The correlation between the micelle morphology of surface-active ionic liquids with self-assembly and thermodynamic characteristics: coarse-grained MD simulation and experiment.

Surface-active ionic liquids (SAILs) show great promise as novel green solvents due to their low vapor pressure, high thermal stability, high electrical conductivity, and bio-friendly nature to replace traditional volatile organic solvents in industrial processes. In the present work, the combination of coarse-grained (CG) molecular dynamics (MD) simulations with conductivity measurements was employed to explain the correlation between the micelle morphology and physicochemical and thermodynamic properties of self-assembly. A homologous series of SAIL molecules, 1-n-alkyl-3-methylimidazolium bromide [Cnmim][Br] (n = 4, 6, 8, 10, and 12), were chosen at various concentrations to shed light on this issue. Simultaneously two factors of concentration and alkyl chain length affected the morphology to control the physical and thermodynamic features. Moreover, the nature of the headgroup for two SAILs with the longest alkyl chain was assessed by shifting from imidazolium into ammonium. First, the critical micelle concentration (CMC), the degree of counterion dissociation of micelles, and the standard Gibbs energy of micellization of SAILs were determined using conductivity data. The micelle morphology such as the aggregation number, micelle radius, and moment of inertia was computed before, around, and after the CMC by MD simulation. Simulated results in accordance with the experimental measurements provide a quantitative understanding of the micellar properties. Increasing the alkyl chain length was associated with a non-spherical bigger micelle while the ammonium-based surfactant with a lower repulsion between neighboring monomers in micelles induced bigger and more spherical aggregates. Raising the SAIL concentration did not considerably influence the sphericity of the micelle except for the SAIL with the longest tail. The umbrella sampling method calculated the potential of mean force (PMF) for pulling a monomer of SAIL from a pre-assembled micelle into the solution. The dissociation energy of a SAIL monomer from a micelle increased with the tail length or with shifting into the ammonium head group and was substantially influenced by micelle morphology. Comparison between a sphere micelle with an oval one demonstrated that the dissociation of a SAIL monomer from a non-spherical shape needed a higher amount of energy. An improved understanding of how the shape of the SAIL micelles controls the physicochemical properties and stability helps to extend their application to different chemical processes.

Screening of indole derivatives as the potent anticancer agents on dihydrofolate reductase: pharmaco-informatics and molecular dynamics simulation.

Dihydrofolate reductase (DHFR) is a ubiquitous cellular enzyme involved in the biosynthesis of nucleotide and protein precursors, thus, the inhibition of human DHFR can be a promising strategy in cancer treatment. The design of effective anticancer drugs is an urgent need today according to the high spread of cancer. The indole molecule with diverse mechanisms of action and anticancer properties is one of the efficient pharmacophores in drug design. Hence, a virtual library of indole derivatives as a scaffold was selected for designing safer and more effective anticancer drugs against DHFR in this work. All indole derivatives utilized in the library design were selected regarding appreciable tumor growth inhibition. Structure-activity relationship (SAR), docking energy, ADMET (absorption, distribution, metabolism, excretion, and toxicity) parameters, and effective non-covalent interactions were used to identify potential anticancer with indole scaffold. Results showed a higher number of indole moieties provide a strong attachment to the DHFR binding pocket and therefore more effective anticancer activity. The indole scaffold in combination with dichlorobenzene improves DHFR inhibition whereas barbituric acid weakens inhibition activity. In the following to validate the docking results, Molecular dynamics (MD) simulation and molecular mechanics generalized-Born surface area (MM-GBSA) indicated the permanent stability of the selected ligands into the DHFR binding pocket and the key amino acids. Therefore, promising pharmacophores based on indole-DHFR interactions were discovered, and the outcome could be useful in guiding future in vitro and in vivo drug discovery in cancer medicine.Communicated by Ramaswamy H. Sarma.

Influence of alkali metals on water dynamics inside imidazolium-based ionic liquid nano-domains.

The global need to expand the design of energy-storage devices led to the investigation of alkali metal - Ionic Liquid (IL) mixtures as a possible class of electrolytes. In this study, 1D and 2D Nuclear Magnetic Resonance (NMR) and Electrochemical Impedance Spectroscopy (EIS) as well as Molecular Dynamics (MD) simulations were used to study the intermolecular interactions in imidazolium-based IL - water - alkali halide ternary mixtures. The 1H and 23Na 1D and 1H DOSY NMR spectra revealed that the presence of small quantities of NaCl does not influence the aggregation of water molecules in the IL nano-domains. The order of adding ionic compounds to water, as well as the certain water and NaCl molecular ratios, lead to the formation of isolated water clusters. Two ternary solutions representing different orders of compounds mixing (H2O+ IL + NaCl or H2O+ NaCl + IL) showed a strong dependence of the initial solvation shell of Na+ and the self-clustering of water. Furthermore, the behaviour of water was found to be independent from the conditions applied during the solution preparation, such as temperature and/or duration of stirring and aging. These findings could be confirmed by large differences in the amount of ionic species, observed in the ternary solutions and depending on the order of mixing/solute preparation.

An atomistic investigation on the interaction of distamycin A and its derivative with the telomeric G-Quadruplex as anticancer agents by molecular dynamics simulation.

