Automation Highlights from Literature

LIMS APPLICATIONS - A MARKET OVERVIEW

Expectations for the functionality of Laboratory Information Management Systems depend on the company type, work profile and personal interests of people. Many LIM systems are established on the market. General tasks of LIM systems include: management of general data and access rights, sample registration, sample delivery, result acquisition, result calculation, data and system management, establishing and storing of data, etc. Since 1999 the requirement of workflow-support has been integrated into new LIM systems to ensure a process-oriented control of lab procedures.

Quality control in chemistry and pharmaceutical sciences are the main application focus of LIMS as these laboratories use clearly structured procedures (e.g. Complex IT Plant Solutions, Beckman Coulter, Creon Lab Control AG). Other systems are focused on environmental analysis (e.g. Advanced Technical Software). The complex requirements of research activities, however, can only be handled by highly specialized systems.

Beside the typical LIMS application, specialized systems for bio and gene technology have been developed within recent years. Their functionality is based on special types of sample handling using microtiter plates, arrays or robots. (e.g. Thermo Lab Systems, Integ Labordatensysteme GmbH)

All LIM systems have the ability to store raw and analytical data. A few systems specialize in delivering their own raw data archives or they enable the integration of the LIMS into specialized systems.

Typically LIMS is realized as a client/server solution supporting Windows NT, 2000 or XP. Many systems can also be used with UNIX. Oracle is the database most used in LIM systems, followed by SQLServer and other databases that can be addressed over SQL. A typical LIMS uses graphical user interface, but there is a new trend toward a browser-based user interface that allows intra- and Internet access to users without requiring any client-side software. (GIT, 46, 2002, 864).

A representative overview about existing Laboratory Information Management Systems is given by J. Wagner (Labo trend, 2002, 8, 76).

ANALYTICAL INSTRUMENTATION AND LIMS: A FULLY INTEGRATED APPROACH

The majority of LIMS today have some kind of interface for directly reading results from instrument data systems, hence avoiding manual transcription errors. However, there are problems associated with losing the link to the original analytical data files. C. Culley et al. discussed progress toward an integrated system where the LIMS reads results directly from the instrument system, while at the same time gathering the corresponding data files and storing them in the same secure LIMS environment. (J. Aut. Methods & Management in Chem., 24 (5), 2002, 170)

CONSTRUCTION OF LIMS SYSTEMS USING ANALYTICAL DATA SYSTEMS

The construction of LIMS systems often requires the development of custom-specific software components. On the other hand many automation features such as sample sequences, data export or OLE automation are integrated in today's analytical data systems. The user interface can be customized for a specific solution. One of the problems is lack of integrity of data from different instruments such as HPLC, GC, LC/MS, GC/MS or other. Shimadzu demonstrated a solution for this problem with the introduction of CLASS-Agent data management software using a back-end database on a network server (J. Aut. Methods & Management in Chem., 24 (6), 2002, 198).

Raw data and calculation results from each instrument are stored to the database together with sample information. As data with the same sample information are easily queried, analysis results of the sample with multiple instruments can be browsed in the same platform. A generic interface to store data to the database is supported for multi-vendor instruments.

PERSONAL DIGITAL ASSISTANT (PDA) LIMS: THE INTEGRATION OF LIMS AND MOBILE TECHNOLOGY

As technology advances, more options become available for developers to create products that are both practical and functional for today's mobile generation. The integration of LIMS functionality on PDAs is thus of great importance for pharmaceutical, chemical and biotech companies. R. Vranken et al. describe the development of a system for automated sample login (J. Aut. Methods & Management in Chem., 24 (6), 2002, 185). With a LIMS application on the PDA, laboratory technicians in the field can easily enter the information about a collection session and upload the data to the LIMS after returning to the laboratory.

The evolution of PDA technology and LIMS allows laboratories to become more efficient in all aspects of sample and data management. With the advancement in PDA technology the implementation of a full-featured LIMS is possible, allowing laboratories to become even more mobile and efficient.

