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Results for “platform design”

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At least 217 records · Page 12Linked to original sources

PubMed1997

Restriction of foot supination by ankle braces in sudden fall situations.

OBJECTIVE: To investigate the restriction of foot supination in different shoe orthotic combinations for unexpected ankle turns. DESIGN: A supination platform was used to experimentally induce sudden ankle turns. BACKGROUND: This study expanded on previous investigations of the effectiveness of different ankle braces and the influence of shoe material on foot supination. METHODS: For 21 male subjects pressure distribution data, achilles tendon angle, and supination velocity were collected. A comparison between a shoe with cut upper material and an intact shoe was done to show the influence of upper material on supination. The effectiveness of four different orthotics inside of an intact shoe were tested in comparison to the same shoe without ankle brace. Additionally, subjects rated their perceived supination movement of the foot. RESULTS: Between experimental conditions no large differences for the pressure distribution patterns were found. Three of the ankle braces reduced foot supination as well as supination velocities. More than two times lower supination values were measured for a footwear condition in which the upper material was cut away. Already during the free-fall most ankle braces caused a substantial reduction of foot inversion. CONCLUSION: The experiments demonstrated the influence of the upper material of a shoe and different orthotics on foot supination. Biomechanical measurements are necessary because of limited capabilities of subjects in detecting subtalar angular motions. RELEVANCE: This study investigated the effectiveness of different shoe conditions and ankle braces under experimental conditions that simulated unexpected ankle turns, the most frequent causes of sport injuries. The results of the study provide insights into which factors influence the amount of foot supination during unexpected ankle turns.

Journal Article↗

PubMed2001

Application of genomics to the definition of the molecular basis for toxicity.

Transcript profiling technology enables quantitative measurement of the transcriptional activity of potentially thousands of genes in biological samples. The application of such technology to toxicology, toxicogenomics, promises substantial dividends in mechanistic toxicity research and also, possibly, the ability to predict adverse toxicity for novel or untested compounds. Our laboratory has developed a custom approach to this technology, designing cDNA microarray platforms specifically for gene expression events of relevance to a large number of toxicological endpoints. Such arrays allow comprehensive coverage of genes associated with entire pathways (such as oxidative stress, signal transduction, stress response, epithelial biology) and enable simultaneous measurement of more than ten thousand gene expression events.

Animals↗

PubMed2006

Electroporation of mammalian cells in a microfluidic channel with geometric variation.

Electroporation has been widely used to load impermeant exogenous molecules into cells. Rapid electrical lysis based on electroporation has also been applied to analyze intracellular materials at single-cell level. There has been increasing demand to implement electroporation in a microfluidic format as a basic tool for applications ranging from screening of drugs and genes to studies of intracellular dynamics. In this report, we have developed a simple technique to electroporate mammalian cells with high throughput on a microfluidic platform. In our design, electroporation only happened in a defined section of a microfluidic channel due to the local field amplification by geometric variation. The time of exposure of the cells to this high field was determined by the velocity of the cells and the length of the section. The change in the cell morphology during electroporation was observed in real time. We determined that electroporation of Chinese hamster ovary cells occurred when the local field strength was increased to approximately 400 V/cm. The internalization of membrane-impermeant molecules (SYTOX green) with cell viability preserved was also carried out to demonstrate transient electropermeabilization. The influence of the operational parameters of the device on cell viability was determined. A large percentage of cells remained viable after electroporation when the parameters were tuned. We also studied rapid cell lysis when the field intensity was in the range of 600-1200 V/cm. The rupture of cell membrane happened within 30 ms when the field strength was 1200 V/cm. Given the simplicity, high throughput, and high compatibility with other devices, this microfluidic electroporation technique may increase the application of microfluidic systems in screening of drugs and biomolecules and chemical cytometry.

Animals↗

PubMed2004

Crystal structure of human phosphodiesterase 3B: atomic basis for substrate and inhibitor specificity.

