1
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Choi H, Kim HD, Choi YW, Lim H, Kim KW, Kim KS, Lee YC, Kim CH. T7 phage display reveals NOLC1 as a GM3 binding partner in human breast cancer MCF-7 cells. Arch Biochem Biophys 2023; 750:109810. [PMID: 37939867 DOI: 10.1016/j.abb.2023.109810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Ganglioside GM3 is a simple monosialoganglioside (NeuAc-Gal-Glc-ceramide) that modulates cell adhesion, proliferation, and differentiation. Previously, we reported isolation of GM3-binding vascular endothelial growth factor receptor and transforming growth factor-β receptor by the T7 phage display method (Chung et al., 2009; Kim et al., 2013). To further identify novel proteins interacting with GM3, we extended the T7 phage display method in this study. After T7 phage display biopanning combined with immobilized biotin-labeled 3'-sialyllactose prepared on a streptavidin-coated microplate, we isolated 100 candidate sequences from the human lung cDNA library. The most frequently detected clones from the blast analysis were the human nucleolar and coiled-body phosphoprotein 1 (NOLC1) sequences. We initially identified NOLC1 as a molecule that possibly binds to GM3 and confirmed this binding ability using the glutathione S-transferase fusion protein. Herein, we report another GM3-interacting protein, NOLC1, that can be isolated by the T7 phage display method. These results are expected to be helpful for elucidating the functional roles of ganglioside GM3 with NOLC1. When human breast cancer MCF-7 cells were examined for subcellular localization of NOLC1, immunofluorescence of NOLC1 was observed in the intracellular region. In addition, NOLC1 expression was increased in the nucleolus after treatment with the anticancer drug doxorubicin. GM3 and NOLC1 levels in the doxorubicin-treated MCF-7 cells were correlated, indicating possible associations between GM3 and NOLC1. Therefore, direct interactions between carbohydrates and cellular proteins can pave the path for new signaling phenomena in biology.
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Affiliation(s)
- Hyunju Choi
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Hee-Do Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Yeon-Woo Choi
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Hakseong Lim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Kyung-Woon Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
| | - Kyoung-Sook Kim
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Saha-Gu, Busan, 604-714, South Korea
| | - Young-Choon Lee
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Saha-Gu, Busan, 604-714, South Korea.
| | - Cheorl-Ho Kim
- Molecular and Cellular Glycobiology Unit, Department of Biological Sciences, SungKyunKwan University, Seoburo 2066, Jangan-Gu, Suwon, 16419, South Korea.
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2
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Zhai F, Wang J, Luo X, Ye M, Jin X. Roles of NOLC1 in cancers and viral infection. J Cancer Res Clin Oncol 2023; 149:10593-10608. [PMID: 37296317 DOI: 10.1007/s00432-023-04934-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The nucleolus is considered the center of metabolic control and an important organelle for the biogenesis of ribosomal RNA (rRNA). Nucleolar and coiled-body phosphoprotein 1(NOLC1), which was originally identified as a nuclear localization signal-binding protein is a nucleolar protein responsible for nucleolus construction and rRNA synthesis, as well as chaperone shuttling between the nucleolus and cytoplasm. NOLC1 plays an important role in a variety of cellular life activities, including ribosome biosynthesis, DNA replication, transcription regulation, RNA processing, cell cycle regulation, apoptosis, and cell regeneration. PURPOSE In this review, we introduce the structure and function of NOLC1. Then we elaborate its upstream post-translational modification and downstream regulation. Meanwhile, we describe its role in cancer development and viral infection which provide a direction for future clinical applications. METHODS The relevant literatures from PubMed have been reviewed for this article. CONCLUSION NOLC1 plays an important role in the progression of multiple cancers and viral infection. In-depth study of NOLC1 provides a new perspective for accurate diagnosis of patients and selection of therapeutic targets.
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Affiliation(s)
- Fengguang Zhai
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China
| | - Jie Wang
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China
| | - Xia Luo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Meng Ye
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China.
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
- The Affiliated First Hospital, Ningbo University, Ningbo, 315020, China.
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3
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Sochacka M, Karelus R, Opalinski L, Krowarsch D, Biadun M, Otlewski J, Zakrzewska M. FGF12 is a novel component of the nucleolar NOLC1/TCOF1 ribosome biogenesis complex. Cell Commun Signal 2022; 20:182. [PMID: 36411431 PMCID: PMC9677703 DOI: 10.1186/s12964-022-01000-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
Among the FGF proteins, the least characterized superfamily is the group of fibroblast growth factor homologous factors (FHFs). To date, the main role of FHFs has been primarily seen in the modulation of voltage-gated ion channels, but a full picture of the function of FHFs inside the cell is far from complete. In the present study, we focused on identifying novel FGF12 binding partners to indicate its intracellular functions. Among the identified proteins, a significant number were nuclear proteins, especially RNA-binding proteins involved in translational processes, such as ribosomal processing and modification. We have demonstrated that FGF12 is localized to the nucleolus, where it interacts with NOLC1 and TCOF1, proteins involved in the assembly of functional ribosomes. Interactions with both NOLC1 and TCOF1 are unique to FGF12, as other FHF proteins only bind to TCOF1. The formation of nucleolar FGF12 complexes with NOLC1 and TCOF1 is phosphorylation-dependent and requires the C-terminal region of FGF12. Surprisingly, NOLC1 and TCOF1 are unable to interact with each other in the absence of FGF12. Taken together, our data link FHF proteins to nucleoli for the first time and suggest a novel and unexpected role for FGF12 in ribosome biogenesis. Video Abstract.
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Affiliation(s)
- Martyna Sochacka
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Radoslaw Karelus
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Lukasz Opalinski
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Daniel Krowarsch
- grid.8505.80000 0001 1010 5103Department of Protein Biotechnology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Martyna Biadun
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Jacek Otlewski
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Malgorzata Zakrzewska
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
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4
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Yu T, Sun Z, Cao X, Pang Q, Deng H. Recent trends in T7 phage application in diagnosis and treatment of various diseases. Int Immunopharmacol 2022; 110:109071. [DOI: 10.1016/j.intimp.2022.109071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/25/2022] [Accepted: 07/14/2022] [Indexed: 11/05/2022]
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5
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Wu M, Lu L, Chen S, Li Y, Zhang Q, Fu S, Deng X. Natural products inducing nucleolar stress: implications in cancer therapy. Anticancer Drugs 2022; 33:e21-e27. [PMID: 34561998 DOI: 10.1097/cad.0000000000001146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The nucleolus is the site of ribosome biogenesis and is found to play an important role in stress sensing. For over 100 years, the increase in the size and number of nucleoli has been considered as a marker of aggressive tumors. Despite this, the contribution of the nucleolus and the biologic processes mediated by it to cancer pathogenesis has been largely overlooked. This state has been changed over the recent decades with the demonstration that the nucleolus controls numerous cellular functions associated with cancer development. Induction of nucleolar stress has recently been regarded as being superior to conventional cytotoxic/cytostatic strategy in that it is more selective to neoplastic cells while sparing normal cells. Natural products represent an excellent source of bioactive molecules and some of them have been found to be able to induce nucleolar stress. The demonstration of these nucleolar stress-inducing natural products has paved the way for a new therapeutic approach to more delicate tumor cell-killing. This review provides a contemporary summary of the role of the nucleolus as a novel promising target for cancer therapy, with particular emphasis on natural products as an exciting new class of anti-cancer drugs with nucleolar stress-inducing properties.
