Automation Highlights from the Literature

Comprehensive Survey of Combinatorial Library Synthesis: 2005

R. E. Dolle et al. present the ninth annual review in an ongoing series of comprehensive reviews in combinatorial chemistry highlighting developments in new methodology and synthesis of small molecule libraries. A total of 434 entries are categorized according to biologically active libraries, libraries without disclosed biological activity, solid- and solution-phase reagents and scavengers, linkers, and polymer-supported chiral ligands as published in 2005 (J. Comb. Chem. 2006, 8, 597–635).

Expediting Drug Discovery: Recent Advances in Fast Medicinal Chemistry—Optimization of Hits and Leads

P. J. Edwards et al. review the literature from January 2004 to January 2006 relating to the use of parallel chemistry compound libraries in drug discovery. Examples of libraries that yield active compounds across a range of biological targets are presented. The backgrounds of the biological target and structure-activity relationships that can be discerned from members of a library series also are discussed. A brief discussion of new technological developments in library design and synthesis, and likely future directions for parallel chemistry in the context of drug discovery, also are presented (Curr. Opin. Drug Discov. Devel. 2006, 9(4), 425–444).

Automated Protein–Ligand Crystallography for Structure-Based Drug Design

An approach to automate protein–ligand crystallography is presented by I. J. Tickle et al., with the aim of increasing the number of structures available to structure-based drug design. The methods proposed by the authors address the automatic interpretation of diffraction data for targets with known protein structures, and provide easy access to the results. Central to the system is a novel procedure that fully automates the placement of ligands into electron density maps. Automation provides an objective way to structure solution, whereas manual placement can be rather subjective, especially for data of low to medium resolution. Ligands are placed by docking into electron density, while taking care of protein–ligand interactions. The ligand fitting procedure is validated on both public domain and in-house examples. Some of the latter deal with cocktails of low-molecular weight compounds as used in fragment-based drug discovery by crystallography. For such library-screening experiments, it is demonstrated that the method can automatically identify which of a cocktail's compounds are bound (Chem. Med. Chem. 2006, 1, 827–838).

Combining Enabling Techniques in Organic Synthesis: Continuous Flow Processes with Heterogenized Catalysts

A. Kirschning et al. describe enabling techniques (solid-phase assisted synthesis, new reactor design, microwave irradiation, and new solvents) in organic chemistry and emphasize the combination of several of them for creating new synthetic technology platforms. Particular focus is on the combination of immobilized catalysts as well as biocatalysts with continuous flow processes. The authors claim that the PASSflow continuous flow technique fulfills both chemical as well as chemical engineering requirements. It combines reactor design with optimized, monolithic solid phases as well as reversible immobilization techniques for performing small- as well as large-scale synthesis with heterogenized catalysts under continuous flow conditions (Chem. Eur. J. 2006, 12, 5972–5990).

A Formal Total Synthesis of Taxol Aided by an Automated Synthesizer

A 36-step synthesis is carried out in automated synthesizers by T. Takahashi et al. to provide a synthetic key intermediate of taxol. A key step involves a microwave-assisted alkylation reaction to construct the ABC ring system from an AC precursor. Subsequent formation of the D ring affords baccatin III, a well-known precursor of taxol (Chem. Asian J. 2006, 1, 370–383).

Efficient Pd(0)-Mediated Microwave-Assisted Arylation of 2-Substituted Imidazo[1,2-a]pyrimidines

A short and practical synthesis of 2,3-substituted imidazo[1,2-a]pyrimidines, based on microwave-assisted Heck-type arylation of 2-substituted imidazo[1,2-a]pyrimidines, is shared by E. van der Eycken et al. A 45-member library of 2,3-substituted imidazo[1,2-a]pyrimidines is obtained with good yields and purities using this optimized protocol (J. Comb. Chem. 2006, 8, 659–663).

