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This study explores the interaction between Vemurafenib (VEM), a potent BRAF inhibitor, and calf thymus DNA (ctDNA) using a comprehensive array of biophysical and computational techniques. The primary objective is to understand the potential off-target effects of VEM on DNA, given its established role in melanoma therapy targeting the BRAF V600E mutation. The investigation employed methods such as ultraviolet–visible absorption spectroscopy, steady-state fluorescence, circular dichroism, isothermal titration calorimetry, and advanced molecular dynamics simulations. The results indicate that VEM interacts with DNA primarily through a minor groove-binding mechanism, causing minimal structural disruption to the DNA double helix. Viscosity measurements and melting temperature analyses further confirmed this non-intercalative mode of binding. Calorimetry data revealed an exothermic, thermodynamically favorable interaction between VEM and ctDNA, driven by both enthalpic and entropic factors. Finally, computer simulations identified the most probable binding site and mode of VEM within the minor groove of the nucleic acid, providing a molecular basis for the experimental findings. [ABSTRACT FROM AUTHOR]

The development of drug resistance in cancer cells poses a significant challenge for treatment, with nearly 90% of cancer-related deaths attributed to it. Over 50% of ovarian cancer patients and 30–40% of breast cancer patients exhibit resistance to therapies such as Taxol. Previous literature has shown that cytotoxic cancer therapies and ionizing radiation damage tumors, prompting cancer cells to exploit the autotaxin (ATX)–lysophosphatidic acid (LPA)–lysophosphatidic acid receptor (LPAR) signaling axis to enhance survival pathways, thus reducing treatment efficacy. Therefore, targeting this signaling axis has become a crucial strategy to overcome some forms of cancer resistance. Addressing this challenge, we identified and assessed ATX-1d, a novel compound targeting ATX, through computational methods and in vitro assays. ATX-1d exhibited an IC50 of 1.8 ± 0.3 μM for ATX inhibition and demonstrated a significant binding affinity for ATX, as confirmed by MM-GBSA, QM/MM-GBSA, and SAPT in silico methods. ATX-1d significantly amplified the potency of paclitaxel, increasing its effectiveness tenfold in 4T1 murine breast carcinoma cells and fourfold in A375 human melanoma cells without inducing cytotoxic effects as a single agent. [ABSTRACT FROM AUTHOR]

The perception of time undergoes a radical shift between the human scale and the nanoscale. In an age of rapidly evolving media and scientific technologies, we need to understand how these impact human perception and visual culture. This essay explores computational molecular simulations through the lenses of temporal media theory and moving image practice. Emerging from a creative fellowship with a physical chemistry research group, I focus on two moving image works that depict crystalline structures. One is a nanoscale computational simulation of soot formation and the other is a durational video artwork showing the dissolution of sugar. Computational molecular simulations are shown to produce a feeling of time by smearing an extremely short duration across a longer perceptible duration. This analysis uncovers how the awareness of media as a construct troubles our chronoception (perception of time), while unexpectedly, the screen becomes complicit in scientists' expert temporal understanding. The videos present vastly different spatial and temporal scales and have different chronoceptive effects: one gives a sense of being within time, the other across time. Ultimately, computational simulations emerge as isomorphic media that have explicit aesthetic properties that connect us to the implicit, abstract energetics of chemical reactivity. [ABSTRACT FROM AUTHOR]

The fat mass and obesity-associated (FTO) protein catalyzes metal-dependent modifications of nucleic acids, namely the demethylation of methyl adenosine inside mRNA molecules. The FTO protein has been identified as a potential target for developing anticancer therapies. Identifying a suitable ligand-targeting FTO protein is crucial to developing chemotherapeutic medicines to combat obesity and cancer. Scientists worldwide have employed many methodologies to discover a potent inhibitor for the FTO protein. This study uses deep learning-based methods and molecular docking techniques to investigate the FTO protein as a target. Our strategy involves systematically screening a database of small chemical compounds. By utilizing the crystal structures of the FTO complexed with ligands, we successfully identified three small-molecule chemical compounds (ZINC000003643476, ZINC000000517415, and ZINC000001562130) as inhibitors of the FTO protein. The identification process was accomplished by employing a combination of screening techniques, specifically deep learning (DeepBindGCN) and Autodock vina, on the ZINC database. These compounds were subjected to comprehensive analysis using 100 nanoseconds of molecular dynamics and binding free energy calculations. The findings of our study indicate the identification of three candidate inhibitors that might effectively target the human fat mass and obesity protein. The results of this study have the potential to facilitate the exploration of other chemicals that can interact with FTO. Conducting biochemical studies to evaluate these compounds' effectiveness may contribute to improving fat mass and obesity treatment strategies. [ABSTRACT FROM AUTHOR]

We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels. [ABSTRACT FROM AUTHOR]

Methacrylate-based polyhedral oligomeric silsesquioxane (POSS) is one of the new composites used as a dental resin. Both monofunctional methacryl isobutyl POSS (MIPOSS) and multifunctional methacryl POSS (MAPOSS) are reported to be possible resins that possess the desired properties for using them as dental resins. Our group's previous comparative study on these two resins showed that the MAPOSS composite has superior mechanical properties compared with the MIPOSS composite. In this article, molecular dynamic simulations (MD simulations) are performed to study the water sorption in these two composites. Water sorption in dental composites can have several effects on the material properties, performance, and longevity of dental restorations. Water sorption in MAPOSS and MIPOSS composites is analyzed by studying the hydrogen bonding, cluster analysis, density projection calculations, and diffusion coefficient calculation of water molecules within the resin matrix. MD simulations results are further used to understand the interaction of water molecules with the resin matrix comprehensively, which governs the composite's mechanical properties. The water sorption study showed that the MAPOSS composite has less water sorption capacity than the MIPOSS composite. The practical significance of this study is to find properties that affect dental restoration and longevity, which can help in the design of better materials for dental applications. [ABSTRACT FROM AUTHOR]

