3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents

Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis monophosphate kinase (TMPKmt) is essential to DNA replication. Thus, this enzyme represents a promising target for developing new drugs against TB. In the present study, the receptor-independent, RI, 4D-QSAR method has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 81 thymidine analogues, and two corresponding subsets, reported as inhibitors of TMPKmt. The resulting optimized models are not only statistically significant with r (2) ranging from 0.83 to 0.92 and q (2) from 0.78 to 0.88, but also are robustly predictive based on test set predictions. The most and the least potent inhibitors in their respective postulated active conformations, derived from each of the models, were docked in the active site of the TMPKmt crystal structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. Moreover, the QSAR models provide insights regarding a probable mechanism of action of the analogues.

Rational Design and 3D-Pharmacophore Mapping of 5 `-Thiourea-Substituted alpha-Thymidine Analogues as Mycobacterial TMPK Inhibitors

Thymidine monophosphate kinase (TMPK) has emerged as an attractive target for developing inhibitors of Mycobacterium tuberculosis growth. In this study the receptor-independent (RI) 4D-QSAR formalism has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 5`-thiourea-substituted alpha-thymidine inhibitors. Models were developed for the entire training set and for a subset of the training set consisting of the most potent inhibitors. The optimized (RI) 4D-QSAR models are statistically significant (r(2) = 0.90, q(2) = 0.83 entire set, r(2) = 0.86, q(2) = 0.80 high potency subset) and also possess good predictivity based on test set predictions. The most and least potent inhibitors, in their respective postulated active conformations derived from the models, were docked in the active site of the TMPK crystallographic structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. This model identifies new regions of the inhibitors that contain pharmacophore sites, such as the sugar-pyrimidine ring structure and the region of the 5`-arylthiourea moiety. These new regions of the ligands can be further explored and possibly exploited to identify new, novel, and, perhaps, better antituberculosis inhibitors of TMPKmt. Furthermore, the 3D-pharmacophores defined by these models can be used as a starting point for future receptor-dependent antituberculosis drug design as well as to elucidate candidate sites for substituent addition to optimize ADMET properties of analog inhibitors.

Molecular modeling and QSAR studies of a set of indole and benzimidazole derivatives as H(4) receptor antagonists

Histamine is an important biogenic amine, which acts with a group of four G-protein coupled receptors (GPCRs), namely H(1) to H(4) (H(1)R - H(4)R) receptors. The actions of histamine at H(4)R are related to immunological and inflammatory processes, particularly in pathophysiology of asthma, and H(4)R ligands having antagonistic properties could be helpful as antiinflammatory agents. In this work, molecular modeling and QSAR studies of a set of 30 compounds, indole and benzimidazole derivatives, as H(4)R antagonists were performed. The QSAR models were built and optimized using a genetic algorithm function and partial least squares regression (WOLF 5.5 program). The best QSAR model constructed with training set (N = 25) presented the following statistical measures: r (2) = 0.76, q (2) = 0.62, LOF = 0.15, and LSE = 0.07, and was validated using the LNO and y-randomization techniques. Four of five compounds of test set were well predicted by the selected QSAR model, which presented an external prediction power of 80%. These findings can be quite useful to aid the designing of new anti-H(4) compounds with improved biological response.

A New Method to Prepare Porous Silk Fibroin Membranes Suitable for Tissue Scaffolding Applications

A new method to prepare porous silk fibroin (SF) membranes without dialysis proposed. Silk fibers were degummed to remove sericin and the resultant fibroin was dissolved in a CaCl(2)-CH(3)CH(2)OH-H(2)O ternary solvent. Rather than undergoing dialysis, a fibroin salty solution was diluted in water and then submitted to a mechanical agitation that led to a phase separation through foam formation on the solution surface. This foam was continually collected and then compacted between plates to remove the excess of water. The membranes presented large pores with diameters of greater than 100 pm (as shown by scanning electron microscopy - SEM), porosity of 68% and water content of 91% w/w. X-ray diffraction (XRD) and infrared spectroscopy (FTIR-ATR) indicated that the membranes present SF in a beta-sheet structure even before the ethanol treatment. A typical elastic deformation profile and degradation under temperature were observed using calorimetric analysis (DSC), thermal gravimetric analysis (TGA) and mechanical tests. As indicated by the in vitro cytotoxicity tests, these membranes present potential for use as scaffolds. (C) 2009 Wiley Periodicals, Inc. J Appl Polym Sci 114: 617-623, 2009

