Identification of protein interaction antagonists using the repressed transactivator two-hybrid system

Genetically Encoded Whole Cell Biosensor for Drug Discovery of HIF-1 Interaction Inhibitors

The heterodimeric transcription factor, hypoxia inducible factor-1 (HIF-1), is an important anticancer target as it supports the adaptation and response of tumors to hypoxia. Here, we optimized the repressed transactivator yeast two-hybrid system to further develop it as part of a versatile yeast-based drug discovery platform and validated it using HIF-1. We demonstrate both fluorescence-based and auxotrophy-based selections that could detect HIF-1α/HIF-1β dimerization inhibition. The engineered genetic selection is tunable and able to differentiate between strong and weak interactions, shows a large dynamic range, and is stable over different growth phases. Furthermore, we engineered mechanisms to control for cellular activity and off-target drug effects. We thoroughly characterized all parts of the biosensor system and argue this tool will be generally applicable to a wide array of protein-protein interaction targets. We anticipate this biosensor will be useful as part of a drug discovery platform, particularly when screening DNA-encoded new modality drugs.

A Multipronged Screening Approach Targeting Inhibition of ETV6 PNT Domain Polymerization

ETV6 is an ETS family transcriptional repressor for which head-to-tail polymerization of its PNT domain facilitates cooperative binding to DNA by its ETS domain. Chromosomal translocations frequently fuse the ETV6 PNT domain to one of several protein tyrosine kinases. The resulting chimeric oncoproteins undergo ligand-independent self-association, autophosphorylation, and aberrant stimulation of downstream signaling pathways, leading to a variety of cancers. Currently, no small-molecule inhibitors of ETV6 PNT domain polymerization are known and no assays targeting PNT domain polymerization have been described. In this study, we developed complementary experimental and computational approaches for identifying such inhibitory compounds. One mammalian cellular approach utilized a mutant PNT domain heterodimer system covalently attached to split Gaussia luciferase fragments. In this protein-fragment complementation assay, inhibition of PNT domain heterodimerization reduces luminescence. A yeast assay took advantage of activation of the reporter HIS3 gene upon heterodimerization of mutant PNT domains fused to DNA-binding and transactivation domains. In this two-hybrid screen, inhibition of PNT domain heterodimerization prevents cell growth in medium lacking histidine. The Bristol University Docking Engine (BUDE) was used to identify virtual ligands from the ZINC8 library predicted to bind the PNT domain polymerization interfaces. More than 75 hits from these three assays were tested by nuclear magnetic resonance spectroscopy for binding to the purified ETV6 PNT domain. Although none were found to bind, the lessons learned from this study may facilitate future approaches for developing therapeutics that act against ETV6 oncoproteins by disrupting PNT domain polymerization.

Yeast-based assays for detecting protein-protein/drug interactions and their inhibitors

Understanding cellular processes at molecular levels in health and disease requires the knowledge of protein-protein interactions (PPIs). In line with this, identification of PPIs at genome-wide scale is highly valuable to understand how different cellular pathways are interconnected, and it eventually facilitates designing effective drugs against certain PPIs. Furthermore, investigating PPIs at a small laboratory scale for deciphering certain biochemical pathways has been demanded for years. In this regard, yeast two hybrid system (Y2HS) has proven an extremely useful tool to discover novel PPIs, while Y2HS derivatives and novel yeast-based assays are contributing significantly to identification of protein-drug/inhibitor interaction at both large- and small-scale set-ups. These methods have been evolving over time to provide more accurate, reproducible and quantitative results. Here we briefly describe different yeast-based assays for identification of various protein-protein/drug/inhibitor interactions and their specific applications, advantages, shortcomings, and improvements. The broad range of yeast-based assays facilitates application of the most suitable method(s) for each specific need.

