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Wang P, Klassmüller T, Karg CA, Kretschmer M, Zahler S, Braig S, Bracher F, Vollmar AM, Moser S. Using the yeast three-hybrid system for the identification of small molecule-protein interactions with the example of ethinylestradiol. Biol Chem 2022; 403:421-431. [PMID: 35224953 DOI: 10.1515/hsz-2021-0355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/10/2022] [Indexed: 12/26/2022]
Abstract
Since the first report on a yeast three-hybrid system, several approaches have successfully utilized different setups for discovering targets of small molecule drugs. Compared to broadly applied MS based target identification approaches, the yeast three-hybrid system represents a complementary method that allows for the straightforward identification of direct protein binders of selected small molecules. One major drawback of this system, however, is that the drug has to be taken up by the yeast cells in sufficient concentrations. Here, we report the establishment of a yeast three-hybrid screen in the deletion strain ABC9Δ, which is characterized by being highly permeable to small molecules. We used this system to screen for protein binding partners of ethinylestradiol, a widely used drug mainly for contraception and hormone replacement therapy. We identified procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 (PLOD2 or lysyl hydroxylase, LH2) as a novel direct target and were able to confirm the interaction identified with the yeast three-hybrid system by a complementary method, affinity chromatography, to prove the validity of the hit. Furthermore, we provide evidence for an interaction between the drug and PLOD2 in vitro and in cellulo.
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Affiliation(s)
- Pengyu Wang
- Pharmaceutical Biology, Department of Pharmacy, Ludwig Maximilians University of Munich, Butenandtstr. 5-13, Building B, D-81377 Munich, Germany
| | - Thomas Klassmüller
- Pharmaceutical Chemistry, Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Building C, D-81377 Munich, Germany
| | - Cornelia A Karg
- Pharmaceutical Biology, Department of Pharmacy, Ludwig Maximilians University of Munich, Butenandtstr. 5-13, Building B, D-81377 Munich, Germany
| | - Maibritt Kretschmer
- Pharmaceutical Biology, Department of Pharmacy, Ludwig Maximilians University of Munich, Butenandtstr. 5-13, Building B, D-81377 Munich, Germany
| | - Stefan Zahler
- Pharmaceutical Biology, Department of Pharmacy, Ludwig Maximilians University of Munich, Butenandtstr. 5-13, Building B, D-81377 Munich, Germany
| | - Simone Braig
- Pharmaceutical Biology, Department of Pharmacy, Ludwig Maximilians University of Munich, Butenandtstr. 5-13, Building B, D-81377 Munich, Germany
| | - Franz Bracher
- Pharmaceutical Chemistry, Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Building C, D-81377 Munich, Germany
| | - Angelika M Vollmar
- Pharmaceutical Biology, Department of Pharmacy, Ludwig Maximilians University of Munich, Butenandtstr. 5-13, Building B, D-81377 Munich, Germany
| | - Simone Moser
- Pharmaceutical Biology, Department of Pharmacy, Ludwig Maximilians University of Munich, Butenandtstr. 5-13, Building B, D-81377 Munich, Germany
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De Clercq DJH, Tavernier J, Lievens S, Van Calenbergh S. Chemical Dimerizers in Three-Hybrid Systems for Small Molecule-Target Protein Profiling. ACS Chem Biol 2016; 11:2075-90. [PMID: 27267544 DOI: 10.1021/acschembio.5b00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The identification of the molecular targets and mechanisms underpinning the beneficial or detrimental effects of small-molecule leads and drugs constitutes a crucial aspect of current drug discovery. Over the last two decades, three-hybrid (3H) systems have progressively taken an important position in the armamentarium of small molecule-target protein profiling technologies. Yet, a prerequisite for successful 3H analysis is the availability of appropriate chemical inducers of dimerization. Herein, we present a comprehensive and critical overview of the chemical dimerizers specifically applied in both yeast and mammalian three-hybrid systems for small molecule-target protein profiling within the broader scope of target deconvolution and drug discovery. Furthermore, examples and alternative suggestions for typical components of chemical dimerizers for 3H systems are discussed. As illustrated, more tools have become available that increase the sensitivity and efficiency of 3H-based screening platforms. Hence, it is anticipated that the great potential of 3H systems will further materialize in important contributions to drug discovery.
