Nucleoside Analog Reverse-Transcriptase Inhibitors in Membrane Environment: Molecular Dynamics Simulations.

The behavior of four drugs from the family of nucleoside analog reverse-transcriptase inhibitors (zalcitabine, stavudine, didanosine, and apricitabine) in a membrane environment was traced using molecular dynamics simulations. The simulation models included bilayers and monolayers composed of POPC and POPG phospholipids. It was demonstrated that the drugs have a higher affinity towards POPG membranes than POPC membranes due to attractive long-range electrostatic interactions. The results obtained for monolayers were consistent with those obtained for bilayers. The drugs accumulated in the phospholipid polar headgroup region. Two adsorption modes were distinguished. They differed in the degree of penetration of the hydrophilic headgroup region. Hydrogen bonds between drug molecules and phospholipid heads were responsible for adsorption. It was shown that apricitabine penetrated the hydrophilic part of the POPC and POPG membranes more effectively than the other drugs. Van der Waals interactions between S atoms and lipids were responsible for this.

Chemometrics as a valuable tool for evaluating interactions between antiretroviral drugs and food.

AIMS: Clinically significant interactions with food occur for more than half of antiretroviral drugs. Different physiochemical properties deriving from the chemical structures of antiretroviral drugs may contribute to the variable food effect. Chemometric methods allow analysing a large number of interrelated variables concomitantly and visualizing correlations between them. We used a chemometric approach to determine the types of correlations among different features of antiretroviral drugs and food that may influence interactions. METHODS: Thirty-three antiretroviral drugs were analysed: ten nucleoside reverse transcriptase inhibitors, six non-nucleoside reverse transcriptase inhibitors, five integrase strand transfer inhibitors, ten protease inhibitors, one fusion inhibitor and one HIV maturation inhibitor. Input data for the analysis were collected from already published clinical studies, chemical records and calculations. We constructed a hierarchical partial least squares (PLS) model with three response parameters: postprandial change of time to reach maximum drug concentration (ΔTmax ), albumin binding (%) and logarithm of partition coefficient (logP). Predictor parameters were the first two principal components of principal component analysis (PCA) models for six groups of molecular descriptors. RESULTS: PCA models explained 64.4% to 83.4% of the variance of the original parameters (average: 76.9%), whereas the PLS model had four significant components and explained 86.2% and 71.4% of the variance in the sets of predictor and response parameters, respectively. We observed 58 significant correlations between ΔTmax , albumin binding (%), logP and constitutional, topological, hydrogen bonding and charge-based molecular descriptors. CONCLUSIONS: Chemometrics is a useful and valuable tool for analysing interactions between antiretroviral drugs and food.

Congo Red as a Supramolecular Carrier System for Doxorubicin: An Approach to Understanding the Mechanism of Action.

The uptake and distribution of doxorubicin in the MCF7 line of breast-cancer cells were monitored by Raman measurements. It was demonstrated that bioavailability of doxorubicin can be significantly enhanced by applying Congo red. To understand the mechanism of doxorubicin delivery by Congo red supramolecular carriers, additional monolayer measurements and molecular dynamics simulations on model membranes were undertaken. Acting as molecular scissors, Congo red particles cut doxorubicin aggregates and incorporated them into small-sized Congo red clusters. The mixed doxorubicin/Congo red clusters were adsorbed to the hydrophilic part of the model membrane. Such behavior promoted transfer through the membrane.

The lung surfactant activity probed with molecular dynamics simulations.

The surface of pulmonary alveolar subphase is covered with a mixture of lipids and proteins. This lung surfactant plays a crucial role in lung functioning. It shows a complex phase behavior which can be altered by the interaction with third molecules such as drugs or pollutants. For studying multicomponent biological systems, it is of interest to couple experimental approach with computational modelling yielding atomic-scale information. Simple two, three, or four-component model systems showed to be useful for getting more insight in the interaction between lipids, lipids and proteins or lipids and proteins with drugs and impurities. These systems were studied theoretically using molecular dynamic simulations and experimentally by means of the Langmuir technique. A better understanding of the structure and behavior of lung surfactants obtained from this research is relevant for developing new synthetic surfactants for efficient therapies, and may contribute to public health protection.

The Molecular Bases of the Interaction between a Saponin from the Roots of Gypsophila paniculata L. and Model Lipid Membranes.

