Reverse MAPPIT: screening for protein-protein interaction modifiers in mammalian cells

Screening for molecular glues - Challenges and opportunities

Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.

Single-Chain Lanthanide Luminescence Biosensors for Cell-Based Imaging and Screening of Protein-Protein Interactions

Lanthanide-based, Förster resonance energy transfer (LRET) biosensors enabled sensitive, time-gated luminescence (TGL) imaging or multiwell plate analysis of protein-protein interactions (PPIs) in living cells. We prepared stable cell lines that expressed polypeptides composed of an alpha helical linker flanked by a Tb(III) complex-binding domain, GFP, and two interacting domains at each terminus. The PPIs examined included those between FKBP12 and the rapamycin-binding domain of m-Tor (FRB) and between p53 (1–92) and HDM2 (1–128). TGL microscopy revealed dramatic differences (>500%) in donor- or acceptor-denominated, Tb(III)-to-GFP LRET ratios between open (unbound) and closed (bound) states of the biosensors. We observed much larger signal changes (>2,500%) and Z′-factors of 0.5 or more when we grew cells in 96- or 384-well plates and analyzed PPI changes using a TGL plate reader. The modular design and exceptional dynamic range of lanthanide-based LRET biosensors will facilitate versatile imaging and cell-based screening of PPIs.

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Non-invasive, microscopic imaging or screening of protein-protein interactions

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Intracellular assembly of sensor polypeptides with luminescent Tb(III) complexes

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High dynamic range with time-gated detection of Tb(III)-to-GFP sensitized emission

The mammalian two-hybrid system as a powerful tool for high-throughput drug screening

Protein-protein interactions (PPIs) are the backbone of signaling pathways, responsible for the basis of cell communication and, when deregulated, several diseases. Consequently, identifying and modulating PPIs can unravel the pathophysiological mechanisms of diseases. The two-hybrid system, particularly the mammalian two-hybrid system (MTH), is an efficient technique to validate PPIs ex vivo. Combining MTH with high-throughput screening has a huge advantage in biomedical research. In this review, we describe methodologies developed from MTH and the role of these adaptations in PPI discovery. We also highlight the powerful contribution of MTH to the identification of disease-related PPIs and its use in the development of potential new drug screens.

Discovering cellular protein-protein interactions: Technological strategies and opportunities

The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.

Medicinal Chemistry Strategies to Disrupt the p53-MDM2/MDMX Interaction

The growth inhibitory activity of p53 tumor suppressor is tightly regulated by interaction with two negative regulatory proteins, murine double minute 2 (MDM2) and X (MDMX), which are overexpressed in about half of all human tumors. The elucidation of crystallographic structures of MDM2/MDMX complexes with p53 has been pivotal for the identification of several classes of inhibitors of the p53-MDM2/MDMX interaction. The present review provides in silico strategies and screening approaches used in drug discovery as well as an overview of the most relevant classes of small-molecule inhibitors of the p53-MDM2/MDMX interaction, their progress in pipeline, and highlights particularities of each class of inhibitors. Most of the progress made with high-throughput screening has led to the development of inhibitors belonging to the cis-imidazoline, piperidinone, and spiro-oxindole series. However, novel potent and selective classes of inhibitors of the p53-MDM2 interaction with promising antitumor activity are emerging. Even with the discovery of the 3D structure of complex p53-MDMX, only two small molecules were reported as selective p53-MDMX antagonists, WK298 and SJ-172550. Dual inhibition of the p53-MDM2/MDMX interaction has shown to be an alternative approach since it results in full activation of the p53-dependent pathway. The knowledge of structural requirements crucial to the development of small-molecule inhibitors of the p53-MDMs interactions has enabled the identification of novel antitumor agents with improved in vivo efficacy.

