Small Molecule-Protein Interaction yeast

Baker K, Sengupta D, Salazar-Jimenez G, Cornish VW. An optimized dexamethasone-methotrexate yeast 3-hybrid system for high-throughput screening of small molecule-protein interactions. 

The yeast three-hybrid (Y3H) system is a cellular assay system designed for the identification and characterization of small molecule-protein interactions in intact cells [25]. It uses yeast Saccharomyces cerevisiae as a host system and combines aspects of the yeast two-hybrid (Y2H) system [26] with recent developments in chemical dimerizer technology [27, 28],... 

A yeast two-hybrid screening system was developed to screen for small molecules that inhibit the interaction of the Ras and the Raf proteins. Hyperpermeable yeast strains useful for high-throughput screening (HTS) for the two-hybrid system were created. Differential inhibition of the Ras-Raf vs the hsRPB4-hsRPB7 interaction allowed the identification of selective inhibitors. 

Fig. 7.1. Different yeast n-hybrid systems that have been developed to study protein-protein, protein-DNA, protein-RNA, and protein - small molecule interactions. A. In the original version of the Y2H system, transcriptional activation of the reporter gene is reconstituted by recruitment of the activation domain (AD) to the promoter region through direct interaction of protein X and Y, since protein X is fused to a DNA-binding domain (DBD) and protein Y is fused to the AD [1], B. In the Y1 H assay, the AD is fused directly to the DBD [109]. This assay can be used to screen either DBDs that can bind to a specific DNA sequence or the in vivo binding site for a given DBD. C.

As with other in vivo selections, it is critical to validate hits at the end of the selection experiment with a secondary screen. The most common secondary screen used with the Y2H assay is a lacZ screen. If either the DBD or AD fusion is under control of an inducible promoter, this screen can be carried out both under inducing and non-inducing conditions to ensure that transcription activation is protein dependent. Y3H systems, where transcription activation depends on a bridging RNA or small molecule, and reverse Y2H systems, where a third protein is disrupting the interaction, provide a built-in control. One can simply check that transcription activation is in fact dependent on the third component. As with any in vivo selection, the evolved plasmid should be isolated and retransformed into a fresh yeast selection strain to ensure that the phenotype is plasmid-dependent. Ultimately, the interaction will be confirmed with co-immunoprecipitation experiments or other in vitro binding assays [39]. 

In many cases, small molecules are found for a TF of interest through assays developed with known protein partners. Structures of the interacting protein domains also have been invaluable for drug discovery. For several important TFs, however, the specific cellular partners with which they interact are unknown. In this case, using small molecule screens on solid supports is an extremely useful tool for dmg discovery. In one such screen, diversity-oriented synthesis (DOS (129) was used to identify a small molecule binder of Hap3p, a yeast protein... 

Figure 1 The classic yeast two-hybrid method and derivatives, (a) Schematic diagram of the yeast two-hybrid approach, describing an interaction between protein X and protein Y. Protein X is fused to a transcription factor DNA-binding domain (the "bait" construct), and protein Y is fused to a transcription factor activation domain (the "prey" construct), (b) High-throughput applications of the yeast two-hybrid method use mating of haploid strains carrying bait and prey, respectively. Hybrids can be mated in arrayed formats (as shown) or as libraries, (c) The reverse two-hybrid method uses a counter-selectable marker to indicate loss of protein interaction because of disruption by an inhibitor protein/small molecule ("/" illustrated in the diagram) or mutation(s) in proteins X and/or Y.

Henthorn DC, Jaxa-Chamiec AA, Meldmm E. A GAL4-based yeast three-hybrid system for the identification of small molecule-target protein interactions. Biochem. Pharmacol. 2002 63 1619-1628. 

Just as a dimeric RNA molecule can be introduced to mediate the interaction between the DNA-binding and ADs, so can a dimeric small molecule [17]. In fact, well before their use in a small molecule three-hybrid assay, dimeric small molecules were used as chemical inducers of dimerization (CIDs) to artificially oligomerize fusion proteins in vivo [18]. In the yeast three-hybrid system, the union of two protein fusions and a CID reconstitute the transcription of a reporter gene (Fig. 4.1-3(d)). In 1996, Licitra and Liu built what they called a yeast three-hybrid assay [19]. This assay consists of two fusion proteins and a heterodimeric small molecule CID that brings these fusion proteins together to activate the transcription of a reporter gene (Fig. 4.1-3 d)). 

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