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Affiliation(s)
- Mi Wu
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University
- Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha
| | - Lu Lu
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University
- Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha
| | - Sisi Chen
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University
- Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha
| | - Ying Li
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University
- Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha
| | - Qiuting Zhang
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University
- Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha
| | - Shujun Fu
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University
- Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha
| | - Xiyun Deng
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University
- Department of Pathophysiology, Hunan Normal University School of Medicine, Changsha
- Department of Pathophysiology, Jishou University School of Medicine, Jishou, Hunan, China
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6
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Bhushan A, Kumari R, Srivastava T. Scouting for common genes in the heterogenous hypoxic tumor microenvironment and their validation in glioblastoma. 3 Biotech 2021; 11:451. [PMID: 34631352 DOI: 10.1007/s13205-021-02987-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/04/2021] [Indexed: 12/17/2022] Open
Abstract
Investigating the therapeutic and prognostic potential of genes in the heterogeneous hypoxic niche of glioblastoma. We have analyzed RNA expression of U87MG cells cultured in hypoxia compared to normoxia. Common differentially expressed genes (DEGs) from GSE45301 and GSE18494 and their functional enrichment was performed using MetaScape and PANTHER. Hub genes and their ontology were identified using MCode cytoHubba and ClueGO and validated with GlioVis, Oncomine, HPA and PrognoScan. Using the GEO2R analysis of GSE45301 and GSE18494 datasets, we have found a total of 246 common DEGs (180 upregulated and 66 downregulated) and identified 2 significant modules involved in ribosome biogenesis and TNF signaling. Meta-analysis of key genes of each module in cytoHubba identified 17 hub genes (ATF3, BYSL, DUSP1, EGFR, JUN, ETS1, LYAR, NIP7, NOLC1, NOP2, NOP56, PNO1, RRS1, TNFAIP3, TNFRSF1B, UTP15, VEGFA). Of the 17 hub genes, ATF3, BYSL, EGFR, JUN, NIP7, NOLC1, PNO1, RRS1, TNFAIP3 and VEGFA were identified as hypoxia signatures associated with poor prognosis in Glioma. Ribosome biogenesis emerged as a vital contender of possible therapeutic potential with BYSL, NIP7, NOLC1, PNO1 and RRS1 showing prognostic value. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02987-2.
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Affiliation(s)
- Ashish Bhushan
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Ranbala Kumari
- National Institute of Pathology (ICMR), Safdarjung Hospital Campus, New Delhi, India
| | - Tapasya Srivastava
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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7
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Wang X, Chen Y, Zhu J, Yang Z, Gong X, Hui R, Huang G, Jin J. A comprehensive screening method for investigating the potential binding targets of doxorubicin based on protein microarray. Eur J Pharmacol 2021; 896:173896. [PMID: 33508279 DOI: 10.1016/j.ejphar.2021.173896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/06/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022]
Abstract
With the development of precision therapy, pharmacological research pays more and more attention to seek and confirm the target of drugs in order to understand the mechanism of drug action and reduce side effects. Screening candidate proteins can be effectively used to predict potential drug targets and toxicity. Therefore, a high-throughput drug-binding protein screening method based on protein microarray which contains over 21,000 human proteins was introduced in this investigation. Doxorubicin, a classical chemotherapeutic agent widely used in clinical treatment, was taken as a drug example in our protein screening study. Through microarray and bioinformatics analysis, more potential targets were found with different binding affinity to doxorubicin, and HRAS stands out as a critical protein from candidate proteins. In addition, the results revealed that the formation of the HRAS-RAF complex is promoted by doxorubicin. It is our expectation that the outcomes could benefit to understand the various effect of the doxorubicin and push the protein microarray screening to apply in the comprehensive pharmacological and toxicological investigation of other drugs.
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Affiliation(s)
- Xu Wang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Yun Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Jingyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Zhaoqi Yang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Xiaohai Gong
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Renjie Hui
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
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8
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Lu L, Yi H, Chen C, Yan S, Yao H, He G, Li G, Jiang Y, Deng T, Deng X. Nucleolar stress: is there a reverse version? J Cancer 2018; 9:3723-3727. [PMID: 30405843 PMCID: PMC6216007 DOI: 10.7150/jca.27660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/04/2018] [Indexed: 12/20/2022] Open
Abstract
The nucleolus is a dynamic structure that has roles in various physiological and pathophysiological processes. Perturbations on many aspects of the nucleolar functions are thought to cause “nucleolar stress”, which occurs in response to a variety of chemotherapeutic drugs. The main characteristic changes of nucleolar stress include: 1) reduction of the size and volume of the nucleolus; 2) inhibition of RNA Pol I-mediated rRNA synthesis; and 3) nucleoplasmic translocation of nucleolar stress-related proteins. In studying the apoptosis-inducing effect of the natural compound lovastatin (LV) on breast cancer stem cells, we unexpectedly uncovered a novel form of nucleolar stress, which we call “reverse nucleolar stress”. In our system, the canonical nucleolus stress inducer doxorubicin caused nucleoplasmic translocation of the nucleolar protein NPM and complete abolishment of Nolc1, an NPM-interacting protein and an activator of rRNA transcription. In contrast, the reverse nucleolar stress induced by LV is manifested as a more localized perinucleolar distribution of NPM and an increase in the protein level of Nolc1. Furthermore, translocation of the ribosomal protein RPL3 from the cytoplasm to the nucleolus and increased AgNOR staining were observed. These changes characterize a novel pattern of nucleolar stress doubtlessly distinguishable from the canonical one. The functional consequences of reverse nucleolar stress are not clear at present but may presumably be related to cell death or even normalization of the stressed cell. The discovery of reverse nucleolar stress opens up a new area of research in molecular and cellular biology and might have important implications in cancer therapy.