Application of Lean Manufacturing Concepts to Drug Discovery: Rapid Analogue Library Synthesis

The application of parallel synthesis to lead optimization programs in drug discovery has been an ongoing challenge since the first reports of library synthesis. A number of approaches to the application of parallel array synthesis for lead optimization have been attempted over the years, ranging from widespread deployment by (and in support of) individual medicinal chemists to centralization as a service by an expert core team. H. N. Weller et al. describe their experience with the latter approach, which is undertaken as part of a larger initiative to optimize drug discovery. In particular, the authors highlight how concepts taken from the manufacturing sector can be applied to drug discovery and parallel synthesis to improve the timeliness, and thus, the impact of arrays on drug discovery (J. Comb. Chem. 2006, 8, 664–669).

Preparation of Pilot Library with Tetrahydro-b-Carboline Alkaloid Core Skeleton Using Tandem Intramolecular Pictet–Spengler Cyclization

Tetrahydro-b-carboline is often found in complex natural products and is frequently associated with biological activity, such as anti-cancer, anti-inflammatory, anti-HIV, and antidepressant. A solid phase strategy is described for the synthesis of tetrahydro-b-carboline alkaloid library. The key transformation is an acid-catalyzed tandem intramolecular Pictet–Spengler cyclization from L-tryptophan (Sung-Chan Lee et al., Tetrahedron Lett. 2006, 38(47), 6843–6847). It forms acyl iminiums with synchronous cleavage of products from acid-labile SASRINTM solid support. A pilot library with two diversity points has been successfully synthesized in high purity to demonstrate this strategy.

Preparation of N-arylpiperazines and Other N-aryl Compounds from Aryl Bromides as Scaffolds of Bioactive Compounds

Aryl bromides are coupled with TV-compounds to give corresponding arylamines a suitable ligand and a weak base in the presence of a palladium catalyst (M. Romero et al., Tetrahedron 2006, 38(62), 9010–9016). The catalysts perform well for a large number of different starting material combinations at 100–150 °C with drops of toluene or without solvent. When the starting materials were solid compounds with low catalyst levels (0.12 mol % Pd), Pd[P(o-tolyl)₃]₂Cl₂ is used with a chelating ligand such as 2,20-bis(diphenylphosphino)-1,10-binaphthyl (BINAP) or triphenylphosphine (PPh₃), and cesium carbonate base without solvent or with a few drops of toluene. The reagents can be weighed and manipulated in contact with air to facilitate industrial use. The results of this fast and clean reaction show it is possible to replace the expensive BINAP with the more readily available PPh₃ than other ligands. The low catalyst amounts make the process environment friendly.

Dehydrogenation of Ethane and Hydrogenation of Carbon Dioxide in a Catalytic Membrane Reactor Using Copper-Plated LaNi₅ as a Membrane Material

Yoshimitsu Uemura et al. assess a new membrane reactor (Int. J. Chem. Reactor Eng. 2006, 6, Note P1). A membrane reactor consisting of a reactor and a separation membrane may be suitable to provide hydrogen from hydrocarbon to reduce carbon dioxide. In this study, a catalytic membrane reactor is designed and tested to prove that if both reactions (dehydrogenation of ethane and reduction of carbon dioxide to carbon monoxide) occur on each side of the membrane in the reactor as expected. Copper-plated LaNi₅ and CaNi₅ are used as membrane materials. In the first step, lower hydrocarbons including ethane are dehydrogenated on one side of the membrane whereas the other side is swept by an inert gas. Hydrogen storage alloy particles are plated with copper for disintegration resistance and adhesiveness to the particles. The membrane is set in a tubular reactor of stainless steel (18 mm in diameter and 630 mm in length). In the second step, simultaneous feed of ethane on one side and carbon dioxide on the other side is tried if both reactions (dehydrogenation of ethane and reduction of carbon dioxide) occur. The hydrocarbons are dehydrogenated to hydrogen and coke for the single side reaction. LaNi₅ and CaNi₅ particles were well bound by interparticle copper even after the reaction. On the other hand, the alloy phase changed for both the alloys. This change may be attributed to the high temperature and the atmosphere during the reaction experiment. There is no significant difference in reaction performance between LaNi₅ and CaNi₅.