In view of the possible medical applications of saponins, the molecular structure of a GOTCAB saponin from the roots of Gypsophila paniculata L. was determined by NMR. The biological activity of saponins may depend on the interaction with cell membranes. To obtain more insight in the mechanism of membrane-related saponin function, an experimental and theoretical study was conducted. Ternary lipid systems composed of sphingomyelin, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, and cholesterol were used as models of mammalian cell membranes. The membrane-saponin interaction was studied experimentally by monitoring surface pressure in the monomolecular films formed at the air-aqueous subphase interface. The behavior of GOTCAB saponin in a water box and model monolayer systems was characterized by molecular dynamics simulations. The results obtained showed that, in the systems used, cholesterol had a decisive effect on the interaction between GOTCAB and phosphocholine or sphingomyelin as well as on its location within the lipid film.

Charge distributions for molecular dynamics simulations from self-consistent polarization method.

Partial atomic charges are important force field parameters. They are usually computed by applying quantum-chemical calculations and the assumed population scheme. In this study polarization consistent scheme of deriving a charge distribution inside solute molecule is proposed. The environment effect is explicitly taken into account by distributing solvent molecules around the solute target. The performed analysis includes a few computational schemes (HF, MP2, B3LYP, and M026X), basis sets (cc-pvnz, n = 2, 3, …, 6), and electrostatically derived charge distributions (KS, CHELP, CHELPG, and HLY). It is demonstrated that the environment effect is very important and cannot be disregarded. The second solvation shell should be included to achieve the charge convergence. Huge corrections to charge distribution are due to induction and dispersion. The B3LYP/cc-pvqz level of theory is recommended for deriving the charges within self-consistent polarization scheme.

Impact of Doxorubicin on Self-Organization of Congo Red: Quantum Chemical Calculations and Molecular Dynamics Simulations.

Quantum-chemical calculations and molecular dynamics simulation were applied to a model self-organization process of Congo red (CR) molecules in aqueous solution and the impact of doxorubicin (DOX) molecules on such a process. It was demonstrated that both pure CR/CR and mixed CR/DOX dimers were stable. Van der Waals interactions between aromatic units were responsible for a stacked dimer formation. An important source of stabilization in the CR/CR dimer was the polarization energy. In the CR/DOX mixed dimer long range, electrostatic interactions were the main driving force leading to complexation. An implicit solvent model showed that the formation of the CR/CR dimer was favored over the CR/DOX one. Molecular dynamics simulations demonstrated rapid complexation. In the pure CR system, short sequences of ribbon-like structures were formed. Such structures might be glued by hydrogen bonds to form bigger complexes. It was shown that the aromatic part of the DOX molecule enters CR ribbons with the sugar part covering the CR ribbons. These findings demonstrated that CR may find applications as a carrier in delivering DOX molecules; however, further more extensive investigations are required.

Elongation method with intermediate mechanical and electrostatic embedding for geometry optimizations of polymers.

The elongation method with intermediate mechanical and electrostatic embedding (ELG-IMEE) is proposed. The electrostatic embedding uses atomic charges generated by a charge sensitivity analysis (CSA) method and parameterized for three different population analyses, namely, the Merz-Singh-Kollman scheme, the charge model 5, and the atomic polar tensor. The obtained CSA models were tested on two model systems. Test calculations show that the electrostatic embedding provides several times of decrease in the difference of energies of testing and reference calculations in comparison with the conventional elongation approach (ELG). The mechanical embedding is implemented in a combination of the conventional elongation method and the ONIOM approach. Moreover, it was demonstrated that the geometry optimization with the ELG-IMEE reduces the errors in the optimized structures by about one order in root-mean-square deviation, when compared to ELG.

Lung surfactant monolayer - A good natural barrier against dibenzo-p-dioxins.

