Search

Reactive multilayer nanofoils (RMNFs), comprised of alternating layers of metals such as nickel and aluminum, have emerged as a focal point of interest owing to their distinctive properties and versatile applications across semiconductor and micro-electromechanical systems. This nanoengineered material undergoes a self-contained exothermic reaction, initiated by a small external trigger delivering localized heat up to 1500 ℃ in fractions of a second. It can be a heat source material primarily used to make a bond between electric components by melting solders. However, the volume shrinkage during reaction causes void formation and microcracking in the reaction product, and it reduces the reliability of the bonding. In this study, we systematically investigate 11 different Ni–Al RMNFs, including multilayers with 0, 10, 30, 50, 70, and 90% alloyed regions (polycrystalline B2-NiAl or amorphous-NiAl) using molecular dynamic simulations. We found that samples with alloyed interlayers exhibit reduced reaction temperatures and volume shrinkage after the reaction. By controlling the thickness of the alloyed interlayers and structures, we can reduce the damage caused by volume shrinkage during the reaction while obtaining a sufficient reaction temperature. [ABSTRACT FROM AUTHOR]

Seismological studies have exposed numerous ultralow velocity zones (ULVZs) exhibiting extraordinary physical attributes at Earth's core-mantle boundary, yet their compositions and origins remain controversial. Water-iron reaction can generate unique phases under lowermost-mantle conditions and likely plays a crucial role in forming ULVZs. Through first-principles molecular dynamic simulations with machine learning techniques, we determine that iron hydride, the product of water-iron reaction, is stable as a superionic phase at the core-mantle boundary. This superionic iron hydride has much slower velocities and a higher density than the ambient mantle under lowermost-mantle conditions. Accumulation of iron hydride, created through either a chemical reaction between subducted water and iron or solidification of core material entrained in the lower mantle by convection, can explain the seismic observations of ULVZs particularly those associated with subduction. This work suggests that water may have a substantial role in creating seismic heterogeneities at the core-mantle boundary. [ABSTRACT FROM AUTHOR]

The premelting layer on crystal surfaces significantly affects the stability, surface reactivity, and phase transition behaviors of crystals. Traditional methods for studying this layer—experimental techniques, classical simulations, and even first-principle simulations—have significant limitations in accuracy and scalability. To overcome these challenges, we employ molecular dynamic simulations based on neural network potentials to investigate the structural and dynamic behavior of the premelting layer on ice. This approach matches the accuracy of first-principle calculations while greatly improving computational efficiency, allowing us to simulate the ice–vapor interface on a much larger scale. In this study, we conducted a one-nanosecond simulation of the ice–vapor interface involving 1024 water molecules. This significantly exceeds the time and size scales of previous first-principle studies. Our simulation results indicate complete surface melting. Furthermore, our simulation results reveal dynamic heterogeneity within the premelting layer, with molecules segregated into clusters of low and high mobility. [ABSTRACT FROM AUTHOR]

Histone deacetylase 3 (HDAC3) is a member of the histone deacetylase family that has emerged as a crucial target in the quest for novel therapeutic interventions against various complex diseases, including cancer. The repositioning of FDAapproved drugs presents a promising avenue for the rapid discovery of potential HDAC3 inhibitors. In this study, we performed a structure-based virtual screening of FDA-approved drugs obtained from DrugBank. Candidate hits were selected based on their binding affinities and interactions with HDAC3. These promising hits were then subjected to a comprehensive assessment of their biological properties and drug profiles. Our investigation identified two FDA-approved drugs, Imatinib and Carpipramine, characterized by their exceptional affinity and specificity for the binding pocket of HDAC3. These molecules demonstrated a strong preference for HDAC3 binding site and formed interactions with functionally significant residues within the active site pocket. To gain deeper insights into the binding dynamics, structural stability, and interaction mechanisms, we performed molecular dynamics (MD) simulations spanning 300 nanoseconds (ns). The results of MD simulations indicated that Imatinib and Carpipramine stabilized the structure of HDAC3 and induced fewer conformational changes. Taken together, the findings from this study suggest that Imatinib and Carpipramine may offer significant therapeutic potential for treating complex diseases, especially cancer. [ABSTRACT FROM AUTHOR]

Flemingia macrophylla has traditionally been applied to relieve inflammation, diabetes, and circulatory complications. The leaf extract of F. macrophylla and its fractions were investigated for their in-vitro antioxidant and anti-diabetic properties. The phytochemical screening showed valuable phytochemicals, including glycosides, flavonoids, saponins, etc. GC-MS analysis of the phytochemicals in the methanol extract detected 19 bioactive compounds. Among the diverse fractions, the ethyl acetate fraction (EFM) exhibited the highest phenol and flavonoid contents of 557 mg GAE/g and 326 mg QCE/g, respectively. The total antioxidant content of EFM was found to be 292.41±19.16 mg AAE/g, while its antidiabetic study showed the greatest level of α -glucosidase (IC50: 11.27±1.25 µg/mL) and α -amylase (IC50: 10.04±0.63 µg/mL) inhibitory effects. The docking results showed that C6 had the highest binding scores of -9.0, -7.4, and -7.6 kcal/mol against antioxidant (6NGJ), α-glucosidase (5NN5), and α-amylase (4GQR) proteins, respectively. The dynamics simulation disclosed that C6-receptor protein complexes remained stable at the binding pocket under human body conditions and retained their stiff morphology for 100 nanoseconds (ns). ADMET results demonstrated their noncarcinogenic and well-absorbed properties, where PASS prediction data confirmed their efficacy as an antioxidant, antiulcerative, thrombolytic, and antidiabetic. Therefore, F. macrophylla has potential health benefits. [ABSTRACT FROM AUTHOR]

Quercetin is a flavonoid with notable pharmacological effects and promising therapeutic potential. Quercetin plays a significant role in neuroinflammation, which helps reduce Alzheimer's disease (AD) severity. Quercetin (Q) and quercetin 3-O-glucuronide (Q3OG) are some of the most potent antioxidants available from natural sources. However, the natural form of quercetin converted into Q3OG when reacted with intestinal microbes. The study aims to ensure the therapeutic potential of Q and Q3OG. In this study, potential molecular targets of Q and Q3OG were first identified using the Swiss Target Prediction platform and pathogenic targets of AD were identified using the DisGeNET database. Followed by compound and disease target overlapping, 77 targets were placed in that AKT1, EGFR, MMP9, TNF, PTGS2, MMP2, IGF1R, MCL1, MET and PARP1 was the top-ranked target, which was estimated by CytoHubba plug-in. The Molecular docking was performed for Q and Q3OG towards the PDB:1UNQ target. The binding score of Q and Q3OG was − 6.2 kcal/mol and − 6.58 kcal/mol respectively. Molecular dynamics simulation was conducted for Q and Q3OG towards the PDB:1UNQ target at 200 ns. This study's results help identify the multiple target sites for the bioactive compounds. Thus, synthesizing new chemical entity-based quercetin on structural modification may aid in eradicating AD complications. [ABSTRACT FROM AUTHOR]

The primary aim of the current investigation is to contribute to SARS-CoV-2 research by identifying potential lead compounds for clinical applications, with a specific focus on inhibitors targeting the main protease (Mpro). In this research, molecular docking analysis was conducted using the software molecular operating environmental (MOE) to evaluate the potency of bioactive compounds sourced from medicinal plants as inhibitors of SARS--CoV-2 Mpro. Among 118 natural compounds with anti-HIV characteristics, the top seven candidates (h3, h84, h85, h87, h90, h108 and h110), were identified based on their superior binding energies with comparison to the reference ligand N3. These selected compounds exhibited binding affinities of -33.996, -35.336, -32.615, -32.154, -33.452, -31.903 and -40.360 kJ mol-1, respectively. To further refine our shortlist of potential candidates for human application, we examined the drug-likeness, and the pharmaceutical attributes of these compounds using the SwissADME web server. Among them, only two compounds, namely h85 and h87, demonstrated favorable pharmacological properties suitable for human administration. These two compounds were subsequently shortlisted for further investigation. To explore the conformational stability of ligands within the Mpro active site, we performed molecular dynamics (MD) simulations. These simulations showed reliable and steady trajectories, supported by analyses of root-mean-square-fluctuation (RMSF) and root--mean-square deviation (RMSD). These findings and favorable molecular properties as well as interaction profiles suggest that these two lead compounds may be promising SARS-CoV-2 therapeutic candidates. They present exciting starting points for further drug design. [ABSTRACT FROM AUTHOR]

