Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic nature of the protein and the possible variety of ligand-binding orientations, while keeping computational costs tractable. Recently, an iterative Linear Interaction Energy (LIE) approach was introduced, in which results from multiple simulations of a protein-ligand complex are combined into a single binding free energy using a Boltzmann weighting-based scheme. This method was shown to reach experimental accuracy for flexible proteins while retaining the computational efficiency of the general LIE approach. Here, we show that the iterative LIE approach can be used to predict binding affinities in an automated way. A workflow was designed using preselected protein conformations, automated ligand docking and clustering, and a (semi-)automated molecular dynamics simulation setup. We show that using this workflow, binding affinities of aryloxypropanolamines to the malleable Cytochrome P450 2D6 enzyme can be predicted without a priori knowledge of dominant protein-ligand conformations. In addition, we provide an outlook for an approach to assess the quality of the LIE predictions, based on simulation outcomes only.     

Exact 3D boundary representation in finite element analysis based on Cartesian grids independent of the geometry

This paper proposes a novel Immersed Boundary Method where the embedded domain is exactly described by using its Computer‐Aided Design (CAD) boundary representation with Non‐Uniform Rational B‐Splines (NURBS) or T‐splines. The common feature with other immersed methods is that the current approach substantially reduces the burden of mesh generation. In contrast, the exact boundary representation of the embedded domain allows to overcome the major drawback of existing immersed methods that is the inaccurate representation of the physical domain. A novel approach to perform the numerical integration in the region of the cut elements that is internal to the physical domain is presented and its accuracy and performance evaluated using numerical tests. The applicability, performance, and optimal convergence of the proposed methodology is assessed by using numerical examples in three dimensions. It is also shown that the accuracy of the proposed methodology is independent on the CAD technology used to describe the geometry of the embedded domain. Copyright © 2015 John Wiley & Sons, Ltd.     

Forum The role of CIB: some reflections

An explanation for the low innovation activity in construction is put forward. The central argument is that the current theory of construction is one root cause for low innovation activity. Instead, an explicit and more powerful theory of construction is needed for further innovation, which is ‘to manage new ideas into good currency’. There are three main mechanisms in the current theory of construction which are identified as causing this hindrance. Firstly, production theories in general, as well as construction theories specifically, have been implicit. Therefore, it has not been possible to transfer radical managerial innovations, such as lean production, from manufacturing to construction at a theoretical level. Direct application of this production template to construction has been limited due to the different context of construction in comparison with manufacturing. Secondly, the current theoretical model of construction is based on the transformation model of production. It is argued that the principles of this model are counterproductive, because uncertainty and interdependence are abstracted away. This leads to fragmented and myopic management and inflated variability. Practical examples show that these deficiencies and related practical constraints hinder the implementation of top-down innovations. Thirdly, empirical research shows that also bottom-up innovations - systematic learning and problem solving - are being hindered by the current theory. Thus, the advancement of innovations in construction requires that a new, explicit and valid theory of construction is created, and business models and control methods are developed on the basis of that new theory. Cet article propose une explication concernant le taux bas de l'activité d'innovation dans la secteur du bâtiment. L'argument central étant que la théorie actuelle de la construction est une des raisons fondamentales de cette activité basse d'innover. Au lieu de cela, on a besoin d'une théorie de la construction explicite et plus efficace afin d'innover. Dans la théorie actuelle du bâtiment, il y a trois mécanismes fondamentaux qui sont identifiés comme causes gênant cette innovation. Premièrement, les théories de production en général, ainsi que les théories de la construction en particulier, ont été implicites. Ainsi, il était impossible de transférer des innovations gestionnaires radicales, comme la production allégée (lean production), à partir du domaine de la fabrication à celui du bâtiment à un niveau théorique. L'application directe de ce modèle de production au secteur bâtiment a été limitée à cause du contexte différent de celui-ci en comparaison de celui de la fabrication. Deuxièmement, le modèle théorique actuel de la construction bâtiment est basé sur le modèle de la transformation de production. On avance que les principes de ce modèle agissent négativement sur la productivité parce que l'incertitude et l'interdépendance en sont exclues. Ceci mène à une gestion fragmentée et myope ainsi qu'à une inflation de la variabilité. Des exemples pratiques montrent que ces déficiences et les contraintes pratiques qui leur sont liées, gênent les implémentations des innovations de haut en bas. Troisièmement, une étude empirique montre que les innovations de bas en haut - c'est-à-dire l'apprentissage systématique et la résolution de problèmes - sont gênés par la théorie actuelle. Ainsi, le progrès dan les innovations du secteur bâtiment exige qu'une nouvelle théorie explicite et valide soit créée, et que des modèles d'affaires et des méthodes de contrôle soient développés sur la base de cette nouvelle théorie.     

