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At least 271 records · Page 15Linked to original sources

PubMed2004

Instant ligand libraries. Parallel synthesis of monodentate phosphoramidites and in situ screening in asymmetric hydrogenation.

Chiral phosphoramidites have been identified as excellent ligands for various metal-catalyzed enantioselective transformations. Taking advantage of their easy preparation and modular nature, we designed a fully automated protocol for the parallel preparation of a library of 32 phosphoramidites and its screening in asymmetric hydrogenation of amino acid precursors. This initial study led to the discovery of a new ligand for the preparation of an enantiopure beta(3)-homoalanine precursor. [structure--see text]

Amides↗

PubMedDate not supplied

High-throughput microcoil NMR of compound libraries using zero-dispersion segmented flow analysis.

An automated system for loading samples into a microcoil NMR probe has been developed using segmented flow analysis. This approach enhanced 2-fold the throughput of the published direct injection and flow injection methods, improved sample utilization 3-fold, and was applicable to high-field NMR facilities with long transfer lines between the sample handler and NMR magnet. Sample volumes of 2 microL (10-30 mM, approximately 10 microg) were drawn from a 96-well microtiter plate by a sample handler, then pumped to a 0.5-microL microcoil NMR probe as a queue of closely spaced "plugs" separated by an immiscible fluorocarbon fluid. Individual sample plugs were detected by their NMR signal and automatically positioned for stopped-flow data acquisition. The sample in the NMR coil could be changed within 35 s by advancing the queue. The fluorocarbon liquid wetted the wall of the Teflon transfer line, preventing the DMSO samples from contacting the capillary wall and thus reducing sample losses to below 5% after passage through the 3-m transfer line. With a wash plug of solvent between samples, sample-to-sample carryover was <1%. Significantly, the samples did not disperse into the carrier liquid during loading or during acquisitions of several days for trace analysis. For automated high-throughput analysis using a 16-second acquisition time, spectra were recorded at a rate of 1.5 min/sample and total deuterated solvent consumption was <0.5 mL (1 US dollar) per 96-well plate.

Combinatorial Chemistry Techniques↗

PubMed2007

MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results.

MS-based protein identification is an important part of both gel-based and gel-free proteome studies. The MASCOT search engine (http://www.matrixscience.com) provides one of the most popular automated algorithms for this task. Here we present an open-source software library written in Java that parses raw MASCOT results into an easily accessible and fully functional object model (http://genesis.ugent.be/MascotDatfile). Several scripts based on this library are provided as examples, allowing direct automation of important routine tasks involved in processing peptide identifications.

Algorithms↗

PubMed1997

Peptide and nonpeptide lead discovery using robotically synthesized soluble libraries.

The method of combinatorial synthesis of peptide and nonpeptide libraries on solid phase is analyzed and the automation of the mix and divide key step described. A set of amino acids leading to a high molecular diversity is proposed as well as a number of scaffolds for the preparation of variable polyamide libraries. Adequacy of the resin bead quantities to library size and to the ratio of the synthesized peptide types is discussed. Examples of the use of capillary electrophoresis and of spectroscopic methods (MS, MS/MS, and NMR) for the analysis of the library content are given. The iterative deconvolution SURF (synthetic unrandomization of randomized fragments) is compared with positional scanning and the success of coupling of mixtures evaluated. It is concluded that extension of the original mix and divide method and the SURF deconvolution (as proposed by Houghten et al. Nature (London), 354: 84-86 1991) to nonpeptide libraries affords new leads that can be optimized towards useful therapeutics.

Amino Acids↗

PubMedDate not supplied

Continuous-flow high pressure hydrogenation reactor for optimization and high-throughput synthesis.

This paper reports on a novel continuous-flow hydrogenation reactor and its integration with a liquid handler to generate a fully automated high-throughput hydrogenation system for library synthesis. The reactor, named the H-Cube, combines endogenous hydrogen generation from the electrolysis of water with a continuous flow-through system. The system makes significant advances over current batch hydrogenation reactors in terms of safety, reaction validation efficiency, and rates of reaction. The hydrogenation process is described along with a detailed description of the device's main parts. The reduction of a series of functional groups, varying in difficulty up to 70 degrees C and 70 bar are also described. The paper concludes with the integration of the device into an automated liquid handler followed by the reduction of a nitro compound in a high throughput manner. The system is fully automated and can conduct 5 reactions in the time it takes to perform and workup one reaction manually on a standard batch reactor.