Arthropod-borne viruses within the Flaviviridae family such as Zika (ZIKV) and dengue (DENV) are responsible for major outbreaks in tropical countries, and there are no specific treatments against them. Naringenin and 7-O-methyl naringenin are flavonoids that can be extracted from geopropolis, a natural material that the Brazilian Jandaira stingless bee (Melipona subnitida Ducke) produces to protect its nest. Here, these flavonoids were tested against ZIKV and DENV using Vero cells as a cellular model to perform a cytotoxicity assay and to define the effective concentrations of TCID50 as the readout method. The results demonstrated the antiviral activity of the compounds against both viruses upon the treatment of infected cells. The tested flavonoids had antiviral activity comparable with 6-methylmercaptopurine riboside (6-MMPr), used here as a positive control. In addition, to identify the possible action mechanism of the antiviral candidates, we carried out a docking analysis followed by a molecular dynamics simulation to elucidate naringenin and 7-O-methyl naringenin binding sites to each virus. Altogether, these results demonstrate that both flavonoids have potent antiviral effects against both viruses and warrant further in vivo trials. [ABSTRACT FROM AUTHOR]

In this study, atomistic simulations were carried out to study the difference in the adsorption process between two similar molecules, diazepam and oxazepam, on Na+-montmorillonite. Kinetic and XRD measurements showed a contrasting adsorption mechanism of these two molecules, differing only by the presence/absence of methyl and hydroxyl groups, with a larger adsorption amount and intercalation for the oxazepam. The structural characterization of these molecules was investigated through DFT calculations and showed the vicinity of hydroxyl and carbonyl groups for only the chair conformation of oxazepam compared to the boat conformation. Classical molecular dynamics simulations of diazepam and the two forms of oxazepam on the external surface of Na+-montmorillonite highlighted the better coordination of the oxazepam-chair conformation, compared to its boat counterpart and diazepam. This has been confirmed through DFT calculations, from which a coordination energy that is greater by 10 kcal·mol−1 is observed. This strongly suggests that the experimentally observed intercalation of oxazepam occurs only in the chair form because of the strong coordination with the Na+ cation present in the Na-Mt interlayer. Classical MD simulations of the intercalated oxazepam chair molecule in the Na-Mt interlayer allowed the evaluation of the interlayer spacing d001, which was in very good agreement with the experimental XRD measurement. [ABSTRACT FROM AUTHOR]

3D-RISM-KH molecular solvation theory based on statistical mechanics has been an engine of the multiscale methods framework, which also includes molecular simulation techniques. Its applications range from the solvation energy of small molecules to the phase behavior of polymers and biomolecules. Molecular solvation theory predicts and explains the molecular mechanisms and functioning of a variety of chemical and biomolecular systems. This includes the self-assembly and conformational stability of synthetic organic rosette nanotubes (RNTs), the aggregation of peptides and proteins related to neurodegeneration, the binding of ligands to proteins, and the solvation properties of biomolecules related to their functions. The replica RISM-KH-VM molecular solvation theory predicts and explains the structure, thermodynamics, and electrochemistry of electrolyte solutions sorbed in nanoporous carbon supercapacitor electrodes, and is part of recent research and development efforts. A new quasidynamics protocol couples multiple time step molecular dynamics (MTS-MD) stabilized with an optimized isokinetic Nosé–Hoover (OIN) thermostat driven by 3D-RISM-KH mean solvation forces at gigantic outer time steps of picoseconds, which are extrapolated forward at short inner time steps of femtoseconds with generalized solvation force extrapolation (GSFE). The OIN/3D-RISM-KH/GSFE quasidynamics is implemented in the Amber Molecular Dynamics package. It is validated on miniprotein 1L2Y and protein G in ambient aqueous solution, and shows the rate of sampling 150 times faster than in standard MD simulations on these biomolecules in explicit water. The self-consistent field version of Kohn–Sham DFT in 3D-RISM-KH mean solvation forces is implemented in the Amsterdam Density Functional (ADF) package. Its applications range from solvation thermochemistry, conformational equilibria, and photochemistry to activation barriers of different nanosystems in solutions and ionic liquids. [ABSTRACT FROM AUTHOR]

Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of antiviral activities. The pandemic emergencies have further increased the interest in finding antiviral agents, and efforts are oriented to investigate possible activities of secondary plant metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection. In this review, we performed a comprehensive analysis of studies through in silico and in vitro investigations, also including in vivo applications and clinical trials, to evaluate the state of knowledge on the antiviral activities of secondary metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection, with a particular focus on natural compounds present in food plants. Although some of the food plant secondary metabolites seem to be useful in the prevention and as a possible therapeutic management against SARS-CoV-2, up to now, no molecules can be used as a potential treatment for COVID-19; however, more research is needed. [ABSTRACT FROM AUTHOR]

Novel polymers applied in economic membrane technologies are a perennial hot topic in the fields of natural gas purification and O2 enrichment. Herein, novel hypercrosslinked polymers (HCPs) incorporating 6FDA-based polyimide (PI) MMMs were prepared via a casting method for enhancing transport of different gases (CO2, CH4, O2, and N2). Intact HCPs/PI MMMs could be obtained due to good compatibility between the HCPs and PI. Pure gas permeation experiments showed that compared with pure PI film, the addition of HCPs effectively promotes gas transport, increases gas permeability, and maintains ideal selectivity. The permeabilities of HCPs/PI MMMs toward CO2 and O2 were as high as 105.85 Barrer and 24.03 Barrer, respectively, and the ideal selectivities of CO2/CH4 and O2/N2 were 15.67 and 3.00, respectively. Molecular simulations further verified that adding HCPs was beneficial to gas transport. Thus, HCPs have potential utility in fabrication of MMMs for facilitating gas transport in the fields of natural gas purification and O2 enrichment. [ABSTRACT FROM AUTHOR]

