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Yang CR, Park E, Chen L, Datta A, Chou CL, Knepper MA. Proteomics and AQP2 regulation. J Physiol 2024; 602:3011-3023. [PMID: 36571566 PMCID: PMC10686537 DOI: 10.1113/jp283899] [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: 10/04/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022] Open
Abstract
The advent of modern quantitative protein mass spectrometry techniques around the turn of the 21st century has contributed to a revolution in biology referred to as 'systems biology'. These methods allow identification and quantification of thousands of proteins in a biological specimen, as well as detection and quantification of post-translational protein modifications including phosphorylation. Here, we discuss these methodologies and show how they can be applied to understand the effects of the peptide hormone vasopressin to regulate the molecular water channel aquaporin-2. The emerging picture provides a detailed framework for understanding the molecular mechanisms involved in water balance disorders.
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Affiliation(s)
- Chin-Rang Yang
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Euijung Park
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Lihe Chen
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Arnab Datta
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
- Division of Neuroscience, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Mark A. Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
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2
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Müller J, Boubaker G, Müller N, Uldry AC, Braga-Lagache S, Heller M, Hemphill A. Investigating Antiprotozoal Chemotherapies with Novel Proteomic Tools-Chances and Limitations: A Critical Review. Int J Mol Sci 2024; 25:6903. [PMID: 39000012 PMCID: PMC11241152 DOI: 10.3390/ijms25136903] [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: 05/31/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Identification of drug targets and biochemical investigations on mechanisms of action are major issues in modern drug development. The present article is a critical review of the classical "one drug"-"one target" paradigm. In fact, novel methods for target deconvolution and for investigation of resistant strains based on protein mass spectrometry have shown that multiple gene products and adaptation mechanisms are involved in the responses of pathogens to xenobiotics rather than one single gene or gene product. Resistance to drugs may be linked to differential expression of other proteins than those interacting with the drug in protein binding studies and result in complex cell physiological adaptation. Consequently, the unraveling of mechanisms of action needs approaches beyond proteomics. This review is focused on protozoan pathogens. The conclusions can, however, be extended to chemotherapies against other pathogens or cancer.
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Affiliation(s)
- Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Ghalia Boubaker
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Norbert Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Sophie Braga-Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
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3
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Van Vranken JG, Li J, Mintseris J, Gadzuk-Shea M, Gygi SP, Schweppe DK. Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577428. [PMID: 38328090 PMCID: PMC10849652 DOI: 10.1101/2024.01.26.577428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to characterize compound-dependent changes in thermal stability, the proteome-wide thermal shift assay has emerged as a powerful tool in this arsenal. The most recent iterations have drastically improved the overall efficiency of these assays, providing an opportunity to screen compounds at a previously unprecedented rate. Taking advantage of this advance, we quantified 1.498 million thermal stability measurements in response to multiple classes of therapeutic and tool compounds (96 compounds in living cells and 70 compounds in lysates). When interrogating the dataset as a whole, approximately 80% of compounds (with quantifiable targets) caused a significant change in the thermal stability of an annotated target. There was also a wealth of evidence portending off-target engagement despite the extensive use of the compounds in the laboratory and/or clinic. Finally, the combined application of cell- and lysate-based assays, aided in the classification of primary (direct ligand binding) and secondary (indirect) changes in thermal stability. Overall, this study highlights the value of these assays in the drug development process by affording an unbiased and reliable assessment of compound mechanism of action.
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Affiliation(s)
| | - Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115 USA
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115 USA
| | - Meagan Gadzuk-Shea
- Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115 USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA
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4
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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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5
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Polypharmacology: The science of multi-targeting molecules. Pharmacol Res 2022; 176:106055. [PMID: 34990865 DOI: 10.1016/j.phrs.2021.106055] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 12/28/2022]
Abstract
Polypharmacology is a concept where a molecule can interact with two or more targets simultaneously. It offers many advantages as compared to the conventional single-targeting molecules. A multi-targeting drug is much more efficacious due to its cumulative efficacy at all of its individual targets making it much more effective in complex and multifactorial diseases like cancer, where multiple proteins and pathways are involved in the onset and development of the disease. For a molecule to be polypharmacologic in nature, it needs to possess promiscuity which is the ability to interact with multiple targets; and at the same time avoid binding to antitargets which would otherwise result in off-target adverse effects. There are certain structural features and physicochemical properties which when present would help researchers to predict if the designed molecule would possess promiscuity or not. Promiscuity can also be identified via advanced state-of-the-art computational methods. In this review, we also elaborate on the methods by which one can intentionally incorporate promiscuity in their molecules and make them polypharmacologic. The polypharmacology paradigm of "one drug-multiple targets" has numerous applications especially in drug repurposing where an already established drug is redeveloped for a new indication. Though designing a polypharmacological drug is much more difficult than designing a single-targeting drug, with the current technologies and information regarding different diseases and chemical functional groups, it is plausible for researchers to intentionally design a polypharmacological drug and unlock its advantages.
