1
|
Schneider C, Hilbert J, Genevaux F, Höfer S, Krauß L, Schicktanz F, Contreras CT, Jansari S, Papargyriou A, Richter T, Alfayomy AM, Falcomatà C, Schneeweis C, Orben F, Öllinger R, Wegwitz F, Boshnakovska A, Rehling P, Müller D, Ströbel P, Ellenrieder V, Conradi L, Hessmann E, Ghadimi M, Grade M, Wirth M, Steiger K, Rad R, Kuster B, Sippl W, Reichert M, Saur D, Schneider G. A Novel AMPK Inhibitor Sensitizes Pancreatic Cancer Cells to Ferroptosis Induction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2307695. [PMID: 38885414 DOI: 10.1002/advs.202307695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/12/2024] [Indexed: 06/20/2024]
Abstract
Cancer cells must develop strategies to adapt to the dynamically changing stresses caused by intrinsic or extrinsic processes, or therapeutic agents. Metabolic adaptability is crucial to mitigate such challenges. Considering metabolism as a central node of adaptability, it is focused on an energy sensor, the AMP-activated protein kinase (AMPK). In a subtype of pancreatic ductal adenocarcinoma (PDAC) elevated AMPK expression and phosphorylation is identified. Using drug repurposing that combined screening experiments and chemoproteomic affinity profiling, it is identified and characterized PF-3758309, initially developed as an inhibitor of PAK4, as an AMPK inhibitor. PF-3758309 shows activity in pre-clinical PDAC models, including primary patient-derived organoids. Genetic loss-of-function experiments showed that AMPK limits the induction of ferroptosis, and consequently, PF-3758309 treatment restores the sensitivity toward ferroptosis inducers. The work established a chemical scaffold for the development of specific AMPK-targeting compounds and deciphered the framework for the development of AMPK inhibitor-based combination therapies tailored for PDAC.
Collapse
Affiliation(s)
- Carolin Schneider
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Jorina Hilbert
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Franziska Genevaux
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
| | - Stefanie Höfer
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Lukas Krauß
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Felix Schicktanz
- Institute of Pathology, Technical University of Munich, 81675, Munich, Germany
| | - Constanza Tapia Contreras
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Shaishavi Jansari
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Aristeidis Papargyriou
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum Muenchen, D-85764, Neuherberg, Germany
- Translational Pancreatic Research Cancer Center, Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
- Center for Organoid Systems (COS), Technical University of Munich, 85747, Garching, Germany
| | - Thorsten Richter
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Abdallah M Alfayomy
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
- Department of Pharmaceutical Chemistry, Al-Azhar University, Assiut, 71524, Egypt
| | - Chiara Falcomatà
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, 81675, Munich, Germany
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian Schneeweis
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, 81675, Munich, Germany
| | - Felix Orben
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
| | - Ruppert Öllinger
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675, Munich, Germany
| | - Florian Wegwitz
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Angela Boshnakovska
- Department of Cellular Biochemistry, University Medical Center, 37073, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center, 37073, Göttingen, Germany
- Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Denise Müller
- Institute of Pathology, University Medical Center, 37075, Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center, 37075, Göttingen, Germany
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075, Göttingen, Germany
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany
| | - Volker Ellenrieder
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075, Göttingen, Germany
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Lena Conradi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075, Göttingen, Germany
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany
| | - Elisabeth Hessmann
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075, Göttingen, Germany
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Michael Ghadimi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany
| | - Matthias Wirth
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203, Berlin, Germany
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, 81675, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and University Hospital Klinikum rechts der Isar, 81675, München, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and University Hospital Klinikum rechts der Isar, 81675, München, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and University Hospital Klinikum rechts der Isar, 81675, München, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Maximilian Reichert
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
- Translational Pancreatic Research Cancer Center, Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
- Center for Organoid Systems (COS), Technical University of Munich, 85747, Garching, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and University Hospital Klinikum rechts der Isar, 81675, München, Germany
- Center for Protein Assemblies (CPA), Technical University of Munich, 85747, Garching, Germany
| | - Dieter Saur
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, 81675, Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich, a partnership between DKFZ and University Hospital Klinikum rechts der Isar, 81675, München, Germany
| | - Günter Schneider
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, 81675, Munich, Germany
- Clinical Research Unit 5002, KFO5002, University Medical Center Göttingen, 37075, Göttingen, Germany
- CCC-N (Comprehensive Cancer Center Lower Saxony), 37075, Göttingen, Germany
| |
Collapse
|
2
|
Reinecke M, Brear P, Vornholz L, Berger BT, Seefried F, Wilhelm S, Samaras P, Gyenis L, Litchfield DW, Médard G, Müller S, Ruland J, Hyvönen M, Wilhelm M, Kuster B. Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Nat Chem Biol 2024; 20:577-585. [PMID: 37904048 PMCID: PMC11062922 DOI: 10.1038/s41589-023-01459-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/22/2023] [Indexed: 11/01/2023]
Abstract
Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Compounds targeting PKN3 were discovered and phosphoproteomics identified substrates that indicate target engagement in cells. We anticipate that this molecular resource will aid research in drug discovery and chemical biology.
