1
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Noel D, Hallsworth JE, Gelhaye E, Darnet S, Sormani R, Morel-Rouhier M. Modes-of-action of antifungal compounds: Stressors and (target-site-specific) toxins, toxicants, or Toxin-stressors. Microb Biotechnol 2023. [PMID: 37191200 DOI: 10.1111/1751-7915.14242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 05/17/2023] Open
Abstract
Fungi and antifungal compounds are relevant to the United Nation's Sustainable Development Goals. However, the modes-of-action of antifungals-whether they are naturally occurring substances or anthropogenic fungicides-are often unknown or are misallocated in terms of their mechanistic category. Here, we consider the most effective approaches to identifying whether antifungal substances are cellular stressors, toxins/toxicants (that are target-site-specific), or have a hybrid mode-of-action as Toxin-stressors (that induce cellular stress yet are target-site-specific). This newly described 'toxin-stressor' category includes some photosensitisers that target the cell membrane and, once activated by light or ultraviolet radiation, cause oxidative damage. We provide a glossary of terms and a diagrammatic representation of diverse types of stressors, toxic substances, and Toxin-stressors, a classification that is pertinent to inhibitory substances not only for fungi but for all types of cellular life. A decision-tree approach can also be used to help differentiate toxic substances from cellular stressors (Curr Opin Biotechnol 2015 33: 228-259). For compounds that target specific sites in the cell, we evaluate the relative merits of using metabolite analyses, chemical genetics, chemoproteomics, transcriptomics, and the target-based drug-discovery approach (based on that used in pharmaceutical research), focusing on both ascomycete models and the less-studied basidiomycete fungi. Chemical genetic methods to elucidate modes-of-action currently have limited application for fungi where molecular tools are not yet available; we discuss ways to circumvent this bottleneck. We also discuss ecologically commonplace scenarios in which multiple substances act to limit the functionality of the fungal cell and a number of as-yet-unresolved questions about the modes-of-action of antifungal compounds pertaining to the Sustainable Development Goals.
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Affiliation(s)
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Eric Gelhaye
- Université de Lorraine, INRAE, IAM, Nancy, France
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2
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Small bioactive molecules designed to be probes as baits “fishing out” cellular targets: finding the fish in the proteome sea. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Wagh SB, Maslivetc VA, La Clair JJ, Kornienko A. Lessons in Organic Fluorescent Probe Discovery. Chembiochem 2021; 22:3109-3139. [PMID: 34062039 PMCID: PMC8595615 DOI: 10.1002/cbic.202100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/22/2021] [Indexed: 02/03/2023]
Abstract
Fluorescent probes have gained profound use in biotechnology, drug discovery, medical diagnostics, molecular and cell biology. The development of methods for the translation of fluorophores into fluorescent probes continues to be a robust field for medicinal chemists and chemical biologists, alike. Access to new experimental designs has enabled molecular diversification and led to the identification of new approaches to probe discovery. This review provides a synopsis of the recent lessons in modern fluorescent probe discovery.
