1
|
Huang H, Jones LH. Covalent drug discovery using sulfur(VI) fluoride exchange warheads. Expert Opin Drug Discov 2023:1-11. [PMID: 37243622 DOI: 10.1080/17460441.2023.2218642] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
INTRODUCTION Covalent drug discovery has traditionally focused on targeting cysteine, but the amino acid is often absent in protein binding sites. This review makes the case to move beyond cysteine labeling using sulfur (VI) fluoride exchange (SuFEx) chemistry to expand the druggable proteome. AREAS COVERED Recent advances in SuFEx medicinal chemistry and chemical biology are described, which have enabled the development of covalent chemical probes that site-selectively engage amino acid residues (including tyrosine, lysine, histidine, serine, and threonine) in binding pockets. Areas covered include chemoproteomic mapping of the targetable proteome, structure-based design of covalent inhibitors and molecular glues, metabolic stability profiling, and synthetic methodologies that have expedited the delivery of SuFEx modulators. EXPERT OPINION Despite recent innovations in SuFEx medicinal chemistry, focused preclinical research is required to ensure the field moves from early chemical probe discovery to the delivery of transformational covalent drug candidates. The authors believe that covalent drug candidates designed to engage residues beyond cysteine using sulfonyl exchange warheads will likely enter clinical trials in the coming years.
Collapse
Affiliation(s)
- Huang Huang
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Brulet JW, Ciancone AM, Yuan K, Hsu K. Advances in Activity‐Based Protein Profiling of Functional Tyrosines in Proteomes. Isr J Chem 2023. [DOI: 10.1002/ijch.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Jeffrey W. Brulet
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Anthony M. Ciancone
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Kun Yuan
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Ku‐Lung Hsu
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
- Department of Pharmacology University of Virginia School of Medicine Charlottesville Virginia 22908 United States
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia 22908 United States
- University of Virginia Cancer Center University of Virginia Charlottesville VA 22903 USA
| |
Collapse
|
4
|
Che J, Jones LH. Covalent drugs targeting histidine - an unexploited opportunity? RSC Med Chem 2022; 13:1121-1126. [PMID: 36325394 PMCID: PMC9579939 DOI: 10.1039/d2md00258b] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/26/2022] [Indexed: 09/30/2023] Open
Abstract
Covalent drugs and chemical probes often possess pharmacological advantages over reversible binding ligands, such as enhanced potency and pharmacodynamic duration. The highly nucleophilic cysteine thiol is commonly targeted using acrylamide electrophiles, but the amino acid is rarely present in protein binding sites. Sulfonyl exchange chemistry has expanded the covalent drug discovery toolkit by enabling the rational design of irreversible inhibitors targeting tyrosine, lysine, serine and threonine. Probes containing the sulfonyl fluoride warhead have also been shown to serendipitously label histidine residues in proteins. Histidine targeting is an attractive prospect because the residue is frequently proximal to protein small molecule ligands and the imidazole side chain possesses desirable nucleophilicity. We recently reported the design of cereblon molecular glues to site-selectively modify a histidine in the thalidomide binding site using sulfonyl exchange chemistry. We believe that histidine targeting holds great promise for future covalent drug development and this Opinion highlights these opportunities.
Collapse
Affiliation(s)
- Jianwei Che
- Center for Protein Degradation, Dana-Farber Cancer Institute 360 Longwood Avenue Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA USA
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute 360 Longwood Avenue Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA USA
| |
Collapse
|
5
|
Kline GM, Nugroho K, Kelly JW. Inverse Drug Discovery identifies weak electrophiles affording protein conjugates. Curr Opin Chem Biol 2022; 67:102113. [PMID: 35065430 PMCID: PMC8940698 DOI: 10.1016/j.cbpa.2021.102113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
Abstract
Traditional biochemical target-based and phenotypic cell-based screening approaches to drug discovery have produced the current covalent and non-covalent pharmacopoeia. Strategies to expand the druggable proteome include Inverse Drug Discovery, which involves incubating one weak organic electrophile at a time with the proteins of a living cell to identify the conjugates formed. An alkyne substructure in each organic electrophile enables affinity chromatography-mass spectrometry, which produces a list of proteins that each distinct compound reacts with. Herein, we review Inverse Drug Discovery in the context of organic compounds of intermediate complexity harboring Sulfur(VI)-fluoride exchange (SuFEx) electrophiles used to expand the cellular proteins that can be targeted covalently.
