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Micheletti G, Boga C, Drius G, Bordoni S, Calonghi N. Suberoylanilide Hydroxamic Acid Analogs with Heteroaryl Amide Group and Different Chain Length: Synthesis and Effect on Histone Deacetylase. Molecules 2024; 29:238. [PMID: 38202821 PMCID: PMC10781187 DOI: 10.3390/molecules29010238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
This review covers the last 25 years of the literature on analogs of suberoylanilide hydroxamic acid (SAHA, known also as vorinostat) acting as an HDAC inhibitor. In particular, the topic has been focused on the synthesis and biological activity of compounds where the phenyl group (the surface recognition moiety, CAP) of SAHA has been replaced by an azaheterocycle through a direct bond with amide nitrogen atom, and the methylene chain in the linker region is of variable length. Most of the compounds displayed good to excellent inhibitory activity against HDACs and in many cases showed antiproliferative activity against human cancer cell lines.
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Affiliation(s)
- Gabriele Micheletti
- Department of Industrial Chemistry ‘Toso Montanari’, Alma Mater Studiorum, Università di Bologna, Viale Del Risorgimento 4, 40136 Bologna, Italy; (G.D.); (S.B.)
| | - Carla Boga
- Department of Industrial Chemistry ‘Toso Montanari’, Alma Mater Studiorum, Università di Bologna, Viale Del Risorgimento 4, 40136 Bologna, Italy; (G.D.); (S.B.)
| | - Giacomo Drius
- Department of Industrial Chemistry ‘Toso Montanari’, Alma Mater Studiorum, Università di Bologna, Viale Del Risorgimento 4, 40136 Bologna, Italy; (G.D.); (S.B.)
| | - Silvia Bordoni
- Department of Industrial Chemistry ‘Toso Montanari’, Alma Mater Studiorum, Università di Bologna, Viale Del Risorgimento 4, 40136 Bologna, Italy; (G.D.); (S.B.)
| | - Natalia Calonghi
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
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2
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Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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3
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Zhang J, Peng J, Huang Y, Meng L, Li Q, Xiong F, Li X. Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling. Angew Chem Int Ed Engl 2020; 59:17525-17532. [DOI: 10.1002/anie.202001205] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/14/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Qingrong Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
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4
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Zhang J, Peng J, Huang Y, Meng L, Li Q, Xiong F, Li X. Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Qingrong Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
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5
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Howard RT, Hemsley P, Petteruti P, Saunders CN, Molina Bermejo JA, Scott JS, Johannes JW, Tate EW. Structure-Guided Design and In-Cell Target Profiling of a Cell-Active Target Engagement Probe for PARP Inhibitors. ACS Chem Biol 2020; 15:325-333. [PMID: 32017532 PMCID: PMC7146755 DOI: 10.1021/acschembio.9b00963] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Inhibition of the
poly(ADP-ribose) polymerase (PARP) family of
enzymes has become an attractive therapeutic strategy in oncology
and beyond; however, chemical tools to profile PARP engagement in
live cells are lacking. Herein, we report the design and application
of PARPYnD, the first photoaffinity probe (AfBP) for
PARP enzymes based on triple PARP1/2/6 inhibitor AZ9482, which induces multipolar spindle (MPS) formation in breast cancer
cells. PARPYnD is a robust tool for profiling PARP1/2
and is used to profile clinical PARP inhibitor olaparib, identifying
several novel off-target proteins. Surprisingly, while PARPYnD can enrich recombinant PARP6 spiked into cellular lysates and inhibits
PARP6 in cell-free assays, it does not label PARP6 in intact cells.
These data highlight an intriguing biomolecular disparity between
recombinant and endogenous PARP6. PARPYnD provides a
new approach to expand our knowledge of the targets of this class
of compounds and the mechanisms of action of PARP inhibitors in cancer.
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Affiliation(s)
- Ryan T. Howard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Paul Hemsley
- Oncology, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Philip Petteruti
- Oncology, R&D, AstraZeneca, Boston, Waltham, Massachusetts 02451, United States
| | - Charlie N. Saunders
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Javier A. Molina Bermejo
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - James S. Scott
- Oncology, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Jeffrey W. Johannes
- Oncology, R&D, AstraZeneca, Boston, Waltham, Massachusetts 02451, United States
| | - Edward W. Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
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Aboukhatwa SM, Hanigan TW, Taha TY, Neerasa J, Ranjan R, El-Bastawissy EE, Elkersh MA, El-Moselhy TF, Frasor J, Mahmud N, McLachlan A, Petukhov PA. Structurally Diverse Histone Deacetylase Photoreactive Probes: Design, Synthesis, and Photolabeling Studies in Live Cells and Tissue. ChemMedChem 2019; 14:1096-1107. [PMID: 30921497 DOI: 10.1002/cmdc.201900114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/28/2019] [Indexed: 01/27/2023]
Abstract
Histone deacetylase (HDAC) activity is modulated in vivo by post-translational modifications and formation of multiprotein complexes. Novel chemical tools to study how these factors affect engagement of HDAC isoforms by HDAC inhibitors (HDACi) in cells and tissues are needed. In this study, a synthetic strategy to access chemically diverse photoreactive probes (PRPs) was developed and used to prepare seven novel HDAC PRPs 9-15. The class I HDAC isoform engagement by PRPs was determined in biochemical assays and photolabeling experiments in live SET-2, HepG2, HuH7, and HEK293T cell lines and in mouse liver tissue. Unlike the HDAC protein abundance and biochemical activity against recombinant HDACs, the chemotype of the PRPs and the type of cells were key in defining the engagement of HDAC isoforms in live cells. Our findings suggest that engagement of HDAC isoforms by HDACi in vivo may be substantially modulated in a cell- and tissue-type-dependent manner.