To obtain crystal products with ideal morphology and better quality, it is important to fully understand and grasp the affecting mechanism of solvents on crystal morphology. In this work, the interactions between solvent/solute molecules and different crystal faces of pyriproxyfen are investigated by a combination of experiments and molecular simulations. It is found that pyriproxyfen crystals grow into a lamellar morphology in methanol and ethanol, while the crystal grows into a three-dimensional shuttle morphology in n-butanol and n-heptane. Molecular simulations reveal that the molecular arrangement of crystal faces makes the alcohol hydroxyl adsorption sites exposed in different degrees, and the (002) face is more sensitive to alcohol hydroxyl than other faces. The adsorption of alcohol hydroxyl groups hinders the growth of crystal planes, so (002) and (102) faces become the main crystal planes in methanol and ethanol, and the lamellar crystal is formed. The developed knowledge of the growth mechanism based on the interaction between the solvent and crystal interface can be conducive to the further optimization of the pyriproxyfen crystal products. [ABSTRACT FROM AUTHOR]

Previous studies have been carried out on the effect of silica nanoparticles (SNPs) on the stability of oil–water emulsions. However, the combining configuration of SNPs and oil droplets at the molecular level and the effect of SNP content on the coalescence behavior of oil droplets cannot be obtained through experiments. In this paper, molecular dynamics (MD) simulation was performed to investigate the adsorption configuration of hydrophilic SNPs in an O/W emulsion system, and the effect of adsorption of SNPs on coalescence of oil droplets. The simulation results showed: (i) SNPs adsorbed on the surface of oil droplets, and excessive SNPs self-aggregated and connected by hydrogen bonds. (ii) Partially hydrophilic asphaltene and resin molecules formed adsorption configurations with SNPs, which changed the distribution of oil droplet components. Furthermore, compared with hydrophobic asphaltene, the hydrophilic asphaltene was easier to combine with SNPs. (iii) SNPs would extend the oil droplet coalescence time, and the π–π stacking structures were formed between asphaltene and asphaltene or resin molecules to enhance the connection between oil droplets during the oil droplet contact process. (iv) Enough SNPs tightly wrapped around the oil droplet, similar to the formation of a rigid film on the surface of an oil droplet, which hindered the contact and coalescence of components between oil droplets. [ABSTRACT FROM AUTHOR]

Supercritical carbon dioxide (sCO2) has great potential for displacing shale oil as a result of its high solubility and low surface tension and viscosity, but the underlying mechanisms have remained unclear up to now. By conducting equilibrium molecular dynamics (EMD) simulations, we found that the displacing process could be divided into three steps: the CO2 molecules were firstly injected in the central region of shale slit, then tended to adsorb on the SiO2-OH wall surface and mix with hexane, resulting in loose hexane layer on the shale surface, and finally displaced hexane from the wall due to strong interactions between CO2 and wall. In that process, the displacing velocity and efficiency of hexane exhibit parabolic and increased trends with pressure, respectively. To gain deep insights into this phenomenon, we further performed non-equilibrium molecular dynamics (NEMD) simulations and found that both the Onsager coefficients of CO2 and hexane were correlated to increase with pressure, until the diffusion rate of hexane being suppressed by the highly dense distribution of CO2 molecules at 12 MPa. The rapid transportation of CO2 molecules in the binary components (CO2 and hexane) actually promoted the hexane diffusion, which facilitated hexane flowing out of the nanochannel and subsequently enhanced oil recovery efficiency. The displacing process could occur effectively at pressures higher than 7.5 MPa, after which the interaction energies of the CO2-wall were stronger than that of the hexane-wall. Taking displacing velocity and efficiency and hexane diffusion rate into consideration, the optimal injection pressure was found at 10.5 MPa in this work. This study provides detailed insights into CO2 displacing shale oil and is in favor of deepening the understanding of shale oil exploitation and utilization. [ABSTRACT FROM AUTHOR]

Antifouling polymer coating surfaces are used in widespread industries applications. Zwitterionic polymers have been identified as promising materials in developing polymer coating surfaces. Importantly, the density of the polymer chains is crucial for acquiring superior antifouling performance. This study introduces two different zwitterionic polymer density surfaces by applying molecular modeling tools. To assess the antifouling performance, we mimic static adsorption test, by placing the foulant model bovine serum albumin (BSA) on the surfaces. Our findings show that not only the density of the polymer chain affect antifouling performance, but also the initial orientation of the BSA on the surface. Moreover, at a high-density surface, the foulant either detaches from the surface or anchor on the surface. At low-density surface, the foulant does not detach from the surface, but either penetrates or anchors on the surface. The anchoring and the penetrating mechanisms are elucidated by the electrostatic interactions between the foulant and the surface. While the positively charged ammonium groups of the polymer play major role in the interactions with the negatively charged amino acids of the BSA, in the penetrating mechanism the ammonium groups play minor role in the interactions with the contact with the foulant. The sulfonate groups of the polymer pull the foulant in the penetrating mechanism. Our work supports the design of a high-density polymer chain surface coating to prevent fouling phenomenon. Our study provides for the first-time insights into the molecular mechanism by probing the interactions between BSA and the zwitterion surface, while testing high- and low-densities polymer chains. [ABSTRACT FROM AUTHOR]

The emergence of immune-evading variants of SARS-CoV-2 further aggravated the ongoing pandemic. Despite the deployments of various vaccines, the acquired mutations are capable of escaping both natural and vaccine-induced immune responses. Therefore, further investigation is needed to design a decisive pharmacological treatment that could efficiently block the entry of this virus into cells. Hence, the current study used structure-based methods to target the RBD of the recombinant variant (Deltacron) of SARS-CoV-2, which was used as a model variant. From the virtual drug screenings of various databases, a total of four hits were identified as potential lead molecules. Key residues were blocked by these molecules with favorable structural dynamic features. The binding free energies further validated the potentials of these molecules. The TBE for MNP was calculated to be −32.86 ± 0.10 kcal/mol, for SANC00222 the TBE was −23.41 ± 0.15 kcal/mol, for Liriodenine the TBE was −34.29 ± 0.07 kcal/mol, while for Carviolin the TBE was calculated to be −27.67 ± 0.12 kcal/mol. Moreover, each complex demonstrated distinct internal motion and a free energy profile, indicating a different strategy for the interaction with and inhibition of the RBD. In conclusion, the current study demands further in vivo and in vitro validation for the possible usage of these compounds as potential drugs against SARS-CoV-2 and its variants. [ABSTRACT FROM AUTHOR]