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6
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Van Vranken JG, Li J, Mitchell DC, Navarrete-Perea J, Gygi SP. Assessing target engagement using proteome-wide solvent shift assays. eLife 2021; 10:e70784. [PMID: 34878405 PMCID: PMC8654358 DOI: 10.7554/elife.70784] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Recent advances in mass spectrometry (MS) have enabled quantitative proteomics to become a powerful tool in the field of drug discovery, especially when applied toward proteome-wide target engagement studies. Similar to temperature gradients, increasing concentrations of organic solvents stimulate unfolding and precipitation of the cellular proteome. This property can be influenced by physical association with ligands and other molecules, making individual proteins more or less susceptible to solvent-induced denaturation. Herein, we report the development of proteome-wide solvent shift assays by combining the principles of solvent-induced precipitation (Zhang et al., 2020) with modern quantitative proteomics. Using this approach, we developed solvent proteome profiling (SPP), which is capable of establishing target engagement through analysis of SPP denaturation curves. We readily identified the specific targets of compounds with known mechanisms of action. As a further efficiency boost, we applied the concept of area under the curve analysis to develop solvent proteome integral solubility alteration (solvent-PISA) and demonstrate that this approach can serve as a reliable surrogate for SPP. We propose that by combining SPP with alternative methods, like thermal proteome profiling, it will be possible to increase the absolute number of high-quality melting curves that are attainable by either approach individually, thereby increasing the fraction of the proteome that can be screened for evidence of ligand binding.
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Affiliation(s)
| | - Jiaming Li
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Dylan C Mitchell
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
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7
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Yazdanparast S, Benvidi A, Abbasi S, Sabbagh SK. Monitoring the mechanism of anti-cancer agents to inhibit colorectal cancer cell proliferation: Enzymatic biosensing of glucose combined with molecular docking. Enzyme Microb Technol 2021; 148:109804. [PMID: 34116755 DOI: 10.1016/j.enzmictec.2021.109804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 10/24/2022]
Abstract
Glucose, a major energy source in cellular metabolism, has a significant role in cell growth. The increase in glucose uptake is a distinguishing hallmark in cancer cells. A key step in glucose utilization is the transport of glucose to the cancer cells for supplying their additional energy. The glucose transporter (or GLUT) family is a membrane protein which facilitates the uptake of glucose in most cancer cell types. Given the increased glucose level in cancer cells and the regulatory role of GLUTs in glucose uptake, it is required to combine both experimental and theoretical studies to develop new methods to monitor cell proliferation. Herein, for the first time, a new strategy was proposed to evaluate the cell proliferation of HT-29 based on glucose consumption in the presence of resveratrol (RSV) as an anticancer agent. A hybrid nanocomposite of carbon nanofibers and nitrogen-doped graphene quantum dots was used to design an enzymatic sensor for the selective and sensitive determination of glucose in cancer cells. The results obtained from the voltammetric technique were compared with the conventional colorimetric assay. A good correlation was observed between the proliferation rate and glucose utilization by cancer cells. As it was observed, RSV induces a decrease in glucose consumption, indicating lower glucose uptake efficiency for HT-29 cells. Molecular docking studies reveal that RSV can block the interaction of glucose with the GLUT family. This is one of the possible mechanisms for the decrease of glucose level followed by the reduction of cell proliferation in the presence of RSV. Compared with traditional methods, in vitro electrochemical techniques benefit from simple, nontoxic, sensitive and low-cost detection assays and hence serve as a novel tool to pursue the growth inhibition of cancer cell in response to anti-cancer agents.