Collapse
Affiliation(s)
- Gabriel M Kline
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Karina Nugroho
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
6
|
Using sulfuramidimidoyl fluorides that undergo sulfur(VI) fluoride exchange for inverse drug discovery. Nat Chem 2020; 12:906-913. [PMID: 32868886 PMCID: PMC7541551 DOI: 10.1038/s41557-020-0530-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/23/2020] [Indexed: 12/20/2022]
Abstract
Drug candidates that form covalent linkages with their target proteins have been under-explored compared to conventional counterparts that modulate biological function by reversible binding to proteins, in part due to concerns about off-target reactivity. But toxicity linked to off-target reactivity can be minimized by using latent electrophiles that only become activated towards covalent bond formation upon binding a specific protein. Here, we study sulfuramidimidoyl fluorides (SAFs), a class of weak electrophiles that undergo sulfur(VI) fluoride exchange (SuFEx) chemistry. We show that equilibrium binding of a SAF to a protein can allow nucleophilic attack by a specific amino acid side chain leading to conjugate formation. Sixteen small molecules, each bearing a SAF electrophile, were incubated with human cell lysate, and the protein conjugates formed were identified by affinity chromatography–mass spectrometry. This inverse drug discovery approach identified a compound that covalently binds to, and irreversibly inhibits the activity of PARP1, an important anti-cancer target in living cells.
Collapse
|
7
|
Teng M, Ficarro SB, Yoon H, Che J, Zhou J, Fischer ES, Marto JA, Zhang T, Gray NS. Rationally Designed Covalent BCL6 Inhibitor That Targets a Tyrosine Residue in the Homodimer Interface. ACS Med Chem Lett 2020; 11:1269-1273. [PMID: 32551010 DOI: 10.1021/acsmedchemlett.0c00111] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/03/2020] [Indexed: 12/29/2022] Open
Abstract
B-cell lymphoma 6 (BCL6) is a transcriptional repressor frequently deregulated in lymphoid malignancies. BCL6 engages with number of corepressors, and these protein-protein interactions are being explored as a strategy for drug development. Here, we report the development of an irreversible BCL6 inhibitor TMX-2164 that uses a sulfonyl fluoride to covalently react with the hydroxyl group of Tyrosine 58 located in the lateral groove. TMX-2164 exhibits significantly improved inhibitory activity compared to that of its reversible parental compound and displays sustained target engagement and antiproliferative activity in cells. TMX-2164 therefore represents an example of a tyrosine-directed covalent inhibitor of BCL6 which demonstrates advantages relative to reversible targeting.
Collapse
Affiliation(s)
- Mingxing Teng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Scott B. Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Hojong Yoon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jing Zhou
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jarrod A. Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
8
|
Jelcic M, Wang K, Hui KL, Cai XC, Enyedi B, Luo M, Niethammer P. A Photo-clickable ATP-Mimetic Reveals Nucleotide Interactors in the Membrane Proteome. Cell Chem Biol 2020; 27:1073-1083.e12. [PMID: 32521230 DOI: 10.1016/j.chembiol.2020.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/13/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022]
Abstract
ATP is an important energy metabolite and allosteric signal in health and disease. ATP-interacting proteins, such as P2 receptors, control inflammation, cell death, migration, and wound healing. However, identification of allosteric ATP sites remains challenging, and our current inventory of ATP-controlled pathways is likely incomplete. Here, we develop and verify mipATP as a minimally invasive photoaffinity probe for ATP-interacting proteins. Its N6 functionalization allows target enrichment by UV crosslinking and conjugation to reporter tags by "click" chemistry. The additions are compact, allowing mipATP to completely retain the calcium signaling responses of native ATP in vitro and in vivo. mipATP specifically enriched for known nucleotide binders in A549 cell lysates and membrane fractions. In addition, it retrieved unannotated ATP interactors, such as the FAS receptor, CD44, and various SLC transporters. Thus, mipATP is a promising tool to identify allosteric ATP sites in the proteome.
Collapse
Affiliation(s)
- Mark Jelcic
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ke Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - King Lam Hui
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiao-Chuan Cai
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Balázs Enyedi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Lendület Tissue Damage Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary; HCEMM-SE Inflammatory Signaling Research Group, Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Philipp Niethammer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
9
|
Vaz C, Reales-Calderon JA, Pitarch A, Vellosillo P, Trevisan M, Hernáez ML, Monteoliva L, Gil C. Enrichment of ATP Binding Proteins Unveils Proteomic Alterations in Human Macrophage Cell Death, Inflammatory Response, and Protein Synthesis after Interaction with Candida albicans. J Proteome Res 2019; 18:2139-2159. [PMID: 30985132 DOI: 10.1021/acs.jproteome.9b00032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Macrophages are involved in the primary human response to Candida albicans. After pathogen recognition, signaling pathways are activated, leading to the production of cytokines, chemokines, and antimicrobial peptides. ATP binding proteins are crucial for this regulation. Here, a quantitative proteomic and phosphoproteomic approach was carried out for the study of human macrophage ATP-binding proteins after interaction with C. albicans. From a total of 547 nonredundant quantified proteins, 137 were ATP binding proteins and 59 were detected as differentially abundant. From the differentially abundant ATP-binding proteins, 6 were kinases (MAP2K2, SYK, STK3, MAP3K2, NDKA, and SRPK1), most of them involved in signaling pathways. Furthermore, 85 phosphopeptides were quantified. Macrophage proteomic alterations including an increase of protein synthesis with a consistent decrease in proteolysis were observed. Besides, macrophages showed changes in proteins of endosomal trafficking together with mitochondrial proteins, including some involved in the response to oxidative stress. Regarding cell death mechanisms, an increase of antiapoptotic over pro-apoptotic signals is suggested. Furthermore, a high pro-inflammatory response was detected, together with no upregulation of key mi-RNAs involved in the negative feedback of this response. These findings illustrate a strategy to deepen the knowledge of the complex interactions between the host and the clinically important pathogen C. albicans.