Human telomerase that activates within cancer cells has a telomeric sequence at the 3' end. Each factor that stabilizes the G-quadruplex in guanine-rich telomeric sequences can inhibit the regular telomerase activity. Therefore, the telomeric G-quadruplex is known as a promising target in cancer treatment. In this work, we studied the binding of positively charged distamycin A and its uncharged derivative to the G-quadruplex in a solution environment by Molecular Dynamics (MD) simulation. The binding mechanism and subtle conformational changes were investigated as a result of the ligand attachment. Moreover, binding free energy and clustering analysis describe the stability and flexibility of G-quadruplexes upon ligand binding. Structural analyses displayed that the favorable binding of both ligands imposes significant stability and rigidity in G-quadruplex conformation compared to free G-quadruplex, especially charged distamycin. Hydration pattern and ion distribution were different for free G-quadruplex and both of the ligand complexes. Energy decomposition reveals the electrostatic effect on the stability of G-quadruplex. The radial distribution function displayed the solvent shell and ion moving away from the groove. The hydrogen bond played an essential role in the binding of both ligands, especially for the charged derivative. van der Waals interaction is the only factor that is more important in binding uncharged distamycin into G-quadruplex than the charged one. The calculated ΔGbind showed the stability of both ligands within grooves and good agreement with the experimental binding free energy data. Finally, the results suggest that ligand modification improves the binding mode toward stabilizing G-quadruplexes.

The influence of a type III antifreeze protein and its mutants on methane hydrate adsorption-inhibition: a molecular dynamics simulation study.

Antifreeze proteins (AFPs) inhibit ice growth in various organisms at subzero temperature. Recently, AFPs as a hydrate inhibitor have been a topic of intense discussion, while the detailed mechanism remains obscure. The present work aims to explore molecular insight into the adsorption and inhibition of an AFP III on methane hydrate. Three polar, hydrophilic, and neutral amino acids (Asn14, Thr18, and Gln44) are mutated to elucidate the molecular mechanism of AFP III antifreeze activity. Another triple mutation is also designed to investigate the effect of the side chain. Atomistic molecular dynamics simulations provide detailed structural and dynamical aspects of protein residues and water molecules at the hydrate/water interface. Initially, it was proposed that the AFP III operates by the adsorption-inhibition mechanism on hydrates, almost similar to that of ice. The exchange of amide and hydroxyl groups by mutagenesis alters the shape of the side chain and the capability of hydrogen bonding and demonstrates that hydrogen bonds are not directly responsible for the AFP III antifreeze activity. Moreover, we deciphered that the length of the pendant group is an important factor in the entrapment of the AFP III on the hydrate cages, which is compatible with van der Waals interactions between the side chains and hydrate surface. The results suggest that this interaction is sensitive to the geometry and shape of the hydrate-binding surface (HBS) of the AFP, which implies that the interface between hydrates and the AFP is relatively rigid.

Hydrodynamic volume of trehalose and its water uptake mechanism.

Trehalose ability to preserve water in biology has spawned research on this special disaccharide and its solutions. Trehalose unlike any other disaccharide, tend to mix with almost any amount of water. In water, Trehalose forms a hydrodynamic volume with bound waters (both coordination water and semicircular heterogeneities), capable of perturbing the very nature of normal bulk water. Switching of the two major conformational forms, defined by their helicities (i, i-H2O with lower helicity and ii, ii-H2O with higher helicity), were closely examined, using DFT/B3LYP- 6-311 + G** level of theory, along with molecular dynamic (MD) calculations in aqueous media. Patterns in radial distribution functions (RDF) confirmed semicircular heterogeneities, including spines of water (rows of slow water molecules), in Trehalose hydration shell. Dynamics of Trehalose conformational switch and its coordination water are coupled to dynamics of these spines of water, which are themselves coupled to dynamics of the rest of Trehalose hydration shell waters. Like seamless cogwheels such energy cascade links the upstream slow dynamics of spines to the downstream collective bulk water dynamics. This lubricates Trehalose conformational switch through coordination water uptake, for which we proposed a mechanism here. We show how the coupling between Trehalose and bound waters in its hydrodynamic volume encompass both function and dynamic of the molecule and its hydration shell. Further simulations are needed to see how this ability is related to the evading and percolating nature of cryoprotectant water, also reported for the self-coordinating jelly behavior of biological water.

Determinative factors in inhibition of aquaporin by different pharmaceuticals: Atomic scale overview by molecular dynamics simulation.

The inhibition of water permeation through aquaporins by ligands of pharmaceutical compounds is considered as a method to control the cell lifetime. The inhibition of aquaporin 1 (AQP1) by bacopaside-I and torsemide, was explored and its atomistic nature was elucidated by molecular docking and molecular dynamics (MD) simulation collectively along with Poisson-Boltzmann surface area (PBSA) method. Docking results revealed that torsemide has a lower level of docking energy in comparison with bacopaside-I at the cytoplasmic side. Furthermore, the effect of steric constraints on water permeation was accentuated. Bacopaside-I inhibits the channel properly due to the strong interaction with the channel and larger spatial volume, whereas torsemide blocks the cytoplasmic side of the channel imperfectly. The most probable active sites of AQP1 for the formation of hydrogen bonds between the inhibitor and the channel were identified by numerical analysis of the bonds. Eventually, free energy assessments indicate that binding of both inhibitors is favorable in complex with AQP1, and van der Waals interaction has an important contribution in stabilizing the complexes.