Search Results (54)

The increasing emission of harmful gases into the atmosphere represents a major environmental challenge, driving the need for efficient air purification materials. Poly(methyl methacrylate) (PMMA) has emerged as a promising candidate due to its favorable physicochemical properties and adsorption potential. In this study, the interactions between PMMA and selected sulfur-containing pollutants (CH₃SH, COS, CS₂, H₂S, and SO₂) were systematically investigated using a multiscale computational approach. Initial structural exploration was performed using extended tight-binding (xTB) methods, followed by refinement at the density functional theory (DFT) level, while molecular dynamics (MD) simulations were employed to capture the dynamic behavior of the systems. The results suggest that all investigated gases exhibit attractive interactions with PMMA, with interaction strength strongly dependent on molecular polarity and electronic structure. Among the studied systems, SO₂ shows the strongest binding, while CS₂ exhibits the weakest interaction. Energy decomposition based on symmetry-adapted perturbation theory (SAPT) and electronic structure analyses suggest that electrostatic and donor–acceptor interactions play a dominant role for strongly interacting systems, whereas weaker interactions are primarily governed by dispersion forces. Full article

Background/Objectives: Microtubule-targeting agents remain foundational components of anticancer chemotherapy, yet their clinical utility is constrained by resistance and toxicity. Methods: Here, we present a theoretical exploration of a plausible “dual” binding pocket that spans the α-tubulin pironetin site and the inter-subunit todalam site. Eight virtual chimeric ligands, each merging key pharmacophoric elements of pironetin and todalam, were constructed and covalently docked to Cys316 of α-tubulin. Results: Covalent docking followed by 200 ns all-atom molecular dynamics simulations revealed that two derivatives (compounds 4 and 8) stably occupy the merged cavity, simultaneously anchoring in the pironetin region via Michael addition and in the todalam region via π-stacking and hydrogen bonding. These hybrids preserved the critical hydrogen-bonding networks of both parent ligands and exhibited low ligand RMSD values (~1.5 Å) and compact radii of gyration throughout the simulations, indicating a tight, persistent binding. Estimated HYDE affinities of 1.5 µM for compound 4 and 17.6 µM for compound 8, calculated with SeeSAR, suggest that covalent engagement can compensate for moderate non-covalent binding scores. Conclusions: In summary, our results provide compelling grounds for developing a new class of α-tubulin inhibitors that engage the hybrid pocket, laying a foundation for the structure-guided synthesis of first-in-class dual-site compounds capable of overcoming resistance to conventional microtubule-targeting drugs. Full article

Pharmacotherapy in the geriatric population is one of the greatest challenges in modern medicine. Elderly patients, characterized by multimorbidity and the resulting polypharmacy, are significantly more exposed to adverse drug reactions (ADRs), which often lead to hospitalization and a decline in quality of life. Understanding the reasons for this difference requires an analysis of the physiological changes that occur during the aging process at the molecular level. This article presents a perspective on the molecular aspects of geriatric pharmacotherapy, focusing on the fundamental mechanisms that are modified with age. The analysis covers changes in pharmacokinetics, including the role and regulation of cytochrome P450 (CYP) enzymes, whose activity, especially in phase I reactions, is significantly reduced. The age-dependent dysfunction of drug transporters from the ABC (ATP-binding cassette) and SLC (solute carrier) families in key organs such as the intestines, liver and kidneys is discussed, which affects the absorption, distribution and elimination of xenobiotic compounds, including drugs. The article also provides a comprehensive analysis of the blood–brain barrier (BBB), describing changes in neurovascular integrity, including the dysfunction of tight junctions and a decrease in the activity of P-glycoprotein, sometimes referred to as multidrug resistance protein (MDR). This increases the susceptibility of the central nervous system to the penetration and action of drugs. In the realm of pharmacodynamics, changes in the density and sensitivity of key receptors (serotonergic, dopaminergic, adrenergic) are described based on neuroimaging data, explaining the molecular basis for increased sensitivity to certain drug classes, such as anticholinergics. The paper also explores new research perspectives, such as the role of the gut microbiome in modulating pharmacokinetics by influencing gene expression and the importance of pharmacoepigenetics, which dynamically regulates drug response throughout life via changes in DNA methylation and histone modifications. The clinical implications of these molecular changes are also discussed, emphasizing the potential of personalized medicine, including pharmacogenomics, in optimizing therapy and minimizing the risk of adverse reactions. Such an integrated approach, incorporating data from multiple fields (genomics, epigenomics, microbiomics) combined with a comprehensive geriatric assessment, appears to be the future of safe and effective pharmacotherapy in the aging population. Full article