Novel Redox-Dependent Esterase Activity (EC 3.1.1.2) for DJ-1: Implications for Parkinson’s Disease

Mutations the in human DJ-1 (hDJ-1) gene are associated with early-onset autosomal recessive forms of Parkinson’s disease (PD). hDJ-1/parkinsonism associated deglycase (PARK7) is a cytoprotective multi-functional protein that contains a conserved cysteine-protease domain. Given that cysteine-proteases can act on both amide and ester substrates, we surmised that hDJ-1 possessed cysteine-mediated esterase activity. To test this hypothesis, hDJ-1 was overexpressed, purified and tested for activity towards 4-nitrophenyl acetate (pNPA) as µmol of pNPA hydrolyzed/min/mg·protein (U/mg protein). hDJ-1 showed maximum reaction velocity esterase activity (V_max = 235.10 ± 12.00 U/mg protein), with a sigmoidal fit (S_0.5 = 0.55 ± 0.040 mM) and apparent positive cooperativity (Hill coefficient of 2.05 ± 0.28). A PD-associated mutant of DJ-1 (M26I) lacked activity. Unlike its protease activity which is inactivated by reactive oxygen species (ROS), esterase activity of hDJ-1 is enhanced upon exposure to low concentrations of hydrogen peroxide (<10 µM) and plateaus at elevated concentrations (>100 µM) suggesting that its activity is resistant to oxidative stress. Esterase activity of DJ-1 requires oxidation of catalytic cysteines, as chemically protecting cysteines blocked its activity whereas an oxido-mimetic mutant of DJ-1 (C106D) exhibited robust esterase activity. Molecular docking studies suggest that C106 and L126 within its catalytic site interact with esterase substrates. Overall, our data show that hDJ-1 contains intrinsic redox-sensitive esterase activity that is abolished in a PD-associated mutant form of the hDJ-1 protein.     

Estimation of the effects of an intensive solar intervention in the historical centre of jaén (Spain)

This paper is directed at evaluating the theoretical potential of an intensive solar intervention in the historical centre of the city of Jaén (Spain). Using the outputs of a solar intervention proposal comprising biomass, photovoltaics and solar thermal domestic hot water (DHW) over a 50-building sample (in which those suitable for solar measures have been selected by evaluating each one over a collection of parameters), energy savings, environmental benefits and economic aspects of the envisaged actions are extrapolated over the entire historical centre. A saving of about 70% of conventional source energy annual consumption and a decrease of some 70% and 73% of CO₂ and SO_x annual releases, respectively, could be reached with respect to the present situation. Besides, an amount of conventionally generated electricity equivalent to the yearly photovoltaic-generated electricity would require 131500 m³ of water a year, which is a rather significant feature for a dry climate like that of the city. the unitary cost of energy in the new scenario would be 60.7 pta kWh-¹ for photovoltaics, 329.9 pta m-³ for DHW using solar thermal installations and 4.6 Pta kWh-¹ for biomass heating (1 US$ = 132.7 pta; 1 ECU = 160.9 pta).     

Assembly and Characterization of Biocompatible Coenzyme Q10-Enriched Lipid Nanoparticles

Coenzyme Q₁₀ (CoQ₁₀) is a strongly hydrophobic lipid that functions in the electron transport chain and as an antioxidant. CoQ₁₀ was conferred with aqueous solubility by incorporation into nanoparticles containing phosphatidylcholine (PtdCho) and apolipoprotein (apo) A-I. These particles, termed CoQ₁₀ nanodisks (ND), contain 1.0 mg CoQ₁₀/5 mg PtdCho/2 mg apoA-I (97% CoQ₁₀ solubilization efficiency). UV/Vis absorbance spectroscopy of CoQ₁₀ ND revealed a characteristic absorbance peak centered at 275 nm. Incorporation of CoQ₁₀ into ND resulted in quenching of apoA-I tryptophan fluorescence emission. Gel filtration chromatography of CoQ₁₀ ND gave rise to a single major absorbance peak and HPLC of material extracted from this peak confirmed the presence of CoQ₁₀. Incubation of cultured cells with CoQ₁₀ ND, but not empty ND, resulted in a significant increase in the CoQ₁₀ content of mitochondria as well as enhanced oxidative phosphorylation, as observed by a ~24% increase in maximal oxygen consumption rate. Collectively, a facile method to solubilize significant quantities of CoQ₁₀ in lipid nanoparticles has been developed. The availability of CoQ₁₀ ND provides a novel means to investigate biochemical aspects of CoQ₁₀ uptake by cells and/or administer it to subjects deficient in this key lipid as a result of inborn errors of metabolism, statin therapy, or otherwise.     