This article focuses on the study related to the estimation of packaging material properties of cellulose–wax nanocomposite using molecular dynamics simulation (MDS). Cellulose based packaging material is gaining lot of importance due to its good material properties and low cost. Cellulose with small amount of plant-derived wax (nonacosane-10-ol and nonacosane-5,10-diol) offers higher mechanical strength and modulus of elasticity compared to the conventional synthetic polymer materials. In this article, in addition to the estimation of mechanical properties, the thermal stability of the proposed ecofriendly cellulose–wax composite is evaluated by estimating the glass transition temperature which essentially provides critical information on the glassy state and rubbery state of this biopolymer. The glass transition temperature of this composite changes significantly compared to that of pure cellulose (which also suffers from poor mechanical strength). Transport properties such as diffusion volume and diffusion coefficient of oxygen, nitrogen, and water are estimated using the results obtained from MDS. The diffusion coefficients of these species within the cellulose–wax composite are analyzed using the diffusion volume and interaction energies of these constituents with the wax and cellulose. [ABSTRACT FROM AUTHOR]

Soluble sulfur (S8) and insoluble sulfur (IS) have different application fields, and molecular dynamics simulation can reveal their differences in solubility in solvents. It is found that in the simulated carbon disulfide (CS2) solvent, soluble sulfur in the form of clusters mainly promotes the dissolution of clusters through van der Waals interaction between solvent molecules (CS2) and S8, and the solubility gradually increases with the increase in temperature. However, the strong interaction between polymer chains of insoluble sulfur in the form of polymer hinders the diffusion of IS into CS2 solvent, which is not conducive to high-temperature dissolution. The simulated solubility parameter shows that the solubility parameter of soluble sulfur is closer to that of the solvent, which is consistent with the above explanation that soluble sulfur is easy to dissolve. [ABSTRACT FROM AUTHOR]

Packaging material has a significant role in maintaining or altering the shelf life of different products. Polymer materials are extensively used as packaging materials for different perishable and non-perishable products both during transportation and storage. This article aims at developing a new polymer composite which can be used as packaging material. This new composite addresses the challenge of controlling oxygen diffusion rates during the storage of perishable goods such as vegetables, meat and produce, etc. The proposed new composite primarily consists of nonacosan-10-ol and polyethylene. Molecular dynamics simulations (MDS) are performed by mixing 5.2%, 17.1%, 29.2%, 40.8% and 45.2% (wt/wt) of nonacosan-10-ol to amorphous polyethylene. Mechanical properties such as Young's modulus/glass transition temperature, and gas transport properties such as diffusion coefficient and diffusion volume are estimated from the MDS and diffusion related simulations consisting of different oxygen concentrations in polyethylene-alone system and polyethylene- nonacosan-10-ol blends. The impact of adding different weight percent of nonacosan-10-ol to polyethylene is quantitatively assessed and optimal composition of the proposed additive is suggested corresponding to minimal oxygen diffusion rate, high elastic modulus and good thermal stability. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A1AR, A2AAR, A2BAR and A3AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A1AR and A3AR preferentially couple to the Gi/o proteins, while the A2AAR and A2BAR prefer coupling to the Gs proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities. [ABSTRACT FROM AUTHOR]

The intractability of bacterial resistance presents a dilemma for therapies against Staphylococcus aureus (S. aureus) infection. Effective anti-virulence strategies are urgently needed, reflecting the proliferation of resistant strains. Inhibitors of sortase A (SrtA), enzymes that anchor virulence-related surface proteins, are regarded as promising candidates for countermeasures against bacterial infections. In the present study, the inhibitory effect of dryocrassin ABBA (ABBA) against SrtA and its molecular basis has been examined. Fluorescence resonance energy transfer (FRET) assays were used to determine the inhibitory activity of ABBA against SrtA. To identify the mechanism underlying this activity, molecular dynamics simulations and mutagenesis assays were applied, and the results revealed that the direct engagement of SrtA via ABBA through binding to V166 and V168 significantly attenuated the catalytic activity of SrtA. Taken together, these findings indicated that ABBA is a potential novel antimicrobial agent for S. aureus infection via targeting SrtA. [ABSTRACT FROM AUTHOR]

Threading charged polymers through a nanopore, driven by electric fields E, is investigated by means of Langevin dynamics simulations. The mean translocation time 〈τ〉 is shown to follow a scaling law Nα, and the exponent α increases monotonically from 1.16(4) to 1.40(3) with E. The result is double-checked by the calculation of mean square displacement of translocation coordinate, which asserts a scaling behavior tβ (for t near τ) with β complying with the relation αβ = 2. At a fixed chain length N, 〈τ〉 displayed a reciprocal scaling behavior E-1 in the weak and also in the strong fields, connected by a transition E-1.64(5) in the intermediate fields. The variations of the radius of gyration of chain and the positions of chain end are monitored during a translocation process; far-from-equilibrium behaviors are observed when the driving field is strong. A strong field can strip off the condensed ions on the chain when it passes the pore. The total charges of condensed ions are hence decreased. The studies for the probability and density distributions reveal that the monomers in the trans-region are gathered near the wall and form a pancake-like density profile with a hump cloud over it in the strong fields, due to fast translocation. [ABSTRACT FROM AUTHOR]

Nanotechnology has arisen as a key player in the field of nanomedicine. Although the use of engineered nanoparticles is rapidly increasing, safety assessment is also important for the beneficial use of new nanomaterials. Considering that the experimental assessment of new nanomaterials is costly and laborious, in silico approaches hold promise. Several major challenges in nanotechnology indicate a need for nanoinformatics. New database initiatives such as ISA-TAB-Nano, caNanoLab, and Nanomaterial Registry will help in data sharing and developing data standards, and, as the amount of nanomaterials data grows, will provide a way to develop methods and tools specific to the nanolevel. In this review, we describe emerging databases and tools that should aid in the progress of nanotechnology research. [ABSTRACT FROM AUTHOR]