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Affiliation(s)
- Sachin B Wagh
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
| | - Vladimir A Maslivetc
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
| | - James J La Clair
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1062, USA
| | - Alexander Kornienko
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
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4
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Friedman Ohana R, Levin S, Hurst R, Rosenblatt MM, Zimmerman K, Machleidt T, Wood KV, Kirkland TA. Streamlined Target Deconvolution Approach Utilizing a Single Photoreactive Chloroalkane Capture Tag. ACS Chem Biol 2021; 16:404-413. [PMID: 33543920 DOI: 10.1021/acschembio.0c00987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of physiologically relevant targets for lead compounds emerging from drug discovery screens is often the rate-limiting step toward understanding their mechanism of action and potential for undesired off-target effects. To this end, we developed a streamlined chemical proteomic approach utilizing a single, photoreactive cleavable chloroalkane capture tag, which upon attachment to bioactive compounds facilitates selective isolation of their respective cellular targets for subsequent identification by mass spectrometry. When properly positioned, the tag does not significantly affect compound potency and membrane permeability, allowing for binding interactions with the tethered compound (probe) to be established within intact cells under physiological conditions. Subsequent UV-induced covalent photo-cross-linking "freezes" the interactions between the probe and its cellular targets and prevents their dissociation upon cell lysis. Targets cross-linked to the capture tag are then efficiently enriched through covalent capture onto HaloTag coated beads and subsequent selective chemical release from the solid support. The tag's built-in capability for selective enrichment eliminates the need for ligation of a capture tag, thereby simplifying the workflow and reducing variability introduced through additional operational steps. At the same time, the capacity for adequate cross-linking without structural optimization permits modular assembly of photoreactive chloroalkane probes, which reduces the burden of customized chemistry. Using three model compounds, we demonstrate the capability of this approach to identify known and novel cellular targets, including those with low affinity and/or low abundance as well as membrane targets with several transmembrane domains.
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Affiliation(s)
| | - Sergiy Levin
- Promega Biosciences LLC, 277 Granada Drive, San Luis Obispo, California 93401, United States
| | - Robin Hurst
- Promega Corporation, 2800 Woods Hollow, Fitchburg, Wisconsin 53711, United States
| | | | - Kristopher Zimmerman
- Promega Corporation, 2800 Woods Hollow, Fitchburg, Wisconsin 53711, United States
| | - Thomas Machleidt
- Promega Corporation, 2800 Woods Hollow, Fitchburg, Wisconsin 53711, United States
| | - Keith V. Wood
- Promega Corporation, 2800 Woods Hollow, Fitchburg, Wisconsin 53711, United States
| | - Thomas A. Kirkland
- Promega Biosciences LLC, 277 Granada Drive, San Luis Obispo, California 93401, United States
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5
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Müskens FM, Ward RJ, Herkt D, van de Langemheen H, Tobin AB, Liskamp RMJ, Milligan G. Design, Synthesis, and Evaluation of a Diazirine Photoaffinity Probe for Ligand-Based Receptor Capture Targeting G Protein-Coupled Receptors. Mol Pharmacol 2019; 95:196-209. [PMID: 30514721 PMCID: PMC6324650 DOI: 10.1124/mol.118.114249] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
Chemoproteomic approaches to identify ligand-receptor interactions have gained popularity. However, identifying transmembrane receptors remains challenging. A new trifunctional probe to aid the nonbiased identification of such receptors was developed and synthesized using a convenient seven-step synthesis. This probe contained three functional groups: 1) an N-hydroxysuccinimide ester for ligand-coupling through free amines, 2) a diazirine moiety to capture the receptor of interest upon irradiation with UV light, and 3) a biotin group which allowed affinity purification of the final adduct using streptavidin. The interaction between the G protein-coupled tachykinin neurokinin 1 (NK1) receptor, expressed in an inducible manner, and the peptidic ligand substance P was used as a test system. Liquid chromatography-mass spectrometry analysis confirmed successful coupling of the probe to substance P, while inositol monophosphate accumulation assays demonstrated that coupling of the probe did not interfere substantially with the substance P-NK1 receptor interaction. Confocal microscopy and western blotting provided evidence of the formation of a covalent bond between the probe and the NK1 receptor upon UV activation. As proof of concept, the probe was used in full ligand-based receptor-capture experiments to identify the substance P-binding receptor via liquid chromatography-tandem mass spectrometry, resulting in the successful identification of only the NK1 receptor. This provides proof of concept toward general utilization of this probe to define interactions between ligands and previously unidentified plasma-membrane receptors.