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Affiliation(s)
- Samira Yazdanparast
- Department of Chemistry, Faculty of Science, Yazd University, Yazd, 89195-741, Iran
| | - Ali Benvidi
- Department of Chemistry, Faculty of Science, Yazd University, Yazd, 89195-741, Iran.
| | - Saleheh Abbasi
- Department of Chemistry, Faculty of Science, Yazd University, Yazd, 89195-741, Iran
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8
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Qi L, Zhang Y, Song F, Han Y, Ding Y. A newly identified small molecular compound acts as a protein kinase inhibitor to suppress metastasis of colorectal cancer. Bioorg Chem 2021; 107:104625. [PMID: 33454506 DOI: 10.1016/j.bioorg.2021.104625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND Targeted therapy has demonstrated high efficacy in the treatment of advanced cancer, and protein kinase inhibitors are a major focus of that therapy; therefore, our study aimed to identify a new protein kinase inhibitor that could be used in the treatment of advanced cancers. METHODS We analyzed the expression profile of colorectal cancer (CRC), combined the driver gene and drug target databases, and identified protein kinase kalirin RhoGEF kinase (kalirin/KALRN) which is related to CRC metastasis. Based on the structure of kalirin, we screened for the small molecular compound ZINC65387069. We first compared the kinase inhibitory activities and molecular properties of ZINC65387069 and tyrosine kinase inhibitors (TKIs). We then determined the effects of ZINC65387069 on the phosphorylation of protein kinase B-Raf. Finally, we determined the effects of ZINC65387069 on migration and apoptosis of HCT116 cells as well as RKO cells. The cell cytoskeleton was also determined. RESULTS Compared with traditional TKIs, ZINC65387069 had stronger kinase inhibitory activity, a simpler structure, higher water solubility, a smaller polar surface area, and lower molecular weight and volume. In CRC cells, ZINC65387069 could significantly inhibit the phosphorylation of B-Raf as well as inhibit cell migration, destroy the cell cytoskeleton, and promote cell apoptosis. CONCLUSION ZINC65387069 is a newly identified protein kinase inhibitor that deserves additional research as a lead compound for drug development to help create targeted therapy against CRC.
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Affiliation(s)
- Lu Qi
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, China.
| | - Ying Zhang
- Department of Radiation Medicine, School of Public Health, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou 510515, China
| | - Fuyao Song
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, China
| | - Yue Han
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, China
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, China.
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9
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Robers MB, Friedman-Ohana R, Huber KVM, Kilpatrick L, Vasta JD, Berger BT, Chaudhry C, Hill S, Müller S, Knapp S, Wood KV. Quantifying Target Occupancy of Small Molecules Within Living Cells. Annu Rev Biochem 2020; 89:557-581. [PMID: 32208767 DOI: 10.1146/annurev-biochem-011420-092302] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The binding affinity and kinetics of target engagement are fundamental to establishing structure-activity relationships (SARs) for prospective therapeutic agents. Enhancing these binding parameters for operative targets, while minimizing binding to off-target sites, can translate to improved drug efficacy and a widened therapeutic window. Compound activity is typically assessed through modulation of an observed phenotype in cultured cells. Quantifying the corresponding binding properties under common cellular conditions can provide more meaningful interpretation of the cellular SAR analysis. Consequently, methods for assessing drug binding in living cells have advanced and are now integral to medicinal chemistry workflows. In this review, we survey key technological advancements that support quantitative assessments of target occupancy in cultured cells, emphasizing generalizable methodologies able to deliver analytical precision that heretofore required reductionist biochemical approaches.
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Affiliation(s)
- M B Robers
- Promega Corporation, Madison, Wisconsin 53711, USA; , ,
| | | | - K V M Huber
- Target Discovery Institute and Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom; .,Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - L Kilpatrick
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom; , .,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, United Kingdom
| | - J D Vasta
- Promega Corporation, Madison, Wisconsin 53711, USA; , ,
| | - B-T Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany; ,
| | - C Chaudhry
- Lead Discovery and Optimization, Bristol-Myers Squibb, Princeton, New Jersey 08648, USA;
| | - S Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom; , .,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, United Kingdom
| | - S Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany; , .,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, 60438 Frankfurt, Germany;
| | - S Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany; , .,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, 60438 Frankfurt, Germany; .,German Cancer Network (DKTK), Frankfurt/Mainz, 60438 Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Goethe University, 60596 Frankfurt am Main, Germany
| | - K V Wood
- Promega Corporation, Madison, Wisconsin 53711, USA; , , .,Current affiliation: Light Bio, Inc., Mount Horeb, Wisconsin 53572, USA;
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10
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Montenegro RC, Howarth A, Ceroni A, Fedele V, Farran B, Mesquita FP, Frejno M, Berger BT, Heinzlmeir S, Sailem HZ, Tesch R, Ebner D, Knapp S, Burbano R, Kuster B, Müller S. Identification of molecular targets for the targeted treatment of gastric cancer using dasatinib. Oncotarget 2020; 11:535-549. [PMID: 32082487 PMCID: PMC7007292 DOI: 10.18632/oncotarget.27462] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 01/13/2020] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) remains the third leading cause of cancer-related death despite several improvements in targeted therapy. There is therefore an urgent need to investigate new treatment strategies, including the identification of novel biomarkers for patient stratification. In this study, we evaluated the effect of FDA-approved kinase inhibitors on GC. Through a combination of cell growth, migration and invasion assays, we identified dasatinib as an efficient inhibitor of GC proliferation. Mass-spectrometry-based selectivity profiling and subsequent knockdown experiments identified members of the SRC family of kinases including SRC, FRK, LYN and YES, as well as other kinases such as DDR1, ABL2, SIK2, RIPK2, EPHA2, and EPHB2 as dasatinib targets. The expression levels of the identified kinases were investigated on RNA and protein level in 200 classified tumor samples from patients, who had undergone gastrectomy, but had received no treatment. Levels of FRK, DDR1 and SRC expression on both mRNA and protein level were significantly higher in metastatic patient samples regardless of the tumor stage, while expression levels of SIK2 correlated with tumor size. Collectively, our data suggest dasatinib for treatment of GC based on its unique property, inhibiting a small number of key kinases (SRC, FRK, DDR1 and SIK2), highly expressed in GC patients.