The power of the yeast two-hybrid system in the identification of novel drug targets: building and modulating PPP1 interactomes

Since the description of the yeast two-hybrid (Y2H) method, it has become more and more evident that it is the most commonly used method to identify protein-protein interactions (PPIs). The improvements in the original Y2H methodology in parallel with the idea that PPIs are promising drug targets, offer an excellent opportunity to apply the principles of this molecular biology technique to the pharmaceutical field. Additionally, the theoretical developments in the networks field make PPI networks very useful frameworks that facilitate many discoveries in biomedicine. This review highlights the relevance of Y2H in the determination of PPIs, specifically phosphoprotein phosphatase 1 interactions, and its possible outcomes in pharmaceutical research.

Multi-scale perturbations of protein interactomes reveal their mechanisms of regulation, robustness and insights into genotype-phenotype maps

Cellular architectures and signaling machineries are organized through protein-protein interactions (PPIs). High-throughput methods to study PPIs in yeast have opened a new perspective on the organization of the cell by allowing the study of whole protein interactomes. Recent investigations have moved from the description of this organization to the analysis of its dynamics by experimenting how protein interaction networks (PINs) are rewired in response to perturbations. Here we review studies that have used the budding yeast as an experimental system to explore these altered networks. Given the large space of possible PPIs and the diversity of potential genetic and environmental perturbations, high-throughput methods are an essential requirement to survey PIN perturbations on a large scale. Network perturbations are typically conceptualized as the removal of entire proteins (nodes), the modification of single PPIs (edges) or changes in growth conditions. These studies have revealed mechanisms of PPI regulation, PIN architectural organization, robustness and sensitivity to perturbations. Despite these major advances, there are still inherent limits to current technologies that lead to a trade-off between the number of perturbations and the number of PPIs that can be considered simultaneously. Nevertheless, as we exemplify here, targeted approaches combined with the existing resources remain extremely powerful to explore the inner organization of cells and their responses to perturbations.

Mutations in the ArsA ATPase that restore interaction with the ArsD metallochaperone

The ArsA ATPase is the catalytic subunit of the ArsAB As(III) efflux pump. It receives trivalent As(III) from the intracellular metallochaperone ArsD. The interaction of ArsA and ArsD allows for resistance to As(III) at environmental concentrations. A quadruple mutant in the arsD gene encoding a K2A/K37A/K62A/K104A ArsD is unable to interact with ArsA. An error-prone mutagenesis approach was used to generate random mutations in the arsA gene that restored interaction with the quadruple arsD mutant in yeast two-hybrid assays. A number of arsA genes with multiple mutations were isolated. These were analyzed in more detail by separation into single arsA mutants. Three such mutants encoding Q56R, F120I and D137V ArsA were able to restore interaction with the quadruple ArsD mutant in yeast two-hybrid assays. Each of the three single ArsA mutants also interacted with wild type ArsD. Only the Q56R ArsA derivative exhibited significant metalloid-stimulated ATPase activity in vitro. Purified Q56R ArsA was stimulated by wild type ArsD and to a lesser degree by the quadruple ArsD derivative. The F120I and D137V ArsAs did not show metalloid-stimulated ATPase activity. Structural models generated by in silico docking suggest that an electrostatic interface favors reversible interaction between ArsA and ArsD. We predict that mutations in ArsA propagate changes in hydrogen bonding and salt bridges to the ArsA-ArsD interface that affect their interactions.

Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system

The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.

Two isoforms of Flk-1 transcripts in early diabetic rat retinas

BACKGROUND

We studied the expression levels of genes encoding the two isoforms of fetal liver kinase-1 (Flk-1) and the effect of intravitreal injection of triamcinolone acetonide (IVTA) in diabetic rat retinas on the isoforms.

METHODS

The right eyes of both streptozotocin-induced diabetic and non-diabetic rats received triamcinolone treatment, while the left eyes were sham-treated, thereby providing four treatment groups. Three pairs of polymerase chain reaction (PCR) primers were designed to specifically amplify the total, long and truncated isoforms of rat Flk-1 mRNA. Gene transcriptional levels of the two isoforms were evaluated using quantitative PCR reaction (real time RT-PCR). To detect the gene activities, standard efficiency standard curves were set up for each of the candidate isoforms.

