Computational and experimental approaches for assessing the interactions between the model calycin β-lactoglobulin and two antibacterial fluoroquinolones

Binding interaction of a potential statin with β-lactoglobulin: An in silico approach

This article reports the interaction between a synthetic statin, fluvastatin with bovine milk protein, β-lactoglobulin (BLG) through docking, constant pH molecular dynamics simulation (cpHMD) and binding free energy calculations. Docking provides the best fitted binding mode of the ligand with the receptor. We have carried out MD simulations of the protein and protein-ligand complex at two different pH viz. 7.0 and 1.5. We have found that the protein shows more compact behavior at pH 1.5 and this behavior is more prominent on complexation with the ligand. In support of this we have utilized the properties viz. root mean square deviations, root mean square fluctuations, radius of gyration, protein-ligand hydrogen bond and binding free energy calculations. Calculation of radius of gyration shows that the value decreases from 14.51 Å to 14.03 Å on complexation at pH 1.5. Calculations of hydrogen bonds at pH 1.5 confirms that hydrogen bonding interactions of the binding residues of the protein with the ligand provides stability to the complex. We have used molecular mechanics-generalized Born surface area (MMGBSA) method to estimate binding free energies of the protein with the ligand. MMGBSA calculations suggest that there is favorable binding interactions between the protein and the ligand with major contributions from Van der Waals interactions. We have found that the net average binding free energy is -29.394 kcal/mol that reveals a favorable binding interactions of BLG with the ligand. This study suggests that in spite of the acidic environment in the stomach BLG can act as a carrier for the acid-sensitive drug molecules such as fluvastatin because of its highly stable conformational behavior in the acidic pH.

Tracking of β-Lactoglobulin Binding Compounds with Biofingerprinting Chromatogram Analysis of Natural Products

The addition of milk to tea has been shown to prevent the vascular protective effects of the tea. Thus we had an interest in evaluating the possible binding of compounds in extracts of black tea, Camellia sinensis (L.) O. Kunze, and nettle, Urtica dioica L, to β-lactoglobulin (βLG), which is the main proteinaceous component of whey. Since our previously miniaturised 96-well plate method based on fluorescence quenching is suitable only for pure compounds, we have developed a method of ultrafiltration sampling combined with HPLC to study the βLG-binding property of the extracts. The method development was made with extract of Piper nigrum L. (black pepper), because its major component is piperine, which has been earlier shown to bind to βLG. The results showed that piperine from P. nigrum was highly and rutin from U. dioica slightly bound to βLG. No components from C. sinensis were bound to βLG. We showed for the first time, that the ultrafiltration/HPLC system can be used in βLG-binding studies with plant extracts. Furthermore, we demonstrated that βLG could bind compounds from extracts and in this way either enhance, or decrease, their health benefits, for example in food preparations.

Stereoselective reduction of aromatic ketones by a new ketoreductase from Pichia glucozyma

A new NADPH-dependent benzil reductase (KRED1-Pglu) was identified from the genome of the non-conventional yeast Pichia glucozyma CBS 5766 and overexpressed in E. coli. The new protein was characterised and reaction parameters were optimised for the enantioselective reduction of benzil to (S)-benzoin. A thorough study of the substrate range of KRED1-Pglu was conducted; in contrast to most other known ketoreductases, KRED1-Pglu prefers space-demanding substrates, which are often converted with high stereoselectivity. A molecular modelling study was carried out for understanding the structural determinants involved in the stereorecognition experimentally observed and unpredictable on the basis of steric properties of the substrates. As a result, a new useful catalyst was identified, enabling the enantioselective preparation of different aromatic alcohols and hydroxyketones.

All-Purpose Containers? Lipid-Binding Protein - Drug Interactions

The combined use of in vitro (¹⁹F-NMR) and in silico (molecular docking) procedures demonstrates the affinity of a number of human calycins (lipid-binding proteins from ileum, liver, heart, adipose tissue and epidermis, and retinol-binding protein from intestine) for different drugs (mainly steroids and vastatins). Comparative evaluations on the complexes outline some of the features relevant for interaction (non-polar character of the drugs; amino acids and water molecules in the protein calyx most often involved in binding). Dissociation constants (K_i) for drugs typically lie in the same range as K_i for natural ligands; in most instances (different proteins and docking conditions), vastatins are the strongest interactors, with atorvastatin ranking top in half of the cases. The affinity of some calycins for some of the vastatins is in the order of magnitude of the drug C_max after systemic administration in humans. The possible biological implications of this feature are discussed in connection with drug delivery parameters (route of administration, binding to carrier proteins, distribution to, and accumulation in, human tissues).