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Affiliation(s)
- Lu Lu
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China.,Departments of Pathology and Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan 410013, China
| | - Huimei Yi
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China.,Departments of Pathology and Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan 410013, China
| | - Chao Chen
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China.,Departments of Pathology and Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan 410013, China
| | - Shichao Yan
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China.,Departments of Pathology and Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan 410013, China
| | - Hui Yao
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China.,Departments of Pathology and Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan 410013, China
| | - Guangchun He
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China.,Departments of Pathology and Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan 410013, China
| | - Guifei Li
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China
| | - Yiqun Jiang
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China
| | - Tuo Deng
- Diabetes Research Center and Center for Bioenergetics, Houston Methodist Research Institute, Houston, Texas 77030, USA.,Department of Medicine, Weill Cornell Medical College at Cornell University, New York, New York 10021, USA
| | - Xiyun Deng
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University, Changsha, Hunan 410013, China.,Departments of Pathology and Pathophysiology, Hunan Normal University School of Medicine, Changsha, Hunan 410013, China
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9
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Yuan F, Xu C, Li G, Tong T. Nucleolar TRF2 attenuated nucleolus stress-induced HCC cell-cycle arrest by altering rRNA synthesis. Cell Death Dis 2018; 9:518. [PMID: 29725012 PMCID: PMC5938709 DOI: 10.1038/s41419-018-0572-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/14/2023]
Abstract
The nucleolus is an important organelle that is responsible for the biogenesis of ribosome RNA (rRNA) and ribosomal subunits assembly. It is also deemed to be the center of metabolic control, considering the critical role of ribosomes in protein translation. Perturbations of rRNA synthesis are closely related to cell proliferation and tumor progression. Telomeric repeat-binding factor 2 (TRF2) is a member of shelterin complex that is responsible for telomere DNA protection. Interestingly, it was recently reported to localize in the nucleolus of human cells in a cell-cycle-dependent manner, while the underlying mechanism and its role on the nucleolus remained unclear. In this study, we found that nucleolar and coiled-body phosphoprotein 1 (NOLC1), a nucleolar protein that is responsible for the nucleolus construction and rRNA synthesis, interacted with TRF2 and mediated the shuttle of TRF2 between the nucleolus and nucleus. Abating the expression of NOLC1 decreased the nucleolar-resident TRF2. Besides, the nucleolar TRF2 could bind rDNA and promoted rRNA transcription. Furthermore, in hepatocellular carcinoma (HCC) cell lines HepG2 and SMMC7721, TRF2 overexpression participated in the nucleolus stress-induced rRNA inhibition and cell-cycle arrest.
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Affiliation(s)
- Fuwen Yuan
- Research Center on Aging, Department of Medical Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chenzhong Xu
- Research Center on Aging, Department of Medical Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Guodong Li
- Research Center on Aging, Department of Medical Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Tanjun Tong
- Research Center on Aging, Department of Medical Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, China.
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10
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Nucleolar and coiled-body phosphoprotein 1 (NOLC1) regulates the nucleolar retention of TRF2. Cell Death Discov 2017; 3:17043. [PMID: 28875039 PMCID: PMC5582526 DOI: 10.1038/cddiscovery.2017.43] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/24/2017] [Accepted: 06/03/2017] [Indexed: 01/24/2023] Open
Abstract
Telomeric repeat-binding factor 2 (TRF2) was reported to localize in the nucleolus of human cells in a cell cycle-dependent manner; however, the underlying mechanism remains unclear. Here, we found that nucleolar and coiled-body phosphoprotein 1 (NOLC1) interacted with TRF2 and mediated the shuttling of TRF2 between the nucleolus and nucleus in human 293T and HepG2 cells. Ablation of NOLC1 expression increased the number of nuclear TRF2 foci and decreased the nucleolar level of TRF2. Conversely, NOLC1 overexpression promoted the nucleolar accumulation of TRF2. NOLC1 overexpression also increased the number of 53BP1 foci and induced the DNA damage response. In addition, co-expression of TRF2 rescued NOLC1 overexpression-induced cell cycle arrest and apoptosis.
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11
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Yuan F, Zhang Y, Ma L, Cheng Q, Li G, Tong T. Enhanced NOLC1 promotes cell senescence and represses hepatocellular carcinoma cell proliferation by disturbing the organization of nucleolus. Aging Cell 2017; 16:726-737. [PMID: 28493459 PMCID: PMC5506443 DOI: 10.1111/acel.12602] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 01/11/2023] Open
Abstract
The nucleolus is a key organelle that is responsible for the synthesis of rRNA and assembly of ribosomal subunits, which is also the center of metabolic control because of the critical role of ribosomes in protein synthesis. Perturbations of rRNA biogenesis are closely related to cell senescence and tumor progression; however, the underlying molecular mechanisms are not well understood. Here, we report that cellular senescence‐inhibited gene (CSIG) knockdown up‐regulated NOLC1 by stabilizing the 5′UTR of NOLC1 mRNA, and elevated NOLC1 induced the retention of NOG1 in the nucleolus, which is responsible for rRNA processing. Besides, the expression of NOLC1 was negatively correlated with CSIG in the aged mouse tissue and replicative senescent 2BS cells, and the down‐regulation of NOLC1 could rescue CSIG knockdown‐induced 2BS senescence. Additionally, NOLC1 expression was decreased in human hepatocellular carcinoma (HCC) tissue, and the ectopic expression of NOLC1 repressed the proliferation of HCC cells and tumor growth in a HCC xenograft model.
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Affiliation(s)
- Fuwen Yuan
- Peking University Research Center on Aging; Department of Biochemistry and Molecular Biology; Peking University Health Science Center, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function; Beijing 100191 China
| | - Yu Zhang
- Peking University Research Center on Aging; Department of Biochemistry and Molecular Biology; Peking University Health Science Center, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function; Beijing 100191 China
| | - Liwei Ma
- Peking University Research Center on Aging; Department of Biochemistry and Molecular Biology; Peking University Health Science Center, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function; Beijing 100191 China
| | - Qian Cheng
- Peking University Research Center on Aging; Department of Biochemistry and Molecular Biology; Peking University Health Science Center, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function; Beijing 100191 China
- Department of Hepatobilliary Surgery; Beijing, Key Surgical Basic Research Laboratory of Liver Cirrhosis and Liver Cancer; Peking University People's Hospital; Beijing 100044 China
| | - Guodong Li
- Peking University Research Center on Aging; Department of Biochemistry and Molecular Biology; Peking University Health Science Center, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function; Beijing 100191 China
| | - Tanjun Tong
- Peking University Research Center on Aging; Department of Biochemistry and Molecular Biology; Peking University Health Science Center, Beijing, Key Laboratory of Protein Posttranslational Modifications and Cell Function; Beijing 100191 China
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12
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Soininen SK, Vellonen KS, Heikkinen AT, Auriola S, Ranta VP, Urtti A, Ruponen M. Intracellular PK/PD Relationships of Free and Liposomal Doxorubicin: Quantitative Analyses and PK/PD Modeling. Mol Pharm 2016; 13:1358-65. [PMID: 26950248 DOI: 10.1021/acs.molpharmaceut.6b00008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanomedicines are widely studied for intracellular delivery of cancer drugs. However, the relationship between intracellular drug concentrations and drug responses are poorly understood. In this study, cellular and nuclear concentrations of doxorubicin were quantified with LC/MS after cell exposure with free and liposomal doxorubicin (pH-sensitive and pegylated liposomes). Cellular uptake of pegylated liposomes was low (∼3-fold extracellular concentrations) compared with doxorubicin in free form and pH-sensitive liposomes (up to 280-fold extracellular concentrations) in rat glioma (BT4C) and renal clear cell carcinoma (Caki-2) cells. However, after the cell exposure with pegylated liposomes, intracellular doxorubicin was distributed into the nuclear compartment in both cell types. Despite high drug concentrations in the nuclei, Caki-2 cells showed strong resistance toward doxorubicin. A model was successfully built to describe PK/PD relationship between drug concentrations in nucleus and cytotoxic responses in BT4C cells. This model is the first step to link target site concentration of doxorubicin into its effect and can be a useful part of more comprehensive future in vivo PK/PD models.