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Affiliation(s)
| | - Alison Howarth
- Novo Nordisk Research Centre Oxford (NNRCO), Discovery Technologies and Genomics, Oxford, UK
| | - Alessandro Ceroni
- Novo Nordisk Research Centre Oxford (NNRCO), Discovery Technologies and Genomics, Oxford, UK
| | - Vita Fedele
- Novo Nordisk Research Centre Oxford (NNRCO), Discovery Technologies and Genomics, Oxford, UK
| | - Batoul Farran
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Felipe Pantoja Mesquita
- Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE, Brazil
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Benedict-Tilman Berger
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Frankfurt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heba Z Sailem
- Institute of Biomedical Engineering, Department of Engineering, University of Oxford, Oxford, UK.,Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus Research Building, Oxford, UK
| | - Roberta Tesch
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Frankfurt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Daniel Ebner
- Novo Nordisk Research Centre Oxford (NNRCO), Discovery Technologies and Genomics, Oxford, UK
| | - Stefan Knapp
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Frankfurt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, Freising, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Frankfurt, Germany
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11
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Tomaselli D, Lucidi A, Rotili D, Mai A. Epigenetic polypharmacology: A new frontier for epi-drug discovery. Med Res Rev 2020; 40:190-244. [PMID: 31218726 PMCID: PMC6917854 DOI: 10.1002/med.21600] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Recently, despite the great success achieved by the so-called "magic bullets" in the treatment of different diseases through a marked and specific interaction with the target of interest, the pharmacological research is moving toward the development of "molecular network active compounds," embracing the related polypharmacology approach. This strategy was born to overcome the main limitations of the single target therapy leading to a superior therapeutic effect, a decrease of adverse reactions, and a reduction of potential mechanism(s) of drug resistance caused by robustness and redundancy of biological pathways. It has become clear that multifactorial diseases such as cancer, neurological, and inflammatory disorders, may require more complex therapeutic approaches hitting a certain biological system as a whole. Concerning epigenetics, the goal of the multi-epi-target approach consists in the development of small molecules able to simultaneously and (often) reversibly bind different specific epi-targets. To date, two dual histone deacetylase/kinase inhibitors (CUDC-101 and CUDC-907) are in an advanced stage of clinical trials. In the last years, the growing interest in polypharmacology encouraged the publication of high-quality reviews on combination therapy and hybrid molecules. Hence, to update the state-of-the-art of these therapeutic approaches avoiding redundancy, herein we focused only on multiple medication therapies and multitargeting compounds exploiting epigenetic plus nonepigenetic drugs reported in the literature in 2018. In addition, all the multi-epi-target inhibitors known in literature so far, hitting two or more epigenetic targets, have been included.
