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The formation of amyloid fibrils is a common feature of many protein systems. It has implications in both health, as amyloid fibrils are implicated in over 30 degenerative diseases, and in the biological functions of proteins. Surfaces have long been known to affect the formation of fibrils but the specific effect depends on the details of both the surface and protein. Fully understanding the role of surfaces in fibrillization requires microscopic information on protein conformation on surfaces. In this paper replica exchange molecular dynamics simulation is used to investigate the model fibril forming protein, A β (10–40) (a 31-residue segment of the amyloid-beta protein) on surfaces of different hydrophobicity. Similar to other proteins A β (10–40) is found to adsorb strongly onto hydrophobic surfaces. It also adopts significantly different sets of conformations on hydrophobic and polar surfaces, as well as in bulk solution. On hydrophobic surfaces, it adopts partially helical structures, with the helices overlapping with beta-strand regions in the mature fibril. These may be helical intermediates on the fibril formation pathway, suggesting a mechanism for the enhanced fibril formation seen on hydrophobic surfaces. [ABSTRACT FROM AUTHOR]

The combination of wet-lab experimental data on multi-site combinatorial mutations and machine learning is an innovative method in protein engineering. In this study, we used an innovative sequence-activity relationship (innov'SAR) methodology based on novel descriptors and digital signal processing (DSP) to construct a predictive model. In this paper, 21 experimental (R)-selective amine transaminases from Aspergillus terreus (AT-ATA) were used as an input to predict higher thermostability mutants than those predicted using the existing data. We successfully improved the coefficient of determination (R2) of the model from 0.66 to 0.92. In addition, root-mean-squared deviation (RMSD), root-mean-squared fluctuation (RMSF), solvent accessible surface area (SASA), hydrogen bonds, and the radius of gyration were estimated based on molecular dynamics simulations, and the differences between the predicted mutants and the wild-type (WT) were analyzed. The successful application of the innov'SAR algorithm in improving the thermostability of AT-ATA may help in directed evolutionary screening and open up new avenues for protein engineering. [ABSTRACT FROM AUTHOR]

Inhibition of the Embryonic Ectoderm Development (EED) subunit in Polycomb Repressive Complex 2 (PRC2) can inhibit tumor growth. In this paper, we selected six experimentally designed EED competitive Inhibitors of the triazolopyrimidine derivatives class. We investigated the difference in the binding mode of the natural substrate to the Inhibitors and the effects of differences in the parent nuclei, heads, and tails of the Inhibitors on the inhibitory capacity. The results showed that the binding free energy of this class of Inhibitors was close to or lower compared to the natural substrate, providing an energetic basis for competitive inhibition. For the Inhibitors, the presence of a strong negatively charged group at the 6-position of the parent nucleus or the 8′-position of the head would make the hydrogen atom on the head imino group prone to flip, resulting in the vertical movement of the parent nucleus, which significantly decreased the inhibitory ability. When the 6-position of the parent nucleus was a nonpolar group, the parent nucleus would move horizontally, slightly decreasing the inhibitory ability. When the 8′-position of the head was methylene, it formed an intramolecular hydrophobic interaction with the benzene ring on the tail, resulting in a significant increase in inhibition ability. [ABSTRACT FROM AUTHOR]

Recently calcium alginate has been successfully applied to encapsulate asphalt rejuvenator, which can protect asphalt rejuvenator from early leakage and release asphalt rejuvenator when triggered by specific factors such as cracks. The interfacial adhesion property of asphalt binder with calcium alginate carrier is of great importance to its actual performance. In this paper, the molecular model of the interface region between asphalt binder and calcium alginate was established, and molecular dynamics simulations were performed on it to investigate the molecular interaction at the interface region. By extracting and processing the data during the simulation process, the interfacial adhesion behavior was expounded using the spreading coefficient (S), permeation depth and permeation degree. Furthermore, the interfacial adhesion strength was evaluated by adopting the interfacial adhesion work. Results showed that the value of S was greater than 0, implying that asphalt binder could wet the surface of calcium alginate. Saturate had the highest value of permeation degree, followed by resin, aromatic and asphaltene. However, asphalt binder could not infiltrate into the interior of TiO2, only accumulating and spreading on the surface of TiO2. The interfacial adhesion work of unaged and aged asphalt binder to calcium alginate was −114.18 mJ/m2 and −186.37 mJ/m2, respectively, similar to that of asphalt–aggregate interface. The van der Waals interactions contributed the most to the formation of the interfacial adhesion strength. In addition, a certain degree aging of asphalt binder and addition of titanium dioxide in the calcium alginate carrier were helpful to enhance the interfacial adhesion strength. [ABSTRACT FROM AUTHOR]

In order to investigate the self-healing behavior of asphalt binder at the molecule scale, the self-healing models of neat and aged asphalt binder with different damage degrees were established by introducing a vacuum pad between two layers filled with asphalt molecules. With this model, the self-healing process was simulated at various healing conditions to reveal the effects of oxidative aging, damage degree and healing temperature on the self-healing property. In addition, self-healing efficiency was evaluated using the indexes representative of the characteristics of different self-healing stages. Our results show that the oxidative aging weakened the stacked structure of the asphalt binder and increased the healing activation energy barrier. The increasing damage degree extended the distance for particles to travel, thus prolonging the time required for the crack interfaces contacting with each other. The elevated temperature improved the molecular mobility by supplying more energy to the molecular system. Furthermore, the self-healing process was evaluated quantitatively by the density variation at the crack closing stage and the diffusion coefficient at the intrinsic healing stage. The duration of each stage was influenced by the oxidative aging, damage degree and healing temperature. The findings in this paper are helpful to reveal and evaluate the self-healing property of asphalt binder. [ABSTRACT FROM AUTHOR]

Rutin is a natural flavonoid that carries out a variety of biological activities, but its application in medicine and food is limited by its water solubility. One of the classical methods used to enhance drug solubility is encapsulation with cyclodextrins. In this paper, the encapsulation of different cyclodextrins with rutin was investigated using a combination of experimental and simulation methods. Three inclusions of rutin/beta-cyclodextrin (β-CD), rutin/2-hydroxypropyl beta-cyclodextrin (HP-β-CD) and rutin/2,6-dimethyl beta-cyclodextrin (DM-β-CD) were prepared by the freeze-drying method, and the inclusions were analyzed using Fourier infrared spectroscopy (FTIR), X-ray diffraction analysis (XRD), differential scanning calorimetry (DSC) and ultraviolet–visible spectroscopy (UV) to characterize and demonstrate the formation of the inclusion complexes. Phase solubility studies showed that rutin formed a 1:1 stoichiometric inclusion complex and significantly increased its solubility. β-CD, HP-β-CD, DM-β-CD, rutin and the three inclusion complexes were modeled by using MS2018 and AutoDock 4.0, and molecular dynamics simulations were performed to calculate the solubility parameters, binding energies, mean square displacement (MSD), hydrogen bonding and radial distribution functions (RDF) after the equilibration of the systems. The results of simulation and experiment showed that rutin/DM-β-CD had the best encapsulation effect among the three cyclodextrin inclusion complexes. [ABSTRACT FROM AUTHOR]