In aqueous and solid media, 2-HP-β/γ-CD inclusion complexes with poly aromatic hydrocarbon (PAH) Phenanthrene (PHN), Anthracene (ANT), Benz(a)pyrene (BaP), and Fluoranthene (FLT) were investigated for the first time. The inclusion complexes were characterized and investigated using fluorescence and 1HNMR spectroscopy. The most prevalent complexes consisting of both guests and hosts were those with a 1:1 guest-to-host ratio. The stability constants for the complexes of PHN with 2-HP-β-CD and 2-HP-γ-CD were 85 ± 12 M−1 and 49 ± 29 M−1, respectively. Moreover, the stability constants were found to be 502 ± 46 M−1 and 289 ± 44 M−1 for the complexes of ANT with both hosts. The stability constants for the complexes of BaP with 2-HP-β-CD and 2-HP-γ-CD were (1.5 ± 0.02) × 103 M−1 and (9.41 ± 0.03) × 103 M−1, respectively. The stability constant for the complexes of FLT with 2-HP-β-CD was (1.06 ± 0.06) × 103 M−1. However, FLT was observed to form a weak complex with 2-HP-γ-CD. Molecular dynamic (MD) simulations were used to investigate the mechanism and mode of inclusion processes, and to monitor the atomic-level stability of these complexes. The analysis of MD trajectories demonstrated that all guests formed stable inclusion complexes with both hosts throughout the duration of the simulation time, confirming the experimental findings. However, the flexible Hydroxypropyl arms prevented the PAHs from being encapsulated within the cavity; however, a stable exclusion complex was observed. The main forces that influenced the complexation included van der Waals interactions, hydrophobic forces, and C–H⋯π interaction, which contribute to the stability of these complexes. [ABSTRACT FROM AUTHOR]

Based on nanoarchitectonics and molecular dynamics simulations, we investigate the structural properties and diffusion pathway of Na atoms in sodium trisilicate over a wide temperature range. The structural and dynamics properties are analyzed through the radial distribution function (RDF), the Voronoi Si- and O-polyhedrons, the cluster function fCL(r), and the sets of fastest (SFA) and slowest atoms (SSA). The results indicate that Na atoms are not placed in Si-polyhedrons and bridging oxygen (BO) polyhedrons; instead, Na atoms are mainly placed in non-bridging oxygen (NBO) polyhedrons and free oxygen (FO) polyhedrons. Here BO, NBO, and FO represent O bonded with two, one, and no Si atoms, respectively. The simulation shows that O atoms in sodium trisilicate undergo numerous transformations: NBF0 ↔ NBF1, NBF1 ↔ NBF2, and BO0 ↔ BO1, where NBF is NBO or FO. The dynamics in sodium trisilicate are mainly distributed by the hopping and cooperative motion of Na atoms. We suppose that the diffusion pathway of Na atoms is realized via hopping Na atoms alone in BO-polyhedrons and the cooperative motion of a group of Na atoms in NBO- and FO-polyhedrons. [ABSTRACT FROM AUTHOR]

Rieske non-heme dioxygenase family enzymes play an important role in the aerobic biodegradation of nitroaromatic pollutants, but no active dioxygenases are available in nature for initial reactions in the degradation of many refractory pollutants like 2,4-dichloronitrobenzene (24DCNB). Here, we report the engineering of hotspots in 2,3-dichloronitrobenzene dioxygenase from Diaphorobacter sp. strain JS3051, achieved through molecular dynamic simulation analysis and site-directed mutagenesis, with the aim of enhancing its catalytic activity toward 24DCNB. The computationally predicted activity scores were largely consistent with the detected activities in wet experiments. Among them, the two most beneficial mutations (E204M and M248I) were obtained, and the combined mutant reached up to a 62-fold increase in activity toward 24DCNB, generating a single product, 3,5-dichlorocatechol, which is a naturally occurring compound. In silico analysis confirmed that residue 204 affected the substrate preference for meta-substituted nitroarenes, while residue 248 may influence substrate preference by interaction with residue 295. Overall, this study provides a framework for manipulating nitroarene dioxygenases using computational methods to address various nitroarene contamination problems. [ABSTRACT FROM AUTHOR]

The manufacturing process for wrought Ti alloys with the hexagonal close-packed (HCP) structure introduces a complicated microstructure with abundant intra- and inter-grain boundaries, which greatly influence performance. In the hexagonal close-packed (HCP) structure, two types of grain boundaries are commonly observed between grains with ~90° misorientation: the basal/prismatic boundary (BPB) and the coherent twin boundary (CTB). The mechanical response of the BPB and CTB under external loading was studied through molecular dynamic simulations of HCP-Ti. The results revealed that CTB undergoes transformation into BPB through the accumulation of twin boundary (TB) steps and subsequent emission of Shockley partial dislocations. When the total mismatch vector is close to the Burgers vector of a Shockley partial dislocation, BPB emits partial dislocations and further grows along the stacking faults. When a pair of CTBs are close to each other, severe boundary distortion occurs, facilitating the emission and absorption of partial dislocations, which further assists the CTB-BPB transformation. The present results thus help to explain the frequent observation of coexisting CTB and BPB in HCP alloys and further contribute to the understanding of their microstructure and property regulation. [ABSTRACT FROM AUTHOR]

Shale oil in China is widely distributed and has enormous resource potential. The pores of shale are at the nanoscale, and traditional research methods encounter difficulty in accurately describing the fluid flow mechanism, which has become a bottleneck restricting the industrial development of shale oil in China. To clarify the distribution and migration laws of fluid microstructure in shale nanopores, we constructed a heterogeneous inorganic composite shale model and explored the fluid behavior in different regions of heterogeneous surfaces. The results revealed the adsorption capacity for alkanes in the quartz region was stronger than that in the illite region. When the aperture was small, solid–liquid interactions dominated; as the aperture increased, the bulk fluid achieved a more uniform and higher flow rate. Under conditions of small aperture/low temperature/low pressure gradient, the quartz region maintained a negative slip boundary. Illite was more hydrophilic than quartz; when the water content was low, water molecules formed a "liquid film" on the illite surface, and the oil flux percentages in the illite and quartz regions were 87% and 99%, respectively. At 50% water content, the adsorbed water in the illite region reached saturation, the quartz region remained unsaturated, and the difference in the oil flux percentage of the two regions decreased. At 70% water content, the adsorbed water in the two regions reached a fully saturated state, and a layered structure of "water–two-phase region–water" was formed in the heterogeneous nanopore. This study is of great significance for understanding the occurrence characteristics and flow mechanism of shale oil within inorganic nanopores. [ABSTRACT FROM AUTHOR]

The diterpene 7α-acetoxy-6β-hydroxyroyleanone isolated from Plectranthus grandidentatus demonstrates promising antibacterial, anti-inflammatory and anticancer properties. However, its bioactivity may be enhanced via strategic structural modifications of such natural products through semisynthesis. The anticancer potential of 7α-acetoxy-6β-hydroxyroyleanone and five derivatives was analyzed in silico via the prediction of chemicals absorption, distribution, metabolism, excretion, and toxicity (ADMET), quantum mechanical calculations, molecular docking and molecular dynamic simulation. The protein targets included regulators of apoptosis and cell proliferation. Additionally, network pharmacology was used to identify potential targets and signaling pathways. Derivatives 7α-acetoxy-6β-hydroxy-12-O-(2-fluoryl)royleanone and 7α-acetoxy-6β-(4-fluoro)benzoxy-12-O-(4-fluoro)benzoylroyleanone achieved high predicted binding affinities towards their respective protein panels, with stable molecular dynamics trajectories. Both compounds demonstrated favorable ADMET parameters and toxicity profiles. Their stability and reactivity were confirmed via geometry optimization. Network analysis revealed their involvement in cancer-related pathways. Our findings justify the inclusion of 7α-acetoxy-6β-hydroxy-12-O-(2-fluoryl)royleanone and 7α-acetoxy-6β-(4-fluoro)benzoxy-12-O-(4-fluoro)benzoylroyleanone in in vitro analyses as prospective anticancer agents. Our binding mode analysis and stability simulations indicate their potential as selective inhibitors. The data will guide studies into their structure optimization, enhancing efficacy and drug-likeness. [ABSTRACT FROM AUTHOR]

Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models. Here, the authors report the development of heterogeneous domain decomposition with load balancing for large biological molecular dynamics simulations using residue-level coarse-grained models. [ABSTRACT FROM AUTHOR]

Huperzine A (HUP) plays a crucial role in Alzheimer's therapy by enhancing cognitive function through increased cholinergic activity as a reversible acetylcholinesterase (AChE) inhibitor. Despite some limitations being seen in AChE inhibitors, ongoing research remains dedicated to finding innovative and more effective treatments for Alzheimer's disease. To achieve the goal of the discovery of potential HUP analogues with improved physicochemical properties, less toxic properties, and high biological activity, many in silico methods were applied. Based on the acetylcholinesterase–ligand complex, an e-pharmacophore model was developed. Subsequently, a virtual screening involving a collection of 1762 natural compounds, sourced from the PubChem database, was performed. This screening yielded 131 compounds that exhibited compatibility with the established pharmacophoric hypothesis. These selected ligands were then subjected to molecular docking within the active site of the 4EY5 receptor. As a result, we identified four compounds that displayed remarkable docking scores and exhibited low free binding energy to the target. These top four compounds, CID_162895946, CID_44461278, CID_44285285, and CID_81108419, were submitted to ADMET prediction and molecular dynamic simulations, yielding encouraging findings in terms of their pharmacokinetic characteristics and stability. Finally, the molecular dynamic simulation, cross-dynamic correlation matrix, free energy landscape, and MM-PBSA calculations demonstrated that two ligands from the selected ligands formed very resilient complexes with the enzyme acetylcholinesterase, with significant binding affinity. Therefore, these two compounds are recommended for further experimental research as possible (AChE) inhibitors. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 virus and its mutations have affected human health globally and created significant danger for the health of people all around the world. To cure this virus, the human Angiotensin Converting Enzyme-2 (ACE2) receptor, the SARS-CoV-2 main protease (Mpro), and spike proteins were found to be likely candidates for the synthesis of novel therapeutic drug. In the past, proteins were capable of engaging in interaction with a wide variety of ligands, including both manmade and plant-derived small molecules. Pyrus communis L., Ginko bibola, Carica papaya, Syrian rue, and Pimenta dioica were some of the plant species that were studied for their tendency to interact with SARS-CoV-2 main protease (Mpro) in this research project (6LU7). This scenario investigates the geometry, electronic, and thermodynamic properties computationally. Assessing the intermolecular forces of phytochemicals with the targets of the SARS-CoV-2 Mpro spike protein (SP) resulted in the recognition of a compound, kaempferol, as the most potent binding ligand, −7.7 kcal mol−1. Kaempferol interacted with ASP-187, CYS-145, SER-144, LEU 141, MET-165, and GLU-166 residues. Through additional molecular dynamic simulations, the stability of ligand–protein interactions was assessed for 100 ns. GLU-166 remained intact with 33% contact strength with phenolic OH group. We noted a change in torsional conformation, and the molecular dynamics simulation showed a potential variation in the range from 3.36 to 7.44 against a 45–50-degree angle rotation. SAR, pharmacokinetics, and drug-likeness characteristic investigations showed that kaempferol may be the suitable candidate to serve as a model for designing and developing new anti-COVID-19 medicines. [ABSTRACT FROM AUTHOR]

The addition of nano-sized filler particles to polymers leads to significant improvements in their mechanical properties. These can be traced back to the matrix–filler interactions of the interphase, which can be analyzed using molecular dynamic simulations. Usually, research in this context studies the general number of entanglements or the radius of gyration. However, this publication presents a novel approach by investigating the radial distribution of entanglements in an effort to characterize the interphase. To this end, we employ a coarse-grained model for a generic polymer composite and study multiple systems with varying particle radius and matrix–filler adhesion. Furthermore, the highly customizable and computationally efficient nanocomposite system developed during this research serves as a foundation for the further characterization of polymer nanocomposites and their interphases. [ABSTRACT FROM AUTHOR]

Context: The interface of Hsp70-Bim protein–protein interaction (PPI) has been identified as a specific target for Chronic Myeloid Leukemia (CML) therapy and the specific inhibitors were developed to exhibit in vivo anti-leukemia activities. Herein, we explored the binding mechanism of a Hsp70-Bim inhibitor, 6-(cyclohexylthio)-3-((2-morpholinoethyl) amino)-1-oxo-1H-phenalene-2-carbonitrile (S1g-6), to Hsp70 at the atomic level by MD simulation. TYR-149, THR-222, ALA-223, and GLY-224 on Hsp70 were identified as four key residues that contribute to Hsp70/S1g-6 complex. Moreover, the site mutation validation demonstrated the TYR-149 of Hsp70 is a "hot-spot" in the Hsp70-Bim PPI interface. These results could benefit the design of further inhibitors to occupy the Bim binding site on the Hsp70 surface. Methods: The binding mechanism of S1g-6 and Hsp70 was predicted through the molecular dynamics (MD) method by Gromacs-2021.3. The MD simulation was performed with 100-ps NVT and 100-ps NPT ensemble, and the force field was chosen as the Charmm36 force field. The temperature was set as 300 K, the time step was 2 fs and the total MD simulation time was 500 ns. [ABSTRACT FROM AUTHOR]

Isoxazolidine derivatives were designed, synthesized, and characterized using different spectroscopic techniques and elemental analysis and then evaluated for their ability to inhibit both α-amylase and α-glucosidase enzymes to treat diabetes. All synthesized derivatives demonstrated a varying range of activity, with IC50 values ranging from 53.03 ± 0.106 to 232.8 ± 0.517 μM (α-amylase) and from 94.33 ± 0.282 to 258.7 ± 0.521 μM (α-glucosidase), revealing their high potency compared to the reference drug, acarbose (IC50 = 296.6 ± 0.825 µM and 780.4 ± 0.346 µM), respectively. Specifically, in vitro results revealed that compound 5d achieved the most inhibitory activity with IC50 values of 5.59-fold and 8.27-fold, respectively, toward both enzymes, followed by 5b. Kinetic studies revealed that compound 5d inhibits both enzymes in a competitive mode. Based on the structure–activity relationship (SAR) study, it was concluded that various substitution patterns of the substituent(s) influenced the inhibitory activities of both enzymes. The server pkCSM was used to predict the pharmacokinetics and drug-likeness properties for 5d, which afforded good oral bioavailability. Additionally, compound 5d was subjected to molecular docking to gain insights into its binding mode interactions with the target enzymes. Moreover, via molecular dynamics (MD) simulation analysis, it maintained stability throughout 100 ns. This suggests that 5d possesses the potential to simultaneously target both enzymes effectively, making it advantageous for the development of antidiabetic medications. [ABSTRACT FROM AUTHOR]

We report ab initio molecular dynamic simulations of the organic structure-directing agent (OSDA) in the channels of SCM-14 and SCM-15 germanosilicates for models with different germanium distribution. Since OSDA was free to move inside the channels, independent of its initial orientation after the simulations in all structures the OSDA, protonated 4-pyrrolidinopyridine, is positioned almost perpendicular to the large channels of SCM-14. The structures obtained from the dynamic simulation are more stable by 157 to 331 kJ/mol than the structures obtained by initial geometry optimization. After simulations, the average distance between the N atom of the pyridine moiety of the OSDA and O from Ge-O-Ge is shorter by 0.2 Å than the same distance obtained from initial optimization. The stretching N-H frequencies in the IR spectra of the OSDA and other calculated vibrational frequencies are not characteristic of the orientation of the molecule and cannot be used to detect it. [ABSTRACT FROM AUTHOR]