Trapping mammalian protein complexes in viral particles

Cell lysis is an inevitable step in classical mass spectrometry–based strategies to analyse protein complexes. Complementary lysis conditions, in situ cross-linking strategies and proximal labelling techniques are currently used to reduce lysis effects on the protein complex. We have developed Virotrap, a viral particle sorting approach that obviates the need for cell homogenization and preserves the protein complexes during purification. By fusing a bait protein to the HIV-1 GAG protein, we show that interaction partners become trapped within virus-like particles (VLPs) that bud from mammalian cells. Using an efficient VLP enrichment protocol, Virotrap allows the detection of known binary interactions and MS-based identification of novel protein partners as well. In addition, we show the identification of stimulus-dependent interactions and demonstrate trapping of protein partners for small molecules. Virotrap constitutes an elegant complementary approach to the arsenal of methods to study protein complexes.

A large portion of the proteome carries out its cellular function as part of macromolecular complexes. Here the authors describe Virotrap, a novel lysis-free approach for the isolation and identification of biologically relevant protein-protein and small molecule-protein interactions.

Fundamentals of protein interaction network mapping

Studying protein interaction networks of all proteins in an organism (“interactomes”) remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases. Over the past two decades, diverse biochemical, genetic, and cell biological methods have been developed to map interactomes. In this review, we highlight basic principles of interactome mapping. Specifically, we discuss the strengths and weaknesses of individual assays, how to select a method appropriate for the problem being studied, and provide general guidelines for carrying out the necessary follow‐up analyses. In addition, we discuss computational methods to predict, map, and visualize interactomes, and provide a summary of some of the most important interactome resources. We hope that this review serves as both a useful overview of the field and a guide to help more scientists actively employ these powerful approaches in their research.

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.

Kinase Substrate Sensor (KISS), a mammalian in situ protein interaction sensor

Probably every cellular process is governed by protein-protein interaction (PPIs), which are often highly dynamic in nature being modulated by in- or external stimuli. Here we present KISS, for KInase Substrate Sensor, a mammalian two-hybrid approach designed to map intracellular PPIs and some of the dynamic features they exhibit. Benchmarking experiments indicate that in terms of sensitivity and specificity KISS is on par with other binary protein interaction technologies while being complementary with regard to the subset of PPIs it is able to detect. We used KISS to evaluate interactions between different types of proteins, including transmembrane proteins, expressed at their native subcellular location. In situ analysis of endoplasmic reticulum stress-induced clustering of the endoplasmic reticulum stress sensor ERN1 and ligand-dependent β-arrestin recruitment to GPCRs illustrated the method's potential to study functional PPI modulation in complex cellular processes. Exploring its use as a tool for in cell evaluation of pharmacological interference with PPIs, we showed that reported effects of known GPCR antagonists and PPI inhibitors are properly recapitulated. In a three-hybrid setup, KISS was able to map interactions between small molecules and proteins. Taken together, we established KISS as a sensitive approach for in situ analysis of protein interactions and their modulation in a changing cellular context or in response to pharmacological challenges.

Using proteomics to identify the HBx interactome in hepatitis B virus: how can this inform the clinic?

Hepatitis B virus (HBV) is a small and enveloped DNA virus, of which chronic infection is the main risk factor of liver cirrhosis and hepatocellular carcinoma. Hepatitis B virus X protein (HBx) is a multifunctional protein encoded by HBV genome, which have significant effects on HBV replication and pathogenesis. Through directly interacting with cellular proteins, HBx is capable to promote HBV replication, regulate transcription of host genes, disrupt protein degradation, modulate signaling pathway, manipulate cell death and deregulate cell cycle. In this review, we briefly discuss the diversified effects of HBx-interactome and their potential clinical significances.

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.