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Affiliation(s)
- Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Alessia Lucidi
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Dante Rotili
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs,
“Sapienza” University of Rome, P.le A. Moro 5, 00185 Roma, Italy
- Pasteur Institute - Cenci Bolognetti Foundation, Viale
Regina Elena 291, 00161 Roma, Italy
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12
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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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13
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Discovery of Small-Molecule Selective mTORC1 Inhibitors via Direct Inhibition of Glucose Transporters. Cell Chem Biol 2019; 26:1203-1213.e13. [PMID: 31231029 DOI: 10.1016/j.chembiol.2019.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/12/2019] [Accepted: 05/22/2019] [Indexed: 12/30/2022]
Abstract
The mechanistic target of rapamycin (mTOR) is a central regulator of cellular metabolic processes. Dysregulation of this kinase complex can result in a variety of human diseases. Rapamycin and its analogs target mTORC1 directly; however, chronic treatment in certain cell types and in vivo results in the inhibition of both mTORC1 and mTORC2. We have developed a high-throughput cell-based screen for the detection of phosphorylated forms of the mTORC1 (4E-BP1, S6K1) and mTORC2 (Akt) substrates and have identified and characterized a chemical scaffold that demonstrates a profile consistent with the selective inhibition of mTORC1. Stable isotope labeling of amino acids in cell culture-based proteomic target identification revealed that class I glucose transporters were the primary target for these compounds yielding potent inhibition of glucose uptake and, as a result, selective inhibition of mTORC1. The link between the glucose uptake and selective mTORC1 inhibition are discussed in the context of a yet-to-be discovered glucose sensor.
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14
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Ctortecka C, Palve V, Kuenzi BM, Fang B, Sumi NJ, Izumi V, Novakova S, Kinose F, Remsing Rix LL, Haura EB, Koomen JM, Rix U. Functional Proteomics and Deep Network Interrogation Reveal a Complex Mechanism of Action of Midostaurin in Lung Cancer Cells. Mol Cell Proteomics 2018; 17:2434-2447. [PMID: 30217950 PMCID: PMC6283294 DOI: 10.1074/mcp.ra118.000713] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/16/2018] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is associated with high prevalence and mortality, and despite significant successes with targeted drugs in genomically defined subsets of lung cancer and immunotherapy, the majority of patients currently does not benefit from these therapies. Through a targeted drug screen, we found the recently approved multi-kinase inhibitor midostaurin to have potent activity in several lung cancer cells independent of its intended target, PKC, or a specific genomic marker. To determine the underlying mechanism of action we applied a layered functional proteomics approach and a new data integration method. Using chemical proteomics, we identified multiple midostaurin kinase targets in these cells. Network-based integration of these targets with quantitative tyrosine and global phosphoproteomics data using protein-protein interactions from the STRING database suggested multiple targets are relevant for the mode of action of midostaurin. Subsequent functional validation using RNA interference and selective small molecule probes showed that simultaneous inhibition of TBK1, PDPK1 and AURKA was required to elicit midostaurin's cellular effects. Immunoblot analysis of downstream signaling nodes showed that combined inhibition of these targets altered PI3K/AKT and cell cycle signaling pathways that in part converged on PLK1. Furthermore, rational combination of midostaurin with the potent PLK1 inhibitor BI2536 elicited strong synergy. Our results demonstrate that combination of complementary functional proteomics approaches and subsequent network-based data integration can reveal novel insight into the complex mode of action of multi-kinase inhibitors, actionable targets for drug discovery and cancer vulnerabilities. Finally, we illustrate how this knowledge can be used for the rational design of synergistic drug combinations with high potential for clinical translation.
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Affiliation(s)
- Claudia Ctortecka
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Vinayak Palve
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Brent M Kuenzi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612; Cancer Biology PhD Program, University of South Florida, Tampa, Florida 33620
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Natalia J Sumi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612; Cancer Biology PhD Program, University of South Florida, Tampa, Florida 33620
| | - Victoria Izumi
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Silvia Novakova
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - John Matthew Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612.