Potentilla nepalensis belongs to the Rosaceae family and has numerous therapeutic applications as potent plant-based medicine. Forty phytoconstituents (PCs) from the root and stem through n-hexane (NR and NS) and methanolic (MR and MS) extracts were identified in earlier studies. However, the PCs affecting human genes and their roles in the body have not previously been disclosed. In this study, we employed network pharmacology, molecular docking, molecular dynamics simulations (MDSs), and MMGBSA methodologies. The SMILES format of PCs from the PubChem was used as input to DIGEP-Pred, with 764 identified as the inducing genes. Their enrichment studies have shown inducing genes' gene ontology descriptions, involved pathways, associated diseases, and drugs. PPI networks constructed in String DB and network topological analyzing parameters performed in Cytoscape v3.10 revealed three therapeutic targets: TP53 from MS-, NR-, and NS-induced genes; HSPCB and Nf-kB1 from MR-induced genes. From 40 PCs, two PCs, 1b (MR) and 2a (MS), showed better binding scores (kcal/mol) with p53 protein of −8.6 and −8.0, and three PCs, 3a, (NR) 4a, and 4c (NS), with HSP protein of −9.6, −8.7, and −8.2. MDS and MMGBSA revealed these complexes are stable without higher deviations with better free energy values. Therapeutic targets identified in this study have a prominent role in numerous cancers. Thus, further investigations such as in vivo and in vitro studies should be carried out to find the molecular functions and interlaying mechanism of the identified therapeutic targets on numerous cancer cell lines in considering the PCs of P. nepalensis. [ABSTRACT FROM AUTHOR]

A combined experimental and molecular dynamic simulation approach was used to examine the structure and interfacial properties of solute-saturated micelles. The properties of dodecylbenzenesulfonate (DBS) micelles were examined in dodecane and benzene hydrocarbon systems. Pyrene fluorescence was used to determine the aggregation number of surfactant monomers in the micelle systems. Molecular dynamic (MD) simulations using energy minimization applying the CHARMm force field with the TIP3P model for water. Comparison of the DBS/benzene and DBS/Dodecane micelles equilibrium structures via radial distribution function (RDF) and probability distribution function (PDF) analysis indicates that the area per head group for the DBS/Benzene micelle interface is significantly larger than that of the DBS/Dodecane at the interface. It was also determined that benzene molecules can move freely within the micelle while dodecane is strictly confined in the core of the micelle. The increased interfacial area per monomer caused by the insertion of benzene also reduces the effectiveness of the surfactant, which has implications for use in various environmental applications. However, the DBS/benzene micelle can solubilize many more hydrocarbon molecules in one micelle with less surfactant monomer (i.e., lower aggregation number) per micelle due to the increased available packing positions within the micelle. This, in turn, increases the efficiency of the surfactant in real-world applications which is consistent with previous laboratory results. Understanding the differing solubilization characteristics of surfactants against various classes of hydrocarbons in single solute systems is a necessary step to beginning to understand their solubilization properties in the mixed waste systems prevalent in most surfactant enhanced remediation (SEAR) strategies. [ABSTRACT FROM AUTHOR]

Significant advancements have been made in the domain of targeted anticancer therapy for the management of malignancies in recent times. VEGFR-2 is characterised by its pivotal involvement in angiogenesis and subsequent mechanisms that promote tumour cells survival. Herein, novel N-arylmethyl-aniline/chalcone hybrids 5a–5n were designed and synthesised as potential anticancer and VEGFR-2 inhibitors. The anticancer activity was evaluated at the NCI-USA, resulting in the identification of 10 remarkably potent molecules 5a–5j that were further subjected to the five-dose assays. Thereafter, they were explored for their VEGFR-2 inhibitory activity where 5e and 5h emerged as the most potent inhibitors. 5e and 5h induced apoptosis with cell cycle arrest at the SubG0-G1 phase within HCT-116 cells. Moreover, their impact on some key apoptotic genes was assessed, suggesting caspase-dependent apoptosis. Furthermore, molecular docking and molecular dynamics simulations were conducted to explore the binding modes and stability of the protein–ligand complexes. [ABSTRACT FROM AUTHOR]

Nickel-coated multi-walled carbon nanotubes (Ni-MWCNTs), through combining the high tensile strength and Young's modulus of multi-walled carbon nanotubes with the good wetting characteristics of nanoscale nickel particle, substantially increase their dispersion and composite efficiency in composites. Therefore, Ni-MWCNTs are a promising nano-reinforcement to strengthen the tensile performances of ultra-high performance concrete (UHPC). This study investigated the effects of Ni-MWCNTs with different aspect ratios on the uniaxial tensile behaviors of UHPC and explored the underlaying modification mechanisms by molecular dynamics simulation and microstructural analysis. The results indicated that the presence of Ni-MWCNTs notably modifies the tensile performances of UHPC. Ni-MWCNTs with large aspect ratios are preferable for improving the tensile strength and toughness of UHPC. Adding 0.5 wt.% Ni-MWCNTs with an aspect ratio of 1000 can lead to a maximum increase of 31.9 and 46.4% in the tensile strength and toughness, respectively. While Ni-MWCNTs with small aspect ratios of 125/200 are more effective in enhancing the Young's modulus and Poisson's ratio of UHPC, the increase rate of which can reach 31–53 and 11–30%. Such modifications derive from the enhancement of the interfacial bonding ability between MWCNTs and matrix due to the presence of nanoscale nickel particle and the improvement of matrix compactness owing to the introduction of Ni-MWCNTs. Additionally, the Ni-MWCNTs' bridging/pull-out effects, enhanced by the existence of nanoscale nickel particle, can retard crack development and consume energy under tensile loading. [ABSTRACT FROM AUTHOR]

Introduction: Signal transducer and activator of transcription 3 (STAT3) is ubiquitously hyper-activated in numerous cancers, rendering it an appealing target for therapeutic intervention. Methods and results: In this study, using structure-based virtual screening complemented by molecular dynamics simulations, we identified ten potential STAT3 inhibitors. The simulations pinpointed compounds 8, 9, and 10 as forming distinct hydrogen bonds with the SH2 domain of STAT3. In vitro cytotoxicity assays highlighted compound 4 as a potent inhibitor of gastric cancer cell proliferation across MGC803, KATO III, and NCI-N87 cell lines. Further cellular assays substantiated the ability of compound 4 to attenuate IL- 6-mediated STAT3 phosphorylation at Tyr475. Additionally, oxygen consumption rate assays corroborated compound 4's deleterious effects on mitochondrial function. Discussion: Collectively, our findings position compound 4 as a promising lead candidate warranting further exploration in the development of anti-gastric cancer therapeutics. [ABSTRACT FROM AUTHOR]

Tanshinone IIA is a lipophilic organic compound from the root of Danshen (Salvia miltiorrhiza) and is one of the most well-known Tanshinone molecules by pharmacologists. In recent years, in addition to effects of anti-cardiovascular and neurological diseases, Tanshinone IIA has also shown some degrees of anti-prostate cancer potential. Although they do have some studies focusing on the molecular mechanism of Tanshinone IIA's anti-prostate cancer effects, a further understanding on the transcriptomic and structural level is still lacking. In this study, transcriptomic sequencing technology and computer technology were employed to illustrate the effects of Tanshinone IIA on prostate cancer through bioinformatic analysis and molecular dynamics simulation, and PPARG was considered to be one of the targets for Tanshinone IIA according to docking scoring and dynamic calculation. Our study provides a novel direction to further understand the mechanism of the effects of Tanshinone IIA on prostate cancer, and further molecular biological studies need to be carried on to further investigate the molecular mechanism of Tanshinone IIA's anti-prostate cancer effect through PPARG. [ABSTRACT FROM AUTHOR]

