Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models

Cryptotanshinone-Induced Permeabilization of Model Phospholipid Membranes: A Biophysical Study

The Danshen terpenoid cryptotanshinone (CPT) is gaining enormous interest in light of its various outstanding biological activities. Among those, CPT has been shown to interact with cell membranes and, for instance, to have antibacterial activity. Several works have shown that CPT alone, or in combination with other drugs, can effectively act as an antibiotic against various infectious bacteria. Some authors have related the mechanism underlying this action to CPT-membrane interaction. This work shows that CPT readily partitions into phosphatidylcholine membranes, but there is a limiting capacity of accommodation of ca. 1 mol CPT to 3 mol phospholipid. The addition of CPT to unilamellar liposomes composed of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) causes membrane permeabilization, as shown by fluorescent probe leakage. This process has been kinetically studied, as well as its modulation by incorporation of phosphatidylethanolamine or phosphatidylglycerol, as a model for pathogenic cell membranes. The thermotropic behavior of 1,2-dimyristoylphosphatidylcholine (DMPC) model membranes is weakly affected by CPT, but the terpenoid causes significant dehydration of the polar region of the bilayer and weak disordering of the acyl chain palisade, as observed in Fourier-transform infrared spectroscopy (FTIR) results. Small-angle X-ray scattering (SAXS) shows that CPT increases DMPC bilayer thickness, which could be due to localization near the phospholipid/water interface. Molecular dynamics (MD) simulations show that the lateral diffusion coefficient of the phospholipid increases with the presence of CPT. CPT extends from the polar head region to the center of the bilayer, being centered between the carbonyl groups and the unsaturated region of the POPC, where there is greater overlap. Interestingly, the free energy profiles of a water molecule crossing the lipid membrane show that the POPC membrane becomes more permeable in the presence of CPT. In summary, our results show that CPT perturbs the physicochemical properties of the phospholipid membrane and compromises its barrier function, which could be of relevance to explain part of its antimicrobial or anticancer activities.

The density of anionic lipids modulates the adsorption of α-Synuclein onto lipid membranes

α-Synuclein is an intrinsically disordered presynaptic protein associated with Parkinson's disease. The physiological role of α-Synuclein is not fully understood, but the protein is known to interact with lipid membranes. We here study how membrane charge affects the adsorption of α-Synuclein to (i) supported lipid bilayers and (ii) small unilamellar vesicles with varying amounts of anionic lipids. The results showed that α-Synuclein adsorbs onto membranes containing ≥5% anionic phosphatidylserine (DOPS) lipids, but not to membranes containing ≤1% DOPS. The density of adsorbed α-Synuclein increased steadily with the DOPS content up to 20% DOPS, after which it leveled off. The vesicles were saturated with α-Synuclein at a 3-5 times higher protein density compared to the supported bilayers, which suggests that a more deformable membrane binds more α-Synuclein. Altogether, the results show that both membrane charge density and flexibility influence the association of α-Synuclein to lipid membranes.

Identification of a potent and selective LAPTc inhibitor by RapidFire-Mass Spectrometry, with antichagasic activity

BACKGROUND

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi and leads to ~10,000 deaths each year. Nifurtimox and benznidazole are the only two drugs available but have significant adverse effects and limited efficacy. New chemotherapeutic agents are urgently required. Here we identified inhibitors of the acidic M17 leucyl-aminopeptidase from T. cruzi (LAPTc) that show promise as novel starting points for Chagas disease drug discovery.

METHODOLOGY/PRINCIPAL FINDINGS

A RapidFire-MS screen with a protease-focused compound library identified novel LAPTc inhibitors. Twenty-eight hits were progressed to the dose-response studies, from which 12 molecules inhibited LAPTc with IC50 < 34 μM. Of these, compound 4 was the most potent hit and mode of inhibition studies indicate that compound 4 is a competitive LAPTc inhibitor, with Ki 0.27 μM. Compound 4 is selective with respect to human LAP3, showing a selectivity index of >500. Compound 4 exhibited sub-micromolar activity against intracellular T. cruzi amastigotes, and while the selectivity-window against the host cells was narrow, no toxicity was observed for un-infected HepG2 cells. In silico modelling of the LAPTc-compound 4 interaction is consistent with the competitive mode of inhibition. Molecular dynamics simulations reproduce the experimental binding strength (-8.95 kcal/mol), and indicate a binding mode based mainly on hydrophobic interactions with active site residues without metal cation coordination.

