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Takakusagi Y, Takakusagi K, Sakaguchi K, Sugawara F. Phage display technology for target determination of small-molecule therapeutics: an update. Expert Opin Drug Discov 2020; 15:1199-1211. [DOI: 10.1080/17460441.2020.1790523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yoichi Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
- Institute of Quantum Life Science (iQLS), National Institutes of Quantum and Radiological Science and Technology (QST), Chiba, Japan
| | - Kaori Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
- Institute of Quantum Life Science (iQLS), National Institutes of Quantum and Radiological Science and Technology (QST), Chiba, Japan
| | - Kengo Sakaguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Fumio Sugawara
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
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Rozhon W, Akter S, Fernandez A, Poppenberger B. Inhibitors of Brassinosteroid Biosynthesis and Signal Transduction. Molecules 2019; 24:E4372. [PMID: 31795392 PMCID: PMC6930552 DOI: 10.3390/molecules24234372] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022] Open
Abstract
Chemical inhibitors are invaluable tools for investigating protein function in reverse genetic approaches. Their application bears many advantages over mutant generation and characterization. Inhibitors can overcome functional redundancy, their application is not limited to species for which tools of molecular genetics are available and they can be applied to specific tissues or developmental stages, making them highly convenient for addressing biological questions. The use of inhibitors has helped to elucidate hormone biosynthesis and signaling pathways and here we review compounds that were developed for the plant hormones brassinosteroids (BRs). BRs are steroids that have strong growth-promoting capacities, are crucial for all stages of plant development and participate in adaptive growth processes and stress response reactions. In the last two decades, impressive progress has been made in BR inhibitor development and application, which has been instrumental for studying BR modes of activity and identifying and characterizing key players. Both, inhibitors that target biosynthesis, such as brassinazole, and inhibitors that target signaling, such as bikinin, exist and in a comprehensive overview we summarize knowledge and methodology that enabled their design and key findings of their use. In addition, the potential of BR inhibitors for commercial application in plant production is discussed.
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Affiliation(s)
- Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Straße 1, 85354 Freising, Germany
| | | | | | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Straße 1, 85354 Freising, Germany
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Butnariu M, Butu A. Plant Nanobionics: Application of Nanobiosensors in Plant Biology. PLANT NANOBIONICS 2019. [PMCID: PMC7123577 DOI: 10.1007/978-3-030-16379-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nanobiosensors (NBSs) are a class of chemical sensors which are sensitive to a physical or chemical stimulus (heat, acidity, metabolism transformations) that conveys information about vital processes. NBSs detect physiological signals and convert them into standardized signals, often electrical, to be quantified from analog to digital. NBSs are classified according to the transducer element (electrochemical, piezoelectric, optical, and thermal) in accordance with biorecognition principle (enzyme recognition, affinity immunoassay, whole sensors, DNA). NBSs have varied forms, depending on the degree of interpretation of natural processes in plants. Plant nanobionics uses mathematical models based on qualitative and less quantitative records. NBSs can give information about endogenous concentrations or endogenous fluxes of signaling molecules (phytohormones). The properties of NBSs are temporal and spatial resolution, the ability of being used without significantly interfering with the system. NBSs with the best properties are the optically genetically coded NBSs, but each NBS needs specific development efforts. NBS technologies using antibodies as a recognition domain are generic and tend to be more invasive, and there are examples of their use in plant nanobionics. Through opportunities that develop along with technologies, we hope that more and more NBSs will become available for plant nanobionics. The main advantages of NBSs are short analysis time, low-cost tests and portability, real-time measurements, and remote control.
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Using the QCM Biosensor-Based T7 Phage Display Combined with Bioinformatics Analysis for Target Identification of Bioactive Small Molecule. Methods Mol Biol 2018; 1795:159-172. [PMID: 29846927 DOI: 10.1007/978-1-4939-7874-8_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Identification of target proteins that directly bind to bioactive small molecule is of great interest in terms of clarifying the mode of action of the small molecule as well as elucidating the biological phenomena at the molecular level. Of the experimental technologies available, T7 phage display allows comprehensive screening of small molecule-recognizing amino acid sequence from the peptide libraries displayed on the T7 phage capsid. Here, we describe the T7 phage display strategy that is combined with quartz-crystal microbalance (QCM) biosensor for affinity selection platform and bioinformatics analysis for small molecule-recognizing short peptides. This method dramatically enhances efficacy and throughput of the screening for small molecule-recognizing amino acid sequences without repeated rounds of selection. Subsequent execution of bioinformatics programs allows combinatorial and comprehensive target protein discovery of small molecules with its binding site, regardless of protein sample insolubility, instability, or inaccessibility of the fixed small molecules to internally located binding site on larger target proteins when conventional proteomics approaches are used.