The structural changes of cellulose in non-solvent liquid media can provide insights into the high-value utilization of cellulose. This study includes molecular dynamics simulations of 36-chain cellulose Iβ microfibril model (Iβ-MF) behavior in 16 non-solvent liquids with different polarities at room temperature using two carbohydrate force fields (CHARMM36, GLYCAM06). Iβ-MF in CHARMM36 retains more than 70% of the tg conformation in 16 liquids, and the retention of the tg conformation increased with decreasing liquid polarity. Liquid polarity can affect the hydroxymethyl conformation of cellulose, which is only an appearance, and the real driving force behind is the electrostatic interaction between liquid molecules and cellulose. Furthermore, changing the 1,4 electrostatic scaling factor of GLYCAM06 can effectively affect the structural convergence of Iβ-MF. The Iβ-MF forms an alternating layer structure in the gg/gt conformation in a medium to high polarity non-solvent liquid, while the model undergoes untwisting. Model untwisting is inextricably linked to the degree of alternate layer structure formation. This paper provides a theoretical basis for the molecular study of nanocellulose structures from an energy-structure-property perspective. [ABSTRACT FROM AUTHOR]

As a subclass of the biopharmaceutical classification system (BCS) class II, basic drugs (BCS IIB) exhibit pH-dependent solubility and tend to generate supersaturation in the gastrointestinal tract, leading to less qualified in vitro–in vivo correlation (IVIVC). This study aims to develop a physiologically based multi-cup dissolution approach to improve the evaluation of the supersaturation for a higher quality of IVIVC and preliminarily explores the molecular mechanism of supersaturation and precipitation of ketoconazole affected by Polyvinylpyrrolidone–vinyl acetate copolymer (PVPVA) and hydroxypropyl methyl-cellulose (HPMC). The concentration of ketoconazole in each cup of the dynamic gastrointestinal model (DGIM) was measured using fiber optical probes. Molecular interactions between ketoconazole and PVPVA or HPMC were simulated by Materials Studio. The results demonstrated that PVPVA and HPMC improved and maintained the supersaturation of ketoconazole. PVPVA exhibited superior precipitation inhibitory effect on ketoconazole molecule aggregation due to slightly stronger van der Waals forces as well as unique electrostatic forces, thereby further enhancing in vitro drug absorption, which correlated well with in vivo drug absorption. Compared with a conventional dissolution apparatus paddle method, the DGIM improved the mean prediction error through the IVIVC from 19.30% to 9.96%, reaching the qualification criteria. In conclusion, the physiologically based multi-cup dissolution approach enables improved evaluation of supersaturation in gastrointestinal transportation of BCS IIB drug ketoconazole, enabling screening screen precipitation inhibitors and achieving qualified IVIVC for drug formulation studies. [ABSTRACT FROM AUTHOR]

The crystal orientation effect on the mechanical properties and micro-deformation behavior of single-crystal iron (SC Fe) were revealed by molecular dynamics (MD) simulations. The results show that the surviving defects in the SC Fe models are [110] < [100] < [111], and only the vacancy and interstitial atomic clusters are formed in the [111] SC Fe model. Irradiation leads to the increase of elastic modulus owing to the annihilation of irradiation point defects. However, the non-annihilable irradiation clusters reduced the strength. The decrease of yield strain and yield strength of the [111] SC Fe model is significantly higher than those of [110] and [100] SC Fe models, exhibiting worse radiation damage resistance. This is due to the number and types of operation of slip systems in the [110] and [100] SC Fe after irradiation, which is caused by its poor inhibition of [111] crystal orientation on clusters under irradiation, being much lower than those in the [111] SC Fe. The yield strength of SC Fe increases with the increase of the number and length of 1/2 111 and 100 dislocations, while the plasticity decreases with the increase of the falling gradient of dislocations after yield. The purpose is to provide theoretical guidance for the microstructure design and regulation of radiation-damage-resistant iron-based materials. [ABSTRACT FROM AUTHOR]

TAK1 (transforming growth factor-beta-activated kinase 1) is a crucial therapeutic target in inflammation-related diseases. This study investigated the inhibitory potential of cannflavin A, a flavonoid found in Cannabis sativa, against TAK1. Through in silico approaches, including drug-likeness analysis, ADMET assessment, molecular docking, and molecular dynamics simulation, the binding affinity and stability of cannflavin A were evaluated. The results demonstrate that cannflavin A exhibits excellent ADMET properties and displays superior binding affinity and stability at the ATP binding site of TAK1 when compared to the known inhibitor takinib. Notably, the decomposition of binding free energy unveils critical amino acid residues involved in TAK1 binding, underscoring the inhibitory effect of cannflavin A through TAK1 inhibition. These findings highlight the potential of cannflavin A as a TAK1 inhibitor and its significant implications for the development of targeted therapies in inflammation-related diseases. Through modulating inflammatory signaling pathways, cannflavin A holds promise for more effective and tailored treatment strategies, particularly in rheumatoid arthritis. This study contributes to the current understanding of cannflavin A's application and provides a foundation for further research and innovative approaches in targeted therapies for inflammatory conditions. [ABSTRACT FROM AUTHOR]

Current practices in synthesizing molecularly imprinted polymers face challenges—lengthy process, low-productivity, the need for expensive and sophisticated equipment, and they cannot be controlled in situ synthesis. Herein, we present a micro-reactor for in situ and continuously synthesizing trillions of molecularly imprinted polymeric nanoparticles that contain molecular fingerprints of bovine serum albumin in a short period of time (5-30 min). Initially, we performed COMSOL simulation to analyze mixing efficiency with altering flow rates, and experimentally validated the platform for synthesizing nanoparticles with sizes ranging from 52-106 nm. Molecular interactions between monomers and protein were also examined by molecular docking and dynamics simulations. Afterwards, we benchmarked the micro-reactor parameters through dispersity and concentration of molecularly imprinted polymers using principal component analysis. Sensing assets of molecularly imprinted polymers were examined on a metamaterial sensor, resulting in 81% of precision with high selectivity (4.5 times), and three cycles of consecutive use. Overall, our micro-reactor stood out for its high productivity (48-288 times improvement in assay-time and 2 times improvement in reagent volume), enabling to produce 1.4-1.5 times more MIPs at one-single step, and continuous production compared to conventional strategy. Molecularly imprinted polymers are useful elements in sensing and biomedical research but their fabrication is challenging. Here, the authors report a micro-reactor for in situ and continuous production of molecularly imprinted polymers. [ABSTRACT FROM AUTHOR]

Globally, breast cancer (BC), the second-biggest cause of cancer death, occurs due to unregulated cell proliferation leading to metastasis to other parts of the human organ. Recently, the exploration of naturally derived anticancer agents has become popular due to their fewer adverse effects. Among the natural products, soybean is a very well-known legume that contains important bioactive compounds such as diadazine, glycetin, genistein, and genistin. Therefore, keeping its therapeutic potential in mind, multi-targeted molecular docking and simulation studies were conducted to explore the potential role of soybean-derived isoflavone genistin against several breast cancer-signaling proteins (ER-alpha, ER-Beta, collapsin response mediator protein 2, CA 15-3, human epidermal growth factor receptor 2). A comparative study of the genistin-protein docked complex was explored to investigate its potential role in BC. The molecular binding energy (∆G) of the docked complex was calculated along with ADMET properties. The molecular docking score of genistin with ubiquitin-like protein activation complex-a type of Cancer Antigen (CA) 15.3 (PDB ID-2NVU, 5T6P, and 1YX8) showed the highest binding energy, ranging from −9.5 to −7.0 Kcal/mol, respectively. Furthermore, the highest docking scores of the complex were additionally put through molecular dynamics (MD) simulation analysis. MD simulations of the selected complex were performed at 100 ns to study the stability of the genistin-ubiquitin-like protein CA 15.3 complex, which appeared to be quite stable. Additionally, the ADMET study demonstrated that genistin complies with all drug-likeness standards, including Lipinski, Egan, Veber, Ghose, and Muegge. Therefore, based on the results, genistin can be considered as one of the potential drugs for the management and treatment of BC. In addition, the obtained results suggest that genistin could pave the way for new drug discovery to manage breast cancer and has potential in the development of nutraceuticals. [ABSTRACT FROM AUTHOR]

