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Aloisio A, Nisticò N, Mimmi S, Maisano D, Vecchio E, Fiume G, Iaccino E, Quinto I. Phage-Displayed Peptides for Targeting Tyrosine Kinase Membrane Receptors in Cancer Therapy. Viruses 2021; 13:649. [PMID: 33918836 PMCID: PMC8070105 DOI: 10.3390/v13040649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) regulate critical physiological processes, such as cell growth, survival, motility, and metabolism. Abnormal activation of RTKs and relative downstream signaling is implicated in cancer pathogenesis. Phage display allows the rapid selection of peptide ligands of membrane receptors. These peptides can target in vitro and in vivo tumor cells and represent a novel therapeutic approach for cancer therapy. Further, they are more convenient compared to antibodies, being less expensive and non-immunogenic. In this review, we describe the state-of-the-art of phage display for development of peptide ligands of tyrosine kinase membrane receptors and discuss their potential applications for tumor-targeted therapy.
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Affiliation(s)
| | | | | | | | | | | | | | - Ileana Quinto
- Correspondence: (A.A.); (I.Q.): Tel.: +39-0961-3694057 (I.Q.)
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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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Target Identification of the Marine Natural Products Dictyoceratin-A and -C as Selective Growth Inhibitors in Cancer Cells Adapted to Hypoxic Environments. Mar Drugs 2019; 17:md17030163. [PMID: 30857246 PMCID: PMC6471994 DOI: 10.3390/md17030163] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
Hypoxia-adapted cancer cells in tumors contribute to the pathological progression of cancer. The marine spongean sesquiterpene phenols dictyoceratin-A (1) and -C (2) have been shown to induce hypoxia-selective growth inhibition in cultured cancer cells and exhibit in vivo antitumor effects. These compounds inhibit the accumulation of hypoxia-inducible factor-1α (HIF-1α), which is a drug target in hypoxia-adapted cancer cells, under hypoxic conditions. However, the target molecules of compounds 1 and 2, which are responsible for decreasing HIF-1α expression under hypoxic conditions, remain unclear. In this study, we synthesized probe molecules for compounds 1 and 2 to identify their target molecules and found that both compounds bind to RNA polymerase II-associated protein 3 (RPAP3), which is a component of the R2TP/Prefoldin-like (PEDL) complex. In addition, RPAP3-knockdown cells showed a phenotype similar to that of compound-treated cells.
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The power of combining phenotypic and target-focused drug discovery. Drug Discov Today 2019; 24:526-532. [DOI: 10.1016/j.drudis.2018.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/10/2018] [Accepted: 10/16/2018] [Indexed: 01/09/2023]
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Morales MA, Halpern JM. Guide to Selecting a Biorecognition Element for Biosensors. Bioconjug Chem 2018; 29:3231-3239. [PMID: 30216055 DOI: 10.1021/acs.bioconjchem.8b00592] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biosensors are powerful diagnostic tools defined as having a biorecognition element for analyte specificity and a transducer for a quantifiable signal. There are a variety of different biorecognition elements, each with unique characteristics. Understanding the advantages and disadvantages of each biorecognition element and their influence on overall biosensor performance is crucial in the planning stages to promote the success of novel biosensor development. Therefore, this review will focus on selecting the optimal biorecognition element in the preliminary design phase for novel biosensors. Included is a review of the typical characteristics and binding mechanisms of various biorecognition elements, and how they relate to biosensor performance characteristics, specifically sensitivity, selectivity, reproducibility, and reusability. The goal is to point toward language needed to improve the design and development of biosensors toward clinical success.