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Affiliation(s)
- Frederike M Müskens
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Richard J Ward
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Dominik Herkt
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Helmus van de Langemheen
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Andrew B Tobin
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Rob M J Liskamp
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Graeme Milligan
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
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6
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Drewes G, Knapp S. Chemoproteomics and Chemical Probes for Target Discovery. Trends Biotechnol 2018; 36:1275-1286. [DOI: 10.1016/j.tibtech.2018.06.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 12/28/2022]
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7
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Moraru A, Wiederstein J, Pfaff D, Fleming T, Miller AK, Nawroth P, Teleman AA. Elevated Levels of the Reactive Metabolite Methylglyoxal Recapitulate Progression of Type 2 Diabetes. Cell Metab 2018; 27:926-934.e8. [PMID: 29551588 DOI: 10.1016/j.cmet.2018.02.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 07/27/2017] [Accepted: 02/06/2018] [Indexed: 10/17/2022]
Abstract
The molecular causes of type 2 diabetes (T2D) are not well understood. Both type 1 diabetes (T1D) and T2D are characterized by impaired insulin signaling and hyperglycemia. From analogy to T1D, insulin resistance and hyperglycemia are thought to also play causal roles in T2D. Recent clinical studies, however, found that T2D patients treated to maintain glycemia below the diabetes definition threshold (HbA1c < 6.5%) still develop diabetic complications. This suggests additional insulin- and glucose-independent mechanisms could be involved in T2D progression and/or initiation. T2D patients have elevated levels of the metabolite methylglyoxal (MG). We show here, using Drosophila glyoxalase 1 knockouts, that animals with elevated methylglyoxal recapitulate several core aspects of T2D: insulin resistance, obesity, and hyperglycemia. Thus elevated MG could constitute one root cause of T2D, suggesting that the molecular causes of elevated MG warrant further study.
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Affiliation(s)
- Alexandra Moraru
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg University, 69120 Heidelberg, Germany
| | - Janica Wiederstein
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg University, 69120 Heidelberg, Germany
| | - Daniel Pfaff
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg University, 69120 Heidelberg, Germany; Department of Internal Medicine I and Clinical Chemistry, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Helmholtz-Zentrum, 85764 Munich, Germany
| | - Thomas Fleming
- Department of Internal Medicine I and Clinical Chemistry, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Helmholtz-Zentrum, 85764 Munich, Germany
| | - Aubry K Miller
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Peter Nawroth
- Department of Internal Medicine I and Clinical Chemistry, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Helmholtz-Zentrum, 85764 Munich, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg University, 69120 Heidelberg, Germany.
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8
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Blex C, Michaelis S, Schrey AK, Furkert J, Eichhorst J, Bartho K, Gyapon Quast F, Marais A, Hakelberg M, Gruber U, Niquet S, Popp O, Kroll F, Sefkow M, Schülein R, Dreger M, Köster H. Targeting G Protein-Coupled Receptors by Capture Compound Mass Spectrometry: A Case Study with Sertindole. Chembiochem 2017; 18:1639-1649. [PMID: 28557180 DOI: 10.1002/cbic.201700152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Indexed: 01/06/2023]
Abstract
Unbiased chemoproteomic profiling of small-molecule interactions with endogenous proteins is important for drug discovery. For meaningful results, all protein classes have to be tractable, including G protein-coupled receptors (GPCRs). These receptors are hardly tractable by affinity pulldown from lysates. We report a capture compound (CC)-based strategy to target and identify GPCRs directly from living cells. We synthesized CCs with sertindole attached to the CC scaffold in different orientations to target the dopamine D2 receptor (DRD2) heterologously expressed in HEK 293 cells. The structure-activity relationship of sertindole for DRD2 binding was reflected in the activities of the sertindole CCs in radioligand displacement, cell-based assays, and capture compound mass spectrometry (CCMS). The activity pattern was rationalized by molecular modelling. The most-active CC showed activities very similar to that of unmodified sertindole. A concentration of DRD2 in living cells well below 100 fmol used as an experimental input was sufficient for unambiguous identification of captured DRD2 by mass spectrometry. Our new CCMS workflow broadens the arsenal of chemoproteomic technologies to close a critical gap for the comprehensive characterization of drug-protein interactions.