Collapse
Affiliation(s)
- Catarina Vaz
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain
| | - Jose Antonio Reales-Calderon
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain
| | - Aida Pitarch
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain
| | - Perceval Vellosillo
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | - Marco Trevisan
- Laboratorio de Proteómica Cardiovascular , Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid , Spain
| | - María Luisa Hernáez
- Unidad de Proteómica , Universidad Complutense de Madrid , 28040 Madrid , Spain
| | - Lucía Monteoliva
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain
| | - Concha Gil
- Departamento de Microbiologı́a y Parasitología, Facultad de Farmacia , Universidad Complutense de Madrid , 28040 Madrid , Spain.,Instituto Ramón y Cajal de Investigación Sanitaria IRYCIS , 28034 Madrid , Spain.,Unidad de Proteómica , Universidad Complutense de Madrid , 28040 Madrid , Spain
| |
Collapse
|
10
|
Jones LH. Understanding the chemically-reactive proteome. MOLECULAR BIOSYSTEMS 2017; 12:1728-30. [PMID: 26726011 DOI: 10.1039/c5mb00760g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The reactivity of amino acid residues in proteins is context-dependent and difficult to predict. Chemical biology can be used to understand the chemical modifications of proteins to help elucidate the nature of the reactive proteome. The resulting insights can be applied to pharmacoproteomics, target identification and molecular pathology.
Collapse
Affiliation(s)
- Lyn H Jones
- Worldwide Medicinal Chemistry, Pfizer, 610 Main Street, Cambridge MA, 02139, USA.
| |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
| | - Yinsheng Wang
- Correspondence to: Yinsheng Wang, Department of Chemistry, University of California, Riverside, CA 92521-0403.
| |
Collapse
|
12
|
Müller AC, Giambruno R, Weißer J, Májek P, Hofer A, Bigenzahn JW, Superti-Furga G, Jessen HJ, Bennett KL. Identifying Kinase Substrates via a Heavy ATP Kinase Assay and Quantitative Mass Spectrometry. Sci Rep 2016; 6:28107. [PMID: 27346722 PMCID: PMC4921819 DOI: 10.1038/srep28107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 05/31/2016] [Indexed: 01/17/2023] Open
Abstract
Mass spectrometry-based in vitro kinase screens play an essential role in the discovery of kinase substrates, however, many suffer from biological and technical noise or necessitate genetically-altered enzyme-cofactor systems. We describe a method that combines stable γ-[(18)O2]-ATP with classical in vitro kinase assays within a contemporary quantitative proteomic workflow. Our approach improved detection of known substrates of the non-receptor tyrosine kinase ABL1; and identified potential, new in vitro substrates.
Collapse
Affiliation(s)
- André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Roberto Giambruno
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Juliane Weißer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandre Hofer
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Henning J Jessen
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| |
Collapse
|
13
|
Lehmann KC, Gulyaeva A, Zevenhoven-Dobbe JC, Janssen GMC, Ruben M, Overkleeft HS, van Veelen PA, Samborskiy DV, Kravchenko AA, Leontovich AM, Sidorov IA, Snijder EJ, Posthuma CC, Gorbalenya AE. Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses. Nucleic Acids Res 2015; 43:8416-34. [PMID: 26304538 PMCID: PMC4787807 DOI: 10.1093/nar/gkv838] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/08/2015] [Indexed: 11/13/2022] Open
Abstract
RNA viruses encode an RNA-dependent RNA polymerase (RdRp) that catalyzes the synthesis of their RNA(s). In the case of positive-stranded RNA viruses belonging to the order Nidovirales, the RdRp resides in a replicase subunit that is unusually large. Bioinformatics analysis of this non-structural protein has now revealed a nidoviral signature domain (genetic marker) that is N-terminally adjacent to the RdRp and has no apparent homologs elsewhere. Based on its conservation profile, this domain is proposed to have nucleotidylation activity. We used recombinant non-structural protein 9 of the arterivirus equine arteritis virus (EAV) and different biochemical assays, including irreversible labeling with a GTP analog followed by a proteomics analysis, to demonstrate the manganese-dependent covalent binding of guanosine and uridine phosphates to a lysine/histidine residue. Most likely this was the invariant lysine of the newly identified domain, named nidovirus RdRp-associated nucleotidyltransferase (NiRAN), whose substitution with alanine severely diminished the described binding. Furthermore, this mutation crippled EAV and prevented the replication of severe acute respiratory syndrome coronavirus (SARS-CoV) in cell culture, indicating that NiRAN is essential for nidoviruses. Potential functions supported by NiRAN may include nucleic acid ligation, mRNA capping and protein-primed RNA synthesis, possibilities that remain to be explored in future studies.