Phosphodiesterases (PDEs) are enzymes that modulate cyclic nucleotide signaling and as such are clinical targets for a range of disorders including congestive heart failure, erectile dysfunction, and inflammation. The PDE3 family comprises two highly homologous subtypes expressed in different tissues, and inhibitors of this family have been shown to increase lipolysis in adipocytes. A specific PDE3B (the lipocyte-localized subtype) inhibitor would be a very useful tool to evaluate the effects of PDE3 inhibition on lipolysis and metabolic rate and might become a novel tool for treatment of obesity. We report here the three-dimensional structures of the catalytic domain of human PDE3B in complex with a generic PDE inhibitor and a novel PDE3 selective inhibitor. These structures explain the dual cAMP/cGMP binding capabilities of PDE3, provide the molecular basis for inhibitor specificity, and can supply a valid platform for the design of improved compounds.

1-Methyl-3-isobutylxanthine↗

PubMed2005

Inhibition of class D beta-lactamases by diaroyl phosphates.

The production of beta-lactamases is an important component of bacterial resistance to beta-lactam antibiotics. These enzymes catalyze the hydrolytic destruction of beta-lactams. The class D serine beta-lactamases have, in recent years, been expanding in sequence space and substrate spectrum under the challenge of currently dispensed beta-lactams. Further, the beta-lactamase inhibitors now employed in medicine are not generally effective against class D enzymes. In this paper, we show that diaroyl phosphates are very effective inhibitory substrates of these enzymes. Reaction of the OXA-1 beta-lactamase, a typical class D enzyme, with diaroyl phosphates involves acylation of the active site with departure of an aroyl phosphate leaving group. The interaction of the latter with polar active-site residues is most likely responsible for the general reactivity of these molecules with the enzyme. The rate of acylation of the OXA-1 beta-lactamase by diaroyl phosphates is not greatly affected by the electronic effects of substituents, probably because of compensation phenomena, but is greatly enhanced by hydrophobic substituents; the second-order rate constant for acylation of the OXA-1 beta-lactamase by bis(4-phenylbenzoyl) phosphate, for example, is 1.1 x 10(7) s(-)(1) M(-)(1). This acylation reactivity correlates with the hydrophobic nature of the beta-lactam side-chain binding site of class D beta-lactamases. Deacylation of the enzyme is slow, e.g., 1.24 x 10(-)(3) s(-)(1) for the above-mentioned phosphate and directly influenced by the electronic effects of substituents. The effective steady-state inhibition constants, K(i), are nanomolar, e.g., 0.11 nM for the above-mentioned phosphate. The diaroyl phosphates, which have now been shown to be inhibitory substrates of all serine beta-lactamases, represent an intriguing new platform for the design of beta-lactamase inhibitors.

Bacterial Proteins↗

PubMed1998

Penetration and intracellular routing of nucleus-directed peptide-based shuttles (loligomers) in eukaryotic cells.

Loligomers are multitasking, peptide-based shuttles that are able to penetrate cells and self-localize into distinct cellular compartments. In particular, loligomer 4 incorporates internalization and nuclear import sequences as well as reporter groups. The intracellular routing of loligomer 4 was analyzed by microscopy and flow cytometry, to define and demonstrate localization events. Electron micrographs of CHO cells exposed to a biotinylated derivative of loligomer 4 as well as confocal images of CHO cells treated with rhodamine-labeled loligomer 4 indicate their presence in the cytosol, endocytic vesicles, and the nucleus of CHO cells. Loligomer 4 accumulates irreversibly inside cells. Uptake of loligomer 4 by six mammalian cell lines (Daudi, EL4, CHO, COS-7, VERO, and HeLa) was proven by flow cytometry, establishing the generality of the principle. Cells presented as monolayers typically were less able to endocytose the construct than cells grown in suspension. Cellular accumulation of loligomer 4 varied between cell lines with COS-7 and VERO cells showing the highest level of uptake. Plasmids harboring reporter genes could be transported efficiently inside CHO cells, suggesting that loligomer 4 either alone or noncovalently associated with large macromolecules can effectively reach the nucleus of cells. In summary, loligomer 4 constructs provide a simple synthetic platform for the design of guided intracellular agents.