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15
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Cann ML, McDonald IM, East MP, Johnson GL, Graves LM. Measuring Kinase Activity-A Global Challenge. J Cell Biochem 2017; 118:3595-3606. [PMID: 28464261 DOI: 10.1002/jcb.26103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/22/2022]
Abstract
The kinase enzymes within a cell, known collectively as the kinome, play crucial roles in many signaling pathways, including survival, motility, differentiation, stress response, and many more. Aberrant signaling through kinase pathways is often linked to cancer, among other diseases. A major area of scientific research involves understanding the relationships between kinases, their targets, and how the kinome adapts to perturbations of the cellular system. This review will discuss many of the current and developing methods for studying kinase activity, and evaluate their applications, advantages, and disadvantages. J. Cell. Biochem. 118: 3595-3606, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Marissa L Cann
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Ian M McDonald
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Michael P East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
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16
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Arend KC, Lenarcic EM, Vincent HA, Rashid N, Lazear E, McDonald IM, Gilbert TSK, East MP, Herring LE, Johnson GL, Graves LM, Moorman NJ. Kinome Profiling Identifies Druggable Targets for Novel Human Cytomegalovirus (HCMV) Antivirals. Mol Cell Proteomics 2017; 16:S263-S276. [PMID: 28237943 PMCID: PMC5393402 DOI: 10.1074/mcp.m116.065375] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/23/2017] [Indexed: 11/06/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a significant cause of disease in immune-compromised adults and immune naïve newborns. No vaccine exists to prevent HCMV infection, and current antiviral therapies have toxic side effects that limit the duration and intensity of their use. There is thus an urgent need for new strategies to treat HCMV infection. Repurposing existing drugs as antivirals is an attractive approach to limit the time and cost of new antiviral drug development. Virus-induced changes in infected cells are often driven by changes in cellular kinase activity, which led us to hypothesize that defining the complement of kinases (the kinome), whose abundance or expression is altered during infection would identify existing kinase inhibitors that could be repurposed as new antivirals. To this end, we applied a kinase capture technique, multiplexed kinase inhibitor bead-mass spectrometry (MIB-MS) kinome, to quantitatively measure perturbations in >240 cellular kinases simultaneously in cells infected with a laboratory-adapted (AD169) or clinical (TB40E) HCMV strain. MIB-MS profiling identified time-dependent increases and decreases in MIB binding of multiple kinases including cell cycle kinases, receptor tyrosine kinases, and mitotic kinases. Based on the kinome data, we tested the antiviral effects of kinase inhibitors and other compounds, several of which are in clinical use or development. Using a novel flow cytometry-based assay and a fluorescent reporter virus we identified three compounds that inhibited HCMV replication with IC50 values of <1 μm, and at doses that were not toxic to uninfected cells. The most potent inhibitor of HCMV replication was OTSSP167 (IC50 <1.2 nm), a MELK inhibitor, blocked HCMV early gene expression and viral DNA accumulation, resulting in a >3 log decrease in virus replication. These results show the utility of MIB-MS kinome profiling for identifying existing kinase inhibitors that can potentially be repurposed as novel antiviral drugs.
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Affiliation(s)
- Kyle C Arend
- From the ‡Department of Microbiology & Immunology
- ¶Lineberger Comprehensive Cancer Center
| | - Erik M Lenarcic
- From the ‡Department of Microbiology & Immunology
- ¶Lineberger Comprehensive Cancer Center
| | - Heather A Vincent
- From the ‡Department of Microbiology & Immunology
- ¶Lineberger Comprehensive Cancer Center
| | - Naim Rashid
- ¶Lineberger Comprehensive Cancer Center
- ‖Department of Biostatistics
| | - Eric Lazear
- From the ‡Department of Microbiology & Immunology
- ¶Lineberger Comprehensive Cancer Center
| | | | | | | | - Laura E Herring
- §Department of Pharmacology
- **UNC Michael Hooker Proteomics Core Facility University of North Carolina, Chapel Hill, 27599 North Carolina
| | | | - Lee M Graves
- §Department of Pharmacology
- **UNC Michael Hooker Proteomics Core Facility University of North Carolina, Chapel Hill, 27599 North Carolina
| | - Nathaniel J Moorman
- From the ‡Department of Microbiology & Immunology,
- ¶Lineberger Comprehensive Cancer Center
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17
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Faria SS, Morris CFM, Silva AR, Fonseca MP, Forget P, Castro MS, Fontes W. A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer Research. Front Oncol 2017; 7:13. [PMID: 28265552 PMCID: PMC5316539 DOI: 10.3389/fonc.2017.00013] [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] [Received: 09/01/2016] [Accepted: 01/17/2017] [Indexed: 01/10/2023] Open
Abstract
The fact that cancer is a leading cause of death all around the world has naturally sparked major efforts in the pursuit of novel and more efficient biomarkers that could better serve as diagnostic tools, prognostic predictors, or therapeutical targets in the battle against this type of disease. Mass spectrometry-based proteomics has proven itself as a robust and logical alternative to the immuno-based methods that once dominated the field. Nevertheless, intrinsic limitations of classic proteomic approaches such as the natural gap between shotgun discovery-based methods and clinically applicable results have called for the implementation of more direct, hypothesis-based studies such as those made available through targeted approaches, that might be able to streamline biomarker discovery and validation as a means to increase survivability of affected patients. In fact, the paradigm shifting potential of modern targeted proteomics applied to cancer research can be demonstrated by the large number of advancements and increasing examples of new and more useful biomarkers found during the course of this review in different aspects of cancer research. Out of the many studies dedicated to cancer biomarker discovery, we were able to devise some clear trends, such as the fact that breast cancer is the most common type of tumor studied and that most of the research for any given type of cancer is focused on the discovery diagnostic biomarkers, with the exception of those that rely on samples other than plasma and serum, which are generally aimed toward prognostic markers. Interestingly, the most common type of targeted approach is based on stable isotope dilution-selected reaction monitoring protocols for quantification of the target molecules. Overall, this reinforces that notion that targeted proteomics has already started to fulfill its role as a groundbreaking strategy that may enable researchers to catapult the number of viable, effective, and validated biomarkers in cancer clinical practice.