RESULTS

The transcripts level of the long form Flk-1 is about 4.3 times higher than the level of the short form in the sham-treated normal rat retinas. The expression of the total, long and short form of Flk-1 was up-regulated by 1.5, 1.8 and 0.7 fold, respectively in sham-treated diabetic retinas compared with the sham-treated non-diabetic retinas. IVTA inhibited the expression of the total, long and short forms of Flk-1 by 1.2, 2.0 and 0.3 fold, respectively in the IVTA-treated diabetic compared with sham-treated retinas. There was no statistically significant difference in the expression of the total and short form of Flk-1 in IVTA-treated diabetic/non-diabetic retinas compared with the sham-treated diabetic/non diabetic retinas.

CONCLUSION

The long form of Flk-1 is the predominant mediator of VEGF-A in the pathogenesis of diabetic retinopathy (DR) and can be significantly inhibited by the IVTA treatment. The short form, which cannot be phosphorylated, does not appear to contribute to the pathogenesis of DR. Further research is warranted to establish whether the truncated form of Flk-1 can be used clinically as a dominant negative inhibitor of the effects of Vascular Endothelial Growth Factor (VEGF).

A screen to identify small molecule inhibitors of protein-protein interactions in mycobacteria

Despite extensive efforts in tuberculosis (TB) drug research, very few novel inhibitors have been discovered. This issue emphasizes the need for innovative methods to discover new anti-TB drugs. In this study, we established a new high-throughput screen (HTS) platform technology that differs from traditional TB drug screens because it utilizes Mycobacterial-Protein Fragment Complementation (M-PFC) to identify small molecule inhibitors of protein-protein interactions in mycobacteria. Several examples of protein-protein interactions were tested with M-PFC to highlight the diversity of selectable drug targets that could be used for screening. These included interactions of essential regulators (IdeR dimerization), enzymatic complexes (LeuCD), secretory antigens (Cfp10-Esat6), and signaling pathways (DevR dimerization). The feasibility of M-PFC in a HTS platform setting was tested by performing a proof-of-concept quantitative HTS of 3,600 small molecule compounds on DevR-DevR interaction, which was chosen because of its strong implications in Mycobacterium tuberculosis persistence and the need for effective drugs against latent TB. The calculated Z'-factor was consistently ≥0.8, indicating a robust and reproducible assay. Completion of the proof-of-concept screen allowed for the identification of advantages and disadvantages in the current assay design, where improvements made will further pioneer M-PFC-based applications in a large-scale HTS format.

Genetic mapping of the interface between the ArsD metallochaperone and the ArsA ATPase

The ArsD metallochaperone delivers trivalent metalloids, As(III) or Sb(III), to the ArsA ATPase, the catalytic subunit of the ArsAB As(III) efflux pump. Transfer of As(III) increases the affinity of ArsA for As(III), allowing resistance to environmental arsenic concentrations. As(III) transfer is channelled from chaperone to ATPase, implying that ArsD and ArsA form an interface at their metal binding sites. A genetic approach was used to test this hypothesis. Thirteen ArsD mutants exhibiting either weaker or stronger interaction with ArsA were selected by either repressed transactivator yeast two-hybrid or reverse yeast two-hybrid assays. Additionally, Lys-37 and Lys-62 were identified as being involved in ArsD function by site-directed mutagenesis and chemical modification. Substitution at either position with arginine was tolerated, suggesting participation of a positive charge. By yeast two-hybrid analysis K37A and K62A mutants lost interaction with ArsA. All 15 mutations were mapped on the surface of the ArsD structure, and their locations are consistent with a structural model generated by in silico docking. Four are close to metalloid binding site residues Cys-12, Cys-13 and Cys-18, and seven are on the surface of helix 1. These results suggest that the interface involves one surface of helix 1 and the metalloid binding site.