Animals↗

PubMed2002

Iterative high-throughput polymorphism studies on acetaminophen and an experimentally derived structure for form III.

Three crystal forms of acetaminophen were prepared and characterized using a newly developed high-throughput crystallization platform, CrystalMax. The platform consists of design software, robotic sample dispensing and handling, and high-throughput microanalytics and is capable of running thousands of crystallizations in parallel using several different methods to drive supersaturation and subsequent crystallization. Additionally, structural models of the elusive third form of acetaminophen will be discussed on the basis of powder X-ray diffraction data. One structure suggested has a bilayer motif, held together by O-H...O(H) hydrogen bonds, and helps explain the difficulty associated with preparing this form from solution.

Acetaminophen↗

PubMed2002

Structure and dynamics of metallomacrocycles: recognition of zinc xylyl-bicyclam by an HIV coreceptor.

As platforms for the design of metal-based therapeutic and diagnostic agents, macrocycles are rigid enough to provide strong metal binding sites and orient functional groups stereoselectively, yet flexible enough to accommodate structural changes required for induced-fit recognition of biological targets. We consider the recognition of the Zn(II) complex of the bis-tetraazamacrocycle xylyl-bicyclam, a potent anti-HIV agent, by the coreceptor CXCR4, a G-protein-coupled receptor used by HIV for membrane fusion and cell entry. NMR studies show that the macrocycles of Zn(II)(2)-xylyl-bicyclam perchlorate exist in aqueous solution as two major configurations, trans-I (nitrogen chirality R,S,R,S), and trans-III (S,S,R,R). Acetate addition induced a major structural change. X-ray crystallography shows that the acetate complex contains the unusual cis-V cyclam configuration (R,R,R,R and folded) with bidentate coordination of acetate to Zn(II) plus second-coordination-sphere double H-bond formation between diagonal NH protons on the opposite cyclam face and acetate carboxylate oxygens. Detailed 1D and 2D NMR studies show that the major configuration of Zn(II)(2)-xylyl-bicyclam acetate in aqueous solution is cis-V/trans-I. Molecular modeling shows that an analogous cis-V site can be formed when Zn(II)(2)-xylyl-bicyclam binds to CXCR4, involving the carboxylate groups of Asp262 (Zn(II) coordination) and Glu288 (double H-bonding). The second cyclam can adopt the trans-I (or trans-III) configuration with Zn(II) binding to Asp171. These interactions are consistent with the known structure-activity relationships for bicyclam anti-HIV activity and receptor mutation. Consideration of the anti-HIV activity of xylyl-bicyclam complexes of other metal ions suggests that affinity for carboxylates, configurational flexibility, and kinetic factors may all play roles in receptor recognition. For example, Pd(II) cyclam complexes interact only weakly with axial ligands and are inflexible and inactive, whereas Co(III) cyclams bind carboxylates strongly, are configurationally flexible, and yet have low activity. Our findings should aid the design of new generations of active macrocycles including highly specific chemokine receptor antagonists.

Benzylamines↗

PubMed2004

Self-assembly of biocidal nanotubes from a single-chain diacetylene amine salt.

We describe the facile two-step synthesis of nanotubes that form pure, well-defined, nanostructured materials. We have synthesized a secondary amine HBr salt as the headgroup of a single-chain diacetylenic lipid. This molecule can form a number of different self-assembled nanostructures in aqueous or organic solvents. In water, this lipid forms a monodisperse preparation of nanotubes at high yields. Partially dissolving a preparation of nanotubes dried from aqueous solution results in a remarkably organized structure that resembles a nanocarpet. Details of the nanotube structure were investigated by scanning electron microscopy, transmission electron microscopy, and small-angle X-ray spectroscopy. The aqueous nanotubes have a cross-sectional diameter of 89 nm. The walls of the tubes are an exquisitely uniform 27 nm thick and are shown to consist of five lipid bilayers with a repeat spacing of 57.8 A. The chemical structure of the material shows no chiral centers, but suspensions of the nanotubes in an aqueous medium show an unexpected circular dichroism signal. The versatility of this new material as a platform for nanostructure design and synthesis is enhanced by its biocidal activity. This antimicrobial activity along with the regularity the nanostructures will enhance the development of a range of applications from biosensors to artificial retinas.