CONCLUSIONS/SIGNIFICANCE

Our data indicates that these new LAPTc inhibitors should be considered for further development as antiparasitic agents for the treatment of Chagas disease.

Impact of Single-Walled Carbon Nanotube Functionalization on Ion and Water Molecule Transport at the Nanoscale

Nanofluidics has a very promising future owing to its numerous applications in many domains. It remains, however, very difficult to understand the basic physico-chemical principles that control the behavior of solvents confined in nanometric channels. Here, water and ion transport in carbon nanotubes is investigated using classical force field molecular dynamics simulations. By combining one single walled carbon nanotube (uniformly charged or not) with two perforated graphene sheets, we mimic single nanopore devices similar to experimental ones. The graphitic edges delimit two reservoirs of water and ions in the simulation cell from which a voltage is imposed through the application of an external electric field. By analyzing the evolution of the electrolyte conductivity, the role of the carbon nanotube geometric parameters (radius and chirality) and of the functionalization of the carbon nanotube entrances with OH or COO- groups is investigated for different concentrations of group functions.

Passive permeability controls synthesis for the allelochemical sorgoleone in sorghum root exudate

Competition for soil nutrients and water with other plants foster competition within the biosphere for access to these limited resources. The roots for the common grain sorghum produce multiple small molecules that are released via root exudates into the soil to compete with other plants. Sorgoleone is one such compound, which suppresses weed growth near sorghum by acting as a quinone analog and interferes with photosynthesis. Since sorghum also grows photosynthetically, and may be susceptible to sorgoleone action if present in tissues above ground, it is essential to exude sorgoleone efficiently. However, since the P450 enzymes that synthesize sorgoleone are intracellular, the release mechanism for sorgoleone remain unclear. In this study, we conducted an in silico assessment for sorgoleone and its precursors to passively permeate biological membranes. To facilitate accurate simulation, CHARMM parameters were newly optimized for sorgoleone and its precursors. These parameters were used to conduct 1 μs of unbiased molecular dynamics simulations to compare the permeability of sorgoleone with its precursors molecules. We find that interleaflet transfer is maximized for sorgoleone, suggesting that the precursor molecules may remain in the same leaflet for access by biosynthetic P450 enzymes. Since no sorgoleone was extracted during unbiased simulations, we compute a permeability coefficient using the inhomogeneous solubility diffusion model. The requisite free energy and diffusivity profiles for sorgoleone through a sorghum membrane model were determined through Replica Exchange Umbrella Sampling (REUS) simulations. The REUS calculations highlight that any soluble sorgoleone would quickly insert into a lipid bilayer, and would readily transit. When sorgoleone forms aggregates in root exudate as indicated by our equilibrium simulations, aggregate formation would lower the effective concentration in aqueous solution, creating a concentration gradient that would facilitate passive transport. This suggests that sorgoleone synthesis occurs within sorghum root cells and that sorgoleone is exuded by permeating through the cell membrane without the need for a transport protein once the extracellular sorgoleone aggregate is formed.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions

Polyelectrolytes continue to find wide interest and application in science and engineering, including areas such as water purification, drug delivery, and multilayer thin films. We have been interested in the dynamics of small molecules in a variety of polyelectrolyte (PE) environments; in this paper, we report simulations and analysis of the small dye molecule rhodamine B (RB) in several very simple polyelectrolyte solutions. Translational diffusion of the RB zwitterion has been measured in fully atomistic, 2 μs long molecular dynamics simulations in four different polyelectrolyte solutions. Two solutions contain the common polyanion sodium poly(styrene sulfonate) (PSS), one with a 30-mer chain and the other with 10 trimers. The other two solutions contain the common polycation poly(allyldimethylammonium) chloride (PDDA), one with two 15-mers and the other with 10 trimers. RB diffusion was also simulated in several polymer-free solutions to verify its known experimental value for the translational diffusion coefficient, D_RB, of 4.7 × 10^-6 cm²/s at 300 K. RB diffusion was slowed in all four simulated PE solutions, but to varying degrees. D_RB values of 3.07 × 10^-6 and 3.22 × 10^-6 cm²/s were found in PSS 30-mer and PSS trimer solutions, respectively, whereas PDDA 15-mer and trimer solutions yielded values of 2.19 × 10^-6 and 3.34 × 10^-6 cm²/s. Significant associations between RB and the PEs were analyzed and interpreted via a two-state diffusion model (bound and free diffusion) that describes the data well. Crowder size effects and anomalous diffusion were also analyzed. Finally, RB translation along the polyelectrolytes during association was characterized.