The present study deals with interaction of two air pollutants: dibenzodioxin, DD, and its' monochlorinated derivative, 2-chlorodibenzodioxin, 2CLDD, with models of the lung surfactant (LS) system. A monolayer composed of DPPC and POPC in 1:1 molar ratio was used as a model of LS. One component monolayers of DPPC and POPC were also examined, to model the interiors of LC and LE domains in LS, respectively. Molecular dynamics simulations and measurements of surface pressure isotherms, as well as polarization modulation-infrared reflection-absorption spectra were employed to study the influence of dioxins on the monolayers. We demonstrate, that both dioxins adsorb and accumulate in the hydrophobic parts of all three monolayers. DD molecules prefer flat orientation on the surface at large areas. Upon compression, they lift and orient perpendicularly to the monolayer. Flat orientation of DD molecules leads to their large surface area. In consequence they preferentially locate in vicinity of unsaturated chains of POPC - they are small enough to fill void spaces created by kinks in unsaturated chains. 2CLDD orient along monolayer normal already at the largest areas and preference for POPC was not observed for them. In laterally relaxed states, a condensing effect, connected with reduction of surface area available to the lipids was observed for both dioxins. In the case of 2CLDD, additional locally ordering influence of dioxin molecules was detected. In compressed states, the presence of dioxin molecules hinders alignment and uniform ordering of lipid chains.

The role of DPPG in lung surfactant exposed to benzo[a]pyrene.

Lung surfactant (LS) occurs at the air-water interface in the alveoli. Its main function is to reduce the work needed to expand the alveoli during inhalation and prevent the alveolar collapse during exhalation. Disturbance of this complex interfacial system by the uptake of pollutant molecules can lead to changes in fluidity, permeability, phase separation and domain formation, which in turn can lead to serious impairment in lung function. Knowledge of the LS-pollutant interaction is essential for understanding the mechanism of this process. In this study, we investigate the interaction of LS models with benzo[a]pyrene (BaP). Dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylglycerol (DPPG) sodium salt, and their 4 : 1 mixture are used as LS models. Surface pressure-area isotherms and molecular dynamics simulations are employed to study the properties of LS monolayers. It was found that the addition of BaP has a destabilizing effect on the mixed DPPC/DPPG monolayer, manifested by the decrease in surface pressure. Compression of a monolayer during a respiratory cycle may expel BaP to the bulk solution. It was demonstrated that DPPG is an active component that prevents the BaP molecule from entering the water subphase; as a minor component of LS it can effectively reduce this process. In addition, the presence of BaP in LS models induces the reduction of monolayer hydration in the hydrophilic region and the increase in chain ordering in the hydrophobic region. The observed changes in monolayer fluidity and phase behavior can be a source of various lung function disorders.

Modeling Lung Surfactant Interactions with Benzo[a]pyrene.

By reducing the surface tension of the air-water interface in alveoli, lung surfactant (LS) is crucial for proper functioning of the lungs. It also forms the first barrier against inhaled pathogens. In this study we inspect the interactions of LS models with a dangerous air pollutant, benzo[a]pyrene (BaP). Dipalmitoylphosphatidylcholine (DPPC), 1-palmitoyl-2-oleoylphosphatidylcholine, and their 1:1 mixture are used as LS models. Pressure-area isotherms are employed to study macroscopic properties of the monolayers. We find that addition of BaP has a condensing effect, manifested by lowering the values of surface pressure and shifting the isotherms to smaller areas. Atomistic details of this process are examined by means of molecular dynamics simulations. We show that initially BaP molecules are accumulated in the monolayers. Upon compression, they are forced to the headgroups region and eventually expelled to the subphase. BaP presence results in reduction of monolayer hydration in the hydrophilic region. In the hydrophobic region it induces increased chain ordering, reduction of monolayer fluidity, and advances transition to the liquid condensed phase in the DPPC system.

Mixed DPPC/POPC Monolayers: All-atom Molecular Dynamics Simulations and Langmuir Monolayer Experiments.

To elucidate the consequences of the saturated-unsaturated nature of lipid surface films, monolayers formed by an equimolar mixture of 1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipids are investigated in a wide range of surface pressures. As such mixtures share some features with naturally-occurring surfactants, for example the lung surfactant, the systems are studied at the temperature relevant for human body. All-atom molecular dynamics simulations and Langmuir trough experiments are employed. The binary lipid mixture is compared with the corresponding one-component systems. Atomistic-level alterations of monolayer molecular properties upon lateral compression are scrutinized. These involve elevation of lateral ordering of lipid chains, modulation of chain and headgroup orientation, and reduction of lipid hydration. The presence of the unsaturated POPC in the DPPC/POPC mixture reduces the liquid expanded-liquid condensed coexistence region and moderates the phase transition. Simulations predict that nanoscale lipid de-mixing occurs with small transient DPPC clusters emerging due to local fluctuations of the lateral lipid arrangement. A vertical sorting of lipids induced by lateral compression is also observed, with DPPC transferred toward the water phase. Both the conformational lipid alterations due to monolayer compression as well as the existence of lateral dynamic inhomogeneities of the lipid film are potentially pertain to dynamic and non-homogeneous lipid interfacial systems.

Formation of ß-cyclodextrin complexes in an anhydrous environment.

The formation of inclusion complexes of ß-cyclodextrin was studied at the melting temperature of guest compounds by differential scanning calorimetry. The complexes of long-chain n-alkanes, polyaromatics, and organic acids were investigated by calorimetry and IR spectroscopy. The complexation ratio of ß-cyclodextrin was compared with results obtained in an aqueous environment. The stability and structure of inclusion complexes with various stoichiometries were estimated by quantum chemistry and molecular dynamics calculations. Comparison of experimental and theoretical results confirmed the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds. This finding gives new insight into the mechanism of formation of host-guest complexes and shows that hydrophobic interactions play a secondary role in this case. Graphical abstract The formation of complexes of ß-cyclodextrin with selected n-alkanes, polyaromatics, and organic acids in an anhydrous environment is studied by differential scanning calorimetry, IR spectroscopy, and molecular modeling. The results obtained confirm the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds and give a new perspective on the mechanism of formation of host-guest complexes.

Structure - membrane activity relationship in a family of peptide-based gemini amphiphiles: An insight from experimental and theoretical model systems.

A study of the interaction between five gemini amphiphilic valine-based pseudopeptides (GAPs) differing by the length of the central aliphatic spacer linking two amino acid subunits, and a model bacterial membrane lipid, 1,2-dimyristoyl-sn-glycero-3-phospho-rac-(1-glycerol) (DMPG), is here presented. Pure DMPG, pure GAPs and mixed GAPs/DMPG monolayers were formed at the air-water interface using Langmuir technique. The properties of the Langmuir films were investigated using surface pressure measurements, polarization modulation-infrared reflection-absorption spectroscopy, and Brewster angle microscopy. The atomic level information concerning the orientation of molecules in the monolayer and hydration of the polar headgroups was obtained from molecular dynamics simulations. It was demonstrated that the length of the central spacer in the GAPs structure is important for the properties of the mixed films; the disorganization of the membrane increases with the length of the spacer. The latter point is important for developing possible antimicrobial agents based on GAPs.

Two antibacterial nalidixate calixarene derivatives in cholesterol monolayers: Molecular dynamics and physicochemical effects.

The interaction of two antibacterial calixarene derivatives with cholesterol, a eukaryotic cell membrane lipid, was investigated with the aim to get more insight in the potential advers effects on our cells. The derivatives used had one or two nalidixic acid arms grafted on the lower rim of the calixarene aromatic crown. Monomolecular films spread at the air-water interface were used as model lipid membranes. Pure cholesterol and pure calixarene derivatives, as well as binary cholesterol - calixarene derivative mixtures were studied using surface pressure measurements, polarization-modulation infrared reflection absorption spectroscopy and molecular dynamics simulations. The properties of the mixed monolayers were described quantitatively using thermodynamic models. The analysis of surface pressure-area isotherms of mixed monolayers shows that cholesterol may form homogenous but metastable domains with both nalidixate derivatives. This phenomenon is more clearly observed with mono-substituted calixarene. A detailed modeling analysis indicates that cholesterol favors dehydration of the calixarene polar headgroups and transfer of the derivatives from the aqueous to the gas phase. This effect, more pronounced in the case of the monosubstituted calixarene, can be linked to the hydrophobic interaction with cholesterol. This observation may be useful for developing new calixarene derivatives allowing us to control disease-causing bacteria without harming our own cells.

The selective interactions of cationic tetra-p-guanidinoethylcalix[4]arene with lipid membranes: theoretical and experimental model studies.