Collapse
Affiliation(s)
- Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Larsen Vornholz
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Benedict-Tilmann Berger
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Florian Seefried
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David William Litchfield
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Jürgen Ruland
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
| |
Collapse
|
3
|
Saltzman AB, Chan DW, Holt MV, Wang J, Jaehnig EJ, Anurag M, Singh P, Malovannaya A, Kim BJ, Ellis MJ. Kinase inhibitor pulldown assay (KiP) for clinical proteomics. Clin Proteomics 2024; 21:3. [PMID: 38225548 PMCID: PMC10790396 DOI: 10.1186/s12014-023-09448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/07/2023] [Indexed: 01/17/2024] Open
Abstract
Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential. For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method. Data are available via ProteomeXchange with identifiers PXD044655 and PXD046169.
Collapse
Affiliation(s)
- Alexander B Saltzman
- Mass Spectrometry Proteomics Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX, USA
| | - Doug W Chan
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Matthew V Holt
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Junkai Wang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Purba Singh
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Johnson & Johnson, Springhouse, PA, USA
| | - Anna Malovannaya
- Mass Spectrometry Proteomics Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- AstraZeneca, Gaithersburg, MD, 20878, USA.
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
4
|
Lechner S, Steimbach RR, Wang L, Deline ML, Chang YC, Fromme T, Klingenspor M, Matthias P, Miller AK, Médard G, Kuster B. Chemoproteomic target deconvolution reveals Histone Deacetylases as targets of (R)-lipoic acid. Nat Commun 2023; 14:3548. [PMID: 37322067 PMCID: PMC10272112 DOI: 10.1038/s41467-023-39151-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
Lipoic acid is an essential enzyme cofactor in central metabolic pathways. Due to its claimed antioxidant properties, racemic (R/S)-lipoic acid is used as a food supplement but is also investigated as a pharmaceutical in over 180 clinical trials covering a broad range of diseases. Moreover, (R/S)-lipoic acid is an approved drug for the treatment of diabetic neuropathy. However, its mechanism of action remains elusive. Here, we performed chemoproteomics-aided target deconvolution of lipoic acid and its active close analog lipoamide. We find that histone deacetylases HDAC1, HDAC2, HDAC3, HDAC6, HDAC8, and HDAC10 are molecular targets of the reduced form of lipoic acid and lipoamide. Importantly, only the naturally occurring (R)-enantiomer inhibits HDACs at physiologically relevant concentrations and leads to hyperacetylation of HDAC substrates. The inhibition of HDACs by (R)-lipoic acid and lipoamide explain why both compounds prevent stress granule formation in cells and may also provide a molecular rationale for many other phenotypic effects elicited by lipoic acid.
Collapse
Affiliation(s)
- Severin Lechner
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Raphael R Steimbach
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biosciences Faculty, Heidelberg University, Heidelberg, Germany
| | - Longlong Wang
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
- Faculty of Sciences, University of Basel, 4031, Basel, Switzerland
| | - Marshall L Deline
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Tobias Fromme
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- EKFZ - Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
- Faculty of Sciences, University of Basel, 4031, Basel, Switzerland
| | - Aubry K Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.