A NEW AUTOMATION PLATFORM

MWG Biotech AG (Ebersberg, Germany) and Sias AG (Hombrechtikon, Switzerland) collaboratively developed a new automation platform called Theonyx (Simon May, GIT Labor-Fachzeitschrift 3, 2003, 242). A completely new pump mechanism enables pipetting in a dynamic range of less than 1 μl up to more than 3 ml within a single pipetting action. In addition to micro-annular gear pumps, the system also incorporates “flexi-span” tip movement, whereby the spacing between each tip is variable. In addition each tip is likewise under independent Z-axis control, allowing the user to “cherry pick” samples with all or a combination of the 8 tips. The platform also features a plate gripper that can be turned up to 270°.

A FULLY INTEGRATED HIGH-THROUGHPUT SCREENING METHODOLOGY FOR THE DISCOVERY OF NEW POLYOLEFIN CATALYSTS: DISCOVERY OF A NEW CLASS OF HIGH TEMPERATURE SINGLE-SITE GROUP (IV) COPOLYMERIZATION CATALYSTS

In a joint publication from Symyx Technologies and Dow Chemical, V. Murphy et al. (J. Am. Chem. Soc., 2003, 125, 4306) claim that for the first time, new catalysts for olefin polymerization have been discovered through the application of fully integrated high-throughput primary and secondary screening techniques supported by rapid polymer characterization methods. Microscale 1-octene primary screening polymerization experiments combining arrays of ligands with reactive metal complexes and multiple activation conditions represent a new high-throughput technique for discovering novel group (IV) polymerization catalysts. Using this approach, 384 microscale primary screening polymerization experiments were performed in just a few hours and resulted in the identification of 10 interesting 1-octene polymerization catalysts. Larger scale secondary screening experiments performed on a focused 96-member library led to the development of a new and versatile high temperature catalyst class based upon a nonmetallocene ligand. This high-throughput infrastructure was also used in a variety of applications to rapidly screen many thousands of catalyst candidates. The authors state that numerous catalyst discoveries have emerged which were entirely unpredictable and that most likely would not have been discovered through more conventional methods of catalyst research.

NEW CATALYSTS FOR THE ASYMMETRIC HYDROSILYLATION OF KETONES DISCOVERED BY MASS SPECTROMETRY SCREENING

Asymmetric catalysis is a very important field of chemical research aiming for the large-scale production of enantiomerically pure substances. In the development of asymmetric catalytic reactions usually a lot of different conditions have to be tested and often the analytical determination of the enantiomeric excess (ee) of the desired product e.g. by chiral HPLC becomes the bottleneck of the experimental study. Therefore new methods for the rapid determination of ee-values is of great importance. M. G. Finn et al. developed a mass spectroscopy assay for the determination of enantiomeric excess and employed it to screen a family of chiral phosphite P, N-ligands for activity in the rhodium-catalyzed asymmetric hydrosilylation of ketones (J. Org. Chem., 2003, 68, 2540). The identification of an effective set of ligands was followed by preliminary studies of the reaction scope and mechanism. Asymmetric induction of 84–88% ee for larger-scale reactions was observed, which is close to the level of the best alternative catalysts previously discovered. The screening method was shown to be applicable to a variety of substrates without the need for special optimization.

ELECTRONIC EFFECTS IN THE (DIIMINE)PALLADIUM(II)-CATALALYSED AEROBIC OXIDATION OF ALCOHOLS

In recent years many groups have investigated palladium-catalysed aerobic oxidations of alcohols as this is very attractive both from an economic as well as an environmental protection point of view. In a joint study from the Delft University of Technology and Avantium Technologies, Roger Sheldon et al. investigated the electronic effects in the (diimine)Pd(II)-catalysed aerobic oxidation of alcohols from the viewpoint of both the catalyst and the alcohol (Adv. Synth. Catal., 2003, 345, 497). To shorten the experimental time they advantageously made use of parallel experimentation methods: the catalytic experiments on the substituted benzylic alcohols were conducted in a special reactor array of 24 miniautoclaves. The parallel catalytic experiments allowed quick catalyst screening and optimisation of reaction conditions and also allowed for rapid generation of data for Hammett plots. It was found that a ‘push-pull’ mechanism is operative, where both electron-donating substituents on the benzyl alcohol and electron-withdrawing groups on the 4, 4′-disubstituted-2, 2′-bipyridine ligand increase the reaction rate.