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Affiliation(s)
- Shaimaa M Aboukhatwa
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt
| | - Thomas W Hanigan
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
| | - Taha Y Taha
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
| | - Jayaprakash Neerasa
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
| | - Rajeev Ranjan
- Section of Hematology/Oncology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Eman E El-Bastawissy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt
| | - Mohamed A Elkersh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University, Alexandria, 21311, Egypt
| | - Tarek F El-Moselhy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt
| | - Jonna Frasor
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Nadim Mahmud
- Section of Hematology/Oncology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Alan McLachlan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Pavel A Petukhov
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
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7
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Xu H, Roberts LR, Chou S, Pierce B, Narayanan A, Jones LH. Quantitative measurement of intracellular HDAC1/2 drug occupancy using a trans-cyclooctene largazole thiol probe. MEDCHEMCOMM 2017; 8:767-770. [PMID: 30108795 DOI: 10.1039/c6md00633g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 12/23/2016] [Indexed: 11/21/2022]
Abstract
Histone deacetylases (HDACs) regulate diverse cellular processes, and are promising targets for a number of diseases. Here we describe the design and utilization of a largazole-based chemical probe to quantitatively measure the intracellular occupancy of HDAC1 and HDAC2 by dacinostat. Surprisingly, the probe was unable to enrich HDAC3 despite its nanomolar potency in a biochemical assay, further proving the necessity of cell-based target occupancy assays to understand compound potency in physiologically-relevant settings. This occupancy assay has the potential to aid the development of novel HDAC1/2 inhibitors in drug discovery.
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Affiliation(s)
- Hua Xu
- Pfizer Inc. Medicine Design , 610 Main Street , Cambridge , MA 02135 , USA .
| | - Lee R Roberts
- Pfizer Inc. Medicine Design , 610 Main Street , Cambridge , MA 02135 , USA .
| | - Song Chou
- Pfizer Inc. Rare Diseases Research Unit , 610 Main Street , Cambridge , MA 02135 , USA
| | - Betsy Pierce
- Pfizer Inc. Medicine Design , Eastern Point Road , Groton , CT 06340 , USA
| | - Arjun Narayanan
- Pfizer Inc. Medicine Design , 610 Main Street , Cambridge , MA 02135 , USA .
| | - Lyn H Jones
- Pfizer Inc. Medicine Design , 610 Main Street , Cambridge , MA 02135 , USA .
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8
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Strmiskova M, Desrochers GF, Shaw TA, Powdrill MH, Lafreniere MA, Pezacki JP. Chemical Methods for Probing Virus-Host Proteomic Interactions. ACS Infect Dis 2016; 2:773-786. [PMID: 27933785 DOI: 10.1021/acsinfecdis.6b00084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interactions between host and pathogen proteins constitute an important aspect of both infectivity and the host immune response. Different viruses have evolved complex mechanisms to hijack host-cell machinery and metabolic pathways to redirect resources and energy flow toward viral propagation. These interactions are often critical to the virus, and thus understanding these interactions at a molecular level gives rise to opportunities to develop novel antiviral strategies for therapeutic intervention. This review summarizes current advances in chemoproteomic methods for studying these molecular altercations between different viruses and their hosts.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew A. Lafreniere
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
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9
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Weigt D, Hopf C, Médard G. Studying epigenetic complexes and their inhibitors with the proteomics toolbox. Clin Epigenetics 2016; 8:76. [PMID: 27437033 PMCID: PMC4950666 DOI: 10.1186/s13148-016-0244-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/05/2016] [Indexed: 12/27/2022] Open
Abstract
Some epigenetic modifier proteins have become validated clinical targets. With a few small molecule inhibitors already approved by national health administrations and many more in the pharmaceutical industry pipelines, there is a need for technologies that can promote full comprehension of the molecular action of these drugs. Proteomics, with its relatively unbiased nature, can contribute to a thorough understanding of the complexity of the megadalton complexes, which write, read and erase the histone code, and it can help study the on-target and off-target effect of the drugs designed to modulate their action. This review on the one hand gathers the published affinity probes able to decipher small molecule targets and off-targets in a close-to-native environment. These are small molecule analogues of epigenetic drugs conceived as protein target enrichment tools after they have engaged them in cells or lysates. Such probes, which have been designed for deacetylases, bromodomains, demethylases, and methyltransferases not only enrich their direct protein targets but also their stable interactors, which can be identified by mass spectrometry. Hence, they constitute a tool to study the epigenetic complexes together with other techniques also reviewed here: immunoaffinity purification with antibodies against native protein complex constituents or epitope tags, affinity matrices designed to bind recombinantly tagged protein, and enrichment of the complexes using histone tail peptides as baits. We expect that this toolbox will be adopted by more and more researchers willing to harness the spectacular advances in mass spectrometry to the epigenetic field.
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Affiliation(s)
- David Weigt
- />Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- />HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Carsten Hopf
- />Center for Applied Research in Biomedical Mass Spectrometry (ABIMAS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- />HBIGS International Graduate School of Molecular and Cellular Biology, Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Guillaume Médard
- />Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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