Catalysis↗

PubMedDate not supplied

Purification of combinatorial libraries.

In the early days of combinatorial chemistry, much attention focused on preparation of large libraries for lead discovery. Recently, though, the focus has shifted toward smaller, more focused libraries for lead optimization. These focused libraries generally consist of individual discrete compounds. Biological assay requirements often require compounds of high purity, thus development of automated high throughput purification methods has received new attention in the past several years. This paper covers automated high throughput purification methods that have been applied to libraries of discrete compounds. Literature published through February 1998 is included. Purification methods discussed include extraction methods, scavenger methods, solid phase extraction, and preparative HPLC.

Chemistry Techniques, Analytical↗

PubMed1988

A local network for sharing resources and technical support: BACS/PHILNET.

Within the framework of large regional and national networks, local libraries can benefit by working together. We report the establishment of an online health sciences library network to share resources and technical support in the greater St. Louis area. BACS/PHILNET has evolved beyond a local automated interlibrary loan network to pilot off-site integrated library and information management systems in hospitals.

Computer Communication Networks↗

PubMed1991

QuickDOC: an interlibrary loan department in a microcomputer.

Interlibrary loan (ILL) is a critical service in most libraries and one that may consume much staff time. QuickDOC, a software program written by a medical librarian, has been designed to expedite and organize the process of requesting loans, keeping records, and preparing reports on ILL activity. The software communicates with DOCLINE, the automated ILL and referral system of the National Library of Medicine (NLM), and simplifies the management of all borrowing and lending, regardless of how requests are transmitted. QuickDOC's creator is very responsive to suggestions from users and continues to enhance the capabilities of this excellent software package.

Data Display↗

PubMed1994

Evaluating library renovation at the University of Rochester Medical Center.

In 1987, the Edward G. Miner Library of the University of Rochester Medical Center completed the second major renovation in its 62-year history. The goal of the renovation was to provide additional space for the library's 3 main constituencies: its readers, its collections, and its staff. A case study of the renovation is presented, outlining processes and issues that shaped the final outcome. The success of the renovation is assessed in terms of project goals, design, and functionality. Changes made since 1987 to accommodate automation are also summarized. The conclusion suggests that library renovation be viewed as a continuing process, and proposes that principles of interface design are appropriate guidelines for evaluating library design across time.

Facility Design and Construction↗

PubMedDate not supplied

Combinatorial electrochemical synthesis and characterization of tungsten-based mixed-metal oxides.

Automated systems for electrochemical synthesis and high-throughput screening of photoelectrochemical materials were developed and used to prepare tungsten-based mixed-metal oxides, W(n)O(m)M(x) [M = Ni, Co, Cu, Zn, Pt, Ru, Rh, Pd, and Ag], specifically for hydrogen production by photoelectrolysis of water. Two-dimensional arrays (libraries) of diverse metal oxides were synthesized by automated cathodic electrodeposition of the oxides on Ti foil substrates. Electrolytes for the mixed oxides were prepared from various metal salts added to a solution containing tungsten stabilized as a peroxo complex. Electrodeposition of the peroxo-stabilized cations gave rise to three distinguishable oxide groups: (1) mixed-metal oxides [Ni], (2) metal-doped tungsten oxides [Pt, Ru, Rh, Pd, Ag], and (3) metal-metal oxide composites [Co, Cu, Zn]. The oxides typically showed n-type semiconducting behavior. Automated measurement of photocurrent using a scanning photoelectrochemical cell showed the W-Ni mixed oxide had the largest relative zero bias photocurrent, particularly at a low Ni concentration (5-10 atomic percent Ni). Pt and Ru were also found to increase the photoactivity of bulk tungsten oxide at relatively low concentrations; however, at concentrations above 5 atomic percent, crystallization of WO(3) was inhibited and photoactivity was diminished. Addition of Co, Cu, and Zn to WO(3) was not found to improve the photoelectrochemical activity.

