1
|
Dürr-Mayer T, Schmidt A, Wiesler S, Huck T, Mayer A, Jessen HJ. Non-Hydrolysable Analogues of Cyclic and Branched Condensed Phosphates: Chemistry and Chemical Proteomics. Chemistry 2023; 29:e202302400. [PMID: 37646539 DOI: 10.1002/chem.202302400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/18/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Studies into the biology of condensed phosphates almost exclusively cover linear polyphosphates. However, there is evidence for the presence of cyclic polyphosphates (metaphosphates) in organisms and for enzymatic digestion of branched phosphates (ultraphosphates) with alkaline phosphatase. Further research of non-linear condensed phosphates in biology would profit from interactome data of such molecules, however, their stability in biological media is limited. Here we present syntheses of modified, non-hydrolysable analogues of cyclic and branched condensed phosphates, called meta- and ultraphosphonates, and their application in a chemical proteomics approach using yeast cell extracts. We identify putative interactors with overlapping hits for structurally related capture compounds underlining the quality of our results. The datasets serve as starting point to study the biological relevance and functions of meta- and ultraphosphates. In addition, we examine the reactivity of meta- and ultraphosphonates with implications for their "hydrolysable" analogues: Efforts to increase the ring-sizes of meta- or cyclic ultraphosphonates revealed a strong preference to form trimetaphosphate-analogue structures by cyclization and/or ring-contraction. Using carbodiimides for condensation, the so far inaccessible dianhydro product of ultraphosphonate, corresponding to P4 O11 2- , was selectively obtained and then ring-opened by different nucleophiles yielding modified cyclic ultraphosphonates.
Collapse
Affiliation(s)
- Tobias Dürr-Mayer
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
| | - Andrea Schmidt
- Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-CH-1066, Epalinges, Switzerland
| | - Stefan Wiesler
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
| | - Tamara Huck
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
| | - Andreas Mayer
- Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-CH-1066, Epalinges, Switzerland
| | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg
| |
Collapse
|
2
|
Brown T, Nguyen T, Zhou B, Zheng YG. Chemical probes and methods for the study of protein arginine methylation. RSC Chem Biol 2023; 4:647-669. [PMID: 37654509 PMCID: PMC10467615 DOI: 10.1039/d3cb00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023] Open
Abstract
Protein arginine methylation is a widespread post-translational modification (PTM) in eukaryotic cells. This chemical modification in proteins functionally modulates diverse cellular processes from signal transduction, gene expression, and DNA damage repair to RNA splicing. The chemistry of arginine methylation entails the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet, SAM) onto a guanidino nitrogen atom of an arginine residue of a target protein. This reaction is catalyzed by about 10 members of protein arginine methyltransferases (PRMTs). With impacts on a variety of cellular processes, aberrant expression and activity of PRMTs have been shown in many disease conditions. Particularly in oncology, PRMTs are commonly overexpressed in many cancerous tissues and positively correlated with tumor initiation, development and progression. As such, targeting PRMTs is increasingly recognized as an appealing therapeutic strategy for new drug discovery. In the past decade, a great deal of research efforts has been invested in illuminating PRMT functions in diseases and developing chemical probes for the mechanistic study of PRMTs in biological systems. In this review, we provide a brief developmental history of arginine methylation along with some key updates in arginine methylation research, with a particular emphasis on the chemical aspects of arginine methylation. We highlight the research endeavors for the development and application of chemical approaches and chemical tools for the study of functions of PRMTs and arginine methylation in regulating biology and disease.
Collapse
Affiliation(s)
- Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Terry Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Bo Zhou
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| |
Collapse
|
3
|
Fedorov II, Lineva VI, Tarasova IA, Gorshkov MV. Mass Spectrometry-Based Chemical Proteomics for Drug Target Discoveries. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:983-994. [PMID: 36180990 DOI: 10.1134/s0006297922090103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
Chemical proteomics, emerging rapidly in recent years, has become a main approach to identifying interactions between the small molecules and proteins in the cells on a proteome scale and mapping the signaling and/or metabolic pathways activated and regulated by these interactions. The methods of chemical proteomics allow not only identifying proteins targeted by drugs, characterizing their toxicity and discovering possible off-target proteins, but also elucidation of the fundamental mechanisms of cell functioning under conditions of drug exposure or due to the changes in physiological state of the organism itself. Solving these problems is essential for both basic research in biology and clinical practice, including approaches to early diagnosis of various forms of serious diseases or prediction of the effectiveness of therapeutic treatment. At the same time, recent developments in high-resolution mass spectrometry have provided the technology for searching the drug targets across the whole cell proteomes. This review provides a concise description of the main objectives and problems of mass spectrometry-based chemical proteomics, the methods and approaches to their solution, and examples of implementation of these methods in biomedical research.
Collapse
Affiliation(s)
- Ivan I Fedorov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
- Moscow Institute of Physics and Technology (National University), Dolgoprudny, Moscow Region, 141700, Russia
| | - Victoria I Lineva
- Moscow Institute of Physics and Technology (National University), Dolgoprudny, Moscow Region, 141700, Russia
| | - Irina A Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
| |
Collapse
|
4
|
Khiar‐Fernández N, Macicior J, Marcos‐Ramiro B, Ortega‐Gutiérrez S. Chemistry for the Identification of Therapeutic Targets: Recent Advances and Future Directions. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nora Khiar‐Fernández
- Department of Organic Chemistry School of Chemistry Universidad Complutense de Madrid Plaza de las Ciencias s/n 28040 Madrid Spain
| | - Jon Macicior
- Department of Organic Chemistry School of Chemistry Universidad Complutense de Madrid Plaza de las Ciencias s/n 28040 Madrid Spain
| | - Beatriz Marcos‐Ramiro
- Department of Organic Chemistry School of Chemistry Universidad Complutense de Madrid Plaza de las Ciencias s/n 28040 Madrid Spain
| | - Silvia Ortega‐Gutiérrez
- Department of Organic Chemistry School of Chemistry Universidad Complutense de Madrid Plaza de las Ciencias s/n 28040 Madrid Spain
| |
Collapse
|
5
|
Molino D, Pila-Castellanos I, Marjault HB, Dias Amoedo N, Kopp K, Rochin L, Karmi O, Sohn YS, Lines L, Hamaï A, Joly S, Radreau P, Vonderscher J, Codogno P, Giordano F, Machin P, Rossignol R, Meldrum E, Arnoult D, Ruggieri A, Nechushtai R, de Chassey B, Morel E. Chemical targeting of NEET proteins reveals their function in mitochondrial morphodynamics. EMBO Rep 2020; 21:e49019. [PMID: 33180995 DOI: 10.15252/embr.201949019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/24/2020] [Accepted: 10/08/2020] [Indexed: 01/27/2023] Open
Abstract
Several human pathologies including neurological, cardiac, infectious, cancerous, and metabolic diseases have been associated with altered mitochondria morphodynamics. Here, we identify a small organic molecule, which we named Mito-C. Mito-C is targeted to mitochondria and rapidly provokes mitochondrial network fragmentation. Biochemical analyses reveal that Mito-C is a member of a new class of heterocyclic compounds that target the NEET protein family, previously reported to regulate mitochondrial iron and ROS homeostasis. One of the NEET proteins, NAF-1, is identified as an important regulator of mitochondria morphodynamics that facilitates recruitment of DRP1 to the ER-mitochondria interface. Consistent with the observation that certain viruses modulate mitochondrial morphogenesis as a necessary part of their replication cycle, Mito-C counteracts dengue virus-induced mitochondrial network hyperfusion and represses viral replication. The newly identified chemical class including Mito-C is of therapeutic relevance for pathologies where altered mitochondria dynamics is part of disease etiology and NEET proteins are highlighted as important therapeutic targets in anti-viral research.
