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.

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.

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.

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.

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.

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.

The impact of lipid oxidation on the functioning of a lung surfactant model

Apart from being responsible for sufficient pulmonary compliance and preventing alveolar collapse, lung surfactant (LS) also forms the first barrier for uptake of inhaled pathogens. As such it is susceptible to damage caused by various deleterious compounds present in air, e.g. oxidants capable of oxidizing unsaturated LS lipids. This study examines the consequences of oxidizing 20% of unsaturated lipids in an LS model: a mixed 1 : 1 DPPC : POPC monolayer. POxnoPC (1-palmitoyl-2-(9-oxo-nonanoyl)-sn-glycero-3-phosphocholine) is considered as the main oxidation product. Experimental surface pressure-area isotherms and polarization-modulation infrared reflection-absorption spectroscopy are employed to probe changes in the macroscopic properties of the unsaturated lipid monolayer induced by oxidation. Microscopic details of the influence of oxidation on the monolayer's phase behavior are elucidated by molecular dynamics simulations at varying lipid packing. We demonstrate that unsaturated lipid oxidation shifts the isotherm towards larger areas and advances monolayer collapse. This is caused by a reversal of the oxidized sn-2 chains of POxnoPC towards the subphase, driven by electrostatic interactions between the aldehyde, glycerin, and water. Increased lipid bulkiness, hindered transition to the LC phase, and transfer of oxidized chain terminals to the subphase have been identified as the most troublesome consequences of this process. They result in the reduction of monolayer stability and its capability to withstand high surface pressures. This may lead to uncontrolled and irreversible loss of lipids from the surface.

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.

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.

Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective

Charge sensitivity analysis (CSA) in force-field atoms resolution was applied to describe the mutual polarization of reactants as well as charge-transfer (CT) effects. An inclusion complex of β-cyclodextrin with salicylic acid was used as a model system. Three CSA models were taken into account and verified on a Born–Oppenheimer molecular dynamics (BOMD) trajectory. The models differed in terms of the equilibrium conditions imposed on the system. It was demonstrated that mutual polarization is an important source of stabilization, in contrast to the results obtained from static charge calculations. The energy lowering induced by CT was small and comparable to the CT stabilization that occurs in hydrogen-bonded systems. All models correctly described the main topological features of the BOMD energy surface. CSA in force-field atoms resolution qualitatively reproduced the charge reorganization accompanying hydrogen-bond formation. It was shown that CSA parameters are very sensitive to the bond formation process, which suggests that they could be applied in reactive force fields as detectors of newly formed chemical bonds.

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Application of explicitly localized molecular orbitals to electronic structure calculations

We have recently generalized the method for localizing orbitals on a set of predefined molecular fragments [Phys. Chem. Chem. Phys. 2012, 14, 546]. The regional localized molecular orbitals (RLMO) are well suited for exploiting the locality of electronic correlation at post-Hartree-Fock level of theory. In this paper, the adequacy of RLMO representation is tested in the second-order local Møller-Plesset (LMP2) perturbation theory. Two model systems, namely, n-pentadecane and trans-retinal, are considered. Adequacy of RLMO/LMP2 method is discussed in conjunction with 'exact' MP2 and Pipek-Mezey LMP2 calculations. It is demonstrated that RLMO/MP2 method reduces correlation space and reproduces more than 99% of the correlation energy.

Fast orbital localization scheme in molecular fragments resolution

The method for localizing orbitals on a set of predefined molecular fragments is introduced. Regional localized molecular orbitals (RLMO) are obtained through block diagonalization of the one-electron density matrix and further refinement of the resulting eigenvectors. The algorithm is fast and reliable, as is illustrated by a few examples. Potential applications range from conceptual insight into a chemical bonding to reduced scaling computational techniques. RLMOs are particularly well suited for fragmentation computational methods and for exploiting the locality of electronic correlation in post-HF methods.

Charge sensitivity analysis in force-field-atom resolution

Charge sensitivity analysis (CSA) was extended to AMBER force-field resolution. The effective electronegativity and hardness data were found using evolutionary algorithms. Four model hardness matrices based on the classical electrostatic, Mataga-Nishimoto, Ohno, and Louwen-Vogt interpolation formulae were considered. Mulliken population analysis and electrostatically derived charges (CHELPG) were taken into account. It was demonstrated that the Ohno interpolation formula gives the best fit to Mulliken charges. For all molecules from the training set and all model hardness matrices, Mulliken charges were reproduced more accurately than CHELPG charges, indicating their good transferability from system to system. The effective electronegativities and hardnesses obtained were further verified by applying CSA to molecules from a validation set that was different from the training set. The correlation between CSA and Mulliken charges was of the same quality as that obtained for the training set.