The overexpression of p21-activated kinase 4 (PAK4) is associated with a variety of cancers. In this paper, the binding modes and inhibitory mechanisms of four 7H-pyrrolo[2,3-d]pyrimidine competitive inhibitors of PAK4 were investigated at the molecular level, mainly using molecular dynamics simulations and binding free energy calculations. The results show that the inhibitors had strong interactions with the hinge region, the β-sheets, and the residues with charged side chains around the 4-substituent. The terminal amino group of the inhibitor 5n was different from the other three, which could cause the enhancement of hydrogen bonds or electrostatic interactions formed with the surrounding residues. Thus, inhibitor 5n had the strongest inhibition capacity. The different halogen atoms on the 2-substituents of the inhibitors 5h, 5g, and 5e caused differences in the positions of the 2-benzene rings and affected the interactions of the hinge region. It also affected to some extent the orientations of the 4-imino groups and consequently their affinities for the surrounding charged residues. The combined results lead to the weakest inhibitory capacity of inhibitor 5e. [ABSTRACT FROM AUTHOR]

Restricted economic conditions and limited sewage treatment facilities in rural areas lead to the discharge of small-scale breeding wastewater containing higher values of residual beta-lactam antibiotics (β-lactams), which seriously threatens the aquatic environment. In this paper, molecular docking and a comprehensive method were performed to quantify and fit the source modification for the combined biodegradation of β-lactams. Using penicillin (PNC) as the target molecule, combined with contour maps for substitute modification, a three-dimensional quantitative structure–activity relationship (3D-QSAR) model was constructed for the high-performance combined biodegradation of β-lactams. The selected candidate with better environmental friendliness, functionality, and high performance was screened. By using the homology modeling algorithms, the mutant penicillin-binding proteins (PBPs) of Escherichia coli were constructed to have antibacterial resistance against β-lactams. The molecular docking was applied to obtain the target substitute by analyzing the degree of antibacterial resistance of β-lactam substitute. The combined biodegradation of β-lactams and substitute in the constructed wetland (CW) by different wetland plant root secretions was studied using molecular dynamics simulations. The result showed a 49.28% higher biodegradation of the substitutes than PNC when the combined wetland plant species of Eichhornia crassipes, Phragmites australis, and Canna indica L. were employed. [ABSTRACT FROM AUTHOR]

Hydrocarbon vapor adsorption experiments (HVAs) are one of the most prevalent methods used to evaluate the proportion of adsorbed state oil, critical in understanding the recoverable resources of shale oil. HVAs have some limitations, which cannot be directly used to evaluate the proportion of adsorbed state oil. The proportion of adsorbed state oil from HVA is always smaller than that in shale oil reservoirs, which is caused by the difference in adsorption characteristics of liquid and gaseous hydrocarbons. The results of HVA need to be corrected. In this paper, HVA was conducted with kaolinite, an important component of shale. A new method is reported here to evaluate the proportion of adsorbed state oil. Molecular dynamics simulations (MDs) of gaseous/liquid hydrocarbons with the same temperature and pressure as the HVAs were used as a reference to reveal the errors in the HVAs evaluation from the molecular scale. We determine the amount of free state of hydrocarbons by HVAs, and then calculate the proportion of adsorbed state oil by the liquid hydrocarbon MD simulation under the same conditions. The results show that gaseous hydrocarbons adsorptions are monolayer at low relative pressures and bilayer at high relative pressures. The liquid hydrocarbons adsorption is multilayer adsorption. The adsorption capacity of liquid hydrocarbons is over 2.7 times higher than gaseous hydrocarbons. The new method will be more effective and accurate to evaluate the proportion of adsorbed state oil. [ABSTRACT FROM AUTHOR]

The relationship between structure and reactivity plays a dominant role in water dissociation on the various TiO2 crystallines. To observe the adsorption and dissociation behavior of H2O, the reaction force field (ReaxFF) is used to investigate the dynamic behavior of H2O on rutile (110) and anatase (101) surfaces in an aqueous environment. Simulation results show that there is a direct proton transfer between the adsorbed H2O (H2Oad) and the bridging oxygen (Obr) on the rutile (110) surface. Compared with that on the rutile (110) surface, an indirect proton transfer occurs on the anatase (101) surface along the H-bond network from the second layer of water. This different mechanism of water dissociation is determined by the distance between the 5-fold coordinated Ti (Ti5c) and Obr of the rutile and anatase TiO2 surfaces, resulting in the direct or indirect proton transfer. Additionally, the hydrogen bond (H-bond) network plays a crucial role in the adsorption and dissociation of H2O on the TiO2 surface. To describe interfacial water structures between TiO2 and bulk water, the double-layer model is proposed. The first layer is the dissociated H2O on the rutile (110) and anatase (101) surfaces. The second layer forms an ordered water structure adsorbed to the surface Obr or terminal OH group through strong hydrogen bonding (H-bonding). Affected by the H-bond network, the H2O dissociation on the rutile (110) surface is inhibited but that on the anatase (101) surface is promoted. [ABSTRACT FROM AUTHOR]

A bidirectional pulsed electric field (BPEF) method is considered a simple and novel technique to demulsify O/W emulsions. In this paper, molecular dynamics simulation was used to investigate the transformation and aggregation behavior of oil droplets in O/W emulsion under BPEF. Then, the effect of surfactant (sodium dodecyl sulfate, SDS) on the demulsification of O/W emulsion was investigated. The simulation results showed that the oil droplets transformed and moved along the direction of the electric field. SDS molecules can shorten the aggregation time of oil droplets in O/W emulsion. The electrostatic potential distribution on the surface of the oil droplet, the elongation length of the oil droplets, and the mean square displacement (MSD) of SDS and asphaltene molecules under an electric field were calculated to explain the aggregation of oil droplets under the simulated pulsed electric field. The simulation also showed that the two oil droplets with opposite charges have no obvious effect on the aggregation of the oil droplets. However, van der Waals interactions between oil droplets was the main factor in the aggregation. [ABSTRACT FROM AUTHOR]

