Abstract
Laboratory Automation and High-Throughput Chemistry
Advances in Solid-Phase Cycloadditions for Heterocyclic Synthesis
M. Alvarez et al. summarize recent developments in solid-phase cycloadditions in a review of literature to December 2006. Their article is the first review focused on the preparation of heterocyclic small molecules assembled via solid-phase (2 + 2), (4 + 2), and (3 + 2) cycloadditions (J. Comb. Chem.
Optimization of Three- and Four-Component Reactions for Polysubstituted Piperidines: Application to the Synthesis and Preliminary Biological Screening of a Prototype Library
Several solid- and solution-phase strategies are evaluated by D. G. Hall et al. for the preparation of libraries of polysubstituted piperidines using the tandem aza (4 + 2) cycloaddition/allylboration multicomponent reaction between l-aza-4-boronobu-tadienes, maleimides, and aldehydes. A novel four-component variant of this chemistry is developed in solution phase, and circumvents the need for preforming the azabutadiene component. A parallel synthesis coupled with compound purification by HPLC with mass-based fraction collection allows the preparation of a library of 944 polysubstituted piperidines with a high degree of purity suitable for biological screening. In addition, a representative subset of 244 compounds is screened against a panel of phosphatase enzymes and modest levels of activity are found (J. Comb. Chem.
Survey of the Diversity Space Coverage of Reported Combinatorial Libraries
H. M. Geysen et al. evaluate all three-point diverse libraries reported in literature since 1992 according to their similarity at the library level (Diversity Space approach). This comparison enables the identification of several particularly promising scaffold hopping opportunities, and highlights a number of optimal libraries expected to reveal binding information characteristic of an entire area of chemical space. The authors claim that future library design pursuits would benefit from a methodology such as the Diversity Space approach to ensure access to novel areas within the chemical landscape, thereby avoiding the expenditure of additional resources to cover a previously explored region (J. Comb. Chem.
High-Throughput Synthesis and Screening of Cyclic Peptide Antibiotics
Cyclic peptides are a rich source of biologically active compounds and are produced in nature by plants, bacteria, fungi, and lower sea animals. A high-throughput methodology has been developed by D. Pei and Q. Xiao for the combinatorial synthesis, screening, and identification of cyclic peptide natural-product analogues with improved biological activities or useful new activities. The methodology is applied to generate a library of 1716 tyrocidine A analogues, which are screened for antibacterial activity in 96-well plates. The identity of the active peptides is determined by partial Edman degradation/mass spectrometry. The availability of tyrocidine analogues with varying antibacterial activities provides important insight into the structure–function relationship of tyrocidine A, which should help reveal its mechanism of action (J. Med. Chem.
Peptidic Catalysts Developed by Combinatorial Screening Methods
Oligopeptides have been developed as efficient catalysts for a range of important organic reactions, including acylation, silylation, oxidation, ester hydrolysis, and aldol reactions. With many peptidic catalysts, high yields and chiral induction can be achieved under mild reaction conditions. Discovery and optimization of these catalysts typically involve the testing of compound collections and are therefore strongly linked to advances in combinatorial screening methods. H. Wennemers and J. D. Revell summarize recent developments in the field of catalytically active short-chain peptides, highlighting the combinatorial techniques that have facilitated their discovery (Curr. Opin. Chem. Biol.
Solving Chemical Problems through the Application of Evolutionary Principles
Molecular evolution has been widely applied in the laboratory to generate novel biological macromolecules. The principles underlying evolution have more recently been used to address problems in the chemical sciences, including the discovery of functional synthetic small molecules, catalysts, materials, and new chemical reactions. The application of these principles in dynamic combinatorial chemistry and in efforts involving small molecule–nucleic acid conjugates has facilitated the evaluation of large numbers of candidate structures or reactions for desired characteristics. D. R. Liu et al. discuss recent trends and claim that these early efforts suggest the promise of pairing evolutionary approaches with synthetic chemistry (Curr. Opin. Chem. Biol.
High-Throughput, Microarray-Based Synthesis of Natural-Product Analogues via in vitro Metabolic Pathway Construction
The generation of biological diversity by engineering the biosynthetic gene assembly of metabolic pathway enzymes has led to a wide range of unnatural variants of natural products. However, current biosynthetic techniques do not allow the rapid manipulation of pathway components and are often fundamentally limited by the compatibility of new pathways, their gene expression, and the resulting biosynthetic products and pathway intermediates with cell growth and function. To overcome these limitations, J. S. Dordick et al. have developed an entirely in vitro approach to synthesize analogues of natural products in high throughput. Using several type III polyketide synthases (PKS) together with oxidative post-PKS tailoring enzymes, they perform 192 individual and multienzymatic reactions on a single glass microarray. Subsequent array-based screening with a human tyrosine kinase leads to the identification of three compounds that act as modest inhibitors in the low micromolar range. This approach could enable the rapid construction of analogues of natural products as potential pharmaceutical lead compounds (ACS Chem. Biol.
