the rebound rate following the pullback signal reflects the progression of damage within the spallation region. By integrating results across macro- and microscales, this work offers comprehensive insights into the complex spallation behavior of ductile tantalum under extreme conditions, advancing the understanding of its failure mechanisms at high strain rates. Full article

Alzheimer’s disease (AD) is an age-associated neurodegenerative condition marked by amyloid plaques, synaptic dysfunction, and neuronal loss. Besides conventional medical care, herbal therapies, both raw and refined, have attracted researchers for their potential therapeutic effects. As a proof-of-concept, our study combined HPLC-DAD analysis of bioactive constituents, network pharmacology, molecular dynamics (MD), molecular docking, post-MD analysis, and experimental verification to investigate the mechanisms of crude drug formulations as a therapeutic strategy for AD. We identified nine bioactive compounds targeting 188 proteins and 1171 AD-associated genes. Using a Venn diagram, we found 47 overlapping targets, forming “herb-compound-target (HCT)” interaction networks and a protein‒protein interaction (PPI) network. Simulations analyzed binding interactions among the three core targets and their compounds. MD assessed the stability of the best-ranked poses and beneficial compounds for each protein. Among the top 22 hub genes, AChE, BChE, and MAO, ranked 10, 14, and 34, respectively, were selected for further analysis. Two tetraherbal formulations, Form A and Form B, showed notable activity against AChE. Form A exhibited significant (p < 0.0001) inhibitory activity (IC50 = 114.842 ± 2.084 µg/mL) compared to Form B (IC50 = 142.829 ± 4.258 µg/mL), though weaker than galantamine (IC50 = 27.950 ± 0.122 µg/mL). Form B had significant inhibitory effects on BChE (IC50 = 655.860 ± 32.812 µg/mL) compared to Form A (IC50 = 679.718 ± 20.656 µg/mL), but lower than galantamine (IC50 = 23.126 ± 0.683 µg/mL). Both forms protected against Fe2+-mediated brain injury by inhibiting MAO. Docking identified quercetin (−10.2 kcal/mol) and myricetin (−10.1 kcal/mol) for AChE; rutin (−10.6 kcal/mol) and quercetin (−9.7 kcal/mol) for BChE; and kaempferol (−9.1 kcal/mol) and quercetin (−8.9 kcal/mol) for MAO. These compounds were thermodynamically stable based on MD analysis. Collectively, the results offer a scientific rationale for the use of these specifically selected medicinal herbs as AD medications. Full article

Human serum albumin (HSA) is an endogenous inhibitor of angiotensin I-converting enzyme (ACE) and, thus, plays a key role in the renin–angiotensin–aldosterone system (RAAS). However, little is known about the mechanism of interaction between these proteins, and the structure of the HSA–ACE complex has not yet been obtained experimentally. The purpose of the presented work is to apply computer modeling methods to study the interaction of HSA with ACE in order to obtain preliminary details about the mechanism of their interaction. Ten possible HSA–ACE complexes were obtained by the procedure of macromolecular docking. Based on the number of steric and polar contacts between the proteins, three leading complexes were selected, the stabilities of which were then tested by molecular dynamics (MD) simulation. Based on the results of MD simulation, the two most probable conformations of the HSA–ACE complex were selected. The analysis of these conformations revealed that the processes of oxidation of the thiol group of Cys34 of HSA and the binding of albumin to ACE can reciprocally affect each other. Known point mutations in the albumin molecules Glu82Lys, Arg114Gly, Glu505Lys, Glu565Lys and Lys573Glu can also affect the interaction with ACE. According to the result of MD simulation, the known ACE mutations, albeit associated with various diseases, do not affect the HSA–ACE interaction. A comparative analysis was performed of the resulting HSA–ACE complexes with those obtained by AlphaFold 3 as well as with the crystal structure of the HSA and the neonatal Fc receptor (FcRn) complex. It was found that domains DI and DIII of albumin are involved in binding both ACE and FcRn. The obtained results of molecular modeling outline the direction for further study of the mechanisms of HSA–ACE interaction in vitro. Information about these mechanisms will help in the design and improvement of pharmacotherapy aimed at modulation of the physiological activity of ACE. Full article

A series of edaravone derivatives and the corresponding Cu(II) complexes were synthesized and characterized using spectroscopic and analytical techniques such as IR, UV, NMR and elemental analysis. Antioxidant activities of all compounds were examined using free radical scavenging methods such as hydrogen peroxide scavenging activity (HPSA), 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2-2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) assays. All of the tested compounds exhibited good antioxidant activity. Further, the frontier orbital energy levels, as well as various chemical properties, were determined using the density functional theory (DFT) calculations. The MEP maps of all of the derivatives were plotted to identify the nucleophilic and electrophilic reactive sites. Further, binding energies of all of the organic compounds with the protein tyrosinase was investigated to determine their potential anti-melanogenic applications. The selected ligand, L6 was subjected to molecular dynamics simulation analysis to determine the stability of the ligand–protein complex. The MD simulation was performed (150 ns) to estimate the stability of the tyrosinase–L6 complex. Other key parameters, such as, RMSD, RMSF, Rg, hydrogen bonds, SASA and MMPBSA were also analyzed to understand the interaction of L6 with the tyrosinase protein. Full article