Background: In recent years, the advancement of computational chemistry has offered new insights into the rational design of molecularly imprinted polymers (MIPs). From this aspect, our study tried to give quantitative parameters for evaluating imprinting efficiency and exploring the formation mechanism of MIPs by combining simulation and experiments. Methods: The pre-polymerization system of sulfadimethoxine (SDM) was investigated using a combination of quantum chemical (QC) calculations and molecular dynamics (MD) simulations. MIPs were prepared on the surface of silica gel by a surface-initiated supplemental activator and reducing agent atom transfer radical polymerization (SI-SARA ATRP). Results: The results of the QC calculations showed that carboxylic monomers exhibited higher bonding energies with template molecules than carboxylic ester monomers. MD simulations confirmed the hydrogen bonding sites predicted by QC calculations. Furthermore, it was observed that only two molecules of monomers could bind up to one molecule of SDM, even when the functional monomer ratio was up to 10. Two quantitative parameters, namely, the effective binding number (EBN) and the maximum hydrogen bond number (HBNMax), were defined. Higher values of EBN and HBNMax indicated a higher effective binding efficiency. Hydrogen bond occupancies and RDF analysis were performed to analyze the hydrogen bond formation between the template and the monomer from different perspectives. Furthermore, under the influence of the EBN and collision probability of the template and the monomers, the experimental results show that the optimal molar ratio of template to monomer is 1:3. Conclusions: The method of monomer screening presented in this study can be extended to future investigations of pre-polymerization systems involving different templates and monomers. [ABSTRACT FROM AUTHOR]

Triethanolamine (TEA) is a promising eco-friendly alternative to inorganic ammonia for enhancing surface sulfidization and flotation recovery of smithsonite. Micro-flotation experiments revealed an enhancement in smithsonite recovery to 95.21% with TEA modification, comparable to the results obtained using ammonia. The mechanisms behind the ability of TEA to enhance the sulfidization process were investigated through surface analysis and molecular dynamics simulations. TEA modification increased the content of sulfidization products, the proportion of crucial S22− in adsorbed products, and the thickness and size of the sulfidization product layer. The complexation of TEA with Zn sites formed positively charged Zn–TEA complexes that adsorb onto the smithsonite surface. These complexes promoted negatively charged HS− adsorption, creating a multi-layered adsorption structure. Moreover, TEA modification reduced the total energy required for the sulfidization. These findings open up new possibilities for using eco-friendly reagents in mineral processing, highlighting the potential of TEA in green mineral processing practices. [ABSTRACT FROM AUTHOR]

In many practical applications involving surfactants, achieving defoaming without affecting interfacial activity is a challenge. In this study, the antifoaming performance of REP-type block polymer nonionic surfactant C12EOmPOn was determined, and molecular dynamics simulation method was employed to investigate the molecular behaviors of surfactants at a gas/water interface, the detailed arrangement information of the different structural segments of the surfactant molecules and the inter-/intra-interactions between all the structural motifs in the interfacial layer were analyzed systematically, by which the antifoaming mechanisms of the surfactants were revealed. The results show that the EO and PO groups of REP-type polyether molecules are located in the aqueous phase near the interface, and the hydrophobic tails distribute separately, lying almost flat on the gas/water interface. The interaction between the same groups of EOs and POs is significantly stronger than with water. REP block polyethers with high polymerization degrees of EO and PO are more inclined to overlap into dense layers, resulting in the formation of aggregates resembling "oil lenses" spreading on the gas/water interface, which exerts a stronger antifoaming effect. This study provides a smart approach to obtaining efficient antifoaming performance at room temperature without adding other antifoam ingredients. [ABSTRACT FROM AUTHOR]

The research and development of alternatives to long-chain fluorocarbon surfactants are desperately needed because they are extremely toxic, difficult to break down, seriously harm the environment, and limit the use of conventional aqueous film-forming foam fire extinguishing agents. In this study, mixed surfactant systems containing the short-chain fluorocarbon surfactant perfluorohexanoic acid (PFHXA) and the hydrocarbon surfactant sodium dodecyl sulfate (SDS) were investigated by molecular dynamics simulation to investigate the microscopic properties at the air/water interface at different molar ratios. Some representative parameters, such as surface tension, degree of order, density distribution, radial distribution function, number of hydrogen bonds, and solvent-accessible surface area, were calculated. Molecular dynamics simulations show that compared with a single type of surfactant, mixtures of surfactants provide superior performance in improving the interfacial properties of the gas–liquid interface. A dense monolayer film is formed by the strong synergistic impact of the two surfactants. Compared to the pure SDS system, the addition of PFHXA caused SDS to be more vertically oriented at the air/water interface with a reduced tilt angle, and a more ordered structure of the mixed surfactants was observed. Hydrogen bonding between SDS headgroups and water molecules is enhanced with the increasing PFHXA. The surface activity is arranged in the following order: PFHXA/SDS = 1:1 > PFHXA/SDS = 3:1 > PFHXA/SDS = 1:3. These results indicate that a degree of synergistic relationship exists between PFHXA and SDS at the air/water interface. [ABSTRACT FROM AUTHOR]

Shut-in after fracturing is generally adopted for wells in shale oil reservoirs, and imbibition occurring in matrix nanopores has been proven as an effective way to improve recovery. In this research, a molecular dynamics (MD) simulation was used to investigate the effects of wettability and pressure on nanopore imbibition during shut-in for a typical shale reservoir, Jimsar. The results indicate that the microscopic advancement mechanism of the imbibition front is the competitive adsorption between "interfacial water molecules" at the imbibition front and "adsorbed oil molecules" on the pore wall. The essence of spontaneous imbibition involves the adsorption and aggregation of water molecules onto the hydroxyl groups on the pore wall. The flow characteristics of shale oil suggest that the overall push of the injected water to the oil phase is the main reason for the displacement of adsorbed oil molecules. Thus, shale oil, especially the heavy hydrocarbon component in the adsorbed layer, tends to slip on the walls. However, the weak slip ability of heavy components on the wall surface is an important reason that restricts the displacement efficiency of shale oil during spontaneous imbibition. The effectiveness of spontaneous imbibition is strongly dependent on the hydrophilicity of the matrix pore's wall. The better hydrophilicity of the matrix pore wall facilitates higher levels of adsorption and accumulation of water molecules on the pore wall and requires less time for "interfacial water molecules" to compete with adsorbed oil molecules. During the forced imbibition process, the pressure difference acts on both the bulk oil and the boundary adsorption oil, but mainly on the bulk oil, which leads to the occurrence of wetting hysteresis. Meanwhile, shale oil still existing in the pore always maintains a good, stratified adsorption structure. Because of the wetting hysteresis phenomenon, as the pressure difference increases, the imbibition effect gradually increases, but the actual capillary pressure gradually decreases and there is a loss in the imbibition velocity relative to the theoretical value. Simultaneously, the decline in hydrophilicity further weakens the synergistic effect on the imbibition of the pressure difference because of the more pronounced wetting hysteresis. Thus, selecting an appropriate well pressure enables cost savings and maximizes the utilization of the formation's natural power for enhanced oil recovery (EOR). [ABSTRACT FROM AUTHOR]

