Automation Highlights from the Literature

Laboratory Automation and High-Throughput Chemistry

Parallel Strategies for the Preparation and Selection of Liver-Targeted Glucocorticoid Receptor Antagonists

Libraries of mifepristone analogs, MP-Acids, designed and synthesized by B. J. Backes et al. increase the chances of identifying glucocorticoid receptor (GR) antagonists that possess liver-selective pharmacological profiles. MP-Acids are uniformly potent GR antagonists in binding and in cell-based functional assays. A high-throughput pharmacokinetic selection strategy that uses the cassette dosing of MP-Acids identifies liver-targeting compounds. Thus, resource-intensive in vivo assays to measure liver-selective pharmacology are enriched with GR antagonists that achieve high concentrations in the liver (Bioorganic & Medicinal Chemistry Letters 2007, 17, 40–44).

SC²: A Novel Process for Manufacturing Multipurpose High-Density Chemical Microarrays

Various formats of miniaturized arrays of cellulose-bound synthetic probe molecules to suit a broad range of technical and assay configurations have been produced by R. Frank et al. via a novel process they name spotting compound-support conjugates, SC². This process involves parallel chemical assembly of the probe molecules by SPOT-synthesis on a special cellulose membrane, postsynthesis separation of the tethered compound spots, solubilization of the cellulose matrix, and spotting of the soluble cellulose–probe conjugates onto various types of planar surfaces. The performance of such arrays is demonstrated using a set of synthetic peptide analogs, assayed with a monoclonal antibody, as well as using a small molecule library of diketopiperazines assayed with fluorescently labeled calmodulin (QSAR Comb. Sci., 2006, 11, 1069–1080).

DNA-Encoded Chemical Libraries

Conventional libraries of chemical compounds, which are individually screened for binding to pharmaceutical targets, are typically limited by screening costs and logistics to several hundred thousand compounds. The use of DNA-encoded chemical libraries promises advantages regarding the way chemical libraries are screened, allowing the synthesis and selection of libraries of unprecedented size. D. Neri et al. summarize the most recent strategies for the construction and selection of DNA-encoded chemical libraries (QSAR Comb. Sci., 2006, 11, 1081–1087).

Design and Synthesis of an Array of Selective Androgen Receptor Modulators

R. P. Trump et al. describe the design, using shape comparison and fast docking computer algorithms, and rapid parallel synthesis of a 1300-member array based on GSK7721, a 4-aminobenzonitrile androgen receptor (AR) antagonist identified by focused screening of the GSK compound collection. The array yielded 352 submicromolar and 17 subnanomolar AR agonists as measured by a cell-based reporter gene functional assay. The rapid synthesis of a large number of active compounds provides valuable information on the optimization of AR modulators, which may be useful in treating androgen deficiency in aging males (J. Comb. Chem., 2007, 9, 107–114).

Microfluidic Chip Technology and Micro Reactor Technology

Large-Scale Synthesis of Immunoactivating Natural Product, Pristane, by Continuous Microfluidic Dehydration as the Key Step

An efficient protocol of dehydration under microfluidic conditions by K. Fukase et al. is applied to a multikilogram synthesis of pristane, a biologically important natural product, which is now widely used as an adjuvant for monoclonal antibody production (Org. Lett. 2007, 9, 299–302).

Reactions in Microfluidic Droplets

Droplet-based microfluidic systems enable the miniaturization of reactions, and the compartments in droplets enable a rapid and efficient mixing of reagents. R. F. Ismagilov et al. summarize theory and recent applications in a review article (Angew. Chem. 2007, 118, 7494–7516).

Countercurrent Laminar Microflow for Highly Efficient Solvent Extraction

T. Kitamori et al. describe a countercurrent laminarflow microsystem that uses selective surface modification of a microchannel. The extraction of a metal chelate is demonstrated with high recovery efficiency (Angew. Chem. 2007, 119, 896–898).