Collapse
Affiliation(s)
- Kathleen C Lehmann
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Anastasia Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Jessika C Zevenhoven-Dobbe
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Mark Ruben
- Leiden Institute of Chemistry, Leiden University, 2300 CC, Leiden, The Netherlands
| | - Hermen S Overkleeft
- Leiden Institute of Chemistry, Leiden University, 2300 CC, Leiden, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Dmitry V Samborskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Alexander A Kravchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Andrey M Leontovich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Igor A Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, 2300 RC, Leiden, The Netherlands Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899 Moscow, Russia
| |
Collapse
|
14
|
Hett EC, Xu H, Geoghegan KF, Gopalsamy A, Kyne RE, Menard CA, Narayanan A, Parikh MD, Liu S, Roberts L, Robinson RP, Tones MA, Jones LH. Rational targeting of active-site tyrosine residues using sulfonyl fluoride probes. ACS Chem Biol 2015; 10:1094-8. [PMID: 25571984 DOI: 10.1021/cb5009475] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This work describes the first rational targeting of tyrosine residues in a protein binding site by small-molecule covalent probes. Specific tyrosine residues in the active site of the mRNA-decapping scavenger enzyme DcpS were modified using reactive sulfonyl fluoride covalent inhibitors. Structure-based molecular design was used to create an alkyne-tagged probe bearing the sulfonyl fluoride warhead, thus enabling the efficient capture of the protein from a complex proteome. Use of the probe in competition experiments with a diaminoquinazoline DcpS inhibitor permitted the quantification of intracellular target occupancy. As a result, diaminoquinazoline upregulators of survival motor neuron protein that are used for the treatment of spinal muscular atrophy were confirmed as inhibitors of DcpS in human primary cells. This work illustrates the utility of sulfonyl fluoride probes designed to react with specific tyrosine residues of a protein and augments the chemical biology toolkit by these probes uses in target validation and molecular pharmacology.
Collapse
Affiliation(s)
- Erik C. Hett
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Hua Xu
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kieran F. Geoghegan
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ariamala Gopalsamy
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Robert E. Kyne
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Carol A. Menard
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Arjun Narayanan
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mihir D. Parikh
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Shenping Liu
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lee Roberts
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ralph P. Robinson
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael A. Tones
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lyn H. Jones
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| |
Collapse
|
15
|
Narayanan A, Jones LH. Sulfonyl fluorides as privileged warheads in chemical biology. Chem Sci 2015; 6:2650-2659. [PMID: 28706662 PMCID: PMC5489032 DOI: 10.1039/c5sc00408j] [Citation(s) in RCA: 350] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/16/2015] [Indexed: 01/10/2023] Open
Abstract
The use of sulfonyl fluoride probes in chemical biology is reviewed.
Sulfonyl fluoride electrophiles have found significant utility as reactive probes in chemical biology and molecular pharmacology. As warheads they possess the right balance of biocompatibility (including aqueous stability) and protein reactivity. Their functionality is privileged in this regard as they are known to modify not only reactive serines (resulting in their common use as protease inhibitors), but also context-specific threonine, lysine, tyrosine, cysteine and histidine residues. This review describes the application of sulfonyl fluoride probes across various areas of research and explores new approaches that could further enhance the chemical biology toolkit. We believe that sulfonyl fluoride probes will find greater utility in areas such as covalent enzyme inhibition, target identification and validation, and the mapping of enzyme binding sites, substrates and protein–protein interactions.
Collapse
Affiliation(s)
- Arjun Narayanan
- Chemical Biology Group , BioTherapeutics Chemistry , WorldWide Medicinal Chemistry , Pfizer , 610 Main Street , Cambridge , MA 02139 , USA .
| | - Lyn H Jones
- Chemical Biology Group , BioTherapeutics Chemistry , WorldWide Medicinal Chemistry , Pfizer , 610 Main Street , Cambridge , MA 02139 , USA .