| |
Collapse
|
5
|
Tröster A, DiPrima M, Jores N, Kudlinzki D, Sreeramulu S, Gande SL, Linhard V, Ludig D, Schug A, Saxena K, Reinecke M, Heinzlmeir S, Leisegang MS, Wollenhaupt J, Lennartz F, Weiss MS, Kuster B, Tosato G, Schwalbe H. Optimization of the Lead Compound NVP-BHG712 as a Colorectal Cancer Inhibitor. Chemistry 2023; 29:e202203967. [PMID: 36799129 PMCID: PMC10133194 DOI: 10.1002/chem.202203967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
The ephrin type-A receptor 2 (EPHA2) kinase belongs to the largest family of receptor tyrosine kinases. There are several indications of an involvement of EPHA2 in the development of infectious diseases and cancer. Despite pharmacological potential, EPHA2 is an under-examined target protein. In this study, we synthesized a series of derivatives of the inhibitor NVP-BHG712 and triazine-based compounds. These compounds were evaluated to determine their potential as kinase inhibitors of EPHA2, including elucidation of their binding mode (X-ray crystallography), affinity (microscale thermophoresis), and selectivity (Kinobeads assay). Eight inhibitors showed affinities in the low-nanomolar regime (KD <10 nM). Testing in up to seven colon cancer cell lines that express EPHA2 reveals that several derivatives feature promising effects for the control of human colon carcinoma. Thus, we have developed a set of powerful tool compounds for fundamental new research on the interplay of EPH receptors in a cellular context.
Collapse
Affiliation(s)
- Alix Tröster
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Michael DiPrima
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), 37 Convent Drive, NIH Bethesda Campus, Building 37, Room 4124, Bethesda, MD 20892, USA
| | - Nathalie Jores
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Santosh L. Gande
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Verena Linhard
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Damian Ludig
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Alexander Schug
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
| | - Matthias S. Leisegang
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main (Germany)
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Frank Lennartz
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
| | - Giovanna Tosato
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), 37 Convent Drive, NIH Bethesda Campus, Building 37, Room 4124, Bethesda, MD 20892, USA
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| |
Collapse
|
6
|
Zecha J, Bayer FP, Wiechmann S, Woortman J, Berner N, Müller J, Schneider A, Kramer K, Abril-Gil M, Hopf T, Reichart L, Chen L, Hansen FM, Lechner S, Samaras P, Eckert S, Lautenbacher L, Reinecke M, Hamood F, Prokofeva P, Vornholz L, Falcomatà C, Dorsch M, Schröder A, Venhuizen A, Wilhelm S, Médard G, Stoehr G, Ruland J, Grüner BM, Saur D, Buchner M, Ruprecht B, Hahne H, The M, Wilhelm M, Kuster B. Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science 2023; 380:93-101. [PMID: 36926954 PMCID: PMC7615311 DOI: 10.1126/science.ade3925] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 02/21/2023] [Indexed: 03/18/2023]
Abstract
Although most cancer drugs modulate the activities of cellular pathways by changing posttranslational modifications (PTMs), little is known regarding the extent and the time- and dose-response characteristics of drug-regulated PTMs. In this work, we introduce a proteomic assay called decryptM that quantifies drug-PTM modulation for thousands of PTMs in cells to shed light on target engagement and drug mechanism of action. Examples range from detecting DNA damage by chemotherapeutics, to identifying drug-specific PTM signatures of kinase inhibitors, to demonstrating that rituximab kills CD20-positive B cells by overactivating B cell receptor signaling. DecryptM profiling of 31 cancer drugs in 13 cell lines demonstrates the broad applicability of the approach. The resulting 1.8 million dose-response curves are provided as an interactive molecular resource in ProteomicsDB.
Collapse
Affiliation(s)
- Jana Zecha
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Florian P. Bayer
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Svenja Wiechmann
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Julia Woortman
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Nicola Berner
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Julian Müller
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Annika Schneider
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Karl Kramer
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Mar Abril-Gil
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Thomas Hopf
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Leonie Reichart
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Lin Chen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Fynn M. Hansen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Severin Lechner
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Patroklos Samaras
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Stephan Eckert
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Ludwig Lautenbacher
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Maria Reinecke
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Firas Hamood
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Polina Prokofeva
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Larsen Vornholz
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Chiara Falcomatà
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, 80336 Munich, Germany
| | - Madeleine Dorsch
- West German Cancer Center, University Hospital Essen, Department of Medical Oncology, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Ayla Schröder
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Anton Venhuizen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Stephanie Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Guillaume Médard
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Gabriele Stoehr
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Jürgen Ruland
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), 81675 Munich, Germany
| | - Barbara M. Grüner
- West German Cancer Center, University Hospital Essen, Department of Medical Oncology, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Dieter Saur
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, 80336 Munich, Germany
| | - Maike Buchner
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Benjamin Ruprecht
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Hannes Hahne
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Matthew The
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Mathias Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Bernhard Kuster
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| |
Collapse
|
7
|
Němec V, Khirsariya P, Janovská P, Moyano PM, Maier L, Procházková P, Kebková P, Gybel' T, Berger BT, Chaikuad A, Reinecke M, Kuster B, Knapp S, Bryja V, Paruch K. Discovery of Potent and Exquisitely Selective Inhibitors of Kinase CK1 with Tunable Isoform Selectivity. Angew Chem Int Ed Engl 2023; 62:e202217532. [PMID: 36625768 DOI: 10.1002/anie.202217532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
Casein kinases 1 (CK1) are key signaling molecules that have emerged recently as attractive therapeutic targets in particular for the treatment of hematological malignancies. Herein, we report the identification of a new class of potent and highly selective inhibitors of CK1α, δ and ϵ. Based on their optimal in vitro and in vivo profiles and their exclusive selectivity, MU1250, MU1500 and MU1742 were selected as quality chemical probes for those CK1 isoforms. At proper concentrations, MU1250 and MU1500 allow for specific targeting of CK1δ or dual inhibition of CK1δ/ϵ in cells. The compound MU1742 also efficiently inhibits CK1α and, to our knowledge, represents the first potent and highly selective inhibitor of this enzyme. In addition, we demonstrate that the central 1H-pyrrolo[2,3-b]pyridine-imidazole pharmacophore can be used as the basis of highly selective inhibitors of other therapeutically relevant protein kinases, e.g. p38α, as exemplified by the compound MU1299.