The study of the gas-phase behavior of proteins has recently gained momentum due to numerous prospective applications in, e.g., the construction of molecular sensors or nano-machines. The study of proteins outside their standard water environment, necessary to arrive at their successful applied use, is, however, limited by the loss of the structure and function of the macromolecules in the gas phase. We selected two enzymatic proteins with great potential for applied use, the digestive enzyme trypsin and the cytochrome sterol demethylase, for which to develop gas-phase structural models. The employed levels of theory were semiempirical, density functional tight binding, and polarizable force-field techniques. The convergence of the self-consistent field equations was very slow and in most cases led to oscillatory behavior, encouraging careful tuning of the convergence parameters. The structural optimization and molecular dynamics simulations indicated the parts of the proteins most prone to structural distortion under gas-phase conditions with unscreened electrostatics. This problem was more pronounced for cationic trypsin, for which the stability of the simulation was lower. The fate of the hydrogen bonding network of the catalytic triad in the gas phase was also investigated. Full article

The main protease (M^pro or 3CL^pro or nsp5) of SARS-CoV-2 is crucial to the life cycle and pathogenesis of SARS-CoV-2, making it an attractive drug target to develop antivirals. This study employed the virtual screening of a few phytochemicals, and the resultant best compound, Scopoletin, was further investigated by a FRET-based enzymatic assay, revealing an experimental IC₅₀ of 15.75 µM. The impact of Scopoletin on M^pro was further investigated by biophysical and MD simulation studies. Fluorescence spectroscopy identified a strong binding constant of 3.17 × 10⁴ M⁻¹ for Scopoletin binding to M^pro, as demonstrated by its effective fluorescence quenching of M^pro. Additionally, CD spectroscopy showed a significant reduction in the helical content of M^pro upon interaction with Scopoletin. The findings of thermodynamic measurements using isothermal titration calorimetry (ITC) supported the spectroscopic data, indicating a tight binding of Scopoletin to M^pro with a K_A of 2.36 × 10³ M⁻¹. Similarly, interaction studies have also revealed that Scopoletin forms hydrogen bonds with the amino acids nearest to the active site, and this has been further supported by molecular dynamics simulation studies. These findings indicate that Scopoletin may be developed as a potential antiviral treatment for SARS-CoV-2 by targeting M^pro. Full article

Nanocomposites composed of Cu and Mo were investigated by means of molecular dynamics (MD) simulations to study the incoherent interface between Cu and Mo. In order to select an appropriate potential capable of accurately describing the Cu-Mo system, five many-body potentials were compared: three Embedded Atom Method (EAM) potentials, a Tight Binding Second Moment Approximation (TB-SMA) potential, and a Modified Embedded Atom Method (MEAM) potential. Among these, the EAM potential proposed by Zhou in 2001 was determined to provide the best compromise for the current study. The simulated system was constructed with two layers of Cu and Mo forming an incoherent fcc-Cu(111)/bcc-Mo(110) interface, based on the Nishiyama–Wassermann (NW) and Kurdjumov–Sachs (KS) orientation relationships (OR). The interfacial energies were calculated for each orientation relationship. The NW configuration emerged as the most stable, with an interfacial energy of 1.83 J/m², compared to 1.97 J/m² for the KS orientation. Subsequent simulations were dedicated to modeling Cu atomic deposition onto a Mo(110) substrate at 300 K. These simulations resulted in the formation of a dense layer with only a few defects in the two Cu planes closest to the interface. The interfacial structures were characterized by computing selected area electron diffraction (SAED) patterns. A direct comparison of theoretical and numerical SAED patterns confirmed the presence of the NW orientation relationship in the nanocomposites formed during deposition, corroborating the results obtained with the model fcc-Cu(111)/bcc-Mo(110) interfaces. Full article

The thermal stability of bimetallic nanoparticles plays a crucial role in their performance in applications in catalysis, biotechnology, and materials science. In this study, we employ molecular dynamics simulations to investigate the melting behavior of Au-Pd nanoparticles with cuboctahedral, icosahedral, and decahedral geometries. Using a tight-binding potential, we systematically explore the effects of particle size and composition on the melting transition. Our analysis, based on caloric curves, Lindemann coefficients, and orientational order parameters, reveals distinct premelting behaviors influenced by geometry. Larger particles exhibit a coexistence of a pseudo-crystalline core and a partially melted shell, but, in decahedra and icosahedra, melting of the core occurs unevenly, with twin boundaries promoting the melting of one or two of the tetrahedral subunits before the rest of the particle. Notably, icosahedral nanoparticles display higher thermal stability, while both icosahedral and decahedral structures exhibit localized melting within twin boundaries. Additionally, we generate HAADF-STEM simulations to aid the interpretation of in situ electron microscopy experiments. Full article