The use of mammalian two-hybrid technologies for high-throughput drug screening

Developing agents that target protein-protein interactions (PPIs) is an emerging field in drug discovery. Although this target class has hitherto remained underexplored, it holds exceptional promise related to the large amount of potential PPI targets compared to single protein targets and it offers important opportunities to increase the specificity of therapeutic molecules. While several PPI modulating therapeutics have recently been reported and a number of these are in clinical trial, progress in the field has been hampered by the lack of efficient screening systems. Recently, a number of cellular approaches have been developed that complement classical in vitro screening methods and which exhibit a number of important assets related to the physiological context they provide. Here we discuss the utility of two-hybrid technologies towards high-throughput screening for PPI inhibitors, in particular those that operate in a mammalian cellular background. We review a number of cases where mammalian two-hybrids have been successfully applied to identify small molecule disruptors of PPIs and zoom in further on the MAPPIT (Mammalian Protein-Protein Interaction Trap) technology platform. The value of this approach for drug discovery is illustrated by recent data from MAPPIT-based screening projects.

LUCIFERASES FOR THE STUDY OF PROTEIN–PROTEIN INTERACTIONS IN LIVE CELLS AND ANIMALS

Many imaging technologies based on luminescent proteins have proven useful for detecting protein–protein interactions, tracking cells in mice, and monitoring transcriptional regulation of specific genes. Especially, novel bioluminescent proteins have advanced the study of induced protein interactions and protein modification in live cells and animals. This review focuses on recent developments of bioluminescent probes for quantitative evaluation of specific protein–protein interactions and their spatio-temporal imaging by means of split luciferase complementation techniques. From the comparison between fluorescent and bioluminescent proteins, advantages and drawbacks of the bioluminescence techniques are described.

Network approaches to the functional analysis of microbial proteins

Large amounts of detailed biological data have been generated over the past few decades. Much of these data is freely available in over 1000 online databases; an enticing, but frustrating resource for microbiologists interested in a systems-level view of the structure and function of microbial cells. The frustration engendered by the need to trawl manually through hundreds of databases in order to accumulate information about a gene, protein, pathway, or organism of interest can be alleviated by the use of computational data integration to generated network views of the system of interest. Biological networks can be constructed from a single type of data, such as protein-protein binding information, or from data generated by multiple experimental approaches. In an integrated network, nodes usually represent genes or gene products, while edges represent some form of interaction between the nodes. Edges between nodes may be weighted to represent the probability that the edge exists in vivo. Networks may also be enriched with ontological annotations, facilitating both visual browsing and computational analysis via web service interfaces. In this review, we describe the construction, analysis of both single-data source and integrated networks, and their application to the inference of protein function in microbes.

MAPPIT: a protein interaction toolbox built on insights in cytokine receptor signaling

MAPPIT (mammalian protein-protein interaction trap) is a two-hybrid interaction mapping technique based on functional complementation of a type I cytokine receptor signaling pathway. Over the last decade, the technology has been extended into a platform of complementary assays for the detection of interactions among proteins and between chemical compounds and proteins, and for the identification of small molecules that interfere with protein-protein interactions. Additionally, several screening approaches have been developed to broaden the utility of the platform. In this review we provide an overview of the different components of the MAPPIT toolbox and highlight a number of applications in interactomics, drug screening and compound target profiling.

A cell-based high-throughput assay for the screening of small-molecule inhibitors of p53-MDM2 interaction

The p53 tumor suppressor is a potent transcription factor that regulates cell growth inhibition and apoptosis. The oncoprotein MDM2 suppresses p53 activity by direct inhibition of its transcriptional activity and enhances the degradation of p53 via the ubiquitin-proteosome pathway. Overexpression of MDM2, found in many human tumors, impairs p53-mediated cell death effectively. Inhibition of the p53-MDM2 interaction can stabilize p53 and may offer a novel strategy for cancer therapy. To search for new inhibitors of the p53-MDM2 interaction, the authors developed a cell-based high-throughput assay system based on mammalian two-hybrid technology. They also used a dual-luciferase reporter system to rule out false- positive hits due to the cytotoxic effect of compounds. Using this assay, they screened a library consisting of 3840 compounds and identified one compound that activates p53 pathway and induces growth arrest in tumor cells.

