Automation Highlights from Literature

Directed-Sorting Method for Synthesis of Bead-Based Combinatorial Libraries of Heterogeneous Catalysts

The synthesis and analysis of inorganic material combinatorial libraries by a directed-sorting, split-pool bead method is demonstrated by T. E. Mallouk et al. Directed-sorting, split-pool, metal-loaded libraries are synthesized by adsorbing metal salts (H₂PtCl₆, SnCl₂, CuCl₂, and NiCl₂) and metal standards (Pt, Cu, Ni in HCl) onto 2 mg porous alumina beads in 96- or 384-well plates. A matrix algorithm for the synthesis of bead libraries treats each bead as a member of a row or column of a given matrix. Computer simulations and manual tracking of the sorting process are used to assess library diversity. The metal-loaded beads are analyzed by laser-activated membrane introduction mass spectroscopy (LAMIMS) for catalytic activity using the dehydrogenation of methyl cyclohexane to toluene as a probe reaction. The catalytic activity of individual beads that shows minimal (app. 20% of that of Pt on alumina) to high conversion could be determined semiquantitatively by LAMIMS. This method, therefore, provides an alternative to screening using microreactors for reactors that use catalysts in the form of beads. The directed-sorting method offers the potential for synthesis of focused libraries of inorganic materials through relatively simple benchtop split-pool chemistry (J. Comb. Chem. 2006, 8, 199–212).

High-Throughput Selection for Heterogeneous Catalysts

A catalyst library of 80 samples with different mass ratios of rare earth elements is prepared by L. Wang et al. by impregnation of a fresh HZSM-5 zeolite support. A high-throughput detection setup, based on UV absorption spectroscopy, is developed for heterogeneous catalyst selection. The catalytic properties of the library are tested in the selective catalytic reduction of NO by methane at 673 K. Several active catalyst combinations are identified in these initial experiments. According to the variation of the UV light intensity, resulting from the absorption of the reactant or product, it is possible to monitor the relative quantity of reactants or products during a catalytic reaction (J. Comb. Chem. 2006, 8, 247–251).

The Impact of Microwave-Assisted Organic Synthesis in Drug Discovery

Microwave-assisted organic synthesis has revolutionized organic synthesis. Small molecules can be built in a fraction of the time required by classical thermal methods. As a result, this technique has rapidly gained acceptance as a valuable tool for accelerating drug discovery and development processes. F. Mavandadi and A. Pilotti summarize the basic principles behind microwave technology, recent trends, and areas in drug discovery where this technology is making an impact (Drug Discov. Today 2006, 11, 165–174).

Microtiter Plate-Based Chemistry and In Situ Screening: A Useful Approach for Rapid Inhibitor Discovery

C.-H. Wong et al. report a method for enzyme inhibitor discovery using an approach that allows diversification of a common core structure in a microtiter plate followed by in situ screening. Their method relies on an organic reaction that is highly selective, high yielding, amenable to the microscale and preferably can be performed in water. The core can be a designed molecule based on the structural and mechanistic information of the target, a compound with a weak binding affinity, or a natural product. Several reactions are found useful for this approach, and are applied to the rapid discovery of potent inhibitors of representative enzymes (Org. Biomol. Chem. 2006, 4, 1446–1457).

Catalysis in Capillaries by Pd Thin Films Using Microwave-Assisted Continuous-Flow Organic Synthesis

M. G. Organ et al. report on the use of Pd thin film-coated capillaries for catalysis in microwave-assisted continuous-flow organic synthesis. The Pd films prepared are highly porous and composed of nanometer-sized grains (94.0 wt% Pd and 5.5 wt% carbon). The films are robust and stand up well to the physical challenges of flow conditions and the high temperatures associated with microwave irradiation. It is demonstrated that these Pd films serve as excellent catalysts for Suzuki–Miyama and Heck reactions, given the very short durations that the reaction mixture actually spends in the capillary, which is far less than 1 min (Angew. Chem. 2006, 118, 2827–2832).

Miniaturization of Microwave-Assisted Carbohydrate Functionalization to Create Oligosaccharide Microarrays

P. H. Seeberger et al. report that a microwave-assisted Kochetkov reaction can be used to rapidly obtain glycosylamines from a variety of different reducing carbohydrates. This material can then be treated with 2-iminothiolane hydrochloride to yield N-iminoglycosylamidines in a simple two-step procedure that requires no purification. This reaction sequence can also be used on as little as 100 μg of material, which can bind to a protein when immobilized onto a surface. These glycoconjugates are used in the construction of microarrays to test known carbohydrate–protein interactions. This method streamlines the efforts required to functionalize carbohydrates for the construction of arrays. Therefore, these transformations should prove useful to increase the content of carbohydrate microarray platforms for high-throughput screening (Chembiochem 2006, 7, 421–424).