Collapse
Affiliation(s)
- Diana Molino
- Institut Necker-Enfants Malades (INEM), INSERM U1151-CNRS UMR 8253, Université de Paris, Paris, France
| | - Irene Pila-Castellanos
- Institut Necker-Enfants Malades (INEM), INSERM U1151-CNRS UMR 8253, Université de Paris, Paris, France.,ENYO-Pharma, Lyon, France
| | - Henri-Baptiste Marjault
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Katja Kopp
- Department of Infectious Diseases, Molecular Virology, Centre for Integrative Infectious Disease Research (CIID), University of Heidelberg, Heidelberg, Germany
| | - Leila Rochin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Sud University, Saclay University, Paris, Gif-sur-Yvette, France
| | - Ola Karmi
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yang-Sung Sohn
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Ahmed Hamaï
- Institut Necker-Enfants Malades (INEM), INSERM U1151-CNRS UMR 8253, Université de Paris, Paris, France
| | | | | | | | - Patrice Codogno
- Institut Necker-Enfants Malades (INEM), INSERM U1151-CNRS UMR 8253, Université de Paris, Paris, France
| | - Francesca Giordano
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Sud University, Saclay University, Paris, Gif-sur-Yvette, France
| | | | - Rodrigue Rossignol
- Cellomet, Genomic Functional Center, Bordeaux, France.,Maladies Rares: Génétique et Métabolisme (MRGM), INSERM U1211, Bordeaux, France
| | | | - Damien Arnoult
- Institut André Lwoff, INSERM UMRS1197, Hôpital Paul Brousse, Université Paris-Saclay, Villejuif, France
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Centre for Integrative Infectious Disease Research (CIID), University of Heidelberg, Heidelberg, Germany
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Etienne Morel
- Institut Necker-Enfants Malades (INEM), INSERM U1151-CNRS UMR 8253, Université de Paris, Paris, France
| |
Collapse
|
6
|
Ngo C, Mehta R, Aggarwal K, Fikes AG, Santos IC, Greer SM, Que EL. Pull-Down of Metalloproteins in Their Native States by Using Desthiobiotin-Based Probes. Chembiochem 2019; 20:1003-1007. [PMID: 30520207 PMCID: PMC6530555 DOI: 10.1002/cbic.201800613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 11/07/2022]
Abstract
One-third of all proteins are estimated to require metals for structural stability and/or catalytic activity. Desthiobiotin probes containing metal binding groups can be used to capture metalloproteins with exposed active-site metals under mild conditions so as to prevent changes in metallation state. The proof-of-concept was demonstrated with carbonic anhydrase (CA), an open active site, Zn2+ -containing protein. CA was targeted by using sulfonamide derivatives. Linkers of various lengths and structures were screened to determine the optimal structure for capture of the native protein. The optimized probes could selectively pull down CA from red blood cell lysate and other protein mixtures. Pull-down of differently metallated CAs was also investigated.
Collapse
Affiliation(s)
- Chinh Ngo
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Kanchan Aggarwal
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Audrey G. Fikes
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Ines C. Santos
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Emily L. Que
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| |
Collapse
|
7
|
Wang B, Dai P, Ding D, Del Rosario A, Grant RA, Pentelute BL, Laub MT. Affinity-based capture and identification of protein effectors of the growth regulator ppGpp. Nat Chem Biol 2018; 15:141-150. [PMID: 30559427 PMCID: PMC6366861 DOI: 10.1038/s41589-018-0183-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 10/29/2018] [Indexed: 01/29/2023]
Abstract
The nucleotide ppGpp is a highly conserved regulatory molecule in prokaryotes that helps tune growth rate to nutrient availability. Despite decades of study, how ppGpp regulates growth remains poorly understood. Here, we develop and validate a capture-compound mass spectrometry approach that identifies >50 putative ppGpp targets in Escherichia coli. These targets control many key cellular processes and include 13 enzymes required for nucleotide synthesis. We demonstrate that ppGpp inhibits the de novo synthesis of all purine nucleotides by directly targeting the enzyme PurF. By solving a structure of PurF bound to ppGpp, we design a mutation that ablates ppGpp-based regulation, leading to a dysregulation of purine nucleotide synthesis following ppGpp accumulation. Collectively, our results provide new insights into ppGpp-based growth control and a nearly comprehensive set of targets for future exploration. The capture compounds developed will also now enable the rapid identification of ppGpp targets in any species, including pathogens.
Collapse
Affiliation(s)
- Boyuan Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David Ding
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda Del Rosario
- Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Environmental Health Sciences MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
8
|
Abstract
‘Drug promiscuity’ refers to a drug that can act on multiple molecular targets, exhibiting similar or different pharmacological effects. Drugs may interact with unwanted targets, leading to off-target effects (one of the main reasons for side effects). Thus, intervention to prevent off-target effects in the early stages of drug discovery could reduce the risk of failure. The conversion between target and off-target effects is important for drug repurposing. Drug repurposing strategies could reduce research and development costs. This review details the research progress in the rational application of drug promiscuity for the discovery of multi-target drugs, drug repurposing and improving druggability in medicinal chemistry over the last 5 years.