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Affiliation(s)
- Sara S Faria
- Mastology Program, Federal University of Uberlandia (UFU) , Uberlandia , Brazil
| | - Carlos F M Morris
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Adriano R Silva
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Micaella P Fonseca
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patrice Forget
- Department of Anesthesiology and Perioperative Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit of Brussel , Brussels , Belgium
| | - Mariana S Castro
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Wagner Fontes
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
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18
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Urisman A, Levin RS, Gordan JD, Webber JT, Hernandez H, Ishihama Y, Shokat KM, Burlingame AL. An Optimized Chromatographic Strategy for Multiplexing In Parallel Reaction Monitoring Mass Spectrometry: Insights from Quantitation of Activated Kinases. Mol Cell Proteomics 2017; 16:265-277. [PMID: 27940637 PMCID: PMC5294213 DOI: 10.1074/mcp.m116.058172] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Reliable quantitation of protein abundances in defined sets of cellular proteins is critical to numerous biological applications. Traditional immunodetection-based methods are limited by the quality and availability of specific antibodies, especially for site-specific post-translational modifications. Targeted proteomic methods, including the recently developed parallel reaction monitoring (PRM) mass spectrometry, have enabled accurate quantitative measurements of up to a few hundred specific target peptides. However, the degree of practical multiplexing in label-free PRM workflows remains a significant limitation for the technique. Here we present a strategy for significantly increasing multiplexing in label-free PRM that takes advantage of the superior separation characteristics and retention time stability of meter-scale monolithic silica-C18 column-based chromatography. We show the utility of the approach in quantifying kinase abundances downstream of previously developed active kinase enrichment methodology based on multidrug inhibitor beads. We examine kinase activation dynamics in response to three different MAP kinase inhibitors in colorectal carcinoma cells and demonstrate reliable quantitation of over 800 target peptides from over 150 kinases in a single label-free PRM run. The kinase activity profiles obtained from these analyses reveal compensatory activation of TGF-β family receptors as a response to MAPK blockade. The gains achieved using this label-free PRM multiplexing strategy will benefit a wide array of biological applications.
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Affiliation(s)
- Anatoly Urisman
- From the ‡Department of Pathology, University of California San Francisco, San Francisco, California;
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Rebecca S Levin
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
- ¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California
| | - John D Gordan
- ¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California
- ‖Department of Medicine, University of California San Francisco, San Francisco, California
| | - James T Webber
- **Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
| | - Hilda Hernandez
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Yasushi Ishihama
- ‡‡Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kevan M Shokat
- ¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California
- §§Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California
| | - Alma L Burlingame
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
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19
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Horning BD, Suciu RM, Ghadiri DA, Ulanovskaya OA, Matthews ML, Lum KM, Backus KM, Brown SJ, Rosen H, Cravatt BF. Chemical Proteomic Profiling of Human Methyltransferases. J Am Chem Soc 2016; 138:13335-13343. [PMID: 27689866 DOI: 10.1021/jacs.6b07830] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methylation is a fundamental mechanism used in Nature to modify the structure and function of biomolecules, including proteins, DNA, RNA, and metabolites. Methyl groups are predominantly installed into biomolecules by a large and diverse class of S-adenosyl methionine (SAM)-dependent methyltransferases (MTs), of which there are ∼200 known or putative members in the human proteome. Deregulated MT activity contributes to numerous diseases, including cancer, and several MT inhibitors are in clinical development. Nonetheless, a large fraction of the human MT family remains poorly characterized, underscoring the need for new technologies to characterize MTs and their inhibitors in native biological systems. Here, we describe a suite of S-adenosyl homocysteine (SAH) photoreactive probes and their application in chemical proteomic experiments to profile and enrich a large number of MTs (>50) from human cancer cell lysates with remarkable specificity over other classes of proteins. We further demonstrate that the SAH probes can enrich MT-associated proteins and be used to screen for and assess the selectivity of MT inhibitors, leading to the discovery of a covalent inhibitor of nicotinamide N-methyltransferase (NNMT), an enzyme implicated in cancer and metabolic disorders. The chemical proteomics probes and methods for their utilization reported herein should prove of value for the functional characterization of MTs, MT complexes, and MT inhibitors in mammalian biology and disease.