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Affiliation(s)
- Marissa A Morales
- Department of Chemical Engineering , University of New Hampshire , Durham , New Hampshire 03824 , United States
| | - Jeffrey Mark Halpern
- Department of Chemical Engineering , University of New Hampshire , Durham , New Hampshire 03824 , United States
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Comess KM, McLoughlin SM, Oyer JA, Richardson PL, Stöckmann H, Vasudevan A, Warder SE. Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective. J Med Chem 2018; 61:8504-8535. [DOI: 10.1021/acs.jmedchem.7b01921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenneth M. Comess
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Shaun M. McLoughlin
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Jon A. Oyer
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Paul L. Richardson
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Henning Stöckmann
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Scott E. Warder
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
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Ruike T, Kanai Y, Iwabata K, Matsumoto Y, Murata H, Ishima M, Ohta K, Oshige M, Katsura S, Kuramochi K, Kamisuki S, Sahara H, Miura M, Sugawara F, Sakaguchi K. Distribution and metabolism of 14C-sulfoquinovosylacylpropanediol ( 14C-SQAP) after a single intravenous administration in tumor-bearing mice. Xenobiotica 2018. [PMID: 29543539 DOI: 10.1080/00498254.2018.1448949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Sulfoquinovosylacylpropanediol (SQAP) is a novel potent radiosensitizer that inhibits angiogenesis in vivo and results in increased oxigenation and reduced tumor volume. We investigated the distribution, metabolism, and excretion of SQAP in male KSN-nude mice transplanted with a human pulmonary carcinoma, Lu65. For the metabolism analysis, a 2 mg (2.98 MBq)/kg of [glucose-U-14C]-SQAP (CP-3839) was intravenously injected. The injected SQAP was decomposed into a stearic acid and a sulfoquinovosylpropanediol (SQP) in the body. The degradation was relatively slow in the carcinoma tissue.1,3-propanediol[1-14C]-SQAP (CP-3635) was administered through intravenous injection of a 1 mg (3.48 MBq)/kg dose followed by whole body autoradiography of the mice. The autoradiography analysis demonstrated that SQAP rapidly distributed throughout the whole body and then quickly decreased within 4 hours except the tumor and excretion organs such as liver, kidney. Retention of SQAP was longer in tumor parts than in other tissues, as indicated by higher levels of radioactivity at 4 hours. The radioactivity around the tumor had also completely disappeared within 72 hours.
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Affiliation(s)
- Tatsushi Ruike
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Yoshihiro Kanai
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Kazuki Iwabata
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Yuki Matsumoto
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Hiroshi Murata
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Masahiro Ishima
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Keisuke Ohta
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Masahiko Oshige
- b Department of Environmental Engineering Science, Graduate School of Science and Technology , Gunma University , Kiryu , Gunma , Japan
| | - Shinji Katsura
- b Department of Environmental Engineering Science, Graduate School of Science and Technology , Gunma University , Kiryu , Gunma , Japan
| | - Koji Kuramochi
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Shinji Kamisuki
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Hiroeki Sahara
- c Laboratory of Biology , Azabu University School of Veterinary Medicine , Chuou-ku, Sagamihara , Kanagawa , Japan
| | - Masahiko Miura
- d Oral Radiation Oncology, Department of Oral Restitution, Graduate School , Tokyo Medical and Dental University , Bunkyo-ku , Tokyo , Japan
| | - Fumio Sugawara
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
| | - Kengo Sakaguchi
- a Department of Applied Biological Science, Faculty of Science and Technology , Tokyo University of Science , Noda , Chiba , Japan
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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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Lee H, Lee JW. Target identification for biologically active small molecules using chemical biology approaches. Arch Pharm Res 2016; 39:1193-201. [DOI: 10.1007/s12272-016-0791-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022]
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Marsh A, Casey-Green K, Probert F, Withall D, Mitchell DA, Dilly SJ, James S, Dimitri W, Ladwa SR, Taylor PC, Singer DRJ. Simvastatin Sodium Salt and Fluvastatin Interact with Human Gap Junction Gamma-3 Protein. PLoS One 2016; 11:e0148266. [PMID: 26863535 PMCID: PMC4749215 DOI: 10.1371/journal.pone.0148266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 01/15/2016] [Indexed: 11/26/2022] Open
Abstract
Finding pleiomorphic targets for drugs allows new indications or warnings for treatment to be identified. As test of concept, we applied a new chemical genomics approach to uncover additional targets for the widely prescribed lipid-lowering pro-drug simvastatin. We used mRNA extracted from internal mammary artery from patients undergoing coronary artery surgery to prepare a viral cardiovascular protein library, using T7 bacteriophage. We then studied interactions of clones of the bacteriophage, each expressing a different cardiovascular polypeptide, with surface-bound simvastatin in 96-well plates. To maximise likelihood of identifying meaningful interactions between simvastatin and vascular peptides, we used a validated photo-immobilisation method to apply a series of different chemical linkers to bind simvastatin so as to present multiple orientations of its constituent components to potential targets. Three rounds of biopanning identified consistent interaction with the clone expressing part of the gene GJC3, which maps to Homo sapiens chromosome 7, and codes for gap junction gamma-3 protein, also known as connexin 30.2/31.3 (mouse connexin Cx29). Further analysis indicated the binding site to be for the N-terminal domain putatively ‘regulating’ connexin hemichannel and gap junction pores. Using immunohistochemistry we found connexin 30.2/31.3 to be present in samples of artery similar to those used to prepare the bacteriophage library. Surface plasmon resonance revealed that a 25 amino acid synthetic peptide representing the discovered N-terminus did not interact with simvastatin lactone, but did bind to the hydrolysed HMG CoA inhibitor, simvastatin acid. This interaction was also seen for fluvastatin. The gap junction blockers carbenoxolone and flufenamic acid also interacted with the same peptide providing insight into potential site of binding. These findings raise key questions about the functional significance of GJC3 transcripts in the vasculature and other tissues, and this connexin’s role in therapeutic and adverse effects of statins in a range of disease states.