Collapse
|
9
|
Laventie BJ, Glatter T, Jenal U. Pull-Down with a c-di-GMP-Specific Capture Compound Coupled to Mass Spectrometry as a Powerful Tool to Identify Novel Effector Proteins. Methods Mol Biol 2018; 1657:361-376. [PMID: 28889308 DOI: 10.1007/978-1-4939-7240-1_28] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Capture compound technology coupled to mass spectrometry (CCMS) allows to biochemically identify ligand receptors. Using a c-di-GMP-specific Capture Compound, we adapted this method for the identification and characterization of c-di-GMP binding proteins in any bacterial species. Because in silico analysis often fails to predict novel c-di-GMP effectors, this universal method aims at better defining the cellular c-di-GMP network in a wide range of bacteria. CCMS was successfully applied in several bacterial species (Nesper et al., J Proteom 75:4874-4878, 2012; Steiner et al., EMBO J 32:354-368, 2013; Tschowri et al., Cell 158:1136-1147, 2014; Trampari et al., J Biol Chem 290:24470-24483, 2015; Rotem et al., J Bacteriol 198:127-137, 2015). To outline the detailed protocol and to illustrate its power, we use Pseudomonas aeruginosa, an opportunistic pathogen in which c-di-GMP plays a critical role in virulence and biofilm control, as an example. CCMS identified 74% (38/51) of the known or predicted components of the c-di-GMP network.
Collapse
Affiliation(s)
| | - Timo Glatter
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
- Facility for Mass Spectrometry and Proteomics, Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Urs Jenal
- Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| |
Collapse
|
10
|
Comess KM, McLoughlin SM, Oyer JA, Richardson PL, Stöckmann H, Vasudevan A, Warder SE. Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective. J Med Chem 2018; 61:8504-8535. [DOI: 10.1021/acs.jmedchem.7b01921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenneth M. Comess
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Shaun M. McLoughlin
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Jon A. Oyer
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Paul L. Richardson
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Henning Stöckmann
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Scott E. Warder
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| |
Collapse
|
11
|
Schlossmann J, Wolfertstetter S. Identification of cCMP and cUMP Substrate Proteins and Cross Talk Between cNMPs. Handb Exp Pharmacol 2017; 238:149-167. [PMID: 26721673 DOI: 10.1007/164_2015_38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
cCMP and cUMP are pyrimidine cyclic nucleotides which are present in several types of cells. These molecules could exert diverse cellular functions and might act as second messengers. In the last years, diverse approaches were performed to analyze possible cellular substrates and signaling pathways of cCMP and cUMP. In this review these approaches are summarized, and probable cross talk of these signaling molecules is described. These analyses might lead to the (patho)physiological and pharmacological relevance of these noncanonical cyclic nucleotides.
Collapse
Affiliation(s)
- Jens Schlossmann
- Pharmacology and Toxicology, Institute of Pharmacy, University Regensburg, Universitätsstr. 31, D-93040, Regensburg, Germany.
| | - Stefanie Wolfertstetter
- Pharmacology and Toxicology, Institute of Pharmacy, University Regensburg, Universitätsstr. 31, D-93040, Regensburg, Germany
| |
Collapse
|
12
|
Budzyński MA, Crul T, Himanen SV, Toth N, Otvos F, Sistonen L, Vigh L. Chaperone co-inducer BGP-15 inhibits histone deacetylases and enhances the heat shock response through increased chromatin accessibility. Cell Stress Chaperones 2017; 22:717-728. [PMID: 28474205 PMCID: PMC5573690 DOI: 10.1007/s12192-017-0798-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/22/2017] [Accepted: 04/07/2017] [Indexed: 01/20/2023] Open
Abstract
Defects in cellular protein homeostasis are associated with many severe and prevalent pathological conditions such as neurodegenerative diseases, muscle dystrophies, and metabolic disorders. One way to counteract these defects is to improve the protein homeostasis capacity through induction of the heat shock response. Despite numerous attempts to develop strategies for chemical activation of the heat shock response by heat shock transcription factor 1 (HSF1), the underlying mechanisms of drug candidates' mode of action are poorly understood. To lower the threshold for the heat shock response activation, we used the chaperone co-inducer BGP-15 that was previously shown to have beneficial effects on several proteinopathic disease models. We found that BGP-15 treatment combined with heat stress caused a substantial increase in HSF1-dependent heat shock protein 70 (HSPA1A/B) expression already at a febrile range of temperatures. Moreover, BGP-15 alone inhibited the activity of histone deacetylases (HDACs), thereby increasing chromatin accessibility at multiple genomic loci including the stress-inducible HSPA1A. Intriguingly, treatment with well-known potent HDAC inhibitors trichostatin A and valproic acid enhanced the heat shock response and improved cytoprotection. These results present a new pharmacological strategy for restoring protein homeostasis by inhibiting HDACs, increasing chromatin accessibility, and lowering the threshold for heat shock response activation.
Collapse
Affiliation(s)
- Marek A Budzyński
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, FI-20520, Turku, Finland
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku, FI-20520, Turku, Finland
| | - Tim Crul
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Samu V Himanen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, FI-20520, Turku, Finland
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku, FI-20520, Turku, Finland
| | - Noemi Toth
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Ferenc Otvos
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, FI-20520, Turku, Finland.
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku, FI-20520, Turku, Finland.
| | - Laszlo Vigh
- Biological Research Centre of the Hungarian Academy of Sciences, Szeged, 6726, Hungary.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Identification of apilimod as a first-in-class PIKfyve kinase inhibitor for treatment of B-cell non-Hodgkin lymphoma. Blood 2017; 129:1768-1778. [PMID: 28104689 DOI: 10.1182/blood-2016-09-736892] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/12/2017] [Indexed: 12/15/2022] Open
Abstract
We identified apilimod as an antiproliferative compound by high-throughput screening of clinical-stage drugs. Apilimod exhibits exquisite specificity for phosphatidylinositol-3-phosphate 5-kinase (PIKfyve) lipid kinase and has selective cytotoxic activity in B-cell non-Hodgkin lymphoma (B-NHL) compared with normal cells. Apilimod displays nanomolar activity in vitro, and in vivo studies demonstrate single-agent efficacy as well as synergy with approved B-NHL drugs. Using biochemical and knockdown approaches, and discovery of a kinase domain mutation conferring resistance, we demonstrate that apilimod-mediated cytotoxicity is driven by PIKfyve inhibition. Furthermore, a critical role for lysosome dysfunction as a major factor contributing to apilimod's cytotoxicity is supported by a genome-wide CRISPR screen. In the screen, TFEB (master transcriptional regulator of lysosomal biogenesis) and endosomal/lysosomal genes CLCN7, OSTM1, and SNX10 were identified as important determinants of apilimod sensitivity. These findings thus suggest that disruption of lysosomal homeostasis with apilimod represents a novel approach to treat B-NHL.