While nanoporous graphene oxide (GO) is recognized as one of the most promising reverse osmosis desalination membranes, limited attention has been paid to controlling desalination performance through the large GO pores, primarily due to significant ion leakage resulting in the suboptimal performance of these pores. In this study, we employed a molecular dynamics simulation approach to demonstrate that Mg2+ ions, adhered to carboxylated GO nanopores, can function as gates, regulating the transport of ions (Na+ and Cl−) through the porous GO membrane. Specifically, the presence of divalent cations near a nanopore reduces the concentration of salt ions in the vicinity of the pore and prolongs their permeation time across the pore. This subsequently leads to a notable enhancement in salt rejection rates. Additionally, the ion rejection rate increases with more adsorbed Mg2+ ions. However, the presence of the adsorbed Mg2+ ions compromises water transport. Here, we also elucidate the impact of graphene oxidation degree on desalination. Furthermore, we design an optimal combination of adsorbed Mg2+ ion quantity and oxidation degree to achieve high water flux and salt rejection rates. This work provides valuable insights for developing new nanoporous graphene oxide membranes for controlled water desalination. [ABSTRACT FROM AUTHOR]

In this work, the modified attachment energy model was used to predict the crystal morphology of isosorbide mononitrate (ISMN) in the dichloromethane (CH2Cl2) solvent system and dichloromethane-n-hexane (CH2Cl2-C6H14) mixed solvent system. The solvent effect can significantly affect the crystal morphology, which can profoundly impact both the drug's physicochemical properties and the subsequent technological treatment process. In addition, the interactions between solvent molecules and crystal faces were investigated using molecular dynamics simulation, and radial distribution function (RDF) analysis was performed to determine the types of interactions. The structural parameter S was introduced to characterize the roughness of each crystal surface; the change in the CH2Cl2 diffusion coefficient before and after the addition of C6H14 was analyzed using mean square displacement (MSD). The calculation results of the modified attachment energy from the two solvent systems revealed that C6H14 could accelerate crystal growth, while the crystal morphology was not greatly affected, which is of some significance as a guide for the industrial crystallization process. [ABSTRACT FROM AUTHOR]

The "Long-COVID syndrome" has posed significant challenges due to a lack of validated therapeutic options. We developed a novel multi-step virtual screening strategy to reliably identify inhibitors against 3-chymotrypsin-like protease of SARS-CoV-2 from abundant flavonoids, which represents a promising source of antiviral and immune-boosting nutrients. We identified 57 interacting residues as contributors to the protein-ligand binding pocket. Their energy interaction profiles constituted the input features for Machine Learning (ML) models. The consensus of 25 classifiers trained using various ML algorithms attained 93.9% accuracy and a 6.4% false-positive-rate. The consensus of 10 regression models for binding energy prediction also achieved a low root-mean-square error of 1.18 kcal/mol. We screened out 120 flavonoid hits first and retained 50 drug-like hits after predefined ADMET filtering to ensure bioavailability and safety profiles. Furthermore, molecular dynamics simulations prioritized nine bioactive flavonoids as promising anti-SARS-CoV-2 agents exhibiting both high structural stability (root-mean-square deviation < 5 Å for 218 ns) and low MM/PBSA binding free energy (<−6 kcal/mol). Among them, KB-2 (PubChem-CID, 14630497) and 9-O-Methylglyceofuran (PubChem-CID, 44257401) displayed excellent binding affinity and desirable pharmacokinetic capabilities. These compounds have great potential to serve as oral nutraceuticals with therapeutic and prophylactic properties as care strategies for patients with long-COVID syndrome. [ABSTRACT FROM AUTHOR]

Carbon dioxide flooding is one of the main methods used to improve crude oil recovery. It can not only improve oil recovery but also reduce greenhouse gas emissions. However, the addition of carbon dioxide makes crude oil become a more complex multiphase fluid; that is, carbon dioxide flooding-produced fluid, in which CO2 and various components in crude oil mass transfer each other. This results in significant changes in the structure and properties of crude oil that increase the hazards associated with its gathering and transportation. Therefore, it is very important to explore the microscopic mechanism for the diffusion mass transfer of CO2 and crude oil in this fluid, especially during its gathering and transportation. In this study, the diffusion mass transfer process of CO2 and crude oil in fluids produced via CO2 flooding is studied using molecular dynamics, and the influences of temperature, gas–oil ratio and water content are explored. Observations of the configuration and dynamic behaviour of the system show that after the system reaches equilibrium, the majority of the CO2 molecules are distributed at the oil–water interface, and CO2 is more prone to diffusing into the oil phase than the water phase. Increases in temperature and water content inhibit, while increases in the gas–oil ratio promote, the diffusion mass transfer of CO2 in the crude oil system. The results of this study reveal the mechanism for the diffusion mass transfer of CO2 and crude oil in fluids produced via CO2 flooding and account for the influence of the water phase, which is consistent with actual production conditions and has certain guiding significance for the safe operation of oil and gas gathering and transportation. [ABSTRACT FROM AUTHOR]

Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand–protein complexes may shed light on rational design of potent ligands in the future. [ABSTRACT FROM AUTHOR]

Novel peptide dendrimer with Lys-2His repeating units was recently synthesized, studied by NMR (Molecules, 2019, 24, 2481) and tested as a nanocontainer for siRNA delivery (Int. J. Mol. Sci., 2020, 21, 3138). Histidine amino acid residues were inserted in the spacers of this dendrimer. Increase of their charge with a pH decrease turns a surface-charged dendrimer into a volume-charged one and should change all properties. In this paper, the molecular dynamics simulation method was applied to compare the properties of the dendrimer in water with explicit counterions at two different pHs (at normal pH with neutral histidines and at low pH with fully protonated histidines) in a wide interval of temperatures. We obtained that the dendrimer at low pH has essentially larger size and size fluctuations. The electrostatic properties of the dendrimers are different but they are in good agreement with the theoretical soft sphere model and practically do not depend on temperature. We have shown that the effect of pairing of side imidazole groups is much stronger in the dendrimer with neutral histidines than in the dendrimer with protonated histidines. We also demonstrated that the capacity of a nanocontainer based on this dendrimer with protonated histidines is significantly larger than that of a nanocontainer with neutral histidines. [ABSTRACT FROM AUTHOR]

Cancer cells can evade immune surveillance through binding of its transmembrane receptor CD47 to CD172a on myeloid cells. CD47 is recognized as a promising immune checkpoint for cancer immunotherapy inhibiting macrophage phagocytosis. N-terminal post-translated modification (PTM) via glutaminyl cyclase is a landmark event in CD47 function maturation, but the molecular mechanism underlying the mechano-chemical regulation of the modification on CD47/CD172a remains unclear. Here, we performed so-called "ramp-clamp" steered molecular dynamics (SMD) simulations, and found that the N-terminal PTM enhanced interaction of CD172a with CD47 by inducing a dynamics-driven contraction of the binding pocket of the bound CD172a, an additional constraint on CYS15 on CD47 significantly improved the tensile strength of the complex with or without PTM, and a catch bond phenomenon would occur in complex dissociation under tensile force of 25 pN in a PTM-independent manner too. The residues GLN52 and SER66 on CD172a reinforced the H-bonding with their partners on CD47 in responding to PTM, while ARG69 on CD172 with its partner on CD47 might be crucial in the structural stability of the complex. This work might serve as molecular basis for the PTM-induced function improvement of CD47, should be helpful for deeply understanding CD47-relevant immune response and cancer development, and provides a novel insight in developing of new strategies of immunotherapy targeting this molecule interaction. [ABSTRACT FROM AUTHOR]