Lymphatic malformations (LMs) are benign, congenital vascular anomalies caused by abnormal lymphangiogenesis during embryology, often presenting as fluid-filled cystic lesions. Though LMs can affect any part of the body except the brain, they primarily manifest in the head and neck or axilla regions of children. With a prevalence of approximately 1 in 4000 births, LMs are commonly diagnosed by age two, with symptoms varying based on lesion location and size. This paper reviews the classification of LMs and discusses the de Serres staging system, which aids in assessing prognosis based on lesion site. Mutations in the (PIK3CA) gene are implicated in most cases, and LMs are also associated with syndromic conditions like Turner and Noonan syndromes. They are diagnosed by ultrasound (USS) or magnetic resonance imaging (MRI), while a histologic analysis can confirm lymphatic origin. Treatment options range from conservative approaches, such as observation, to sclerotherapy, pharmacotherapy, and surgery. Sclerotherapy, particularly with agents like OK-432, bleomycin, and doxycycline, has shown significant efficacy in reducing LM size and symptoms with minimal side effects. Pharmacological therapies, such as sirolimus, that target the mTOR pathway are also increasingly being used, with a good effect on the burden of disease. While surgical excision remains a choice for symptomatic or large lesions, minimally invasive approaches are often preferred due to lower morbidity. Emerging techniques include gravity-dependent sclerotherapy, electrosclerotherapy, alpelisib, everolimus, and Wnt/β-catenin pathway stimulators (e.g., tankyrase inhibitors, porcupine inhibitors). Computational atomistic molecular dynamics (MD) and density functional tight binding (DFTB) techniques may offer an experimental approach to future therapeutic targets. This paper highlights a multidisciplinary approach to LM management, emphasising individualised treatment based on lesion characteristics and patient needs. Full article

Bio-based corrosion inhibitor formulations are incredibly promising for mitigating corrosion, offering an environmentally sustainable approach while providing effective protection against material degradation. This study explores the corrosion inhibition potential of Ammi visnaga essential oil (AVEO) on carbon steel (CS) in a 1 mol/L hydrochloric acid (HCl) medium, combining electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), linear polarization resistance (LPR), weight loss (WL) analysis, density functional theory (DFT), density-functional tight-binding (DFTB) modeling, and molecular dynamics (MD) simulation. The AVEO was extracted through hydrodistillation, and its chemical profile was characterized to identify key active compounds. EIS and PDP results revealed that the AVEO effectively inhibited corrosion through the formation of a protective layer on the steel surface, exhibiting inhibition efficiencies of up to 84% at 3 g/L, with a mixed-type corrosion inhibition action. Nyquist plots displayed an increased polarization resistance with the AVEO concentration, indicating an enhanced surface coverage and reduction in active corrosion sites. WL studies further supported these findings, showing decreased corrosion rates proportional to the AVEO concentration, while temperature variation studies showed a decreased performance at higher temperatures. Scanning electron microscope (SEM) analysis supported the formation of an effective protective layer on the CS surface upon the addition of AVEO to the HCl medium. DFTB modeling and MD simulations were employed to evaluate the interaction between major AVEO constituents and the steel surface, providing insight into the adsorption behavior and the electronic contributions at the molecule–metal interface. The combined experimental and theoretical findings indicate that AVEO holds promise as a natural, eco-friendly corrosion inhibitor, with implications for sustainable metal protection in acidic environments. Full article

Aluminum (Al) ion implantation is one of the most important technologies in SiC device manufacturing processes due to its ability to produce the p-type doping effect, which is essential to building p–n junctions and blocking high voltages. However, besides the doping effect, defects are also probably induced by the implantation. Here, the impacts of Al ion implantation-induced defects on 4H-SiC MOSFET channel transport behaviors are studied using a multiscale simulation flow, including the molecular dynamics (MD) simulation, density functional theory (DFT) calculation, and tight-binding (TB) model-based quantum transport simulation. The simulation results show that an Al ion can not only replace a Si lattice site to realize the p-doping effect, but it can also replace the C lattice site to induce mid-gap trap levels or become an interstitial to induce the n-doping effect. Moreover, the implantation tends to bring additional point defects to the 4H-SiC body region near the Al ions, which will lead to more complicated coupling effects between them, such as degrading the p-type doping effect by trapping free hole carriers and inducing new trap states at the 4H-SiC bandgap. The quantum transport simulations indicate that these coupling effects will impede local electron transports, compensating for the doping effect and increasing the leakage current of the 4H-SiC MOSFET. In this study, the complicated coupling effects between the implanted Al ions and the implantation-induced point defects are revealed, which provides new references for experiments to increase the accepter activation rate and restrain the defect effect in SiC devices. Full article