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Affiliation(s)
- Christian Blex
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Present address: Department of Neurology and Experimental Neurology, Charité, University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Simon Michaelis
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Anna K Schrey
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Institute for Physiology/Structural Bioinformatics Group, Charité, University Medicine Berlin, Philippstrasse 12, 10115, Berlin, Germany
| | - Jens Furkert
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Jenny Eichhorst
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Kathrin Bartho
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Thermo Fisher Scientific GmbH, Im Steingrund 4-6, 63303, Dreieich, Germany
| | - Frederick Gyapon Quast
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Glycotope GmbH, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Anett Marais
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Medical Bioinformatics, Centogene AG, Schillingstrasse 68, 18057, Berlin, Germany
| | | | - Uschi Gruber
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Sylvia Niquet
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Oliver Popp
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Friedrich Kroll
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,YARA International, Hanninghof 35, 48249, Duelmen, Germany
| | - Michael Sefkow
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany.,Celares GmbH, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Ralf Schülein
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Mathias Dreger
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
| | - Hubert Köster
- caprotec bioanalytics GmbH, Magnusstrasse 11, 12489, Berlin, Germany
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9
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Murale DP, Hong SC, Haque MM, Lee JS. Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs). Proteome Sci 2017; 15:14. [PMID: 28652856 PMCID: PMC5483283 DOI: 10.1186/s12953-017-0123-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/15/2017] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.
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Affiliation(s)
- Dhiraj P Murale
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Seong Cheol Hong
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Md Mamunul Haque
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
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10
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Das J, Roy S, Halnor S, Das AK, Basak A. Enediyne-based protein capture agents: demonstration of an enediyne moiety acting as a photoaffinity label. Org Biomol Chem 2017; 15:1122-1129. [DOI: 10.1039/c6ob02075e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Two enediyne based protein-capture compounds 1 and 2 were synthesized.
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Affiliation(s)
- Joyee Das
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur-721302
- India
| | - Sayantani Roy
- School of Bioscience
- Indian Institute of Technology Kharagpur
- Kharagpur-721302
- India
| | - Swapnil Halnor
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur-721302
- India
| | - Amit Kumar Das
- School of Bioscience
- Indian Institute of Technology Kharagpur
- Kharagpur-721302
- India
| | - Amit Basak
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur-721302
- India
- School of Bioscience
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11
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Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
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12
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Bauermeister A, Zucchi TD, Moraes LAB. Mass spectrometric approaches for the identification of anthracycline analogs produced by actinobacteria. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:437-445. [PMID: 27270867 DOI: 10.1002/jms.3772] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/28/2016] [Accepted: 04/07/2016] [Indexed: 06/06/2023]
Abstract
Anthracyclines are a well-known chemical class produced by actinobacteria used effectively in cancer treatment; however, these compounds are usually produced in few amounts because of being toxic against their producers. In this work, we successfully explored the mass spectrometry versatility to detect 18 anthracyclines in microbial crude extract. From collision-induced dissociation and nuclear magnetic resonance spectra, we proposed structures for five new and identified three more anthracyclines already described in the literature, nocardicyclins A and B and nothramicin. One new compound 8 (4-[4-(dimethylamino)-5-hydroxy-4,6-dimethyloxan-2-yl]oxy-2,5,7,12-tetrahydroxy-3,10-dimethoxy-2-methyl-3,4-dihydrotetracene-1,6,11-trione) was isolated and had its structure confirmed by (1) H nuclear magnetic resonance. The anthracyclines identified in this work show an interesting aminoglycoside, poorly found in natural products, 3-methyl-rhodosamine and derivatives. This fact encouraged to develop a focused method to identify compounds with aminoglycosides (rhodosamine, m/z 158; 3-methyl-rhodosamine, m/z 172; 4'-O-acethyl-3-C-methyl-rhodosamine, m/z 214). This method allowed the detection of four more anthracyclines. This focused method can also be applied in the search of these aminoglycosides in other microbial crude extracts. Additionally, it was observed that nocardicyclin A, nothramicin and compound 8 were able to interact to DNA through a DNA-binding study by mass spectrometry, showing its potential as anticancer drugs. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Anelize Bauermeister