Journal Article↗

PubMed2002

Glycosamino acids: building blocks for combinatorial synthesis-implications for drug discovery.

The unique functions of carbohydrates, including energy storage, transport, modulation of protein function, intercellular adhesion, signal transduction, malignant transformation, and viral and bacterial cell-surface recognition, underlie a significant pharmaceutical potential. The development of combinatorial carbohydrate libraries in this important arena has been slow, in contrast to the rapid development of combinatorial synthesis in the area of small-molecule libraries and biopolymers. This is largely as a result of the inherent difficulties presented by this class of polyfunctional compounds. Nevertheless, strategies to cope with these problems have been devised over the past seven years, and combinatorial carbohydrate libraries have appeared. The incorporation of an amino acid moiety into the carbohydrate scaffold generates glycosamino acids, which are attractive building blocks for the preparation of carbohydrate-based libraries because of the well-established automated peptide synthesis. Derivatization as well as homo- and heterooligomerization of glycosamino acids can be used to create novel structures with unique properties. Glycosamino acids are hybrid structures of carbohydrates and amino acids which can be utilized to generate potential glycomimetics and peptidomimetics. The incorporation of glycosamino acids into peptides allows the engineering of carbohydrate-binding sites into synthetic polypeptides, which may also influence the pharmacokinetic and dynamic properties of the peptides. Furthermore, sugar-amino acid hybrids offer a tremendous structural and functional diversity, which is largely unexplored and requires combinatorial strategies for efficient exploitation. This article provides an overview of previous work on glycosamino acids and discusses their use in combinatorial synthesis and drug discovery. Supporting information for this article is available on the WWW under http://www.angewandte.com or from the author.

Amino Acids↗

PubMed2002

High-throughput approaches for the discovery and optimization of new olefin polymerization catalysts.

The discovery of new olefin polymerization catalysts is currently a time-intensive trial-and-error process with no guarantee of success. A fully integrated high-throughput screening workflow for the discovery of new catalysts for polyolefin production has been implemented at Symyx Technologies. The workflow includes the design of the metal-ligand libraries using custom-made computer software, automated delivery of metal precursors and ligands into the reactors using a liquid-handling robot, and a rapid primary screen that serves to assess the potential of each metalligand-activator combination as an olefin polymerization catalyst. "Hits" from the primary screen are subjected to secondary screens using a 48-cell parallel polymerization reactor. Individual polymerization reactions are monitored in real time under conditions that provide meaningful information about the performance capabilities of each catalyst. Rapid polymer characterization techniques support the primary and secondary screens. We have discovered many new and interesting catalyst classes using this technology.

Journal Article↗

PubMed2006

A bioluminescent assay for monoamine oxidase activity.

This article describes a novel two-step homogeneous bioluminescent assay for monoamine oxidase (MAO) that is simple, sensitive, and amenable to high-throughput screening. In the first step, MAO reacts with an aminopropylether analog of methyl ester luciferin. In the second step, a luciferin detection reagent inactivates MAO and converts the product of the first step into a luminescent signal. The amount of light produced is proportional to the amount of MAO and the time of incubation in the first step, but the luminescent signal is stable in the second step with a half-life greater than 5h. The assay has high precision, is more sensitive than current fluorescent methods, and can accurately measure the binding constants of known substrates and inhibitors. An automated screen of the Sigma-RBI Library of Pharmacologically Active Compounds (LOPAC(1280)) revealed a surprisingly high percentage of MAO inhibitors (16%) with a low false hit rate (0.9%). This implies that a significant number of compounds interact with the MAO enzymes and suggests that it is important to include MAO assays in drug metabolism studies. Other advantages of this bioluminescent assay over comparable fluorescent assays are discussed.

Animals↗

PubMed1998

Solid-phase synthesis of a library of piperazinediones and diazepinediones via Kaiser oxime resin.

A combinatorial library of piperazinediones has been prepared by automated parallel solid-phase synthesis. The five-step reaction protocol makes use of Kaiser oxime resin, to enable cleavage from the polymeric support concomitant with an intramolecular displacement reaction, under very mild conditions. The methodology was also successfully extended to the preparation of the seven-membered ring homologs, diazepinediones.