β-lactoglobulin as a vector for β-carotene food fortification

Food fortification is a strategy to overcome vitamin A deficiency in developing countries. Our aim was to investigate the involvement of the bovine milk protein β-lactoglobulin (β-Lg), a potential retinoid carrier, in vitamin A absorption. In vivo experiments were conducted by force-feeding mice with retinol or β-carotene associated with either β-Lg or oil-in-water emulsion, with subsequent determination of both vitamin A intestinal mucosa and plasma contents. Caco-2 cells were then used to investigate the mechanisms of vitamin A uptake when delivered by either β-Lg or mixed micelles. We showed that β-Lg was as efficient as emulsion to promote β-carotene, but not retinol, absorption in mice. Similar results were obtained in vitro. Interestingly, an inhibitor of the Scavenger Receptor Class B Type I significantly decreased the uptake of micellar β-carotene but not that of β-carotene bound to β-Lg. Overall, we showed that β-Lg would be a good vector for β-carotene food fortification.

Wards in the keyway: amino acids with anomalous pK(a)s in calycins

As a follow-up to our recent analysis of the electrostatics of bovine β-lactoglobulin (Eberini et al. in Amino Acids 42:2019-2030, 2011), we investigated whether the occurrence in the native structure of calycins-the superfamily to which β-lactoglobulin belongs-of amino acids with anomalous pK (a)s is an infrequent or, on the contrary, a common occurrence, and whether or not a general pattern may be recognized. To this aim, we randomly selected four calycins we had either purified from natural sources or prepared with recombinant DNA technologies during our previous and current structural and functional studies on this family. Their pIs vary over several pH units and their known functions are as diverse as carriers, enzymes, immunomodulators and/or extracellular chaperones. In our survey, we used both in silico prediction methods and in vitro procedures, such as isoelectric focusing, electrophoretic titration curves and spectroscopic techniques. By comparing the results under native conditions (no exposure of the proteins to chaotropic agents) to those after protein unfolding (in the presence of 8 M urea), a shift is observed in the pK (a) of at least one amino acid per protein, which results in a measurable change in pI. Three types of amino acids are involved: Cys, Glu, and His, their position varies along the calycin sequence. Although no common mechanism may thus be recognized, we hypothesize that the 'normalization' of anomalous pK (a)s may be the phenomenon that accompanies, and favors, structural rearrangements such as those involved in ligand binding by these proteins. An interesting, if anecdotal, validation to this view comes from the behavior of human retinol binding protein, for which the pI of the folded and liganded protein is intermediate between those of the folded and unliganded and of the unfolded protein forms. Likewise, both solid (from crystallography) and solution state (from CD spectroscopy) data confirm that the protein undergoes structural rearrangement upon retinol binding.

In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases

GPR17, a previously orphan receptor responding to both uracil nucleotides and cysteinyl-leukotrienes, has been proposed as a novel promising target for human neurodegenerative diseases. Here, in order to specifically identify novel potent ligands of GPR17, we first modeled in silico the receptor by using a multiple template approach, in which extracellular loops of the receptor, quite complex to treat, were modeled making reference to the most similar parts of all the class-A GPCRs crystallized so far. A high-throughput virtual screening exploration of GPR17 binding site with more than 130,000 lead-like compounds was then applied, followed by the wet functional and pharmacological validation of the top-scoring chemical structures. This approach revealed successful for the proposed aim, and allowed us to identify five agonists or partial agonists with very diverse chemical structure. None of these compounds could have been expected 'a priori' to act on a GPCR, and all of them behaved as much more potent ligands than GPR17 endogenous activators.