Behavior of cationic tetra-p-guanidinoethylcalix[4]arene (CX1) and its building block, p-guanidinoethylphenol (mCX1) in model monolayer lipid membranes was investigated using all atom molecular dynamics simulations and surface pressure measurements. Members of two classes of lipids were taken into account: zwitterionic 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and anionic 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine sodium salt (DMPS) as models of eukaryotic and bacterial cell membranes, respectively. It was demonstrated that CX1 and mCX1 accumulate near the negatively charged DMPS monolayers. The adsorption to neutral monolayers was negligible. In contrast to mCX1, CX1 penetrated into the hydrophobic part of the monolayer. The latter effect, which is possible due to a flip-flop inversion of the CX1 orientation in the lipid layer compared to the aqueous phase, may be responsible for its antibacterial activity.

A Study of the Interaction between a Family of Gemini Amphiphilic Pseudopeptides and Model Monomolecular Film Membranes Formed with a Cardiolipin.

The interaction between five gemini amphiphilic pseudopeptides (GAPs) differing by the length of the central spacer and a model membrane lipid, 1,3-bis[1,2-dimyristoyl-sn-glycero-3-phospho]-sn-glycerol (cardiolipin) were studied with the aim to evaluate their possible antimicrobial properties. To this end, monomolecular films were formed at the air/water interface with pure cardiolipin or cardiolipin/GAPs mixtures; film properties were determined using surface pressure and surface potential measurements, as well as polarization-modulation infrared reflection-absorption spectroscopy. Moreover, to better understand the GAPs-phospholipid interaction at the molecular level, molecular dynamics simulations were performed. The results obtained indicate that the length of the central spacer has an effect on the interaction of GAPs with cardiolipin and on the properties of the lipid film. The GAPs with the longer linkers can be expected to be useful for biological membrane modification and for possible antimicrobial applications.

Intermediate electrostatic field for the generalized elongation method.

An intermediate electrostatic field is introduced to improve the accuracy of fragment-based quantum-chemical computational methods by including long-range polarizations of biomolecules. The point charge distribution of the intermediate field is generated by a charge sensitivity analysis that is parameterized for five different population analyses, namely, atoms-in-molecules, Hirshfeld, Mulliken, natural orbital, and Voronoi population analysis. Two model systems are chosen to demonstrate the performance of the generalized elongation method (ELG) combined with the intermediate electrostatic field. The calculations are performed for the STO-3G, 6-31G, and 6-31G(d) basis sets and compared with reference Hartree-Fock calculations. It is shown that the error in the total energy is reduced by one order of magnitude, independently of the population analyses used. This demonstrates the importance of long-range polarization in electronic-structure calculations by fragmentation techniques.

Molecular organization of nalidixate conjugated calixarenes in bacterial model membranes probed by molecular dynamics simulation and Langmuir monolayer studies.

Two p-tert-butylcalix[4]arene derivatives bearing one or two nalidixic acid groups connected to the lower rim of p-tert-butylcalix[4]arene through the propylenic spacer were studied upon interaction with model bacterial membranes. Indeed, these derivatives were developed recently as new macrocyclic antibiotic carriers for antibacterial therapy. To obtain molecular level information about the interaction between the calixarene conjugates and a membrane lipid, atomistic molecular dynamics simulation, as well as surface pressure, surface potential, polarization modulation infrared reflection-absorption spectroscopy, and Brewster angle microscopy studies of 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE)-calixarene derivative films were performed. The results obtained indicate that the interaction between the calixarene derivatives and DMPE occurs via the phosphate and carbonyl groups present in the lipid. Although both calixarene derivatives increase the chain tilt and conformational disordering of the DMPE molecules, these effects are more important in the case of the monosubstituted derivative. Importantly, the two derivatives have an opposite impact on hydration of the phosphoglyceride polar head.

Intermediate electrostatic field for the elongation method.

A simple way to improve the accuracy of the fragmentation methods is proposed. The formalism was applied to the elongation (ELG) method at restricted open-shell Hartree-Fock (ROHF) level of theory. The α-helix conformer of polyglycine was taken as a model system. The modified ELG method includes a simplified electrostatic field resulting from point-charge distribution of the system's environment. In this way the long-distance polarization is approximately taken into account. The field attenuates during the ELG process to eventually disappear when the final structure is reached. The point-charge distributions for each ELG step are obtained from charge sensitivity analysis (CSA) in force-field atoms resolution. The presence of the intermediate field improves the accuracy of ELG calculations. The errors in total energy and its kinetic and potential contributions are reduced by at least one-order of magnitude. In addition the SCF convergence of ROHF scheme is improved.