1
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Picco G, Rao Y, Al Saedi A, Lee Y, Vieira SF, Bhosle S, May K, Herranz-Ors C, Walker SJ, Shenje R, Dincer C, Gibson F, Banerjee R, Hewitson Z, Werner T, Cottom JE, Peng Y, Deng N, Landis P, Conticelli D, McCarten K, Bush J, Sharma M, Lightfoot H, House D, Milford E, Grant EK, Glogowski MP, Wagner CD, Bantscheff M, Rutkowska-Klute A, Network Uk Group CM, Zappacosta F, Pettinger J, Barthorpe S, Eberl HC, Jones BT, Schneck JL, Murphy DJ, Voest EE, Taygerly JP, DeMartino MP, Coelho MA, Houseley J, Sharma G, Schwartz BJ, Garnett MJ. Novel WRN Helicase Inhibitors Selectively Target Microsatellite Unstable Cancer Cells. Cancer Discov 2024:742950. [PMID: 38587317 DOI: 10.1158/2159-8290.cd-24-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024]
Abstract
Microsatellite-unstable (MSI) cancers require WRN helicase to resolve replication stress due to expanded DNA (TA)n-dinucleotide repeats. WRN is a promising synthetic lethal target for MSI tumours, and WRN inhibitors are in development. Here, we used CRISPR-Cas9 base editing to map WRN residues critical for MSI cells, validating the helicase domain as the primary drug target. Fragment-based screening led to the development of potent and highly selective WRN helicase covalent inhibitors. These compounds selectively suppressed MSI model growth In vitro and In vivo by mimicking WRN loss, inducing DNA double-strand breaks at expanded TA-repeats and DNA damage. Assessment of biomarkers in preclinical models linked TA-repeat expansions and mismatch repair (MMR) alterations to compound activity. Efficacy was confirmed in immunotherapy-resistant organoids and patient-derived xenograft (PDX) models. The discovery of potent, selective covalent WRN inhibitors provides proof of concept for synthetic-lethal targeting of WRN in MSI cancer and tools to dissect WRN biology.
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Affiliation(s)
| | - Yanhua Rao
- GSK, Upper Providence, PA, US 19426, United States
| | | | - Yang Lee
- GSK, Upper Providence, PA, US 19426, United States
| | | | | | - Kieron May
- Babraham Institute, Cambridge, United Kingdom
| | | | | | | | - Cansu Dincer
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Freddy Gibson
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Zoe Hewitson
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Joshua E Cottom
- GlaxoSmithKline (United States), Upper Providence, PA, United States
| | - Yang Peng
- The University of Texas MD Anderson Cancer Center, Houston, TEXAS, United States
| | | | | | - Daniela Conticelli
- University of Torino, Candiolo Cancer Institute - FPO,IRCCS, Candiolo, TO, Italy
| | | | | | - Mamta Sharma
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | - Syd Barthorpe
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | | | | | | | - Emile E Voest
- Netherlands Cancer Institute, Amsterdam, Netherlands
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2
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Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P, Bergamini G, Bantscheff M, Fälth-Savitski M, Saez-Rodriguez J. Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition. Mol Syst Biol 2024; 20:458-474. [PMID: 38454145 PMCID: PMC10987601 DOI: 10.1038/s44320-024-00025-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
Complex disease phenotypes often span multiple molecular processes. Functional characterization of these processes can shed light on disease mechanisms and drug effects. Thermal Proteome Profiling (TPP) is a mass-spectrometry (MS) based technique assessing changes in thermal protein stability that can serve as proxies of functional protein changes. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a multi-omics integration framework, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover consequences of Poly (ADP-ribose) polymerase (PARP) inhibition in ovarian cancer cells on cell cycle and DNA damage response as well as interferon and hippo signaling. We found that TPP offers a complementary perspective to other omics data modalities, and that its integration allowed us to obtain a more complete molecular overview of PARP inhibition. We anticipate that this strategy can be used to integrate functional proteomics with other omics to study molecular processes.
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Affiliation(s)
- Mira L Burtscher
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Martin Garrido-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | | | | | - Katharina Zirngibl
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
| | | | | | | | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany.
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3
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Sauer P, Bantscheff M. Thermal Proteome Profiling for Drug Target Identification and Probing of Protein States. Methods Mol Biol 2023; 2718:73-98. [PMID: 37665455 DOI: 10.1007/978-1-0716-3457-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Proteins are central drivers of physiological and pathological processes in the cell. Methods evaluating protein functional states are therefore vital to fundamental research as well as drug discovery. Thermal proteome profiling (TPP) to this date constitutes the only approach that permits examining protein states in live cells, under native conditions and at a proteome-wide scale. TPP harnesses ligand/perturbation-induced changes in protein thermal stability, which are monitored by multiplexed quantitative mass spectrometry. In this chapter, we describe a modular experimental workflow for TPP experiments using live cells or crude cell extracts. We provide the tools to perform different TPP formats, i.e., temperature range experiments, TPP-TR; isothermal compound titrations, TPP-CCR; and a combination thereof, 2D-TPP.