EFFECT OF CHEMICAL INTERESTERIFICATION ON PHYSICOCHEMICAL PROPERTIES AND INDUSTRIAL APPLICATIONS OF CANOLA OIL AND FULLY HYDROGENATED COTTONSEED OIL BLENDS

Blends of canola oil (CO) and fully hydrogenated cottonseed oil (FHCSO), with 20, 25, 30, 35 and 40% FHCSO (w/w) were interesterified under the following conditions: 0.4% sodium methoxide, 500 rpm stirring, 100C, 20 min. The original and interesterified blends were examined for triacylglycerol composition, melting point, solid fat content (SFC) and consistency. Interesterification caused considerable rearrangement of triacylglycerol species, reduction of trisaturated triacylglycerol content and increase in disaturated-monounsaturated and monosaturated-diunsaturated triacylglycerols in all blends, resulting in lowering of respective melting points. The interesterified blends showed reduced SFC at all temperatures and more linear melting profiles if compared with the original blends. Consistency, expressed as yield value, significantly decreased after the reaction. Iso-solid curves indicated eutectic interactions for the original blends, which were eliminated after randomization. The 80:20, 75:25, 70:30 and 65:35 (w/w) CO: FHCSO interesterified blends showed characteristics which are appropriate for their application as soft margarines, spreads, fat for bakery/all-purpose shortenings, and icing shortenings, respectively. PRACTICAL APPLICATIONS Recently, a number of studies have suggested a direct relationship between trans isomers and increased risk of vascular disease. In response, many health organizations have recommended reducing consumption of foods containing trans fatty acids. In this connection, chemical interesterification has proven the main alternative for obtaining plastic fats that have low trans isomer content or are even trans isomer free. This work proposes to evaluate the chemical interesterification of binary blends of canola oil and fully hydrogenated cottonseed oil and the specific potential application of these interesterified blends in food products.

Zero trans fats from soybean oil and fully hydrogenated soybean oil: Physico-chemical properties and food applications

Blends of soybean oil (50) and fully hydrogenated soybean oil (FHSBO), with 10%, 20%, 30%, 40% and 50% FHSBO (w/w) content were interesterified under the following conditions: 0.4% sodium methoxide, 500 rpm stirring, 100 degrees C, 20 min. The original and interesterified blends were examined for triacylglycerol composition, melting point, solid fat content (SFC) and consistency. Interesterification caused considerable rearrangement of triacylglycerol species, reduction of trisaturated triacylglycerol content and increase in monounsaturated and diunsaturated triacylglycerols, resulting in lowering of respective melting points. The interesterified blends displayed reduced SFC at all temperatures and more linear melting profiles as compared with the original blends. Yield values showed increased plasticity in the blends after the reaction. Isosolid diagrams before and after the reaction showed no eutectic interactions. The 90:10, 80:20, 70:30 and 60:40 interesterified SO:FHSBO blends displayed characteristics suited to application, respectively, as liquid shortening, table margarine, baking/confectionery fat and all-purpose shortenings/biscuit-filing base. (C) 2009 Elsevier Ltd. All rights reserved.

Generation and Analysis of Interaction Energy Maps of p-Substituted Benzoic Acid [(5-Nitro-thiophen-2-yl)-methylene]-Hydrazides Active against MRSA

In this preliminary study eighteen p-substituted benzoic acid [(5-nitro-thiophen-2-yl)-methylene]-hydrazides with antimicrobial activity were evaluated against multidrug-resistant Staphylococcus aureus, correlating the three-dimensional characteristics of the ligands with their respective bioactivities. The computer programs Sybyl and CORINA were used, respectively, for the design and three-dimensional conversion of the ligands. Molecular interaction fields were calculated using GRID program. Calculations using Volsurf resulted in a statistically consistent model with 48 structural descriptors showing that hydrophobicity is a fundamental property in the analyzed biological response.