Visualizing dynamic interaction between calmodulin and calmodulin-related kinases via a monitoring method in live mammalian cells

A new visualizing method was developed for monitoring protein-protein (P-P) interactions in live mammalian cells. P-P interactions are visualized by directing localization of a bait protein to endosomes. This method is sufficiently robust to analyze signal-dependent P-P interactions such as calcium-dependent protein interactions. We visualized interactions between activated calmodulin and calmodulin-binding proteins, and observed oscillatory interactions via time-lapse imaging. In addition, this new method can simultaneously monitor multiple P-P interactions in a single live cell, which allows comparison of interactions between several prey proteins and a single bait protein. We observed that CaMKK1 and CaMKIIalpha bind calmodulin with distinct binding affinities in live cell, which indicates that calcium signaling is fine-tuned by distinct activation patterns of CaM kinases. This method will enable investigation of cellular processes based on dynamic P-P interactions.

Mammalian two-hybrids come of age

A diverse series of mammalian two-hybrid technologies for the detection of protein-protein interactions have emerged in the past few years, complementing the established yeast two-hybrid approach. Given the mammalian background in which they operate, these assays open new avenues to study the dynamics of mammalian protein interaction networks, i.e. the temporal, spatial and functional modulation of protein-protein associations. In addition, novel assay formats are available that enable high-throughput mammalian two-hybrid applications, facilitating their use in large-scale interactome mapping projects. Finally, as they can be applied in drug discovery and development programs, these techniques also offer exciting new opportunities for biomedical research.

Array MAPPIT: high-throughput interactome analysis in mammalian cells

Physical interactions between proteins play a key role in probably every cellular process. Efforts to chart the protein interaction networks are ongoing in a number of model organisms using a diversity of approaches. The resulting genome-wide interaction maps will provide a scaffold for further detailed functional analysis. We developed MAPPIT, a mammalian two-hybrid approach that allows identification and analysis of mammalian protein-protein interactions in their native environment. Here, we introduce an efficient MAPPIT assay that permits high-throughput screening of arrayed collections of proteins and complements a previously published cDNA library screening approach. We validated both methods in screens for interaction partners of the Cullin-based E3 ubiquitin ligase subunits SKP1 and Elongin C. In addition to a number of known interactors, novel SKP1 and Elongin C binding proteins were identified. The array assay is an important addition to the MAPPIT suite of technologies that is expected to significantly increase its utility as a toolbox to screen for novel interactors of proteins or small molecules.

A network medicine approach to human disease

High-throughput interaction discovery initiatives are providing thousands of novel protein interactions which are unveiling many unexpected links between apparently unrelated biological processes. In particular, analyses of the first draft human interactomes highlight a strong association between protein network connectivity and disease. Indeed, recent exciting studies have exploited the information contained within protein networks to disclose some of the molecular mechanisms underlying complex pathological processes. These findings suggest that both protein-protein interactions and the networks themselves could emerge as a new class of targetable entities, boosting the quest for novel therapeutic strategies.

Prioritizing genes for pathway impact using network analysis

Prioritization, or ranking, of gene lists is becoming increasingly important for analyzing data generated from high-throughput assays like expression profiling and RNAi-based screening. This is especially the case when specific genes in a list need to be further validated using low-throughput experiments. In addition to gene set overlap enrichment methods, a complementary approach is to examine molecular interaction networks. These can provide putative functional insights based on gene connectivity, especially when many genes contain little or no annotation. For bench and computational biologists alike, using networks requires an informed selection of interaction data for network construction and strategies for managing network complexity. Moreover, graph theory and social network analysis methods can be used to isolate critical subnetworks and quantify network properties. Here, I discuss the basic components of networks, implications of their structure for functional interpretation, and common metrics used for prioritization. Although this is still an ongoing area of research, networks are providing new ways for gauging pathway impact in large-scale data sets.