Bovine β-lactoglobulin acts as an acid-resistant drug carrier by exploiting its diverse binding regions

Binding of fluorine-containing drugs to bovine β-lactoglobulin, the most abundant whey protein in bovine milk, was investigated by means of 19F NMR and mass spectrometry. The stoichiometry of the binding and its stability in acidic medium, where β-lactoglobulin is folded and stable, were also studied, along with competition from molecules that can be regarded as analogs of physiological ligands to bovine β-lactoglobulin. Conditional binding data were combined with protein structural information derived from circular dichroism and limited proteolysis studies. Spectroscopic techniques were also used to assess whether the bound drugs stabilize the protein structure against denaturation by chaotropes or temperature at various pH values. The results obtained provide evidence for the presence of multiple binding regions on the protein, with a specific and different affinity for structurally different classes of hydrophobic drugs and, more generally, that bovine β-lactoglobulin can bind and protect against low pH values various classes of drugs of pharmaceutical relevance.

Binding of phenolic compounds and their derivatives to bovine and reindeer beta-lactoglobulin

In plant-based food, phenolic compounds usually do not exist in their native form, but as esters, glycosides, or polymers. The native forms, however, require deglycosylation for their intestinal absorption, and aglycone has been considered to be the potential health-protecting/promoting form. The binding of the aglycones of phenolic compounds to bovine and reindeer beta-lactoglobulins (betaLG) using fluorescence quenching was studied. The effects of pH and storage were also studied. Of the compounds investigated, the majority of flavones, flavonols, flavanones, and isoflavones were bound to betaLG. In the pH studies, no significant effects were found. The fact that the phenolic compounds were not released at pH 2 might indicate that they bind to an external part rather than to the central cavity. Studies implicated that betaLG could act as a binder or carrier for phenolic compounds in acidic, basic, or neutral conditions and that the ligand/betaLG complex can remain stable during storage.

Transport properties of bovine and reindeer β-lactoglobulin in the Caco-2 cell model

Beta-lactoglobulin (betaLG) is a protein that binds ligands like fatty acids and retinol into the hydrophobic pocket. Our purpose was to study bovine and reindeer betaLG as transporter molecules and compare their transport properties across Caco-2 cell membrane. The reindeer betaLG has more valuable binder characteristics than bovine betaLG because it has only one genetic phenotype and it seems to exhibit better immunological properties. The permeation of betaLG in Caco-2 cells was evaluated by immunoblotting, and the permeation of the model substances retinol, palmitic acid and cholesterol with and without betaLG was determined using [(3)H]-labelled ligands. Both bovine and reindeer betaLG were able to pass across a Caco-2 cell monolayer similarly. Unbound and betaLG-bound [(3)H]retinol and [(3)H]palmitic acid were equally transported across the Caco-2 cell layer, whereas [(3)H]cholesterol could not pass across Caco-2 cells with or without betaLG at any of the studied circumstances. Thus, the bovine and reindeer milk betaLG is not a suitable protein to enhance transport of ligands across the Caco-2 cell membrane, used for predicting intestinal absorption.

Computational and experimental approaches assess the interactions between bovine beta-lactoglobulin and synthetic compounds of pharmacological interest

Extending a previous investigation, the ability of binding to the model calycin beta-lactoglobulin (BLG) was evaluated both in silico and in vitro for several fluorine-containing (semi-)synthetic molecules of pharmacological and pharmaceutical interest (antibiotics, vastatins, steroid drugs). Simulation procedures included molecular docking according to a Montecarlo-simulated annealing protocol and molecular dynamics; heteronuclear NMR and denaturant gradient gel electrophoresis were the selected experimental techniques. For the tested drugs, ranking of the binding affinity was consistently assessed by computation and by experiment. The affinity for BLG increased in the sequence: 5-fluorosalycilic acid<dexamethasone<<sulindac=norfloxacin<fluvastatin. The computed Ki for fluorosalycilate was in the order of 10(-4)M; accordingly, in a molecular dynamics simulation the chemical diffused out of the BLG calyx in less than 2ns, and no evidence of binding was found by NMR or electrophoresis. Conversely, the Ki for fluvastatin and norfloxacin were in the order of 10(-7) and 10(-6)M, similar to the affinity for BLG by natural ligands, such as retinoids and long-chain fatty acids. Moreover fluvastatin was found still bound to the protein after 5ns of molecular dynamics simulation. Interaction of fluvastatin and norfloxacin with BLG was made evident by changes in chemical shift and dynamic parameters in the 19F NMR spectra and in effective urea concentration and cooperativity features in denaturant gradient gel electrophoresis. Such findings prove BLG may act as a drug carrier accepting in its cavity molecules of different bulk, rigidity and hydrophobicity.