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Affiliation(s)
- Suvi K Soininen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland , Kuopio campus, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Kati-Sisko Vellonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland , Kuopio campus, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Aki T Heikkinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland , Kuopio campus, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Seppo Auriola
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland , Kuopio campus, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Veli-Pekka Ranta
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland , Kuopio campus, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - Arto Urtti
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland , Kuopio campus, P.O. Box 1627, FI-70211, Kuopio, Finland.,Centre for Drug Research, Faculty of Pharmacy, University of Helsinki , P.O. Box 56, FI-00014, Helsinki, Finland
| | - Marika Ruponen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland , Kuopio campus, P.O. Box 1627, FI-70211, Kuopio, Finland
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13
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Chang J, Kwon HJ. Discovery of novel drug targets and their functions using phenotypic screening of natural products. ACTA ACUST UNITED AC 2016; 43:221-31. [DOI: 10.1007/s10295-015-1681-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/27/2015] [Indexed: 12/27/2022]
Abstract
Abstract
Natural products are valuable resources that provide a variety of bioactive compounds and natural pharmacophores in modern drug discovery. Discovery of biologically active natural products and unraveling their target proteins to understand their mode of action have always been critical hurdles for their development into clinical drugs. For effective discovery and development of bioactive natural products into novel therapeutic drugs, comprehensive screening and identification of target proteins are indispensable. In this review, a systematic approach to understanding the mode of action of natural products isolated using phenotypic screening involving chemical proteomics-based target identification is introduced. This review highlights three natural products recently discovered via phenotypic screening, namely glucopiericidin A, ecumicin, and terpestacin, as representative case studies to revisit the pivotal role of natural products as powerful tools in discovering the novel functions and druggability of targets in biological systems and pathological diseases of interest.
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Affiliation(s)
- Junghwa Chang
- grid.15444.30 0000000404705454 Department of Biotechnology, Translational Research Center for Protein Function Control, College of Life Science and Biotechnology Yonsei University 120-749 Seoul Republic of Korea
| | - Ho Jeong Kwon
- grid.15444.30 0000000404705454 Department of Biotechnology, Translational Research Center for Protein Function Control, College of Life Science and Biotechnology Yonsei University 120-749 Seoul Republic of Korea
- grid.15444.30 0000000404705454 Department of Internal Medicine, College of Medicine Yonsei University 120-752 Seoul Republic of Korea
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14
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Piggott AM, Karuso P. Identifying the cellular targets of natural products using T7 phage display. Nat Prod Rep 2016; 33:626-36. [DOI: 10.1039/c5np00128e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A description of the T7 phage biopanning procedure is provided with tips and advice suitable for setup in a chemistry laboratory.
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Affiliation(s)
- Andrew M. Piggott
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
| | - Peter Karuso
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
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15
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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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16
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Lee CC, Tsai YT, Kao CW, Lee LW, Lai HJ, Ma TH, Chang YS, Yeh NH, Lo SJ. Mutation of a Nopp140 gene dao-5 alters rDNA transcription and increases germ cell apoptosis in C. elegans. Cell Death Dis 2014; 5:e1158. [PMID: 24722283 PMCID: PMC5424100 DOI: 10.1038/cddis.2014.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 02/17/2014] [Accepted: 02/20/2014] [Indexed: 01/03/2023]
Abstract
Human diseases of impaired ribosome biogenesis resulting from disruption of rRNA biosynthesis or loss of ribosomal components are collectively described as ‘ribosomopathies'. Treacher Collins syndrome (TCS), a representative human ribosomopathy with craniofacial abnormalities, is attributed to mutations in the tcof1 gene that has a homologous gene called nopp140. Previous studies demonstrated that the dao-5 (dauer and aged animal overexpression gene 5) of Caenorhabditis elegans is a member of nopp140 gene family and plays a role in nucleogenesis in the early embryo. Here, we established a C. elegans model for studying Nopp140-associated ribosomopathy. A null dao-5 mutant ok542 with a semi-infertile phenotype showed a delay in gonadogenesis, as well as a higher incidence of germline apoptosis. These phenotypes in dao-5(ok542) are likely resulted from inefficient rDNA transcription that was observed by run-on analyses and chromatin immunoprecipitation (ChIP) assays measuring the RNA Pol I occupancy on the rDNA promoter. ChIP assays further showed that the modifications of acetylated histone 4 (H4Ac) and dimethylation at the lysine 9 of histone 3 (H3K9me2) around the rDNA promoter were altered in dao-5 mutants compared with the N2 wild type. In addition, activated CEP-1 (a C. elegans p53 homolog) activity was also linked to the loss of DAO-5 in terms of the transcriptional upregulation of two CEP-1 downstream effectors, EGL-1 and CED-13. We propose that the dao-5 mutant of C. elegans can be a valuable model for studying human Nopp140-associated ribosomopathy at the cellular and molecular levels.
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Affiliation(s)
- C-C Lee
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan
| | - Y-T Tsai
- 1] Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan [2] Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - C-W Kao
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - L-W Lee
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - H-J Lai
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - T-H Ma
- 1] Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan [2] Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Y-S Chang
- 1] Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan [2] Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - N-H Yeh
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan
| | - S J Lo
- 1] Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan [2] Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
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17
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Wada A, Hara S, Osada H. Ribosome display and photo-cross-linking techniques for in vitro identification of target proteins of bioactive small molecules. Anal Chem 2014; 86:6768-73. [PMID: 24380432 DOI: 10.1021/ac4030208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The identification of target proteins of bioactive small molecules as bioprobe candidates or drug seeds is indispensable for elucidating their actions and predicting their side effects. To meet the current need, we developed a scheme for detection and identification of target proteins by using ribosome display and photo-cross-linking techniques, and demonstrated the feasibility. The mRNAs encoding full-length human proteins (FHPs) were constructed and translated in vitro to prepare pools of FHP-ribosome-mRNA complexes used for ribosome display selection. Expression levels of the FHPs were confirmed by Western blot analysis, and photo-cross-linked small-molecule beads were assessed through cell-free synthesized FHP binding assay. After ribosome display selection against photo-cross-linked small-molecule beads, RT-PCR using mRNAs recovered from the selected ternary complexes and electrophoresis of the PCR products allowed specific detection of the target proteins binding to the beads. In addition, a repeat of ribosome display selection enabled us to identify the target proteins even if the molar quantity was one ten-thousandth of that of the other proteins in a cell-free synthesized FHP pool. Therefore, these results showed that ribosome display using photo-cross-linked small-molecule beads and further extended FHP pool could be one of the powerful techniques for identification of unknown target proteins of bioactive small molecules.
