Combinatorial Chemistry & High
Throughput Screening, Vol. 6, No. 7, 2003
Contents
Bead
Technologies and Post-Genomic Drug Discovery
Guest
Editor: Gerard Rosse
Parallel
and Multiplexed Bead-Based Assays and Encoding Strategies Pp.577-587
Boon-ek
Yingyongnarongkul, Siew-Eng How, Juan Jose Diaz-Mochon, Mathilde Muzerelle and
Mark Bradley
PEG
Based Resins for Protease Drug Discovery Synthesis, Screening and Analysis of
Combinatorial On-Bead Libraries Pp.589-610
Thomas
Groth, Mana Renil and Ernst Meinjohanns
Chemogenomics
with Peptide Secondary Structure Mimetics Pp.611-621
Masakatsu
Eguchi, Michael McMillan, Cu Nguyen, Jia-Ling Teo, Emil Y. Chi, William R.
Henderson, Jr and Michael Kahn
Forward
& Reverse Chemical Genetics Using SPOS-Based Combinatorial Chemistry
Pp.623-647
David
S. Thorpe
Library
Design Practices for Success in Lead Generation With Small Molecule Libraries
Pp.649-660
R.A.
Goodnow Jr., W. Guba and W. Haap
Chemical
Libraries Towards Protein Kinase Inhibitors Pp.661-672
R.D.A.
Kimmich and W.K.-C. Park
Natural
Product-Like and Other Biologically Active Heterocyclic Libraries Using
Solid-Phase Techniques in the Post-Genomic Era Pp.673-691
K.
Knepper, C. Gil and S. Brase
Use
of Multicomponent, Domino, and Other One-Pot Syntheses on Solid Phase: Powerful
Tools for the Generation of Libraries of Diverse and
M.
Pulici, G. Cervi, K. Martina and F. Quartieri
Application
of Non-Covalently Solid-Phase Bound Catalysts Pp.729-740
F.
Michalek, J. Horn, C.C. Tzschucke and W. Bannwarth
High
Resolution Magic Angle Spinning NMR for Analyzing Small Molecules Attached to
Solid Support Pp.741-753
Harald
Schroder
Abstracts
[Back to top] Parallel
and Multiplexed Bead-Based Assays and Encoding Strategies
Boon-ek
Yingyongnarongkul, Siew-Eng How, Juan Jose Diaz-Mochon, Mathilde Muzerelle and
Mark Bradley
Advances in high throughput screening (HTS), together with the rapid progress in combinatorial chemistry, genomic and proteomic sciences have dramatically stimulated the development of a variety tools to enable the drug discovery process to become more efficient. Major future challenges in HTS include obtaining high density and good quality data based on assays that are rapid, reliable, inexpensive, sensitive, simple and miniaturised. This paper reviews the development and role of bead-based assays for HTS including DNA and single nucleotide polymorphism (SNP) assays, particularly from a multiplex perspective and evaluating the recent advances in bead-based arrays. The encoding strategies that are commonly used in bead-based assays are highlighted, while the importance of magnetic beads in genomic and proteomic purifications is discussed. In conclusion, bead-based assays offer a powerful promising approach for many aspects of drug discovery.
[Back to top] PEG Based Resins for Protease Drug
Discovery Synthesis, Screening and Analysis of Combinatorial On-Bead Libraries
Thomas
Groth, Mana Renil and Ernst Meinjohanns
This review will cover the entire hit identification process performed with biocompatible, aqueous solvated, poly[ethylene glycol] (PEG) based resins – from synthesis, through screening, to analysis. The different types of resins (including their preparation) will be discussed and compared individually. Examples of one-bead-one-compound substrate libraries will be presented, as will one-bead-two-compounds libraries used for the discovery of enzyme inhibitors. The review includes a section covering organic and bio-organic reactions performed on all-PEG resins and discusses on-bead screening of the libraries with biomolecules. Finally, analysis of compounds on single beads, either via investigation by on-bead NMR or by ladder-coding of the combinatorial compound is covered. In general, the review will focus on chemistry, libraries, synthesis, screening, and analysis, using all-PEG based resins.
[Back to top] Chemogenomics
with Peptide Secondary Structure Mimetics
Masakatsu
Eguchi, Michael McMillan, Cu Nguyen, Jia-Ling Teo, Emil Y. Chi, William R.
Henderson, Jr and Michael Kahn
There is increasing evidence that redox regulation of transcription, particularly activator protein-1 (AP-1) and nuclear factor kappa B (NF-κB), is important in inflammatory diseases. Human thioredoxin (TRX), a member of the oxidoreductase superfamily, was initially identified, as a factor which augments the production of interleukin-2 receptor alpha (IL-2R α) in human T-cell lymphotropic virus type 1 (HTLV-1) infected patient T-cells. Substrates for the redox activity of TRX bind the active site cleft in extended strand structure. The rapid generation of high numbers of peptide secondary structure mimetics through solid-phase synthesis is a key technology for the identification of pharmaceutical leads based on such protein-peptide interactions. In this manuscript, we describe a chemogenomic approach utilizing an extended strand templated library to develop small molecule inhibitors to validate oxidoreductase molecular targets in a murine asthma model.