Utility of 4,6-Dichloro-2-(methylthio)-5-Nitropyrimidine. Part 3: Regioselective Solid-Phase Synthesis of a 2,6,8,9-Tetrasubstituted Purine Library
The first regiocontrolled solid-phase synthesis of a 2,6,8,9-tetrasubstituted purine library has been performed through on-resin elaboration of 4,6-dichloro-2-(methylthio)-5-nitro-pyrimidine (Lars G. J. Hammarström, David B. Smith, and Francisco X. Talamás in Tetrahedron Lett.
A series of primary amines are loaded on ArgoGel-MB-CHO resin via reductive amination to yield secondary amines. Subsequent attachment of the starting pyrimidine core unit and C6-chloride substitution by primary amines yields the resin-bound 4,6-disubstituted-2-methylthio-5-nitropyrimidines. Oxone-mediated oxidation of the 2-methylthio moiety to the corresponding sulfone allows facile substitution at the 2-position. CrCl2 assists reduction of the nitro group, followed by acid-catalyzed orthoester cyclization, and finally, trifluoro acetic acid (TFA)-mediated cleavage provides the tetrasubstituted purine final products. Most of the final purines are cleaved in good to excellent yield and purity; however, it is noted that bulky groups at N9 hinder cyclization in C8-substituted derivatives. For these systems, LC purification of the crude cleavage products provides the target purines in high purity.
A Novel One-Pot Reductive Amination of Aldehydes and Ketones with Lithium Perchlorate and Zirconium Borohydride–Piperazine Complexes
A novel, one-pot reductive mono-alkylation method of amines (primary and secondary), 1,2-phenylenediamine, O-trimethylsilylhydroxylamine, and N,N-dimethylhydrazine is shared by Akbar Heydari et al. (Tetrahedron
LiClO4 has been used as a source for in situ generation of imine, iminium ion, oxime, and hydrazone, and zirconium borohydride–piperazine complex as reducing agent. This condition is especially useful for situations in which it is not practical to use the amine in excess (as is typically the case under acid-catalyzed conditions) or for acid-sensitive compounds.
Microfluidic Chip Technology and Mlcroreactor Technology
Mesoscale Flow Chemistry: A Plug-Flow Approach to Reaction Optimization
In recent years, chemistry in flowing systems has become a prominent method for conducting chemical transformations that range from analytical-scale (microchemistry) through kilogram-scale synthesis (macrochemistry). Despite obvious advantages, such as increased control of conditions leading to greater reproducibility, scaleability, increased safety, and reduced loss, its acceptance as a viable synthesis technique has been limited because of its drawbacks. These drawbacks include primarily precipitation, liquid handling, and diffusion of the reaction within the reactor. R. C. Wheeler et al. present details of a system that bridges the gap between micro- and macroreactors and enables fast reaction optimization (using small amounts of reagents) and subsequent multigram scale-up using a commercial reactor (Org. Proc. Res. Dev.
Multistep Continuous-Flow Microchemical Synthesis Involving Multiple Reactions and Separations
K. F. Jensen et al. perform a continuous multistep microchemical synthesis consisting of three transformations with separation steps in between by using the Curtius rearrangement as a model system. The work demonstrates the simultaneous use of a network of microreactors and separators for parallel synthesis of a family of compounds, in situ generation, and consumption of hazardous intermediates such as isocyanates, safe operation of microreactor systems for reactive compounds such as azides, and small-scale synthesis of chemicals for screening and optimization purposes (Angew. Chem.
Greener Approaches to Organic Synthesis Using Microreactor Technology
In a review article, D. T. McQuade et al. discuss recent trends in microreactor technology and their applications in a broad spectrum of chemical reactions (Chem. Rev.
Analysis of a Membrane Reactor: Influence of Membrane Characteristics and Operating Conditions
Investigations of the influence of membrane characteristics and operating conditions of a membrane reactor are the topic of a novel article by Nikunj P. Tanna and S. Mayadevi (Int. J. Chem. Reactor Eng.
The authors show that the membrane flux affects the performance of the PVMR in the intermediate region. In the equilibrium regime, the membrane selectivity affects the performance. The limitation introduced by a low-flux membrane can be overcome by appropriate selection of the membrane area. To a certain extent, poor selectivity can be compensated by adjusting the feed ratio. By using this model, it is possible to predict the membrane characteristics that give the best performance for specific reaction kinetics.
Multicomponent Reactions to Form Heterocycles by Microwave-Assisted Continuous-Flow Organic Synthesis
Investigations of multicomponent reaction (MCR)s in a microwave-assisted continuous microreactor are described by W. Stacy Bremner and Michael G. Organ (J. Comb. Chem.
The article is focused on the investigation of MCRs by microwave-assisted, continuous-flow organic synthesis. The MCR is one strategy for meeting goals of total synthesis and library production. In this MCR chemistry, three or more starting materials are brought together in a highly convergent approach to rapidly build up molecular structure and complexity.