| |
Collapse
|
16
|
Mahajan S, Manetsch R, Merkler DJ, Stevens Jr. SM. Synthesis and evaluation of a novel adenosine-ribose probe for global-scale profiling of nucleoside and nucleotide-binding proteins. PLoS One 2015; 10:e0115644. [PMID: 25671571 PMCID: PMC4324776 DOI: 10.1371/journal.pone.0115644] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/25/2014] [Indexed: 01/09/2023] Open
Abstract
Proteomics is a powerful approach used for investigating the complex molecular mechanisms of disease pathogenesis and progression. An important challenge in modern protein profiling approaches involves targeting of specific protein activities in order to identify altered molecular processes associated with disease pathophysiology. Adenosine-binding proteins represent an important subset of the proteome where aberrant expression or activity changes of these proteins have been implicated in numerous human diseases. Herein, we describe an affinity-based approach for the enrichment of adenosine-binding proteins from a complex cell proteome. A novel N6-biotinylated-8-azido-adenosine probe (AdoR probe) was synthesized, which contains a reactive group that forms a covalent bond with the target proteins, as well as a biotin tag for affinity enrichment using avidin chromatography. Probe specificity was confirmed with protein standards prior to further evaluation in a complex protein mixture consisting of a lysate derived from mouse neuroblastoma N18TG2 cells. Protein identification and relative quantitation using mass spectrometry allowed for the identification of small variations in abundance of nucleoside- and nucleotide-binding proteins in these samples where a significant enrichment of AdoR-binding proteins in the labeled proteome from the neuroblastoma cells was observed. The results from this study demonstrate the utility of this method to enrich for nucleoside- and nucleotide-binding proteins in a complex protein mixture, pointing towards a unique set of proteins that can be examined in the context of further understanding mechanisms of disease, or fundamental biological processes in general.
Collapse
Affiliation(s)
- Shikha Mahajan
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL, 33620, United States of America
| | - Roman Manetsch
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL, 33620, United States of America
- Department of Chemistry and Chemical Biology and Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States of America
| | - David J. Merkler
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL, 33620, United States of America
| | - Stanley M. Stevens Jr.
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, FL, 33620, United States of America
| |
Collapse
|
17
|
Lee JE, Park JH, Moon PG, Baek MC. Identification of differentially expressed proteins by treatment with PUGNAc in 3T3-L1 adipocytes through analysis of ATP-binding proteome. Proteomics 2014; 13:2998-3012. [PMID: 23946262 DOI: 10.1002/pmic.201200549] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 06/27/2013] [Accepted: 07/13/2013] [Indexed: 12/13/2022]
Abstract
O-GlcNAc (2-acetamino-2-deoxy-β-D-glucopyranose), an important modification for cellular processes, is catalyzed by O-GlcNAc transferase and O-GlcNAcase. O-(2-acetamido-2-deoxy-D-glucopyranosylidene) amino-N-phenylcarbamate (PUGNAc) is a nonselective inhibitor of O-GlcNAcase, which increases the level of protein O-GlcNAcylation and is known to induce insulin-resistance in adipose cells due to uncharacterized targets of this inhibitor. In this study, using ATP affinity chromatography, we applied a targeted proteomic approach for identification of proteins induced by treatment with PUGNAc. For optimization of proteomic methods using ATP affinity chromatography, comparison of two cell lines (3T3-L1 adipocytes and C2C12 myotubes) and two different digestion steps was performed using four different structures of immobilized ATP-bound resins. Using this approach, based on DNA sequence homologies, we found that the identified proteins covered almost half of ATP-binding protein families classified by PROSITE. The optimized ATP affinity chromatography approach was applied for identification of proteins that were differentially expressed in 3T3-L1 adipocytes following treatment with PUGNAc. For label-free quantitation, a gel-assisted method was used for digestion of the eluted proteins, and analysis was performed using two different MS modes, data-independent (671 proteins identified) and data-dependent (533 proteins identified) analyses. Among identified proteins, 261 proteins belong to nucleotide-binding proteins and we focused on some nucleotide-binding proteins, ubiquitin-activation enzyme 1 (E1), Hsp70, vasolin-containing protein (Vcp), and Hsp90, involved in ubiquitin-proteasome degradation and insulin signaling pathways. In addition, we found that treatment with PUGNAc resulted in increased ubiquitination of proteins in a time-dependent manner, and a decrease in both the amount of Akt and the level of phosphorylation of Akt, a key component in insulin signaling, through downregulation of Hsp90. In this study, based on a targeted proteomic approach using ATP affinity chromatography, we found four proteins related to ubiquitination and insulin signaling pathways that were induced by treatment with PUGNAc. This result would provide insight into understanding functions of PUGNAc in 3T3-L1 cells.