Two extracellular domains of the adhesive receptor DNAM-1 are involved in various cellular biological processes through binding to ligand CD155, usually under a mechano-microenvironment. The first extracellular domain (D1) plays a key role in recognition, but the function of the second extracellular domain (D2) and effects of force on the interaction of DNAM-1 with CD155 remain unclear. We herein studied the interaction of DNAM-1 with CD155 by performing steered molecular dynamics (MD) simulations, and observed the roles of tensile force and D2 on the affinity of DNAM-1 to CD155. The results showed that D2 improved DNAM-1 affinity to CD155; the DNAM-1/CD155 complex had a high mechanical strength and a better mechanical stability for its conformational conservation either at pulling with constant velocity or under constant tensile force (≤100 pN); the catch–slip bond transition governed CD155 dissociation from DNAM-1; and, together with the newly assigned key residues in the binding site, force-induced conformation changes should be responsible for the mechanical regulation of DNAM-1′s affinity to CD155. This work provided a novel insight in understanding the mechanical regulation mechanism and D2 function in the interaction of DNAM-1 with CD155, as well as their molecular basis, relevant transmembrane signaling, and cellular immune responses under a mechano-microenvironment. [ABSTRACT FROM AUTHOR]

The monkeypox outbreak has become a global public health emergency. The lack of valid and safe medicine is a crucial obstacle hindering the extermination of orthopoxvirus infections. The identification of potential inhibitors from natural products, including Traditional Chinese Medicine (TCM), by molecular modeling could expand the arsenal of antiviral chemotherapeutic agents. Monkeypox DNA topoisomerase I (TOP1) is a highly conserved viral DNA repair enzyme with a small size and low homology to human proteins. The protein model of viral DNA TOP1 was obtained by homology modeling. The reliability of the TOP1 model was validated by analyzing its Ramachandran plot and by determining the compatibility of the 3D model with its sequence using the Verify 3D and PROCHECK services. In order to identify potential inhibitors of TOP1, an integrated library of 4103 natural products was screened via Glide docking. Surface Plasmon Resonance (SPR) was further implemented to assay the complex binding affinity. Molecular dynamics simulations (100 ns) were combined with molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) computations to reveal the binding mechanisms of the complex. As a result, three natural compounds were highlighted as potential inhibitors via docking-based virtual screening. Rosmarinic acid, myricitrin, quercitrin, and ofloxacin can bind TOP1 with KD values of 2.16 μM, 3.54 μM, 4.77 μM, and 5.46 μM, respectively, indicating a good inhibitory effect against MPXV. The MM/PBSA calculations revealed that rosmarinic acid had the lowest binding free energy at −16.18 kcal/mol. Myricitrin had a binding free energy of −13.87 kcal/mol, quercitrin had a binding free energy of −9.40 kcal/mol, and ofloxacin had a binding free energy of −9.64 kcal/mol. The outputs (RMSD/RMSF/Rg/SASA) also indicated that the systems were well-behaved towards the complex. The selected compounds formed several key hydrogen bonds with TOP1 residues (TYR274, LYS167, GLY132, LYS133, etc.) via the binding mode analysis. TYR274 was predicted to be a pivotal residue for compound interactions in the binding pocket of TOP1. The results of the enrichment analyses illustrated the potential pharmacological networks of rosmarinic acid. The molecular modeling approach may be acceptable for the identification and design of novel poxvirus inhibitors; however, further studies are warranted to evaluate their therapeutic potential. [ABSTRACT FROM AUTHOR]

Citrus greening, also known as Huanglongbing (HLB), is caused by the unculturable bacterium Candidatus Liberibacter spp. (e.g., CLas), and has caused a devastating decline in citrus production in many areas of the world. As of yet, there are no definitive treatments for controlling the disease. Antimicrobial peptides (AMPs) that have the potential to block secretion-dependent effector proteins at the outer-membrane domains were screened in silico. Predictions of drug-receptor interactions were built using multiple in silico techniques, including molecular docking analysis, molecular dynamics, molecular mechanics generalized Born surface area analysis, and principal component analysis. The efflux pump TolC of the Type 1 secretion system interacted with natural bacteriocin plantaricin JLA-9, blocking the β barrel. The trajectory-based principal component analysis revealed the possible binding mechanism of the peptides. Furthermore, in vitro assays using two closely related culturable surrogates of CLas (Liberibacter crescens and Rhizobium spp.) showed that Plantaricin JLA-9 and two other screened AMPs inhibited bacterial growth and caused mortality. The findings contribute to designing effective therapies to manage plant diseases associated with Candidatus Liberibacter spp. [ABSTRACT FROM AUTHOR]

In this paper, we explain the amphoteric character of the cartilage surface by studying a lipid bilayer model built from phospholipids. We examined the interfacial tension values and molecular dynamics simulation in solutions of varying pH. The effects of negative and positive charge density (or fixed charges) on the (cartilage/cartilage) friction coefficient were investigated. In physiological (or synovial) fluid, after the isoelectric point (pI), the curve of interfacial tension decreases rapidly as it reaches pH 7.4 and then approaches a constant value at higher pH. It was shown that the curve of the interfacial tension curve exhibits a maximum value at the isoelectric point with a Gaussian shape feature. The phospholipid bilayers facilitate an almost frictionless contact in the joint. Moreover, the slippage of the bilayer and the short-range repulsion between the surfaces of the negatively charged cartilage surfaces are the main determinants of the low frictional properties of the joint. [ABSTRACT FROM AUTHOR]

Adsorption is one of the most successful physicochemical approaches for removing heavy metal contaminants from polluted water. The use of residual biomass for the production of adsorbents has attracted a lot of attention due to its cheap price and environmentally friendly approach. The transformation of Sargassum—an invasive brown macroalga—into activated carbon (AC) via phosphoric acid thermochemical activation was explored in an effort to increase the value of Sargassum seaweed biomass. Several techniques (nitrogen adsorption, pHPZC, Boehm titration, FTIR and XPS) were used to characterize the physicochemical properties of the activated carbons. The SAC600 3/1 was predominantly microporous and mesoporous (39.6% and 60.4%, respectively) and revealed a high specific surface area (1695 m2·g−1). To serve as a comparison element, a commercial reference activated carbon with a large specific surface area (1900 m2·g−1) was also investigated. The influence of several parameters on the adsorption capacity of AC was studied: solution pH, solution temperature, contact time and Cr(VI) concentration. The best adsorption capacities were found at very acid (pH 2) solution pH and at lower temperatures. The adsorption kinetics of SAC600 3/1 fitted well a pseudo-second-order type 1 model and the adsorption isotherm was better described by a Jovanovic-Freundlich isotherm model. Molecular dynamics (MD) simulations confirmed the experimental results and determined that hydroxyl and carboxylate groups are the most influential functional groups in the adsorption process of chromium anions. MD simulations also showed that the addition of MgCl2 to the activated carbon surface before adsorption experiments, slightly increases the adsorption of HCrO4− and CrO42− anions. Finally, this theoretical study was experimentally validated obtaining an increase of 5.6% in chromium uptake. [ABSTRACT FROM AUTHOR]

Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)3 in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions. [ABSTRACT FROM AUTHOR]

Astilbin is a dihydroflavonol glycoside identified in many natural plants and functional food with promising biological activities which is used as an antioxidant in the pharmaceutical and food fields. This work investigated the interaction between astilbin and human serum albumin (HSA) and their effects on the antioxidant activity of astilbin by multi-spectroscopic and molecular modeling studies. The experimental results show that astilbin quenches the fluorescence emission of HSA through a static quenching mechanism. Astilbin and HSA prefer to bind at the Site Ⅰ position, which is mainly maintained by electrostatic force, hydrophobic and hydrogen bonding interactions. Multi-spectroscopic and MD results indicate that the secondary structure of HSA could be changed because of the interaction of astilbin with HSA. DPPH radical scavenging assay shows that the presence of HSA reduces the antioxidant capacity of astilbin. The explication of astilbin–HSA binding mechanism will provide insights into clinical use and resource development of astilbin in food and pharmaceutical industries. [ABSTRACT FROM AUTHOR]

Hydroxamate, as a zinc-binding group (ZBG), prevails in the design of histone deacetylase 6(HDAC6) inhibitors due to its remarkable zinc-chelating capability. However, hydroxamate-associated genotoxicity and mutagenicity have limited the widespread application of corresponding HDAC6 inhibitors in the treatment of human diseases. To avoid such side effects, researchers are searching for novel ZBGs that may be used for the synthesis of HDAC6 inhibitors. In this study, a series of stereoisomeric compounds were designed and synthesized to discover non-hydroxamate HDAC6 inhibitors using α-amino amide as zinc-ion-chelating groups, along with a pair of enantiomeric isomers with inverted L-shaped vertical structure as cap structures. The anti-proliferative activities were determined against HL-60, Hela, and RPMI 8226 cells, and 7a and its stereoisomer 13a exhibited excellent activities against Hela cells with IC50 = 0.31 µM and IC50 = 5.19 µM, respectively. Interestingly, there is a significant difference between the two stereoisomers. Moreover, an evaluation of cytotoxicity toward human normal liver cells HL-7702 indicated its safety for normal cells. X-ray single crystal diffraction was employed to increase insights into molecule structure and activities. It was found that the carbonyl of the amide bond is on the different side from the amino and pyridine nitrogen atoms. To identify possible protein targets to clarify the mechanism of action and biological activity of 7a, a small-scale virtual screen using reverse docking for HDAC isoforms (1–10) was performed and the results showed that HDAC6 was the best receptor for 7a, suggesting that HDAC6 may be a potential target for 7a. The interaction pattern analysis showed that the α-amino amide moiety of 7a coordinated with the zinc ion of HDAC6 in a bidentate chelate manner, which is similar to the chelation pattern of hydroxamic acid. Finally, the molecular dynamics simulation approaches were used to assess the docked complex's conformational stability. In this work, we identified 7a as a potential HDAC6 inhibitor and provide some references for the discovery of non-hydroxamic acid HDAC6 inhibitors. [ABSTRACT FROM AUTHOR]

Opioid receptors are members of the group of G protein-couple receptors, which have been proven to be effective targets for treating severe pain. The interactions between the opioid receptors and corresponding ligands and the receptor's activation by different agonists have been among the most important fields in opioid research. In this study, with compound M1, an active metabolite of tramadol, as the clue compound, several aminomethyl tetrahydronaphthalenes were designed, synthesized and assayed upon opioid receptors. With the resultant compounds FW-AII-OH-1 (Ki = 141.2 nM for the κ opioid receptor), FW-AII-OH-2 (Ki = 4.64 nM for the δ opioid receptor), FW-DI-OH-2 (Ki = 8.65 nM for the δ opioid receptor) and FW-DIII-OH-2 (Ki = 228.45 nM for the δ opioid receptor) as probe molecules, the structural determinants responsible for the subtype selectivity and activation mechanisms were further investigated by molecular modeling and molecular dynamics simulations. It was shown that Y7.43 was a key residue in determining the selectivity of the three opioid receptors, and W6.58 was essential for the selectivity of the δ opioid receptor. A detailed stepwise discovered agonist-induced signal transduction mechanism of three opioid receptors by aminomethyl tetrahydronaphthalene compounds was proposed: the 3–7 lock between TM3 and TM7, the DRG lock between TM3 and TM6 and rearrangement of I3.40, P5.50 and F6.44, which resulted in the cooperative movement in 7 TMs. Then, the structural relaxation left room for the binding of the G protein at the intracellular site, and finally the opioid receptors were activated. [ABSTRACT FROM AUTHOR]

In order to solve the problem of demulsification difficulties in Liaohe Oilfield, 24 kinds of demulsifiers were screened by using the interface generation energy (IFE) module in the molecular dynamics simulation software Materials Studio to determine the ability of demulsifier molecules to reduce the total energy of the oil–water interface after entering the oil–water interface. Neural network analysis (NNA) and genetic function approximation (GFA) were used as technical means to predict the demulsification effect of the Liaohe crude oil demulsifier. The simulation results show that the SDJ9927 demulsifier with ethylene oxide (EO) and propylene oxide (PO) values of 21 (EO) and 44 (PO) reduced the total energy and interfacial tension of the oil–water interface to the greatest extent, and the interfacial formation energy reached −640.48 Kcal/mol. NNA predicted that the water removal amount of the SDJ9927 demulsifier was 7.21 mL, with an overall error of less than 1.83. GFA predicted that the water removal amount of the SDJ9927 demulsifier was 7.41mL, with an overall error of less than 0.9. The predicted results are consistent with the experimental screening results. SDJ9927 had the highest water removal rate and the best demulsification effect. NNA and GFA had high correlation coefficients, and their R2s were 0.802 and 0.861, respectively. The higher R2 was, the more accurate the prediction accuracy was. Finally, the demulsification mechanism of the interfacial film breaking due to the collision of fluorinated polyether demulsifiers was studied. It was found that the carbon–fluorine chain had high surface activity and high stability, which could protect the carbon–carbon bond in the demulsifier molecules to ensure that there was no re-emulsion due to the stirring external force. [ABSTRACT FROM AUTHOR]