Multilabeled classification approach to find a plaint source for terpenoids

Recently, we have built a classification model that is capable of assigning a given sesquiterpene lactone (STL) into exactly one tribe of the plant family Asteraceae from which the STL has been isolated. Although many plant species are able to biosynthesize a set of peculiar compounds, the occurrence of the same secondary metabolites in more than one tribe of Asteraceae is frequent. Building on our previous work, in this paper, we explore the possibility of assigning an STL to more than one tribe (class) simultaneously. When an object may belong to more than one class simultaneously, it is called multilabeled. In this work, we present a general overview of the techniques available to examine multilabeled data. The problem of evaluating the performance of a multilabeled classifier is discussed. Two particular multilabeled classification methods-cross-training with support vector machines (ct-SVM) and multilabeled k-nearest neighbors (M-L-kNN)were applied to the classification of the STLs into seven tribes from the plant family Asteraceae. The results are compared to a single-label classification and are analyzed from a chemotaxonomic point of view. The multilabeled approach allowed us to (1) model the reality as closely as possible, (2) improve our understanding of the relationship between the secondary metabolite profiles of different Asteraceae tribes, and (3) significantly decrease the number of plant sources to be considered for finding a certain STL. The presented classification models are useful for the targeted collection of plants with the objective of finding plant sources of natural compounds that are biologically active or possess other specific properties of interest.

Using Computer-aided Drug Design and Medicinal Chemistry Strategies in the Fight Against Diabetes

The aim of this work is to present a simple, practical and efficient protocol for drug design, in particular Diabetes, which includes selection of the illness, good choice of a target as well as a bioactive ligand and then usage of various computer aided drug design and medicinal chemistry tools to design novel potential drug candidates in different diseases. We have selected the validated target dipeptidyl peptidase IV (DPP-IV), whose inhibition contributes to reduce glucose levels in type 2 diabetes patients. The most active inhibitor with complex X-ray structure reported was initially extracted from the BindingDB database. By using molecular modification strategies widely used in medicinal chemistry, besides current state-of-the-art tools in drug design (including flexible docking, virtual screening, molecular interaction fields, molecular dynamics. ADME and toxicity predictions), we have proposed 4 novel potential DPP-IV inhibitors with drug properties for Diabetes control, which have been supported and validated by all the computational tools used herewith.

O/W Nanoemulsion After 15 Years of Preparation: A Suitable Vehicle for Pharmaceutical and Cosmetic Applications

The application of nanoemulsions is due to have good stability, uniform spreading and enhance active penetration upon skin. Nanometer emulsions can be obtained by low-energy emulsification method. The required hydrophilic and lipophilic balance indicates the better balance of emulsifier for optimum system emulsification. Emulsion stability is evidently controlled for the properties of the adsorbed layer formed in the surface of its globules, know as potential zeta. The aim of this work was to evaluate the oil/water nanoemulsion of formulation obtained after 15 years of preparation. The results suggested that the nanoemulsion have performed stability for many years.

Computer-aided Drug Design of Novel PLA(2) Inhibitor Candidates for Treatment of Snakebite

Phospholipases A(2) (PLA(2)) are enzymes commonly found in snake venoms from Viperidae and Elaphidae families, which are major components thereof. Many plants are used in traditional medicine its active agents against various effects induced by snakebite. This article presents the PLA(2) BthTX-I structure prediction based on homology modeling. In addition, we have performed virtual screening in a large database yielding a set of potential bioactive inhibitors. A flexible docking program was used to investigate the interactions between the receptor and the new ligands. We have performed molecular interaction fields (MIFs) calculations with the phospholipase model. Results confirm the important role of Lys49 for binding ligands and suggest three additional residues as well. We have proposed a theoretically nontoxic, drug-like, and potential novel BthTX-I inhibitor. These calculations have been used to guide the design of novel phospholipase inhibitors as potential lead compounds that may be optimized for future treatment of snakebite victims as well as other human diseases in which PLA(2) enzymes are involved.

