Abstract
Kerstin Thurow, Ph.D.
Hilmar Weinmann, Ph.D.
Laboratory Automation and High-Throughput Chemistry
Rapid Multistep Synthesis of 1,2,4-Oxadiazoles in a Single Continuous Microreactor Sequence
A general method for the synthesis of bis-substituted 1,2,4-oxadiazoles from readily available arylnitriles and activated carbonyls in a single continuous microreactor sequence is described by N.D.P. Cosford et al. The synthesis incorporates three sequential microreactors to produce 1,2,4-oxadiazoles in approximately 30 min in quantities (40–80 mg) sufficient for full characterization and rapid library supply (J. Org. Chem.
Expanding the Chemical Space in Practice: Diversity-Oriented Synthesis
Diversity-oriented synthesis (DOS) aims to broaden the frontier of accessible collections of complex and diverse small molecules. M. Peuchmaur and Y.-S. Wong dissect the DOS concept through three elements of diversity: building block, stereochemistry, and skeleton. Recent examples in the literature that emphasize the efficient combinations of these elements to generate diversity are reported (Comb. Chem. High Throughput Screen.
Selective Monolithiation of Dibromobiaryls Using Microflow Systems
Selective monolithiation of dibromobiaryls with one equivalent of n-butyllithium followed by the reaction with electrophiles is achieved by J.-I. Yoshida et al. using a microflow system by virtue of fast micromixing and precise temperature control. Sequential introduction of two different electrophiles based on this method also is achieved using a microflow system composed of four micromixers and four microtube reactors (Org. Lett.
Combinatorial Materials Research Applied to the Development of New Surface Coatings X: A High-Throughput Electrochemical Impedance Spectroscopy Method for Screening Organic Coatings for Corrosion Inhibition
J. He et al. report a high-throughput electrochemical impedance spectroscopy (HT-EIS) method for rapid and quantitative evaluation of corrosion protective coatings. A 12-element, spatially addressable electrochemical platform has been designed, fabricated, and validated. This platform is interfaced to a commercial electrochemical impedance spectroscopy (EIS) instrument through an automated electronic switching unit. The HT-EIS system enables four parallel EIS measurements to be run simultaneously, which significantly reduces characterization time compared to that of serial EIS measurements using a multiplexer. The performance of the HT-EIS system is validated using a series of model systems, including a Randles equivalent circuit, an electrochemical reaction (Ti/K4FeCN6, K3FeCN6), a highly uniform polymer film, and several polymer coatings. The results of the validation studies show that the HT-EIS system enables a major reduction in characterization time and provides high quality data comparable to data obtained with conventional, single-cell EIS measurement systems (J. Comb. Chem.
Resin Capsules: Permeable Containers for Parallel/Combinatorial Solid-Phase Organic Synthesis
A resin capsule is a permeable container for resin beads designed for combinatorial solid-phase organic synthesis. Resin capsules consist of a high-density polyethylene ring sealed with peek mesh on both sides. The cylindrical shape of resin capsules enables space-saving packing into plastic column-like reaction vessels commonly used for solid-phase organic synthesis. Resin capsules are evaluated by V. Krchnak et al. for use in combinatorial synthesis, and a set of model compounds with excellent purity is prepared (J. Comb. Chem.
High-Throughput Analytics
Ambient Molecular Imaging and Depth Profiling of Live Tissue by Laser Ablation Electrospray Ionization Mass Spectrometry
In conjunction with mass spectrometry, the demand for atmospheric pressure ionization methods that achieve efficient ion generation under native-like experimental conditions arises. A. Vertes and coworkers from W. M. Keck Institute for Proteomics Technology and Applications (George Washington University, Washington, DC) present the lateral mapping of metabolite distributions and their variations with depth on plant leaves with laser ablation electrospray ionization mass spectrometry (LAESI-MS) (Anal. Chem.
In contrast to electrospray-assisted laser desorption/ionization, which also relies on the postionization of neutrals in a laser plum by ESI, the laser energy used for LAESI causes a resonant process in water-rich targets. With the ESI source in axial spraying mode, the laser light (2940 nm) hits the target 18 mm below and 5–8 mm downstream from the tip of the emitter and results in a laser ablation area of 350 μm in diameter and a depth of 50 μm. Details of the produced ablation craters are investigated by scanning electron microscopy and correlated with the recorded MS data. As an example, the distribution of metabolites in the green and yellow sectors of a Zebra plant leaf is analyzed. At this, over 40 metabolites are detected and 36 could be assigned. The results are in good conformance with other techniques. Summarized, their results demonstrate that LAESI-MS opens a new way for ambient molecular three-dimensional imaging of metabolites in biological tissues and live organisms.