Molecular modeling is an important subdomain in the field of computational modeling, regarding both scientific and industrial applications. This is because computer simulations on a molecular level are a virtuous instrument to study the impact of microscopic on macroscopic phenomena. Accurate molecular models are indispensable for such simulations in order to predict physical target observables, like density, pressure, diffusion coefficients or energetic properties, quantitatively over a wide range of temperatures. Thereby, molecular interactions are described mathematically by force fields. The mathematical description includes parameters for both intramolecular and intermolecular interactions. While intramolecular force field parameters can be determined by quantum mechanics, the parameterization of the intermolecular part is often tedious. Recently, an empirical procedure, based on the minimization of a loss function between simulated and experimental physical properties, was published by the authors. Thereby, efficient gradient-based numerical optimization algorithms were used. However, empirical force field optimization is inhibited by the two following central issues appearing in molecular simulations: firstly, they are extremely time-consuming, even on modern and high-performance computer clusters, and secondly, simulation data is affected by statistical noise. The latter provokes the fact that an accurate computation of gradients or Hessians is nearly impossible close to a local or global minimum, mainly because the loss function is flat. Therefore, the question arises of whether to apply a derivative-free method approximating the loss function by an appropriate model function. In this paper, a new Sparse Grid-based Optimization Workflow (SpaGrOW) is presented, which accomplishes this task robustly and, at the same time, keeps the number of time-consuming simulations relatively small. This is achieved by an efficient sampling procedure for the approximation based on sparse grids, which is described in full detail: in order to counteract the fact that sparse grids are fully occupied on their boundaries, a mathematical transformation is applied to generate homogeneous Dirichlet boundary conditions. As the main drawback of sparse grids methods is the assumption that the function to be modeled exhibits certain smoothness properties, it has to be approximated by smooth functions first. Radial basis functions turned out to be very suitable to solve this task. The smoothing procedure and the subsequent interpolation on sparse grids are performed within sufficiently large compact trust regions of the parameter space. It is shown and explained how the combination of the three ingredients leads to a new efficient derivative-free algorithm, which has the additional advantage that it is capable of reducing the overall number of simulations by a factor of about two in comparison to gradient-based optimization methods. At the same time, the robustness with respect to statistical noise is maintained. This assertion is proven by both theoretical considerations and practical evaluations for molecular simulations on chemical example substances. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in our lab aimed at understanding this unique mechanism of action, in particular the development of models that provide a quantitative connection between molecular-level biophysical phenomena and relevant biological effects. Our work is focused on protegrins, a potent class of AMPs that attack bacteria by associating with the bacterial membrane and forming transmembrane pores that facilitate the unrestricted transport of ions. Using fully atomistic molecular dynamics simulations, we have computed the thermodynamics of peptide-membrane association and insertion, as well as peptide aggregation. We also present a multi-scale analysis of the ion transport properties of protegrin pores, ranging from atomistic molecular dynamics simulations to mesoscale continuum models of single-pore electrodiffusion to models of transient ion transport from bacterial cells. Overall, this work provides a quantitative mechanistic description of the mechanism of action of protegrin antimicrobial peptides across multiple length and time scales. [ABSTRACT FROM AUTHOR]

It has been established that the elongational rheology of polymers depends on their chemistry. However, the analysis of experimental data has been reported for only a few polymers. In this study, we analyzed the elongational viscosity of poly (propylene carbonate) (PPC) melts in terms of monomeric friction via primitive chain network simulations. By incorporating a small polydispersity of materials, the linear viscoelastic response was semi-quantitatively reproduced. Owing to this agreement, we determined units of time and modulus to carry out elongational simulations. The simulation with constant monomeric friction overestimated elongational viscosity, whereas it nicely captured the experimental data if friction decreased with increasing segment orientation. To see the effect of chemistry, we also conducted the simulation for a polystyrene (PS) melt, which has a similar entanglement number per chain and a polydispersity index. The results imply that PPC and PS behave similarly in terms of the reduction of friction under fast deformations. [ABSTRACT FROM AUTHOR]

In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibition and binding studies confirmed interaction with the ATPase domain. We constructed a binding model through docking and extensively investigated it with molecular dynamics MD simulations, essential dynamics, and MM-GBSA free energy calculations, thus reconnecting the new results to the initial dynophore-based screening model. We not only demonstrate a new design strategy that incorporates a dynamic component of molecular recognition, but also highlight new derivates in the established flavonoid class of topoisomerase II inhibitors. [ABSTRACT FROM AUTHOR]

Simple Summary: To function correctly, most proteins need to fold into well-defined three-dimensional structures. Destabilization of these structures may not only lead to the loss of function, but also to toxic aggregation and fibril formation. These pathological processes have been linked to a number of neurodegenerative diseases. To prevent such processes, it is important to describe factors causing protein destabilization and identify misfolded structures that are at the origin of the toxic behavior. From the experimental point of view, in many cases, it is useful to construct protein models to better investigate the issues of stability, misfolding, and aggregation. Here, indeed, we focus on a mutant model of superoxide dismutase 1, a protein implicated in amyotrophic lateral sclerosis. We apply a state-of-the-art molecular simulation method to verify whether the current computational machinery is able to describe the features of the biochemical model. Namely, our paper provides a microscopic insight into the unfolding of the superoxide dismutase 1 model while highlighting the strengths and limitations of the computational approach. Overall, our investigation opens the route to the computational study of pathological mutants of the superoxide dismutase 1 protein. In this work, we investigate the β -barrel of superoxide dismutase 1 (SOD1) in a mutated form, the isoleucine 35 to alanine (I35A) mutant, commonly used as a model system to decipher the role of the full-length apoSOD1 protein in amyotrophic lateral sclerosis (ALS). It is known from experiments that the mutation reduces the stability of the SOD1 barrel and makes it largely unfolded in the cell at 37 degrees Celsius. We deploy state-of-the-art computational machinery to examine the thermal destabilization of the I35A mutant by comparing two widely used force fields, Amber a99SB-disp and CHARMM36m. We find that only the latter force field, when combined with the Replica Exchange with Solute Scaling (REST2) approach, reproduces semi-quantitatively the experimentally observed shift in the melting between the original and the mutated SOD1 barrel. In addition, we analyze the unfolding process and the conformational landscape of the mutant, finding these largely similar to those of the wildtype. Nevertheless, we detect an increased presence of partially misfolded states at ambient temperatures. These states, featuring conformational changes in the region of the β -strands β 4 − β 6, might provide a pathway for nonnative aggregation. [ABSTRACT FROM AUTHOR]