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Affiliation(s)
- Akira Wada
- Antibiotics Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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18
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Yu X, Zhao P, Zhang L, Zhang Y. Screening of phage-displayed human liver cDNA library against doxorubicin with drug-immobilized monolithic polyacrylamide cryogel. Biomed Chromatogr 2013; 27:1574-9. [DOI: 10.1002/bmc.2962] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/12/2013] [Accepted: 05/13/2013] [Indexed: 12/18/2022]
Affiliation(s)
| | - Peng Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; 116023; China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; 116023; China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; 116023; China
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19
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Molecular basis for the action of a dietary flavonoid revealed by the comprehensive identification of apigenin human targets. Proc Natl Acad Sci U S A 2013; 110:E2153-62. [PMID: 23697369 DOI: 10.1073/pnas.1303726110] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flavonoids constitute the largest class of dietary phytochemicals, adding essential health value to our diet, and are emerging as key nutraceuticals. Cellular targets for dietary phytochemicals remain largely unknown, posing significant challenges for the regulation of dietary supplements and the understanding of how nutraceuticals provide health value. Here, we describe the identification of human cellular targets of apigenin, a flavonoid abundantly present in fruits and vegetables, using an innovative high-throughput approach that combines phage display with second generation sequencing. The 160 identified high-confidence candidate apigenin targets are significantly enriched in three main functional categories: GTPase activation, membrane transport, and mRNA metabolism/alternative splicing. This last category includes the heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2), a factor involved in splicing regulation, mRNA stability, and mRNA transport. Apigenin binds to the C-terminal glycine-rich domain of hnRNPA2, preventing hnRNPA2 from forming homodimers, and therefore, it perturbs the alternative splicing of several human hnRNPA2 targets. Our results provide a framework to understand how dietary phytochemicals exert their actions by binding to many functionally diverse cellular targets. In turn, some of them may modulate the activity of a large number of downstream genes, which is exemplified here by the effects of apigenin on the alternative splicing activity of hnRNPA2. Hence, in contrast to small-molecule pharmaceuticals designed for defined target specificity, dietary phytochemicals affect a large number of cellular targets with varied affinities that, combined, result in their recognized health benefits.
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20
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Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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21
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Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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22
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Kusayanagi T, Tsukuda S, Shimura S, Manita D, Iwakiri K, Kamisuki S, Takakusagi Y, Takeuchi T, Kuramochi K, Nakazaki A, Sakaguchi K, Kobayashi S, Sugawara F. The antitumor agent doxorubicin binds to Fanconi anemia group F protein. Bioorg Med Chem 2012; 20:6248-55. [DOI: 10.1016/j.bmc.2012.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/30/2022]
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23
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Takakusagi Y, Takakusagi K, Sugawara F, Sakaguchi K. Use of phage display technology for the determination of the targets for small-molecule therapeutics. Expert Opin Drug Discov 2012; 5:361-89. [PMID: 22823088 DOI: 10.1517/17460441003653155] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
IMPORTANCE OF THE FIELD Target discovery of drug-like small-molecules contributes to our understanding of biological phenomena at the molecular level as well as elucidating the mode of action of bioactive compounds. Research in this field is of high value because, in addition to basic observations, the data can be used to directly identify molecular targets or investigate pharmacokinetic characteristics of drugs in clinical use. AREAS COVERED IN THIS REVIEW In addition to providing a brief overview of phage display (PD) technology, we discuss screening platforms, different types of phage libraries and the application of this method to the determination of targets for small-molecule therapeutics over the past decade. WHAT THE READER WILL GAIN Readers will gain an understanding of the basis of PD technology through successful examples of the use of this method for the determination of targets for small-molecule therapeutics. They will learn what kinds of small-molecules were used to identify their binding partner, what characteristics and drawbacks are present in the use of small-molecule as bait, and what kinds of approaches were introduced in order to improve the technique to overcome the limitations of conventional strategies. TAKE HOME MESSAGE A suitable combination of diverse technologies from various different fields can act synergistically to increase throughput and enhance the efficiency of PD technology for the determination of targets for small-molecule therapeutics. The most suitable method for successful target identification of small-molecules of interest using PD technology can often be determined by referring to past examples.
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Affiliation(s)
- Yoichi Takakusagi
- Tokyo University of Science, Faculty of Science and Technology, Department of Applied Biological Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan +81 4 7124 1501 ext. 3409 ; +81 4 7123 9767 ; ;
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24
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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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25
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Lee WK, Lee SY, Na JH, Jang SW, Park CR, Kim SY, Lee SH, Han KH, Yu YG. Mitoxantrone Binds to Nopp140, an Intrinsically Unstructured Protein, and Modulate its Interaction with Protein Kinase CK2. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.6.2005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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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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27
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Yao N, Chen CY, Wu CY, Motonishi K, Kung HJ, Lam KS. Novel flavonoids with antiproliferative activities against breast cancer cells. J Med Chem 2011; 54:4339-49. [PMID: 21599001 DOI: 10.1021/jm101440r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A series of flavone analogues were synthesized and evaluated for their antiproliferation activity against breast cancer cells. The IC(50) of compound 10 and 24 were determined to be at 5 μM. These compounds were used as baits to screen breast cancer cDNA expression phage display proteome library. DNA sequencing of the binding phages suggests that eEF1A1 is a target protein for 10 and 24. Further optimization of these compounds led to the discovery of 39 with higher cytotoxic potency (IC(50) = 1 μM) and binding to eEF1A2. Biological and biochemical data suggest that eEF1A2 might be a therapeutic target and that 39 is an excellent lead compound for further development.
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Affiliation(s)
- Nianhuan Yao
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, California 95817, United States
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28
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Woolard J, Vousden W, Moss SJ, Krishnakumar A, Gammons MVR, Nowak DG, Dixon N, Micklefield J, Spannhoff A, Bedford MT, Gregory MA, Martin CJ, Leadlay PF, Zhang MQ, Harper SJ, Bates DO, Wilkinson B. Borrelidin modulates the alternative splicing of VEGF in favour of anti-angiogenic isoforms. Chem Sci 2011; 2011:273-278. [PMID: 22822423 PMCID: PMC3399765 DOI: 10.1039/c0sc00297f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The polyketide natural product borrelidin 1 is a potent inhibitor of angiogenesis and spontaneous metastasis. Affinity biopanning of a phage display library of colon tumor cell cDNAs identified the tandem WW domains of spliceosome-associated protein formin binding protein 21 (FBP21) as a novel molecular target of borrelidin, suggesting that borrelidin may act as a modulator of alternative splicing. In support of this idea, 1, and its more selective analog 2, bound to purified recombinant WW domains of FBP21. They also altered the ratio of vascular endothelial growth factor (VEGF) isoforms in retinal pigmented endothelial (RPE) cells in favour of anti-angiogenic isoforms. Transfection of RPE cells with FBP21 altered the ratio in favour of pro-angiogenic VEGF isoforms, an effect inhibited by 2. These data implicate FBP21 in the regulation of alternative splicing and suggest the potential of borrelidin analogs as tools to deconvolute key steps of spliceosome function.
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Affiliation(s)
- Jeanette Woolard
- Microvascular Research Laboratories, Bristol Heart Institute, Department of Physiology and Pharmacology, School of Veterinary Sciences, University of Bristol, Southwell Street Bristol, BS2 8EJ, UK. Fax: +44 (0)117 9288151; Tel: +44 (0)117 9289818;
| | - William Vousden
- Biotica, Chesterford Research Park, Cambridge, CB10 1XL, UK. Fax: +44 (0)1799 532921; Tel: +44 (0)1799 532925;
| | - Steven J. Moss
- Biotica, Chesterford Research Park, Cambridge, CB10 1XL, UK. Fax: +44 (0)1799 532921; Tel: +44 (0)1799 532925;
| | - Arjun Krishnakumar
- Microvascular Research Laboratories, Bristol Heart Institute, Department of Physiology and Pharmacology, School of Veterinary Sciences, University of Bristol, Southwell Street Bristol, BS2 8EJ, UK. Fax: +44 (0)117 9288151; Tel: +44 (0)117 9289818;
| | - Melissa VR Gammons
- Microvascular Research Laboratories, Bristol Heart Institute, Department of Physiology and Pharmacology, School of Veterinary Sciences, University of Bristol, Southwell Street Bristol, BS2 8EJ, UK. Fax: +44 (0)117 9288151; Tel: +44 (0)117 9289818;
| | - David G Nowak
- Microvascular Research Laboratories, Bristol Heart Institute, Department of Physiology and Pharmacology, School of Veterinary Sciences, University of Bristol, Southwell Street Bristol, BS2 8EJ, UK. Fax: +44 (0)117 9288151; Tel: +44 (0)117 9289818;
| | - Neil Dixon
- School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jason Micklefield
- School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Astrid Spannhoff
- The University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
| | - Mark T. Bedford
- The University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
| | - Matthew A. Gregory
- Biotica, Chesterford Research Park, Cambridge, CB10 1XL, UK. Fax: +44 (0)1799 532921; Tel: +44 (0)1799 532925;
| | - Christine J. Martin
- Biotica, Chesterford Research Park, Cambridge, CB10 1XL, UK. Fax: +44 (0)1799 532921; Tel: +44 (0)1799 532925;
| | - Peter F. Leadlay
- Department of Biochemistry, 80 Tennis Court Road, University of Cambridge, Cambridge CB2 1GA, UK
| | - Ming Q. Zhang
- Biotica, Chesterford Research Park, Cambridge, CB10 1XL, UK. Fax: +44 (0)1799 532921; Tel: +44 (0)1799 532925;
| | - Steven J. Harper
- Microvascular Research Laboratories, Bristol Heart Institute, Department of Physiology and Pharmacology, School of Veterinary Sciences, University of Bristol, Southwell Street Bristol, BS2 8EJ, UK. Fax: +44 (0)117 9288151; Tel: +44 (0)117 9289818;
| | - David O. Bates
- Microvascular Research Laboratories, Bristol Heart Institute, Department of Physiology and Pharmacology, School of Veterinary Sciences, University of Bristol, Southwell Street Bristol, BS2 8EJ, UK. Fax: +44 (0)117 9288151; Tel: +44 (0)117 9289818;
| | - Barrie Wilkinson
- Biotica, Chesterford Research Park, Cambridge, CB10 1XL, UK. Fax: +44 (0)1799 532921; Tel: +44 (0)1799 532925;
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Sunbul M, Emerson N, Yin J. Enzyme-catalyzed substrate attachment to phage surfaces for the selection of catalytic activities. Chembiochem 2011; 12:380-6. [PMID: 21290537 DOI: 10.1002/cbic.201000475] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Murat Sunbul
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, GCIS E505, Chicago, IL 60637, USA
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30
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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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31
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Van Dorst B, Mehta J, Rouah-Martin E, Somers V, De Coen W, Blust R, Robbens J. cDNA phage display as a novel tool to screen for cellular targets of chemical compounds. Toxicol In Vitro 2010; 24:1435-40. [DOI: 10.1016/j.tiv.2010.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/07/2010] [Accepted: 04/12/2010] [Indexed: 11/26/2022]
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32
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Liu S, Sun Y, Chen H, Song S, Xu Y. Magnetic screening of the potential targeted protein of salvianolic acid B using T7 phage display library. Appl Biochem Biotechnol 2010; 162:1206-13. [PMID: 20049555 DOI: 10.1007/s12010-009-8888-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Accepted: 12/08/2009] [Indexed: 10/20/2022]
Abstract
Salvianolic acid B is one of the effective components from the Chinese traditional drug Salvia miltiorrhiza (Danshen), which is widely used as a usual clinic drug for atherosclerosis-related disorder patients in China. But the targeting protein of salvianolic acid B is still not known. The possible targeting proteins of salvianolic acid B were explored by high throughput screening in this paper. Attached to the magnetic nanoparticles, salvianolic acid B was used for screening the high-affinity protein from the displaying cDNA peptide library phage. After biopanning, the selected protein or peptide sequences were used to explore the whole proteins containing the selected sequences in the National Center for Biotechnology Information website using blast. One of the selected phages was carried out by affinity analysis with salvianolic acid B using capillary electrophoresis (CE). The CE results indicated that the protein or peptide on the surface of the selected phages could bind the drug salvianolic acid B. The results are helpful to preliminarily explain the pharmacology of salvianolic acid B.
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Affiliation(s)
- Shupeng Liu
- Institute of Biomedical Engineering, Shanghai University, Shanghai 200072, People's Republic of China.
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33
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Piggott AM, Kriegel AM, Willows RD, Karuso P. Rapid isolation of novel FK506 binding proteins from multiple organisms using gDNA and cDNA T7 phage display. Bioorg Med Chem 2009; 17:6841-50. [DOI: 10.1016/j.bmc.2009.08.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 08/14/2009] [Accepted: 08/16/2009] [Indexed: 01/27/2023]
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34
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Gresham V, McLeod HL. Genomics: applications in mechanism elucidation. Adv Drug Deliv Rev 2009; 61:369-74. [PMID: 19166886 DOI: 10.1016/j.addr.2008.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 12/15/2008] [Indexed: 12/01/2022]
Abstract
The inability to predict the pharmacology and toxicology of drug candidates in preclinical studies has led to the decline in the number of new drugs which make it to market and the rise in cost associated with drug development. Identifying molecular interactions associated with therapeutic and toxic drug effects early in development is a top priority. Traditional mechanism elucidation strategies are narrow, often focusing on the identification of solely the molecular target. Methods which can offer additional insight into wide-ranging molecular interactions required for drug effect and the biochemical consequences of these interactions are in demand. Genomic strategies have made impressive advances in defining a more global view of drug action and are expected to increasingly be used as a complimentary tool in drug discovery and development.
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Affiliation(s)
- Venita Gresham
- UNC Institute for Pharmacogenomics and Individualized Therapy, Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, NC 27599-7360, USA
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35
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Kuramochi K, Miyano Y, Enomoto Y, Takeuchi R, Ishi K, Takakusagi Y, Saitoh T, Fukudome K, Manita D, Takeda Y, Kobayashi S, Sakaguchi K, Sugawara F. Identification of small molecule binding molecules by affinity purification using a specific ligand immobilized on PEGA resin. Bioconjug Chem 2009; 19:2417-26. [PMID: 19035789 DOI: 10.1021/bc8002716] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We investigated the application of resins used in solid-phase synthesis for affinity purification. A synthetic ligand for FK506-binding protein 12 (SLF) was immobilized on various resins, and the binding assays between the SLF-immobilized resins and FK506-binding protein 12 (FKBP12) were performed. Of the resins tested in this study, PEGA resin was the most effective for isolating FKBP12. This matrix enabled the isolation of FKBP12 from a cell lysate, and the identification of SLF-binding peptides from a phage cDNA library. We confirmed the interaction between SLF and these peptides using a cuvette type quartz crystal microbalance (QCM) apparatus. Our study suggests that PEGA resin has great potential as a tool not only for the purification and identification of small-molecule binding proteins but also for the selection of peptides that recognize target molecules.
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Affiliation(s)
- Kouji Kuramochi
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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36
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37
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He QL, Jiang H, Zhang F, Chen HB, Tang GL. Simultaneous identification of multiple receptors of natural product using an optimized cDNA phage display cloning. Bioorg Med Chem Lett 2008; 18:3995-8. [PMID: 18571405 DOI: 10.1016/j.bmcl.2008.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 06/03/2008] [Indexed: 10/22/2022]
Abstract
Simultaneously isolating more than one receptor of natural product remains a challenge to chemical genetics. Using cyclosporine A as an affinity probe and an optimized phage display cloning procedure, not only cyclophilin A, but also cyclophilin B was isolated as the full-length gene clone from a human brain cDNA library. This optimized protocol can be used to select protein targets of chemicals dependent on the binding affinity rather than on the relative abundance in cells.
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Affiliation(s)
- Qing-Li He
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai 200032, China
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38
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Saitoh T, Kuramochi K, Imai T, Takata KI, Takehara M, Kobayashi S, Sakaguchi K, Sugawara F. Podophyllotoxin directly binds a hinge domain in E2 of HPV and inhibits an E2/E7 interaction in vitro. Bioorg Med Chem 2008; 16:5815-25. [DOI: 10.1016/j.bmc.2008.03.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/17/2008] [Accepted: 03/21/2008] [Indexed: 02/08/2023]
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39
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Screening of phage displayed human liver cDNA library against dexamethasone. J Pharm Biomed Anal 2007; 45:701-5. [DOI: 10.1016/j.jpba.2007.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 08/30/2007] [Accepted: 09/08/2007] [Indexed: 11/23/2022]
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40
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Takakusagi Y, Takakusagi K, Kuramochi K, Kobayashi S, Sugawara F, Sakaguchi K. Identification of C10 biotinylated camptothecin (CPT-10-B) binding peptides using T7 phage display screen on a QCM device. Bioorg Med Chem 2007; 15:7590-8. [PMID: 17897832 DOI: 10.1016/j.bmc.2007.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 09/05/2007] [Accepted: 09/06/2007] [Indexed: 11/20/2022]
Abstract
A peptide sequence that can bind to camptothecin (CPT), a natural cytotoxic compound, was screened for using a T7 phage display system combined with a cuvette type quartz crystal microbalance (QCM) device. In this screen, after only 10min of monitoring of the interaction between injected T7 phage pool with immobilized C10 biotinylated CPT (CPT-10-B) on a gold electrode surface, six different kinds of phage (A-F) were identified as judged by the size of PCR product on agarose gel electrophoresis. Injection of each single phage (A-E) pool individually caused a frequency decrease, suggesting interaction with the immobilized CPT-10-B. In addition, the peptide sequence displayed on phages A-C is consistent with chemical and biological studies of the interaction of CPTs with topoisomerase I (TopI), human E prostanoid receptor third cytoplasmic polypeptide, and a series of esterases. The efficacy of T7 phage display screening for small molecules on QCM devices, target discovery from primary peptide sequence, and application of this strategy to various drug-like small molecules are discussed.
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Affiliation(s)
- Yoichi Takakusagi
- 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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41
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Aoki S, Morohashi K, Sunoki T, Kuramochi K, Kobayashi S, Sugawara F. Screening of paclitaxel-binding molecules from a library of random peptides displayed on T7 phage particles using paclitaxel-photoimmobilized resin. Bioconjug Chem 2007; 18:1981-6. [PMID: 17979224 DOI: 10.1021/bc700287v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paclitaxel (Taxol), an effective anticancer agent, is known to bind to tubulin and induce tubulin polymerization. Several other binding proteins of paclitaxel, such as Bcl-2, heat shock proteins, and NSC-1, have also been reported. Here, we describe a T7 phage-based display to screen for paclitaxel-binding molecules from a random peptide library using paclitaxel-photoimmobilized TentaGel resin. Specific phage particles that bind the paclitaxel-immobilized resin were obtained. Among them, two phage clones included the same consensus amino acid sequence (KACGRTRVTS). Analysis of the protein database using BLAST revealed that a portion of this sequence is conserved in the zinc finger domain of human NFX1. Binding affinity of paclitaxel against the partial recombinant protein of NFX1 (424aa-876aa) was confirmed by pull-down assays and surface plasmon resonance analyses.
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Affiliation(s)
- Sota Aoki
- Department of Applied Biological Science, Genome and Drug Research Center, and Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
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42
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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43
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Kim H, Deng L, Xiong X, Hunter WD, Long MC, Pirrung MC. Glyceraldehyde 3-phosphate dehydrogenase is a cellular target of the insulin mimic demethylasterriquinone B1. J Med Chem 2007; 50:3423-6. [PMID: 17595071 PMCID: PMC2556249 DOI: 10.1021/jm070437i] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study was undertaken to identify cellular proteins that bind an orally active natural product insulin mimic. Phage display cloning was used with a biotinylated derivative of this molecule as bait. Among the proteins identified was glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which has recently been shown to affect insulin receptor signaling. Binding data support a role for human GAPDH as another target of the insulin mimic, which could explain its action as a selective insulin receptor modulator.
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Affiliation(s)
| | | | | | | | | | - Michael C. Pirrung
- To whom correspondence should be addressed: f: 951-827-2749; p: 951-827-2722; e:
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44
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Kim YK, Chang YT. Tagged library approach facilitates forward chemical genetics. MOLECULAR BIOSYSTEMS 2007; 3:392-7. [PMID: 17533452 DOI: 10.1039/b702321a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Forward chemical genetics has been highlighted as a new method for the study of various biological pathways using exogenous ligands. However, limited success in the field has demonstrated that, in many cases, it is not feasible to determine the protein targets of small-molecule probes. Identifying protein targets is an integral part of forward chemical genetics and is also the most challenging. Over the past decade, several biochemical and genetic methods have been developed to facilitate target identification processes. Even so, one of the major difficulties is that these methods require the chemical modification of active compounds, with a significant amount of structure-activity relationship (SAR) study to ensure that the small-molecule tags do not compromise bioactivity. In this article, we will highlight a new strategy for small molecule libraries that have built-in linkers in order to avoid this well-known problem and demonstrate their successful use in forward chemical genetics.
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Affiliation(s)
- Yun Kyung Kim
- Department of Chemistry, New York University, New York, NY 10003, USA
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45
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Kim YK, Lee WK, Jin Y, Lee KJ, Jeon H, Yu YG. Doxorubicin Binds to Un-phosphorylated Form of hNopp140 and Reduces Protein Kinase CK2-Dependent Phosphorylation of hNopp140. BMB Rep 2006; 39:774-81. [PMID: 17129415 DOI: 10.5483/bmbrep.2006.39.6.774] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human nucleolar phosphoprotein p140 (hNopp140) is a nucleolar phosphoprotein that can bind to doxorubicin, an anti-cancer agent. We have examined the interaction between hNopp140 and doxorubicin as well as the folding property of hNopp140. Also, the effects of ATP and phosphorylation on the affinity of hNopp140 to doxorubicin are investigated by affinity dependent co-precipitation and surface plasmon resonance methods. Doxorubicin preferentially binds to un-phosphorylated form of hNopp140 with a KD value of 3.3 x 10(-7) M. Furthermore, doxorubicin reduces the protein kinase CK2-dependent phosphorylation of hNopp140, indicating that doxorubicin may perturb the cellular function of hNopp140 by reducing the protein kinase CK2-dependent phosphorylation of hNopp140. Low contents of the secondary structures of hNopp140 and the fast rate of proteolysis imply that hNopp140 has a high percentage of flexible regions or extended loop structures.
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Affiliation(s)
- Yun-Kyoung Kim
- Biomedical Research Center, Korea Institute of Science and Technology, 39-1, Hwawolkok-dong, Songbuk-gu, Seoul 136-791, Korea
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46
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Abstract
The nucleolus is the most prominent compartment in the nucleus and known as the site for ribosome biogenesis in eucaryotes. In contrast, there is no such equivalent structure for ribosome synthesis in procaryotes. This raises two concerns that how does the nucleolus evolve and that whether the nucleolus remains playing a single role in ribosome biogenesis along the evolution. Increasing data support new nucleolus functions, including signal recognition particle assembly, small RNA modification, telomerase maturation, cell-cycle and aging control, and cell stress sensor. Multiple functions of the nucleolus possibly result from the plurifunctionality of nucleolar proteins, such as nucleolin and Nopp140. Proteomic analyses of human and Arabidopsis nucleolus lead a remarkable progress in understanding the evolution and new functions of nucleoli. In this review, we present a brief history of nucleolus research and new concepts and unresolved questions. Also, we introduce hepatitis D virus for studying the communication between the nucleolus and other subnuclear compartments, and Caenorhabditis elegans for the role of nucleolus in the development and the epistatic control of nucleologenesis.
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Affiliation(s)
- Szecheng J Lo
- Department of Life Science, Graduate Institute of Basic Medical Science, 259, Wen-Hwa 1st Road, Chang Gung University, TaoYuan 333.
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47
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Marxfeld H, Staedtler F, Harleman JH. Characterisation of two rat mammary tumour models for breast cancer research by gene expression profiling. ACTA ACUST UNITED AC 2006; 58:133-43. [PMID: 16857353 DOI: 10.1016/j.etp.2006.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 05/15/2006] [Indexed: 11/20/2022]
Abstract
Breast cancer is the most frequently occurring cancer in women. Treatment options are still an active area of research. Models used for this purpose include induced models in rodents. By the advent of microarrays it has become possible to evaluate models not only for similar morphology or selected markers by polymerase chain reaction (PCR) or immunohistochemistry but also for the expression of thousands of genes at once. This study presents gene expression profiles of the hormone-sensitive 7,12-dimethylbenzanthracene-induced and the metastasising MTLn3-model. The models are discussed for their relevance to breast cancer in humans.
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Affiliation(s)
- Heike Marxfeld
- Preclinical Safety, Novartis Pharma AG, Basel, Switzerland.
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48
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Morimura T, Noda N, Kato Y, Watanabe T, Saitoh T, Yamazaki T, Takada K, Aoki S, Ohta K, Ohshige M, Sakaguchi K, Sugawara F. Identification of Antibiotic Clarithromycin Binding Peptide Displayed by T7 Phage Particles. J Antibiot (Tokyo) 2006; 59:625-32. [PMID: 17191677 DOI: 10.1038/ja.2006.83] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide libraries displayed by T7 phage, which contain random cDNA fragments insets, were screened for their ability to bind to a biotinylated derivative of clarithromycin. Phage particles bound to an immobilized derivative of the antibiotic were isolated and the inserted cDNA was amplified and sequenced. A common selected peptide sequence, composed of 19 amino acids, was obtained and a synthetic peptide with this sequence was produced. Surface plasmon resonance experiments showed that the synthetic peptide immobilized on a sensor chip bound to clarithromycin and the dissociation constant was determined to be 2.1 x 10(-3) M. The dissociation constants of other macrolide antibiotics, erythromycin, roxithromycin, azithromycin and josamycin were also determined to be 5.4 x 10(-3) M, 6.2 x 10(-5) M, 1.1 M and 3.4 x 10(-2) M, respectively. These results indicated that T7 phage display method might be useful to determine relatively weak interactions between small molecule drugs and the selected peptides which could represent a possible binding site conserved in binding proteins.
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Affiliation(s)
- Tetsuro Morimura
- Genome and Drug Research Center, Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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49
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Shi JH, Zhou Y, He ML, Jin J, Xiao YC, Xiao JH, Wei DZ. Synthesis of a novel 18β-glycyrrhetinic acid derivative. Chem Nat Compd 2006. [DOI: 10.1007/s10600-006-0111-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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50
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Feng L, Jin J, Zhang LF, Yan T, Tao WY. Analysis of the resveratrol-binding protein using phage-displayed random peptide library. Acta Biochim Biophys Sin (Shanghai) 2006; 38:342-8. [PMID: 16680375 DOI: 10.1111/j.1745-7270.2006.00163.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Resveratrol, a plant polyphenol, is found in significant amounts in the skin of grapes and in some traditional herbs. It is reported to exert different biological activities, such as inhibiting lipid peroxidation, scavenging free radicals, inhibiting platelet aggregation, and anticancer activity. In order to screen the resveratrol-binding proteins, we synthesized biotinylated resveratrol, purified by liquid chromatography and immobilized it into streptavidin-coated microplate wells. 3-(4,5-Demethylthiazol-)-2,5-diphenyl tetrazolium bromide assay showed little change in the anticancer activity of biotinylated resveratrol in vitro. A random library of phage-displayed peptides was screened for binding to immobilized resveratrol to isolate resveratrol-binding proteins. Several peptides were found to bind to resveratrol specifically, which was proven by enzyme-linked immunosorbent assay. Through amino acid sequence analysis of the selected peptides and human proteins using the BLAST program, the results showed that resveratrol has an affinity for various proteins such as breast cancer-associated antigen, breast cancer resistance protein, death-associated transcription factor, and human cyclin-dependent kinase. These results demonstrate that our study provides a feasible method for the study of binding proteins of natural compounds using a phage-displayed random peptide library.
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Affiliation(s)
- Lei Feng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Southern Yangtze University, Wuxi 214036, China
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