- Mass Spectrometry Applied to Natural Products Laboratory, Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, CEP: 14040-901, Ribeirão Preto, SP, Brazil
| | - Tiago Domingues Zucchi
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000, Jaguariúna, Brazil
| | - Luiz Alberto Beraldo Moraes
- Mass Spectrometry Applied to Natural Products Laboratory, Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, CEP: 14040-901, Ribeirão Preto, SP, Brazil
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13
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Hsu YL, Yang CC, Chou TC, Tai CH, Chen LY, Fu SL, Lin JJ, Lo LC. Design, synthesis, and evaluation of cell permeable probes for protein kinases. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.10.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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14
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Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
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15
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Saathoff H, Brofelth M, Trinh A, Parker BL, Ryan DP, Low JKK, Webb SR, Silva APG, Mackay JP, Shepherd NE. A peptide affinity reagent for isolating an intact and catalytically active multi-protein complex from mammalian cells. Bioorg Med Chem 2015; 23:960-5. [PMID: 25678017 DOI: 10.1016/j.bmc.2015.01.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 10/24/2022]
Abstract
We have developed an approach for directly isolating an intact multi-protein chromatin remodeling complex from mammalian cell extracts using synthetic peptide affinity reagent 4. FOG1(1-15), a short peptide sequence known to target subunits of the nucleosome remodeling and deacetylase (NuRD) complex, was joined via a 35-atom hydrophilic linker to the StreptagII peptide. Loading this peptide onto Streptactin beads enabled capture of the intact NuRD complex from MEL cell nuclear extract. Gentle biotin elution yielded the desired intact complex free of significant contaminants and in a form that was catalytically competent in a nucleosome remodeling assay. The efficiency of 4 in isolating the NuRD complex was comparable to other reported methods utilising recombinantly produced GST-FOG1(1-45).
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Affiliation(s)
- Hinnerk Saathoff
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mattias Brofelth
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anne Trinh
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Daniel P Ryan
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| | - Jason K K Low
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sarah R Webb
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ana P G Silva
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Nicholas E Shepherd
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia.
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16
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Schülke JP, McAllister LA, Geoghegan KF, Parikh V, Chappie TA, Verhoest PR, Schmidt CJ, Johnson DS, Brandon NJ. Chemoproteomics demonstrates target engagement and exquisite selectivity of the clinical phosphodiesterase 10A inhibitor MP-10 in its native environment. ACS Chem Biol 2014; 9:2823-32. [PMID: 25295858 DOI: 10.1021/cb500671j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phosphodiesterases (PDEs) regulate the levels of the second messengers cAMP and cGMP and are important drug targets. PDE10A is highly enriched in medium spiny neurons of the striatum and is an attractive drug target for the treatment of basal ganglia diseases like schizophrenia, Parkinson's disease, or Huntington's disease. Here we describe the design, synthesis, and application of a variety of chemical biology probes, based on the first clinically tested PDE10A inhibitor MP-10, which were used to characterize the chemoproteomic profile of the clinical candidate in its native environment. A clickable photoaffinity probe was used to measure target engagement of MP-10 and revealed differences between whole cell and membrane preparations. Moreover, our results illustrate the importance of the linker design in the creation of functional probes. Biotinylated affinity probes allowed identification of drug-interaction partners in rodent and human tissue and quantitative mass spectrometry analysis revealed highly specific binding of MP-10 to PDE10A with virtually no off-target binding. The profiling of PDE10A chemical biology probes described herein illustrates a strategy by which high affinity inhibitors can be converted into probes for determining selectivity and target engagement of drug candidates in complex biological matrices from native sources.