Collapse
Affiliation(s)
- Václav Němec
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Prashant Khirsariya
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Pavlína Janovská
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Paula Martín Moyano
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Lukáš Maier
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Petra Procházková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Pavlína Kebková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Tomáš Gybel'
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354, Freising, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kamil Paruch
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| |
Collapse
|
8
|
Lo WT, Belabed H, Kücükdisli M, Metag J, Roske Y, Prokofeva P, Ohashi Y, Horatscheck A, Cirillo D, Krauss M, Schmied C, Neuenschwander M, von Kries JP, Médard G, Kuster B, Perisic O, Williams RL, Daumke O, Payrastre B, Severin S, Nazaré M, Haucke V. Development of selective inhibitors of phosphatidylinositol 3-kinase C2α. Nat Chem Biol 2023; 19:18-27. [PMID: 36109648 PMCID: PMC7613998 DOI: 10.1038/s41589-022-01118-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/20/2022] [Indexed: 01/01/2023]
Abstract
Phosphatidylinositol 3-kinase type 2α (PI3KC2α) and related class II PI3K isoforms are of increasing biomedical interest because of their crucial roles in endocytic membrane dynamics, cell division and signaling, angiogenesis, and platelet morphology and function. Herein we report the development and characterization of PhosphatidylInositol Three-kinase Class twO INhibitors (PITCOINs), potent and highly selective small-molecule inhibitors of PI3KC2α catalytic activity. PITCOIN compounds exhibit strong selectivity toward PI3KC2α due to their unique mode of interaction with the ATP-binding site of the enzyme. We demonstrate that acute inhibition of PI3KC2α-mediated synthesis of phosphatidylinositol 3-phosphates by PITCOINs impairs endocytic membrane dynamics and membrane remodeling during platelet-dependent thrombus formation. PITCOINs are potent and selective cell-permeable inhibitors of PI3KC2α function with potential biomedical applications ranging from thrombosis to diabetes and cancer.