Multicomponent Reactions to Form Heterocycles by Microwave-Assisted Continuous Flow Organic Synthesis

M. G. Organ and W. S. Bremner offer a unique approach to multicomponent reactions by microwave-assisted, continuous flow organic synthesis. Flowed synthesis holds multiple advantages over batch reactions. One of the principal features is that when a reaction exits the reaction chamber, it is complete or at least as complete as it is going to be. As a result, with the implementation of real-time, in-line reaction monitoring, optimization can be performed rapidly with instantaneous changes of feedstock into the capillary reactor (J. Comb. Chem., 2007, 9, 14–16).

Solvent-Resistant Microfluidic DNA Synthesizer

S. R. Quake et al. have fabricated a microfluidic DNA synthesizer out of perfluoropolyether, an elastomer with excellent chemical compatibility that makes it possible to perform organic chemical reactions, and synthesized 20-mer oligonucleotides on chip (Lab. Chips 2007, 7, 24–26).

“Syn&Sort”: A Chip-Based Tool for Combinatorial Synthesis

A. Schober et al. present a new method and process for combinatorial solid-phase library synthesis. The new method, entitled “Syn&Sort,” combines the advantages of the directed sorting technique with those of miniaturized parallel synthesis. Directed sorting steps are realized by combination of two encoding principles: spatially resolved encoding is used for a carrier chip, bearing 60 solid-phase units and an individual barcode-marker for each carrier. Solid-phase supports are made of glass with a magnetic core coated with functionalized polymer support. Sixty synthesis units are arranged on each carrier chip using the magnetic “clip board” principle. No special synthesis equipment is necessary because all carriers can be used in standard laboratory equipment (QSAR Comb. Sci., 2006, 11, 1063–1068).

Microreactor Array Assembly Designed for Diversity-Oriented Synthesis Using a Multiple Core Structure Library on Solid Support

The application of spatially encoded principles in solid-phase combinatorial synthesis requires no chemical or physical coding strategies. The resulting products are encoded by their position inside the array and their synthesis history. The advantages of microreactor arrays for solid-phase synthesis as one of the embodiments in the field of microreaction technology are discussed by A. Schober et al. The reactor design, necessary process steps, and a strategy for the diversityoriented array synthesis are reviewed. In particular, the glass-made microreactor and its assembly for 1563 parallel solid-phase reactions, which can be performed at temperatures up to 120°C, are described. A multiple core structure library approach for the efficient synthesis of diverse heterocyclic libraries also is described (QSAR Comb. Sci., 2006, 11, 1055–1062).

Recent Advances in Carbohydrate Microarrays

Carbohydrate microarrays have become a powerful tool to elucidate the biological role of these important biomolecules. A minireview by P. H. Seeberger and J. L. de Paz focuses on the most recent advances involving carbohydrate microarrays, including the use of sugar arrays to study carbohydrate–cell interactions and detection of pathogens. Other important developments are novel immobilization strategies to covalently attach unmodified carbohydrates, and the application of this robotic technology to the printing of medium-size (more than 200 compounds) glycan libraries using reproducible amide bond formation and standard DNA array protocols. Recent advances in synthetic carbohydrate chemistry, such as the development of the automated solid-phase oligosaccharide synthesizer, increase the complexity and utility of carbohydrate microarrays (QSAR Comb. Sci., 2006, 11, 1027–1032).

High-Throughput Analytics

Containerless Reaction Monitoring in Ionic Liquids by Means of Raman Microspectroscopy

Reaction monitoring by Raman microspectroscopy in levitated room temperature ionic liquid (RTIL) droplets is reported by B. Lendl et al. Due to their nonvolatility, RTIL droplets are well suited to act as wall-less microreactors. The droplets are produced by a piezoelectric flow-through microdispenser connected to an automated flow injection system, and are levitated by an acoustic trap. Taking advantage of the flow system versatility, the sequence of reagents is easily changed to study a model organic reaction: the Knoevenagel condensation. The reaction is followed by Raman microspectrometry, and the obtained spectra are analyzed using multivariate curve resolution to retrieve the concentration profiles and pure spectra of reactants, intermediates, and products involved in the reaction (Lab. Chips 2007, 7, 126–132).