Integrative modeling of macromolecular assemblies requires stochastic sampling, for example, via MCMC (Markov Chain Monte Carlo), since exhaustively enumerating all structural degrees of freedom is infeasible. MCMC-based methods usually require tuning several parameters, such as the move sizes for coarse-grained beads and rigid bodies, for sampling to be efficient and accurate. Currently, these parameters are tuned manually. To automate this process, we developed a general heuristic for derivative-free, global, stochastic, parallel, multiobjective optimization, termed StOP (Stochastic Optimization of Parameters) and applied it to optimize sampling-related parameters for the Integrative Modeling Platform (IMP). Given an integrative modeling setup, list of parameters to optimize, their domains, metrics that they influence, and the target ranges of these metrics, StOP produces the optimal values of these parameters. StOP is adaptable to the available computing capacity and converges quickly, allowing for the simultaneous optimization of a large number of parameters. However, it is not efficient at high dimensions and not guaranteed to find optima in complex landscapes. We demonstrate its performance on several examples of random functions, as well as on two integrative modeling examples, showing that StOP enhances the efficiency of sampling the posterior distribution, resulting in more good-scoring models and better sampling precision. [ABSTRACT FROM AUTHOR]

3CL-Pro is the SARS-CoV-2 main protease (MPro). It acts as a homodimer to cleave the large polyprotein 1ab transcript into proteins that are necessary for viral growth and replication. 3CL-Pro has been one of the most studied SARS-CoV-2 proteins and a main target of therapeutics. A number of drug candidates have been reported, including natural products. Here, we employ elaborate computational methods to explore the dimerization of the 3CL-Pro protein, and we formulate a computational context to identify potential inhibitors of this process. We report that fortunellin (acacetin 7-O-neohesperidoside), a natural flavonoid O-glycoside, and its structural analogs are potent inhibitors of 3CL-Pro dimerization, inhibiting viral plaque formation in vitro. We thus propose a novel basis for the search of pharmaceuticals as well as dietary supplements in the fight against SARS-CoV-2 and COVID-19. [ABSTRACT FROM AUTHOR]

Detailed molecular dynamics (MD) simulations are employed to study how the presence of adsorbed domains and nanoparticle bridging chains affect the structural, conformational, thermodynamic, and dynamic properties of attractive polymer nanocomposite melts in the semi-dilute regime. As a model system we have chosen an unentangled poly(ethylene glycol) (PEG) matrix containing amorphous spherical silica nanoparticles with different diameters and at different concentrations. Emphasis is placed on properties such as the polymer mass density profile around nanoparticles, the compressibility of the system, the mean squared end-to-end distance of PEG chains, their orientational and diffusive dynamics, the single chain form factor, and the scattering functions. Our analysis reveals a significant impact of the adsorbed, interfacial polymer on the microscopic dynamic and conformational properties of the nanocomposite, especially under conditions favoring higher surface-to-volume ratios (e.g., for small nanoparticle sizes at fixed nanoparticle loading, or for higher silica concentrations). Simultaneously, adsorbed polymer chains adopt graft-like conformations, a feature that allows them to considerably extend away from the nanoparticle surface to form bridges with other nanoparticles. These bridges drive the formation of a nanoparticle network whose strength (number of tie chains per nanoparticle) increases substantially with increasing concentration of the polymer matrix in nanoparticles, or with decreasing nanoparticle size at fixed nanoparticle concentration. The presence of hydroxyl groups at the ends of PEG chains plays a key role in the formation of the network. If hydroxyl groups are substituted by methoxy ones, the simulations reveal that the number of bridging chains per nanoparticle decreases dramatically, thus the network formed is less dense and less strong mechanically, and has a smaller impact on the properties of the nanocomposite. Our simulations predict further that the isothermal compressibility and thermal expansion coefficient of PEG-silica nanocomposites are significantly lower than those of pure PEG, with their values decreasing practically linear with increasing concentration of the nanocomposite in nanoparticles. [ABSTRACT FROM AUTHOR]

A novel carbazole-containing diamine (M-2,7-CPDA) isomer of our previously reported diamine 2,7-CPDA, has been synthesized using a two-step synthesis. Compared with 2,7-CPDA, the substituted position of amino is changed from para to meta for M-2,7-CPDA. The two diamines were polymerized with pyromellitic dianhydride (PMDA) to prepare two isomeric polyimides (M-2,7-CPPI and 2,7-CPPI), respectively. The effects of para/meta isomerism on microstructures and gas barrier performances of the two isomeric polyimides were studied by positron annihilation test, X-ray diffraction and molecular simulation. The results display that meta-connected M-2,7-CPPI has less ordered chain structure and weaker hydrogen bonding than para-connected 2,7-CPPI, which leads to loose chain stacking and thereby increased free volumes of M-2,7-CPPI. The higher free volumes promote the solubility and diffusivity of gas in M-2,7-CPPI. As a result, the meta-linked M-2,7-CPPI shows a lower gas barrier than its para-linked analog. The work provides guidance for the design and synthesis of high-performance barrier polymers. [ABSTRACT FROM AUTHOR]