Collapse
Affiliation(s)
- Wen-Ting Lo
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Hassane Belabed
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Murat Kücükdisli
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Juliane Metag
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Yvette Roske
- grid.419491.00000 0001 1014 0849Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Berlin, Germany
| | - Polina Prokofeva
- grid.6936.a0000000123222966Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Yohei Ohashi
- grid.42475.300000 0004 0605 769XMRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - André Horatscheck
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Davide Cirillo
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Michael Krauss
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Christopher Schmied
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Martin Neuenschwander
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Jens Peter von Kries
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Guillaume Médard
- grid.6936.a0000000123222966Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- grid.6936.a0000000123222966Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Olga Perisic
- grid.42475.300000 0004 0605 769XMRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Roger L. Williams
- grid.42475.300000 0004 0605 769XMRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Oliver Daumke
- grid.419491.00000 0001 1014 0849Max-Delbrück-Centrum für Molekulare Medizin, Kristallographie, Berlin, Germany
| | - Bernard Payrastre
- Inserm, U1297-Université, Toulouse III, Institut des Maladies Métaboliques et Cardiovasculaires, Toulouse, France ,grid.411175.70000 0001 1457 2980Centre Hospitalier Universitaire de Toulouse, Laboratoire d’Hématologie, Toulouse, France
| | - Sonia Severin
- Inserm, U1297-Université, Toulouse III, Institut des Maladies Métaboliques et Cardiovasculaires, Toulouse, France
| | - Marc Nazaré
- Departments of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany. .,Departments of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| |
Collapse
|
9
|
Prokofeva P, Höfer S, Hornisch M, Abele M, Kuster B, Médard G. Merits of Diazirine Photo-Immobilization for Target Profiling of Natural Products and Cofactors. ACS Chem Biol 2022; 17:3100-3109. [PMID: 36302507 PMCID: PMC9680877 DOI: 10.1021/acschembio.2c00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/05/2022] [Indexed: 01/20/2023]
Abstract
Finding the targets of natural products is of key importance in both chemical biology and drug discovery, and deconvolution of cofactor interactomes contributes to the functional annotation of the proteome. Identifying the proteins that underlie natural compound activity in phenotypic screens helps to validate the respective targets and, potentially, expand the druggable proteome. Here, we present a generally applicable protocol for the photoactivated immobilization of unmodified and microgram quantities of natural products on diazirine-decorated beads and their use for systematic affinity-based proteome profiling. We show that among 31 molecules of very diverse reported activity and biosynthetic origin, 25 could indeed be immobilized. Dose-response competition binding experiments using lysates of human or bacterial cells followed by quantitative mass spectrometry recapitulated targets of 9 molecules with <100 μM affinity. Among them, immobilization of coenzyme A produced a tool to interrogate proteins containing a HotDog domain. Surprisingly, immobilization of the cofactor flavin adenine dinucleotide (FAD) led to the identification of nanomolar interactions with dozens of RNA-binding proteins.
Collapse
Affiliation(s)
- Polina Prokofeva
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Höfer
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Maximilian Hornisch
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Miriam Abele
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| |
Collapse
|
10
|
Characterizing PTP4A3/PRL-3 as the Potential Prognostic Marker Gene for Liver Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:2717056. [PMID: 36213837 PMCID: PMC9546693 DOI: 10.1155/2022/2717056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/17/2022] [Accepted: 07/26/2022] [Indexed: 01/27/2023]
Abstract
Background A large number of cancer-related deaths in the world can be attributed to liver hepatocellular carcinoma (LIHC). The purpose of this study is to explore protein tyrosine phosphatase type IV A member 3 (PTP4A3/PRL-3) as a new and reliable biomarker to predict the prognosis of LIHC and determine the potential therapeutic targets or drugs that can be used for treating LIHC. Methods We included three LIHC datasets with clinical information and expression profiles from public databases. The expression level of PTP4A3 was analyzed, and based on the results, the samples were divided into high- and low-expression groups. The Kaplan–Meier survival analysis method was used to determine the relationship between PTP4A3 and prognosis. The enrichment differences among the functional pathways associated with the high- and low-expression groups were determined using the gene set enrichment analysis (GSEA) method. Five methods were used to determine the differences among the tumor microenvironment in the low- and high-expression groups. The sensitivity of the low- and high-expression groups toward different drug treatment methods was predicted by analyzing the Tumor Immune Dysfunction and Exclusion (TIDE) scores and determining the biochemical half-maximal inhibitory concentration (IC50). Results The expression levels of the LIHC and adjacent samples were analyzed, and it was observed that the expression level of PTP4A3 in tumor tissue was significantly higher than the expression level of the same gene in the adjacent samples. It was also inferred that it might be a cancer-promoting gene. It was concluded that high-expression results in a significantly poor prognosis. The high-expression group was significantly enriched in the tumor-related pathways, such as the PI3K-AKT signaling pathway. In addition, the results obtained by conducting immune infiltration analysis revealed a significant positive correlation between some immune scores and the gene PTP4A3. The drug KIN001−135 and gene PTP4A3 were also found to correlate positively with each other. CP466722, Pyrimethamine, AKT inhibitor VIII, Embelin, Cisplatin, QS11, Bexarotene, and Midostaurin negatively correlated with PTP4A3 associated with the three datasets. Moreover, the drugs Cisplatin, QS11, Midostaurin, and CP466722 were more sensitive toward the high-expression group than the low PTP4A3 expression group. Significant differences were observed in these cases. Conclusion PTP4A3/PRL-3 is potentially associated with the progression, metastasis, and invasion of LIHC. The prognosis of LIHC patients is negatively impacted by the high-expression levels of the gene. The results indicate that PTP4A3/PRL-3 is an important prognostic factor for LIHC and is a new potential prognostic detection target. The discovery of the 8 drugs that were negatively associated with PTP4A3 provided a new direction that can be developed in the future for the treatment of LIHC.