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Affiliation(s)
- Patricia Sauer
- Cellzome GmbH, GlaxoSmithKline (GSK), Heidelberg, Germany
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4
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Singh V, Grzegorzewicz AE, Fienberg S, Müller R, Khonde LP, Sanz O, Alfonso S, Urones B, Drewes G, Bantscheff M, Ghidelli-Disse S, Ioerger TR, Angala B, Liu J, Lee RE, Sacchettini JC, Krieger IV, Jackson M, Chibale K, Ghorpade SR. 1,3-Diarylpyrazolyl-acylsulfonamides Target HadAB/BC Complex in Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:2315-2326. [PMID: 36325756 PMCID: PMC9673142 DOI: 10.1021/acsinfecdis.2c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 11/05/2022]
Abstract
Alternative mode-of-inhibition of clinically validated targets is an effective strategy for circumventing existing clinical drug resistance. Herein, we report 1,3-diarylpyrazolyl-acylsulfonamides as potent inhibitors of HadAB/BC, a 3-hydroxyl-ACP dehydratase complex required to iteratively elongate the meromycolate chain of mycolic acids in Mycobacterium tuberculosis (Mtb). Mutations in compound 1-resistant Mtb mutants mapped to HadC (Rv0637; K157R), while chemoproteomics confirmed the compound's binding to HadA (Rv0635), HadB (Rv0636), and HadC. The compounds effectively inhibited the HadAB and HadBC enzyme activities and affected mycolic acid biosynthesis in Mtb, in a concentration-dependent manner. Unlike known 3-hydroxyl-ACP dehydratase complex inhibitors of clinical significance, isoxyl and thioacetazone, 1,3-diarylpyrazolyl-acylsulfonamides did not require activation by EthA and thus are not liable to EthA-mediated resistance. Further, the crystal structure of a key compound in a complex with Mtb HadAB revealed unique binding interactions within the active site of HadAB, providing a useful tool for further structure-based optimization of the series.
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Affiliation(s)
- Vinayak Singh
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch7701, South Africa
| | - Anna E. Grzegorzewicz
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Stephen Fienberg
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Rudolf Müller
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Lutete Peguy Khonde
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Olalla Sanz
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Salvatore Alfonso
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Beatriz Urones
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Gerard Drewes
- Cellzome
GmbH · A GSK Company, Meyerhofstrasse 1, Heidelberg69117, Germany
| | - Marcus Bantscheff
- Cellzome
GmbH · A GSK Company, Meyerhofstrasse 1, Heidelberg69117, Germany
| | | | - Thomas R. Ioerger
- Department
of Computer Science and Engineering, Texas
A&M University, College
Station, Texas77843, United States
| | - Bhanupriya Angala
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Jiuyu Liu
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee38105, United States
| | - Richard E. Lee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee38105, United States
| | - James C. Sacchettini
- Texas A&M
University, Department of Biochemistry and
Biophysics, ILSB 2138,
301 Old Main Dr, College Station, Texas77843-3474, United States
| | - Inna V. Krieger
- Texas A&M
University, Department of Biochemistry and
Biophysics, ILSB 2138,
301 Old Main Dr, College Station, Texas77843-3474, United States
| | - Mary Jackson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch7701, South Africa
| | - Sandeep R. Ghorpade
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
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5
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Arendse LB, Murithi JM, Qahash T, Pasaje CFA, Godoy LC, Dey S, Gibhard L, Ghidelli-Disse S, Drewes G, Bantscheff M, Lafuente-Monasterio MJ, Fienberg S, Wambua L, Gachuhi S, Coertzen D, van der Watt M, Reader J, Aswat AS, Erlank E, Venter N, Mittal N, Luth MR, Ottilie S, Winzeler EA, Koekemoer LL, Birkholtz LM, Niles JC, Llinás M, Fidock DA, Chibale K. The anticancer human mTOR inhibitor sapanisertib potently inhibits multiple Plasmodium kinases and life cycle stages. Sci Transl Med 2022; 14:eabo7219. [PMID: 36260689 PMCID: PMC9951552 DOI: 10.1126/scitranslmed.abo7219] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Compounds acting on multiple targets are critical to combating antimalarial drug resistance. Here, we report that the human "mammalian target of rapamycin" (mTOR) inhibitor sapanisertib has potent prophylactic liver stage activity, in vitro and in vivo asexual blood stage (ABS) activity, and transmission-blocking activity against the protozoan parasite Plasmodium spp. Chemoproteomics studies revealed multiple potential Plasmodium kinase targets, and potent inhibition of Plasmodium phosphatidylinositol 4-kinase type III beta (PI4Kβ) and cyclic guanosine monophosphate-dependent protein kinase (PKG) was confirmed in vitro. Conditional knockdown of PI4Kβ in ABS cultures modulated parasite sensitivity to sapanisertib, and laboratory-generated P. falciparum sapanisertib resistance was mediated by mutations in PI4Kβ. Parasite metabolomic perturbation profiles associated with sapanisertib and other known PI4Kβ and/or PKG inhibitors revealed similarities and differences between chemotypes, potentially caused by sapanisertib targeting multiple parasite kinases. The multistage activity of sapanisertib and its in vivo antimalarial efficacy, coupled with potent inhibition of at least two promising drug targets, provides an opportunity to reposition this pyrazolopyrimidine for malaria.