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Takakusagi K, Takakusagi Y, Suzuki T, Toizaki A, Suzuki A, Kawakatsu Y, Watanabe M, Saito Y, Fukuda R, Nakazaki A, Kobayashi S, Sakaguchi K, Sugawara F. Multimodal biopanning of T7 phage-displayed peptides reveals angiomotin as a potential receptor of the anti-angiogenic macrolide Roxithromycin. Eur J Med Chem 2015; 90:809-21. [PMID: 25528335 DOI: 10.1016/j.ejmech.2014.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/06/2014] [Accepted: 12/09/2014] [Indexed: 02/07/2023]
Abstract
Roxithromycin (RXM) is a semi-synthetic fourteen-membered macrolide antibiotic that shows anti-angiogenic activity in solid tumors. In the present study, we conducted biopanning of T7 phage-displayed peptides either on a 96-well formatted microplate, a flow injection-type quartz-crystal microbalance (QCM) biosensor, or a cuvette-type QCM. RXM-selected peptides of different sequence, length and number were obtained from each mode of screening. Subsequent bioinformatics analysis of the RXM-selected peptides consistently gave positive scores for the extracellular domain (E458-T596) of angiomotin (Amot), indicating that this may comprise a binding region for RXM. Bead pull down assay and QCM analysis confirmed that RXM directly interacts with Amot via the screen-guided region, which also corresponds to the binding site for the endogenous anti-angiogenic inhibitor angiostatin (Anst). Thus, multimodal biopanning of T7PD revealed that RXM binds to the extracellular domain on Amot as a common binding site with Anst, leading to inhibition of angiogenesis-dependent tumor growth and metastasis. These data might explain the molecular basis underlying the mechanism of action for the anti-angiogenic activity of RXM.
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Affiliation(s)
- Kaori Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yoichi Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Takahiro Suzuki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Aya Toizaki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Aiko Suzuki
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yaichi Kawakatsu
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Madoka Watanabe
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yukihiro Saito
- Meiwafosis Co. Ltd., 1-14-2 Shinjuku, Tokyo 160-0022, Japan
| | - Ryushi Fukuda
- Meiwafosis Co. Ltd., 1-14-2 Shinjuku, Tokyo 160-0022, Japan
| | - Atsuo Nakazaki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Susumu Kobayashi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kengo Sakaguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Fumio Sugawara
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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Dejonghe W, Mishev K, Russinova E. The brassinosteroid chemical toolbox. CURRENT OPINION IN PLANT BIOLOGY 2014; 22:48-55. [PMID: 25282585 DOI: 10.1016/j.pbi.2014.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/29/2014] [Accepted: 09/05/2014] [Indexed: 06/03/2023]
Abstract
Chemical biology approaches have been instrumental in understanding the mode of action of brassinosteroids, a group of plant steroid hormones essential for plant development and growth. The small molecules used for such approaches include inhibitors of biosynthetic enzymes and signaling components. Additionally, recent structural data on the brassinosteroid receptor complex together with its ligand brassinolide, the most active brassinosteroid, and knowledge on its different analogs have given us a better view on the recognition of the hormone and signaling initiation. Moreover, a fluorescently labeled brassinosteroid enabled the visualization of the receptor-ligand pair in the cell. Given the insights obtained, small molecules will continue to provide new opportunities for probing brassinosteroid biosynthesis and for unraveling the dynamic and highly interconnected signaling.
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Affiliation(s)
- Wim Dejonghe
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kiril Mishev
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Eugenia Russinova
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
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Dejonghe W, Russinova E. Target identification strategies in plant chemical biology. FRONTIERS IN PLANT SCIENCE 2014; 5:352. [PMID: 25104953 PMCID: PMC4109434 DOI: 10.3389/fpls.2014.00352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/30/2014] [Indexed: 05/03/2023]
Abstract
The current needs to understand gene function in plant biology increasingly require more dynamic and conditional approaches opposed to classic genetic strategies. Gene redundancy and lethality can substantially complicate research, which might be solved by applying a chemical genetics approach. Now understood as the study of small molecules and their effect on biological systems with subsequent target identification, chemical genetics is a fast developing field with a strong history in pharmaceutical research and drug discovery. In plant biology however, chemical genetics is still largely in the starting blocks, with most studies relying on forward genetics and phenotypic analysis for target identification, whereas studies including direct target identification are limited. Here, we provide an overview of recent advances in chemical genetics in plant biology with a focus on target identification. Furthermore, we discuss different strategies for direct target identification and the possibilities and challenges for plant biology.
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Affiliation(s)
- Wim Dejonghe
- Department of Plant Systems Biology, VIBGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
| | - Eugenia Russinova
- Department of Plant Systems Biology, VIBGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- *Correspondence: Eugenia Russinova, Department of Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, VIB-Ghent University, Technologiepark 927, 9052 Ghent, Belgium e-mail:
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