Collapse
|
11
|
Lechner S, Malgapo MIP, Grätz C, Steimbach RR, Baron A, Rüther P, Nadal S, Stumpf C, Loos C, Ku X, Prokofeva P, Lautenbacher L, Heimburg T, Würf V, Meng C, Wilhelm M, Sippl W, Kleigrewe K, Pauling JK, Kramer K, Miller AK, Pfaffl MW, Linder ME, Kuster B, Médard G. Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target. Nat Chem Biol 2022; 18:812-820. [PMID: 35484434 PMCID: PMC9339481 DOI: 10.1038/s41589-022-01015-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 03/15/2022] [Indexed: 01/22/2023]
Abstract
Histone deacetylase (HDAC) targeting drugs have entered the pharmacopoeia in the 2000s. However, some enigmatic phenotypes suggest off-target engagement. Here, we developed a quantitative chemical proteomics assay using immobilized HDAC inhibitors and mass spectrometry that we deployed to establish the target landscape of 53 drugs. The assay covers 9 of the 11 human zinc-dependent HDACs, questions the reported selectivity of some widely-used molecules, notably for HDAC6, and delineates how the composition of HDAC complexes influences drug potency. Unexpectedly, metallo-beta-lactamase domain-containing protein 2 (MBLAC2) featured as a frequent off-target of hydroxamate drugs. This poorly characterized palmitoyl-CoA hydrolase is inhibited by 24 HDAC inhibitors at low nM potency. MBLAC2 enzymatic inhibition and knock down led to the accumulation of extracellular vesicles. Given the importance of extracellular vesicle biology in neurological diseases and cancer, this HDAC-independent drug effect may qualify MBLAC2 as a target for drug discovery.
Collapse
Affiliation(s)
- Severin Lechner
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Martin Ian P Malgapo
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Christian Grätz
- Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Raphael R Steimbach
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Agnes Baron
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Patrick Rüther
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Simon Nadal
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Carmen Stumpf
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christina Loos
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Xin Ku
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Polina Prokofeva
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Tino Heimburg
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Vivian Würf
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Josch K Pauling
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karl Kramer
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Aubry K Miller
- Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael W Pfaffl
- Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Maurine E Linder
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
12
|
Wiechmann S, Ruprecht B, Siekmann T, Zheng R, Frejno M, Kunold E, Bajaj T, Zolg DP, Sieber SA, Gassen NC, Kuster B. Chemical Phosphoproteomics Sheds New Light on the Targets and Modes of Action of AKT Inhibitors. ACS Chem Biol 2021; 16:631-641. [PMID: 33755436 DOI: 10.1021/acschembio.0c00872] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Due to its important roles in oncogenic signaling, AKT has been subjected to extensive drug discovery efforts leading to small molecule inhibitors investigated in advanced clinical trials. To better understand how these drugs exert their therapeutic effects at the molecular level, we combined chemoproteomic target affinity profiling using kinobeads and phosphoproteomics to analyze the five clinical AKT inhibitors AZD5363 (Capivasertib), GSK2110183 (Afuresertib), GSK690693, Ipatasertib, and MK-2206 in BT-474 breast cancer cells. Kinobead profiling identified between four and 29 nM targets for these compounds and showed that AKT1 and AKT2 were the only common targets. Similarly, measuring the response of the phosphoproteome to the same inhibitors identified ∼1700 regulated phosphorylation sites, 276 of which were perturbed by all five compounds. This analysis expanded the known AKT signaling network by 119 phosphoproteins that may represent direct or indirect targets of AKT. Within this new network, 41 regulated phosphorylation sites harbor the AKT substrate motif, and recombinant kinase assays validated 16 as novel AKT substrates. These included CEP170 and FAM83H, suggesting a regulatory function of AKT in mitosis and cytoskeleton organization. In addition, a specific phosphorylation pattern on the ULK1-FIP200-ATG13-VAPB complex was found to determine the active state of ULK1, leading to elevated autophagy in response to AKT inhibition.