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Affiliation(s)
- Dries J. H. De Clercq
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sam Lievens
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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Abstract
Phenotypic drug discovery (PDD) strategies are defined by screening and selection of hit or lead compounds based on quantifiable phenotypic endpoints without prior knowledge of the drug target. We outline the challenges associated with traditional phenotypic screening strategies and propose solutions and new opportunities to be gained by adopting modern PDD technologies. We highlight both historical and recent examples of approved drugs and new drug candidates discovered by modern phenotypic screening. Finally, we offer a prospective view of a new era of PDD underpinned by a wealth of technology advances in the areas of in vitro model development, high-content imaging and image informatics, mechanism-of-action profiling and target deconvolution.
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Suter B, Zhang X, Pesce CG, Mendelsohn AR, Dinesh-Kumar SP, Mao JH. Next-Generation Sequencing for Binary Protein-Protein Interactions. Front Genet 2015; 6:346. [PMID: 26734059 PMCID: PMC4681833 DOI: 10.3389/fgene.2015.00346] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 11/26/2015] [Indexed: 12/21/2022] Open
Abstract
The yeast two-hybrid (Y2H) system exploits host cell genetics in order to display binary protein-protein interactions (PPIs) via defined and selectable phenotypes. Numerous improvements have been made to this method, adapting the screening principle for diverse applications, including drug discovery and the scale-up for proteome wide interaction screens in human and other organisms. Here we discuss a systematic workflow and analysis scheme for screening data generated by Y2H and related assays that includes high-throughput selection procedures, readout of comprehensive results via next-generation sequencing (NGS), and the interpretation of interaction data via quantitative statistics. The novel assays and tools will serve the broader scientific community to harness the power of NGS technology to address PPI networks in health and disease. We discuss examples of how this next-generation platform can be applied to address specific questions in diverse fields of biology and medicine.
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Affiliation(s)
| | | | | | - Andrew R Mendelsohn
- Next Interactions, Inc., RichmondCA, USA; Regenerative Sciences Institute, SunnyvaleCA, USA
| | | | - Jian-Hua Mao
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA
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Bidlingmaier S, Liu B. Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions. Methods Mol Biol 2015; 1319:203-14. [PMID: 26060077 PMCID: PMC4838597 DOI: 10.1007/978-1-4939-2748-7_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The identification of proteins that interact with small bioactive molecules is a critical but often difficult and time-consuming step in understanding cellular signaling pathways or molecular mechanisms of drug action. Numerous methods for identifying small molecule-interacting proteins have been developed and utilized, including affinity-based purification followed by mass spectrometry analysis, protein microarrays, phage display, and three-hybrid approaches. Although all these methods have been used successfully, there remains a need for additional techniques for analyzing small molecule-protein interactions. A promising method for identifying small molecule-protein interactions is affinity-based selection of yeast surface-displayed human proteome libraries. Large and diverse libraries displaying human protein fragments on the surface of yeast cells have been constructed and subjected to FACS-based enrichment followed by comprehensive exon microarray-based output analysis to identify protein fragments with affinity for small molecule ligands. In a recent example, a proteome-wide search has been successfully carried out to identify cellular proteins binding to the signaling lipids PtdIns(4,5)P2 and PtdIns(3,4,5)P3. Known phosphatidylinositide-binding proteins such as pleckstrin homology domains were identified, as well as many novel interactions. Intriguingly, many novel nuclear phosphatidylinositide-binding proteins were discovered. Although the existence of an independent pool of nuclear phosphatidylinositides has been known about for some time, their functions and mechanism of action remain obscure. Thus, the identification and subsequent study of nuclear phosphatidylinositide-binding proteins is expected to bring new insights to this important biological question. Based on the success with phosphatidylinositides, it is expected that the screening of yeast surface-displayed human proteome libraries will be of general use for the discovery of novel small molecule-protein interactions, thus facilitating the study of cellular signaling pathways and mechanisms of drug action or toxicity.
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Affiliation(s)
- Scott Bidlingmaier
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1001 Potrero Avenue, Box 1305, San Francisco, CA, 94110, USA
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Corrêa IR. Live-cell reporters for fluorescence imaging. Curr Opin Chem Biol 2014; 20:36-45. [PMID: 24835389 DOI: 10.1016/j.cbpa.2014.04.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 01/14/2023]
Abstract
Advances in the development of new fluorescent reporters and imaging techniques have revolutionized our ability to directly visualize biological processes in living systems. Real-time analysis of protein localization, dynamics, and interactions has been made possible by site-specific protein labeling with custom designed probes. This review outlines some of the most recent advances in the design and application of live-cell imaging probes, with a particular focus on SNAP-tag technology. Specific examples illustrating applications in superresolution and single-molecule imaging, protein trafficking and recycling, and protein-protein interactions are presented.
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Affiliation(s)
- Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
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