The nanoscale wood-water interaction strength, accessible sorption sites, and cell wall pore sizes are important factors that drive water sorption and the hysteresis phenomenon in wood. In this work, these factors were quantitatively studied using molecular simulations based on a cell wall pore model, previously developed by the authors. Specifically, the wall-water interaction strength, the sorption sites network including their number, interaction range, strength, and spatial distributions were set at a series of theoretical values as simulation input parameters. The results revealed that most of the investigated parameters significantly affected both sorption isotherms and hysteresis. Water monolayers and clusters were observed on the simulated pore surface when the wood-water interaction and sorption site strength were set at unrealistically high values. Furthermore, multiple linear regression models suggested that wood-water interaction and sorption site parameters were coupled in determining sorption isotherms, but not in determining hysteresis. [ABSTRACT FROM AUTHOR]

Humira is a monoclonal antibody that binds to TNF alpha, inactivates TNF alpha receptors, and inhibits inflammation. Neonatal Fc receptors can mediate the transcytosis of Humira–TNF alpha complex structures and process them toward degradation pathways, which reduces the therapeutic effect of Humira. Allowing the Humira–TNF alpha complex structures to dissociate to Humira and soluble TNF alpha in the early endosome to enable Humira recycling is crucial. We used the cytoplasmic pH (7.4), the early endosomal pH (6.0), and pKa of histidine side chains (6.0–6.4) to mutate the residues of complementarity-determining regions with histidine. Our engineered Humira (W1-Humira) can bind to TNF alpha in plasma at neutral pH and dissociate from the TNF alpha in the endosome at acidic pH. We used the constant-pH molecular dynamics, Gaussian accelerated molecular dynamics, two-dimensional potential mean force profiles, and in vitro methods to investigate the characteristics of W1-Humira. Our results revealed that the proposed Humira can bind TNF alpha with pH-dependent affinity in vitro. The W1-Humira was weaker than wild-type Humira at neutral pH in vitro, and our prediction results were close to the in vitro results. Furthermore, our approach displayed a high accuracy in antibody pH-dependent binding characteristics prediction, which may facilitate antibody drug design. Advancements in computational methods and computing power may further aid in addressing the challenges in antibody drug design. [ABSTRACT FROM AUTHOR]

The rapid growth in energy consumption and environmental pollution have greatly stimulated the exploration and utilization of shale gas. The injection of gases such as CO2, N2, and their mixture is currently regarded as one of the most effective ways to enhance gas recovery from shale reservoirs. In this study, molecular simulations were conducted on a kaolinite–kerogen IID composite shale matrix to explore the displacement characteristics of CH4 using different injection gases, including CO2, N2, and their mixture. The results show that when the injection pressure was lower than 10 MPa, increasing the injection pressure improved the displacement capacity of CH4 by CO2. Correspondingly, an increase of formation temperature also increased the displacement efficiency of CH4, but an increase of pore size slightly increased this displacement efficiency. Moreover, it was found that when the proportion of CO2 and N2 was 1:1, the displacement efficiency of CH4 was the highest, which proved that the simultaneous injection of CO2 and N2 had a synergistic effect on shale gas production. The results of this paper will provide guidance and reference for the displacement exploitation of shale gas by injection gases. [ABSTRACT FROM AUTHOR]

Histone modifications through acetylation are fundamental for remodelling chromatin and consequently activating gene expression. The imbalance between acetylation and deacetylation activity causes transcriptional dysregulation associated with several disorders. Flavones, small molecules of plant origin, are known to interfere with class I histone deacetylase (HDAC) enzymes and to enhance acetylation, restoring cell homeostasis. To investigate the possible physical interactions of flavones on human HDAC1 and 2, we carried out in silico molecular docking simulations. Our data have revealed how flavone, and other two flavones previously investigated, i.e., apigenin and luteolin, can interact as ligands with HDAC1 and 2 at the active site binding pocket. Regulation of HDAC activity by dietary flavones could have important implications in developing epigenetic therapy to regulate the cell gene expression. [ABSTRACT FROM AUTHOR]

A high-barrier polyimide (2,7-CPI) was synthesized through the polymerization of pyromellitic dianhydride (PMDA) and a novel diamine (2,7-CDA) containing carbazole moiety. The synthesized diamine and polyimide were fully characterized by elemental analyses, FTIR and NMR. The 2,7-CPI displays very attractive barrier performances, with oxygen transmission rate (OTR) and water vapor transmission rate (WVTR) low to 0.14 cm3·m−2·day−1 and 0.05 g·m−2·day−1, respectively. Meanwhile, 2,7-CPI also exhibits exceptional thermal stability with a glass transition temperature (Tg) of 467 °C, 5% weight-loss temperature (Td5%) of 550 °C under N2 and coefficient of thermal expansion (CTE) of 3.4 ppm/K. The barrier performances of 2,7-CPI are compared with those of a structural analogue (2,7-CPPI) and a typical polyimide (Kapton). Their barrier performances with respect to microstructure were investigated by molecular simulations, wide angle X-ray diffraction (WAXD), and positron annihilation lifetime spectroscopy (PALS). The results show that 2,7-CPI possesses better coplanar structure and more number of intermolecular hydrogen bonds among the three PIs, which result in tight chain packing and thereby high crystallinity, low free volume, and decreased chains mobility. That is, the high crystallinity and low free volume of 2,7-CPI reduce the diffusion and solubility of gases. Meanwhile, the poor chains mobility further decreases the gases diffusion. The reduced diffusion and solubility of gases consequently promote the improvement of barrier properties for 2,7-CPI. The polyimide has a wide application prospect in the field of flexible electronic packaging industries. [ABSTRACT FROM AUTHOR]