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Affiliation(s)
- Jan-Philip Schülke
- Neuroscience
Research Unit, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139 (United States)
| | - Laura A. McAllister
- Neuroscience
Medicinal Chemistry and Chemical Biology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139 (United States)
| | - Kieran F. Geoghegan
- Center
of Chemistry, Pfizer Worldwide Research and Development, Groton, Connecticut 06340 (United States)
| | - Vinod Parikh
- Center
of Chemistry, Pfizer Worldwide Research and Development, Groton, Connecticut 06340 (United States)
| | - Thomas A. Chappie
- Neuroscience
Medicinal Chemistry and Chemical Biology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139 (United States)
| | - Patrick R. Verhoest
- Neuroscience
Medicinal Chemistry and Chemical Biology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139 (United States)
| | - Christopher J. Schmidt
- Neuroscience
Research Unit, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139 (United States)
| | - Douglas S. Johnson
- Neuroscience
Medicinal Chemistry and Chemical Biology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139 (United States)
| | - Nicholas J. Brandon
- Neuroscience
Research Unit, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139 (United States)
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17
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Wu J, Shen Q, Wang Y, Zhao D, Peng C, Li JX. Fluorescent Probes for Subcellular Localization during Osteclast Formation. ACS Med Chem Lett 2014; 5:911-4. [PMID: 25147613 DOI: 10.1021/ml500181e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/11/2014] [Indexed: 01/03/2023] Open
Abstract
Labeling of a small bioactive molecule with fluorescent probe has been becoming an essential tool in cell biology to reveal the subcellular distribution and the location of a molecular target. QOA-8a is a novel molecule with potent antiosteoporotic effect in vivo. To investigate the molecular mechanism of QOA-8a, novel fluorescence-tagged chemical probes as bioactive as their parent molecule were designed and synthesized. The fluorescent compound 12 showed a more potent inhibitory activity on RANKL-induced osteoclastogenesis at 2 μM compared with that of QOA-8a. Microscopy experiments revealed that almost all of probe 12 accumulated in the fusing region, with little in the osteoclast precursors or the mature osteoclasts during osteoclast formation. The result suggests the location of the binding target of QOA-8a, which might greatly narrow down the search field of the target protein(s).
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Affiliation(s)
- Jing Wu
- State Key Lab of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Qi Shen
- State Key Lab of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yue Wang
- State Key Lab of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Dan Zhao
- State Key Lab of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Chen Peng
- State Key Lab of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Jian-Xin Li
- State Key Lab of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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18
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Yao C, Na N, Huang L, He D, Ouyang J. High-throughput detection of drugs binding to proteins using desorption electrospray ionization mass spectrometry. Anal Chim Acta 2013; 794:60-6. [DOI: 10.1016/j.aca.2013.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/31/2013] [Accepted: 07/05/2013] [Indexed: 01/24/2023]
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19
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Morimoto S, Tomohiro T, Maruyama N, Hatanaka Y. Photoaffinity casting of a coumarin flag for rapid identification of ligand-binding sites within protein. Chem Commun (Camb) 2013; 49:1811-3. [PMID: 23349004 DOI: 10.1039/c3cc38594a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
A photo-switchable fluorescent flagging approach has been developed to identify photoaffinity-labeled peptides in target protein. Upon photochemical release of the ligand, the protein was newly modified with a coumarin in place of the previously attached biotin. It allowed us to simplify complex identification processes for labeled sites.
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Affiliation(s)
- Shota Morimoto
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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20
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Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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21
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Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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22
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Sarathi Addy P, Saha B, Pradeep Singh ND, Das AK, Bush JT, Lejeune C, Schofield CJ, Basak A. 1,3,5-Trisubstituted benzenes as fluorescent photoaffinity probes for human carbonic anhydrase II capture. Chem Commun (Camb) 2013; 49:1930-2. [PMID: 23364467 DOI: 10.1039/c3cc38251f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The synthesis of small molecule based 1,3,5-trisubstituted benzenes for photo-mediated capture of human carbonic anhydrase II with visualisation by fluorescence is described.