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Affiliation(s)
- Benjamin D Horning
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Radu M Suciu
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Darian A Ghadiri
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Olesya A Ulanovskaya
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Megan L Matthews
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Kenneth M Lum
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Keriann M Backus
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Steven J Brown
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Hugh Rosen
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Benjamin F Cravatt
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
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20
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De Lucca GV, Shi Q, Liu Q, Batt DG, Beaudoin Bertrand M, Rampulla R, Mathur A, Discenza L, D’Arienzo C, Dai J, Obermeier M, Vickery R, Zhang Y, Yang Z, Marathe P, Tebben AJ, Muckelbauer JK, Chang CJ, Zhang H, Gillooly K, Taylor T, Pattoli MA, Skala S, Kukral DW, McIntyre KW, Salter-Cid L, Fura A, Burke JR, Barrish JC, Carter PH, Tino JA. Small Molecule Reversible Inhibitors of Bruton’s Tyrosine Kinase (BTK): Structure–Activity Relationships Leading to the Identification of 7-(2-Hydroxypropan-2-yl)-4-[2-methyl-3-(4-oxo-3,4-dihydroquinazolin-3-yl)phenyl]-9H-carbazole-1-carboxamide (BMS-935177). J Med Chem 2016; 59:7915-35. [DOI: 10.1021/acs.jmedchem.6b00722] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- George V. De Lucca
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Qing Shi
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Qingjie Liu
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Douglas G. Batt
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Myra Beaudoin Bertrand
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Rick Rampulla
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Arvind Mathur
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Lorell Discenza
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Celia D’Arienzo
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Jun Dai
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mary Obermeier
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Rodney Vickery
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Yingru Zhang
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Zheng Yang
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Punit Marathe
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Andrew J. Tebben
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Jodi K. Muckelbauer
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - ChiehYing J. Chang
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Huiping Zhang
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Kathleen Gillooly
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Tracy Taylor
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mark A. Pattoli
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Stacey Skala
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Daniel W. Kukral
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Kim W. McIntyre
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Luisa Salter-Cid
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Aberra Fura
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - James R. Burke
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Joel C. Barrish
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Percy H. Carter
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Joseph A. Tino
- Immunosciences Discovery Chemistry, ‡Immunoscience Discovery Biology, §Molecular Structure
and Design, Molecular Discovery Technologies, ∥Metabolism and Pharmacokinetic
Department, Pharmaceutical Candidate Optimization, and ⊥ECTR/CTTO Imaging Department, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
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Dias MH, Kitano ES, Zelanis A, Iwai LK. Proteomics and drug discovery in cancer. Drug Discov Today 2016; 21:264-77. [DOI: 10.1016/j.drudis.2015.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/30/2015] [Accepted: 10/12/2015] [Indexed: 12/14/2022]
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Humphrey SJ, James DE, Mann M. Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation. Trends Endocrinol Metab 2015; 26:676-687. [PMID: 26498855 DOI: 10.1016/j.tem.2015.09.013] [Citation(s) in RCA: 338] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 12/20/2022]
Abstract
Metabolism research is undergoing a renaissance because many diseases are increasingly recognized as being characterized by perturbations in intracellular metabolic regulation. Metabolic changes can be conferred through changes to the expression of metabolic enzymes, the concentrations of substrates or products that govern reaction kinetics, or post-translational modification (PTM) of the proteins that facilitate these reactions. On the 60th anniversary since its discovery, reversible protein phosphorylation is widely appreciated as an essential PTM regulating metabolism. With the ability to quantitatively measure dynamic changes in protein phosphorylation on a global scale - hereafter referred to as phosphoproteomics - we are now entering a new era in metabolism research, with mass spectrometry (MS)-based proteomics at the helm.
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Affiliation(s)
- Sean J Humphrey
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried 82152, Germany
| | - David E James
- Charles Perkins Centre, School of Molecular Bioscience, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried 82152, Germany.
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Rauh D. Special Issue Focused on Two Areas Pertinent to Chemical Biology: Post-Translational Modifications and New Frontiers on Kinases. ACS Chem Biol 2015. [DOI: 10.1021/acschembio.5b00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Rauh
- Technische Universität Dortmund, Fakultät für Chemie
und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
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