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Affiliation(s)
- Andrew Marsh
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
- * E-mail: (AM); (DRJS)
| | | | - Fay Probert
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - David Withall
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Daniel A. Mitchell
- Division of Metabolic and Vascular Health, Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry, CV2 2DX, United Kingdom
| | - Suzanne J. Dilly
- Tangent Reprofiling Ltd, c/o SEEK, Central Point, 45 Beech Street, London, EC2Y 8AD, United Kingdom
| | - Sean James
- University Hospital Coventry and Warwickshire, Clifford Bridge Road, Coventry CV2 2DX, United Kingdom
| | - Wade Dimitri
- University Hospital Coventry and Warwickshire, Clifford Bridge Road, Coventry CV2 2DX, United Kingdom
| | - Sweta R. Ladwa
- Tangent Reprofiling Ltd, c/o SEEK, Central Point, 45 Beech Street, London, EC2Y 8AD, United Kingdom
| | - Paul C. Taylor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Donald R. J. Singer
- University Hospital Coventry and Warwickshire, Clifford Bridge Road, Coventry CV2 2DX, United Kingdom
- Fellowship of Postgraduate Medicine, 11 Chandos St, London W1G 9EB, United Kingdom
- Division of Metabolic and Vascular Health, Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry, CV2 2DX, United Kingdom
- * E-mail: (AM); (DRJS)
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Izaguirre-Carbonell J, Kawakubo H, Murata H, Tanabe A, Takeuchi T, Kusayanagi T, Tsukuda S, Hirakawa T, Iwabata K, Kanai Y, Ohta K, Miura M, Sakaguchi K, Matsunaga S, Sahara H, Kamisuki S, Sugawara F. Novel anticancer agent, SQAP, binds to focal adhesion kinase and modulates its activity. Sci Rep 2015; 5:15136. [PMID: 26456697 PMCID: PMC4601023 DOI: 10.1038/srep15136] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/18/2015] [Indexed: 01/03/2023] Open
Abstract
SQAP is a novel and promising anticancer agent that was obtained by structural modifications from a natural compound. SQAP inhibits angiogenesis in vivo resulting in increased hypoxia and reduced tumor volume. In this study, the mechanism by which SQAP modifies the tumor microenvironment was revealed through the application of a T7 phage display screening. This approach identified five SQAP-binding proteins including sterol carrier protein 2, multifunctional enzyme type 2, proteasomal ubiquitin receptor, UV excision repair protein and focal adhesion kinase (FAK). All the interactions were confirmed by surface plasmon resonance analysis. Since FAK plays an important role in cell turnover and angiogenesis, the influence of SQAP on FAK was the principal goal of this study. SQAP decreased FAK phosphorylation and cell migration in human umbilical vein endothelial cells and A549 cancer cells. These findings suggest that inhibition of FAK phosphorylation works as the mechanism for the anti-angiogenesis activity of SQAP.