This study investigates the crystal structure, physicochemical properties, and pharmacokinetic profile of Ethyl 2-amino-6-methyl-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate (EAMT) as a potential therapeutic agent. The crystal structure was analyzed using Hirshfeld surface analysis in conjunction with the quantum theory of atoms in molecules (QT-AIM). Non-covalent interactions were evaluated through reduced-density gradient reduction, revealing that the EAMT crystal is stabilized by hydrogen bonds between EAMT molecules in the crystal and between EAMT molecules and water molecules. The molecular electrostatic nature of interactions was examined using MESP, while global and local descriptors were calculated to assess the compound's reactivity. Molecular docking with the Adenosine A1 receptor was performed and validated through a 50 ns molecular dynamics simulation (MDS). Results suggest that EAMT influences protein structure, potentially stabilizing specific secondary structure elements. The compactness analysis showed a slightly more compact protein conformation and a marginally increased solvent exposure in the presence of the EAMT ligand, as indicated by Rg and SASA values. The total binding free energy (ΔG total) was determined to be −114.56 kcal/mol. ADMET predictions demonstrated EAMT's compliance with Lipinski's and Pfizer's rule of five, indicating good oral availability. The compound may exhibit low-potency endocrine activity. In conclusion, EAMT presents potential as a therapeutic candidate, warranting further exploration of its molecular interactions, pharmacokinetics, and potential safety concerns. [ABSTRACT FROM AUTHOR]

Introduction: Intellectual disability (ID) is a clinically and genetically heterogeneous disorder. It drastically affects the learning capabilities of patients and eventually reduces their IQ level below 70. Methods: The current genetic study ascertained two consanguineous Pakistani families suffering from autosomal recessive intellectual developmental disorder-5 (MRT5). We have used exome sequencing followed by Sanger sequencing to identify the disease-causing variants. Results and discussion: Genetic analysis using whole exome sequencing in these families identified two novel mutations in the NSUN2 (NM_017755.5). Family-A segregated a novel missense variant c.953A>C; p.Tyr318Ser in exon-9 of the NSUN2. The variant substituted an amino acid Tyr318, highly conserved among different animal species and located in the functional domain of NSUN2 known as "SAM-dependent methyltransferase RsmB/NOP2-type". Whereas in family B, we identified a novel splice site variant c.97-1G>C that affects the splice acceptor site of NSUN2. The identified splice variant (c.97-1G>C) was predicted to result in the skipping of exon-2, which would lead to a frameshift followed by a premature stop codon (p. His86Profs*16). Furthermore, it could result in the termination of translation and synthesis of dysfunctional protein, most likely leading to nonsense-mediated decay. The dynamic consequences of NSUN2 missense variant was further explored together with wildtype through molecular dynamic simulations, which uncovered the disruption of NSUN2 function due to a gain in structural flexibility. The present molecular genetic study further extends the mutational spectrum of NSUN2 to be involved in ID and its genetic heterogeneity in the Pakistani population. [ABSTRACT FROM AUTHOR]

Obesity is a pandemic and a serious health problem in developed and undeveloped countries. Activation of estrogen receptor beta (ERβ) has been shown to promote weight loss without modifying caloric intake, making it an attractive target for developing new drugs against obesity. This work aimed to predict new small molecules as potential ERβ activators. A ligand-based virtual screening of the ZINC15, PubChem, and Molport databases by substructure and similarity was carried out using the three-dimensional organization of known ligands as a reference. A molecular docking screening of FDA-approved drugs was also conducted as a repositioning strategy. Finally, selected compounds were evaluated by molecular dynamic simulations. Compounds 1 (−24.27 ± 0.34 kcal/mol), 2 (−23.33 ± 0.3 kcal/mol), and 6 (−29.55 ± 0.51 kcal/mol) showed the best stability on the active site in complex with ERβ with an RMSD < 3.3 Å. RMSF analysis showed that these compounds do not affect the fluctuation of the Cα of ERβ nor the compactness according to the radius of gyration. Finally, an in silico evaluation of ADMET showed they are safe molecules. These results suggest that new ERβ ligands could be promising molecules for obesity control. [ABSTRACT FROM AUTHOR]

Background: ECEL1 has been presented as a causal gene of an autosomal recessive form distal arthrogryposis (DA) which affects the distal joints. The present study focused on bioinformatic analysis of a novel mutation in ECEL1, c.535A>G (p. Lys179Glu), which was reported in a family with 2 affected boys and fetus through prenatal diagnosis. Methods: Whole‐exome sequencing data analyzed followed by molecular dynamic (MD) simulation of native ECEL1 protein and mutant structures using GROMACS software. One variant c.535A>G, p. Lys179Glu (homozygous) on gene ECEL1 has been detected in proband which was validated in all family members through Sanger sequencing. Results: We demonstrated remarkable constructional differences by MD simulation between wild‐type and novel mutant of ECEL1 gene. The reason for the lack of the Zn ion binding in mutation in the ECEL1 protein has been identified by average atomic distance and SMD analysis among the wild‐type and mutant. Conclusion: Overall, in this study, we present knowledge of the effect of the studied variant on the ECEL1 protein leading to neurodegenerative disorder in humans. This work may hopefully be supplementary to classical molecular dynamics to dissolve the mutational effects of cofactor‐dependent protein. [ABSTRACT FROM AUTHOR]

Alopecia is a condition in which hair on the scalp or other areas of the body is lost or falls out excessively. Nutritional deficiency causes blood flow to the head to decrease causing the hormone testosterone to be changed by the enzyme 5-α-reductase to dihydrotestosterone, which inhibits the growth phase and accelerates the death phase. One of the methods developed to treat alopecia is through inhibition of the 5-α-reductase enzyme, which converts testosterone to its more potent metabolite, dihydrotestosterone (DHT). Ethnomedicinally, Merremia peltata leaf is used by the people of Sulawesi as a remedy for baldness. Therefore, in this research, an in vivo study was conducted on rabbits to determine the anti-alopecia activity of M. peltata leaf compounds. The structure of the compounds isolated from the M. peltata leaf ethyl acetate fraction was determined by analysis of NMR and LC-MS data. An in silico study was then carried out using minoxidil as a comparison ligand; scopolin (1) and scopoletin (2) isolated from M. peltata leaf were identified as anti-alopecia compounds by predicting docking, simulating molecular dynamics and predicting absorption, distribution, metabolism, excretion, and toxicology (ADME-Tox). Compounds 1 and 2 had a better effect on hair growth compared to positive controls, and NMR and LC-MS analysis showed that they had comparable binding energies to receptors in the molecular docking interaction study: −4.51 and −4.65 kcal/mol, respectively, compared to −4.8 kcal/mol for minoxidil. Molecular dynamics simulation analysis with the parameters binding free energy calculated using the MM-PBSA method and complex stability based on SASA, PCA, RMSD, and RMSF showed that scopolin (1) has a good affinity for androgens receptors. The ADME-Tox prediction for scopolin (1) showed good results for the parameters of skin permeability, absorption and distribution. Therefore, scopolin (1) is a potential antagonist to androgen receptors and could be useful in the treatment of alopecia. [ABSTRACT FROM AUTHOR]