Modeling thermodiffusion in aqueous sodium chloride solutions-Which water model is best?

Thermodiffusion is the migration of a species due to a temperature gradient and is the driving phenomenon in many applications ranging from early cancer detection to uranium enrichment. Molecular dynamics (MD) simulations can be a useful tool for exploring the rather complex thermodiffusive behavior of species, such as proteins and ions. However, current MD models of thermodiffusion in aqueous ionic solutions struggle to quantitatively predict the Soret coefficient, which indicates the magnitude and direction of species migration under a temperature gradient. In this work, we aim to improve the accuracy of MD thermodiffusion models by assessing how well different water models can recreate thermodiffusion in a benchmark aqueous NaCl solution. We tested four of the best available rigid non-polarizable water models (TIP3P-FB, TIP4P-FB, OPC3, and OPC) and the commonly used TIP3P and SPC/E water models for their ability to predict the inversion temperature and Soret coefficient in 0.5, 2, and 4M aqueous NaCl solutions. Each water model predicted a noticeably different ion distribution yielding different inversion temperatures and magnitudes of the Soret coefficient. By comparing the modeled Soret coefficients to published experimental values, we determine TIP3P-FB to be the water model that best recreates thermodiffusion in aqueous NaCl solutions. Our findings can aid future works in selecting the most accurate rigid non-polarizable water model, including water and ion parameters for investigating thermodiffusion through MD simulations.

Investigation of Antidepressant Properties of Yohimbine by Employing Structure-Based Computational Assessments

The use of pharmaceuticals to treat Major Depressive Disorder (MDD) has several drawbacks, including severe side effects. Natural compounds with great efficacy and few side effects are in high demand due to the global rise in MDD and ineffective treatment. Yohimbine, a natural compound, has been used to treat various ailments, including neurological conditions, since ancient times. Serotonergic neurotransmission plays a crucial role in the pathogenesis of depression; thus, serotonergic receptor agonist/antagonistic drugs are promising anti-depressants. Yohimbine was investigated in this study to determine its antidepressant activity using molecular docking and pharmacokinetic analyses. Additionally, the in silico mutational study was carried out to understand the increase in therapeutic efficiency using site-directed mutagenesis. Conformational changes and fluctuations occurring during wild type and mutant serotonergic receptor, 5-hydroxytryptamine receptors 1A (5HT1A) and yohimbine were assessed by molecular dynamics MD simulation studies. Yohimbine was found to satisfy all the parameters for drug-likeness and pharmacokinetics analysis. It was found to possess a good dock score and hydrogen-bond interactions with wild type 5HT1A structure. Our findings elaborate the substantial efficacy of yohimbine against MDD; however, further bench work studies may be carried out to prove the same.

Structure-Based Virtual Screening Reveals Ibrutinib and Zanubrutinib as Potential Repurposed Drugs against COVID-19