[Back to top] Forward & Reverse Chemical Genetics Using SPOS-Based Combinatorial
Chemistry
David S. Thorpe
Combinatorial chemistry is being applied to diverse problems in the biological and pharmaceutical sciences. This review will describe an emerging application called “chemical genetics” or “chemical genomics” – genetics and genomics are often used interchangeably in this context. In forward chemical genomics, chemical libraries are tested in living systems to discover compounds that cause a desirable effect. Subsequently, the protein target is identified using various biochemical and molecular biological tools. By this method, we gain insights into the inner workings of life, and indeed, in some forms this has been the path by which most of the pharmacopoeia was discovered. In reverse chemical genetics, proteins of interest are used to probe compound collections, and those compounds that bind the proteins of interest are used to treat living systems and observed for interesting biological responses. Plausible biological roles of these proteins are inferred from the effects of the compounds because they are assumed to generally inhibit, or more rarely, stimulate, the protein’s functions. Interestingly, the reverse genetic approach is emerging as the leading model for drug discovery today. Different methods and cases will be described to illustrate forward and reverse paradigms, including those developed in the author’s laboratory.
[Back to top] Library Design Practices for Success in Lead Generation With
Small Molecule Libraries
R.A. Goodnow Jr., W. Guba and W. Haap
The generation of novel structures amenable to rapid and efficient lead optimization comprises an emerging strategy for success in modern drug discovery. Small molecule libraries of sufficient size and diversity to increase the chances of discovery of novel structures make the high throughput synthesis approach the method of choice for lead generation. Despite an industry trend for smaller, more focused libraries, the need to generate novel lead structures makes larger libraries a necessary strategy. For libraries of a several thousand or more members, solid phase synthesis approaches are the most suitable. While the technology and chemistry necessary for small molecule library synthesis continue to advance, success in lead generation requires rigorous consideration in the library design process to ensure the synthesis of molecules possessing the proper characteristics for subsequent lead optimization. Without proper selection of library templates and building blocks, solid phase synthesis methods often generate molecules which are too heavy, too lipophilic and too complex to be useful for lead optimization. The appropriate filtering of virtual library designs with multiple computational tools allows the generation of information-rich libraries within a druglike molecular property space. An understanding of the hit-to-lead process provides a practical guide to molecular design characteristics. Examples of leads generated from library approaches also provide a benchmarking of successes as well as aspects for continued development of library design practices.
[Back to top] Chemical Libraries Towards Protein Kinase Inhibitors
R.D.A. Kimmich and W.K.-C. Park
Over 500 human protein kinases identified to date are susceptible to play crucial roles in the regulation of many signal transduction pathways, making them significant drug discovery targets. However, their active sites share a high level of similarity, which constitutes a major challenge in the finding of selective and safe inhibitors. In order to meet this challenge, whether via traditional or alternative approaches, the use of chemical libraries to find either unknown natural ligands or specific inhibitors of particular kinases is more important than ever. This review briefly summarizes the recent literature on such libraries of peptides, natural product analogues, and small molecules. Significant chemical scaffolds, some synthetic routes particularly on solid-phase support, and computational tools employed for the efficient design of both selective and bioavailable inhibitors are highlighted.
[Back to top] Natural Product-Like and Other Biologically Active Heterocyclic
Libraries Using Solid-Phase Techniques in the Post-Genomic Era
K. Knepper, C. Gil and S. Brase
High-throughput technologies allow the selection of new biological targets for drug discovery in the post-genomic era. These tools increase the need of new methods to rapidly obtain potent small molecules and natural products to discover new lead structures. In particular, the solid-phase synthesis offers a great potential to obtain large compound sets.
[Back to top] Use
of Multicomponent, Domino, and Other One-Pot Syntheses on Solid Phase: Powerful
Tools for the Generation of Libraries of Diverse and Complex Compounds
M. Pulici, G. Cervi, K. Martina and F. Quartieri
The availability of small organic molecules covering as much chemical space as possible is seen as the only means that guarantees potential modulation of the many biological targets that are ultimately being unveiled by genomics. Therefore diversity oriented organic synthesis is rapidly becoming one of the paradigms in the process of modern drug discovery. This has spurred research in those fields of chemical investigation that lead to the rapid assembly of not only molecular diversity, but also molecular complexity. As a consequence multi-component as well as domino or related reactions are witnessing a new spring. Coupling these one-pot processes with solid-phase synthesis offers new perspectives for the preparation of both primary and thematic libraries. The progresses recently made in this field that perfectly suits the needs of modern drug discovery are the subject of the present review.
[Back to top] Application
of Non-Covalently Solid-Phase Bound Catalysts
F. Michalek, J. Horn, C.C. Tzschucke and W. Bannwarth
Supported catalysts have become valuable tools for simplified product isolation and catalyst recycling. The common method is covalent attachment to a solid support. An alternative strategy is to immobilize catalysts by non-covalent bonding through hydrogen bridges, ionic, hydrophobic or fluorous interactions. Compared to covalent attachment, such non-covalent approaches increase the flexibility in the choice of the support-material, reaction conditions and work-up strategies. Numerous catalytic reactions employing one of these non-covalent fixation strategies have meanwhile appeared in the literature.
[Back to top] High
Resolution Magic Angle Spinning NMR for Analyzing Small Molecules Attached to
Solid Support
Harald Schroder
Solid phase synthesis has become a routine technique in combinatorial chemistry. The need in analytical methods to characterize nondestructively resin bound molecules has been fulfilled by the introduction of High Resolution Magic Angle Spinning (HR MAS) NMR of solvent swollen beads. HR MAS NMR can give solution like proton NMR spectra and one- and two-dimensional NMR techniques are amenable, allowing detailed structure analysis. Recent developments are the application of a diffusion filter to suppress solvent signals and dipolar recoupling techniques to gain spatial information. HR MAS NMR has been applied to monitor reactions and elucidate reaction products.