Collapse
Affiliation(s)
- Svenja Wiechmann
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
- German Cancer Consortium (DKTK), 80336 Munich, Germany
- German Cancer Center (DKFZ), 69120 Heidelberg, Germany
| | - Benjamin Ruprecht
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Theresa Siekmann
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Runsheng Zheng
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Elena Kunold
- Organic Chemistry II, Technical University of Munich, 85748 Garching, Germany
| | - Thomas Bajaj
- Department of Psychiatry, Bonn Clinical Center, 53127 Bonn, Germany
| | - Daniel P. Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Stephan A. Sieber
- Organic Chemistry II, Technical University of Munich, 85748 Garching, Germany
| | - Nils C. Gassen
- Department of Psychiatry, Bonn Clinical Center, 53127 Bonn, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
- German Cancer Consortium (DKTK), 80336 Munich, Germany
- German Cancer Center (DKFZ), 69120 Heidelberg, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, 85354 Freising, Germany
| |
Collapse
|
13
|
Gonçalves E, Segura‐Cabrera A, Pacini C, Picco G, Behan FM, Jaaks P, Coker EA, van der Meer D, Barthorpe A, Lightfoot H, Mironenko T, Beck A, Richardson L, Yang W, Lleshi E, Hall J, Tolley C, Hall C, Mali I, Thomas F, Morris J, Leach AR, Lynch JT, Sidders B, Crafter C, Iorio F, Fawell S, Garnett MJ. Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens. Mol Syst Biol 2020; 16:e9405. [PMID: 32627965 PMCID: PMC7336273 DOI: 10.15252/msb.20199405] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/26/2022] Open
Abstract
Low success rates during drug development are due, in part, to the difficulty of defining drug mechanism-of-action and molecular markers of therapeutic activity. Here, we integrated 199,219 drug sensitivity measurements for 397 unique anti-cancer drugs with genome-wide CRISPR loss-of-function screens in 484 cell lines to systematically investigate cellular drug mechanism-of-action. We observed an enrichment for positive associations between the profile of drug sensitivity and knockout of a drug's nominal target, and by leveraging protein-protein networks, we identified pathways underpinning drug sensitivity. This revealed an unappreciated positive association between mitochondrial E3 ubiquitin-protein ligase MARCH5 dependency and sensitivity to MCL1 inhibitors in breast cancer cell lines. We also estimated drug on-target and off-target activity, informing on specificity, potency and toxicity. Linking drug and gene dependency together with genomic data sets uncovered contexts in which molecular networks when perturbed mediate cancer cell loss-of-fitness and thereby provide independent and orthogonal evidence of biomarkers for drug development. This study illustrates how integrating cell line drug sensitivity with CRISPR loss-of-function screens can elucidate mechanism-of-action to advance drug development.
Collapse
Affiliation(s)
| | - Aldo Segura‐Cabrera
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxtonUK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew R Leach
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxtonUK
| | - James T Lynch
- Research and Early DevelopmentOncology R&DAstraZenecaCambridgeUK
| | - Ben Sidders
- Research and Early DevelopmentOncology R&DAstraZenecaCambridgeUK
| | - Claire Crafter
- Research and Early DevelopmentOncology R&DAstraZenecaCambridgeUK
| | - Francesco Iorio
- Wellcome Sanger InstituteHinxtonUK
- Human TechnopoleMilanoItaly
| | - Stephen Fawell
- Research and Early DevelopmentOncology R&DAstraZenecaWalthamMAUSA
| | | |
Collapse
|
14
|
Ensan D, Smil D, Zepeda-Velázquez CA, Panagopoulos D, Wong JF, Williams EP, Adamson R, Bullock AN, Kiyota T, Aman A, Roberts OG, Edwards AM, O'Meara JA, Isaac MB, Al-Awar R. Targeting ALK2: An Open Science Approach to Developing Therapeutics for the Treatment of Diffuse Intrinsic Pontine Glioma. J Med Chem 2020; 63:4978-4996. [PMID: 32369358 PMCID: PMC8213057 DOI: 10.1021/acs.jmedchem.0c00395] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Diffuse
intrinsic pontine glioma is an aggressive pediatric cancer
for which no effective chemotherapeutic drugs exist. Analysis of the
genomic landscape of this disease has led to the identification of
the serine/threonine kinase ALK2 as a potential target for therapeutic
intervention. In this work, we adopted an open science approach to
develop a series of potent type I inhibitors of ALK2 which are orally
bio-available and brain-penetrant. Initial efforts resulted in the
discovery of M4K2009, an analogue of the previously reported
ALK2 inhibitor LDN-214117. Although highly selective
for ALK2 over the TGF-βR1 receptor ALK5, M4K2009 is also moderately active against the hERG potassium channel. Varying
the substituents of the trimethoxyphenyl moiety gave rise to an equipotent
benzamide analogue M4K2149 with reduced off-target affinity
for the ion channel. Additional modifications yielded 2-fluoro-6-methoxybenzamide
derivatives (26a–c), which possess high inhibitory
activity against ALK2, excellent selectivity, and superior pharmacokinetic
profiles.