Online Coupling of Gas Chromatography to Nuclear Magnetic Resonance Spectroscopy: Method for the Analysis of Volatile Stereoisomers
Although HPLC-NMR has evolved into a versatile tool in the analysis of complex samples, the coupling of GC and NMR is still in an early stage of development, despite the fact that first experiments were conducted in the 1970s. In their article, K. Albert and colleagues (Institute of Organic Chemistry, Chemisches Zentralinstitut, University of Tubingen) describe a new system of coupled GC–NMR for the analysis of volatile cis/trans stereoisomers of alkenes for continuous- and stopped-flow gas-phase experiments (Anal. Chem.
Bioautomation and Screening
New Connections across Pathways and Cellular Processes: Industrialized Mutant Screening Reveals Novel Associations between Diverse Phenotypes in Arabidopsis
It is widely known that high-throughput approaches are not limited to the fields of drug discovery and white biotechnology. These techniques enter into many other areas, among them, different parts of plant biology. High-throughput analyses led to the sequencing of the first genome of a higher eukaryotic organism, the mouse-ear cress Arabidopsis thaliana, and were also essential for setting up large repositories of clones, microarray data and mutants from different model and crop plants. Today, these partially publicly available resources are indispensable for progress in any field of plant research, but the future of high-throughput approaches is not limited to particular fields. These plant biology techniques can be helpful in any area of research.
Lu et al. present an interesting example for this development. The authors analyze 13 different Arabidopsis mutants biochemically and phenotypically. The biochemical analyses are performed with different LC, GC, and MS methods to determine the contents of free amino acids, fatty acids, starch, and chlorophyll in different organs. One result of the data is that several new phenotypes are discovered in particular mutants. In a further approach, statistical and bioinformatic calculations are performed with the data sets, which reveal novel connections and associations between different metabolic and catabolic pathways. In one conclusion by Lu et al., parallel analyses of plant germplasm, like mutants or ecotypes, harbors an enormous potential for plant biology, especially for plant breeding. The exploitation of this potential depends on the application of high-throughput methods, especially of automated ones. Currently, such methods need to be improved or invented in the field of plant research to address future needs for crop plants (Plant Physiol.
Live-Cell High-Content Screening in Drug Development
Cell-based assays are state of the art in drug discovery and development. They provide toxicological data during an early phase of drug discovery and can thus help to reduce costs. The power of high-content screening technology using living cells is summarized by M. Bickle (Eur. Pharm. Rev.
One aspect of the article addresses the challenges and requirements for software solutions, for example, kinetic HCS offer tracking of objects capabilities. There are very few commercially available software products, and one is described briefly (Eur. Pharm. Rev.
Chemogenomics: A Discipline at the Crossroad of High-Throughput Technologies, Biomarker Research, Combinatorial Chemistry, Genomics, Cheminformatics, Bioinformatics, and Artificial Intelligence
E. Marechal gives an overview on chemogenomics and related technologies. Chemogenomics is the study of the interaction of functional biological systems with exogenous small molecules, or in a broader sense, the study of the intersection of biological and chemical spaces. Chemogenomics requires expertises in biology, chemistry, and computational sciences. Chemogenomics is a descendent of conventional pharmaceutical approaches, because it involves the screening of chemical libraries for their effects on biological targets, and benefits from the advances in the corresponding enabling technologies and the introduction of new biological markers (Comb. Chem. High Throughput Screen.
Cell-Based Assays in Practice: Cell Markers from Autofluorescent Proteins of the GFP Family
The recently discovered anthozoan fluorescent proteins (FPs) and the classic Aequorea victoria Green Fluorescent Protein (avGFP) as well as their derivatives have become versatile tools as live-cell markers in fluorescence microscopy. R. Heilker et al. review the use of these FPs in drug discovery assays. Assay examples are given for the application of FPs in multiplexed imaging, as photosensitizers, as fluorescent timers, as pulse-chase labels, and for robotically integrated compound testing. The development of fast microscopic imaging devices enables the application of automated fluorescence microscopy combined with image analysis to pharmaceutical high-throughput drug discovery assays, generally referred to as high-content screening (Comb. Chem. High Throughput Screen.
Design of Phenotypic Screens for Bioactive Chemicals and Identification of Their Targets by Genetic and Proteomic Approaches
Cell-based screening using phenotypic assays is a useful means of identifying bioactive chemicals for use as tools to elucidate complex cellular processes. M. Roberge et al. describe how cell-based screening assays can be designed to maximize the likelihood of discovering selective compounds through the choice of positive readouts, low chemical concentrations, and long incubation periods. Identifying the cellular targets of active chemicals can be especially demanding. Strategies for unbiased target identification by sampling potential targets at the genome-wide and proteome-wide levels also are discussed (Comb. Chem. High Throughput Screen.