MAPPIT (mammalian protein-protein interaction trap) analysis of early steps in toll-like receptor signalling

The mammalian protein-protein interaction trap (MAPPIT) is a two-hybrid technique founded on type I cytokine signal transduction. Thereby, bait and prey proteins are linked to signalling deficient cytokine receptor chimeras. Interaction of bait and prey and ligand stimulation restores functional JAK (Janus kinase)-STAT (signal transducers and activators of transcription) signalling, which ultimately leads to the transcription of a reporter or marker gene under the control of the STAT3-responsive rPAP1 promoter. In the subsequent protocol, we describe the use of MAPPIT to study early events in Toll-like receptor (TLR) signalling. We here demonstrate a "signalling interaction cascade" from TLR4 to IRAK-1.

Targeting and tinkering with interaction networks

Biological interaction networks have been in the scientific limelight for nearly a decade. Increasingly, the concept of network biology and its various applications are becoming more commonplace in the community. Recent years have seen networks move from pretty pictures with limited application to solid concepts that are increasingly used to understand the fundamentals of biology. They are no longer merely results of postgenome analysis projects, but are now the starting point of many of the most exciting new scientific developments. We discuss here recent progress in identifying and understanding interaction networks, new tools that use them in predictive ways in exciting areas of biology, and how they have become the focus of many efforts to study, design and tinker with biological systems, with applications in biomedicine, bioengineering, ecology and beyond.

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.

Interactive proteomics: what lies ahead?

Interactive proteomics addresses the physical associations among proteins and establishes global, disease-, and pathway-specific protein interaction networks. The inherent chemical and structural diversity of proteins, their different expression levels, and their distinct subcellular localizations pose unique challenges for the exploration of these networks, necessitating the use of a variety of innovative and ingenious approaches. Consequently, recent years have seen exciting developments in protein interaction mapping and the establishment of very large interaction networks, especially in model organisms. In the near future, attention will shift to the establishment of interaction networks in humans and their application in drug discovery and understanding of diseases. In this review, we present an impressive toolbox of different technologies that we expect to be crucial for interactive proteomics in the coming years.

Cheiradone: a vascular endothelial cell growth factor receptor antagonist

BACKGROUND

Angiogenesis, the growth of new blood vessels from the pre-existing vasculature is associated with physiological (for example wound healing) and pathological conditions (tumour development). Vascular endothelial growth factor (VEGF), fibroblast growth factor-2 (FGF-2) and epidermal growth factor (EGF) are the major angiogenic regulators. We have identified a natural product (cheiradone) isolated from a Euphorbia species which inhibited in vivo and in vitro VEGF- stimulated angiogenesis but had no effect on FGF-2 or EGF activity. Two primary cultures, bovine aortic and human dermal endothelial cells were used in in vitro (proliferation, wound healing, invasion in Matrigel and tube formation) and in vivo (the chick chorioallantoic membrane) models of angiogenesis in the presence of growth factors and cheiradone. In all cases, the concentration of cheiradone which caused 50% inhibition (IC50) was determined. The effect of cheiradone on the binding of growth factors to their receptors was also investigated.

RESULTS

Cheiradone inhibited all stages of VEGF-induced angiogenesis with IC50 values in the range 5.20-7.50 microM but did not inhibit FGF-2 or EGF-induced angiogenesis. It also inhibited VEGF binding to VEGF receptor-1 and 2 with IC50 values of 2.9 and 0.61 microM respectively.

CONCLUSION

Cheiradone inhibited VEGF-induced angiogenesis by binding to VEGF receptors -1 and -2 and may be a useful investigative tool to study the specific contribution of VEGF to angiogenesis and may have therapeutic potential.

The social network of a cell: recent advances in interactome mapping

Proteins very rarely act in isolation. Biomolecular interactions are central to all biological functions. In human, for example, interference with biomolecular networks often lead to disease. Protein-protein and protein-metabolite interactions have traditionally been studied one by one. Recently, significant progresses have been made in adapting suitable tools for the global analysis of biomolecular interactions. Here we review this suite of powerful technologies that enable an exponentially growing number of large-scale interaction datasets. These new technologies have already contributed to a more comprehensive cartography of several pathways relevant to human pathologies, offering a broader choice for therapeutic targets. Genome-wide scale analyses in model organisms reveal general organizational principles of eukaryotic proteomes. We also review the biochemical approaches that have been used in the past on a smaller scale for the quantification of the binding constant and the thermodynamics parameters governing biomolecular interaction. The adaptation of these technologies to the large-scale measurement of biomolecular interactions in (semi-)quantitative terms represents an important challenge.

