Compound Screening Facility
| Chemical genetics |
 The past two decades, classical genetics has been widely used to unravel complex biological processes in cells or whole organisms. Recently, chemical genetic studies have emerged because of the availability of large commercial compound collections.The major difference between classical and chemical genetics is the manner in which a biological process is dissected. In classical genetics, mutations are introduced at the DNA or RNA level to disturb a biological process of interest. On the other hand, chemical genetics uses small organic molecules (compounds) that exert their effect directly at the protein level.
Chemical Genetics In General A chemical genetic screen involves three important tools. First, a chemical library with 10,000 or more compounds is required. The second tool is a robust biological assay that is down-scalable to a 96-well plate format to study a biological process in a model system. Possible model systems include cell-free or cellular systems or even small model organisms such as Danio rerio embryos, Xenopus laevis embryos and Arabidopsis thaliana. And finally, to study the effect of the compounds on the model system, there is need for a screening platform.
The experimental set-up of a chemical genetic screen is very similar to a classical genetic screen. In accordance with classical genetics, we can distinguish between two chemical genetic approaches. The phenotype-based approach is analogous to forward genetics and comprises three different steps. The first step is the assembly of a set of mutation equivalents, i.e. a chemical library with 10,000 or more compounds capable of altering protein function. Subsequently, a high-throughput screen is performed to identify compounds that affect a biological process of interest. As a final step, the protein targets of these compounds are identified. Target-based chemical genetics is comparable to reverse genetics and entails over-expressing a protein of interest, screening for compounds that interact with the protein and finally using this compound to determine the phenotypic consequences of altering the function of this protein in a cellular context.
Although similar in study design, chemical genetics has several major advantages over the classical genetic approach:
People working on this project in the Root Development Group: Tom Beeckman ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ); Bert De Rybel ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ); Dominique Audenaert ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it , CSF); Long (Le Son) Nguyen ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it , CSF) During the last years, the Department of Plant Systems Biology (UGent) has built up a significant experience in chemical genetic screening technology. This has been translated into a novel VIB service facility: the Compound Screening Facility or CSF. VIB Compound Screening Facility, UGent
A full compound screening project includes the development of a screening assay, analysis of the effect of a large number of compounds and identification of compounds that induce the desired effect. The VIB Compound Screening Facility (VIB-CSF) has built up expertise in assay development and compound screenings and has acquired several high quality chemical libraries for primary screening purposes. In addition, the required robotic systems and equipment are available at the VIB-CSF to allow compound screenings to be performed in a high-throughput fashion.
Platform at the VIB Compound Screening Facility Compound collection The compound screening collection of the VIB-CSF amounts to a total of 42,000 compounds. The collection comprises three different chemical libraries acquired through ChemBridge Corporation (http://chembridge.com/chembridge/); DIVERSet™ (22,000 compounds), CNS-Set™ (10,000 compounds) and NOVACore (10,000 compounds). For selection of the DIVERSet™ compounds, a range of filtering methods are applied to ensure maximal diversity with a minimal number of compound, and to remove unstable, toxic and non-drug-like compounds. The DIVERSet™ library can be used in initial screening programs that require high diversity and qualitative lead-like compounds. For the CNS-Set™ library, additional computational methods are applied to select compounds with increased probability of oral bioavailability and blood-brain-barrier penetration. NOVACore is a diverse and drug-like library comprising compounds that are synthesized via combinatorial chemistry. The main focus of NOVACore is ‘novelty’; all compounds are recently synthesized by ChemBridge and contain mainly proprietary ChemBridge building blocks. All NOVACore compounds have a low molecular weight, which allows more margin for further lead optimization. The three available chemical libraries can be used as primary screening tools for a wide range of biological assays. After hit identification, similar compounds for additional testing can be selected from ChemBridge’s main stock collection of more than 500,000 compounds. Compound storage To maintain compound integrity, the VIB-CSF uses 4titude’s (www.4ti.co.uk) PlateStable™ conditioned storage system. All library compounds are stored in a 100% nitrogen atmosphere to minimize water uptake and the damaging effects of atmospheric oxygen. This significantly reduces the well-known problems with DMSO-dissolved compounds such as degradation, dilution and precipitation. By using the PlateStable™ system, the high quality of the screening libraries is preserved during longer periods of time. High-throughput screening equipment The VIB-CSF has established a state-of-the-art high-throughput platform for screening chemical compound libraries. The platform consists of robotic systems that make it possible to prepare assay plates and to add compounds to the assay system in a high-throughput fashion. The exerted effects of the compounds can be analyzed by using different equipment for visual (microscopy-based) or digital (plate reader-based) read-out. These include light and fluorescence stereomicroscopes, a confocal microscope and plate readers for luminescence and fluorescence measurements.
Core Services The VIB-CSF has the expertise and equipment to perform a full screening project. This includes:
Additional Services At the starting stage of a project, the VIB-CSF can advice on and assist in assay development, i.e. optimizing, validating and downscaling the assay to 96-well or 384-well plate format. After hit compound identification, services for further compound characterization can be provided, i.e. determining the EC50 values, identifying the active substructures of a compound through analysis of structural analogues and initial lead optimization of identified hit compounds. In addition, the VIB-CSF can perform detailed bimolecular interaction analysis by using Biacore technology to study the interaction between a compound and its target protein. Ultimately, the deliverable of the VIB-CSF is a set of chemical compounds in dry format or dissolved in DMSO, which target the biological process under study. The VIB-CSF is operated by technical personnel specialized in the necessary technologies. For prices and project information, please contact Dominique Audenaert, the VIB-CSF manager. Information about the CSF Contact dr. Dominique Audenaert:
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CSF Publications:
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