Coronavirus disease (COVID)-19 is the leading global health threat to date caused by a severe acute respiratory syndrome coronavirus (SARS-CoV-2). Recent clinical trials reported that the use of Bruton's tyrosine kinase (BTK) inhibitors to treat COVID-19 patients could reduce dyspnea and hypoxia, thromboinflammation, hypercoagulability and improve oxygenation. However, the mechanism of action remains unclear. Thus, this study employs structure-based virtual screening (SBVS) to repurpose BTK inhibitors acalabrutinib, dasatinib, evobrutinib, fostamatinib, ibrutinib, inositol 1,3,4,5-tetrakisphosphate, spebrutinib, XL418 and zanubrutinib against SARS-CoV-2. Molecular docking is conducted with BTK inhibitors against structural and nonstructural proteins of SARS-CoV-2 and host targets (ACE2, TMPRSS2 and BTK). Molecular mechanics-generalized Born surface area (MM/GBSA) calculations and molecular dynamics (MD) simulations are then carried out on the selected complexes with high binding energy. Ibrutinib and zanubrutinib are found to be the most potent of the drugs screened based on the results of computational studies. Results further show that ibrutinib and zanubrutinib could exploit different mechanisms at the viral entry and replication stage and could be repurposed as potential inhibitors of SARS-CoV-2 pathogenesis.

Effect of TMAO on the Structure and Phase Transition of Lipid Membranes: Potential Role of TMAO in Stabilizing Cell Membranes under Osmotic Stress

Extremophiles adopt strategies to deal with different environmental stresses, some of which are severely damaging to their cell membrane. To combat high osmotic stress, deep-sea organisms synthesize osmolytes, small polar organic molecules, like trimethylamine-N-oxide (TMAO), and incorporate them in the cell. TMAO is known to protect cells from high osmotic or hydrostatic pressure. Several experimental and simulation studies have revealed the roles of such osmolytes on stabilizing proteins. In contrast, the effect of osmolytes on the lipid membrane is poorly understood and broadly debated. A recent experiment has found strong evidence of the possible role of TMAO in stabilizing lipid membranes. Using the molecular dynamics (MD) simulation technique, we have demonstrated the effect of TMAO on two saturated fully hydrated lipid membranes in their fluid and gel phases. We have captured the impact of TMAO's concentration on the membrane's structural properties along with the fluid/gel phase transition temperatures. On increasing the concentration of TMAO, we see a substantial increase in the packing density of the membrane (estimated by area, thickness, and volume) and enhancement in the orientational order of lipid molecules. Having repulsive interaction with the lipid head group, the TMAO molecules are expelled away from the membrane surface, which induces dehydration of the lipid head groups, increasing the packing density. The addition of TMAO also increases the fluid/gel phase transition temperature of the membrane. All of these results are in close agreement with the experimental observations. This study, therefore, provides a molecular-level understanding of how TMAO can influence the cell membrane of deep-sea organisms and help in combating the osmotic stress condition.

The degree and position of phosphorylation determine the impact of toxic and trace metals on phosphoinositide containing model membranes

This work assessed effects of metal binding on membrane fluidity, liposome size, and lateral organization in biomimetic membranes composed of 1 mol% of selected phosphorylated phosphoinositides in each system. Representative examples of phosphoinositide phosphate, bisphosphate and triphosphate were investigated. These include phosphatidylinositol-(4,5)-bisphosphate, an important signaling lipid constituting a minor component in plasma membranes whereas phosphatidylinositol-(4,5)-bisphosphate clusters support the propagation of secondary messengers in numerous signaling pathways. The high negative charge of phosphoinositides facilitates electrostatic interactions with metals. Lipids are increasingly identified as toxicological targets for divalent metals, which potentially alter lipid packing and domain formation. Exposure to heavy metals, such as lead and cadmium or elevated levels of essential metals, like cobalt, nickel, and manganese, implicated with various toxic effects were investigated.  Phosphatidylinositol-(4)-phosphate and phosphatidylinositol-(3,4,5)-triphosphate containing membranes are rigidified by lead, cobalt, and manganese whilst cadmium and nickel enhanced fluidity of membranes containing phosphatidylinositol-(4,5)-bisphosphate. Only cobalt induced liposome aggregation. All metals enhanced lipid clustering in phosphatidylinositol-(3,4,5)-triphosphate systems, cobalt in phosphatidylinositol-(4,5)-bisphosphate systems, while all metals showed limited changes in lateral film organization in phosphatidylinositol-(4)-phosphate matrices. These observed changes are relevant from the biophysical perspective as interference with the spatiotemporal formation of intricate domains composed of important signaling lipids may contribute to metal toxicity.

