Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer

The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations

Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.

A Mechanoelastic Glimpse on Hyaluronan-Coated Extracellular Vesicles

Cancer cells secrete extracellular vesicles (EVs) covered with a carbohydrate polymer, hyaluronan (HA), linked to tumor malignancy. Herein, we have unravelled the contour lengths of HA on a single cancer cell-derived EV surface using single-molecule force spectroscopy (SMFS), which divulges the presence of low molecular weight HA (LMW-HA < 200 kDa). We also discovered that these LMW-HA-EVs are significantly more elastic than the normal cell-derived EVs. This intrinsic elasticity of cancer EVs could be directly allied to the LMW-HA abundance and associated labile water network on EV surface as revealed by correlative SMFS, hydration dynamics with fluorescence spectroscopy, and molecular dynamics simulations. This method emerges as a molecular biosensor of the cancer microenvironment.

Effect of Ionic Strength on Ibuprofenate Adsorption on a Lipid Bilayer of Dipalmitoylphosphatidylcholine from Molecular Dynamics Simulations

In this work, the free energy change in the process of transferring ibuprofenate from the bulk solution to the center of a model of the dipalmitoylphosphatidylcholine bilayer at different NaCl concentrations was calculated. Two minima were found in the free energy profile: a local minimum, located in the vicinity of the membrane, and the global free energy minimum, found near the headgroup region. The downward shift of free energy minima with increasing NaCl concentration is consistent with the results of previous works. Conversely, the upward shift of the free energy maximum with increasing ionic strength is due to the competition of sodium ions and lipids molecules to coordinate with ibuprofenate and neutralize its charge. In addition, normal molecular dynamics simulations were performed to study the effects of the ibuprofenate on the lipid bilayer and in the presence of a high ibuprofenate concentration. The effect of ionic strength on the properties of the lipid bilayer and on lipid-drug interactions was analyzed. The area per lipid shrinking with increasing ionic strength, volume of lipids, and thickness of the bilayer is consistent with the experimental results. At a very high ibuprofenate concentration, the lipid bilayer dehydrates, and it consequently transforms into the gel phase, thus blocking the permeation.

Functional Group Distributions, Partition Coefficients, and Resistance Factors in Lipid Bilayers Using Site Identification by Ligand Competitive Saturation

Small molecules such as metabolites and drugs must pass through the membrane of the cell, a barrier primarily comprising phospholipid bilayers and embedded proteins. To better understand the process of passive diffusion, knowledge of the ability of various functional groups to partition across bilayers and the associated energetics would be of utility. In the present study, the site identification by ligand competitive saturation (SILCS) methodology has been applied to sample the distributions of a diverse set of chemical solutes representing the functional groups of small molecules across phospholipid bilayers composed of 0.9:0.1 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/cholesterol and a mixture of 0.52:0.18:0.3 1,2-dioleoyl-sn-glycero-3-phospho-l-serine/1,2-dioleoyl-sn-glycero-3-phosphocholine/cholesterol used in parallel artificial membrane permeability assay experiments. A combination of oscillating chemical potential grand canonical Monte Carlo and molecular dynamics in the SILCS simulations was applied to achieve solute sampling through the bilayers and surrounding aqueous environment from which the distribution of solutes and the functional groups they represent were obtained. Results show differential distribution of aliphatic versus aromatic groups with the former having increased sampling in the center of the bilayers versus in the region of the glycerol linker for the latter. Variations in the distribution of different polar groups are evident, with large differences between negative acetate and positive methylammonium with accumulation of the polar-neutral and acetate solutes above the bilayer head groups. Conversion of the distributions to absolute free energies allows for a detailed understanding of energetics of functional groups in different regions of the bilayers and for calculation of absolute free-energy profiles of multifunctional drug-like molecules across the bilayers from which partition coefficients and resistance factors suitable for insertion into the homogenous solubility-diffusion equation for calculation of permeability were obtained. Comparisons of the calculated bilayer/solution partition coefficients with 1-octanol/water experimental data for both drug-like molecules and the solutes show overall good agreement, validating the calculated distributions and associated absolute free-energy profiles.

Influence of Lipid Composition on the Insertion Process of Glyphosate into Membranes: A Thermodynamic Study

In this work, molecular dynamics simulations were applied to investigate the influence of lipid composition of the model membrane on the insertion of glyphosate (in its charged state, GLYP2-). The profiles of free energy, entropy and enthalpy were obtained through umbrella sampling calculations, for lipid bilayers composed by only 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC), only 1,2-dipalmitoyl-sn-glycerol-3-phosphoserine (DPPS) or a symmetric binary mixture of DPPC and DPPS. In general, the location, the values of minima and maxima of the free energy, and the trend of free energy profiles are influenced by the lipid composition of the lipid bilayer. The driving force in the glyphosate insertion process depends on the lipid composition of the membrane model. If the lipid bilayer is composed solely of DPPS or DPPC, GLYP2- insertion is driven by a favorable enthalpic change. However, if the membrane is composed of a mixture of both lipids, this process is driven by a favorable entropic change. In the lipid bilayer containing DPPS, the glyphosate was found to penetrate hydrated and coordinated with Na+ ions, in contrast to the pure zwitterionic lipid bilayer which penetrated only hydrated. This effect is independent of the concentration of sodium ions present in the bulk solution.