A Comprehensive Model for Catalytic Membrane Reactor

A new model for a catalytic membrane reactor is described by Shashi Kumar et al. (Int. J. Chem. Reactor Eng. 2006, 4). The demand for higher conversion and better yield and selectivity of the desired reaction products with energy saving considerations has led to new, ingenious configuration and design of chemical reactors. In this regard, multifunctional reactors that combine reactions with separations have received much attention. Catalytic membrane reactors, which are used mainly for conducting hydrogenation and dehydrogenation reactions, are multifunctional reactors. They can provide improved performance over conventional reactors, and can be used for synthesis of oxyorganic compounds by using inorganic membranes.

The authors present a comprehensive model for a tubular membrane reactor. It may be used with any type of membrane, viz. Pd, Pd alloy, or porous, and considers steady state, isothermal, and adiabatic operations. The model accounts for reactions on either side, tube or shell, isothermal and adiabatic conditions, reactive and nonreactive sweep gas, multicomponent diffusion through gas films on both sides of the membrane, and pressure variations.

Application of the model is demonstrated with a case study of the production of styrene by catalytic dehydrogenation of ethyl benzene. Performances of four catalysts are evaluated by using the model. The model may be used to study a wide variety of catalytic reacting systems in membrane reactors, and also to develop software for this purpose.

Nonstop Integrated—Profinet

In contrast to product engineering, field bus systems are not as common in process automation. Approximately 20% of field bus systems are used in process automation. With the development of new systems for process automation, the question of how to best use a field bus system arises.

Matthias Römer provides an overview of the possibilities and limitations for Profinet in process automation (CITplus. 2006, 7, 58–60). The Ethernet-based Profinet is standardized internationally (ICE 61158), and offers two options: the CBA (Component Based Automation) and the Profinet-IO-Technology. The Profinet can be integrated into existing Ethernet-based communication systems. The TCP/IP compatible infrastructure creates the basis for use with future automatic control engineering technologies. The article describes different concepts for the integration of Profibus PA Systems into an automation system on Profinet basis. The function range of Profinet is larger than existing field bus systems, and it permits a flexible bus-, star-, or a tree-topology. The Profinet cannot replace all field bus systems today. In the short term, users will apply it to many devices. In the long term, new devices with Profinet interfaces will become available in the marketplace. Because of the robustness of some established field bus systems, the Profinent will never be able to replace them. Therefore, it is a special challenge to integrate existing field bus systems into the Profinet.

Supercooled Micro Flows and Application for Asymmetric Synthesis

Supercooled micro flow in microchannels is demonstrated by T. Kitamori. To clarify fundamental properties of the supercooling state in microchannels, freezing temperature is measured in microchannels with widths ranging from 70 mm to 300 mm. The freezing temperature decreases with decreasing width of the microchannel when the microchannel wall is chemically modified with octadecylsilane group. The lowest freezing temperature observed is –28 °C for water in the 70 mm wide microchannel. By contrast, the freezing temperature of –15 °C did not depend on width when a microchannel with a bare glass surface is used. The supercooled micro flow is applied to an asymmetric reaction in two-phase micro flow of aqueous and dichloromethane phases. As expected from thermodynamic prediction, enantiomeric selectivity increases in the supercooled water (Lab Chip. 2006, 6, 1236–1238).

Development of a Mass-Directed Preparative Supercritical Fluid Chromatography Purification System

W. K. Goetzinger et al. report the development of a mass-directed supercritical fluid chromatography (SFC) purification system. The authors address issues of software compatibility, the interface between the preparative SFC and the mass spectrometer, and fraction collection. Good peak shape and signal are achieved in the mass spectrometry (MS) trace, allowing accurate peak detection and reliable fraction collection. Simple modifications on a commercially available fraction collector enable fractionation at atmospheric pressure with high recovery. The SFC/MS purification system is used to support high-throughput library purification, and proves to be a valuable tool for complementing reversed-phase high-performance liquid chromatograph (RP-HPLC/MS)-based technology platforms (J. Comb. Chem. 2006, 8, 705–714).