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Affiliation(s)
- Lauren B. Arendse
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - James M. Murithi
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tarrick Qahash
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Luiz C. Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liezl Gibhard
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | | | - Gerard Drewes
- Cellzome GmbH, a GSK Company, Heidelberg 69117, Germany
| | | | - Maria J. Lafuente-Monasterio
- Tres Cantos Medicines Development Campus-Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
| | - Stephen Fienberg
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Lynn Wambua
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Samuel Gachuhi
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Dina Coertzen
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield 0028, South Africa
| | - Mariëtte van der Watt
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield 0028, South Africa
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield 0028, South Africa
| | - Ayesha S. Aswat
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2193, South Africa
| | - Erica Erlank
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2193, South Africa
| | - Nelius Venter
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2193, South Africa
| | - Nimisha Mittal
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Madeline R. Luth
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sabine Ottilie
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Lizette L. Koekemoer
- Wits Research Institute for Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2193, South Africa
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield 0028, South Africa
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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6
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Sridharan S, Hernandez-Armendariz A, Kurzawa N, Potel CM, Memon D, Beltrao P, Bantscheff M, Huber W, Cuylen-Haering S, Savitski MM. Systematic discovery of biomolecular condensate-specific protein phosphorylation. Nat Chem Biol 2022; 18:1104-1114. [PMID: 35864335 PMCID: PMC9512703 DOI: 10.1038/s41589-022-01062-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/13/2022] [Indexed: 12/27/2022]
Abstract
Reversible protein phosphorylation is an important mechanism for regulating (dis)assembly of biomolecular condensates. However, condensate-specific phosphosites remain largely unknown, thereby limiting our understanding of the underlying mechanisms. Here, we combine solubility proteome profiling with phosphoproteomics to quantitatively map several hundred phosphosites enriched in either soluble or condensate-bound protein subpopulations, including a subset of phosphosites modulating protein–RNA interactions. We show that multi-phosphorylation of the C-terminal disordered segment of heteronuclear ribonucleoprotein A1 (HNRNPA1), a key RNA-splicing factor, reduces its ability to locate to nuclear clusters. For nucleophosmin 1 (NPM1), an essential nucleolar protein, we show that phosphorylation of S254 and S260 is crucial for lowering its partitioning to the nucleolus and additional phosphorylation of distal sites enhances its retention in the nucleoplasm. These phosphorylation events decrease RNA and protein interactions of NPM1 to regulate its condensation. Our dataset is a rich resource for systematically uncovering the phosphoregulation of biomolecular condensates. ![]()
A combination of solubility proteome profiling with phosphoproteomics enables systematic analysis of the phosphorylation status of proteins in soluble and condensate-bound pools.