Collapse
Affiliation(s)
- Jeong-Eun Lee
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | | | | | | |
Collapse
|
18
|
Pham VC, Anania VG, Phung QT, Lill JR. Complementary methods for the identification of substrates of proteolysis. Methods Enzymol 2014; 544:359-80. [PMID: 24974297 DOI: 10.1016/b978-0-12-417158-9.00014-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Proteolysis describes the cleavage of proteins into smaller components, which in vivo occurs typically to either activate or impair the functionality of cellular proteins. Proteolysis can occur during cellular homeostasis or can be induced due to external stress stimuli such as heat, biological or chemical insult, and is mediated by the activity of cellular enzymes, namely, proteases. Proteolytic cleavage of proteins can influence protein activation by exposing an active site or disrupting inhibitor binding. Conversely, proteolytic cleavage of many proteins has also been shown to lead to protein degradation resulting in inactivation of the substrate. Thousands of proteolytic events are known to take place in regulated cellular processes such as apoptosis and pyroptosis, however, their individual contribution to these processes remains poorly understood. Additionally, many cellular homeostatic processes are regulated by proteolytic events, however, in some cases, few proteolytic substrates have been identified. To gain further insight into the mechanism of action of these cellular processes, and to characterize biomarkers of cell death and other pathological indications, it is imperative to utilize a complete arsenal of tools for studying proteolysis events in vivo and in vitro. In this chapter, we focus on alternative methodologies to N-terminomics for profiling substrates of proteolysis and describe an additional suite of tools including orthogonal biophysical separation techniques such as COFRADIC or GASSP, and affinity capture tools that can enrich for newly formed C-termini (C-terminomics) generated as a result of caspase-mediated proteolysis.
Collapse
Affiliation(s)
- Victoria C Pham
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Veronica G Anania
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Qui T Phung
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Jennie R Lill
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California, USA.
| |
Collapse
|
19
|
Rosenblum JS, Nomanbhoy TK, Kozarich JW. Functional interrogation of kinases and other nucleotide-binding proteins. FEBS Lett 2013; 587:1870-7. [PMID: 23684650 DOI: 10.1016/j.febslet.2013.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 05/06/2013] [Indexed: 01/04/2023]
Abstract
The largest mammalian enzyme family is the kinases. Kinases and other nucleotide-binding proteins are key regulators of signal transduction pathways and the mutation or overexpression of these proteins is often the difference between health and disease. As a result, a massive research effort has focused on understanding how these proteins function and how to inhibit them for therapeutic benefit. Recent advances in chemical biological tools have enabled functional interrogation of these enzymes to provide a deeper understanding of their physiological roles. In addition, these innovative platforms have paved the way for a new generation of drugs whose properties have been guided by functional profiling.
Collapse
|
20
|
Hu L, Paul Fawcett J, Gu J. Protein target discovery of drug and its reactive intermediate metabolite by using proteomic strategy. Acta Pharm Sin B 2012. [DOI: 10.1016/j.apsb.2012.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
21
|
Ohnuma S, Chufan E, Nandigama K, Miller Jenkins LM, Durell SR, Appella E, Sauna ZE, Ambudkar SV. Inhibition of multidrug resistance-linked P-glycoprotein (ABCB1) function by 5'-fluorosulfonylbenzoyl 5'-adenosine: evidence for an ATP analogue that interacts with both drug-substrate-and nucleotide-binding sites. Biochemistry 2011; 50:3724-35. [PMID: 21452853 PMCID: PMC3108491 DOI: 10.1021/bi200073f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5'-Fluorosulfonylbenzonyl 5'-adenosine (FSBA) is an ATP analogue that covalently modifies several residues in the nucleotide-binding domains (NBDs) of several ATPases, kinases, and other proteins. P-glycoprotein (P-gp, ABCB1) is a member of the ATP-binding cassette (ABC) transporter superfamily that utilizes energy from ATP hydrolysis for the efflux of amphipathic anticancer agents from cancer cells. We investigated the interactions of FSBA with P-gp to study the catalytic cycle of ATP hydrolysis. Incubation of P-gp with FSBA inhibited ATP hydrolysis (IC(50 )= 0.21 mM) and the binding of 8-azido[α-(32)P]ATP (IC(50) = 0.68 mM). In addition, (14)C-FSBA cross-links to P-gp, suggesting that FSBA-mediated inhibition of ATP hydrolysis is irreversible due to covalent modification of P-gp. However, when the NBDs were occupied with a saturating concentration of ATP prior to treatment, FSBA stimulated ATP hydrolysis by P-gp. Furthermore, FSBA inhibited the photo-cross-linking of P-gp with [(125)I]iodoarylazidoprazosin (IAAP; IC(50) = 0.17 mM). As IAAP is a transport substrate for P-gp, this suggests that FSBA affects not only the NBDs but also the transport-substrate site in the transmembrane domains. Consistent with these results, FSBA blocked efflux of rhodamine 123 from P-gp-expressing cells. Additionally, mass spectrometric analysis identified FSBA cross-links to residues within or nearby the NBDs but not in the transmembrane domains, and docking of FSBA in a homology model of human P-gp NBDs supports the biochemical studies. Thus, FSBA is an ATP analogue that interacts with both the drug-binding and ATP-binding sites of P-gp, but fluorosulfonyl-mediated cross-linking is observed only at the NBDs.
