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Ligand Screening (ligand + screening)
Selected AbstractsAutolabo: an automated system for ligand-soaking experiments with protein crystalsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2010Michihiro Sugahara Ligand soaking of protein crystals is important for the preparation of heavy-atom derivative crystals for experimental phasing as well as for large-scale ligand screening in pharmaceutical developments. To facilitate laborious large-scale ligand screening, to reduce the risk of human contact with hazardous ligand reagents and to increase the success rate of the soaking experiments, a protein crystallization robot `Autolabo' has been developed and implemented in the high-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center. The main functions of this robotic system are the production of protein crystals for experiments, the ligand soaking of these crystals and the observation of soaked crystals. The separate eight-channel dispensers of Autolabo eliminate the cross-contamination of reagents which should be strictly avoided in the ligand-soaking experiment. Furthermore, the automated approach reduces physical damage to crystals during experiments when compared with the conventional manual approach, and thereby has the potential to yield better quality diffraction data. Autolabo's performance as a ligand-soaking system was evaluated with a crystallization experiment on ten proteins from different sources and a heavy-atom derivatization experiment on three proteins using a versatile cryoprotectant containing heavy-atom reagents as ligands. The crystallization test confirmed reliable crystal reproduction in a single condition and the capability for crystallization with nucleants to improve crystal quality. Finally, Autolabo reproducibly derivatized the test protein crystals with sufficient diffraction quality for experimental phasing and model building, indicating a high potentiality of this automated approach in ligand-soaking experiments. [source] Parallel implementation of AutoDockJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2007Prashant Khodade Computational docking of ligands to protein structures is a key step in structure-based drug design. Currently, the time required for each docking run is high and thus limits the use of docking in a high-throughput manner, warranting parallelization of docking algorithms. AutoDock, a widely used tool, has been chosen for parallelization. Near-linear increases in speed were observed with 96 processors, reducing the time required for docking ligands to HIV-protease from 81,min, as an example, on a single IBM Power-5 processor (1.65,GHz), to about 1,min on an IBM cluster, with 96 such processors. This implementation would make it feasible to perform virtual ligand screening using AutoDock. [source] Protein-free ligand screening: simplification of chiral chromatographic development via novel adaptation of NMR screening methodologiesMAGNETIC RESONANCE IN CHEMISTRY, Issue 7 2009Melissa R. Thompson Abstract We demonstrate here a promising NMR method that provides evidence for chiral compound selector interaction as a first-pass screening method. A novel adaptation of commonly used protein-based screening technologies, this approach relies upon ligand-to-stationary phase interaction wherein the stationary phase is tethered to sepharose beads. At only minutes per experiment, this methodology significantly reduces the time required for chiral separation methodology development and complements currently available chromatographic purity technologies.Copyright © 2009 John Wiley & Sons, Ltd. [source] Odor discrimination by G protein-coupled olfactory receptorsMICROSCOPY RESEARCH AND TECHNIQUE, Issue 3 2002Kazushige Touhara Abstract The vertebrate olfactory system possesses a remarkable capacity to recognize and discriminate a variety of odorants by sending the coding information from peripheral olfactory sensory neurons in the olfactory epithelium to the olfactory bulb of the brain. The recognition of odorants appear to be mediated by a G protein-coupled receptor superfamily that consists of ,1% of total genes in vertebrates. Since the first discovery of the olfactory receptor gene superfamily in the rat, similar chemosensory receptors have been found in various species across different phyla. The functions of these receptors, however, had been uncharacterized until the recently successful functional expression and ligand screening of some olfactory receptors in various cell expression systems. The functional cloning of odorant receptors from single olfactory neurons allowed for the identification of multiple receptors that recognized a particular odorant of interest. Reconstitution of the odorant responses demonstrated that odorant receptors recognized various