Connexins (Cxs) are a family of integral membrane proteins, which function as both hexameric hemichannels (HCs) and dodecameric gap junction channels (GJCs), behaving as conduits for the electrical and molecular communication between cells and between cells and the extracellular environment, respectively. Their proper functioning is crucial for many processes, including development, physiology, and response to disease and trauma. Abnormal GJC and HC communication can lead to numerous pathological states including inflammation, skin diseases, deafness, nervous system disorders, and cardiac arrhythmias. Over the last 15 years, high-resolution X-ray and electron cryomicroscopy (cryoEM) structures for seven Cx isoforms have revealed conservation in the four-helix transmembrane (TM) bundle of each subunit; an αβ fold in the disulfide-bonded extracellular loops and inter-subunit hydrogen bonding across the extracellular gap that mediates end-to-end docking to form a tight seal between hexamers in the GJC. Tissue injury is associated with cellular Ca²⁺ overload. Surprisingly, the binding of 12 Ca²⁺ ions in the Cx26 GJC results in a novel electrostatic gating mechanism that blocks cation permeation. In contrast, acidic pH during tissue injury elicits association of the N-terminal (NT) domains that sterically blocks the pore in a “ball-and-chain” fashion. The NT domains under physiologic conditions display multiple conformational states, stabilized by protein–protein and protein–lipid interactions, which may relate to gating mechanisms. The cryoEM maps also revealed putative lipid densities within the pore, intercalated among transmembrane α-helices and between protomers, the functions of which are unknown. For the future, time-resolved cryoEM of isolated Cx channels as well as cryotomography of GJCs and HCs in cells and tissues will yield a deeper insight into the mechanisms for channel regulation. The cytoplasmic loop (CL) and C-terminal (CT) domains are divergent in sequence and length, are likely involved in channel regulation, but are not visualized in the high-resolution X-ray and cryoEM maps presumably due to conformational flexibility. We expect that the integrated use of synergistic physicochemical, spectroscopic, biophysical, and computational methods will reveal conformational dynamics relevant to functional states. We anticipate that such a wealth of results under different pathologic conditions will accelerate drug discovery related to Cx channel modulation. Full article

Malaria is one of the infectious illnesses causing a public health burden worldwide. Plasmodium vivax (P. vivax) is the most prevalent malaria parasite in Asia and Asia Pacific. P. vivax is resistant to sulfadoxine–pyrimethamine (SP) and mefloquine. This resistance makes it extremely difficult to control and eradicate due to its ability to survive in the liver and reactivate if the person infected has a weakened immune system. Thus, this study aims to inhibit P. vivax via targeting Duffy-binding protein (DBP) with active compounds from Hops (Humulus lupulus). The inhibition of DBP is essential to reduce malaria invasion of human red blood cells. We performed a quality assessment and prediction of the active site of DBP to determine the effectiveness and prediction of ligands in inhibiting DBP. Furthermore, the mechanism and structural stability of active compounds against DBP were evaluated using a combination of molecular docking and molecular dynamics simulation and a density-functional theory (DFT) study. The results showed that rutin had the highest binding of 8.852 kcal/mol. However, after the molecular dynamics simulation was run for 50 ns, the ligand 6-prenylnaringenin via MM-PBSA calculation showed the most positive value of 106.760 kJ/mol. In addition, 6-prenylnaringenin is the most stable ligand via the analysis of root-mean-square deviation backbone (RMSDBb), root-mean-square deviation c-alpha (RMSDCa), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), radius of gyration (Rg), and the hydrogen bond formation. We conclude that 6-prenylnaringenin has a tight and stable bond with the targeted DBP protein. Finally, we propose the use of 6-prenylnaringenin as a potential antimalarial compound via in silico studies. Full article