MCR transformation reacts in a sequence of steps. This involves an equilibrium-driven step followed by a nonequilibrium process. This means MCR processes can be kinetically quite slow. By using a microwave support for such reactions, the rate of MCR procedures can be increased. The authors have been developing the area of microwave-assisted continuous-flow organic synthesis (MACOS) that combines the sample-handling advantage of flow with the rate-enhancing features of microwave-assisted organic synthesis. The use of MACOS to prepare medicinally relevant, heterocyclic compounds in an MCR format is the main topic of this article.
The reactor system contains a capillary with a diameter of 1200 μm and some integrated syringe pumps. The capillary is positioned by the magnetron. Two reagents flow laminar through the capillary, and the microwave assists mixing. The reason may well be a result of the microwave's heating that helps to promote turbulent flow. Furthermore, the authors investigate reactions with three reagents.
For reaction optimization, the parameters for capillary diameter, microwave power, flow rate, reaction concentration, and solvent must vary. With a newly developed methodology to implement backpressure into the flow system, the temperature can be higher than without backpressure. When using backpressure with other solvents that have higher boiling points, it is possible to achieve suitable temperatures to drive reactions to completion in a very brief time period.
Overall, it can be said that flowed synthesis, in general, 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, inline reaction monitoring (e.g., LC and GC), optimization can be performed rapidly with instantaneous changes of feedstock in the capillary reactor. Optimization of conventional batch reactions is a slow, iterative process that includes reaction set-up, quench, workup, analysis, and set-up of the next set of conditions. Thus, MCR MACOS methodology holds great promise for both total synthesis and medicinal chemistry applications.
Bioautomation and Screening
Image-Based Chemical Screening
Technological advances make it feasible to conduct high-throughput small-molecule screens based on visual phenotypes of individual cells using automated imaging and analysis. These screens are rapidly moving from being small, proof-of-principle tests to robust and widespread screens of hundreds of thousands of compounds. Automated imaging screens maximize the information obtained in an initial screen and improve the ability to select high-quality leads. In a perspective article, A. Carpenter highlights the key steps necessary for conducting a high-throughput image-based chemical compound screen (Nature Chem. Bio.
High-Throughput Screening Assays for the Identification of Chemical Probes
The biological responses measured in high-throughput screening (HTS) assays span isolated biochemical systems containing purified receptors or enzymes to signal transduction pathways and complex networks functioning in cellular environments. In a tutorial review by J. Inglese et al., factors that need to be considered when implementing assays for HTS are addressed. The authors discuss assay design strategies, the major detection technologies, and examples of HTS assays for common target classes, cellular pathways, and simple cellular phenotypes (Nature Chem. Bio.
The Interdependence between Screening Methods and Screening Libraries
The most common methods for discovery of chemical compounds capable of manipulating biological function involve some form of screening. The success of such screens is highly dependent on the chemical libraries that are assayed. Classic methods for the design of screening libraries have mainly depended on knowledge of target structure and relevant pharmacophores for target focus. The recent proliferation of two novel screening paradigms, structure-based screening and high-content screening, prompts a profound reconsideration of the ideal composition of small-molecule screening libraries. Anang A. Shelat and R. Kiplin Guy discuss interdependence between screening methods and screening libraries, and why current libraries are not optimal for addressing new targets by high-throughput screening, or complex phenotypes by high-content screening (Curr. Opin. Chem. Biol.
Microarrays in Infection and Immunity
When using DNA microarrays to uncover gene expression patterns that are diagnostic and prognostic of cancer, understanding the interplay between immune responses and disease has been a prime application of microarray technology. More recent efforts move beyond genetic analysis to functional analysis of the molecules involved, including identification of immuno-dominant antigens and peptides as well as the role of post-translational glycosylation. J. A. Maynard et al. summarize recent applications of microarray technology in understanding the detailed chemical biology of immune responses to disease in an effort to guide development of vaccines and other protective therapies (Curr. Opin. Chem. Biol.
Automated Electrophysiology in Drug Discovery
Ion channels play essential roles in nervous system signaling, electrolyte transport, and muscle contraction. Therefore, ion channels are important therapeutic targets, and the search for compounds that modulate ion channels is accelerating. To identify and optimize ion channel modulators, assays are needed that are reliable and provide sufficient throughput for all stages of the drug discovery process. Electrophysiological assays offer the most direct and accurate characterization of channel activity, and by controlling membrane potential, can provide information about drug interactions with different conformational states. However, these assays are technically challenging and notoriously low throughput. The recent development of several automated electrophysiology platforms has greatly increased the throughput of whole cell electrophysiological recordings, allowing them to play a more central role in ion channel drug discovery. O. M. McManus et al. point out how this new technology facilitates the pharmaceutical development of ion channel modulators despite remaining challenges (Current Pharm. Design