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Affiliation(s)
- Partha Sarathi Addy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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23
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Bush JT, Walport LJ, McGouran JF, Leung IKH, Berridge G, van Berkel SS, Basak A, Kessler BM, Schofield CJ. The Ugi four-component reaction enables expedient synthesis and comparison of photoaffinity probes. Chem Sci 2013. [DOI: 10.1039/c3sc51708j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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24
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Messana I, Cabras T, Iavarone F, Vincenzoni F, Urbani A, Castagnola M. Unraveling the different proteomic platforms. J Sep Sci 2012; 36:128-39. [PMID: 23212829 DOI: 10.1002/jssc.201200830] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/05/2012] [Accepted: 10/06/2012] [Indexed: 01/06/2023]
Abstract
This review is addressed to scientists working outside the field of proteomics and wishes to shed a light on the possibility offered by the latest proteomics strategies. Bottom-up and top-down platforms are critically examined outlining advantages and limitations of their application to qualitative and quantitative investigations. Discovery, directed and targeted proteomics as different options for the management of the MS instrument are defined emphasizing their integration in the experimental plan to accomplish meaningful results. The issue of data validation is analyzed and discussed. The most common qualitative proteomic platforms are described, with a particular emphasis on enrichment methods to elucidate PTMs codes (i.e. ubiquitin and histone codes). Label-free and labeled methods for relative and absolute quantification are critically compared. The possible contribution of proteomics platforms to the transition from structural proteomics to functional proteomics (study of the functional connections between different proteins) and to the challenging system biology (integrated study of all the functional cellular functions) is also briefly discussed.
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Affiliation(s)
- Irene Messana
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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25
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Wiedner SD, Burnum KE, Pederson LM, Anderson LN, Fortuin S, Chauvigné-Hines LM, Shukla AK, Ansong C, Panisko EA, Smith RD, Wright AT. Multiplexed activity-based protein profiling of the human pathogen Aspergillus fumigatus reveals large functional changes upon exposure to human serum. J Biol Chem 2012; 287:33447-59. [PMID: 22865858 PMCID: PMC3460446 DOI: 10.1074/jbc.m112.394106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/27/2012] [Indexed: 11/06/2022] Open
Abstract
Environmental adaptability is critical for survival of the fungal human pathogen Aspergillus fumigatus in the immunocompromised host lung. We hypothesized that exposure of the fungal pathogen to human serum would lead to significant alterations to the organism's physiology, including metabolic activity and stress response. Shifts in functional pathway and corresponding enzyme reactivity of A. fumigatus upon exposure to the human host may represent much needed prognostic indicators of fungal infection. To address this, we employed a multiplexed activity-based protein profiling (ABPP) approach coupled to quantitative mass spectrometry-based proteomics to measure broad enzyme reactivity of the fungus cultured with and without human serum. ABPP showed a shift from aerobic respiration to ethanol fermentation and utilization over time in the presence of human serum, which was not observed in serum-free culture. Our approach provides direct insight into this pathogen's ability to survive, adapt, and proliferate. Additionally, our multiplexed ABPP approach captured a broad swath of enzyme reactivity and functional pathways and provides a method for rapid assessment of the A. fumigatus response to external stimuli.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ellen A. Panisko
- the Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, Washington 99352
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26
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Direct identification of ligand-receptor interactions on living cells and tissues. Nat Biotechnol 2012; 30:997-1001. [PMID: 22983091 DOI: 10.1038/nbt.2354] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 08/08/2012] [Indexed: 12/11/2022]
Abstract
Many cellular responses are triggered by proteins, drugs or pathogens binding to cell-surface receptors, but it can be challenging to identify which receptors are bound by a given ligand. Here we describe TRICEPS, a chemoproteomic reagent with three moieties--one that binds ligands containing an amino group, a second that binds glycosylated receptors on living cells and a biotin tag for purifying the receptor peptides for identification by quantitative mass spectrometry. We validated this ligand-based, receptor-capture (LRC) technology using insulin, transferrin, apelin, epidermal growth factor, the therapeutic antibody trastuzumab and two DARPins targeting ErbB2. In some cases, we could also determine the approximate ligand-binding sites on the receptors. Using TRICEPS to label intact mature vaccinia viruses, we identified the cell surface proteins AXL, M6PR, DAG1, CSPG4 and CDH13 as binding factors on human cells. This technology enables the identification of receptors for many types of ligands under near-physiological conditions and without the need for genetic manipulations.