Chemogenomics and Cancer Chemotherapy: Cell-Based Assays to Screen for Small Molecules That Impair Microtubule Dynamics
Microtubules are still a promising target for new therapeutic agents. Thus, there is ongoing interest in compounds that are able to modify microtubule assembly. Because of its dynamic characteristics, the microtubule cytoskeleton is a suitable target for small molecules that rapidly diffuse in the cell cytoplasm. Moreover, compounds targeting the microtubule cytoskeleton prove to be valuable tools for basic research in cell biology. L. Lafanechere reviews the potential and impact of chemogenomics and cell-based assays in the discovery of new therapeutic compounds and of new regulators of the microtubule cytoskeleton (Comb. Chem. High Throughput Screen.
Chemogenomics and Parasitology: Small Molecules and Cell-Based Assays to Study Infectious Processes
Infectious diseases caused by protozoan parasites remain chronic problems for humanity. Current advances in high-throughput screening (HTS) technologies and availability of diverse small molecule libraries offer the promise of accelerated discovery of new drug targets and new drugs that will reduce disease burdens imposed on humanity by parasitic protozoa. M.-J. Gubbels et al. provide a status report on HTS technologies in hand and cell-based assays under development for biological investigations and drug discovery directed toward the three best characterized parasitic protozoa: Trypanosoma brucei, Plasmodium falciparum, and Toxoplasma gondii. Small molecules that interfere with specific aspects of protozoan biology, identified in such screens, will be valuable tools for dissecting parasite cell biology and developing antiprotozoan drugs (Comb. Chem. High Throughput Screen.
Plant Pathogen Recognition as a Natural, Original, and Simple Model for Chemogenomics: A Brief Overview of Cell-Based Assays to Screen for Peptides Acting as Plant Defense Activators
As plants lack a circulatory system and adaptive immune system, they have evolved their own defense systems distinct from animals in which each plant cell is capable of defending itself from pathogens. Plants induce a number of defense responses, which are triggered by a variety of molecules derived from pathogenic microorganisms, referred to as microbe-associated molecular patterns (MAMPs). MAMPs include peptides, proteins, lipopolysaccharide, β-glucan, chitin, and ergosterol. The interaction between plants and chemicals in the context of plant defense represents a natural and simple model for chemogenomics at the intersection of chemical and biological diversities. To protect crop plants from diseases, it has been shown to effectively stimulate plant immunity by chemical compounds, the so-called plant defense activators. Combinatorial chemistry techniques can be applied to the search for novel plant defense activators, but it is essential to establish an efficient and reliable screening system for library screening. M. Miyashita et al. describe the cell-based lawn format assay for identification of peptides acting as plant defense activators from combinatorial peptide libraries. The requirements and limitations in constructing the screening system using combinatorial libraries in the studies of plant sciences are also discussed (Comb. Chem. High Throughput Screen.
Building a Biological Space Based on Protein Sequence Similarities and Biological Ontologies
Assignment of function to protein sequence is a task of growing importance in the life sciences as new high-throughput sequencing DNA technologies generate ever-increasing quantities of genomic data. Clustering similar sequences is a useful technique for finding conserved sequences. The CluSTr database is a publicly available database that arranges proteins in a hierarchy structured by similarity. The protein classification tool InterProScan builds on this approach by applying a range of methods to detect proteins that contain signatures indicative of the presence of particular conserved domains. P. Kersey et al. review the use of ontologies to describe a protein function that provides a flexible and abstract language to classify proteins (Comb. Chem. High Throughput Screen.
Building a Chemical Space Based on Fragment Descriptors
I. Baskin and A. Varnek review the application of fragment descriptors at different stages of virtual screening—filtering, similarity search, and direct activity assessment—using QSAR/QSPR models. They demonstrate that the power of fragment descriptors stems from their universality, very high computational efficiency, simplicity of interpretation, and versatility (Comb. Chem. High Throughput Screen.
A Ligand-Based Approach to Mining the Chemogenomic Space of Drugs
The practical implementation and validation of a ligand-based approach to mining the chemogenomic space of drugs is presented by J. Mestres et al. and applied to the in silico target profiling of 767 drugs against 684 targets of therapeutic relevance. The results reveal that drugs targeting aminergic G protein-coupled receptors (GPCRs) show the most promiscuous pharmacological profiles. The detection of cross-pharmacologies between aminergic GPCRs and the opioid, sigma, NMDA, and 5-HT3 receptors aggravate the potential promiscuity of those drugs, which predominantly include analgesics, antidepressants, and antipsychotics (Comb. Chem. High Throughput Screen.
Machine Learning for In Silico Virtual Screening and Chemical Genomics: New Strategies
Support vector machines and kernel methods belong to the same class of machine learning algorithms that has recently become prominent in both computational biology and chemistry, although both fields have largely ignored each other. These methods are based on a sound mathematical and computationally efficient framework that implicitly embeds the data of interest, respectively, proteins and small molecules, in high-dimensional feature spaces where various classification or regression tasks can be performed with linear algorithms. J.-P. Vert and L. Jacob present the main ideas underlying these approaches, survey how both the biological and the chemical spaces have been separately constructed using the same mathematical framework and tricks, and suggest different avenues to unify both spaces for the purpose of in silico chemogenomics (Comb. Chem. High Throughput Screen.