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Affiliation(s)
- Jesus Izaguirre-Carbonell
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Hirofumi Kawakubo
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Hiroshi Murata
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Atsushi Tanabe
- Laboratory of Biology, Azabu University School of Veterinary Medicine, Sagamihara 229-8501, Japan
| | - Toshifumi Takeuchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Tomoe Kusayanagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Senko Tsukuda
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takeshi Hirakawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kazuki Iwabata
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yoshihiro Kanai
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Keisuke Ohta
- Department of Oral Radiation Oncology, Graduate school, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-85-10, Japan
| | - Masahiko Miura
- Department of Oral Radiation Oncology, Graduate school, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-85-10, Japan
| | - Kengo Sakaguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Hiroeki Sahara
- Laboratory of Biology, Azabu University School of Veterinary Medicine, Sagamihara 229-8501, Japan
| | - Shinji Kamisuki
- 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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Ridaifen G, tamoxifen analog, is a potent anticancer drug working through a combinatorial association with multiple cellular factors. Bioorg Med Chem 2015; 23:6118-24. [DOI: 10.1016/j.bmc.2015.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 07/31/2015] [Accepted: 08/01/2015] [Indexed: 12/31/2022]
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13
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Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
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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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Identification and characterization of the direct interaction between methotrexate (MTX) and high-mobility group box 1 (HMGB1) protein. PLoS One 2013; 8:e63073. [PMID: 23658798 PMCID: PMC3643934 DOI: 10.1371/journal.pone.0063073] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/28/2013] [Indexed: 11/19/2022] Open
Abstract
Background Methotrexate (MTX) is an agent used in chemotherapy of tumors and autoimmune disease including rheumatoid arthritis (RA). In addition, MTX has some anti-inflammatory activity. Although dihydrofolate reductase (DHFR) is a well-known target for the anti-tumor effect of MTX, the mode of action for the anti-inflammatory activity of MTX is not fully understood. Methodology/Result Here, we performed a screening of MTX-binding proteins using T7 phage display with a synthetic biotinylated MTX derivative. We then characterized the interactions using surface plasmon resonance (SPR) analysis and electrophoretic mobility shift assay (EMSA). Using a T7 phage display screen, we identified T7 phages that displayed part of high-mobility group box 1 (HMGB1) protein (K86-V175). Binding affinities as well as likely binding sites were characterized using genetically engineered truncated versions of HMGB1 protein (Al G1-K87, Bj: F88-K181), indicating that MTX binds to HMGB1 via two independent sites with a dissociation constants (KD) of 0.50±0.03 µM for Al and 0.24±0.01 µM for Bj. Although MTX did not inhibit the binding of HMGB1 to DNA via these domains, HMGB1/RAGE association was impeded in the presence of MTX. These data suggested that binding of MTX to part of the RAGE-binding region (K149-V175) in HMGB1 might be significant for the anti-inflammatory effect of MTX. Indeed, in murine macrophage-like cells (RAW 264.7), TNF-α release and mitogenic activity elicited by specific RAGE stimulation with a truncated monomeric HMGB1 were inhibited in the presence of MTX. Conclusions/Significance These data demonstrate that HMGB1 is a direct binding protein of MTX. Moreover, binding of MTX to RAGE-binding region in HMGB1 inhibited the HMGB1/RAGE interaction at the molecular and cellular levels. These data might explain the molecular basis underlying the mechanism of action for the anti-inflammatory effect of MTX.
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Takakusagi Y, Manita D, Kusayanagi T, Izaguirre-Carbonell J, Takakusagi K, Kuramochi K, Iwabata K, Kanai Y, Sakaguchi K, Sugawara F. Mapping a disordered portion of the Brz2001-binding site on a plant monooxygenase, DWARF4, using a quartz-crystal microbalance biosensor-based T7 phage display. Assay Drug Dev Technol 2013; 11:206-15. [PMID: 23514038 DOI: 10.1089/adt.2012.478] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In small-molecule/protein interaction studies, technical difficulties such as low solubility of small molecules or low abundance of protein samples often restrict the progress of research. Here, we describe a quartz-crystal microbalance (QCM) biosensor-based T7 phage display in combination use with a receptor-ligand contacts (RELIC) bioinformatics server for application in a plant Brz2001/DWARF4 system. Brz2001 is a brassinosteroid biosynthesis inhibitor in the less-soluble triazole series of compounds that targets DWARF4, a cytochrome P450 (Cyp450) monooxygenase containing heme and iron. Using a Brz2001 derivative that has higher solubility in 70% EtOH and forms a self-assembled monolayer on gold electrode, we selected 34 Brz2001-recognizing peptides from a 15-mer T7 phage-displayed random peptide library using a total of four sets of one-cycle biopanning. The RELIC/MOTIF program revealed continuous and discontinuous short motifs conserved within the 34 Brz2001-selected 15-mer peptide sequences, indicating the increase of information content for Brz2001 recognition. Furthermore, an analysis of similarity between the 34 peptides and the amino-acid sequence of DWARF4 using the RELIC/MATCH program generated a similarity plot and a cluster diagram of the amino-acid sequence. Both of these data highlighted an internally located disordered portion of a catalytic site on DWARF4, indicating that this portion is essential for Brz2001 recognition. A similar trend was also noted by an analysis using another 26 Brz2001-selected peptides, and not observed using the 27 gold electrode-recognizing control peptides, demonstrating the reproducibility and specificity of this method. Thus, this affinity-based strategy enables high-throughput detection of the small-molecule-recognizing portion on the target protein, which overcomes technical difficulties such as sample solubility or preparation that occur when conventional methods are used.