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27
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Moggs J, Moulin P, Pognan F, Brees D, Leonard M, Busch S, Cordier A, Heard DJ, Kammüller M, Merz M, Bouchard P, Chibout SD. Investigative safety science as a competitive advantage for Pharma. Expert Opin Drug Metab Toxicol 2012; 8:1071-82. [DOI: 10.1517/17425255.2012.693914] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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28
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Zinn N, Hopf C, Drewes G, Bantscheff M. Mass spectrometry approaches to monitor protein-drug interactions. Methods 2012; 57:430-40. [PMID: 22687620 DOI: 10.1016/j.ymeth.2012.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/16/2012] [Accepted: 05/28/2012] [Indexed: 12/16/2022] Open
Abstract
Recent advances in mass spectrometry-based approaches have enabled the investigation of drug-protein interactions in various ways including the direct detection of drug-target complexes, the examination of drug-induced changes in the target protein structure, and the monitoring of enzymatic target activity. Mass spectrometry-based proteomics methods also permit the unbiased analysis of changes in protein abundance and post-translational modifications induced by drug action. Finally, chemoproteomic affinity enrichment studies enable the deconvolution of drug targets under close to physiological conditions. This review provides an overview of current methods for the characterization of drug-target interactions by mass spectrometry and describes a protocol for chemoproteomic target binding studies using immobilized bioactive molecules.
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Affiliation(s)
- Nico Zinn
- Cellzome AG, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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29
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Nesper J, Reinders A, Glatter T, Schmidt A, Jenal U. A novel capture compound for the identification and analysis of cyclic di-GMP binding proteins. J Proteomics 2012; 75:4874-8. [PMID: 22652488 DOI: 10.1016/j.jprot.2012.05.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/16/2012] [Accepted: 05/18/2012] [Indexed: 11/16/2022]
Abstract
The second messenger cyclic di-GMP is a near-ubiquitous signaling molecule that globally alters bacterial cell physiology to promote biofilm formation and community behavior. Much progress was made in recent years towards the identification and characterization of diguanylate cyclases and phosphodiersterases, enzymes involved in the synthesis and degradation of this signaling compound. In contrast, our knowledge of the nature and mechanistic details of c-di-GMP effector proteins lags behind, primarily because effective tools for their specific enrichment and rapid analysis are missing. In this report we demonstrate that a novel tri-functional c-di-GMP-specific Capture Compound (cdG-CC) can be effectively used to identify and validate c-di-GMP binding proteins. The cdG-CC was able to specifically and efficiently pull down bona fide c-di-GMP effector proteins. Furthermore, in combination with mass spectrometry (CCMS), this technology robustly identified a substantial fraction of the known c-di-GMP signaling components directly from cell extracts of different model organisms. Finally, we applied the CCMS technique to profile c-di-GMP binding proteins of Pseudomonas aeruginosa and Salmonella enterica serovar typhimurium. Our studies establish CCMS as a powerful and versatile tool to identify and analyze components of the cellular c-di-GMP pathway in a wide range of different organisms.
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Affiliation(s)
- Jutta Nesper
- Biozentrum of the University of Basel, Klingelbergstrasse 50, CH-4054 Basel, Switzerland
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