Reusable Polymer-Supported Catalyst for the [3+2] Huisgen Cycloaddition in Automation Protocols

A polymer-supported catalyst for Huisgen's [3+2] cycloaddition reaction between azides and alkynes is prepared by C. Girard et al. from copper(I) iodide and Amberlyst A-21. This catalyst is then used in an automated synthesis of 1,4-disubstituted 1,2,3-triazoles giving access to these products in good yields. The reactions are performed in 13 mL glass reactors equipped with a plunging filter on a Chemspeed ASW-2000. The catalyst shows good activity, stability, and recycling capabilities (Org. Lett. 2006, 8, 1689–1692).

Emerging Chemical and Biological Approaches for the Preparation of Discovery Libraries

In academic as well as in industrial laboratories, the development of many combinatorial techniques is driven by a desire to generate diverse libraries of molecules. Recent chemical approaches range from alternative library design concepts to new synthetic procedures that allow for selective product formation in extremely short reaction times. Furthermore, biological techniques have made great advances by adapting naturally occurring strategies for library preparation and screening. K. D. Janda et al. summarize these recent trends in an interesting review article (Drug Discov. Today 2006, 11, 143–148).

A Simple, Convenient Method for the Synthesis of Maleic Anhydrides from Alpha-Keto Esters and Alkanoic Acid Anhydrides Using the TiCl₄/n-Bu₃N Reagent System

A new method for the synthesis of maleic anhydrides is described by Neela Kishorebabu and Mariappan Periasamy (Tetrahedron Lett. 2006, 13(47), 2107–2109). The reaction of a-keto esters with alkanoic acid anhydrides using the TiCl4/n-Bu3N reagent system gives the corresponding maleic anhydrides in 62–95% yields.

The TiCl4/n-Bu3N reagent system as well as the substrate alkanoic acid anhydrides and a-keto esters are inexpensive, and are easy to prepare and handle compared to the reagent systems and substrates used previously for the synthesis of these maleic anhydrides. Accordingly, this method offers good synthetic potential.

A Novel Linker for Solid-Phase Synthesis Cleavable Under Neutral Conditions

According to Asako Murata and Takeshi Wada, a novel linker cleavable under neutral and reductive conditions has been developed for the solid-phase synthesis of base-labile compounds. The linker is comprised of a 3-azidomethyl-4-hydroxybenzyl alcohol moiety, and the azidomethyl group in the linker is readily converted to an aminomethyl group by treatment with a phosphine reagent in the presence of water to result in an intramolecular cyclization to release the compounds. Using the linker, a base-labile dinucleoside methyl phosphate is synthesized on a highly cross-linked polystyrene support, and cleaved successfully from the resin without decomposition of the product.

Using the linker, a base-labile 3′-phosphorylated dithymidine methyl phosphate is synthesized and successfully cleaved from the solid support without decomposition of the product. The linker may be useful for the synthesis of other oligonucleotide analogs, peptides, and natural products as well as a wide variety of organic molecules, which are unstable under basic and acidic conditions.

Enantioselective Catalysis and Analysis on a Microchip

M. T. Reetz and D. Belder et al. share a system that combines a microfluidic reactor with an analytical device on one chip. This chip is used successfully for the rapid determination of enantiomeric excess of reaction products that are formed by mutated enzymes from directed evolution studies. As a model system, the authors use the kinetic racemate separation of glycidyl phenylether by an epoxide hydrolase-catalyzed hydrolysis that is combined with a chiral electrophoresis on the chip (Angew. Chem. 2006, 118, 2523–2526).

Lab-on-a-Chip: Microfluidics in Drug Discovery

Miniaturization can expand the capability of existing bioassays, separation technologies, and chemical synthesis techniques. Although a reduction in size to the micrometer scale usually will not change the nature of molecular reactions, laws of scale for surface per volume, molecular diffusion, and heat transport enable dramatic increases in throughput. Besides the many microwell-plate- or bead-based methods, microfluidic chips are widely used to provide small volumes and fluid connections, and could eventually outperform conventional robotic fluid handling. Moreover, completely novel applications without a macroscopic equivalent have recently been developed. P. S. Dittrich and A. Manz have reviewed current and future applications of microfluidics and the potential of lab-on-a-chip technologies for drug discovery (Nat. Rev. Drug Discov. 2006, 5, 206–218).