Over the past few years, COVID-19 has caused widespread suffering worldwide. There is great research potential in this domain and it is also necessary. The main objective of this study was to identify potential inhibitors against acid sphingomyelinase (ASM) in order to prevent coronavirus infection. Experimental studies revealed that SARS-CoV-2 causes activation of the acid sphingomyelinase/ceramide pathway, which in turn facilitates the viral entry into the cells. The objective was to inhibit acid sphingomyelinase activity in order to prevent the cells from SARS-CoV-2 infection. Previous studies have reported functional inhibitors against ASM (FIASMAs). These inhibitors can be exploited to block the entry of SARS-CoV-2 into the cells. To achieve our objective, a drug library containing 257 functional inhibitors of ASM was constructed. Computational molecular docking was applied to dock the library against the target protein (PDB: 5I81). The potential binding site of the target protein was identified through structural alignment with the known binding pocket of a protein with a similar function. AutoDock Vina was used to carry out the docking steps. The docking results were analyzed and the inhibitors were screened based on their binding affinity scores and ADME properties. Among the 257 functional inhibitors, Dutasteride, Cepharanthine, and Zafirlukast presented the lowest binding affinity scores of −9.7, −9.6, and −9.5 kcal/mol, respectively. Furthermore, computational ADME analysis of these results revealed Cepharanthine and Zafirlukast to have non-toxic properties. To further validate these findings, the top two inhibitors in complex with the target protein were subjected to molecular dynamic simulations at 100 ns. The molecular interactions and stability of these compounds revealed that these inhibitors could be a promising tool for inhibiting SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

Epoxy resins are formed when epoxy monomers react with crosslinkers that have active hydrogen sites on them such as amine and anhydrides. These cross-linked structures are highly unpredictable and depend on different parameters during curing. Epoxy material when reinforced with nanoparticles has got importance because of its extraordinary enhanced mechanical and thermal properties for structural application. Experimentally it is challenging to tailor these nanostructures and manufacture epoxy-based nanocomposites with desired properties. An experimental approach to preparing these is tedious and costly. The improvement of such materials requires huge experimentation and a better level of control of their properties can't be accomplished up till now. There is a need for numerical experimentation to guide these experimental procedures. With the headway of computational techniques, an alternative for these experiments had given an effective method to characterize these nanocomposites and study their reaction kinetics. Molecular dynamics (MD) simulation is one such technique that works on density function theory and Newton's second law to characterize these materials with different permutations and combinations during their curing. This review is carried out for MD simulation studies done to date on different epoxies and epoxy-based nanocomposites for their thermal, mechanical, and thermo-mechanical characterization. [ABSTRACT FROM AUTHOR]

Aluminum nanoparticle (ANP) in liquid Cellulose dinitrate decamer sol was investigated by ReaxFF molecular dynamics simulations. The mechanism of nitrocellulose (NC) single chain adsorption was researched as a chemisorption process. New Al–O bonds are formed by dehydrogenation and denitrification of the nitrate ester groups. The adsorbed part of the NC chain drags other parts to the surface as a horizontal adsorption state. We also simulated the processes of liquid Cellulose dinitrate decamer sol (ethanol, diethyl ether, and NC three components) coating the ANPs at different temperatures. The results indicate that the organic coating near surface is mainly consisted of ethanol and diethyl ether molecules. The NC chains are adsorbed on the ANPs surface in two states, including the horizontal adsorption or the nearly vertical adsorption. Heating can increase the coating rate without significantly changing the composition of the coating. Finally, the oxidation simulation shows that the organic layer can maintain good stability and oxidation resistance. [ABSTRACT FROM AUTHOR]

Natural rubber (NR) exhibits good elasticity, flexural resistance, wear resistance, and excellent mechanical properties, and it has been widely used in aerospace, transportation, medical, and health fields. For NR, however, the resistance to thermal-oxidation and ozone aging is fairly poor. Although aging properties of NR can be significantly improved with the incorporation of chloroprene rubber (CR) according to some references, the miscibility between NR and CR, the morphologies of the binary blends, and so on are revealed ambiguously. In this work, molecular dynamics simulation (MD) and dissipative particle dynamics (DPD) simulation were carried out to predict the compatibility between natural rubber and chloroprene rubber in view of Flory–Huggins parameters. The morphologies of the blends were obtained with the use of the DPD method. The simulation results were furtherly examined by means of Fourier transform infrared spectroscopy (FT-IR) and dynamic mechanical analysis (DMA). It was found that the miscibility between NR and CR is poor. Nevertheless, the miscibility could be improved when the content of CR is 50% or 90%. In addition, spinodal decomposition with a critical temperature of 390 K would take place according to the phase diagram. Microphase structure such as spherical, lamellar, and bicontinuous phases can be found with different contents of CR in the blends with the results of morphologies analysis. [ABSTRACT FROM AUTHOR]

Shikonin, a phytochemical present in the roots of Lithospermum erythrorhizon, is well-known for its broad-spectrum activity against cancer, oxidative stress, inflammation, viruses, and anti-COVID-19 agents. A recent report based on a crystallographic study revealed a distinct conformation of shikonin binding to the SARS-CoV-2 main protease (Mpro), suggesting the possibility of designing potential inhibitors based on shikonin derivatives. The present study aimed to identify potential shikonin derivatives targeting the Mpro of COVID-19 by using molecular docking and molecular dynamics simulations. A total of 20 shikonin derivatives were screened, of which few derivatives showed higher binding affinity than shikonin. Following the MM-GBSA binding energy calculations using the docked structures, four derivatives were retained with the highest binding energy and subjected to molecular dynamics simulation. Molecular dynamics simulation studies suggested that alpha-methyl-n-butyl shikonin, beta-hydroxyisovaleryl shikonin, and lithospermidin-B interacted with two conserved residues, His41 and Cys145, through multiple bonding in the catalytic sites. This suggests that these residues may effectively suppress SARS-CoV-2 progression by inhibiting Mpro. Taken together, the present in silico study concluded that shikonin derivatives may play an influential role in Mpro inhibition. [ABSTRACT FROM AUTHOR]

Bilayers of mycolic acids (MAs) form the outer membrane of Mycobacterium tuberculosis that has high strength and extremely low permeability for external molecules (including antibiotics). For the first time, we were able to study them using the all-atom long-term molecular dynamic simulations (from 300 ns up to 1.2 μs) in order to investigate the conformational changes and most favorable structures of the mycobacterial membranes. The structure and properties of the membranes are crucially dependent on the initial packing of the α-mycolic acid (AMA) molecules, as well as on the presence of the secondary membrane components, keto- and methoxy mycolic acids (KMAs and MMAs). In the case of AMA-based membranes, the most labile conformation is W while other types of conformations (sU as well as sZ, eU, and eZ) are much more stable. In the multicomponent membranes, the presence of the KMA and MMA components (in the W conformation) additionally stabilizes both the W and eU conformations of AMA. The membrane in which AMA prevails in the eU conformation is much thicker and, at the same time, much denser. Such a packing of the MA molecules promotes the formation of a significantly stronger outer mycobacterial membrane that should be much more resistant to the threatening external factors. [ABSTRACT FROM AUTHOR]

To investigate the crystallization of DNTF in modified double-base propellants, glycidyl azide polymer (GAP) was used as the coating material for the in situ coating of DNTF, and the performance of the coating was investigated to inhibit the crystallization. The results show that GAP can form a white gel on the surface of DNTF crystals and has a good coating effect which can significantly reduce the impact sensitivity and friction sensitivity of DNTF. Molecular dynamics was used to construct a bilayer interface model of GAP and DNTF with different growth crystal surfaces, and Molecular dynamics calculations of the binding energy and mechanical properties of the composite system were carried out. The results showed that GAP could effectively improve the mechanical properties of DNTF. The values of K/G, γ and ν are higher than those of DNTF crystals, and the values of C12-C44 are positive, indicating that GAP can improve DNTF ductility while also improving toughness. Combining the experimental results with the simulation calculations, energetic binder GAP can be referred to as a better cladding layer for DNTF, which is feasible for inhibiting the DNTF crystallization problem in propellants. [ABSTRACT FROM AUTHOR]