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Affiliation(s)
- Yoichi Takakusagi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan
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17
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Lee J, Bogyo M. Target deconvolution techniques in modern phenotypic profiling. Curr Opin Chem Biol 2013; 17:118-26. [PMID: 23337810 DOI: 10.1016/j.cbpa.2012.12.022] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/19/2012] [Accepted: 12/30/2012] [Indexed: 01/12/2023]
Abstract
The past decade has seen rapid growth in the use of diverse compound libraries in classical phenotypic screens to identify modulators of a given process. The subsequent process of identifying the molecular targets of active hits, also called 'target deconvolution', is an essential step for understanding compound mechanism of action and for using the identified hits as tools for further dissection of a given biological process. Recent advances in 'omics' technologies, coupled with in silico approaches and the reduced cost of whole genome sequencing, have greatly improved the workflow of target deconvolution and have contributed to a renaissance of 'modern' phenotypic profiling. In this review, we will outline how both new and old techniques are being used in the difficult process of target identification and validation as well as discuss some of the ongoing challenges remaining for phenotypic screening.
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Affiliation(s)
- Jiyoun Lee
- Department of Global Medical Science, Sungshin Women's University, Seoul 142-732, Republic of Korea.
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18
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Tsukuda S, Kusayanagi T, Umeda E, Watanabe C, Tosaki YT, Kamisuki S, Takeuchi T, Takakusagi Y, Shiina I, Sugawara F. Ridaifen B, a tamoxifen derivative, directly binds to Grb10 interacting GYF protein 2. Bioorg Med Chem 2012. [PMID: 23199482 DOI: 10.1016/j.bmc.2012.10.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ridaifen B (RID-B) is a tamoxifen derivative that potently inhibits breast tumor growth. RID-B was reported to show anti-proliferating activity for a variety of estrogen receptor (ER)-positive human cancer cells. Interestingly, RID-B was also reported to possess higher potency than that of tamoxifen even for some ER-negative cells, suggesting an ER-independent mechanism of action. In this study, a T7 phage display screen and subsequent binding analyses have identified Grb10 interacting GYF protein 2 (GIGYF2) as a RID-B-binding protein. Using a cell-based assay, the Akt phosphorylation level mediated by GIGYF2 was found to have decreased in the presence of RID-B.
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Affiliation(s)
- Senko Tsukuda
- 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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19
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Van Dorst B, Mehta J, Rouah-Martin E, Blust R, Robbens J. Phage display as a method for discovering cellular targets of small molecules. Methods 2012; 58:56-61. [PMID: 22819857 DOI: 10.1016/j.ymeth.2012.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 07/11/2012] [Indexed: 12/12/2022] Open
Abstract
Phage display can be used for the discovery of cellular targets of small molecules in order to unravel their mechanism of action, which is important in the drug discovery field to assess biological effects of drugs at the molecular level and to investigate pharmacokinetic characteristics of drugs in clinical use. The potential of phage display in the drug discovery field is shown by a lot of successful cellular target identifications of drug-like small molecules in the last decade. More recently, phage display was also introduced in environmental science to predict risks of small molecules, like nickel, 17β estradiol and bisphenol A on both environmental and human health, wherefore knowledge about the mechanism of action and cellular targets is essential. This paper discusses some important aspects of the phage display approach for the discovery of cellular targets of small molecules. The different phage display libraries and immobilization strategies used for the discovery of cellular target of small molecules are described. In general, the phage display approach is very useful in drug discovery and environmental science as a fast and cost-effective in vitro tool to determine cellular targets of small molecules, which increases our understanding of the mechanisms of action of small molecules.