Quantum-chemical, NMR and X-ray diffraction studies on (+/-)-1-[3,4-(methylenedioxy)phenyl]-2-methylaminopropane

Time-averaged conformations of (+/-)-1-[3,4-(methylenedioxy)phenyl]-2-methylaminopropane hydrochloride (MDMA, ""ecstasy"") in D(2)O, and of its free base and trifluoroacetate in CDCl(3), were deduced from their (1)H NMR spectra and used to calculate their conformer distribution. Their rotational potential energy surface (PES) was calculated at the RHF/6-31G(d,p), 133LYP/6-31G(d,p), B3LYP/cc-pVDZ and AM1 levels. Solvent effects were evaluated using the polarizable continuum model. The NMR and theoretical studies showed that, in the free base, the N-methyl group and the ring are preferentially trans. This preference is stronger in the salts and corresponds to the X-ray structure of the hydrochloride. However, the energy barriers separating these forms are very low. The X-ray diffraction crystal structures of the anhydrous salt and its monohydrate differed mainly in the trans or cis relationship of the N-methyl group to the a-methyl, although these two forms interconvert freely in solution. (C) 2007 Elsevier Inc. All rights reserved.

Visual Display Height

We examined the influence of backrest inclination and vergence demand on the posture and gaze angle that-workers adopt to view visual targets placed in different vertical locations. In the study 12 participants viewed a small video monitor placed in 7 locations around a 0.65-m radius arc (from 650 below to 300 above horizontal eye height). Trunk posture was manipulated by changing the backrest inclination of an adjustable chair. Vergence demand was manipulated by using ophthalmic lenses and prisms to mimic the visual consequences of varying target distance. Changes in vertical target location caused large changes in atlantooccipital posture and gaze angle. Cervical posture was altered to a lesser extent by changes in vertical target location. Participants compensated for changes in backrest inclination by changing cervical posture, though they did not significantly alter atlanto-occipital posture and gaze angle. The posture adopted to view any target represents a compromise between visual and musculoskeletal demands. These results provide support for the argument that the optimal location of visual targets is at least 15 below horizontal eye level. Actual or potential applications of this work include the layout of computer workstations and the viewing of displays from a seated posture.

It's all very well, in theory: Theoretical perspectives and their applications in contemporary pedagogical research

Current debates about educational theory are concerned with the relationship between knowledge and power and thereby issues such as who possesses a truth and how have they arrived at it, what questions are important to ask, and how should they best be answered. As such, these debates revolve around questions of preferred, appropriate, and useful theoretical perspectives. This paper overviews the key theoretical perspectives that are currently used in physical education pedagogy research and considers how these inform the questions we ask and shapes the conduct of research. It also addresses what is contested with respect to these perspectives. The paper concludes with some cautions about allegiances to and use of theories in line with concerns for the applicability of educational research to pressing social issues.

Mesoporous dye-doped titanium dioxide for micro-optoelectronic applications

Optically transparent, mesostructured titanium dioxide thin films were fabricated using an amphiphilic poly(alkylene oxide) block copolymer template in combination with retarded hydrolysis of a titanium isopropoxide precursor. Prior to calcination, the films displayed a stable hexagonal mesophase and high refractive indices (1.5 to 1.6) relative to mesostructured silica (1.43). After calcination, the hexagonal mesophase was retained with surface areas >300 m2 g-1. The dye Rhodamine 6G (commonly used as a laser dye) was incorporated into the copolymer micelle during the templating process. In this way, novel dye-doped mesostructured titanium dioxide films were synthesised. The copolymer not only directs the film structure, but also provides a solubilizing environment suitable for sustaining a high monomer-to-aggregate ratio at elevated dye concentrations. The dye-doped films displayed optical thresholdlike behaviour characteristic of amplified spontaneous emission. Soft lithography was successfully applied to micropattern the dye-doped films. These results pave the way for the fabrication and demonstration of novel microlaser structures and other active optical structures. This new, high-refractive index, mesostructured, dye-doped material could also find applications in areas such as optical coatings, displays and integrated photonic devices.