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems. [ABSTRACT FROM AUTHOR]

Tribological surgical adjuvants constitute a therapeutic discipline made possible by surgical advances in the treatment of damaged articular cartilage beyond palliative care. The purpose of this study is to analyze interactions between hyaluronic acid and phospholipid molecules, and the formation of geometric forms, that play a role in the facilitated lubrication of synovial joint organ systems. The analysis includes an evaluation of the pathologic state to detail conditions that may be encountered by adjuvants during surgical convalescence. The synovial fluid changes in pH, hyaluronic acid polydispersity, and phospholipid concentration associated with osteoarthritis are presented as features that influence the lubricating properties of adjuvant candidates. Molecular dynamic simulation studies are presented, and the Rouse model is deployed, to rationalize low molecular weight hyaluronic acid behavior in an osteoarthritic environment of increased pH and phospholipid concentration. The results indicate that the hyaluronic acid radius of gyration time evolution is both pH- and phospholipid concentration-dependent. Specifically, dipalmitoylphosphatidylcholine induces hydrophobic interactions in the system, causing low molecular weight hyaluronic acid to shrink and at high concentration be absorbed into phospholipid vesicles. Low molecular weight hyaluronic acid appears to be insufficient for use as a tribological surgical adjuvant because an increased pH and phospholipid concentration induces decreased crosslinking that prevents the formation of supramolecular lubricating forms. Dipalmitoylphosphatidylcholine remains an adjuvant candidate for certain clinical situations. The need to reconcile osteoarthritic phenotypes is a prerequisite that should serve as a framework for future adjuvant design and subsequent tribological testing. [ABSTRACT FROM AUTHOR]

Energetic molecular crystals are widely applied for military and civilian purposes, and molecular forcefields (FF) are indispensable for treating the microscopic issues therein. This article reviews the three types of molecular FFs that are applied widely for describing energetic crystals—classic FFs, consistent FFs, and reactive FFs (ReaxFF). The basic principle of each type of FF is briefed and compared, with the application introduced, predicting polymorph, morphology, thermodynamics, vibration spectra, thermal property, mechanics, and reactivity. Finally, the advantages and disadvantages of these FFs are summarized, and some directions of future development are suggested. [ABSTRACT FROM AUTHOR]

Sub-Saharan Africa is profoundly challenged with African Animal Trypanosomiasis and the available trypanocides are faced with drawbacks, necessitating the search for novel agents. Herein, the chemotherapeutic potential of phloroglucinol on T. congolense infection and its inhibitory effects on the partially purified T. congolense sialidase and phospholipase A2 (PLA2) were investigated. Treatment with phloroglucinol for 14 days significantly (p < 0.05) suppressed T. congolense proliferation, increased animal survival and ameliorated anemia induced by the parasite. Using biochemical and histopathological analyses, phloroglucinol was found to prevent renal damages and splenomegaly, besides its protection against T. congolense-associated increase in free serum sialic acids in infected animals. Moreover, the compound inhibited bloodstream T. congolense sialidase via mixed inhibition pattern with inhibition binding constant (Ki) of 0.181 µM, but a very low uncompetitive inhibitory effects against PLA2 (Ki > 9000 µM) was recorded. Molecular docking studies revealed binding energies of −4.9 and −5.3 kcal/mol between phloroglucinol with modeled sialidase and PLA2 respectively, while a 50 ns molecular dynamics simulation using GROMACS revealed the sialidase-phloroglucinol complex to be more compact and stable with higher free binding energy (−67.84 ± 0.50 kJ/mol) than PLA2-phloroglucinol complex (−77.17 ± 0.52 kJ/mol), based on MM-PBSA analysis. The sialidase-phloroglucinol complex had a single hydrogen bond interaction with Ser453 while none was observed for the PLA2-phloroglucinol complex. In conclusion, phloroglucinol showed moderate trypanostatic activity with great potential in ameliorating some of the parasite-induced pathologies and its anti-anemic effects might be linked to inhibition of sialidase rather than PLA2. [ABSTRACT FROM AUTHOR]

In this work, molecular dynamics simulations were performed to study the pH-induced structural transitions for a CTAB/p-toluic acid solution. Spherical and cylindrical micelles were obtained for aqueous surfactants at pH 2 and 7, respectively, which agrees well with the experimental observations. The structural properties of two different micelles were analyzed through the density distributions of components and the molecular orientations of CTA+ and toluic acid inside the micelles. It was found that the bonding interactions between CTA+ and toluic in spherical and cylindrical micelles are very different. Almost all the ionized toluic acid (PTA−) in the solution at pH 7 was solubilized into the micelles, and it was located in the CTA+ headgroups region. Additionally, the bonding between surfactant CTA+ and PTA− was very tight due to the electrostatic interactions. The PTA− that penetrated into the micelles effectively screened the electrostatic repulsion among the cationic headgroups, which is considered to be crucial for maintaining the cylindrical micellar shape. As the pH decreased, the carboxyl groups were protonated. The hydration ability of neutral carboxyl groups weakened, resulting in deeper penetration into the micelles. Meanwhile, their bonding interactions with surfactant headgroups also weakened. Accompanied by the strengthen of electrostatic repulsion among the positive headgroups, the cylindrical micelle was broken into spherical micelles. Our work provided an atomic-level insights into the mechanism of pH-induced structural transitions of a CTAB/p-toluic solution, which is expected to be useful for further understanding the aggregate behavior of mixed cationic surfactants and aromatic acids. [ABSTRACT FROM AUTHOR]

Water transport inside carbon nano-tubes (CNTs) has attracted considerable attention due to its nano-fluidic properties, its importance in nonporous systems, and the wide range of applications in membrane desalination and biological medicine. Recent studies show an enhancement of water diffusion inside nano-channels depending on the size of the nano-confinement. However, the underlying mechanism of this enhancement is not well understood yet. In this study, we performed Molecular Dynamics (MD) simulations to study water flow inside CNT systems. The length of CNTs considered in this study is 20 nm, but their diameters vary from 1 to 10 nm. The simulations are conducted at temperatures ranging from 260 K to 320 K. We observe that water molecules are arranged into coaxial water tubular sheets. The number of these tubular sheets depends on the CNT size. Further analysis reveals that the diffusion of water molecules along the CNT axis deviates from the Arrhenius temperature dependence. The non-Arrhenius relationship results from a fragile liquid-like water component persisting at low temperatures with fragility higher than that of the bulk water. [ABSTRACT FROM AUTHOR]

