Chemical genetics small-molecule probes

By analogy to the framework for classical genetics developed by Morgan and colleagues, the development of an experimentally driven, computational framework for chemical genetics, which allows the mapping of the functional units (chemicals) that can induce variation in biological systems, holds the potential to revolutionize the discovery of small-molecule probes for basic... 

The Chemical Genetic Approach The Interrogation of Biological Mechanisms with Small Molecule Probes... 

The chapter is not an exhaustive review of chemical genetics the field, and its impact on our understanding of fundamental biological mechanisms, has already been comprehensively reviewed elsewhere. Rather, the chapter will emphasise the approaches that may be used to diseover small molecule probes, the solutions that address the challenges raised by chemical genetics, and the insights into fundamental biological mechanisms that may be revealed. 

Figure 1.1 Schematic overview of forward and reverse chemical genetics. In forward chemical genetics (left panel), a small molecule probe is discovered on the basis of its phenotypic effect the small molecule probe may then be subsequently used to identify the protein responsible for the phenotypic effect. In contrast, in reverse chemical genetics (right panel), a small molecule probe is discovered on the basis of its ability to modulate a specific protein the small molecule probe may then be used to modulate the cellular function of that specific protein, and the phenotypic effects that result.

Discovery of Small Molecule Probes Using a Reverse Chemical Genetic Approach... 

A major challenge associated with the forward chemical genetic approach is the identification of the target of the small molecule probe.Affinity chromatography is a common approach to target identification. This approach requires the attachment of the small molecule probe to a solid support the site of the attachment of the linker must be chosen carefully to avoid the ablation of the probe s biological activity. Trapoxin, is a cyclic tetrapeptide whose... 

In this chapter, we describe a protocol for the systematic perturbation of patient-derived cell lines using small-molecule probes, which is both scalable to high-throughput workflow and generalizable to a variety of assays. In the protocol presented here, multiple patient-derived lymphoblastoid cell lines either mutant or wild type at a defined genetic locus (e.g., HNF4a) are perturbed by an annotated chemical library. After sufficient incubation, cells are subjected to a phenotypic assay, in this case a luminescence-based readout of cellular ATP content, that aims to quantify the effect of compounds on oxidative phosphorylation, viability, or other relevant traits. The effect of each compound is expressed as a metric that reflects the difference in compound-induced phenotypes between mutant and wild-type cells. These ratios are then... 

Examples of small molecules, altered cell culture conditions, proteins, and genetic constructs used to probe RME. CID chemical inducer of dimerization. 

Fig. 6-3 Forward versus reverse chemical molecules that can be used to probe the genetics. While forward chemical genetics function of the selected protein. Both relies on a phenotype of interest to guide the approaches require the use of small selection of biologically active small molecules and phenotypic assays but differ...

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