A biophysical approach to phospholipase A2 activity and inhibition by anti-inflammatory drugs

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230 000 experimentally determined structures. The chemical reactivity of proteins is based on the electron density distribution, which is usually approximated by partial atomic charges. However, because of the size and high variability, there is not yet a universal and accurate tool for calculating the partial atomic charges of these structures. For this reason, we introduce the web application PDBCharges: a tool for quick calculation of partial atomic charges for protein structures from PDB. The charges are calculated using the recent semi-empirical quantum-mechanical method GFN1-xTB, which reproduces PBE0/TZVP/CM5 charges. The computed partial atomic charges can be downloaded in common data formats or visualized online via the powerful Mol* Viewer. The PDBCharges application is freely available at https://pdbcharges.biodata.ceitec.cz and has no login requirement.

Role of respiratory uncoupling in drug-induced mitochondrial permeability transition

Mitochondrial injury contributes to severe drug-induced liver injury. Particularly, mitochondrial permeability transition (MPT) is thought to be relevant to cytolytic hepatitis. However, the mechanism of drug-induced MPT is unclear and prediction of MPT is not adequately evaluated in the preclinical stage. In a previous study, we found that troglitazone, a drug withdrawn due to liver injury, induced MPT via mild depolarization probably resulting from uncoupling. Herein, we investigated whether other drugs that induce MPT share similar properties as troglitazone, using isolated mitochondria from rat liver. Of the 22 test drugs examined, six drugs, including troglitazone, induced MPT and showed an uncoupling effect. Additionally, receiver operating characteristic analysis was conducted to predict the MPT potential from the respiratory control ratio, an indicator of uncoupling intensity. Results showed that 2.5 was the best threshold that exhibited high sensitivity (1.00) and high specificity (0.81), indicating that uncoupling was correlated with MPT potential. Activation of calcium-independent phospholipase A2 appeared to be involved in uncoupling-induced MPT. Furthermore, a strong relationship between MPT intensity and the uncoupling effect among similar compounds was confirmed. These results may help in predicting MPT potential using cultured cells and modifying the chemical structures of the drugs to reduce MPT risk.

Subtle chemical modification for enrichment of Fmoc-amino acid at a phospholipid interface

Amino acids including the Fmoc group (9-fluorenylmethyloxycarbonyl) are bioinspired molecules that display intriguing features in self-assembly and biological applications. The influence of a delicate chemical modification between Fmoc-F and Fmoc-Y on the interaction with a phospholipid surface was analyzed. Langmuir monolayers of the 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA) phospholipid were used to mimic the eukaryotic cell membrane. In situ Brewster angle microscopy and UV-vis reflection spectroscopy provided insights on the effect of the Fmoc-amino acid derivatives on the DMPA phospholipid. The formation of H-bonds between the Fmoc-Y and the DMPA molecules was assessed, demonstrating the crucial role of the hydroxyl group of Fmoc-Y in enhancing the interaction with biosurfaces.

A modest chemical modification of the Fmoc-amino acids led to enhanced interaction with a model surface for biomembrane.

Effects of ibuprofen and carbamazepine on the ion transport system and fatty acid metabolism of temperature conditioned juveniles of Solea senegalensis

The increasing presence of pharmaceuticals in aquatic environments in the last decades, derived from human and veterinary use, has become an important environmental problem. Previous studies have shown that ibuprofen (IB) and carbamazepine (CBZ) modify physiological and biochemical processes in Senegalese sole (Solea senegalensis) in a temperature-dependent manner. In other vertebrates, there is evidence that both of these pharmaceuticals interfere with the 'arachidonic acid (AA) cascade', which is responsible for the biosynthesis of numerous enzymes that are involved in the osmoregulatory process. The present work aims to study the temperature-dependent effects of these two pharmaceuticals on several biochemical and molecular parameters in Senegalese sole. Regarding osmoregulation, Na⁺, K⁺ -ATPase enzyme activity was determined in the gills, kidney and intestine, and the expressions of both Na⁺, K⁺ -ATPase 1α-subunit isoforms (ATP1A1a and ATP1A1b) were quantified in gills. Gill prostaglandin-endoperoxide synthase-2 (PTGS2) gene expression and fatty acid composition were selected to determine the interference of both pharmaceuticals with the AA cascade. Senegalese sole juveniles, acclimatised at 15°C or 20°C, were exposed through intraperitoneal injection to IB (10mg/kg) and CBZ (1mg/kg) for 48h. Non-injected fish (Control) and those injected with the carrier (sunflower oil; S.O.), acclimated at each of the two temperatures, were used for comparison. The results show that IB directly affected the osmoregulatory mechanisms that alter gill and intestine Na⁺, K⁺ -ATPase activities. In addition, the copy number of ATP1A1a was higher at 20°C than at 15°C, which could be a direct response to the temperature variation. The gene expression of PTGS2 was affected by neither drug administration nor acclimation temperature. Nevertheless, detailed analysis of AA and eicosapentaenoic acid (EPA) percentages revealed a CBZ-derived effect in the fatty acid composition of the gills.