Practical Synthesis of (S)-Pyrrolidin-2-yl-1H-tetrazole, Incorporating Efficient Protecting Group Removal by Flow-Reactor Hydrogenolysis

A practical, safe, high yielding, and efficient synthesis of (S)-pyrrolidin-2-yl-1H-tetrazole is reported by S. V. Ley et al. It avoids the generation of ammonium azide in the cyclization step, and uses a 9:1 acetic acid–water mixture as the solvent in the hydrogenation. The hydrogenolysis reaction time is decreased from 3 days to hours through the use of an H-Cube (a continuous-flow reactor using a mixed hydrogen–liquid flow stream) (Synlett 2006, 6, 889–892).

Continuous Flow Separation of Particles Within an Asymmetric Microfluidic Device

A microfluidic-based device has been developed by S. J. Haswell et al. for the continuous separation of polymer microspheres, taking advantage of the flow characteristics of systems. The chip consists of an asymmetric cavity with variable channel width that enables continuous amplification of the particle separation for different sized particles within the laminar flow profile. The process is examined by varying the sample inlet position, the sample to media flow rate ratio, and the total flow rate. This technique can be used for manipulating both microscale biological and colloidal particles within microfluidic systems (Lab Chip 2006, 6, 561–566).

Miniaturized Continuous-Flow Reaction Vessels: Influence on Chemical Reactions

M. Brivio et al. summarize the relatively young research area of continuous-flow lab-on-a chip for synthetic applications. A short introduction on the basic aspects of lab-on-a-chip is given in the first part. The effects of downscaling reaction vessels as well as the advantages of the continuous flow microfluidic approach over conventional chemical laboratory batch methodologies are illustrated by a number of examples of organic reactions carried out in microfluidic devices. The last part addresses the integration of the microreactor with the analytical instrumentation to achieve high-throughput reaction monitoring, which is a key issue of the lab-on-a-chip approach (Lab Chip 2006, 6, 329–344).

EGEE Speeds Up Hunt for New Malaria Drugs

Martin Hofmann offers a new method for finding potential new drugs to combat malaria by running a drug discovery application on the Enabling Grids for E-sciencE (EGEE) production service (G-I.T. Lab. J. 2005, 10, 804).

Originally, the EGEE Grid infrastructure was developed for nuclear research. But in general, it is perfect for any scientific research including bioinformatics and biomedicine. The application for finding new malaria drugs is currently used by the Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) in Germany and the Corpuscular Physics Laboratory (IN2P3) of Clermont-Ferrand in France. In about 40 days, a virtual screening experiment on a 1000 computer cluster in 15 countries, calculates 46 millions substance combinations. On a single PC, the calculations would require 80 years. By using data mining methods it is possible to filter potentially new drug combinations. The Grid Computing is helpful in decreasing the time and costs for drug discovery.

High-Throughput Axial MALDI-TOF MS Using a 2-kHz Repetition Rate Laser

B. L. Karger and co-workers construct and test a new high-throughput capable axial MALDI-TOF mass spectrometer, using a laser with a 2-kHz pulse repetition rate (Anal. Chem. 2006, 78, 912–919). The comparison with a commercially available 200-Hz axial MALDI-TOF mass spectrometer shows a 10 times faster data acquisition rate. Furthermore, the achieved limits of detection are comparable (200 amol of Glu fib peptide), and the mass resolution for peptides with m/z <2700 is only slightly less (10,000 vs. 14,000). The general specification of the 2-kHz MALDI-TOF instrument contains features about instrumentation, optical design, experimental control, and data acquisition, and further methodical information. Considerations concerning the new technical instrument design included the suitability of a 2-kHz laser, and how the new 40-mm MCP detector tolerates the 10-fold increase in average ion current in terms of its saturation behavior. Another important requirement to increase the sample analysis rate is mastered with a novel strategy for rapid sample plate movement during acquisition. The final overall performance is demonstrated on the basis of the analysis of multidimensional LC fractions. MS analysis of a MALDI plate of 650 spots requires only 12 min, using the 2-kHz MALDI instrument with the continuous plate motion strategy.

Photofading of Ballpoint Dyes Studied on Paper by LDI and MALDI MS

In forensic science, determining the age of an ink is often a decisive issue. B. Spengler and co-workers share and evaluate a method to characterize the degradation processes of methyl violet and ethyl violet, typical ballpoint dyes, by using laser desorption/ionization (LDI) and MALDI mass spectrometry (J. Am. Soc. Mass Spectrom. 2006, 17, 297–306). To obtain precise and reliable results for this exceptional analytical problem, special attention is given to understanding the fundamental influences of the methodically caused degradation, and the natural and artificial aging of the dyes. The analysis of the dye directly from the paper, without preparational chemical treatment, is facilitated by the use of LDI–MS, minimizes sample preparation, and avoids the destruction of the document. As a result, the recorded aging curves represent a reliable and informative tool to characterize degradation processes. In conclusion, knowledge of storage conditions and the initial composition of the dyes in the ink are critical for interpreting the age of an ink entry.