Acetylene↗

PubMed2006

Insight through molecular mechanics Poisson-Boltzmann surface area calculations into the binding affinity of triclosan and three analogues for FabI, the E. coli enoyl reductase.

Keeping pace with emerging drug resistance in clinically important pathogens will be greatly aided by inexpensive yet reliable computational methods that predict the binding affinities of ligands for drug targets. We present results using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method to calculate the affinity of a series of triclosan analogues for the E. coli enoyl reductase FabI, spanning a 450000-fold range of binding affinities. Significantly, a high correlation is observed between the calculated binding energies and those determined experimentally. Further examination indicates that the van der Waals energies are the most correlated component of the total affinity (r2 = 0.74), indicating that the shape of the inhibitor is very important in defining the binding energies for this system. The validation of MM-PBSA for the E coli FabI system serves as a platform for inhibitor design efforts focused on the homologous enzyme in Staphylococcus aureus and Mycobacterium tuberculosis.

Binding Sites↗

PubMed2005

Di- and trinuclear Zn2+ complexes of calix[4]arene based ligands as catalysts of acyl and phosphoryl transfer reactions.

The calix[4]arene scaffold, blocked in the cone conformation by proper alkylation of the lower rim hydroxyls, was used as a convenient molecular platform for the design of bi- and trimetallic Zn2+ catalysts. The catalytic activity of the Zn2+ complexes of calix[4]arenes decorated at the 1,2-, 1,3-, and 1,2,3-positions of the upper rim with 2,6-bis[(dimethylamino)methyl]pyridine units were investigated in the cleavage of ester 6 and of the RNA model compound HPNP. High rate enhancements, up to 4 orders of magnitude, were observed in a number of catalyst-substrate combinations. Interestingly the order of catalytic efficiency among regioisomeric dinuclear complexes in the cleavage of ester 6 is 1,2-vicinal >> 1,3-distal, but it is reversed in the reaction of HPNP. The higher efficiency of trinuclear compared to dinuclear complexes provides an indication of the cooperation of three Zn2+ ions in the catalytic mechanism.

Journal Article↗

PubMed2006

Expanding the synthetic method and structural diversity potential for the intramolecular Aza Diels-Alder cyclization.

New experimental facets have been examined to expand upon the known methods for an aromatic variant of the intramolecular Aza Diels-Alder cyclization. The specific transformation under study is one that uses functionalized anilines and an aldehyde-olefin tether to provide tetrahydroquinoline cycloadducts under mild acidic conditions. Variations investigated encompass the use of N-alkylated anilines, including one with ring-constrained nitrogen, in the context of glycine, phenylalanine, and glyoxyl ester bridging elements; bridge components with structural perturbations; modified dienophile segments; and different acid catalysts. Substituted tetrahydroquinolines obtained from many of the preceding experiments were obtained in good chemical yield, generally in excess of 80%. Designed as a platform for combinatorial chemical synthesis, this reaction manifold accommodates a range of starting materials with structurally and electronically distinct characteristics. The results of this report, in combination with the discoveries from previous work in this area, enhance the ability of the intramolecular Aza Diels-Alder transformation to generate a diverse array of quinolinic structures with multiple stereogenic centers, many of which resemble lignan and arylnaphthalene-type natural products.

Aldehydes↗

PubMed2006

Systematic approach to understanding macrolide-ribosome interactions: NMR and modeling studies of oleandomycin and its derivatives.