Adverse effects associated with synthetic drugs in diabetes therapy has prompted the search for novel natural lead compounds with little or no side effects. Effects of phenolic compounds from Carpobrotus edulis on carbohydrate-metabolizing enzymes through in vitro and in silico methods were assessed. Based on the half-maximal inhibitory concentrations (IC50), the phenolic extract of the plant had significant (p < 0.05) in vitro inhibitory effect on the specific activity of alpha-amylase (0.51 mg/mL), alpha-glucosidase (0.062 mg/mL) and aldose reductase (0.75 mg/mL), compared with the reference standards (0.55, 0.72 and 7.05 mg/mL, respectively). Molecular interactions established between the 11 phenolic compounds identifiable from the HPLC chromatogram of the extract and active site residues of the enzymes revealed higher binding affinity and more structural compactness with procyanidin (−69.834 ± 6.574 kcal/mol) and 1,3-dicaffeoxyl quinic acid (−42.630 ± 4.076 kcal/mol) as potential inhibitors of alpha-amylase and alpha-glucosidase, respectively, while isorhamnetin-3-O-rutinoside (−45.398 ± 4.568 kcal/mol) and luteolin-7-O-beta-d-glucoside (−45.102 ± 4.024 kcal/mol) for aldose reductase relative to respective reference standards. Put together, the findings are suggestive of the compounds as potential constituents of C. edulis phenolic extract responsible for the significant hypoglycemic effect in vitro; hence, they could be exploited in the development of novel therapeutic agents for type-2 diabetes and its retinopathy complication. [ABSTRACT FROM AUTHOR]

A short self-assembly peptide A6K (H2N−AAAAAAK−OH) with unmodified N− and C−terminus was designed, and the charge distribution model of this short peptide at different pH was established by computer simulation. The pH of the solution was adjusted according to the model and the corresponding self-assembled structure was observed using a transmission electron microscope (TEM). As the pH changes, the peptide will assemble into blocks or nanoribbons, which indicates that the A6K peptide is a pH-responsive peptide. Circular dichroism (CD) and molecular dynamics (MD) simulation showed that the block structure was formed by random coils, while the increase in β-turn content contributes to the formation of intact nanoribbons. A reasonable explanation of the self-assembling structure was made according to the electrostatic distribution model and the effect of electrostatic interaction on self-assembly was investigated. This study laid the foundation for further design of nanomaterials based on pH-responsive peptides. [ABSTRACT FROM AUTHOR]

Coumarin phytoestrogens, as one of the important classes of phytoestrogens, have been proved to play an important role in various fields of human life. In this study, molecular simulation method including molecular docking and molecular dynamics methods were performed to explore the various effects between four classical coumarin phytoestrogens (coumestrol, 4-methoxycoumestrol, psoralen and isopsoralen), and estrogen receptors (ERα, ERβ), respectively. The calculated results not only proved that the four coumarin phytoestrogens have weaker affinity than 17β-estradiol to both ERα, and ERβ, but also pointed out that the selective affinity for ERβ is greater than ERα. In addition, the binding mode indicated that the formation of hydrogen bond and hydrophobic interaction have an important effect on the stability of the complexes. Further, the calculation and decomposition of binding free energy explored the main contribution interactions to the total free energy. [ABSTRACT FROM AUTHOR]

Proteins are among the most important molecules on Earth. Their structure and aggregation behavior are key to their functionality in living organisms and in protein-rich products. Innovations, such as increased computer size and power, together with novel simulation tools have improved our understanding of protein structure-function relationships. This review focuses on various proteins present in plants and modeling tools that can be applied to better understand protein structures and their relationship to functionality, with particular emphasis on plant storage proteins. Modeling of plant proteins is increasing, but less than 9% of deposits in the Research Collaboratory for Structural Bioinformatics Protein Data Bank come from plant proteins. Although, similar tools are applied as in other proteins, modeling of plant proteins is lagging behind and innovative methods are rarely used. Molecular dynamics and molecular docking are commonly used to evaluate differences in forms or mutants, and the impact on functionality. Modeling tools have also been used to describe the photosynthetic machinery and its electron transfer reactions. Storage proteins, especially in large and intrinsically disordered prolamins and glutelins, have been significantly less well-described using modeling. These proteins aggregate during processing and form large polymers that correlate with functionality. The resulting structure-function relationships are important for processed storage proteins, so modeling and simulation studies, using up-to-date models, algorithms, and computer tools are essential for obtaining a better understanding of these relationships. [ABSTRACT FROM AUTHOR]

β-Glucosidases are enzymes with high importance for many industrial processes, catalyzing the last and limiting step of the conversion of lignocellulosic material into fermentable sugars for biofuel production. However, β-glucosidases are inhibited by high concentrations of the product (glucose), which limits the biofuel production on an industrial scale. For this reason, the structural mechanisms of tolerance to product inhibition have been the target of several studies. In this study, we performed in silico experiments, such as molecular dynamics (MD) simulations, free energy landscape (FEL) estimate, Poisson–Boltzmann surface area (PBSA), and grid inhomogeneous solvation theory (GIST) seeking a better understanding of the glucose tolerance and inhibition mechanisms of a representative GH1 β-glucosidase and a GH3 one. Our results suggest that the hydrophobic residues Y180, W350, and F349, as well the polar one D238 act in a mechanism for glucose releasing, herein called "slingshot mechanism", dependent also on an allosteric channel (AC). In addition, water activity modulation and the protein loop motions suggest that GH1 β-Glucosidases present an active site more adapted to glucose withdrawal than GH3, in consonance with the GH1s lower product inhibition. The results presented here provide directions on the understanding of the molecular mechanisms governing inhibition and tolerance to the product in β-glucosidases and can be useful for the rational design of optimized enzymes for industrial interests. [ABSTRACT FROM AUTHOR]

Autotaxin (ATX) is a potential drug target that is associated with inflammatory diseases and various cancers. In our previous studies, we have designed several inhibitors targeting ATX using computational and experimental approaches. Here, we have analyzed topological water networks (TWNs) in the binding pocket of ATX. TWN analysis revealed a pharmacophoric site inside the pocket. We designed and synthesized compounds considering the identified pharmacophoric site. Furthermore, we performed biological experiments to determine their ATX inhibitory activities. High potency of the designed compounds supports the predictions of the TWN analysis. [ABSTRACT FROM AUTHOR]

Protein kinases are deeply involved in immune-related diseases and various cancers. They are a potential target for structure-based drug discovery, since the general structure and characteristics of kinase domains are relatively well-known. However, the ATP binding sites in protein kinases, which serve as target sites, are highly conserved, and thus it is difficult to develop selective kinase inhibitors. To resolve this problem, we performed molecular dynamics simulations on 26 kinases in the aqueous solution, and analyzed topological water networks (TWNs) in their ATP binding sites. Repositioning of a known kinase inhibitor in the ATP binding sites of kinases that exhibited a TWN similar to interleukin-1 receptor-associated kinase 4 (IRAK4) allowed us to identify a hit molecule. Another hit molecule was obtained from a commercial chemical library using pharmacophore-based virtual screening and molecular docking approaches. Pharmacophoric features of the hit molecules were hybridized to design a novel compound that inhibited IRAK4 at low nanomolar levels in the in vitro assay. [ABSTRACT FROM AUTHOR]