Collapse
|
15
|
Singha M, Roy S, Pandey SD, Bag SS, Bhattacharya P, Das M, Ghosh AS, Ray D, Basak A. Use of azidonaphthalimide carboxylic acids as fluorescent templates with a built-in photoreactive group and a flexible linker simplifies protein labeling studies: applications in selective tagging of HCAII and penicillin binding proteins. Chem Commun (Camb) 2017; 53:13015-13018. [DOI: 10.1039/c7cc08209f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A simple design of versatile template-based protein labeling agents has been successfully demonstrated with HCA and PBPs.
Collapse
Affiliation(s)
- Monisha Singha
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
| | - Sayantani Roy
- School of Bioscience
- Indian Institute of Technology Kharagpur
- India
| | - Satya Deo Pandey
- Department of Biotechnology
- Indian Institute of Technology Kharagpur
- India
| | | | | | - Mainak Das
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
| | - Anindya S. Ghosh
- Department of Biotechnology
- Indian Institute of Technology Kharagpur
- India
| | - Debashis Ray
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
| | - Amit Basak
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
McLellan M, Doyle MGJ, Bodnar ED, Lopez PG, Domalaon R, Roy R, Cordova K, Schweizer F, Perreault H. Multiplexed azido-group isotopic capture (MAGIC) beads: Selective analysis of azido compounds using a propargyl-based cleavable linker, a proof of concept. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2497-2507. [PMID: 27650360 DOI: 10.1002/rcm.7744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/13/2016] [Accepted: 09/18/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE A cleavable linker is designed and synthesized for the selective capture of azide-containing compounds. This article presents a proof of concept methodology involving the use of peptide-functionalized aminopropyl silica, on which the peptide is constructed by solid-phase peptide synthesis. METHODS The peptide linker has L-propargylglycine (Pra) at one terminal end to allow the conjugation of azide-containing molecules by copper assisted azide alkyne cycloaddition, also known as click reaction. L-Arginine (Arg) is placed just before Pra to permit the release of the captured product by tryptic cleavage. Three glycine (Gly) residues, as part of the linker, are appended to the silica bead to present a spacer section that allows efficient tryptic cleavage devoid of steric hindrance imposed by the bulky bead. The bead composition is Si-O-propyl-NH-Gly-Gly-Gly-Arg-Pra. RESULTS This solid-phase material can be used to capture and release azide-functionalized compounds. The beads are first tested on three azido compounds, 2-azido-2-deoxyglucose (ADG), BOC-p-azido-Phe-OH (BAzPhe), where BOC = tert-butoxycarbonyl, and tetraacetylated-N-azidomannosamine (Ac4 ManNAz). Copper-mediated click reaction conditions are used and released products are characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and tandem MS (MS/MS). CONCLUSIONS This method allows easy identification of captured compounds based on mass and fragmentation analysis. Moreover, it is useful for the analysis of small azide-containing compounds by MALDI-TOF-MS which may not be possible otherwise due to matrix interferences. The insertion of isotopically labeled Arg residues provides the possibility of multiplex analysis, from which the beads have been called MAGIC (for Multiplexed Azido-Group Isotopic Capture). Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Michelle McLellan
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Michael G J Doyle
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Edward D Bodnar
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Paul G Lopez
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Ronald Domalaon
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Rini Roy
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Katherine Cordova
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Frank Schweizer
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| | - Hélène Perreault
- University of Manitoba, Chemistry Parker 550, 144 Dysart Road, Winnipeg, Manitoba, Canada, R3T 2N2
| |
Collapse
|
18
|
Joosten M, Ginzel S, Blex C, Schmidt D, Gombert M, Chen C, Linka RM, Gräbner O, Hain A, Hirsch B, Sommerfeld A, Seegebarth A, Gruber U, Maneck C, Zhang L, Stenin K, Dieks H, Sefkow M, Münk C, Baldus CD, Thiele R, Borkhardt A, Hummel M, Köster H, Fischer U, Dreger M, Seitz V. A novel approach to detect resistance mechanisms reveals FGR as a factor mediating HDAC inhibitor SAHA resistance in B-cell lymphoma. Mol Oncol 2016; 10:1232-44. [PMID: 27324824 DOI: 10.1016/j.molonc.2016.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 01/15/2023] Open
Abstract
Histone deacetylase (HDAC) inhibitors such as suberoylanilide hydroxamic acid (SAHA) are not commonly used in clinical practice for treatment of B-cell lymphomas, although a subset of patients with refractory or relapsed B-cell lymphoma achieved partial or complete remissions. Therefore, the purpose of this study was to identify molecular features that predict the response of B-cell lymphomas to SAHA treatment. We designed an integrative approach combining drug efficacy testing with exome and captured target analysis (DETECT). In this study, we tested SAHA sensitivity in 26 B-cell lymphoma cell lines and determined SAHA-interacting proteins in SAHA resistant and sensitive cell lines employing a SAHA capture compound (CC) and mass spectrometry (CCMS). In addition, we performed exome mutation analysis. Candidate validation was done by expression analysis and knock-out experiments. An integrated network analysis revealed that the Src tyrosine kinase Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog (FGR) is associated with SAHA resistance. FGR was specifically captured by the SAHA-CC in resistant cells. In line with this observation, we found that FGR expression was significantly higher in SAHA resistant cell lines. As functional proof, CRISPR/Cas9 mediated FGR knock-out in resistant cells increased SAHA sensitivity. In silico analysis of B-cell lymphoma samples (n = 1200) showed a wide range of FGR expression indicating that FGR expression might help to stratify patients, which clinically benefit from SAHA therapy. In conclusion, our comprehensive analysis of SAHA-interacting proteins highlights FGR as a factor involved in SAHA resistance in B-cell lymphoma.