Collapse
Affiliation(s)
- Shinobu Ohnuma
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Eduardo Chufan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Krishnamachary Nandigama
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Lisa M. Miller Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Stewart R. Durell
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Zuben E. Sauna
- Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland 20892
| | - Suresh V. Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4256
| |
Collapse
|
22
|
Helsens K, Martens L, Vandekerckhove J, Gevaert K. Mass spectrometry-driven proteomics: an introduction. Methods Mol Biol 2011; 753:1-27. [PMID: 21604112 DOI: 10.1007/978-1-61779-148-2_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Proteins are reckoned to be the key actors in a living organism. By studying proteins, one engages into deciphering a complex series of events occurring during a protein's life span. This starts at the creation of a protein, which is tightly controlled on both a transcriptional (Williams and Tyler, 2007, Curr Opin Genet Dev 17, 88-93) and a translational level (Van Der Kelen et al., 2009, Crit Rev Biochem Mol Biol 44, 143-168). During translation, a primary strand of amino acids undergoes a complex folding process in order to obtain a native three-dimensional protein structure (Gross et al., 2003, Cell 115, 739-750). Proteins take on a plethora of functions, such as complex formation, receptor activity, and signal transduction, which ultimately adds up to a cellular phenotype. Consequently, protein analysis is of major interest in molecular biology and involves annotating their presence and localization, as well as their modification state and biochemical context. To accomplish this, many methods have been developed over the last decades, and their general principles and important recent advances in large-scale protein analysis or proteomics are discussed in this review.
Collapse
Affiliation(s)
- Kenny Helsens
- Department of Medical Protein Research, VIB, Ghent University, B-9000, Ghent, Belgium.
| | | | | | | |
Collapse
|
23
|
Impens F, Colaert N, Helsens K, Plasman K, Van Damme P, Vandekerckhove J, Gevaert K. MS-driven protease substrate degradomics. Proteomics 2010; 10:1284-96. [PMID: 20058249 DOI: 10.1002/pmic.200900418] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteolytic processing has recently received increased attention in the field of signal propagation and cellular differentiation. Because of its irreversible nature, protein cleavage has been associated with committed steps in cell function. One aspect of protease biology that boomed the past few years is the detailed characterization of protease substrates by both shotgun as well as targeted MS-driven proteomics techniques. The most promising techniques are discussed in this review and we further elaborate on the bioinformatics challenges that accompany mainly qualitative, MS-driven protease substrate degradome studies.
Collapse
Affiliation(s)
- Francis Impens
- Department of Medical Protein Research, VIB, Ghent, Belgium
| | | | | | | | | | | | | |
Collapse
|
24
|
Kramer G, Sprenger RR, Back J, Dekker HL, Nessen MA, van Maarseveen JH, de Koning LJ, Hellingwerf KJ, de Jong L, de Koster CG. Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography. Mol Cell Proteomics 2009; 8:1599-611. [PMID: 19321432 DOI: 10.1074/mcp.m800392-mcp200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A method is presented to identify and quantify several hundreds of newly synthesized proteins in Escherichia coli upon pulse labeling cells with the methionine analogue azidohomoalanine (azhal). For the first 30 min after inoculation, a methionine-auxotrophic strain grows equally well on azhal as on methionine. Upon a pulse of 15 min and digestion of total protein, azhal-labeled peptides are isolated by a retention time shift between two reversed phase chromatographic runs. The retention time shift is induced by a reaction selective for the azido group in labeled peptides using tris(2-carboxyethyl)phosphine. Selectively modified peptides are identified by reversed phase liquid chromatography and on-line tandem mass spectrometry. We identified 527 proteins representative of all major Gene Ontology categories. Comparing the relative amounts of 344 proteins synthesized in 15 min upon a switch of growth temperature from 37 to 44 degrees C showed that nearly 20% increased or decreased more than 2-fold. Among the most up-regulated proteins many were chaperones and proteases in accordance with the cells response to unfolded proteins due to heat stress. Comparison of our data with results from previous microarray experiments revealed the importance of regulation of gene expression at the level of transcription of the most elevated proteins under heat shock conditions and enabled identification of several candidate genes whose expression may predominantly be regulated at the level of translation. This work demonstrates for the first time the use of a bioorthogonal amino acid for proteome-wide detection of changes in the amounts of proteins synthesized during a brief period upon variations in cellular growth conditions. Comparison of such data with relative mRNA levels enables assessment of the separate contributions of transcription and translation to the regulation of gene expression.