Efficient Evaluation of Microarrays

High-throughput analytics, together with the increasing use of microarrays, generates enormous amount of data in laboratories. From a mathematical point of view, the greatest challenge is the management and evaluation of this giant amount of data. This requires reliable, fast, and user-friendly software. For Axxima Pharmaceuticals, the database system ScreenBase has been developed and adapted to meet the specific requirements of its molecular biological laboratories. The raw data, together with the experiment protocols and parameters, can be imported directly into ScreenBase after being measured. For evaluation purposes, the measured signal intensities are normalized using the attached controls so that a comparison of signals becomes possible. Thresholds assigned to the calculated data make the evaluation easier. As soon as the calculations are made, the first chart becomes available. The points of the expressive scatter plot are linked with the detailed information of this measure point, and can be displayed in a window with just one mouse click. In the same way, a link to data bases with extended information via the Internet can be realized (LaborPraxis 2005, 3, 48–51).

Market Survey LIMS

During the past years, LIMS has grown from a simple management tool for samples to a complex IT solution for integrated workflows in a lab. Many LIMS applications are available. This article provides an overview of more than 20 of these applications with attributes like operation system, fields of application, scope of functions, costs for implementation, etc. In addition to comparisons, the article also highlights how customization of a basic LIMS or LIMS framework is often needed to satisfy the requirements of a given system environment.

The primary purpose of a LIMS is to support paperless work in labs. To achieve this goal, the supply of heterogeneous interfaces becomes a very important LIMS product feature. This market study is the result of interviews with LIMS vendors (LaborPraxis 2005, 12(29), 48–51).

An Efficient Rapid System for Profiling the Cellular Activities of Molecular Libraries

Rapid quantitative methods for characterizing small molecules in a broad array of cellular assays are crucial for the discovery of new biological activities associated with these molecules, and for providing a more comprehensive profile of drug candidates early in the drug development process. P. G. Schultz et al. describe a robotic system, termed the automated compound profiler, that is capable of both propagating a large number of cell lines in parallel, and assaying large collections of molecules simultaneously against a matrix of cellular assays in a highly reproducible manner. As a test system, the authors characterize a set of 1400 kinase inhibitors in a panel of 35 activated tyrosine-kinase dependent cellular assays in a dose–response format in a single experiment. Analysis of the resulting multidimensional dataset reveals subclusters of both inhibitors and kinases with closely correlated activities. This methodology provides a powerful tool for unraveling the cellular biology and molecular pharmacology of diverse chemical libraries (PNAS 2006, 103, 3153–3158).

High-Throughput Screening of Biocatalytic Activity: Applications in Drug Discovery

High-throughput biocatalytic assay platforms enable rapid screening against enzymatic targets, and have great potential to impact various stages of the drug discovery process, including lead identification and optimization, and ADME/Tox assessment. R. A. Kumar and D. S. Clark summarize advances that are paving the way for the adoption of high-throughput biocatalytic assays as an indispensable tool for the pharmaceutical industry. The biocatalytic assays described in this review are largely used at preliminary stages for inhibitor identification and for inhibition profiling of lead compounds. Later in the drug discovery process, a major cause of failure is toxicity related to CYP inhibition, or deleterious effects of CYP-generated metabolites. High-throughput biocatalytic assays using drug metabolizing enzymes can predict such toxicity (Curr. Opin. Chem. Biol. 2006, 10,162–168).

Combinatorial Materials Research Applied to the Development of New Surface Coatings I: A Multiwell Plate Screening Method for the High-Throughput Assessment of Bacterial Biofilm Retention on Surfaces

Combinatorial, high-throughput capabilities can aid in the rapid development of new and effective antifouling marine coatings for naval applications. A biological screening process involving marine bacteria by S. J. Stafslien et al. allows for rapid and effective quantification of bacterial biofilm growth and retention on large numbers of coating surfaces in parallel. The screening process involves multiwell plate modifications for coating deposition, deposition of combinatorial coating libraries via an automated liquid dispensing robot, coating thickness measurements of cured coatings, preconditioning of coatings via immersion in deionized water, bacterial incubation, plate processing, and data analysis for identification of promising candidates (J. Comb. Chem. 2006, 8, 156–162).