Collapse
Affiliation(s)
- Maria Joosten
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Sebastian Ginzel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany; Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Grantham-Allee 20, 53757 Sankt Augustin, Germany
| | - Christian Blex
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Dmitri Schmidt
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Cai Chen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - René Martin Linka
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Olivia Gräbner
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Anika Hain
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Burkhard Hirsch
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Anke Sommerfeld
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Anke Seegebarth
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Uschi Gruber
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Corinna Maneck
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Langhui Zhang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany; Department of Hematology, Union Hospital, Fujian Medical University, NO.29,Xinquan Road, Fuzhou City, Fujian Province, China
| | - Katharina Stenin
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Henrik Dieks
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Michael Sefkow
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Claudia D Baldus
- Department of Hematology and Oncology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Ralf Thiele
- Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Grantham-Allee 20, 53757 Sankt Augustin, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Michael Hummel
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Hubert Köster
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Mathias Dreger
- caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Volkhard Seitz
- Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
| |
Collapse
|
19
|
von Kleist L, Michaelis S, Bartho K, Graebner O, Schlief M, Dreger M, Schrey AK, Sefkow M, Kroll F, Koester H, Luo Y. Identification of Potential Off-target Toxicity Liabilities of Catechol-O-methyltransferase Inhibitors by Differential Competition Capture Compound Mass Spectrometry. J Med Chem 2016; 59:4664-75. [PMID: 27074629 DOI: 10.1021/acs.jmedchem.5b01970] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Structurally related inhibitors of a shared therapeutic target may differ regarding potential toxicity issues that are caused by different off-target bindings. We devised a differential competition capture compound mass spectrometry (dCCMS) strategy to effectively differentiate off-target profiles. Tolcapone and entacapone are potent inhibitors of catechol-O-methyl transferase (COMT) for the treatment of Parkinson's disease. Tolcapone is also known for its hepatotoxic side effects even though it is therapeutically more potent than entacapone. Here, we identified 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) as a possible toxicity-causing off-target of tolcapone, and this protein is not bound by the less toxic COMT inhibitor entacapone. Moreover, two novel compounds from a focused library synthesized in-house, N(2),N(2),N(3),N(3)-tetraethyl-6,7-dihydroxy-5-nitronaphthalene-2,3-dicarboxamide and 5-(3,4-dihydroxy-5-nitrobenzylidene)-3-ethylthiazolidine-2,4-dione, were utilized to gain insight into the structure-activity relationships in binding to COMT and the novel off-target HIBCH. These compounds, especially N(2),N(2),N(3),N(3)-tetraethyl-6,7-dihydroxy-5-nitronaphthalene-2,3-dicarboxamide, could serve as starting point for the development of improved and more specific COMT inhibitors.
Collapse
Affiliation(s)
- Lisa von Kleist
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Simon Michaelis
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Kathrin Bartho
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Olivia Graebner
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Marén Schlief
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Mathias Dreger
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Anna K Schrey
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Michael Sefkow
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Friedrich Kroll
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Hubert Koester
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| | - Yan Luo
- Caprotec Bioanalytics GmbH , Magnusstraße 11, 12489 Berlin, Germany
| |
Collapse
|
20
|
Abstract
S-Adenosyl-L-methionine (SAM) is a sulfonium molecule with a structural hybrid of methionine and adenosine. As the second largest cofactor in the human body, its major function is to serve as methyl donor for SAM-dependent methyltransferases (MTases). The resultant transmethylation of biomolecules constitutes a significant biochemical mechanism in epigenetic regulation, cellular signaling, and metabolite degradation. Recently, numerous SAM analogs have been developed as synthetic cofactors to transfer the activated groups on MTase substrates for downstream ligation and identification. Meanwhile, new compounds built upon or derived from the SAM scaffold have been designed and tested as selective inhibitors for important MTase targets. Here, we summarized the recent development and application of SAM analogs as chemical biology tools for MTases.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
21
|
Lennicke C, Rahn J, Heimer N, Lichtenfels R, Wessjohann LA, Seliger B. Redox proteomics: Methods for the identification and enrichment of redox-modified proteins and their applications. Proteomics 2015; 16:197-213. [PMID: 26508685 DOI: 10.1002/pmic.201500268] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/14/2015] [Accepted: 10/15/2015] [Indexed: 01/24/2023]
Abstract
PTMs are defined as covalent additions to functional groups of amino acid residues in proteins like phosphorylation, glycosylation, S-nitrosylation, acetylation, methylation, lipidation, SUMOylation as well as oxidation. Oxidation of proteins has been characterized as a double-edged sword. While oxidative modifications, in particular of cysteine residues, are widely involved in the regulation of cellular homeostasis, oxidative stress resulting in the oxidation of biomolecules along with the disruption of their biological functions can be associated with the development of diseases, such as cancer, diabetes, and neurodegenerative diseases, respectively. This is also the case for advanced glycation end products, which result from chemical reactions of keto compounds such as oxidized sugars with proteins. The role of oxidative modifications under physiological and pathophysiological conditions remains largely unknown. Recently, novel technologies have been established that allow the enrichment, identification, and characterization of specific oxidative PTMs (oxPTMs). This is essential to develop strategies to prevent and treat diseases that are associated with oxidative stress. Therefore this review will focus on (i) the methods and technologies, which are currently applied for the detection, identification, and quantification of oxPTMs including the design of high throughput approaches and (ii) the analyses of oxPTMs related to physiological and pathological conditions.
Collapse
Affiliation(s)
- Claudia Lennicke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Jette Rahn
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Nadine Heimer
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Rudolf Lichtenfels
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | | | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| |
Collapse
|
22
|
Mello AA, Leal MF, Rey JA, Pinto GR, Lamarão LM, Montenegro RC, Alves APNN, Assumpção PP, Borges BDN, Smith MC, Burbano RR. Deregulated Expression of SRC, LYN and CKB Kinases by DNA Methylation and Its Potential Role in Gastric Cancer Invasiveness and Metastasis. PLoS One 2015; 10:e0140492. [PMID: 26460485 PMCID: PMC4604160 DOI: 10.1371/journal.pone.0140492] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/25/2015] [Indexed: 12/29/2022] Open
Abstract
Kinases are downstream modulators and effectors of several cellular signaling cascades and play key roles in the development of neoplastic disease. In this study, we aimed to evaluate SRC, LYN and CKB protein and mRNA expression, as well as their promoter methylation, in gastric cancer. We found elevated expression of SRC and LYN kinase mRNA and protein but decreased levels of CKB kinase, alterations that may have a role in the invasiveness and metastasis of gastric tumors. Expression of the three studied kinases was also associated with MYC oncogene expression, a possible biomarker for gastric cancer. To understand the mechanisms that regulate the expression of these genes, we evaluated the DNA promoter methylation of the three kinases. We found that reduced SRC and LYN methylation and increased CKB methylation was associated with gastric cancer. The reduced SRC and LYN methylation was associated with increased levels of mRNA and protein expression, suggesting that DNA methylation is involved in regulating the expression of these kinases. Conversely, reduced CKB methylation was observed in samples with reduced mRNA and protein expression, suggesting CKB expression was found to be only partly regulated by DNA methylation. Additionally, we found that alterations in the DNA methylation pattern of the three studied kinases were also associated with the gastric cancer onset, advanced gastric cancer, deeper tumor invasion and the presence of metastasis. Therefore, SRC, LYN and CKB expression or DNA methylation could be useful markers for predicting tumor progression and targeting in anti-cancer strategies.