PHASE-TRANSFER ALKYLATION REACTIONS USING MICROREACTORS

Recent microchip technology has enabled versatile applications in chemistry. In particular, applications in the field of analytical chemistry have been established as one of the promising research fields. Furthermore, applications in synthetic organic chemistry are getting more and more attention. Shu Kobayashi and coworkers studied phase-transfer alkylation reactions in a microchip reactor (Chem. Commun., 2003, 936).

OPEN IN VIEWER Figure 1.

They found that the reaction proceeded smoothly and that it was more efficient compared than that in a round-bottom flask with vigorous stirring. After 10 minutes the isolated yield in the microchip reactor was 96%. By an optical microscope study they observed that the interfacial area between organic and aqueous phases is more extended in a microreactor.

AUTOMATED CARBOHYDRATE SYNTHESIS TO DRIVE CHEMICAL GLYCOMICS

In a feature article by P. Seeberger (Massachusetts Institute of Technology) the development of the first automated solid-phase oligosaccharide synthesizer is described (Chem. Commun., 2003, 1115). A series of chemical challenges had to be addressed to accomplish this breakthrough and provide rapid access to oligosaccharides of biological significance. Rather than designing an entirely new system an ABI 433 peptide synthesizer was reengineered. The saccharide building blocks are stored in cartridges that are advanced toward an intake needle in the order of incorporation. All other reagents and solvents are kept in argon-pressurized bottles and delivered to the reaction bottles via a series of valves. The reactions occur in a custom designed, double walled, coolable reaction vessel that may be vortexed. A chiller allows for the adjustment of the reaction temperature from −25 °C to +40 °C. The reaction vessel can be purged by forcing the solution through the frit at the bottom of the reaction vessel by argon pressure. By using this synthesizer, structures as large as dodecasaccharides have been accessed about twenty times faster than with previous methods. Accelerated synthesis of glycoconjugates promises to greatly impact the emerging field of glycobiology. The automated synthesis of a novel malaria vaccine candidate is discussed to illustrate the medical potential of chemical glycomics.

FLUOROPHORIC ASSAY FOR THE HIGH-THROUGHPUT DETERMINATION OF AMIDASE ACTIVITY

Modern biocatalysis research has generated a need for simple, inexpensive and fast assay systems for high-throughput screening of enzyme activity. E. Henke and U.T. Bornscheuer developed a method based on coupling the enzyme-released amines with 4-nitro-7-chloro-benzo-2-oxa-1, 3-diazole (Anal. Chem. 2003, 75, 255). This reaction leads to a highly fluorescent dye that can be detected in aqueous or even in organic solvents. It could be shown that this assay works with high reproducibility and sensitivity with no further need of purification of the resulting reaction mixture.

OPEN IN VIEWER Figure 2.

PRECISE PEPTIDE SEQUENCING AND PROTEIN QUANTIFICATION IN THE HUMAN PROTEOME THROUGH IN VIVO LYSINE-SPECIFIC MASS TAGGING

Proteomics studies demand new scalable and automatable MS-based methods for peptide sequencing and protein quantification with higher specificity and accuracy. The unique feature of the method from S. Gu et al. (J. Am. Soc. Mass Spectrom 2003, 14, 1) is based on the incorporation of deuterium-labeled lysine into proteins through in vivo cell culturing. This introduces specific mass tags at the carbonyl termini of proteolytic peptides when cleaved by certain proteases. The mass shift between the unlabeled and the deuterated lysine (lys-d₄ ) assigns a mass signature to all lysine-containing peptides in any pool of proteolytic peptides. Furthermore this new method eliminates the chemical processes required for chemical tagging, which is one of the most common peptide sequencing methods today.