Bioautomation and Screening

Combinatorial Dispensing as a Fast and Efficient Means to Create Complex Screens

Liquid handling robots carry out tasks from simple plate filling to complex operations such as creating reagent mixtures from multiple stock solutions. The latter task is conceptually a combinatorial process where each mixture is created by combining a subset of stock solutions in user-defined volumes. General-purpose liquid handlers can perform this task, but their hardware lacks the inherent properties needed to exploit the combinatorial nature of the problem at hand. B. Hazes describes the use of noncontact dispensing technologies to create complex screens at low volume and high density. This approach is based on the “inkjet printer principle” where a block of dispensers (print head) travels over a multiwell plate (paper) to deliver the reagents (inks) in a user-defined pattern. Impact-induced mixing and the lack of tip contamination remove the need for extensive tip washing or the use of large numbers of disposable tips (Combinatorial Chemistry & High Throughput Screening, 2006, 9, 785–790).

A Screening Platform for Compounds with Potential Immunoregulatory Activities Using Human Cord Blood Mononuclear Cells

A systematic and combinatorial approach is adopted by S. T. Chen et al. using human umbilical cord blood mononuclear cells (hUCB-MNCs) to screen for potential immunoregulatory compounds. The hUCB-MNCs contain several types of immunogenic cells, which are a suitable material to mimic the in vivo immunoresponse after drug treatment. After treatment with various natural products, phenotypic expression analysis revealed that the subpopulation of CD3+ T cells, CD56+ natural killer (NK) cells, and CD1a+ dendritic cells apparently increased after being treated with γ-dodecalactone for 6 days. These experiments demonstrate that γ-dodecalactone has immunoregulatory effects to enhance cord blood NK cells population and bio-activities. Such a high-throughput methodology using hUCB-MNCs might be an effective platform for systematically screening potential immunoregulatory compounds (Combinatorial Chemistry & High Throughput Screening, 2006, 9, 777–784).

Application of Small Molecule Microarrays in Comparative Chemical Proteomics

The simultaneous identification of disease-specific protein targets and their small molecule–binding partners, suitable as drug candidates, could radically reduce the timeline and costs of drug discovery and development. Comparative chemical proteomics provides a novel approach to achieve this goal through rapid detection of overexpressed proteins in diseased samples by the application of small molecule microarrays. The interacting small molecules enable direct affinity-based isolation and identification of the proteins. L. G. Puskas et al. report comparative chemical proteomics studies on melanocytes and melanoma cell lines, which lead to the identification of three overexpressed proteins together with their small molecule–binding partner (QSAR Comb. Sci., 2006, 11, 1020–1026).

Small Molecule Screening: Advances in Microarraying and Cell Imaging Technologies

Cell-permeable small molecules can be used to modulate protein function selectively, rapidly, reversibly, and conditionally with temporal and quantitative control in biological systems. The identification of these chemical probes can require the screening of large numbers of small molecules. With the advent of new technologies, small molecule high-throughput screening is widely available. A review by D. R. Spring et al. focuses on the emerging technologies of microarray screening platforms and high-content screening formats (ACS Chemical Biology, 2007, 2, 24–31).

Small Molecule Microarrays: Applications Using Specially Tagged Chemical Libraries

Recent advances in proteomics and combinatorial synthesis have drawn impetus toward the development of robust technologies for the convenient identification of biologically relevant entities from within diverse chemical sets, as well as rapid strategies for the functional profiling of proteins. Among the various exciting platforms that have been developed to address these challenges, spatially addressable microarrays of small molecules have emerged as a versatile, high-density platform for high-throughput screening and analysis. The fabrication process of small molecule microarray demands that diverse molecular species and scaffolds be presented suitably for parallel screening, thereby necessitating unique design and synthetic considerations, particularly in the generation of specialized tags for encoded capture or immobilization on complementary surfaces. S. Q. Yao et al. summarize the strategies that have been established to assemble organized assortments of compounds according to the downstream application requirements on microarrays (QSAR Comb. Sci., 2006, 11, 1009–1019).