Collapse
Affiliation(s)
- Adriano Azevedo Mello
- Centro de Ciências Biológicas e da Saúde, Universidade Federal de Campina Grande, Campina Grande, PB, Brazil
| | - Mariana Ferreira Leal
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- * E-mail:
| | - Juan Antonio Rey
- Laboratorio de Oncogenética Molecular, Hospital Universitario La Paz, Madrid, Madrid, Spain
| | | | - Leticia Martins Lamarão
- Laboratório de Testes de Ácidos Nucleicos, Fundação Centro de Hemoterapia e Hematologia do Pará, Belém, PA, Brazil
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | | | | | - Paulo Pimentel Assumpção
- Núcleo de Pesquisa em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, PA, Brazil
| | - Barbara do Nascimento Borges
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Centro de Tecnologia Agropecuária, Instituto Socioambiental e dos Recursos Hídricos, Universidade Federal Rural da Amazônia, Belém, PA, Brazil
| | - Marília Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rommel Rodriguez Burbano
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Núcleo de Pesquisa em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, PA, Brazil
| |
Collapse
|
23
|
Bartoloni M, Jin X, Marcaida MJ, Banha J, Dibonaventura I, Bongoni S, Bartho K, Gräbner O, Sefkow M, Darbre T, Reymond JL. Bridged bicyclic peptides as potential drug scaffolds: synthesis, structure, protein binding and stability. Chem Sci 2015; 6:5473-5490. [PMID: 29861888 PMCID: PMC5949603 DOI: 10.1039/c5sc01699a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/12/2015] [Indexed: 12/28/2022] Open
Abstract
Double cyclization of short linear peptides obtained by solid phase peptide synthesis was used to prepare bridged bicyclic peptides (BBPs) corresponding to the topology of bridged bicyclic alkanes such as norbornane. Diastereomeric norbornapeptides were investigated by 1H-NMR, X-ray crystallography and CD spectroscopy and found to represent rigid globular scaffolds stabilized by intramolecular backbone hydrogen bonds with scaffold geometries determined by the chirality of amino acid residues and sharing structural features of β-turns and α-helices. Proteome profiling by capture compound mass spectrometry (CCMS) led to the discovery of the norbornapeptide 27c binding selectively to calmodulin as an example of a BBP protein binder. This and other BBPs showed high stability towards proteolytic degradation in serum.
Collapse
Affiliation(s)
- Marco Bartoloni
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Xian Jin
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Maria José Marcaida
- School of Life Sciences , Ecole Polytechnique de Lausanne , 1015 Lausanne , Switzerland
| | - João Banha
- caprotec bioanalytics GmbH , Berlin , Germany
| | - Ivan Dibonaventura
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Swathi Bongoni
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | | | | | | | - Tamis Darbre
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland .
| |
Collapse
|
24
|
Laventie BJ, Nesper J, Ahrné E, Glatter T, Schmidt A, Jenal U. Capture compound mass spectrometry--a powerful tool to identify novel c-di-GMP effector proteins. J Vis Exp 2015. [PMID: 25867682 DOI: 10.3791/51404] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Considerable progress has been made during the last decade towards the identification and characterization of enzymes involved in the synthesis (diguanylate cyclases) and degradation (phosphodiesterases) of the second messenger c-di-GMP. In contrast, little information is available regarding the molecular mechanisms and cellular components through which this signaling molecule regulates a diverse range of cellular processes. Most of the known effector proteins belong to the PilZ family or are degenerated diguanylate cyclases or phosphodiesterases that have given up on catalysis and have adopted effector function. Thus, to better define the cellular c-di-GMP network in a wide range of bacteria experimental methods are required to identify and validate novel effectors for which reliable in silico predictions fail. We have recently developed a novel Capture Compound Mass Spectrometry (CCMS) based technology as a powerful tool to biochemically identify and characterize c-di-GMP binding proteins. This technique has previously been reported to be applicable to a wide range of organisms(1). Here we give a detailed description of the protocol that we utilize to probe such signaling components. As an example, we use Pseudomonas aeruginosa, an opportunistic pathogen in which c-di-GMP plays a critical role in virulence and biofilm control. CCMS identified 74% (38/51) of the known or predicted components of the c-di-GMP network. This study explains the CCMS procedure in detail, and establishes it as a powerful and versatile tool to identify novel components involved in small molecule signaling.
Collapse
Affiliation(s)
| | - Jutta Nesper
- Focal Area Infection Biology, Biozentrum of the University of Basel
| | - Erik Ahrné
- Proteomics Core Facility, Biozentrum of the University of Basel
| | - Timo Glatter
- Proteomics Core Facility, Biozentrum of the University of Basel
| | | | - Urs Jenal
- Focal Area Infection Biology, Biozentrum of the University of Basel;
| |
Collapse
|
25
|
Liu S, Cheng C, Gong H, Wang L. Programmable Mg2+-dependent DNAzyme switch by the catalytic hairpin DNA assembly for dual-signal amplification toward homogeneous analysis of protein and DNA. Chem Commun (Camb) 2015; 51:7364-7. [DOI: 10.1039/c5cc01649e] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The catalytic hairpin DNA assembly-programmed Mg2+-dependent DNAzyme switch was proposed for dual-signal amplified detection of protein and DNA.
Collapse
Affiliation(s)
- Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Chuanbin Cheng
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Hongwei Gong
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| |
Collapse
|
26
|
Addy PS, Bhattacharya A, Mandal SM, Basak A. Label-assisted laser desorption/ionization mass spectrometry (LA-LDI-MS): an emerging technique for rapid detection of ubiquitous cis-1,2-diol functionality. RSC Adv 2014. [DOI: 10.1039/c4ra07499h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
27
|
Brown LJ, Baranowski M, Wang Y, Schrey AK, Lenz T, Taverna SD, Cole PA, Sefkow M. Using S-adenosyl-L-homocysteine capture compounds to characterize S-adenosyl-L-methionine and S-adenosyl-L-homocysteine binding proteins. Anal Biochem 2014; 467:14-21. [PMID: 25172130 DOI: 10.1016/j.ab.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 08/12/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022]
Abstract
S-Adenosyl-l-methionine (SAM) is recognized as an important cofactor in a variety of biochemical reactions. As more proteins and pathways that require SAM are discovered, it is important to establish a method to quickly identify and characterize SAM binding proteins. The affinity of S-adenosyl-l-homocysteine (SAH) for SAM binding proteins was used to design two SAH-derived capture compounds (CCs). We demonstrate interactions of the proteins COMT and SAHH with SAH-CC with biotin used in conjunction with streptavidin-horseradish peroxidase. After demonstrating SAH-dependent photo-crosslinking of the CC to these proteins, we used a CC labeled with a fluorescein tag to measure binding affinity via fluorescence anisotropy. We then used this approach to show and characterize binding of SAM to the PR domain of PRDM2, a lysine methyltransferase with putative tumor suppressor activity. We calculated the Kd values for COMT, SAHH, and PRDM2 (24.1 ± 2.2 μM, 6.0 ± 2.9 μM, and 10.06 ± 2.87 μM, respectively) and found them to be close to previously established Kd values of other SAM binding proteins. Here, we present new methods to discover and characterize SAM and SAH binding proteins using fluorescent CCs.