Handheld Rectilinear Ion Trap Mass Spectrometer

The interest in miniature mass spectrometers for in situ chemical analysis, providing rapid response, high sensitivity, and high specificity, leads to new handheld systems with enhanced portability by minimizing size, weight, and power consumption. G. E. Patterson (Griffin Analytical Technology) and R. G. Cooks and co-workers (Purdue University, West Lafayette) introduce a new handheld mass spectrometer, Mini 10, based on a rectilinear ion trap mass analyzer. (Anal. Chem. 2006, 78, 5994–6002)

The shoebox-sized system, 32 cm in length, 22 cm in width, and 19 cm in height, has a total weight of 10 kg, and is battery-powered (nickel-metal hydride batteries). It can perform chemical analysis on air or water samples while being carried. The inherent advantages of the implemented rectilinear ion trap are its simplified geometry and high capacity. A filament electron source, as well as a glow discharge electron source, is developed for the new mass spectrometer. To achieve the necessary vacuum (< 1 × 10⁻⁵ Torr) and robustness, a two-stage KNF Neuberger diaphragm pump is used as the rough pump for the backing pressure and a Pfeiffer TPD 011 turbo pump is used as the main pump. Analytical performance is characterized using various gaseous and liquid samples, and results in a unit mass resolution, a mass range over m/z 500 and LODs in the 50 ppb range. Multistage tandem mass spectrometry capabilities provide additional structural information and improve the limit of detection for analytes in complex mixtures. The option for wireless networking underscores the validity of the handheld device.

Direct screening of a Dynamic Combinatorial Library Using Mass Spectrometry

The discovery of ligands from dynamic combinatorial libraries (DCLs) generated in the presence of therapeutic target molecules is a promising, but labor- and time-intensive, screening tool in modern drug discovery. Sally-Ann Poulsen from Eskitis Institute for Cell and Molecular Therapies (Griffith University, Australia) presents a Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) approach together with sustained off-resonance irradiation collision activated dissociation (SORI-CAD) to detect noncovalent protein–DCL ligand complexes under native conditions. (J. Am. Soc. Mass Spectrom. 2006, 17, 1074–1080)

For this, the protein target bovine carbonic anhydrase II (bCA II) is screened against a DCL generated by hydrazone exchange. The systematic design of the DCL building block, a benzene sulphonamide hydrazide, with a bCA II recognition element and the experimental data of all synthesized compounds are described in detail. The MS/MS capabilities of the FTICR MS technique are significant because they enable an effective deconvolution of the DCL mixtures without need for further synthesis or conversion steps. Furthermore, the mass spectrometry capabilities and protocol are expected to master the complexity of DCLs with increased dimensions. A conventional solution phase competitive binding assay for bCA II is used for the validation of mass spectrometry screening results, and is fully consistent.

A Chemical Genetics Approach for the Discovery of Apoptosis Inducers: From Phenotypic Cell Based HTS Assay and Structure-Activity Relationship Studies, to Identification of Potential Anticancer Agents and Molecular Targets

Chemical genetics has been widely used to study biological systems and to discover new drugs, signaling pathways, and targets. A recent review by S. X. Cai et al. describe the development and utilization of a cell- and caspase-based apoptosis induction assay for the discovery of apoptosis inducers. The authors begin with the development of a cell-based phenotypic assay, which is used for the identification of small molecules that exhibit apoptosis inducing activities. Through medicinal chemistry and biological studies, in vivo active compounds are identified, such as MX116407 as a tumor vascular disrupting agent with potent in vivo anticancer activity. The molecular targets of in vivo active compounds are identified using reagents designed and synthesized based on the Structure Activity Relation (SAR), including the identification of tail-interacting protein 47 (TIP47), an insulin-like growth factor II (IGF II) receptor binding protein, as the molecular target of 3-aryl-5-aryl-1,2,4-oxadiazoles; and Transferrin receptor I (TfR), a transmembrane protein that interacts with transferrin (Tf) for the transport of iron into cells, as the molecular target of gambogic acid (Curr. Med. Chem. 2006, 13, 2627−2644).