Effects of cholesterol on bilayers with various degrees of unsaturation of their phospholipid tails under mechanical stress

Cholesterol is one of the essential components of the cell membrane. It has a significant influence on various mechanical properties of biomembranes, such as fluidity and elasticity, which have attracted much attention. It is also well known that the concentration of cholesterol affects the mechanical strength of cell membranes. In this paper, we aim to explore the influence of the degree of unsaturation of phospholipid tails on the concentration-effect of cholesterol. Three different phospholipids (DPPC, DIPC and DAPC) were selected as the respective main components of the bilayers and several concentrations of cholesterol were also added to the systems. Our coarse-grained molecular dynamics simulations show that as the cholesterol concentration increases, the saturated phospholipid bilayer is first strengthened, by increasing the rupture tension from 68.9 to 110 mN m⁻¹, and then weakened. The non-monotonic concentration-effect gradually decreases as the degree of unsaturation of the phospholipid tails increases, and in particular, the mechanical strength of the DAPC bilayer hardly changes. The results suggest that cholesterol does not influence a bilayer composed of highly unsaturated phospholipids. Furthermore, lateral density distributions reveal that the distribution of cholesterol in the bilayer is related to the carbon tail unsaturation of the phospholipids.

The concentration-effect of cholesterol on the mechanical strength of biomembranes weakens as the degree of unsaturation of the phospholipid tails increases.

Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

This review gives an overview about the some of the most important possible analyzes, technical challenges, and existing protocols that can be performed on the biological membrane by the molecular dynamics simulation.

Fluorinated CdSe/ZnS quantum dots: Interactions with cell membrane

Fluorescent inorganic quantum dots are highly promising for biomedical applications as sensing and imaging agents. However, the low internalization of the quantum dots, as well as for most of the nanoparticles, by living cells is a critical issue which should be solved for success in translational research. In order to increase the internalization rate of inorganic CdSe/ZnS quantum dots, they were functionalized with a fluorinated organic ligand. The fluorinated quantum dots displayed an enhanced surface activity, leading to a significant cell uptake as demonstrated by in vitro experiments with HeLa cells. We combined the experimental and computational results of Langmuir monolayers of the DPPC phospholipid as a model cell membrane with in vitro experiments for analyzing the mechanism of internalization of the fluorinated CdSe/ZnS quantum dots. Surface pressure-molecular area isotherms suggested that the physical state of the DPPC molecules was greatly affected by the quantum dots. UV-vis reflection spectroscopy and Brewster Angle Microscopy as in situ experimental techniques further confirmed the significant surface concentration of quantum dots. The disruption of the ordering of the DPPC molecules was assessed. Computer simulations offered detailed insights in the interaction between the quantum dots and the phospholipid, pointing to a significant modification of the physical state of the hydrophobic region of the phospholipid molecules. This phenomenon appeared as the most relevant step in the internalization mechanism of the fluorinated quantum dots by cells. Thus, this work sheds light on the role of fluorine on the surface of inorganic nanoparticles for enhancing their cellular uptake.

On the degradation pathway of glyphosate and glycine

The degradation in water of the most widespread herbicide, glyphosate, is still under debate. Experimental disagreements on this process exist and there are only a few theoretical studies to support any conclusions. Moreover, the relationship between glyphosate and glycine is underestimated. Besides the structural similarity, glycine is a product of glyphosate degradation; hence, their studies are complementary. In this study, two mechanisms for the decomposition of the glyphosate molecule and glycine molecule in water are proposed. These mechanisms were explored by using quantum mechanical calculations. A combined microsolvation/PCM approach was employed to find and characterize their transition states, by which the reaction pathways were determined via the IRC method. The results have shown that the degradation processes might occur via a C-C bond cleavage, through a concerted mechanism, whereby the proton transfers and the CO2 detachments occur simultaneously. The second mechanism had two consecutive steps, a decarboxylation followed by the proton transfers. The water molecules served as a conduit for the proton transfers, away from the amine group (or the phosphonate, glyphosate case). Their function was to assist the reactions in a water-mediated decarboxylation. In these particular cases, the free energy of activation was 42.68 and 42.28 kcal mol-1 for the glycine structure and the glyphosate structure, respectively. These results agreed with the photodegradation and thermodegradation of glyphosate, as well as with the spontaneous decarboxylation of glycine. A concerted mechanism might be expected to yield C-P and C-N bond cleavages in the glyphosate molecule.