Insulin receptor substrate 4 couples the leptin receptor to multiple signaling pathways

Leptin is an adipokine that regulates food intake and energy expenditure by activating its hypothalamic leptin receptor (LR). Members of the insulin receptor substrate (IRS) family serve as adaptor proteins in the signaling pathways of several cytokines and hormones and a role for IRS2 in central leptin physiology is well established. Using mammalian protein-protein interaction trap (MAPPIT), a cytokine receptor-based two-hybrid method, in the N38 hypothalamic cell line, we here demonstrate that also IRS4 interacts with the LR. This recruitment is leptin dependent and requires phosphorylation of the Y1077 motif of the LR. Domain mapping of IRS4 revealed the critical role of the pleckstrin homology domain for full interaction. In line with its function as an adaptor protein, IRS4 interacted with the regulatory p85 subunit of the phosphatidylinositol 3-kinase, phospholipase Cgamma, and the suppressor of cytokine signaling (SOCS) family members SOCS2, SOCS6, and SOCS7 and thus can modulate LR signaling.

Neuroproteomics in stem cell differentiation

The term "proteome" is used to describe the entire complement of proteins in a given organism or in a system at a given time. Proteome analysis in neuroscience, also called "neuroproteomics" or "neuromics" is in its initial stage, and shows a deficit of studies in the context of brain development. It is the main objective of this review to illustrate the potential of neuroproteomics as a tool to unravel the differentiation of neural stem or progenitor cells to terminally differentiated neurons. Experimental results regarding the rat striatal progenitor model cell line ST14A are presented to illustrate the large rearrangements of the proteome during the differentiation process of neural progenitor cells and their modification by neurotrophic factors like the glial cell line-derived neurotrophic factor (GDNF). Thereby native stem cells and cells transfected with GDNF gene were investigated at the proliferative state and at seven time points up to 72 h after induction of differentiation. In addition, the immortalized human fetal midbrain stem cell line ReNcell VM was analyzed in order to detect stem cell differentiation associated changes of the protein profile. This review gives also an outlook on technical improvements and perspectives of application of neural stem cell proteomics.

Reverse MAPPIT detects disruptors of protein-protein interactions in human cells

Reverse mammalian protein-protein interaction trap (MAPPIT) is a mammalian reverse two-hybrid technology. The method is adapted from the forward MAPPIT technique, a two-hybrid complementation system in which the interaction between a bait-fusion protein and a prey-fusion protein restores ligand-dependent cytokine receptor signaling. In the reverse mode described in detail here, a positive readout is generated on disruption of the designated protein-protein interactions. Reverse MAPPIT functions in intact human cells, facilitating simultaneous analysis of disruption, toxicity and permeability of the tested compounds, making it particularly suitable for screening for molecules that target therapeutically interesting protein-protein interactions or for mapping the interaction interface between proteins. The total handling time of a typical reverse MAPPIT experiment is approximately 9 h and is spread over 4-5 d.

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

The repressed transactivator (RTA) yeast two-hybrid system was developed to enable genetic identification of interactions with transcriptional activator proteins. We have devised modifications of this system that enable its use in screening for inhibitors of protein interactions from small molecule compound libraries. We show that inhibition of protein interactions can be measured by monitoring growth in selective medium containing 3-aminotriazole (3-AT) and using this assay have identified inhibitors of four independent protein interactions in screens with a 23,000 small molecule compound library. Compounds found to inhibit one of the tested interactions between FKBP12 and the transforming growth factor β receptor (TGFβ-R) were validated in vivo and found to inhibit calcineurin-dependent signaling in T cells. One of these compounds was also found to cause elevated basal expression of a TGFβ-R/SMAD-dependent reporter gene. These results demonstrate the capability of the RTA small molecule screening assay for discovery of potentially novel therapeutic compounds.