Meloxicam and meloxicam-beta-cyclodextrin complex in model membranes: effects on the properties and enzymatic lipolysis of phospholipid monolayers in relation to anti-inflammatory activity

Meloxicam, a nonsteroidal anti-inflammatory drug (NSAID), is known as a selective cyclooxygenase-2 inhibitor. Cyclooxygenase-2 is a membrane protein, functionally coupled to an interfacial enzyme, phospholipase A2. Consequently, it may be supposed that the interactions of NSAIDs with lipid membranes play a role in the anti-inflammatory process. In order to investigate the mechanism of this process, Langmuir films formed with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 1,2-dilauroyl-sn-glycero-3-phosphocholine, 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine, or 1,2-myristoyl-sn-glycero-3-phosphoethanolamine were exposed to meloxicam and its beta-cyclodextrin inclusion complex. The monolayers were studied by measuring surface pressure, electric surface potential, Brewster angle micrographs, polarization-modulation infrared reflection-absorption spectra, and phospholipase A2 activity; the inclusion complex was studied using molecular modeling. The results obtained show that the monolayers formed in the presence of meloxicam and its complex are expanded and more liquid-like compared to pure lipids. Both compounds modify hydration of the lipid polar heads, orientation of the molecules, morphology of the domains, and the rate of lipolysis catalyzed by phospholipase A2. The latter effect may be involved in the anti-inflammatory activity of meloxicam. Importantly, the effects observed with the meloxicam-beta-cyclodextrin complex are more pronounced compared to those of the free meloxicam. This observation may be relevant for developing new meloxicam preparations with increased bioavailability.

Complexation of metal ions in Langmuir films formed with two amphiphilic dioxadithia crown ethers

The two new crown ethers presented in this study were synthesized in order to investigate two important features of ionophores, namely metal cation complexation and interfacial properties, and the way in which they interrelate. The two derivatives were conceived as analogs of membrane phospholipids with respect to their amphiphilicity and geometry. They contain a hydrophilic 1,1'-dioxo-3,3'-dithio-14-crown ether headgroup and bear two myristoyl or stearoyl lateral chains. The length of the myristoyl and stearoyl derivatives in an extended conformation is comparable with the thickness of the individual leaflets of cell membranes. The membrane-related and complexation properties of the two crown ether derivatives were studied in monomolecular films spread on pure water and on aqueous solutions of mono-, di-, and trivalent metal salts. The properties of the monolayers are described quantitatively using thermodynamic models. The compression isotherms of the monolayers formed on different subphases show a clear-cut differentiation of the monovalent and di- or trivalent cations with both ligands. This differentiation was interpreted in terms of conformational changes occurring in the crown ether derivatives upon complexation. Molecular modeling indicates that the mono- and divalent cations are coordinated differently by the ligands, yielding complexes with different conformations. The differences of the conformations of the mono- and di- or trivalent cation complexes may be important from the point of view of the interactions with lipid membranes and the biological activity of these potential ionophores.

Efficiency and accuracy of the elongation method as applied to the electronic structures of large systems

Current state of development of the elongation method originally proposed by Imamura is presented. Recent progress in methodology, including geometry optimization and employment of the fast multiple method, is highlighted. The accuracy and efficiency of the elongation method as compared to exact canonical Hartree-Fock and Kohn-Sham approaches are discussed. Potential applications are illustrated by wide range of calculations for model systems. The elongation calculations are demonstrated to be much more efficient compared to the conventional ones with high accuracy maintained. The elongation CPU time is shown by the model calculations as linear or sub-linear scaling for quasi-one-dimensional systems. Future work of development into post-Hartree-Fock methodologies are pointed out.

A new localization scheme for the elongation method

A different localization scheme for the elongation method is developed based on regional molecular orbitals. This scheme is more efficient and more accurate than the previous one especially for covalently bonded systems with strongly delocalized pi electrons. Ab initio test calculations have been performed on three model systems: water chains, polyglycine, and cationic cyanine chains. The dependence on the size of the starting clusters and the effect of the basis set are investigated. Our results are compared with conventional ab initio calculations and it is found in all cases that the error per added unit levels off to a satisfactorily small value as long as the starting cluster is sufficiently large.