Mutant isocitrate dehydrogenase 1 (mIDH1) is a common driving factor in acute myeloid leukemia (AML), with the R132 mutation accounting for a high proportion. The U.S. Food and Drug Administration (FDA) approved Ivosidenib, a molecular entity that targets IDH1 with R132 mutations, as a promising therapeutic option for AML with mIDH1 in 2018. It was of concern that the occurrence of disease resistance or recurrence, attributed to the IDH1 R132C/S280F second site mutation, was observed in certain patients treated with Ivosidenib within the same year. Furthermore, it should be noted that most mIDH1 inhibitors demonstrated limited efficacy against mutations at this specific site. Therefore, there is an urgent need to investigate novel inhibitors targeting mIDH1 for combating resistance caused by IDH1 R132C/S280F mutations in AML. This study aimed to identify novel mIDH1 R132C/S280F inhibitors through an integrated strategy of combining virtual screening and dynamics simulations. First, 2000 hits were obtained through structure-based virtual screening of the COCONUT database, and hits with better scores than −10.67 kcal/mol were obtained through molecular docking. A total of 12 potential small molecule inhibitors were identified through pharmacophore modeling screening and Prime MM-GBSA. Dynamics simulations were used to study the binding modes between the positive drug and the first three hits and IDH1 carrying the R132C/S280F mutation. RMSD showed that the four dynamics simulation systems remained stable, and RMSF and Rg showed that the screened molecules have similar local flexibility and tightness to the positive drug. Finally, the lowest energy conformation, hydrogen bond analysis, and free energy decomposition results indicate that in the entire system the key residues LEU120, TRP124, TRP267, and VAL281 mainly contribute van der Waals forces to the interaction, while the key residues VAL276 and CYS379 mainly contribute electrostatic forces. Full article

This study evaluates the corrosion inhibition capabilities of two novel hydrazone derivatives, (E)-2-(5-methoxy-2-methyl-1H-indol-3-yl)-N′-(4-methylbenzylidene)acetohydrazide (MeHDZ) and (E)-N′-benzylidene-2-(5-methoxy-2-methyl-1H-indol-3-yl)acetohydrazide (HHDZ), on carbon steel in a 15 wt.% HCl solution. A comprehensive suite of analytical techniques, including gravimetric analysis, potentiodynamic polarization (PDP), electrochemical impedance spectroscopy (EIS), and scanning electron microscopy (SEM), demonstrates their significant inhibition efficiency. At an optimal concentration of 5 × 10⁻³ mol/L, MeHDZ and HHDZ achieve remarkable inhibition efficiencies of 98% and 94%, respectively. EIS measurements reveal a dramatic reduction in effective double-layer capacitance (from 236.2 to 52.8 and 75.3 µF/cm²), strongly suggesting inhibitor adsorption on the steel surface. This effect is further corroborated by an increase in polarization resistance and a significant decrease in corrosion current density at optimal concentrations. Moreover, these inhibitors demonstrate sustained corrosion mitigation over extended exposure durations and maintain effectiveness even under elevated temperatures, highlighting their potential for diverse operational conditions. The adsorption process of these inhibitors aligns well with the Langmuir adsorption isotherm, implying physicochemical interactions at the carbon steel surface. Density functional tight-binding (DFTB) calculations and molecular dynamics simulations provide insights into the inhibitor-surface interaction mechanism, further elucidating the potential of these hydrazone derivatives as highly effective corrosion inhibitors in acidic environments. Full article

The vibrational dynamics of rutile (TiO₂) as a function of temperature has been studied by combining molecular dynamics (MD) simulations in conjunction with the generalized two-dimensional correlation spectroscopy analysis (2D COS) technique. Molecular dynamics simulations within the microcanonical ensemble were performed with the self-consistent charge density functional tight binding formalism at a series of different temperatures. To validate the DFTB MD results against the experimental data, the method of atomic pair distribution functions (PDFs) was used. IR absorption spectra were calculated implementing the time correlation function formalism. Subsequently, the generalized two-dimensional correlation approach was applied to obtain further insights into the temperature-dependent vibrational dynamics. The static DFTB calculations of the vibrational force field of the rutile reproduced excellently the experimental data and allowed for more exact assignments of the corresponding experimental IR/Raman spectral bands. Through the detailed analysis of the synchronous and asynchronous 2D spectra computed on the basis of MD-generated anharmonic spectra, we have provided new insights into the couplings between the modes in the studied system, as well as into the sequential character of the temperature-induced changes in the vibrational force field. The sensitivity of IR active modes to the temperature-induced perturbation of the system decreases in the order 685 cm⁻¹E_u mode > 370 cm⁻¹E_u mode > 982 cm⁻¹A_2u mode. The results presented in this study clearly demonstrate the usefulness of the combination of periodic SCC DFTB MD simulations coupled to the 2D COS analysis techniques in solid-state vibrational spectroscopy. Full article