Salmonellosis in finishing pigs in Spain: prevalence, antimicrobial agent susceptibilities, and risk factor analysis

A herd-based survey of Salmonella in pigs was carried in a major pig producing region of Spain. Mesenteric lymph nodes were collected from the carcasses of 25 pigs from each of 80 herds at time of slaughter. Salmonella spp. were isolated from 31% of animals and 94% of herds. Within-herd prevalence ranged from 4 to 88%, with the prevalence in most herds being greater than 10%. A large diversity of Salmonella serotypes was found, with Typhimurium, 4,[5],12:i:-, and Rissen being the most prevalent. Two or more serotypes coexisted in 73% of the herds. Salmonella Typhimurium was present in 68% of the herds. Most (82%) of the Salmonella isolates belonged to serogroups targeted by enzyme-linked immunosorbent assay tests for pig salmonellosis. Resistance to at least one antimicrobial agent was detected in 73% of the strains, and one or more resistant strains were recovered from pigs in 93% of the herds. Antimicrobial agent resistance (AR) was more frequent among the most prevalent than it was among the rarer serotypes. Twenty-five multi-AR patterns were found. Resistance to three or more families of antimicrobial agents was found in 75% of AR strains. The finding that many of the herds yielded isolates of several multi-AR patterns indicates that Salmonella infections were acquired from multiple sources. High prevalence of Salmonella in herds was associated with lack of rodent control programs, herds from farms with only finishing pigs, herds managed by more than one full-time worker, herds for which the source of drinking water was not a city supply, and relatively long fattening times.     

Biochemical changes during the preservation stage of ripe olive processing

The influences of initial sodium chloride (6% and 0% w/v in tap water) and acetic acid concentrations (0.3%, and 0.6% v/v), use of starter culture, and aerobic versus anaerobic conditions on the biochemical changes that take place throughout the preservation stage of ripe olive processing were investigated. Glucose, fructose and sucrose were completely consumed during preservation. Mannitol and malic acid were metabolized only in the presence of lactic acid bacteria or oxidative yeast (aerobic treatment). The main metabolites produced were lactic and acetic acid in aerobic or anaerobic treatments inoculated with Lactobacillus plantarum. Methanol and ethanol were present in all the brines although in a lower concentration when conditions were aerobic. Thus, induced lactic fermentation led to the most efficient utilization of carbohydrates and yielded the most suitable physicochemical characteristics for ripe olive preservation.     

Influence of arsenate adsorption to ferrihydrite, goethite, and boehmite on the kinetics of arsenate reduction by Shewanella putrefaciens strain CN-32

The kinetics of As(V) reduction by Shewanella putrefaciens strain CN-32 was investigated in suspensions of 0.2, 2, or 20 g L(-1) ferrihydrite, goethite, or boehmite at low As (10 μM) and lactate (25 μM) concentrations. Experimental data were compared with model predictions based on independently determined sorption isotherms and rates of As(V) desorption, As(III) adsorption, and microbial reduction of dissolved As(V), respectively. The low lactate concentration was chosen to prevent significant Fe(III) reduction, but still allowing complete As(V) reduction. Reduction of dissolved As(V) followed first-order kinetics with a 3 h half-life of As(V). Addition of mineral sorbents resulted in pronounced decreases in reduction rates (32-1540 h As(V) half-life). The magnitude of this effect increased with increasing sorbent concentration and sorption capacity (goethite < boehmite < ferrihydrite). The model consistently underestimated the concentrations of dissolved As(V) and the rates of microbial As(V) reduction after addition of S. putrefaciens (～5 × 10(9) cells mL(-1)), suggesting that attachment of S. putrefaciens cells to oxide mineral surfaces promoted As(V) desorption and thereby facilitated As(V) reduction. The interplay between As(V) sorption to mineral surfaces and bacterially induced desorption may thus be critical in controlling the kinetics of As reduction and release in reducing soils and sediments.     

Multiclass method for fast determination of veterinary drug residues in baby food by ultra-high-performance liquid chromatography–tandem mass spectrometry

A simple and rapid multiresidue method for the determination of different veterinary drug residues in meat-based baby food (MBF) and powdered milk-based infant formulae (PMIF) has been developed. The method involves an extraction procedure based on buffered QuEChERS (quick, easy, cheap, effective, rugged and safe) methodology, without any further clean-up step, followed by ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS). The method has been validated in two baby food matrices (MBF and PMIF) at three different concentration levels, obtaining suitable recoveries and precision (inter and intra-day precision) values. Quantification was carried out using matrix-matched standard calibration. Furthermore, the decision limit (CCα) and the decision capability (CCβ) were evaluated, ranging from 0.5 to 16.2 μg/kg and from 1.2 to 22.4 μg/kg, respectively. Finally, the method was applied to the analysis of several kinds of baby food samples and traces of some veterinary drugs were detected.