The three-dimensional structures of oleandomycin (1) and its derivatives oleandomycin-9-oxime (2) and 10,11-anhydrooleandomycin (3) were determined in different solvents by the combined use of NMR and molecular modeling methods. The experimental NMR data were compared with the results of molecular modeling and known crystal structures of the related molecules. It was shown that the dominant conformation of the lactone ring is the folded-out conformation with some amounts of the folded-in one depending on the solvent and temperature, while desosamine and cladinose sugars adopt the usual chair conformations. Modeling calculations provided evidence for conformational changes in the upper lactone region as well. Saturation transfer difference (STD) NMR experiments have provided information on the binding epitopes of 1-3 in complexes with E. coli ribosomes. The obtained molecular surfaces in close contact with ribosomes were compared with recently available 3D structures of the related macrolide-ribosome complexes, and the observed differences were discussed. The knowledge gained from this study can serve as a platform for the design of novel macrolides with an improved biological profile.

Anti-Bacterial Agents↗

PubMed2005

Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter.

It has been widely accepted that DNA can adopt other biologically relevant structures beside the Watson-Crick double helix. One recent important example is the guanine-quadruplex (G-quadruplex) structure formed by guanine tracts found in the MYC (or c-myc) promoter region, which regulates the transcription of the MYC oncogene. Stabilization of this G-quadruplex by ligands, such as the cationic porphyrin TMPyP4, decreases the transcriptional level of MYC. Here, we report the first structure of a DNA fragment containing five guanine tracts from this region. An unusual G-quadruplex fold, which was derived from NMR restraints using unambiguous model-independent resonance assignment approaches, involves a core of three stacked guanine tetrads formed by four parallel guanine tracts with all anti guanines and a snapback 3'-end syn guanine. We have determined the structure of the complex formed between this G-quadruplex and TMPyP4. This structural information, combined with details of small-molecule interaction, provides a platform for the design of anticancer drugs targeting multi-guanine-tract sequences that are found in the MYC and other oncogenic promoters, as well as in telomeres.

Biomarkers, Tumor↗

PubMed2002

Smoking cessation in methadone maintenance.

AIMS: To evaluate relapse prevention (relapse prevention) and contingency management (contingency management) for optimizing smoking cessation outcomes using nicotine replacement therapy for methadone-maintained tobacco smokers. DESIGN: Experimental, 2 (relapse prevention)x2 (contingency management) repeated measures design using a platform of nicotine replacement therapy featuring a 2-week baseline period, followed by randomization to 12 weeks of treatment, and 6- and 12-month follow-up visits. SETTING: Three narcotic treatment centers in Los Angeles. PARTICIPANTS: One hundred and seventy-five participants who met all inclusion and no exclusion criteria. INTERVENTION: Participants received 12 weeks of nicotine replacement therapy and assignment to one of four conditions: patch-only, relapse prevention + patch, contingency management + patch and relapse prevention + contingency management + patch. MEASUREMENTS: Thrice weekly samples of breath (analyzed for carbon monoxide) and urine (analyzed for metabolites of opiates and cocaine) and weekly self-reported numbers of cigarettes smoked. FINDINGS: Participants (73.1%) completed 12 weeks of treatment. During treatment, those assigned to receive contingency management showed statistically higher rates of smoking abstinence than those not assigned to receive contingencies (F3,4680=6.3, P=0.0003), with no similar effect observed for relapse prevention. At follow-up evaluations, there were no significant differences between conditions. Participants provided more opiate and cocaine-free urines during weeks when they met criteria for smoking abstinence than during weeks when they did not meet these criteria (F1,2054=14.38, P=0.0002; F1,2419=16.52, P<0.0001). CONCLUSIONS: Contingency management optimized outcomes using nicotine replacement therapy for reducing cigarette smoking during treatment for opiate dependence, although long-term effects are not generally maintained. Findings document strong associations between reductions in cigarette smoking and reductions in illicit substance use during treatment.