Benchmarking Force Field and the ANI Neural Network Potentials for the Torsional Potential Energy Surface of Biaryl Drug Fragments

Many drug molecules contain biaryl fragments, resulting in a torsional barrier corresponding to rotation around the bond linking the aryls. The potential energy surfaces of these torsions vary significantly because of steric and electronic effects, ultimately affecting the relative stability of the molecular conformations in the protein-bound and solution states. Simulations of protein-ligand binding require accurate computational models to represent the intramolecular interactions to provide accurate predictions of the structure and dynamics of binding. In this article, we compare four force fields [generalized AMBER force field (GAFF), open force field (OpenFF), CHARMM general force field (CGenFF), optimized potentials for liquid simulations (OPLS)] and two neural network potentials (ANI-2x and ANI-1ccx) for their ability to predict the torsional potential energy surfaces of 88 biaryls extracted from drug fragments. The root mean square deviation (rmsd) over the full potential energy surface and the mean absolute deviation of the torsion rotational barrier height (MADB) relative to high-level ab initio reference data (CCSD(T1)*) were used as the measure of accuracy. Uncertainties in these metrics due to the composition of the data set were estimated using bootstrap analysis. In comparison to high-level ab initio data, ANI-1ccx was most accurate for predicting the barrier height (rmsd: 0.5 ± 0.0 kcal/mol, MADB: 0.8 ± 0.1 kcal/mol), followed closely by ANI-2x (rmsd: 0.5 ± 0.0 kcal/mol, MADB: 1.0 ± 0.2 kcal/mol), then CGenFF (rmsd: 0.8 ± 0.1 kcal/mol, MADB: 1.3 ± 0.1 kcal/mol) and OpenFF (rmsd: 0.7 ± 0.1 kcal/mol, MADB: 1.3 ± 0.1 kcal/mol), then GAFF (rmsd: 1.2 ± 0.2 kcal/mol, MADB: 2.6 ± 0.5 kcal/mol), and finally OPLS (rmsd: 3.6 ± 0.3 kcal/mol, MADB: 3.6 ± 0.3 kcal/mol). Significantly, the neural network potentials (NNPs) are systematically more accurate and more reliable than any of the force fields. As a practical example, the NNP/molecular mechanics method was used to simulate the isomerization of ozanimod, a drug used for multiple sclerosis. Multinanosecond molecular dynamics (MD) simulations in an explicit aqueous solvent were performed, as well as umbrella sampling and adaptive biasing force-enhanced sampling techniques. The rate constant for this isomerization calculated using transition state theory was 4.30 × 10^-1 ns^-1, which is consistent with direct MD simulations.

Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches

One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.

Membrane permeability of small molecules from unbiased molecular dynamics simulations

Permeation of many small molecules through lipid bilayers can be directly observed in molecular dynamics simulations on the nano- and microsecond timescale. While unbiased simulations provide an unobstructed view of the permeation process, their feasibility for computing permeability coefficients depends on various factors that differ for each permeant. The present work studies three small molecules for which unbiased simulations of permeation are feasible within less than a microsecond, one hydrophobic (oxygen), one hydrophilic (water), and one amphiphilic (ethanol). Permeabilities are computed using two approaches: counting methods and a maximum-likelihood estimation for the inhomogeneous solubility diffusion (ISD) model. Counting methods yield nearly model-free estimates of the permeability for all three permeants. While the ISD-based approach is reasonable for oxygen, it lacks precision for water due to insufficient sampling and results in misleading estimates for ethanol due to invalid model assumptions. It is also demonstrated that simulations using a Langevin thermostat with collision frequencies of 1/ps and 5/ps yield oxygen permeabilities and diffusion constants that are lower than those using Nosé-Hoover by statistically significant margins. In contrast, permeabilities from trajectories generated with Nosé-Hoover and the microcanonical ensemble do not show statistically significant differences. As molecular simulations become more affordable and accurate, calculation of permeability for an expanding range of molecules will be feasible using unbiased simulations. The present work summarizes theoretical underpinnings, identifies pitfalls, and develops best practices for such simulations.