Chitin, a polymer of N-acetyl-d-glucosamine (GlcNAc), can be degraded by chitinase, which is produced by higher plants, vertebrates, and bacteria. Chitinases are characterized by the ability to hydrolyze the beta-1,4-linkages in the chitin chain by either an endolytic or an exolytic mechanism. Chitinase 1198 is a novel endochitinase from the genome sequence of Chitinibacter tainanensis CT01. Herein, we report the findings of molecular simulations and bioassays for chitinase 1198. Our experimental results suggest that chitinase 1198 can recognize the nonreducing end of chitin and cleave the second or third glycosidic linkage from the nonreducing end of chitin oligomers. Furthermore, our simulations results revealed that chitinase 1198 is more likely to bind chitin oligomers with the main hydrogen bonds of the Asp440, the second GlcNAc unit of chitin oligomers, and degrade chitin oligomers to (GlcNAc)2 molecules. Moreover, chitinase 1198 is less likely to bind chitin oligomers with the main hydrogen bonds of the Asp440, the third GlcNAc unit of chitin oligomers, and degrade chitin oligomers to (GlcNAc)3 molecules. Lastly, chitinase 1198 can bind (GlcNAc)3 molecules with the main hydrogen bonds of the Asp440, the second GlcNAc of the (GlcNAc)3 molecules, and degrade chitin oligomers to GlcNAc and (GlcNAc)2 molecules. [ABSTRACT FROM AUTHOR]

Biology is dominated by polyanions (cell membranes, nucleic acids, and polysaccharides just to name a few), and achieving selective recognition between biological polyanions and synthetic systems currently constitutes a major challenge in many biomedical applications, nanovectors-assisted gene delivery being a prime example. This review work summarizes some of our recent efforts in this field; in particular, by using a combined experimental/computation approach, we investigated in detail some critical aspects in self-assembled nanomicelles and two major polyanions—DNA and heparin. [ABSTRACT FROM AUTHOR]

The comprehensive characterization of Intramolecular Charge Transfer (ICT) stemming in push-pull molecules with a delocalized π-system of electrons is noteworthy for a bespoke design of organic materials, spanning widespread applications from photovoltaics to nanomedicine imaging devices. Photo-induced ICT is characterized by structural reorganizations, which allows the molecule to adapt to the new electronic density distribution. Herein, we discuss recent photophysical advances combined with recent progresses in the computational chemistry of photoactive molecular ensembles. We focus the discussion on femtosecond Transient Absorption Spectroscopy (TAS) enabling us to follow the transition from a Locally Excited (LE) state to the ICT and to understand how the environment polarity influences radiative and non-radiative decay mechanisms. In many cases, the charge transfer transition is accompanied by structural rearrangements, such as the twisting or molecule planarization. The possibility of an accurate prediction of the charge-transfer occurring in complex molecules and molecular materials represents an enormous advantage in guiding new molecular and materials design. We briefly report on recent advances in ultrafast multidimensional spectroscopy, in particular, Two-Dimensional Electronic Spectroscopy (2DES), in unraveling the ICT nature of push-pull molecular systems. A theoretical description at the atomistic level of photo-induced molecular transitions can predict with reasonable accuracy the properties of photoactive molecules. In this framework, the review includes a discussion on the advances from simulation and modeling, which have provided, over the years, significant information on photoexcitation, emission, charge-transport, and decay pathways. Density Functional Theory (DFT) coupled with the Time-Dependent (TD) framework can describe electronic properties and dynamics for a limited system size. More recently, Machine Learning (ML) or deep learning approaches, as well as free-energy simulations containing excited state potentials, can speed up the calculations with transferable accuracy to more complex molecules with extended system size. A perspective on combining ultrafast spectroscopy with molecular simulations is foreseen for optimizing the design of photoactive compounds with tunable properties. [ABSTRACT FROM AUTHOR]

This review work reports a collection of coupled experimental/computational results taken from our own experience in the field of self-assembled dendrimers for heparin binding. These studies present and discuss both the potentiality played by this hybrid methodology to the design, synthesis, and development of possible protamine replacers for heparin anticoagulant activity reversal in biomedical applications, and the obstacles this field has still to overcome before these molecules can be translated into nanomedicines available in clinical settings. [ABSTRACT FROM AUTHOR]

Structural, mechanical, and transport properties of amorphous Li2CO3 were studied using molecular dynamics (MD) simulations and a hybrid MD-Monte Carlo (MC) scheme. A many-body polarizable force field (APPLE&P) was employed in all simulations. Dynamic and mechanical properties of Dilithium carbonate, Li2CO3, in amorphous liquid and glassy phases were calculated over a wide temperature range. At higher temperatures, both anion and cation diffusion coefficients showed similar temperature dependence. However, below the glass transition temperature (T < 450 K) the anions formed a glassy matrix, while Li+ continued to be mobile, showing decoupling of cation and anion diffusion. The conductivity of Li+ at room temperature was estimated to be on the order of 10−6 S/cm. Mechanical analysis revealed that at room temperature the amorphous phase had a shear modulus of about 8 GPa, which was high enough to suppress Li metal dendrite growth on an electrode surface. [ABSTRACT FROM AUTHOR]

This paper reports on synthesis, acid-base properties and self-structuring in water of chiral polyamidoamino acids (PAACs) obtained by polyaddition of N,N′-methylenebisacrylamide with l-alanine, l-valine and l-leucine (M-l-Ala, M-l-Val, M-l-Leu) with potential for selective interactions with biomolecules. The polymers maintained the acid-base properties of amino acids. In water, the circular dichroism spectra of PAACs revealed pH-dependent structuring in the range 3–11 and in the wavelength interval 200–280 nm. Taking as reference the values at pH 3, the differential molar ellipticities were plotted in the pH interval 3–11. Sigmoidal curves were obtained presenting inflection points at pH 8.1, 6.8 and 7.3 for M-l-Ala, M-l-Val and M-l-Leu, respectively, corresponding to the amine half-ionization. Theoretical modeling showed that PAACs assumed stable folded conformations. Intramolecular interactions led to transoid arrangements of the main chain reminiscent of protein hairpin motif. Oligomers with ten repeat units had simulated gyration radii consistent with the hydrodynamic radii obtained by dynamic light scattering. [ABSTRACT FROM AUTHOR]