Collapse
Affiliation(s)
- Lindsey J Brown
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Yun Wang
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Thomas Lenz
- Caprotec Bioanalytics, 12489 Berlin, Germany
| | - Sean D Taverna
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Philip A Cole
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | | |
Collapse
|
28
|
Carrié H, Tran DT, Rousseau S, Chaignepain S, Schmitter JM, Deffieux D, Quideau S. New affinity-based probes for capturing flavonoid-binding proteins. Chem Commun (Camb) 2014; 50:9387-9. [DOI: 10.1039/c4cc04557b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
29
|
A non-canonical function of eukaryotic elongation factor 1A1: Regulation of interleukin-6 expression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:965-75. [DOI: 10.1016/j.bbamcr.2014.01.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/20/2014] [Accepted: 01/23/2014] [Indexed: 11/22/2022]
|
30
|
Addy PS, Saha B, Panja A, Das AK, Basak A. Design and synthesis of azobenzene template based sulfonamide for capture of HCAII: dependence of efficiency on E–Z geometry. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.02.124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
31
|
Blanco-Colio LM, López JA, Martínez-Pinna Albar R, Egido J, Martín-Ventura JL. Vascular proteomics, a translational approach: from traditional to novel proteomic techniques. Expert Rev Proteomics 2014; 6:461-4. [DOI: 10.1586/epr.09.66] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
32
|
Dejonghe W, Russinova E. Target identification strategies in plant chemical biology. FRONTIERS IN PLANT SCIENCE 2014; 5:352. [PMID: 25104953 PMCID: PMC4109434 DOI: 10.3389/fpls.2014.00352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/30/2014] [Indexed: 05/03/2023]
Abstract
The current needs to understand gene function in plant biology increasingly require more dynamic and conditional approaches opposed to classic genetic strategies. Gene redundancy and lethality can substantially complicate research, which might be solved by applying a chemical genetics approach. Now understood as the study of small molecules and their effect on biological systems with subsequent target identification, chemical genetics is a fast developing field with a strong history in pharmaceutical research and drug discovery. In plant biology however, chemical genetics is still largely in the starting blocks, with most studies relying on forward genetics and phenotypic analysis for target identification, whereas studies including direct target identification are limited. Here, we provide an overview of recent advances in chemical genetics in plant biology with a focus on target identification. Furthermore, we discuss different strategies for direct target identification and the possibilities and challenges for plant biology.
Collapse
Affiliation(s)
- Wim Dejonghe
- Department of Plant Systems Biology, VIBGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
| | - Eugenia Russinova
- Department of Plant Systems Biology, VIBGhent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- *Correspondence: Eugenia Russinova, Department of Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, VIB-Ghent University, Technologiepark 927, 9052 Ghent, Belgium e-mail:
| |
Collapse
|
33
|
Brunner R, Ng CL, Aissaoui H, Akabas MH, Boss C, Brun R, Callaghan PS, Corminboeuf O, Fidock DA, Frame IJ, Heidmann B, Le Bihan A, Jenö P, Mattheis C, Moes S, Müller IB, Paguio M, Roepe PD, Siegrist R, Voss T, Welford RWD, Wittlin S, Binkert C. UV-triggered affinity capture identifies interactions between the Plasmodium falciparum multidrug resistance protein 1 (PfMDR1) and antimalarial agents in live parasitized cells. J Biol Chem 2013; 288:22576-83. [PMID: 23754276 DOI: 10.1074/jbc.m113.453159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
A representative of a new class of potent antimalarials with an unknown mode of action was recently described. To identify the molecular target of this class of antimalarials, we employed a photo-reactive affinity capture method to find parasite proteins specifically interacting with the capture compound in living parasitized cells. The capture reagent retained the antimalarial properties of the parent molecule (ACT-213615) and accumulated within parasites. We identified several proteins interacting with the capture compound and established a functional interaction between ACT-213615 and PfMDR1. We surmise that PfMDR1 may play a role in the antimalarial activity of the piperazine-containing compound ACT-213615.
Collapse
Affiliation(s)
- Ralf Brunner
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF. Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound. J Proteomics 2013; 86:97-104. [PMID: 23684787 DOI: 10.1016/j.jprot.2013.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/30/2013] [Accepted: 05/01/2013] [Indexed: 11/17/2022]
Abstract
UNLABELLED Trypanosomatid parasites of the genus Leishmania cause severe human diseases collectively termed leishmaniasis. Parasite ATP-binding proteins have emerged as potent targets for chemotherapeutic intervention. However, many parasite-specific ATP-binding proteins may escape current efforts in drug target identification, validation and deconvolution due to the lack of sequence conservation and functional annotation of these proteins in early branching eukaryotic trypanosomatids. Here, we selectively enriched for ATP-binding proteins from Leishmania donovani axenic promastigote and amastigote total protein extracts utilizing a Capture Compound™ (CC) linked to the ATP-competitive inhibitor staurosporine. As judged by in-gel kinase activity assay and competitive inhibition with free staurosporine, the CC specifically enriched for parasite phosphotransferases. Comparative nanoLC-MS(n) analysis identified 70 captured proteins, including 24 conserved protein kinases, and 32 hypothetical proteins with potential ATP-binding function. We identified conserved signature sequence motifs characteristic for staurosporine-binding protein kinases, and identified the hypothetical proteins LinJ.20.0280 and LinJ.09.1630 as novel ATP-binding proteins. Thus, functional enrichment procedures such as described here, combined with bio-informatics analyses and activity assays, provide powerful tools for the discovery of parasite-specific ATP-binding proteins that escape homology-based identification, which can be subsequently targeted for pharmacological intervention. BIOLOGICAL SIGNIFICANCE Functional enrichment using a Capture Compound™ linked to the ATP-competitive inhibitor staurosporine provides a powerful new tool for the discovery of parasite-specific ATP-binding proteins that escape homology-based identification, which can be subsequently targeted for pharmacological intervention.
Collapse
Affiliation(s)
- Olivier Leclercq
- Institut Pasteur, and CNRS URA2581, Department of Parasitology and Mycology, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
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]
|
36
|
Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
Collapse
Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | | | | | | |
Collapse
|
37
|
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.