LIMS and Process Control Systems
Information Automation in R&D Laboratories: Past and Future
Ch. Sodano, author and founder of eOrganizedWorld, considers IT trends of e-records in an article that traces the history of Laboratory Information Management Systems (LIMS) and Electronic Laboratory Journals (ELNs). The way the first commercial LIMS appeared in the 1980s to the future are discussed in terms of general requirements, interfacing, the need of standardization, and IT infrastructure for collaboration networks. The overviews help to interpret new developments. The retention time for experiments captured in paper-based laboratory notebook or by microfilm is compared with electronic records (life time of storage media, etc). One of the problems identified is the availability of system software to interpret analytical data after a lot of years, but one of the central points of long life data access is the question of data or information structures. Therefore, the need and importance of general ISO standards for all types of LIMS- and ELN-related data structures are underlined. The general known convergence between LIMS and ELN is confirmed by the author. If records must be kept in electronic formats for more than 10 years, a strategy of planning for continuous migration becomes imperative (Eur. Pharm. Rev.
Extensible Open Source Content Management Systems and Frameworks: A Solution for Many Needs of a Bioinformatics Group
Authors from the Center for Computational Biology and Bioinformatics at Indiana University School of Medicine, focus on the availability of information via Internet or standard Web browsers. Basics and reviews about well-known Web site management tools are discussed and compared with the needs of user groups that conduct research-specific activities. The use of content management systems (CMSs) is described as an interesting alternative to other IT solutions for exchanging scientific content. The article provides a good overview to existing types of CMS application and standalone tools; and popular open source CMS programming languages and application software are listed with their homepage addresses. The authors divide several types of CMS use in biomedicine, including collaborative Web sites, conference Web sites, content databases in laboratory intranets, and write about the use and development of CMS application plug-ins. The article ends with CMS customization experiences and examples of solutions and recommendations.
Comparability of Data in Process and Laboratory
As in process automation, equipment and data standardization is required for laboratory automation. LIMSs collect and organize information, but are mostly proprietary solutions that do not communicate with an organization's production area.
Profibus is the world's most popular fieldbus, and it offers a fully integrated solution for discrete and process applications. The basic functions, controls, and communication services are defined in standardized device profiles. The Profibus user organization was the first of the major fieldbus organizations, specified a device profile that is especially dedicated to the requirements of laboratory equipment.
U. Jecht and C. Diedrich provide an overview of the device in “LabDevices” (CIT plus.
The new profile “LabDevices” is a door opener for the seamless integration of labs into Profibus systems, and by means of object linking and embedding for process control into other automation worlds. Application of “LabDevices” allows the use of uniform Profibus technology in production and lab automation, and provides significant savings potential even if they are not in the same fieldbus system.
Data Sharing in Distributed Databases and Peer-to-Peer Databases
Content-sharing systems on the Web have renewed interest in the design and development of decentralized database management systems. The need for large-scale data sharing between autonomous and possibly heterogeneous decentralized systems on the Web give rise to the concept of peer-to-peer (P2P) database systems. A recently published paper provides insight into this new P2P data management technology, and compares more established decentralized models, commonly referred to as distributed, federated, and multidatabases. The goal was to clarify some of the essential differences and similarities from a data management point of view.
A database system (DBS) is a software that manages one or more databases. A distributed database system is a software that manages one or more logically related databases, spanning a network. Both a federated database system and a multidatabase system are collections of preexisting DBSs in which operations can be applied to multiple heterogeneous component DBSs in a coordinated manner. The authors distinguish between db-centric and P2P-centric features. The various DBS are characterized by three dimensions: distribution, autonomy, and heterogeneity.
The most important features of P2P paradigm are scalability in terms of the number of nodes and distribution; direct access to the data at the source, which guarantees freshness in contrast to centralized repositories; robustness and resilience against attacks and churn by exploiting self organization principles; and simplified deployment, because resources from the edge of the Internet can be used and no special infrastructure is required to join the network. A P2P database system is conceived as a collection of autonomous local repositories that interact in a P2P style with established correspondences or exchange query and update requests. The local repositories are autonomous peers with equal rights, and are linked to only a small number of neighbors. The main data integration and interoperability idea in peer data management is to avoid a global schema by providing mappings between pairs of information sources. Mappings between all pairs are not necessary. An export schema contains only the elements of the local schema that a peer wants to share with the outside world.
Open and challenging issues in P2P data management are anonymity, security, and access control problems (SIGMOD Rec.