structurally-related odorant molecules with a specific molecular receptive range, and that odor discrimination is established based on a combinatorial receptor code model in which the identities of different odorants are encoded by a combination of odorant receptors. The receptor code for an odorant changes at different odorant concentrations, consistent with our experience that perceived quality of an odorant changes at different concentrations. The molecular bases of odor discrimination at the level of olfactory receptors appear to correlate well with the receptive field in the olfactory bulb where the input signal is further processed to create the specific odor maps. Microsc. Res. Tech. 58:135,141, 2002. © 2002 Wiley-Liss, Inc. [source] Surface plasmon resonance for high-throughput ligand screening of membrane-bound proteinsBIOTECHNOLOGY JOURNAL, Issue 11 2009Jennifer A. Maynard Dr. Abstract Technologies based on surface plasmon resonance (SPR) have allowed rapid, label-free characterization of protein-protein and protein-small molecule interactions. SPR has become the gold standard in industrial and academic settings, in which the interaction between a pair of soluble binding partners is characterized in detail or a library of molecules is screened for binding against a single soluble protein. In spite of these successes, SPR is only beginning to be adapted to the needs of membrane-bound proteins which are difficult to study in situ but represent promising targets for drug and biomarker development. Existing technologies, such as BIAcoreTM, have been adapted for membrane protein analysis by building supported lipid layers or capturing lipid vesicles on existing chips. Newer technologies, still in development, will allow membrane proteins to be presented in native or near-native formats. These include SPR nanopore arrays, in which lipid bilayers containing membrane proteins stably span small pores that are addressable from both sides of the bilayer. Here, we discuss current SPR instrumentation and the potential for SPR nanopore arrays to enable quantitative, high-throughput screening of G protein coupled receptor ligands and applications in basic cellular biology. [source] Synthesis of Enantiomerically Pure 1,2,3,4-Tetrahydro-,-carbolines and N -Acyl-1-aryl Ethylamines by Rhodium-Catalyzed HydrogenationCHEMISTRY - AN ASIAN JOURNAL, Issue 7 2008Stephan Enthaler Dr. Abstract The rhodium-catalyzed asymmetric hydrogenation of different enamides, in particular, dihydro-,-carboline derivates, was investigated in the presence of chiral phosphorus ligands. Enantioselectivities of up to 99,%,ee were obtained after ligand screening and optimization of the reaction conditions. The scope and limitation of the catalysts were shown in the synthesis of optically active tetrahydro-,-carbolines and other benchmark N -acyl-1-aryl ethylamines. Im Rahmen dieser Arbeit wird die Rhodium-katalysierte asymmetrische Hydrierung von Enamiden vorgestellt, wobei ein besonderes Augenmerk auf der Synthese von Vorstufen für Indolalkaloide (1,2,3,4-Tetrahydro-,-carboline) lag. Nach Untersuchung verschiedenster Ligandensysteme und Optimierung der Reaktionsbedingungen konnten Enantioselektivitäten von bis zu 99,%,ee erzielt werden. Dabei erwiesen sich Phospholan-basierte Diphosphane als besonders geeignet zum Chiralitätstransfer. Die hervorragenden Eigenschaften dieser Ligandklasse konnte weiterhin in der asymmetrischen Hydrierung verschiedenster Enamide erfolgreich gezeigt werden. [source] Photo-Cross-Linked Small-Molecule Microarrays as Chemical Genomic Tools for Dissecting Protein,Ligand InteractionsCHEMISTRY - AN ASIAN JOURNAL, Issue 6 2006Naoki Kanoh Dr. Abstract We have developed a unique photo-cross-linking approach for immobilizing a variety of small molecules in a functional-group-independent manner. Our approach depends on the reactivity of the carbene species generated from trifluoromethylaryldiazirine upon UV irradiation. It was demonstrated in model experiments that the photogenerated carbenes were able to react with every small molecule tested, and they produced multiple conjugates in most cases. It was also found in on-array immobilization experiments that various small molecules were immobilized, and the immobilized small molecules retained their ability to interact with their binding proteins. With this approach, photo-cross-linked microarrays of about 2000 natural products and drugs were constructed. This photo-cross-linked microarray format was found to be useful not merely for ligand screening but also to study the structure,activity relationship, that is, the relationship between the structural motif (or pharmacophore) found in small molecules and its binding affinity toward a protein, by taking advantage of the nonselective nature of the photo-cross-linking process. [source] | ||||||||||