In Vitro ADME Medium/High-Throughput Screening in Drug Preclinical Development

The study of ADME features huge numbers of new chemical entities (NCEs) produced mainly by combinatorial chemistry. Because NCEs are a bottleneck in the drug development process, the pharmaceutical industry is developing new medium/high-throughput screening capabilities. M. J. Gómez-Lechón et al. review some of the available in vitro ADME systems that have been adapted to screening requirements, and they review the technological approaches that can be linked to medium/high-throughput molecular screening (JMin-Rev. Med. Chem. 2006, 6, 1053–1062).

Establishment and Application of a High-Throughput Model for Rho Kinase Inhibitors Screening Based on Fluorescence Polarization

In February 2006, Duang et al. (Biol. Pharm. Bull. 2006, 29(6), 1138–1142) state that Rho kinase (ROCK) inhibitors are effective candidates for neural or cardiovascular disorders. To uncover new potential inhibitory candidates, the development of high-throughput applications becomes pivotal for picking up new ROCK inhibitors from thousands of potential drug compounds. The high-throughput model is based on purified recombinant rat ROCK catalytic domain (rROCK-CD) from Escherichia coli (E. coli). The assay facilitates the phosphorylation of a fluorescent S6-peptide (200 nM) relative to the activity of rROCK-CD (2.0 mg/mL) under restriction of subjected compounds. The amount of fluorescence measured after 60 min. of incubation at 37 °C varies from low to high polarization depending on the amount of the phosphorylated peptide. According to the authors, only compounds with IC50 values of less than 10 μM are considered as lead compounds. The bioactivity of such compounds is then evaluated by observing their potential to promote neurite outgrowth. Using this application, five lead compounds are identified, underlining the suitability of the assay for further high-throughput applications.

Description of Complex Devices with the Enhanced Electronic Device Description Language (EDDL)

For 2 years, the Electronic Device Description Language (EDDL) has served as an international standardized language (IEC 61804–2) for describing the automation features and functions process devices EDDL was developed via a cooperative project of Foundation Fieldbus, HART Communication Foundation, PROFIBUS International, and OPC Foundation.

The improved EDDL achieves a unified and complete operation and observation of all installed devices. A manufacturer independent interpreter creates user interfaces for control and parameterization using Electronic Device Descriptions (EDD), which are formulated in EDDL. A great advantage is the unified “look and feel” of all devices and device classes. The EDDL under IEC 61804–2 and the specifications for EDDL Enhancements are technically perfect today. As a result, complex device features, control functions, and user interfaces can be realized efficiently. EDDL is an operation system independent language. Even for complex devices, no operation system dependent enhancements are necessary. All elements that are required for the graphical visualization of the device functions and for the control of devices can be realized in a user-friendly manner with Enhanced EDDL. The necessary time for the development of EDD is shown to be reduced by a factor of at least 10 when compared with conventional software tools (M. Augustin; D. Eckardt.atp, 2006, 4, 18–23).

LIMS and ELN: Integration Vs. Combination

LIMS are specialized for the management of highly structured process information. In contrast, an Electronic Laboratory Notebook (ELN) is designed for the acquisition, processing, and visualization of unstructured information. Quality assurance and the demands of complete electronic process documentation challenge the separation these two IT solutions (LIMS and ELN). In addition, system integration (e.g., ERP, technical lab processes of lab devices and systems) requires additional expenses for realization and system validation by the separate use of LIMS and ELN.

This article justifies the complete integration of ELN properties within a LIMS. Next to the ELN integration, disadvantages of a LIMS interface with networked ELN are discussed. The article is product oriented. Examples of ELN LIMS integration consider recent decision criteria for the modernization and improvement of IT infrastructures in modern life science labs. For the high demands on availability of complete process integration, the integrated LIMS ELN approach is indispensable. (Ehrensberger, LaborPraxis. 2006, 5(30), 96–97)