Collapse
Affiliation(s)
- Deeba Ensan
- Department of Pharmacology and Toxicology, University of Toronto, Medical Sciences Building, Room 4207, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - David Smil
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Carlos A Zepeda-Velázquez
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Dimitrios Panagopoulos
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada.,Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada.,Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jong Fu Wong
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Eleanor P Williams
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Roslin Adamson
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Alex N Bullock
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Taira Kiyota
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada.,Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Owen G Roberts
- M4K Pharma Inc., 101 College Street, MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada.,M4K Pharma Inc., 101 College Street, MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
| | - Jeff A O'Meara
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Methvin B Isaac
- Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Rima Al-Awar
- Department of Pharmacology and Toxicology, University of Toronto, Medical Sciences Building, Room 4207, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| |
Collapse
|
15
|
Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS. Nat Commun 2020; 11:157. [PMID: 31919466 PMCID: PMC6952431 DOI: 10.1038/s41467-019-13973-x] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/10/2019] [Indexed: 02/07/2023] Open
Abstract
Nano-flow liquid chromatography tandem mass spectrometry (nano-flow LC–MS/MS) is the mainstay in proteome research because of its excellent sensitivity but often comes at the expense of robustness. Here we show that micro-flow LC–MS/MS using a 1 × 150 mm column shows excellent reproducibility of chromatographic retention time (<0.3% coefficient of variation, CV) and protein quantification (<7.5% CV) using data from >2000 samples of human cell lines, tissues and body fluids. Deep proteome analysis identifies >9000 proteins and >120,000 peptides in 16 h and sample multiplexing using tandem mass tags increases throughput to 11 proteomes in 16 h. The system identifies >30,000 phosphopeptides in 12 h and protein-protein or protein-drug interaction experiments can be analyzed in 20 min per sample. We show that the same column can be used to analyze >7500 samples without apparent loss of performance. This study demonstrates that micro-flow LC–MS/MS is suitable for a broad range of proteomic applications. Mass spectrometry-based proteomics typically relies on highly sensitive nano-flow liquid chromatography (LC) but this can reduce robustness and reproducibility. Here, the authors show that micro-flow LC enables robust and reproducible high-throughput proteomics experiments at a very moderate loss of sensitivity.
Collapse
|
16
|
Reinecke M, Heinzlmeir S, Wilhelm M, Médard G, Klaeger S, Kuster B. Kinobeads: A Chemical Proteomic Approach for Kinase Inhibitor Selectivity Profiling and Target Discovery. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527818242.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
17
|
Abstract
PURPOSE OF REVIEW Fibrodysplasia ossificans progressiva (FOP) is an extremely rare and severely disabling autosomal dominant disease that is yet to be clearly understood. The purpose of this review is to present recent literature on pathophysiology, clinical features, diagnosis and treatment of FOP. RECENT FINDINGS FOP is characterized by congenital great toe deformity and progressive heterotopic ossifications in connective tissue. Heterotopic ossifications occur after painful flare-ups that can arise spontaneously or can be triggered by minor trauma. Each flare-up ultimately causes restriction of related-joint, and along with the others eventually leads to immobility. Death is usually caused by pulmonary complications because of chest wall involvement. The causative gene of FOP is activin A receptor type 1 (ACVR1), a bone morphogenetic protein-signalling component, which normally acts to inhibit osteoblastogenesis. The treatment of FOP is still preventive and supportive. SUMMARY Although there are still gaps in the underlying mechanism of FOP, effective treatment options, such as potential pharmacologic targets and cell-based therapies are promising for the future. Some of these were tested without a clinical trial setting, and are currently in the process of evidence-based research.
Collapse
Affiliation(s)
- Gulseren Akyuz
- Department of Physical Medicine and Rehabilitation, Marmara University School of Medicine
| | - Kardelen Gencer-Atalay
- Department of Physical Medicine and Rehabilitation, Marmara University School of Medicine
| | - Pinar Ata
- Department of Medical Genetics, Marmara University School of Medicine, Istanbul, Turkey
| |
Collapse
|