Yeast two-hybrid, a powerful tool for systems biology

A key property of complex biological systems is the presence of interaction networks formed by its different components, primarily proteins. These are crucial for all levels of cellular function, including architecture, metabolism and signalling, as well as the availability of cellular energy. Very stable, but also rather transient and dynamic protein-protein interactions generate new system properties at the level of multiprotein complexes, cellular compartments or the entire cell. Thus, interactomics is expected to largely contribute to emerging fields like systems biology or systems bioenergetics. The more recent technological development of high-throughput methods for interactomics research will dramatically increase our knowledge of protein interaction networks. The two most frequently used methods are yeast two-hybrid (Y2H) screening, a well established genetic in vivo approach, and affinity purification of complexes followed by mass spectrometry analysis, an emerging biochemical in vitro technique. So far, a majority of published interactions have been detected using an Y2H screen. However, with the massive application of this method, also some limitations have become apparent. This review provides an overview on available yeast two-hybrid methods, in particular focusing on more recent approaches. These allow detection of protein interactions in their native environment, as e.g. in the cytosol or bound to a membrane, by using cytosolic signalling cascades or split protein constructs. Strengths and weaknesses of these genetic methods are discussed and some guidelines for verification of detected protein-protein interactions are provided.

Two-hybrid technologies in proteomics research

Given that protein-protein interactions (PPIs) regulate nearly every living process; the exploration of global and pathway-specific protein interaction networks is expected to have major implications in the understanding of diseases and for drug discovery. Consequently, the development and application of methodologies that address physical associations among proteins is of major importance in today's proteomics research. The most widely and successfully used methodology to assess PPIs is the yeast two-hybrid system (YTH). Here we present an overview on the current applications of YTH and variant technologies in yeast and mammalian systems. Two-hybrid-based methods will not only continue to have a dominant role in the assessment of protein interactomes but will also become important in the development of novel compounds that target protein interaction interfaces for therapeutic intervention.

The yeast two-hybrid system and its role in drug discovery

BACKGROUND

The yeast two-hybrid system is the most widely used genetic assay to identify and characterize novel protein interactions. Over the past decade, the system has been adapted to cover an increasingly wide range of applications, including various tasks within the drug discovery and development process.

OBJECTIVE

We highlight the role of different two-hybrid systems within the drug discovery process, including target identification and validation and the selection of affinity reagents for protein targets, such as peptides and small molecules.

METHODS

We have focused on applications where the two-hybrid system has been used to great advantage and have sought to put a special emphasis on less conventional but promising approaches, such as the identification of agents which block therapeutically relevant protein interactions.

CONCLUSIONS

The yeast two-hybrid system has evolved from a method mainly used in basic research to a collection of versatile screening systems with the potential to affect many different aspects of drug discovery today.

A yeast two-hybrid system reconstituting substrate recognition of the von Hippel-Lindau tumor suppressor protein

The von Hippel-Lindau tumor suppressor protein (pVHL) is inactivated in the hereditary cancer syndrome von Hippel-Lindau disease and in the majority of sporadic renal carcinomas. pVHL is the substrate-binding subunit of the CBC^VHL ubiquitin ligase complex that negatively regulates cell growth by promoting the degradation of hypoxia-inducible transcription factor subunits (HIF1/2α). Proteomics-based identification of novel pVHL substrates is hampered by their short half-life and low abundancy in mammalian cells. The usefulness of yeast two-hybrid (Y2H) approaches, on the other hand, has been limited by the failure of pVHL to adopt its native structure and by the absence of prolylhydroxylase activity critical for pVHL substrate recognition. Therefore, we modified the Y2H system to faithfully reconstitute the physical interaction between pVHL and its substrates. Our approach relies on the coexpression of pVHL with the cofactors Elongin B and Elongin C and with HIF1/2α prolylhydroxylases. In a proof-of-principle Y2H screen, we identified the known substrates HIF1/2α and new candidate substrates including diacylglycerol kinase iota, demonstrating that our strategy allows detection of stable interactions between pVHL and otherwise elusive cellular targets. Additional future applications may include structure/function analyses of pVHL-HIF1/2α binding and screens for therapeutically relevant compounds that either stabilize or disrupt this interaction.