MEMBRANE-BASED NANOSCALE PROTEOLYTIC REACTOR ENABLING PROTEIN DIGESTION, PEPTIDE SEPARATION AND PROTEIN IDENTIFICATION USING MASS SPECTROMETRY

Information such as protein molecular weight, isoelectric point, sequence and ultimately structure are of great importance in understanding the biological function of a protein. Identification of proteins is generally accomplished through proteolytic digestion and peptide mass mapping prior to electrospray ionisation mass spectrometry (ESI-MS) or matrix-assisted laser desorption/ionisation mass spectrometry. J. W. Cooper et al. (Anal. Chem. 2003, 75, 1067) report a new miniaturized trypsin reactor housed inside a commonly used capillary fitting. This enables rapid and sensitive protein identification by online proteolytic digestion and analysing of protein digests using nano-ESI-MS and MALDI-MS. The design and assembly of the capillary fitting-based trypsin membrane reactor are straightforward and highly robust. In addition, the integration of liquid chromatography or transient capillary isotachophoresis prior to the mass spectrometric analysis is possible.

FACILITIES AND METHODS FOR THE HIGH-THROUGHPUT CRYSTAL STRUCTURAL ANALYSIS OF HUMAN PROTEINS

The structure elucidation of proteins plays a crucial role in modern structure-based drug discovery and the rational design of new small molecule inhibitors. As structure determination of proteins in many cases is still a bottleneck in the drug discovery process, a lot of efforts are undertaken to achieve a higher throughput.

U. Heinemann et al. (Acc. Chem. Res. 2003, 36, 157) reported about facilities and methods for the high-throughput crystal structure analysis of human proteins as recently established in the Protein Structure Factory, a Berlin-area structural genomics project. Genes encoding human proteins are expressed in either recombinant Escherichia coli or yeast. To facilitate and standardize protein purification the target proteins are produced with various tags for affinity chromatography. For high-throughput crystallization, a robotic station based upon a Zinsser Analytic pipetting robot, is being set up with the capacity to handle 960,000 experiments simultaneously. The resulting protein crystals will be subjected to X-ray diffraction experiments at the third-generation synchrotron storage ring BESSY.

THE SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS: A HIGH-THROUGHPUT GENE TO STRUCTURE FACTORY

B.C. Wang et al. (Acc. Chem. Res. 2003, 36, 191) described a similar network initiative consisting of five institutions in the southeastern United States. The protein production group supplies high-output production of selected proteins. The X-ray crystallography group conducts high-throughput structure production in parallel with production-related research and development in nanocrystallization robotics and capillary crystallization cassette and other equipment. The NanoScreen system is a novel technology for automated and efficient screening of crystallization conditions, which greatly reduces the amount of protein necessary. The NanoScreen can accurately dispense as little as 10 nl of solution in each experiment. Several thousand experiments can be performed daily. A novel capillary crystallization cassette system has also been developed. This system combines the crystallization and crystal mounting steps, eliminating the need for crystal transfer - an advantage when handling sensitive or fragile crystals.

HIGH-THROUGHPUT CRYSTALLOGRAPHY AT AN AFFORDABLE COST: THE TB STRUCTURAL GENOMICS CONSORTIUM CRYSTALLIZATION FACILITY

In another paper B. Rupp (Acc. Chem. Res. 2003, 36, 173) reports a cost-effective approach to high-throughput crystallography. In contrast to venture capital-funded commercial enterprises, the TB consortium facilities are decentralized and aim to develop high-throughput crystallography methods and automation with a comparatively small budget. For the crystallization plate setup a Hydra-Plus-One robot is used. It consists of a standard 96-syringe Hydra dispenser, an xyz-table and a single-channel Innovadyne microsolenoid dispenser for the protein. By using this system and starting from premixed cocktails and aspirated protein the total setup time per 96-well plate is 90 s.

COMPOUND MANAGEMENT COMES OF AGE

The changing role of compound management in recent years has seen an often under-valued and under-resourced function become recognized as a key part of the drug discovery process. In an interesting overview article Ian Yates examines the challenges faced by compound management teams, some of the solutions that are currently available, and those that may be available in the future (Drug Discovery World, Spring 2003, 35). Compound management has to cover a wide range of different tasks: from supplying one or two compounds to an in vivo test to supplying a million compounds to a HTS screen. In order to handle these different tasks successfully special hardware, software and labware components are needed. These are discussed in detail with special focus on automated solutions for sample storage and processing. The author states that compound management groups must now consolidate their position and justify the large investments that have been made in them by contributing to an increased discovery output, and proving they are not only capable of managing the “crown jewels” of a company, but also of continuing to adapt to meet the needs of an ever-changing discovery process.