Adolescent↗

PubMed2006

Use of substrate analogs and mutagenesis to study substrate binding and catalysis in the Sir2 family of NAD-dependent protein deacetylases.

The Sir2 family of enzymes is highly conserved throughout evolution and functions in silencing, control of life span, apoptosis, and many other cellular processes. Since the discovery of the NAD-dependent deacetylase activity of Sir2 proteins, there has been a flurry of activity aiming to uncover the mode of substrate binding and catalysis. Structural and biochemical studies have led to several proposed reaction mechanisms, yet the exact catalytic steps remain unclear. Here we present in vitro studies of yeast homolog Hst2 that shed light on the mechanism of Sir2 proteins. Using acetyl-lysine substrate analogs, we demonstrate that the Hst2 reaction proceeds via an initial SN2-type mechanism with the direct formation of an ADP-ribose-acetyl-lysine intermediate. Kinetic studies further suggest that ADP-ribose inhibits the Hst2 reaction in a biologically relevant manner. Through biochemical and kinetic analyses of point mutants, we also clarify the role of several conserved core domain residues in substrate binding, stabilization of the ADP-ribose-acetyl-lysine intermediate, and catalysis. These findings bring us a few steps closer to understanding Sir2 activity and may provide a useful platform for the design of Sir2-specific inhibitors for analysis of Sir2 function and possibly therapeutic applications.

Acetylation↗

PubMed2006

A cell-sparing electric field stimulation technique for high-throughput screening of voltage-gated ion channels.

The Trans Cell Layer Electrical Field Stimulation (TCL-EFS) system has been developed for high-throughput screening (HTS) of voltage-gated ion channels in microplate format on a Voltage-Ion Probe Reader (VIPR) platform. In this design, a wire electrode is placed above the cell layer of each filter well, and a whole plate perimeter electrode resides beneath the filter layer. This configuration allows the electrodes to be placed away from the cell layer to minimize the near electrode field effects on cell function and dye bleaching observed with other existing designs. Mathematical simulation indicates that the electric field at the cell layer becomes uniform as the top electrode is raised to a position near the surface of the solution in the well. Using the TCL-EFS system and membrane potential fluorescence resonance energy transfer (FRET) dyes, the sensitivity of voltage-gated sodium channels to tetrodotoxin and other channel inhibitors was found to be similar to those determined by established electrophysiological and more conventional VIPR techniques. A good correlation was also observed with the TCL-EFS system for inhibition of Cav2.2 by omega-conotoxin-GVIA and for block of Cav1.2 by known small molecule inhibitors. Thus, the TCLEFS system is suitable for both quantitative analysis and HTS of voltage-gated sodium and calcium channels, without the liabilities of previously reported EFS methodologies.

Calcium Channel Blockers↗

PubMed2000

The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).

The synthesis of deoxy-thymidine di-phosphate (dTDP)-L-rhamnose, an important component of the cell wall of many microorganisms, is a target for therapeutic intervention. The first enzyme in the dTDP-L-rhamnose biosynthetic pathway is glucose-1-phosphate thymidylyltransferase (RmlA). RmlA is inhibited by dTDP-L-rhamnose thereby regulating L-rhamnose production in bacteria. The structure of Pseudomonas aeruginosa RmlA has been solved to 1.66 A resolution. RmlA is a homotetramer, with the monomer consisting of three functional subdomains. The sugar binding and dimerization subdomains are unique to RmlA-like enzymes. The sequence of the core subdomain is found not only in sugar nucleotidyltransferases but also in other nucleotidyltransferases. The structures of five distinct enzyme substrate- product complexes reveal the enzyme mechanism that involves precise positioning of the nucleophile and activation of the electrophile. All the key residues are within the core subdomain, suggesting that the basic mechanism is found in many nucleotidyltransferases. The dTDP-L-rhamnose complex identifies how the protein is controlled by its natural inhibitor. This work provides a platform for the design of novel drugs against pathogenic bacteria.

Amino Acid Sequence↗