Collapse
Affiliation(s)
- Gertjan Kramer
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Staes A, Van Damme P, Helsens K, Demol H, Vandekerckhove J, Gevaert K. Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics 2008; 8:1362-70. [PMID: 18318009 DOI: 10.1002/pmic.200700950] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We previously described a proteome-wide, peptide-centric procedure for sorting protein N-terminal peptides and used these peptides as readouts for protease degradome and xenoproteome studies. This procedure is part of a repertoire of gel-free techniques known as COmbined FRActional DIagonal Chromatography (COFRADIC) and highly enriches for alpha-amino-blocked peptides, including alpha-amino-acetylated protein N-terminal peptides. Here, we introduce two additional steps that significantly increase the fraction of such proteome-informative, N-terminal peptides: strong cation exchange (SCX) segregation of alpha-amino-blocked and alpha-amino-free peptides and an enzymatic step liberating pyroglutamyl peptides for 2,4,6-trinitrobenzenesulphonic acid (TNBS) modification and thus COFRADIC sorting. The SCX step reduces the complexity of the analyte mixture by enriching N-terminal peptides and depleting alpha-amino-free internal peptides as well as proline-starting peptides prior to COFRADIC. The action of pyroglutamyl aminopeptidases prior to the first COFRADIC peptide separation results in greatly diminishing numbers of contaminating pyroglutamyl peptides in peptide maps. We further show that now close to 95% of all COFRADIC-sorted peptides are alpha-amino-acetylated and, using the same amount of starting material, our novel procedure leads to an increased number of protein identifications.
Collapse
Affiliation(s)
- An Staes
- Department of Medical Protein Research, VIB, Ghent, Belgium
| | | | | | | | | | | |
Collapse
|
26
|
Gevaert K, Impens F, Van Damme P, Ghesquière B, Hanoulle X, Vandekerckhove J. Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses. FEBS J 2007; 274:6277-89. [PMID: 18021238 DOI: 10.1111/j.1742-4658.2007.06149.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Numerous gel-free proteomics techniques have been reported over the past few years, introducing a move from proteins to peptides as bits of information in qualitative and quantitative proteome studies. Many shotgun proteomics techniques randomly sample thousands of peptides in a qualitative and quantitative manner but overlook the vast majority of protein modifications that are often crucial for proper protein structure and function. Peptide-based proteomic approaches have thus been developed to profile a diverse set of modifications including, but not at all limited, to phosphorylation, glycosylation and ubiquitination. Typical here is that each modification needs a specific, tailor-made analytical procedure. In this minireview, we discuss how one technique - diagonal reverse-phase chromatography - is applied to study two different types of protein modification: protein processing and protein N-glycosylation. Additionally, we discuss an activity-based proteome study in which purine-binding proteins were profiled by diagonal chromatography.
Collapse
Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.
| | | | | | | | | | | |
Collapse
|
27
|
Ghesquière B, Buyl L, Demol H, Van Damme J, Staes A, Timmerman E, Vandekerckhove J, Gevaert K. A new approach for mapping sialylated N-glycosites in serum proteomes. J Proteome Res 2007; 6:4304-12. [PMID: 17918875 DOI: 10.1021/pr0703728] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new approach for proteome-wide analysis of sialylated N-glycopeptides based on the diagonal chromatographic COFRADIC technology is presented here. The use of alpha(2-3,6,8,9) neuraminidase is central to isolate sialylated N-glycopeptides out of a complex peptide mixture. Two different COFRADIC techniques are introduced here, either without or with post-metabolic oxygen-18 labeling (direct versus indirect sorting), and when applied to immuno-depleted mouse serum, we herewith identified 93 sialylated glycosylation sites in 53 serum proteins.
Collapse
Affiliation(s)
- Bart Ghesquière
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Qiu H, Wang Y. Probing adenosine nucleotide-binding proteins with an affinity-labeled nucleotide probe and mass spectrometry. Anal Chem 2007; 79:5547-56. [PMID: 17602667 PMCID: PMC2637870 DOI: 10.1021/ac0622375] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mass spectrometry combined with chemical labeling strategies has become very important in biological analysis. Herein, we described the application of a biotin-conjugated acyl nucleotide for probing adenosine nucleotide-binding proteins. We demonstrated that the probe reacted specifically with the lysine residue at the nucleotide-binding site of two purified adenosine nucleotide-binding proteins, Escherichia coli recombinase A (RecA) and Saccharomyces cerevisiae alcohol dehydrogenase-I (YADH-I). A single conjugate peptide with a specifically labeled lysine residue was identified, by using LC-MS/MS, from the tryptic digestion mixture of the reaction products of the nucleotide analogue with RecA or YADH-I. The strategy, which involved labeling reaction, enzymatic digestion, affinity purification, and LC-MS/MS analysis, was relatively simple, fast, and straightforward. The method should be generally applicable for the identification of lysine residues at the nucleotide-binding site of other proteins. The biotin-conjugated acyl nucleotide probe also allowed for the enrichment and identification of nucleotide-binding proteins from complex protein mixtures; we showed that more than 50 adenosine nucleotide-binding proteins could be identified from the whole-cell lysates of HeLa-S3 and WM-266-4 cells.
Collapse
Affiliation(s)
- Haibo Qiu
- Department of Chemistry-027, University of California, Riverside, California 92521-0403, USA
| | | |
Collapse
|