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Affiliation(s)
- Bieke Van Dorst
- University Antwerp, Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
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20
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Exploration of the binding proteins of perfluorooctane sulfonate by a T7 phage display screen. Bioorg Med Chem 2012; 20:3985-90. [PMID: 22658539 DOI: 10.1016/j.bmc.2012.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/09/2012] [Accepted: 05/09/2012] [Indexed: 01/09/2023]
Abstract
Perfluorooctane sulfonate (PFOS) is a pollutant widely found throughout nature and is toxic to animals. We created a PFOS analogue on a polyethylene glycol polyacrylamide copolymer and isolated peptides that preferentially bound the PFOS analogue using a T7 phage display system. Bioinformatic analysis using the FASTAskan program on the RELIC bioinformatics server showed several human proteins that likely bound PFOS. Among them, we confirmed binding between PFOS and a recombinant soluble form of monocyte differentiation antigen CD14 (sCD14) by a surface plasmon biosensor. Furthermore, PFOS inhibited TNF-α production induced by the sCD14 in mouse macrophage RAW264.7 cells.
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21
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Qi H, Lu H, Qiu HJ, Petrenko V, Liu A. Phagemid Vectors for Phage Display: Properties, Characteristics and Construction. J Mol Biol 2012; 417:129-43. [PMID: 22310045 DOI: 10.1016/j.jmb.2012.01.038] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 01/20/2012] [Accepted: 01/24/2012] [Indexed: 11/20/2022]
Affiliation(s)
- Huan Qi
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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22
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Matsumoto Y, Shindo Y, Takakusagi Y, Takakusagi K, Tsukuda S, Kusayanagi T, Sato H, Kawabe T, Sugawara F, Sakaguchi K. Screening of a library of T7 phage-displayed peptides identifies alphaC helix in 14-3-3 protein as a CBP501-binding site. Bioorg Med Chem 2011; 19:7049-56. [PMID: 22032894 DOI: 10.1016/j.bmc.2011.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 10/04/2011] [Indexed: 01/01/2023]
Abstract
CBP501 is a chemically modified peptide composed of twelve unnatural d-amino acids, which inhibits Chk kinase and abrogates G2 arrest induced by DNA-damaging agents. Here we identified an alphaC helix in 14-3-3 protein as a CBP501-binding site using T7 phage display technology. An affinity selection of T7 phage-displayed peptide using biotinylated CBP501 identified a 14-mer peptide NSDCIISRKIEQKE. This peptide sequence showed similarity to a portion of the alphaC helix of human 14-3-3ε, suggesting that CBP501 may bind to this region. Surface plasmon resonance (SPR) and ELISA demonstrated that CBP501 interacts with 14-3-3ε specifically at the screen-guided region. An avidin-agarose bead pull-down assay showed that CBP501 also binds to other 14-3-3 isoforms in Jurkat cells. Among the other known Chk kinase inhibitors tested, CBP501 showed the strongest affinity for 14-3-3ε. Thus, we conclude that in addition to the direct inhibition of Chk kinase activity, CBP501 directly binds to cellular 14-3-3 proteins through alphaC helix.
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Affiliation(s)
- Yuki Matsumoto
- Department of Applied Biological Sciences, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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23
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Manita D, Toba Y, Takakusagi Y, Matsumoto Y, Kusayanagi T, Takakusagi K, Tsukuda S, Takada K, Kanai Y, Kamisuki S, Sakaguchi K, Sugawara F. Camptothecin (CPT) directly binds to human heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and inhibits the hnRNP A1/topoisomerase I interaction. Bioorg Med Chem 2011; 19:7690-7. [PMID: 22071521 DOI: 10.1016/j.bmc.2011.09.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 09/29/2011] [Indexed: 12/20/2022]
Abstract
Camptothecin (CPT) is an anti-tumor natural product that forms a ternary complex with topoisomerase I (top I) and DNA (CPT-top I-DNA). In this study, we identified the direct interaction between CPT and human heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) using the T7 phage display technology. On an avidin-agarose bead pull down assay, hnRNP A1 protein was selectively pulled down in the presence of C20-biotinylated CPT derivative (CPT-20-B) both in vitro and in vivo. The interaction was also confirmed by an analysis on a quartz-crystal microbalance (QCM) device, yielding a K(D) value of 82.7 nM. A surface plasmon resonance (SPR) analysis revealed that CPT inhibits the binding of hnRNP A1 to top I (K(D): 260 nM) in a non-competitive manner. Moreover, an in vivo drug evaluation assay using Drosophila melanogaster showed that the knockout of the hnRNP A1 homolog Hrb87F gene showed high susceptibility against 5-50 μM of CPT as compared to a wild-type strain. Such susceptibility was specific for CPT and not observed after treatment with other cytotoxic drugs. Collectively, our data suggests that CPT directly binds to hnRNP A1 and non-competitively inhibits the hnRNP A1/top I interaction in vivo. The knockout strain loses the hnRNP A1 homolog as a both CPT-binding partner and naïve brakes of top I, which enhances the formation of the CPT-top I-DNA ternary complexes and subsequently sensitizes the growth inhibitory effect of CPT in D. melanogaster.