Surface dilution kinetics of phospholipase A(2) catalyzed lipid-bilayer hydrolysis

Phospholipase A2 (PLA2) enzymes catalyze hydrolysis of phospholipids in membranes. Elucidation of the kinetics of interfacial enzymatic activity is best accomplished by investigating the interface substrate concentration dependence of the activity for which appropriate diluents are required. PLA2 is stereoselective toward the L_enantiomers of phospholipids. A novel approach employing D_phospholipids as diluents to perform surface dilution kinetic studies of PLA2 is presented. Activity of bee venom PLA2 at mixed L+D_DPPC (dipalmitoylphosphatidylcholine) bilayer interfaces was measured as a function of substrate L_DPPC mole fraction and vesicle concentration using a sensitive fluorescence assay. A model for interface enzymatic activity based on the three-step kinetic scheme of (i) binding of PLA2 to the bilayer interface, (ii) binding of a lipid to PLA2 at the interface, and (iii) hydrolysis was applied to the hydrolysis data. Activity profiles showed that D_enantiomers also bind to the enzyme but resist hydrolysis. Activity dependences on vesicle and substrate concentrations could be disentangled, bringing resolution to an outstanding problem in membrane hydrolysis of separating the effects of the three steps. Individual values of the kinetic parameters of the model, including the vesicle-PLA2 equilibrium dissociation constant of step (i), interface Michaelis-Menten-Henri constant for L and D_DPPC of step (ii), and the rate constant for interface hydrolysis, step (iii), were obtained as solutions to equations resulting from fitting the model to the data.

Interaction of nonsteroidal anti-inflammatory drugs with membranes: in vitro assessment and relevance for their biological actions

Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most commonly used drugs in the world due to their anti-inflammatory, analgesic and antipyretic properties. Nevertheless, the consumption of these drugs is still associated with the occurrence of a wide spectrum of adverse effects. Regarding the major role of membranes in cellular events, the hypothesis that the biological actions of NSAIDs may be related to their effect at the membrane level has triggered the in vitro assessment of NSAIDs-membrane interactions. The use of membrane mimetic models, cell cultures, a wide range of experimental techniques and molecular dynamics simulations has been providing significant information about drugs partition and location within membranes and also about their effect on diverse membrane properties. These studies have indeed been providing evidences that the effect of NSAIDs at membrane level may be an additional mechanism of action and toxicity of NSAIDs. In fact, the pharmacokinetic properties of NSAIDs are closely related to the ability of these drugs to interact and overcome biological membranes. Moreover, the therapeutic actions of NSAIDs may also result from the indirect inhibition of cyclooxygenase due to the disturbing effect of NSAIDs on membrane properties. Furthermore, increasing evidences suggest that the disordering effects of these drugs on membranes may be in the basis of the NSAIDs-induced toxicity in diverse organ systems. Overall, the study of NSAIDs-membrane interactions has proved to be not only important for the better understanding of their pharmacological actions, but also for the rational development of new approaches to overcome NSAIDs adverse effects.

In vitro assessment of NSAIDs-membrane interactions: significance for pharmacological actions

PURPOSE

To study interactions between nonsteroidal anti-inflammatory drugs (NSAIDs) and membrane mimetic models.

METHODS

The interactions of indomethacin and nimesulide with liposomes of dipalmitoylphosphatidylcholine (DPPC) at two physiological pH conditions (pH 7.4 and 5.0) were investigated by time-resolved and steady-state fluorescence techniques and derivative ultraviolet/visible absorption spectrophotometry. Fluorescence quenching studies that assess the location of the drugs interacting with the membrane were carried out using labeled liposomes with trimethylammonium-diphenylhexatriene (TMA-DPH), a fluorescent probe with well-known membrane localization. Partition of the drugs within membranes was determined by calculating their partition coefficients (K p ) between liposomes and water using derivative ultraviolet/visible absorption spectrophotometry in a temperature range of 37-50°C. The Van't Hoff analysis of the temperature dependence of K p values allowed calculating the membrane-water variation of enthalpy (ΔH w→m) and entropy (ΔS w→m) and consequently the Gibbs free energy (ΔG w→m).

RESULTS

Results indicate that quenching, partitioning and thermodynamic parameters inherent to the interaction of the studied drugs with the membrane mimetic model are deeply dependent on the initial organization of the membrane, on the pH medium and on the physical properties of the drug.

CONCLUSIONS

The interactions between NSAIDs and membranes are manifested as changes in the physical and thermodynamic properties of the bilayers. Depending on the composition and physical state of the membrane and the chemical structure of the NSAID, the interaction can support or prevent drug activity or toxicity.

NSAIDs interactions with membranes: a biophysical approach

This work focuses on the interaction of four representative NSAIDs (nimesulide, indomethacin, meloxicam, and piroxicam) with different membrane models (liposomes, monolayers, and supported lipid bilayers), at different pH values, that mimic the pH conditions of normal (pH 7.4) and inflamed cells (pH 5.0). All models are composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) which is a representative phospholipid of most cellular membranes. Several biophysical techniques were employed: Fluorescence steady-state anisotropy to study the effects of NSAIDs in membrane microviscosity and thus to assess the main phase transition of DPPC, surface pressure-area isotherms to evaluate the adsorption and penetration of NSAIDs into the membrane, IRRAS to acquire structural information of DPPC monolayers upon interaction with the drugs, and AFM to study the changes in surface topography of the lipid bilayers caused by the interaction with NSAIDs. The NSAIDs show pronounced interactions with the lipid membranes at both physiological and inflammatory conditions. Liposomes, monolayers, and supported lipid bilayers experiments allow the conclusion that the pH of the medium is an essential parameter when evaluating drug-membrane interactions, because it conditions the structure of the membrane and the ionization state of NSAIDs, thereby influencing the interactions between these drugs and the lipid membranes. The applied models and techniques provided detailed information about different aspects of the drug-membrane interaction offering valuable information to understand the effect of these drugs on their target membrane-associated enzymes and their side effects at the gastrointestinal level.