Additional scalarane sesterterpenes from the sponge Phyllospongia papyracea

A chemical investigation of the marine sponge Phyllospongia papyracea, collected in Papua New Guinea, initiated by the screening result of a beta-catenin/Tcf4 disruption assay afforded six new bishomoscalarane sesterterpenes containing two rare scalaranes with a cyclobutane ring in the molecule, together with one known scalarane sesterterpene. The structures of the new compounds were elucidated by 1D and 2D spectroscopic techniques. The compounds isolated in this study did not show activity against the beta-catenin and Tcf4 complex.

MASPIT: three-hybrid trap for quantitative proteome fingerprinting of small molecule-protein interactions in mammalian cells

Organic small molecules generally act by perturbing the function of one or more cellular target proteins, the identification of which is essential to an understanding of the molecular basis of drug action. Here we describe the application of methotrexate-linked small molecule ligands to a mammalian three-hybrid interaction trap for proteome-wide identification of small molecule targets, quantification of the targeting potency of unmodified small molecules for such targets in intact cells, and screening for inhibitors of small molecule-protein interactions. During the course of this study we also identified the pyrido[2,3-d]pyrimidine PD173955, a known SRC kinase inhibitor, as a potent inhibitor of several ephrin receptor tyrosine kinases. This finding could perhaps be exploited in the design of inhibitors for this kinase subfamily, members of which have been implicated in the pathogenesis of various diseases, including cancer.

A complex interaction pattern of CIS and SOCS2 with the leptin receptor

Hypothalamic leptin receptor signalling plays a central role in weight regulation by controlling fat storage and energy expenditure. In addition, leptin also has direct effects on peripheral cell types involved in regulation of diverse body functions including immune response, bone formation and reproduction. Previous studies have demonstrated the important role of SOCS3 (suppressor of cytokine signalling 3) in leptin physiology. Here, we show that CIS (cytokine-inducible SH2 protein) and SOCS2 can also interact with the leptin receptor. Using MAPPIT (mammalian protein-protein interaction trap), a cytokine receptor-based two-hybrid method operating in intact cells, we show specific binding of CIS with the conserved Y985 and Y1077 motifs in the cytosolic domain of the leptin receptor. SOCS2 only interacts with the Y1077 motif, but with higher binding affinity and can interfere with CIS and STAT5a prey recruitment at this site. Furthermore, although SOCS2 does not associate with Y985 of the leptin receptor, we find that SOCS2 can block interaction of CIS with this position. This unexpected interference can be explained by the direct binding of SOCS2 on the CIS SOCS box, whereby elongin B/C recruitment is crucial to suppress CIS activity.

Techniques: new pharmacological perspectives for the leptin receptor

The function of leptin, initially confined to its role in energy homeostasis and obesity, has now expanded to the regulation of reproduction, glucose homeostasis, bone formation, wound healing and the immune system. Both stimulation and inhibition of the molecular target of leptin, the leptin receptor (LR), might find applications in disease treatment. Recent advances in the understanding of LR activation mechanisms have led to the design of LR antagonists. Several assays have been developed for the screening and evaluation of LR ligands. Both the extracellular and the intracellular domains of the LR are potential drug targets. The bioluminescence resonance energy transfer technique can be used to screen for compounds that target the extracellular part of the LR, and we propose that the novel reverse mammalian protein-protein interaction trap technique can be used to screen compounds that affect intracellular aspects of LR signalling. These assays can be easily adapted to other pharmacologically relevant receptors.

Two-hybrid and its recent adaptations

Interactions between proteins play a pivotal role in virtually all cellular processes, and many of these interactions represent interesting targets for drug development. Among the wide array of interactor-hunting technologies that has emerged, genetic two-hybrid methods account for a large amount of the currently available interaction data and is being successfully applied in interactome-scale mapping projects. Reverse two-hybrid approaches have been developed that allow selected interactions to be assayed for disrupting compounds.: