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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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2
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Shaw AL, Parson MAH, Truebestein L, Jenkins ML, Leonard TA, Burke JE. ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt1. Structure 2023; 31:343-354.e3. [PMID: 36758543 DOI: 10.1016/j.str.2023.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/21/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023]
Abstract
Akt is a master regulator of pro-growth signaling in the cell. Akt is activated by phosphoinositides that disrupt the autoinhibitory interface between the kinase and pleckstrin homology (PH) domains and then is phosphorylated at T308 and S473. Akt hyperactivation is oncogenic, which has spurred development of potent and selective inhibitors as therapeutics. Using hydrogen deuterium exchange mass spectrometry (HDX-MS), we interrogated the conformational changes upon binding Akt ATP-competitive and allosteric inhibitors. We compared inhibitors against three different states of Akt1. The allosteric inhibitor caused substantive conformational changes and restricts membrane binding. ATP-competitive inhibitors caused extensive allosteric conformational changes, altering the autoinhibitory interface and leading to increased membrane binding, suggesting that the PH domain is more accessible for membrane binding. This work provides unique insight into the autoinhibitory conformation of the PH and kinase domain and conformational changes induced by Akt inhibitors and has important implications for the design of Akt targeted therapeutics.
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Affiliation(s)
- Alexandria L Shaw
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, the University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, the University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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3
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Occhiuzzi MA, Lico G, Ioele G, De Luca M, Garofalo A, Grande F. Recent advances in PI3K/PKB/mTOR inhibitors as new anticancer agents. Eur J Med Chem 2023; 246:114971. [PMID: 36462440 DOI: 10.1016/j.ejmech.2022.114971] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022]
Abstract
The biochemical role of the PI3K/PKB/mTOR signalling pathway in cell-cycle regulation is now well known. During the onset and development of different forms of cancer it becomes overactive reducing apoptosis and allowing cell proliferation. Therefore, this pathway has become an important target for the treatment of various forms of malignant tumors, including breast cancer and follicular lymphoma. Recently, several more or less selective inhibitors targeting these proteins have been identified. In general, drugs that act on multiple targets within the entire pathway are more efficient than single targeting inhibitors. Multiple inhibitors exhibit high potency and limited drug resistance, resulting in promising anticancer agents. In this context, the present survey focuses on small molecule drugs capable of modulating the PI3K/PKB/mTOR signalling pathway, thus representing drugs or drug candidates to be used in the pharmacological treatment of different forms of cancer.
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Affiliation(s)
| | - Gernando Lico
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Giuseppina Ioele
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Michele De Luca
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Antonio Garofalo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Fedora Grande
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy.
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4
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Tsai PJ, Lai YH, Manne RK, Tsai YS, Sarbassov D, Lin HK. Akt: a key transducer in cancer. J Biomed Sci 2022; 29:76. [PMID: 36180910 PMCID: PMC9526305 DOI: 10.1186/s12929-022-00860-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/21/2022] [Indexed: 01/27/2023] Open
Abstract
Growth factor signaling plays a pivotal role in diverse biological functions, such as cell growth, apoptosis, senescence, and migration and its deregulation has been linked to various human diseases. Akt kinase is a central player transmitting extracellular clues to various cellular compartments, in turn executing these biological processes. Since the discovery of Akt three decades ago, the tremendous progress towards identifying its upstream regulators and downstream effectors and its roles in cancer has been made, offering novel paradigms and therapeutic strategies for targeting human diseases and cancers with deregulated Akt activation. Unraveling the molecular mechanisms for Akt signaling networks paves the way for developing selective inhibitors targeting Akt and its signaling regulation for the management of human diseases including cancer.
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Affiliation(s)
- Pei-Jane Tsai
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Hsin Lai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Rajesh Kumar Manne
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Yau-Sheng Tsai
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Clinical Medicine Research Center, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Dos Sarbassov
- Biology Department, School of Sciences and Humanities, and National Laboratory Astana, Nazarbayev University, Nur-Sultan City, 010000, Kazakhstan.
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA.
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5
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Toson B, Fortes IS, Roesler R, Andrade SF. Targeting Akt/PKB in pediatric tumors: A review from preclinical to clinical trials. Pharmacol Res 2022; 183:106403. [PMID: 35987481 DOI: 10.1016/j.phrs.2022.106403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/01/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
The serine/threonine kinase Akt is a major player in the phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) signaling pathway, and its modulation impacts multiple cellular processes such as growth, proliferation, and survival. Several abnormalities in this pathway have been documented over the years, and these alterations were shown to have great implications in tumorigenesis and resistance to chemotherapy. Thus, multiple Akt inhibitors have been developed and tested in adult tumors, and some of them are currently undergoing phase I, II, and III clinical trials for distinct cancers that arise during adulthood. Despite that, the impact of these inhibitors is still not fully understood in pediatric tumors, and Akt-specific targeting seems to be a promising approach to treat children affected by cancers. This review summarizes recent available evidence of Akt inhibitors in pediatric cancers, from both preclinical and clinical studies. In short, we demonstrate the impact that Akt inhibition provides in tumorigenesis, and we suggest targeting the PI3K/Akt/mTOR signaling pathway, alone or in combination with other inhibitors, is a feasible tool to achieve better outcomes in pediatric tumors.
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Affiliation(s)
- Bruno Toson
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Isadora S Fortes
- Pharmaceutical Synthesis Group (PHARSG), College of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Pharmaceutical Sciences Graduate Program, Federal University of Rio Grande do Sul (UFRGS), Av. Ipiranga, 2752, Porto Alegre, RS 90610-000, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Saulo F Andrade
- Pharmaceutical Synthesis Group (PHARSG), College of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Pharmaceutical Sciences Graduate Program, Federal University of Rio Grande do Sul (UFRGS), Av. Ipiranga, 2752, Porto Alegre, RS 90610-000, Brazil.
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6
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Chirom K, Malik MZ, Mangangcha IR, Somvanshi P, Singh RKB. Network medicine in ovarian cancer: topological properties to drug discovery. Brief Bioinform 2022; 23:6555408. [PMID: 35352113 DOI: 10.1093/bib/bbac085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/11/2022] [Accepted: 02/20/2022] [Indexed: 12/21/2022] Open
Abstract
Network medicine provides network theoretical tools, methods and properties to study underlying laws governing human interactome to identify disease states and disease complexity leading to drug discovery. Within this framework, we investigated the topological properties of ovarian cancer network (OCN) and the roles of hubs to understand OCN organization to address disease states and complexity. The OCN constructed from the experimentally verified genes exhibits fractal nature in the topological properties with deeply rooted functional communities indicating self-organizing behavior. The network properties at all levels of organization obey one parameter scaling law which lacks centrality lethality rule. We showed that $\langle k\rangle $ can be taken as a scaling parameter, where, power law exponent can be estimated from the ratio of network diameters. The betweenness centrality $C_B$ shows two distinct behaviors one shown by high degree hubs and the other by segregated low degree nodes. The $C_B$ power law exponent is found to connect the exponents of distributions of high and low degree nodes. OCN showed the absence of rich-club formation which leads to the missing of a number of attractors in the network causing formation of weakly tied diverse functional modules to keep optimal network efficiency. In OCN, provincial and connector hubs, which includes identified key regulators, take major responsibility to keep the OCN integrity and organization. Further, most of the key regulators are found to be over expressed and positively correlated with immune infiltrates. Finally, few potential drugs are identified related to the key regulators.
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Affiliation(s)
- Keilash Chirom
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India.,Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, 110019, India
| | - Md Zubbair Malik
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | | | - Pallavi Somvanshi
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - R K Brojen Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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7
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van Alphen C, Cloos J, Beekhof R, Cucchi DGJ, Piersma SR, Knol JC, Henneman AA, Pham TV, van Meerloo J, Ossenkoppele GJ, Verheul HMW, Janssen JJWM, Jimenez CR. Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines. Mol Cell Proteomics 2020; 19:884-899. [PMID: 32102969 PMCID: PMC7196578 DOI: 10.1074/mcp.ra119.001504] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 02/05/2020] [Indexed: 12/20/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disorder arising from hematopoietic myeloid progenitors. Aberrantly activated tyrosine kinases (TK) are involved in leukemogenesis and are associated with poor treatment outcome. Kinase inhibitor (KI) treatment has shown promise in improving patient outcome in AML. However, inhibitor selection for patients is suboptimal.In a preclinical effort to address KI selection, we analyzed a panel of 16 AML cell lines using phosphotyrosine (pY) enrichment-based, label-free phosphoproteomics. The Integrative Inferred Kinase Activity (INKA) algorithm was used to identify hyperphosphorylated, active kinases as candidates for KI treatment, and efficacy of selected KIs was tested.Heterogeneous signaling was observed with between 241 and 2764 phosphopeptides detected per cell line. Of 4853 identified phosphopeptides with 4229 phosphosites, 4459 phosphopeptides (4430 pY) were linked to 3605 class I sites (3525 pY). INKA analysis in single cell lines successfully pinpointed driver kinases (PDGFRA, JAK2, KIT and FLT3) corresponding with activating mutations present in these cell lines. Furthermore, potential receptor tyrosine kinase (RTK) drivers, undetected by standard molecular analyses, were identified in four cell lines (FGFR1 in KG-1 and KG-1a, PDGFRA in Kasumi-3, and FLT3 in MM6). These cell lines proved highly sensitive to specific KIs. Six AML cell lines without a clear RTK driver showed evidence of MAPK1/3 activation, indicative of the presence of activating upstream RAS mutations. Importantly, FLT3 phosphorylation was demonstrated in two clinical AML samples with a FLT3 internal tandem duplication (ITD) mutation.Our data show the potential of pY-phosphoproteomics and INKA analysis to provide insight in AML TK signaling and identify hyperactive kinases as potential targets for treatment in AML cell lines. These results warrant future investigation of clinical samples to further our understanding of TK phosphorylation in relation to clinical response in the individual patient.
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Affiliation(s)
- Carolien van Alphen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam Department of Hematology, De Boelelaan 1117, Amsterdam, Netherlands
| | - Jacqueline Cloos
- Amsterdam UMC, Vrije Universiteit Amsterdam Department of Hematology, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pediatric Oncology, De Boelelaan 1117, Amsterdam, Netherlands
| | - Robin Beekhof
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - David G J Cucchi
- Amsterdam UMC, Vrije Universiteit Amsterdam Department of Hematology, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pediatric Oncology, De Boelelaan 1117, Amsterdam, Netherlands
| | - Sander R Piersma
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Jaco C Knol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Alex A Henneman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Thang V Pham
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Johan van Meerloo
- Amsterdam UMC, Vrije Universiteit Amsterdam Department of Hematology, De Boelelaan 1117, Amsterdam, Netherlands
| | - Gert J Ossenkoppele
- Amsterdam UMC, Vrije Universiteit Amsterdam Department of Hematology, De Boelelaan 1117, Amsterdam, Netherlands
| | - Henk M W Verheul
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Jeroen J W M Janssen
- Amsterdam UMC, Vrije Universiteit Amsterdam Department of Hematology, De Boelelaan 1117, Amsterdam, Netherlands
| | - Connie R Jimenez
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands.
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8
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Bao B, Gao D, Li N, Wu M, Xing C. Near-Infrared Light Regulation of Tumor PI3K/Akt Signaling Pathway for Enhancing Cancer Cell Apoptosis through Conjugated Polymer Nanoparticles. ACS APPLIED BIO MATERIALS 2020; 3:2428-2437. [PMID: 35025292 DOI: 10.1021/acsabm.0c00161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calmodulin (CaM), as a calcium binding protein involved in the signal pathways of many life activities such as cell proliferation and apoptosis, can be regulated with the near-infrared (NIR) light-based photothermal conversion. Here, we build a conjugated polymer nanoparticle (CPNs-C) by assembling polypyrrole dione and dipalmitoyl phosphatidylethanolamine-polyethylene glycol-maleimide with a calmodulin antibody modified on the surface, which is NIR light-responsive for photothermally inducing apoptosis of cancer cells. Under near-infrared light irradiation, protein kinase B (Akt) and phosphatidylinositol 3-kinase, which bind to CaM, reduce the degree of phosphorylation due to the photothermal effect of CPNs-C, thus inhibiting the recruitment of Akt on the cell membrane. Therefore, the phosphorylation of GSK-3β downstream of the signaling pathway is reduced, and the phosphorylation of FoxO3a is enhanced, which can promote apoptosis of cancer cells. Compared with the photothermal effect of traditional CPNs, CPNs-C exhibits higher efficiency to regulate signaling pathways to promote cancer cells toward apoptosis. This strategy of utilizing NIR light to regulate the tumor apoptotic signaling pathway provides an effective way to enhance cancer cell apoptosis with high efficiency.
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Affiliation(s)
- Benkai Bao
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, Hebei University of Technology, Tianjin 300400, P.R. China
| | - Dong Gao
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, Hebei University of Technology, Tianjin 300400, P.R. China
| | - Ning Li
- School of Materials Science and Engineering, Hebei University of Technology Tianjin 300130, P. R. China
| | - Manman Wu
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, Hebei University of Technology, Tianjin 300400, P.R. China
| | - Chengfen Xing
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, Hebei University of Technology, Tianjin 300400, P.R. China
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Barnes EME, Xu Y, Benito A, Herendi L, Siskos AP, Aboagye EO, Nijhuis A, Keun HC. Lactic acidosis induces resistance to the pan-Akt inhibitor uprosertib in colon cancer cells. Br J Cancer 2020; 122:1298-1308. [PMID: 32152504 PMCID: PMC7188671 DOI: 10.1038/s41416-020-0777-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 02/07/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Akt signalling regulates glycolysis and drives the Warburg effect in cancer, thus decreased glucose utilisation is a pharmacodynamic marker of Akt inhibition. However, cancer cells can utilise alternative nutrients to glucose for energy such as lactate, which is often elevated in tumours together with increased acidity. We therefore hypothesised that lactic acidosis may confer resistance to Akt inhibition. METHODS The effect of the pan-Akt inhibitor uprosertib (GSK2141795), on HCT116 and LS174T colon cancer cells was evaluated in the presence and absence of lactic acid in vitro. Expression of downstream Akt signalling proteins was determined using a phosphokinase array and immunoblotting. Metabolism was assessed using 1H nuclear magnetic resonance spectroscopy, stable isotope labelling and gas chromatography-mass spectrometry. RESULTS Lactic acid-induced resistance to uprosertib was characterised by increased cell survival and reduced apoptosis. Uprosertib treatment reduced Akt signalling and glucose uptake irrespective of lactic acid supplementation. However, incorporation of lactate carbon and enhanced respiration was maintained in the presence of uprosertib and lactic acid. Inhibiting lactate transport or oxidative phosphorylation was sufficient to potentiate apoptosis in the presence of uprosertib. CONCLUSIONS Lactic acidosis confers resistance to uprosertib, which can be reversed by inhibiting lactate transport or oxidative metabolism.
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Affiliation(s)
- Emily M E Barnes
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Yitao Xu
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Adrian Benito
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Lili Herendi
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Alexandros P Siskos
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Eric O Aboagye
- Cancer Imaging Centre, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Anke Nijhuis
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Hector C Keun
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK.
- Division of Systems Medicine, Department of Metabolism, Digestion & Reproduction, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK.
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10
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Tolcher AW, Kurzrock R, Valero V, Gonzalez R, Heist RS, Tan AR, Means-Powell J, Werner TL, Becerra C, Wang C, Leonowens C, Kalyana-Sundaram S, Kleha JF, Gauvin J, D'Amelio AM, Ellis C, Ibrahim N, Yan L. Phase I dose-escalation trial of the oral AKT inhibitor uprosertib in combination with the oral MEK1/MEK2 inhibitor trametinib in patients with solid tumors. Cancer Chemother Pharmacol 2020; 85:673-683. [PMID: 32062691 DOI: 10.1007/s00280-020-04038-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/31/2020] [Indexed: 12/31/2022]
Abstract
PURPOSE This study aimed to determine the safety, tolerability, and recommended phase II doses of trametinib plus uprosertib (GSK2141795) in patients with solid tumors likely to be sensitive to MEK and/or AKT inhibition. METHODS This was a phase I, open-label, dose-escalation, and dose-expansion study in patients with triple-negative breast cancer or BRAF-wild type advanced melanoma. The primary outcome of the expansion study was investigator-assessed response. Among 126 enrolled patients, 63 received continuous oral daily dosing of trametinib and uprosertib, 29 received various alternative dosing schedules, and 34 were enrolled into expansion cohorts. Doses tested in the expansion cohort were trametinib 1.5 mg once daily (QD) + uprosertib 50 mg QD. RESULTS Adverse events (AEs) were consistent with those reported in monotherapy studies but occurred at lower doses and with greater severity. Diarrhea was the most common dose-limiting toxicity; diarrhea and rash were particularly difficult to tolerate. Overall, 59% and 6% of patients reported AEs with a maximum severity of grade 3 and 4, respectively. Poor tolerability prevented adequate delivery of uprosertib with trametinib at a concentration predicted to have clinical activity. The study was terminated early based on futility in the continuous-dosing expansion cohorts and a lack of pharmacological or therapeutic advantage with intermittent dosing. The objective response rate was < 5% (1 complete response, 5 partial responses). CONCLUSIONS Continuous and intermittent dosing of trametinib in combination with uprosertib was not tolerated, and minimal clinical activity was observed in all schedules tested.
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Affiliation(s)
- Anthony W Tolcher
- South Texas Accelerated Research Therapeutics, San Antonio, TX, USA. .,NEXT Oncology, San Antonio, USA. .,Texas Oncology, 5206 Research Drive, San Antonio, TX, 78240, USA.
| | - Razelle Kurzrock
- Division of Hematology and Oncology, Moores Cancer Center, University of California, San Diego, CA, USA
| | - Vincente Valero
- Division of Cancer Medicine, Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rene Gonzalez
- Division of Medical Oncology, Melanoma Research Clinics, University of Colorado Cancer Center, Aurora, CO, USA
| | | | - Antoinette R Tan
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Levine Cancer Institute, Atrium Health, Charlotte, USA
| | | | - Theresa L Werner
- Division of Medical Oncology, Department of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Carlos Becerra
- Texas Oncology, US Oncology-Baylor University Medical Center, Dallas, TX, USA
| | | | - Cathrine Leonowens
- GlaxoSmithKline, Collegeville, PA, USA.,Cathrine Leonowens Consulting LLC, Sanford, USA
| | | | - Joseph F Kleha
- Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA.,Array Biopharma, Boulder, CO, USA
| | | | | | | | - Nageatte Ibrahim
- GlaxoSmithKline, Collegeville, PA, USA.,Merck & Co, Kenilworth, USA
| | - Li Yan
- GlaxoSmithKline, Collegeville, PA, USA.,Brii Biosciences Limited, San Francisco, USA
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11
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Reinecke M, Heinzlmeir S, Wilhelm M, Médard G, Klaeger S, Kuster B. Kinobeads: A Chemical Proteomic Approach for Kinase Inhibitor Selectivity Profiling and Target Discovery. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527818242.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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Reinecke M, Ruprecht B, Poser S, Wiechmann S, Wilhelm M, Heinzlmeir S, Kuster B, Médard G. Chemoproteomic Selectivity Profiling of PIKK and PI3K Kinase Inhibitors. ACS Chem Biol 2019; 14:655-664. [PMID: 30901187 DOI: 10.1021/acschembio.8b01020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemical proteomic approaches utilizing immobilized, broad-selective kinase inhibitors (Kinobeads) have proven valuable for the elucidation of a compound's target profile under close-to-physiological conditions and often revealed potentially synergistic or toxic off-targets. Current Kinobeads enrich more than 300 native protein kinases from cell line or tissue lysates but do not systematically cover phosphatidylinositol 3-kinases (PI3Ks) and phosphatidylinositol 3-kinase-related kinases (PIKKs). Some PIKKs and PI3Ks show aberrant activation in many human diseases and are indeed validated drug targets. Here, we report the development of a novel version of Kinobeads that extends kinome coverage to these proteins. This is achieved by inclusion of two affinity probes derived from the clinical PI3K/MTOR inhibitors Omipalisib and BGT226. We demonstrate the utility of the new affinity matrix by the profiling of 13 clinical and preclinical PIKK/PI3K inhibitors. The large discrepancies between the PI3K affinity values obtained and reported results from recombinant assays led us to perform a phosphoproteomic experiment showing that the chemoproteomic assay is the better approximation of PI3K inhibitor action in cellulo. The results further show that NVP-BEZ235 is not a PI3K inhibitor. Surprisingly, the designated ATM inhibitor CP466722 was found to bind strongly to ALK2, identifying a new chemotype for drug discovery to treat fibrodysplasia ossificans progressiva.
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Affiliation(s)
- Maria Reinecke
- German Cancer Consortium
(DKTK), Munich, Germany
- German
Cancer
Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Ruprecht
- Center for Integrated
Protein Science Munich (CIPSM), Freising, Germany
| | | | - Svenja Wiechmann
- German Cancer Consortium
(DKTK), Munich, Germany
- German
Cancer
Research Center (DKFZ), Heidelberg, Germany
| | | | | | - Bernhard Kuster
- German Cancer Consortium
(DKTK), Munich, Germany
- German
Cancer
Research Center (DKFZ), Heidelberg, Germany
- Center for Integrated
Protein Science Munich (CIPSM), Freising, Germany
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13
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Butoxy Mansonone G Inhibits STAT3 and Akt Signaling Pathways in Non-Small Cell Lung Cancers: Combined Experimental and Theoretical Investigations. Cancers (Basel) 2019; 11:cancers11040437. [PMID: 30925736 PMCID: PMC6521096 DOI: 10.3390/cancers11040437] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 01/20/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) is the key molecular target for non-small cell lung cancer (NSCLC) due to its major contribution to complex signaling cascades modulating the survival of cancer cells. Targeting EGFR-mediated signaling pathways has been proved as a potential strategy for NSCLC treatment. In the present study, mansonone G (MG), a naturally occurring quinone-containing compound, and its semi-synthetic ether derivatives were subjected to investigate the anticancer effects on human NSCLC cell lines expressing wild-type EGFR (A549) and mutant EGFR (H1975). In vitro cytotoxicity screening results demonstrated that butoxy MG (MG3) exhibits the potent cytotoxic effect on both A549 (IC50 of 8.54 μM) and H1975 (IC50 of 4.21 μM) NSCLC cell lines with low toxicity against PCS201-010 normal fibroblast cells (IC50 of 21.16 μM). Western blotting and flow cytometric analyses revealed that MG3 induces a caspase-dependent apoptosis mechanism through: (i) inhibition of p-STAT3 and p-Akt without affecting upstream p-EGFR and (ii) activation of p-Erk. The 500-ns molecular dynamics simulations and the molecular mechanics combined with generalized Born surface area (MM/GBSA)-based binding free energy calculations suggested that MG3 could possibly interact with STAT3 SH2 domain and ATP-binding pocket of Akt. According to principal component analysis, the binding of MG3 toward STAT3 and Akt dramatically altered the conformation of proteins, especially the residues in the active site, stabilizing MG3 mainly through van der Waals interactions.
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14
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Song M, Bode AM, Dong Z, Lee MH. AKT as a Therapeutic Target for Cancer. Cancer Res 2019; 79:1019-1031. [PMID: 30808672 DOI: 10.1158/0008-5472.can-18-2738] [Citation(s) in RCA: 470] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/15/2018] [Accepted: 12/26/2018] [Indexed: 11/16/2022]
Abstract
Many cellular processes in cancer are attributed to kinase signaling networks. V-akt murine thymoma viral oncogene homolog (AKT) plays a major role in the PI3K/AKT signaling pathways. AKT is activated by PI3K or phosphoinositide-dependent kinases (PDK) as well as growth factors, inflammation, and DNA damage. Signal transduction occurs through downstream effectors such as mTOR, glycogen synthase kinase 3 beta (GSK3β), or forkhead box protein O1 (FOXO1). The abnormal overexpression or activation of AKT has been observed in many cancers, including ovarian, lung, and pancreatic cancers, and is associated with increased cancer cell proliferation and survival. Therefore, targeting AKT could provide an important approach for cancer prevention and therapy. In this review, we discuss the rationale for targeting AKT and also provide details regarding synthetic and natural AKT-targeting compounds and their associated studies.
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Affiliation(s)
- Mengqiu Song
- Basic Medical College, Zhengzhou University, Zhengzhou, Henan, China.,China-US (Henan) Hormel Cancer Institute, Jinshui District, Zhengzhou, Henan, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Zigang Dong
- Basic Medical College, Zhengzhou University, Zhengzhou, Henan, China. .,China-US (Henan) Hormel Cancer Institute, Jinshui District, Zhengzhou, Henan, China.,The Hormel Institute, University of Minnesota, Austin, Minnesota.,The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, China
| | - Mee-Hyun Lee
- Basic Medical College, Zhengzhou University, Zhengzhou, Henan, China. .,China-US (Henan) Hormel Cancer Institute, Jinshui District, Zhengzhou, Henan, China.,The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, China
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15
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Costa RLB, Han HS, Gradishar WJ. Targeting the PI3K/AKT/mTOR pathway in triple-negative breast cancer: a review. Breast Cancer Res Treat 2018; 169:397-406. [DOI: 10.1007/s10549-018-4697-y] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/29/2018] [Indexed: 01/01/2023]
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16
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Prêtre V, Wicki A. Inhibition of Akt and other AGC kinases: A target for clinical cancer therapy? Semin Cancer Biol 2017; 48:70-77. [PMID: 28473255 DOI: 10.1016/j.semcancer.2017.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/04/2017] [Accepted: 04/25/2017] [Indexed: 01/27/2023]
Abstract
AGC kinases have been identified to contribute to cancer development and progression. Currently, most AGC inhibitors in clinical development are Akt inhibitors such as MK-2206 or GDC-0068, which are known to promote cell growth arrest and to sensitize cancer cells to radiotherapy. Response rates in clinical trials with single agent Akt inhibitors are typically low. The observed adverse events are within the expected limits for compounds inhibiting the PI3K-mTOR axis. Preclinical and early clinical data for combination therapies are accumulating. Based on these data, several Akt inhibitors are about to enter phase 3 trials. Besides drugs that target Akt, p70S6K inhibitors have entered clinical development. Again, the response rates were rather low. In addition, relevant toxicities were identified, including a risk for coagulopathies with these compounds. Multi-AGC kinase inhibitors are also in early clinical development but the data is not sufficient yet to draw conclusions regarding their efficacy and side-effect profile. PKC inhibitors have been tested in the phase 3 setting but were found to lack efficacy. More trials with isoform-specific PKC inhibitors are expected. Taken together, therapies with AGC kinase inhibitors as single agents are unlikely to meet success. However, combination therapies and a precise stratification of patients according to the activation of signaling axes may increase the probability to see relevant efficacy with these compounds. The emergence of onco-immunotherapies holds some new challenges for these agents.
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Affiliation(s)
- Vincent Prêtre
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Andreas Wicki
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland; Department of Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland.
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17
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Zhao Q, Ouyang X, Wan X, Gajiwala KS, Kath JC, Jones LH, Burlingame AL, Taunton J. Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes. J Am Chem Soc 2017; 139:680-685. [PMID: 28051857 PMCID: PMC5858558 DOI: 10.1021/jacs.6b08536] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein kinases comprise a large family of structurally related enzymes. A major goal in kinase-inhibitor development is to selectively engage the desired kinase while avoiding myriad off-target kinases. However, quantifying inhibitor interactions with multiple endogenous kinases in live cells remains an unmet challenge. Here, we report the design of sulfonyl fluoride probes that covalently label a broad swath of the intracellular kinome with high efficiency. Protein crystallography and mass spectrometry confirmed a chemoselective reaction between the sulfonyl fluoride and a conserved lysine in the ATP binding site. Optimized probe 2 (XO44) covalently modified up to 133 endogenous kinases, efficiently competing with high intracellular concentrations of ATP. We employed probe 2 and label-free mass spectrometry to quantify intracellular kinase engagement by the approved drug, dasatinib. The data revealed saturable dasatinib binding to a small subset of kinase targets at clinically relevant concentrations, highlighting the utility of lysine-targeted sulfonyl fluoride probes in demanding chemoproteomic applications.
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Affiliation(s)
- Qian Zhao
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
- Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Xiaohu Ouyang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
| | - Xiaobo Wan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
| | - Ketan S. Gajiwala
- Worldwide Research and Development, Pfizer, San Diego, California 92121, United States
| | - John C. Kath
- Worldwide Research and Development, Pfizer, San Diego, California 92121, United States
| | - Lyn H. Jones
- Medicine Design, Pfizer, Cambridge, Massachusetts 02139, United States
| | - Alma L. Burlingame
- Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
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18
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Xiao Y, Wang Y. Global discovery of protein kinases and other nucleotide-binding proteins by mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:601-19. [PMID: 25376990 PMCID: PMC5609854 DOI: 10.1002/mas.21447] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 08/08/2014] [Accepted: 08/09/2014] [Indexed: 05/11/2023]
Abstract
Nucleotide-binding proteins, such as protein kinases, ATPases and GTP-binding proteins, are among the most important families of proteins that are involved in a number of pivotal cellular processes. However, global study of the structure, function, and expression level of nucleotide-binding proteins as well as protein-nucleotide interactions can hardly be achieved with the use of conventional approaches owing to enormous diversity of the nucleotide-binding protein family. Recent advances in mass spectrometry (MS) instrumentation, coupled with a variety of nucleotide-binding protein enrichment methods, rendered MS-based proteomics a powerful tool for the comprehensive characterizations of the nucleotide-binding proteome, especially the kinome. Here, we review the recent developments in the use of mass spectrometry, together with general and widely used affinity enrichment approaches, for the proteome-wide capture, identification and quantification of nucleotide-binding proteins, including protein kinases, ATPases, GTPases, and other nucleotide-binding proteins. The working principles, advantages, and limitations of each enrichment platform in identifying nucleotide-binding proteins as well as profiling protein-nucleotide interactions are summarized. The perspectives in developing novel MS-based nucleotide-binding protein detection platform are also discussed. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:601-619, 2016.
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Affiliation(s)
| | - Yinsheng Wang
- Correspondence to: Yinsheng Wang, Department of Chemistry, University of California, Riverside, CA 92521-0403.
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19
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Weigt D, Hopf C, Médard G. Studying epigenetic complexes and their inhibitors with the proteomics toolbox. Clin Epigenetics 2016; 8:76. [PMID: 27437033 PMCID: PMC4950666 DOI: 10.1186/s13148-016-0244-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/05/2016] [Indexed: 12/27/2022] Open
Abstract
Some epigenetic modifier proteins have become validated clinical targets. With a few small molecule inhibitors already approved by national health administrations and many more in the pharmaceutical industry pipelines, there is a need for technologies that can promote full comprehension of the molecular action of these drugs. Proteomics, with its relatively unbiased nature, can contribute to a thorough understanding of the complexity of the megadalton complexes, which write, read and erase the histone code, and it can help study the on-target and off-target effect of the drugs designed to modulate their action. This review on the one hand gathers the published affinity probes able to decipher small molecule targets and off-targets in a close-to-native environment. These are small molecule analogues of epigenetic drugs conceived as protein target enrichment tools after they have engaged them in cells or lysates. Such probes, which have been designed for deacetylases, bromodomains, demethylases, and methyltransferases not only enrich their direct protein targets but also their stable interactors, which can be identified by mass spectrometry. Hence, they constitute a tool to study the epigenetic complexes together with other techniques also reviewed here: immunoaffinity purification with antibodies against native protein complex constituents or epitope tags, affinity matrices designed to bind recombinantly tagged protein, and enrichment of the complexes using histone tail peptides as baits. We expect that this toolbox will be adopted by more and more researchers willing to harness the spectacular advances in mass spectrometry to the epigenetic field.
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Affiliation(s)
- David Weigt
- />Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- />HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Carsten Hopf
- />Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- />HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Guillaume Médard
- />Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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20
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Zhang Y, Stefanovic B. Akt mediated phosphorylation of LARP6; critical step in biosynthesis of type I collagen. Sci Rep 2016; 6:22597. [PMID: 26932461 PMCID: PMC4773855 DOI: 10.1038/srep22597] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/17/2016] [Indexed: 12/31/2022] Open
Abstract
La ribonucleoprotein domain family, member 6 (LARP6) is the RNA binding protein, which regulates translation of collagen mRNAs and synthesis of type I collagen. Posttranslational modifications of LARP6 and how they affect type I collagen synthesis have not been studied. We show that in lung fibroblasts LARP6 is phosphorylated at 8 serines, 6 of which are located within C-terminal domain. Phosphorylation of LARP6 follows a hierarchical order; S451 phosphorylation being a prerequisite for phosphorylations of other serines. Inhibition of PI3K/Akt pathway reduced the phosphorylation of LARP6, but had no effect on the S451A mutant, suggesting that PI3K/Akt pathway targets S451 and we have identified Akt as the responsible kinase. Overexpression of S451A mutant had dominant negative effect on collagen biosynthesis; drastically reduced secretion of collagen and induced hyper-modifications of collagen α2 (I) polypeptides. This indicates that LARP6 phosphorylation at S451 is critical for regulating translation and folding of collagen polypeptides. Akt inhibitor, GSK-2141795, which is in clinical trials for treatment of solid tumors, reduced collagen production by human lung fibroblasts with EC50 of 150 nM. This effect can be explained by inhibition of LARP6 phosphorylation and suggests that Akt inhibitors may be effective in treatment of various forms of fibrosis.
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Affiliation(s)
- Yujie Zhang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
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21
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Neel VA, Todorova K, Wang J, Kwon E, Kang M, Liu Q, Gray N, Lee SW, Mandinova A. Sustained Akt Activity Is Required to Maintain Cell Viability in Seborrheic Keratosis, a Benign Epithelial Tumor. J Invest Dermatol 2015; 136:696-705. [PMID: 26739095 DOI: 10.1016/j.jid.2015.12.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/17/2015] [Accepted: 11/06/2015] [Indexed: 10/24/2022]
Abstract
Seborrheic keratoses (SKs) are common benign skin tumors that share many morphological features with their malignant counterpart, squamous cell carcinoma. SKs frequently have acquired oncogenic mutations in the receptor tyrosine kinase/phosphatidylinositol 3-kinase/Akt signaling cascade. We developed a reliable culture system to study SKs in vitro and screened these cells using a library of selective kinase inhibitors to evaluate effects on cell survival. These benign tumors are sensitive to inhibition by ATP-competitive Akt inhibitors, including A-443654 and GSK690693. RNA interference-mediated Akt suppression mimicked the effects of enzyme inhibition in cultured cells. Akt inhibition suppressed phosphorylation of downstream targets of Akt kinase that are critical for cell survival, including MDM2 and FOXO3a, and induced apoptosis. Cell death was also dependent on p53, mutations in which, although common in cutaneous squamous cell carcinoma, have not been identified in SKs. Intact explants of SKs were also sensitive to Akt inhibition. In addition to the obvious therapeutic implications of these findings, identifying the signaling characteristics that differentiate benign and malignant tumors may inform our understanding of the malignant state.
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Affiliation(s)
- Victor A Neel
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.
| | - Kristina Todorova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Jun Wang
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Eunjeong Kwon
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Minjeong Kang
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Qingsong Liu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Nathanael Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sam W Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Anna Mandinova
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA; Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.
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22
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Ruprecht B, Zecha J, Heinzlmeir S, Médard G, Lemeer S, Kuster B. Evaluation of Kinase Activity Profiling Using Chemical Proteomics. ACS Chem Biol 2015; 10:2743-52. [PMID: 26378887 DOI: 10.1021/acschembio.5b00616] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein kinases are important mediators of intracellular signaling and are reversibly activated by phosphorylation. Immobilized kinase inhibitors can be used to enrich these often low-abundance proteins, to identify targets of kinase inhibitors, or to probe their selectivity. It has been suggested that the binding of kinases to affinity beads reflects a kinase's activation status, a concept that is under considerable debate. To assess the merits of the idea, we performed a series of experiments including quantitative phosphoproteomics and purification of kinases by single or mixed affinity matrices from signaling activated or resting cancer cells. The data show that mixed affinity beads largely bind kinases independent of their activation status, and experiments using individual immobilized kinase inhibitors show mixed results in terms of preference for binding the active or inactive conformation. Taken together, activity- or conformation-dependent binding to such affinity resins depends (i) on the kinase, (ii) on the affinity probe, and (iii) on the activation status of the lysate or cell. As a result, great caution should be exercised when inferring kinase activity from such binding data. The results also suggest that assaying kinase activity using binding data is restricted to a limited number of well-chosen cases.
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Affiliation(s)
- Benjamin Ruprecht
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- Center for Protein Science Munich (CIPSM), 85354 Freising, Germany
| | - Jana Zecha
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Stephanie Heinzlmeir
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
| | - Simone Lemeer
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- Center for Protein Science Munich (CIPSM), 85354 Freising, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenemeyer-Forum 5, 85354 Freising, Germany
- Center for Protein Science Munich (CIPSM), 85354 Freising, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
- Bavarian
Biomolecular Mass Spectrometry Center, Technische Universität München, 85354 Freising, Germany
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23
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Höfener M, Pachl F, Kuster B, Sewald N. Inhibitor-based affinity probes for the investigation of JAK signaling pathways. Proteomics 2015; 15:3066-74. [PMID: 25959371 DOI: 10.1002/pmic.201400324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 03/04/2015] [Accepted: 05/05/2015] [Indexed: 11/06/2022]
Abstract
The Janus Kinase (JAK) signaling pathway plays a key role for many cellular processes and has recently been correlated with neuronal disorders. In order to understand new links of JAK family members with other signaling pathways, chemical proteomics tools with broad kinase coverage are desirable. A probe that shows outstanding kinase selectivity and allows for the enrichment of up to 133 kinases including many mitogen activated kinase (MAPK) members and JAK kinases has been developed. Furthermore, this probe was applied to establish the selectivity profile of the JAK1/2 inhibitor momelotinib that is currently evaluated in clinical phase 3 studies. These results render this probe a valuable tool for the investigation of JAK and JAK related signaling pathways and the selectivity profiling of kinase inhibitors.
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Affiliation(s)
- Michael Höfener
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Fiona Pachl
- Chair of Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany.,Center for Integrated Protein Science Munich, Freising, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
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24
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Médard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, Qiao H, Ku X, Wilhelm M, Kuehne T, Wu Z, Dittmann A, Hopf C, Kramer K, Kuster B. Optimized chemical proteomics assay for kinase inhibitor profiling. J Proteome Res 2015; 14:1574-86. [PMID: 25660469 DOI: 10.1021/pr5012608] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Solid supported probes have proven to be an efficient tool for chemical proteomics. The kinobeads technology features kinase inhibitors covalently attached to Sepharose for affinity enrichment of kinomes from cell or tissue lysates. This technology, combined with quantitative mass spectrometry, is of particular interest for the profiling of kinase inhibitors. It often leads to the identification of new targets for medicinal chemistry campaigns where it allows a two-in-one binding and selectivity assay. The assay can also uncover resistance mechanisms and molecular sources of toxicity. Here we report on the optimization of the kinobead assay resulting in the combination of five chemical probes and four cell lines to cover half the human kinome in a single assay (∼ 260 kinases). We show the utility and large-scale applicability of the new version of kinobeads by reprofiling the small molecule kinase inhibitors Alvocidib, Crizotinib, Dasatinib, Fasudil, Hydroxyfasudil, Nilotinib, Ibrutinib, Imatinib, and Sunitinib.
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Affiliation(s)
- Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technische Universität München , Freising, Germany
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25
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Abstract
Small molecule inhibitors of protein kinases are key tools for signal transduction research and represent a major class of targeted drugs. Recent developments in quantitative proteomics enable an unbiased view on kinase inhibitor selectivity and modes of action in the biological context. While chemical proteomics techniques utilizing quantitative mass spectrometry interrogate both target specificity and affinity in cellular extracts, proteome-wide phosphorylation analyses upon kinase inhibitor treatment identify signal transduction pathway and network regulation in an unbiased manner. Thus, critical information is provided to promote new insights into mechanisms of kinase signaling and their relevance for kinase inhibitor drug discovery.
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Affiliation(s)
- Henrik Daub
- Evotec (München) GmbH, Am Klopferspitz
19a, 82152 Martinsried, Germany
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26
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Höfener M, Pachl F, Take T, Fischer von Mollard G, Kuster B, Sewald N. Investigating RET RTK Signaling Pathways Using an IAP-Based Activity-Profiling Approach. J Proteome Res 2014; 13:3628-34. [DOI: 10.1021/pr500163r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Michael Höfener
- Organic
and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Fiona Pachl
- Chair
for Proteomics and Bioanalytics, Center of Life and Food Sciences
Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Tim Take
- Biochemistry,
Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | | | - Bernhard Kuster
- Chair
for Proteomics and Bioanalytics, Center of Life and Food Sciences
Weihenstephan, Technische Universität München, 85354 Freising, Germany
- Center for Integrated Protein Science Munich, 85354 Freising, Germany
| | - Norbert Sewald
- Organic
and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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27
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Ku X, Heinzlmeir S, Helm D, Médard G, Kuster B. New affinity probe targeting VEGF receptors for kinase inhibitor selectivity profiling by chemical proteomics. J Proteome Res 2014; 13:2445-52. [PMID: 24712744 DOI: 10.1021/pr401247t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Solid tumors are dependent for growth on nutrients and the supply of oxygen, which they often acquire via neoangiogenesis. Vascular endothelial growth factors and the corresponding receptors (VEGFRs) play central roles in this process, and consequently, the blockade of this pathway is one therapeutic strategy for cancer treatment. A number of small molecules inhibiting VEGFR inhibitors have been developed for clinical use, and a comprehensive view of target selectivity is important to assess the therapeutic as well as risk potential of a drug molecule. Recent advances in mass spectrometry-based chemical proteomics allow analyses of drug-target interactions under close-to-physiological conditions, and in this study, we report on the design, synthesis, and application of a small molecule affinity probe as a tool for the selectivity profiling of VEGFR and other kinase inhibitors. The probe is capable of binding >132 protein kinases, including angiokinases such as VEGFRs, PDGFRs, and c-KIT from lysates of cancer cell lines or human placenta tissue. Combining the new probe with Kinobeads in competitive binding assays, we were able to identify nanomolar off-targets of the VEGFR/PDGFR inhibitors pazopanib and axitinib. Because of its broad binding spectrum, the developed chemical tool can be generically used for the discovery of kinase inhibitor targets, which may contribute to a more comprehensive understanding of the mechanisms of action of such drugs.
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Affiliation(s)
- Xin Ku
- Chair for Proteomics and Bioanalytics, Technische Universität München , Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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28
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Ku X, Heinzlmeir S, Liu X, Médard G, Kuster B. A new chemical probe for quantitative proteomic profiling of fibroblast growth factor receptor and its inhibitors. J Proteomics 2013; 96:44-55. [PMID: 24184958 DOI: 10.1016/j.jprot.2013.10.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/13/2013] [Accepted: 10/18/2013] [Indexed: 01/09/2023]
Abstract
UNLABELLED Recent advances in mass spectrometry-based chemical proteomics allow unbiased analysis of drug-target interactions under close to physiological conditions. In this study, we designed and synthesized two small molecule probes targeting fibroblast growth factor receptors (FGFRs) and applied them to evaluate the selectivity profiles of the FGFR inhibitors Dovitinib and Orantinib. Probe F2 was capable of enriching all members of the FGF receptor family as well as other kinases involved in cancer such as KDR, FLT4 and RET from lysates of cancer cells or human placenta tissue. In combination with the established Kinobeads™ approach, probe F2 facilitated the identification of the target spectrum of the two inhibitors confirming many of the previously identified (off-) targets such as AURKA, FLT4-VEGFR3, IKBKE and PDGFRβ. The newly synthesized probe enlarges the arsenal of chemical proteomic tools for the expression profiling of kinases and selectivity profiling of their inhibitors. It will also be useful in applications aiming at a better understanding of a drug's cellular mechanisms of action as well as highlighting potential beneficial or adverse side effects. BIOLOGICAL SIGNIFICANCE The synthesis of a new chemical affinity probe targeting FGF-receptors and many other kinases improved the general scope of drug selectivity profiling by chemical proteomics. The application of the developed chemical tool identified most of the known targets for the advanced clinical kinase inhibitors Dovitinib and Orantinib thus exemplify the practical utility of the developed probe and the results obtained shed further light on how these drugs exert their anti-cancer activity in cells. More generally speaking, the significance of the work is that the molecular tools presented here extend the application scope of kinobeads based kinase profiling to FGFR/VEGFR/PDGFR families, which thus may be generically employed for selectivity profiling of kinase inhibitors using chemical proteomics. The overall aim of such studies is to improve our understanding of how target as well as off-target profiles can be used to assess or predict the therapeutic efficacy of a drug.
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Affiliation(s)
- Xin Ku
- Chair for Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Stephanie Heinzlmeir
- Chair for Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Xiaofeng Liu
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, 200237 Shanghai, China
| | - Guillaume Médard
- Chair for Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany; Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany.
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