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

Insight into the structure-antibacterial activity of amino cation-based and acetate anion-based ionic liquids from computational interactions with the POPC phospholipid bilayer

Investigations relevant to ionic liquids (ILs) as antibacterial agents have drawn considerable attention. However, the high cost and potential toxicity of ILs have severely limited their extensive applications, which has motivated researchers to design inexpensive and health-benign ILs. In this work, the interactions between the hydrated zwitterionic phospholipid (POPC) bilayer and a series of hypothetical amino cation-based and acetate anion-based ILs with different counterparts were investigated using molecular dynamics (MD) simulations to predict their antibacterial abilities. The cations of the ILs were found to insert into the lipid bilayer spontaneously, especially amino cations. Reorientation of the inserted imidazolium-based cations was observed, while the inserted amino cations showed no obvious reorientation phenomena, probably because of the strong charge interactions between the positive NH₃ groups of the amino cation and the negative PO₄ groups of the lipid bilayer. Due to their strong affinity with water, acetate-based anions disperse better in water solution, which weakens the insertion of the cations into the lipid bilayer to some extent. The structure and dynamic properties of the lipid bilayer, such as electrostatic potential, local ordering, area per lipid, volume per lipid, bilayer thickness, and lateral diffusion, are significantly influenced by the insertion of the cations, which results in disorder of the lipid bilayer and further disruption of the activity of the cell membrane. The insights into the relationship between the structures of ILs and their antibacterial activity in this work will provide a good reference for the screening and design of less expensive, safer, and greener IL candidates as antibacterial agents.

Permeability of membranes in the liquid ordered and liquid disordered phases

The functional significance of ordered nanodomains (or rafts) in cholesterol rich eukaryotic cell membranes has only begun to be explored. This study exploits the correspondence of cellular rafts and liquid ordered (L_o) phases of three-component lipid bilayers to examine permeability. Molecular dynamics simulations of L_o phase dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol show that oxygen and water transit a leaflet through the DOPC and cholesterol rich boundaries of hexagonally packed DPPC microdomains, freely diffuse along the bilayer midplane, and escape the membrane along the boundary regions. Electron paramagnetic resonance experiments provide critical validation: the measured ratio of oxygen concentrations near the midplanes of liquid disordered (L_d) and L_o bilayers of DPPC/DOPC/cholesterol is 1.75 ± 0.35, in very good agreement with 1.3 ± 0.3 obtained from simulation. The results show how cellular rafts can be structurally rigid signaling platforms while remaining nearly as permeable to small molecules as the L_d phase.

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects

Atomistic biomolecular simulations predominantly utilize additive force fields (FF), where the electrostatic potential is modeled by fixed point charges. Among other consequences, the lack of polarizability in these models undermines the balance of hydrophilic/hydrophobic nonbonded interactions. Simulations of water/alkane systems using the TIP3P water model and CHARMM36 parameters reveal a 1 kcal/mol overestimate of the experimental transfer free energy of water to hexadecane; more recent optimized water models (SPC/E, TIP4P/2005, TIP4P-Ew, TIP3P-FB, TIP4P-FB, OPC, TIP4P-D) overestimate this transfer free energy by approximately 2 kcal/mol. In contrast, the polarizable SWM4-NDP and SWM6 water models reproduce experimental values to within statistical error. As an alternative to explicitly modeling polarizability, this paper develops an efficient automated workflow to optimize pair-specific Lennard-Jones parameters within an additive FF. Water/hexadecane is used as a prototype and the free energy of water transfer to hexadecane as a target. The optimized model yields quantitative agreement with the experimental transfer free energy and improves the water/hexadecane interfacial tension by 6%. Simulations of five different lipid bilayers show a strong increase of water permeabilities compared to the unmodified CHARMM36 lipid FF which consistently improves match with experiment: the order-of-magnitude underestimate for monounsaturated bilayers is rectified and the factor of 2.8-4 underestimate for saturated bilayers is turned into a factor of 1.5-3 overestimate. While agreement with experiment is decreased for the diffusion constant of water in hexadecane, alkane transfer free energies, and the bilayers' area per lipid, the method provides a permeant-specific route to achieve a wide range of heterogeneous observables via rapidly optimized pairwise parameters.

Molecular Dynamics Simulations of Membrane Permeability

This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.