Azepines↗

PubMed1999

The Brigham integrated computing system (BICS): advanced clinical systems in an academic hospital environment.

The Brigham integrated computing system (BICS) provides nearly all clinical, administrative, and financial computing services to Brigham and Women's Hospital, an academic tertiary-care hospital in Boston. The BICS clinical information system includes a very wide range of data and applications, including results review, longitudinal medical records, provider order entry, critical pathway management, operating-room dynamic scheduling, critical-event detection and altering, dynamic coverage lists, automated inpatient summaries, and an online reference library. BICS design emphasizes direct physician interaction and extensive clinical decision support. Impact studies have demonstrated significant value of the system in preventing adverse events and in saving costs, particularly for medications.

Computer Security↗

PubMed2004

A 1536-well cAMP assay for Gs- and Gi-coupled receptors using enzyme fragmentation complementation.

Guanosine triphosphate binding protein (G protein)-coupled receptors (GPCRs) are a large class of pharmaceutical drug targets. With the increasing popularity of functional assays for high throughput screening, there arises an increasing need for robust second messenger assays that reflect GPCR activation and are readily amenable for miniaturization. GPCRs that upon agonist stimulation modulate adenylyl cyclase activity, and, consequently, cellular cyclic adenosine monophosphate (cAMP) levels, via the G protein Gs or Gi, form a subset of therapeutic targets. While there are several cAMP assays currently available, most are not scalable for miniaturization into the 1536-well format employed for automated high throughput screening of large chemical libraries. Here, we describe a cAMP assay based on the enzyme fragmentation complementation (EFC) of beta-galactosidase. In this assay, recombinant cells expressing Gs- or Gi-coupled receptors exhibit robust and reproducible pharmacology for agonists and antagonists, as measured by cAMP levels. Furthermore, the EFC cAMP assay offers sufficient sensitivity to be used with cells expressing endogenous GPCRs. We demonstrate the miniaturization of this assay into a 1536-well format with comparable sensitivity and plate statistics to those of the 384-well assay for both Gs- and Gi-coupled receptors, and its suitability for miniaturized high throughput screening.

Animals↗

PubMed1996

Immobilized metal affinity chromatography of DNA.

Many of the most widely employed operations in molecular biology hinge upon the use of single-stranded DNA as a probe or template. Here we report a straightforward method by which to produce long single-stranded DNA molecules using the polymerase chain reaction (PCR) in combination with immobilized metal affinity chromatography (IMAC). We demonstrate that a tag consisting of six successive 6-histaminylpurine (H) residues (H6-tag) endows a DNA strand with selective retentivity onto a Ni2+-NTA-agarose chromatography matrix. The H6-tagged strand can then be eluted from the resin using 200 mM imidazole. Quantitative phosphorimaging analysis revealed that the PCR/IMAC procedure typically yields unmodified strands comprising >90% of the unbound DNA and H6-tagged strands comprising >95% of the bound fractions. DNA strands generated in this manner are shown to be excellent substrates for template-directed polymerization. The chemistry reported herein should facilitate a wide variety of operations in molecular biology, including automated DNA sequencing, hybridization screening of DNA libraries, assembly of gene cassettes, run-off transcription, site-directed mutagenesis and footprinting of protein-DNA complexes by template-directed interference footprinting.

Chromatography, Affinity↗

PubMed2002

Ongoing developments in CCP4 for high-throughput structure determination.

Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. From these beginnings, CCP4 now distributes a large software suite and is active in developing new software. In this article, an overview is given of recent and ongoing developments in the CCP4 software suite, in particular as they pertain to high-throughput studies. Developments in individual programs are discussed first, although these are covered in more detail elsewhere. The bulk of the article focuses on the infrastructure of the software suite which allows the user to move effortlessly between different programs or to create automated schemas. Major changes to the software library at the heart of the CCP4 suite, developments in the CCP4 graphical user interface, and data management within CCP4 are discussed. The latter is crucial to high-throughput studies, where a large number of data are imported, created and finally archived.

Crystallography, X-Ray↗