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Affiliation(s)
- Daisuke Manita
- 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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24
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A screening of a library of T7 phage-displayed peptide identifies E2F-4 as an etoposide-binding protein. Molecules 2011; 16:4278-94. [PMID: 21610657 PMCID: PMC6263361 DOI: 10.3390/molecules16054278] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 04/22/2011] [Accepted: 05/16/2011] [Indexed: 12/22/2022] Open
Abstract
Etoposide (VP-16) is an anti-tumor compound that targets topoisomerase II (top II). In this study, we have identified an alternative binding protein of etoposide by screening a library of T7 phage-displayed peptides. After four rounds of selection using a biotinylated etoposide derivative immobilized on a streptavidin-coated plate, T7 phage particles that display a 16-mer peptide NSSASSRGNSSSNSVY (ETBP16) or a 10-mer NSLRKYSKLK (ETBP10) were enriched with the ratio of 40 or 11 out of the 69 clones, respectively. Binding of etoposide to these peptides was confirmed by surface plasmon resonance (SPR) analysis, which showed ETBP16 and ETBP10 to have a kinetic constant of 4.85 × 10−5 M or 6.45 × 10−5 M, respectively. ETBP16 displays similarity with the ser-rich domain in E2F-4, a transcription factor in cell cycle-regulated genes, suggesting that etoposide might interact with E2F-4 via this domain. SPR analysis confirmed the specific binding of etoposide to recombinant E2F-4 is in the order of 10−5 M. Furthermore, etoposide was shown to inhibit luciferase reporter gene expression mediated by the heterodimeric E2F-4/DP complex. Taken together, our results suggest that etoposide directly binds to E2F-4 and inhibits subsequent gene transcription mediated by heterodimeric E2F-4/DP complexes in the nucleus.
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25
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Takakusagi Y, Takakusagi K, Ida N, Takami M, Matsumoto Y, Kusayanagi T, Nakabayashi T, Aoki S, Murata H, Ohta K, Sugawara F, Sakaguchi K. Binding region and interaction properties of sulfoquinovosylacylglycerol (SQAG) with human vascular endothelial growth factor 165 revealed by biosensor-based assays. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00180a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Van Dorst B, Mehta J, Rouah-Martin E, De Coen W, Blust R, Robbens J. The identification of cellular targets of 17β estradiol using a lytic (T7) cDNA phage display approach. Toxicol In Vitro 2010; 25:388-93. [PMID: 21034808 DOI: 10.1016/j.tiv.2010.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 10/19/2010] [Accepted: 10/21/2010] [Indexed: 11/18/2022]
Abstract
To unravel the mechanism of action of chemical compounds, it is crucial to know their cellular targets. A novel in vitro tool that can be used as a fast, simple and cost effective alternative is cDNA phage display. This tool is used in our study to select cellular targets of 17β estradiol (E2). It was possible to select two potential cellular targets of E2 out of the T7 Select™ Human Breast cDNA phage library. The selected cellular targets, autophagy/beclin-1 regulator 1 (beclin 1) and ATP synthase F(0) subunit 6 (ATP6) have so far been unknown as binding proteins of E2. To confirm the E2 binding properties of these selected proteins, surface plasmon resonance (SPR) was used. With SPR the K(d) values were determined to be 0.178±0.031 and 0.401±0.142 nM for the ATP6 phage and beclin 1 phage, respectively. These K(d) values in the low nM range verify that the selected cellular proteins are indeed binding proteins for E2. The selection and identification of these two potential cellular targets of E2, can enhance our current understanding of its mechanism of action. This illustrates the potential of lytic (T7) cDNA phage display in toxicology, to provide important information about cellular targets of chemical compounds.
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Affiliation(s)
- Bieke Van Dorst
- University Antwerp, Department of Biology, Antwerp, Belgium.
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