Background and Objective: Mutations in the CYB5R3 gene cause reduced NADH-dependent cytochrome b5 reductase enzyme function and consequently lead to recessive congenital methemoglobinemia (RCM). RCM exists as RCM type I (RCM1) and RCM type II (RCM2). RCM1 leads to higher methemoglobin levels causing only cyanosis, while in RCM2, neurological complications are also present along with cyanosis. Materials and Methods: In the current study, a consanguineous Pakistani family with three individuals showing clinical manifestations of cyanosis, chest pain radiating to the left arm, dyspnea, orthopnea, and hemoptysis was studied. Following clinical assessment, a search for the causative gene was performed using whole exome sequencing (WES) and Sanger sequencing. Various variant effect prediction tools and ACMG criteria were applied to interpret the pathogenicity of the prioritized variants. Molecular dynamic simulation studies of wild and mutant systems were performed to determine the stability of the mutant CYB5R3 protein. Results: Data analysis of WES revealed a novel homozygous missense variant NM_001171660.2: c.670A > T: NP_001165131.1: p.(Ile224Phe) in exon 8 of the CYB5R3 gene located on chromosome 22q13.2. Sanger sequencing validated the segregation of the identified variant with the disease phenotype within the family. Bioinformatics prediction tools and ACMG guidelines predicted the identified variant p.(Ile224Phe) as disease-causing and likely pathogenic, respectively. Molecular dynamics study revealed that the variant p.(Ile224Phe) in the CYB5R3 resides in the NADH domain of the protein, the aberrant function of which is detrimental. Conclusions: The present study expanded the variant spectrum of the CYB5R3 gene. This will facilitate genetic counselling of the same and other similar families carrying mutations in the CYB5R3 gene. [ABSTRACT FROM AUTHOR]

The mechanical properties of HTPE/PEG interpenetrating polymer network (IPN) binders were systemically studied with molecular dynamics (MDs) simulations and experiments. In this study, an algorithm was used to construct the crosslinking interpenetrating polymer network models and then the mechanical behaviors of Hydroxyl-terminated polyethylene glycol-tetrahydrofuran co-polyether/poly ethylene glycol (HTPE/PEG) IPN models were analyzed at a molecular scale. Firstly, glass transition temperatures (Tg), mean square displacement (MSD) and mechanical properties of IPN crosslinked model simulations showed that better thermomechanical parameters appeared at low temperatures, which were in good agreement with the experimental methods, including dynamic mechanical analysis and uniaxial tensile. Then bond-length distribution was performed to verify the crosslinked structures between prepolymers and curing agents. FTIR-ATR spectra analysis of four IPN binder specimens also gave a convictive result to the special interpenetrating polymer network of polyether polyurethane binders. Cohesive energy density and friction-free volume explained how the micro-structures of IPN crosslinked models and the force of inter-molecule chains affected the mechanical behaviors of the HTPE/PEG polyurethane matrix. Lastly, the morphology of IPN binder specimen tensile fracture indicated the mechanism at different temperatures. These studies were helpful in understanding the mechanical properties of HTPE/PEG interpenetrating polymer network binders and provide molecular insight into mechanisms of mechanical behaviors, which would guide the property improvement of HTPE propellant. [ABSTRACT FROM AUTHOR]

Overexpression of polo-like kinase 1 (PLK1) has been found in many different types of cancers. With its essential role in cell proliferation, PLK1 has been determined to be a broad-spectrum anti-cancer target. In this study, 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations were applied on a series of novel pteridinone derivatives as PLK1 inhibitors to discover anti-cancer drug candidates. In this work, three models—CoMFA (Q² = 0.67, R² = 0.992), CoMSIA/SHE (Q² = 0.69, R² = 0.974), and CoMSIA/SEAH (Q² = 0.66, R² = 0.975)—of pteridinone derivatives were established. The three models that were established gave R pred 2 = 0.683, R pred   2 = 0.758, and R pred   2 = 0.767, respectively. Thus, the predictive abilities of the three proposed models were successfully evaluated. The relations between the different champs and activities were well-demonstrated by the contour chart of the CoMFA and CoMSIA/SEAH models. The results of molecular docking indicated that residues R136, R57, Y133, L69, L82, and Y139 were the active sites of the PLK1 protein (PDB code: 2RKU), in which the more active ligands can inhibit the enzyme of PLK1. The results of the molecular dynamic MD simulation diagram were obtained to reinforce the previous molecular docking results, which showed that both inhibitors remained stable in the active sites of the PLK1 protein (PDB code: 2RKU) for 50 ns. Finally, a check of the ADME-Tox properties of the two most active molecules showed that molecular N° 28 could represent a good drug candidate for the therapy of prostate cancer diseases. [ABSTRACT FROM AUTHOR]

Herein we reported the design and synthesis of two series comprising twenty-two benzenesulfonamides that integrate the s-triazine moiety. Target compounds successfully suppressed the hCA IX, with IC50 ranging from 28.6 to 871 nM. Compounds 5d, 11b, 5b, and 7b were the most active analogues, which inhibited hCA IX isoform in the low nanomolar range (KI = 28.6, 31.9, 33.4, and 36.6 nM, respectively). Furthermore, they were assessed for their cytotoxic activity against a panel of 60 cancer cell lines following US-NCI protocol. According to five-dose assay, 13c showed significant anticancer activity than 5c with GI50-MID values of 25.08and 189.01 mM, respectively. Additionally, 13c's effects on wound healing, cell cycle disruption, and apoptosis induction in NCI-H460 cancer cells were examined. Further, docking studies combined with molecular dynamic simulation showed a stable complex with high binding affinity of 5d to hCA IX, exploiting a favourable H-bond and lipophilic interactions. [ABSTRACT FROM AUTHOR]

Hydrogenated amorphous silicon nitride is useful as an anti-reflection coating on solar cells. The addition of hydrogen atoms to amorphous silicon nitride can reduce the dangling bonds that exist on the surface. The objective of this paper is to clarify on the behavior of hydrogen atoms absorbed in silicon nitride during the hydrogenation process at various temperatures. We investigate, in particular, the silicon and hydrogen bonds that are formed by the transfer of electrons from hydrogen to silicon to form Si 1 − , Si 2 − , Si 3 − , and Si 4 − ions. The conversion of Si 1 − ions into Si 2 − ions and then also into Si 3 − and Si 4 − occurs during enhancement of the hydrogen atoms absorbed. Hydrogenated amorphous silicon nitride was stabilized through the passivation of dangling bonds of silicon atoms and nitrogen atoms by the absorbed hydrogen atoms. The passivation was indicated by enhancement of over-coordinated silicon and nitrogen atoms as well as the reduction of under-coordinated silicon and nitrogen atoms. It was found that the thermal energy from high hydrogenation temperature was primarily used by hydrogen atoms to diffuse more and to penetrate deeper into silicon nitride rather than being used for the ionization of silicon atoms. Finally, we stress that these reactive molecular dynamic simulations have led to substantial progress in understanding how hydrogen atoms interact with amorphous silicon nitride during hydrogenation. [ABSTRACT FROM AUTHOR]

The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 is one of the optimum targets for antiviral drug design and development. The hydroxyl groups of cytidine structures were modified with different aliphatic and aromatic groups to obtain 5´-O-acyl and 2´,3´-di-O-acyl derivatives, and then, these derivatives were employed in molecular modeling, antiviral prediction, molecular docking, molecular dynamics, pharmacological and POM studies. Density functional theory (DFT) at the B3LYP/6-31G++ level analyzed biochemical behavior and molecular electrostatic potential (MESP) of the modified cytidine derivatives. The antiviral parameters of the mutated derivatives revealed promising drug properties compared with those of standard antiviral drugs. Molecular docking has determined binding affinities and interactions between the cytidine derivatives and SARS-CoV-2 RdRp. The modified derivatives strongly interacted with prime Pro620 and Lys621 residues. The binding conformation and interactions stability were investigated by 200 ns of molecular dynamics simulations and predicted the compounds to firmly dock inside the RdRp binding pocket. Interestingly, the binding residues of the derivatives were revealed in high equilibrium showing an enhanced binding affinity for the molecules. Intermolecular interactions are dominated by both Van der Waals and electrostatic energies. Finally, the pharmacokinetic characterization of the optimized inhibitors confirmed the safety of derivatives due to their improved kinetic properties. The selected cytidine derivatives can be suggested as potential inhibitors against SARS-CoV-2. The POM Theory supports the hypothesis above by confirming the existence of an antiviral (Oδ-—O'δ-) pharmacophore site of Hits. [ABSTRACT FROM AUTHOR]