Collapse
Affiliation(s)
- Partha Sarathi Addy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Trippier PC. Synthetic strategies for the biotinylation of bioactive small molecules. ChemMedChem 2013; 8:190-203. [PMID: 23303486 DOI: 10.1002/cmdc.201200498] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/07/2012] [Indexed: 01/19/2023]
Abstract
Biotinylation, the functional appendage of a biotin moiety to a bioactive compound (including small molecules and biological macromolecules), represents a common technique for identification of the intracellular binding partners that underlie the foundation of observed biological activity. Introduction of an attachment tether to the framework of a compound of interest must be planned at an early stage of development, and many considerations apply: 1) region of attachment, so as not to impede the pharmacophore; 2) stability of the parent molecular architecture to biotinylation conditions; 3) regioselectivity for the chosen tethering location over other reactive functionalities; 4) toxicity of reagents if biotinylation is to be performed in vitro; and 5) overall ease of synthesis. This review is intended to serve as a guide for the selection of appropriate tethering modalities. Examples of the common techniques used to affix biotin, including amide bond formation, [3+2] cycloadditions through "click" chemistry, Staudinger ligation, and thioether formation will be discussed, along with analysis of the wider applications of synthetic methodology that have been applied toward the biotinylation of small molecules.
Collapse
Affiliation(s)
- Paul C Trippier
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA.
| |
Collapse
|
39
|
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
|
40
|
Maurer A, Zeyher C, Amin B, Kalbacher H. A Periodate-Cleavable Linker for Functional Proteomics under Slightly Acidic Conditions: Application for the Analysis of Intracellular Aspartic Proteases. J Proteome Res 2012; 12:199-207. [DOI: 10.1021/pr300758c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Andreas Maurer
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Claus Zeyher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Bushra Amin
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| |
Collapse
|
41
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Ellen A. Panisko
- the Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, Washington 99352
| | | | | |
Collapse
|
42
|
Sikkema AH, den Dunnen WFA, Diks SH, Peppelenbosch MP, de Bont ESJM. Optimizing targeted cancer therapy: towards clinical application of systems biology approaches. Crit Rev Oncol Hematol 2012; 82:171-86. [PMID: 21641230 DOI: 10.1016/j.critrevonc.2011.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 04/28/2011] [Accepted: 05/04/2011] [Indexed: 12/13/2022] Open
Abstract
In cancer, genetic and epigenetic alterations ultimately culminate in discordant activation of signal transduction pathways driving the malignant process. Pharmacological or biological inhibition of such pathways holds significant promise with respect to devising rational therapy for cancer. Thus, technical concepts pursuing robust characterization of kinase activity in tissue samples from cancer patients have been subject of investigation. In the present review we provide a comprehensive overview of these techniques and discuss their advantages and disadvantages for systems biology approaches to identify kinase targets in oncological disease. Recent advances in the development and application of array-based peptide-substrate kinase activity screens show great promise in overcoming the discrepancy between the evaluation of aberrant cell signaling in specific malignancies or even individual patients and the currently available ensemble of highly specific targeted treatment strategies. These developments have the potential to result in a more effective selection of kinase inhibitors and thus optimize mechanism-based patient-specific therapeutic strategies. Given the results from current research on the tumor kinome, generating network views on aberrant tumor cell signaling is critical to meet this challenge.
Collapse
Affiliation(s)
- Arend H Sikkema
- Beatrix Children's Hospital, Department of Pediatric Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | | | | | | | | |
Collapse
|
43
|
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.
Collapse
Affiliation(s)
- Nico Zinn
- Cellzome AG, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | | | | | | |
Collapse
|
44
|
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.
Collapse
Affiliation(s)
- Jutta Nesper
- Biozentrum of the University of Basel, Klingelbergstrasse 50, CH-4054 Basel, Switzerland
| | | | | | | | | |
Collapse
|
45
|
Abstract
The term "chemical proteomics" refers to a research area at the interface of chemistry, biochemistry, and cell biology that focuses on studying the mechanism of action of bioactive small molecule compounds, which comprises the mapping of their target proteins and their impact on protein expression and posttranslational modifications in target cells or tissues of interest on a proteome-wide level. For this purpose, a large arsenal of approaches has emerged in recent years, many of which employing quantitative mass spectrometry. This review briefly summarizes major experiment types employed in current chemical proteomics research.
Collapse
|
46
|
Bantscheff M, Drewes G. Chemoproteomic approaches to drug target identification and drug profiling. Bioorg Med Chem 2012; 20:1973-8. [DOI: 10.1016/j.bmc.2011.11.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/21/2011] [Accepted: 11/02/2011] [Indexed: 12/21/2022]
|
47
|
Schirle M, Bantscheff M, Kuster B. Mass Spectrometry-Based Proteomics in Preclinical Drug Discovery. ACTA ACUST UNITED AC 2012; 19:72-84. [DOI: 10.1016/j.chembiol.2012.01.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Revised: 01/03/2012] [Accepted: 01/05/2012] [Indexed: 01/14/2023]
|
48
|
Lenz T, Poot P, Weinhold E, Dreger M. Profiling of methyltransferases and other S-Adenosyl-L-homocysteine-binding proteins by Capture Compound mass spectrometry. Methods Mol Biol 2012; 803:97-125. [PMID: 22065221 DOI: 10.1007/978-1-61779-364-6_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
There is a variety of approaches to reduce the complexity of the proteome on the basis of functional small molecule-protein interactions. We describe a generic approach based on trifunctional Capture Compounds, in which the initial equilibrium-driven interaction between a small molecule probe and target proteins is irreversibly fixed upon photo-crosslinking between an independent photo-activable reactivity function of the Capture Compound and the surface of the target protein(s). Subsequently, Capture Compound - protein conjugates are isolated from complex biological mixtures via the sorting function of the Capture Compound. Here, we describe the application of a trifunctional Capture Compound that carries the methyltransferase product inhibitor S-Adenosyl-L -homocysteine as the selectivity function for the isolation of methyltransferases from a complex lysate of Escherichia coli DH5α cells. Photo-activated crosslinking enhances yield and sensitivity of the experiment, and the specificity can be readily tested for in competition experiments using an excess of free S-Adenosyl-L -homocysteine.
Collapse
|
49
|
Lenger J, Kaschani F, Lenz T, Dalhoff C, Villamor JG, Köster H, Sewald N, van der Hoorn RA. Labeling and enrichment of Arabidopsis thaliana matrix metalloproteases using an active-site directed, marimastat-based photoreactive probe. Bioorg Med Chem 2012; 20:592-6. [DOI: 10.1016/j.bmc.2011.06.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/16/2011] [Accepted: 06/24/2011] [Indexed: 01/12/2023]
|
50
|
Probing small molecule–protein interactions: A new perspective for functional proteomics. J Proteomics 2011; 75:100-15. [DOI: 10.1016/j.jprot.2011.07.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 07/01/2011] [Accepted: 07/13/2011] [Indexed: 11/22/2022]
|