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Affiliation(s)
- Sindhuja Sridharan
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Alberto Hernandez-Armendariz
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Clement M Potel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Danish Memon
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Pedro Beltrao
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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7
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Knecht S, Eberl HC, Bantscheff M. Interval-Based Secretomics Unravels Acute-Phase Response in Hepatocyte Model Systems. Mol Cell Proteomics 2022; 21:100241. [PMID: 35525403 PMCID: PMC9184749 DOI: 10.1016/j.mcpro.2022.100241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/21/2022] Open
Abstract
Mass spectrometry-based secretomics approaches frequently utilize serum-free culture conditions to circumvent serum-induced interference and to increase analytical depth. However, this can negatively affect a wide range of cellular functions and cell viability. These effects become particularly apparent when investigating transcriptionally regulated secretion events and feedback-loops in response to perturbations that require 48 h or more to fully manifest. We present an “interval-based” secretomics workflow, which determines protein secretion rates in short serum-free time windows. Relative quantification using tandem mass tags enables precise monitoring of time-dependent changes. We applied this approach to determine temporal profiles of protein secretion in the hepatocyte model cell lines HepG2 and HepaRG after stimulation of the acute-phase response (APR) by the cytokines IL1b and IL6. While the popular hepatocarcinoma cell line HepG2 showed an incomplete APR, secretion patterns derived from differentiated HepaRG cells recapitulated the expected APR more comprehensively. For several APR response proteins, substantial secretion was only observed after 72 h, a time window at which cell fitness is substantially impaired under serum-free cell culture conditions. The interval-based secretomics approach enabled the first comprehensive analysis of time-dependent secretion of liver cell models in response to these proinflammatory cytokines. The extended time range facilitated the observation of distinct chronological phases and cytokine-dependent secretion phenotypes of the APR. IL1b directed the APR toward pathogen defense over three distinct phases—chemotaxis, effector, clearance—while IL6 directed the APR toward regeneration. Protein shedding on the cell surface was pronounced upon IL1b stimulation, and small molecule inhibition of ADAM and matrix metalloproteases identified induced as well as constitutive shedding events. Inhibition of ADAM proteases with TAPI-0 resulted in reduced shedding of the sorting receptor SORT1, and an attenuated cytokine response suggesting a direct link between cell surface shedding and cytokine secretion rates. Interval-based secretomics enables extended time course analysis. Time-resolved acute phase response in liver model systems HepG2 and HepaRG. IL1b response clusters in three phases. Cell surface shedding is amplified during acute-phase response. ADAM inhibition dampens secretion of inflammatory cytokines.
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Affiliation(s)
- Sascha Knecht
- Cellzome GmbH, GlaxoSmithKline (GSK), Heidelberg, Germany
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8
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Yan B, Freiwald T, Chauss D, Wang L, West E, Mirabelli C, Zhang CJ, Nichols EM, Malik N, Gregory R, Bantscheff M, Ghidelli-Disse S, Kolev M, Frum T, Spence JR, Sexton JZ, Alysandratos KD, Kotton DN, Pittaluga S, Bibby J, Niyonzima N, Olson MR, Kordasti S, Portilla D, Wobus CE, Laurence A, Lionakis MS, Kemper C, Afzali B, Kazemian M. SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.125.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Patients with coronavirus disease 2019 (COVID-19) present a wide range of acute clinical manifestations affecting the lungs, liver, kidneys, and gut. Angiotensin-converting enzyme 2 (ACE2), the best-characterized entry receptor for the disease-causing virus SARS-CoV-2, is highly expressed in the aforementioned tissues. However, the pathways that underlie the disease are still poorly understood. Here, we unexpectedly found that the complement system was one of the intracellular pathways most highly induced by SARS-CoV-2 infection in lung epithelial cells. Infection of respiratory epithelial cells with SARS-CoV-2 generated activated complement component C3a and could be blocked by a cell-permeable inhibitor of complement factor B (CFBi), indicating the presence of an inducible cell-intrinsic C3 convertase in respiratory epithelial cells. Within cells of the bronchoalveolar lavage of patients, distinct signatures of complement activation in myeloid, lymphoid, and epithelial cells tracked with disease severity. Genes induced by SARS-CoV-2 and the drugs that could normalize these genes both implicated the interferon-JAK1/2-STAT1 signaling system and NF-κB as the main drivers of their expression. Ruxolitinib, a JAK1/2 inhibitor, normalized interferon signature genes and all complement gene transcripts induced by SARS-CoV-2 in lung epithelial cell lines but did not affect NF-κB–regulated genes. Ruxolitinib, alone or in combination with the antiviral remdesivir, inhibited C3a protein produced by infected cells. Together, we postulate that combination therapy with JAK inhibitors and drugs that normalize NF-κB signaling could potentially have clinical application for severe COVID-19.
This research was financed by the National Heart, Lung, and Blood Institute of the NIH (grant 5K22HL125593 to M. Kazemian; R01HL119215 to J.R.S.); National Institute of General Medical Sciences of the NIH (grant R35GM138283 to M. Kazemian); and Deutsche Forschungsgemeinschaft (fellowship FR3851/2-1 to T. Freiwald) and supported, in part, by the Intramural Research Program of the NIH; the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) (project number ZIA/DK075149 to B.A.); the National Heart, Lung, and Blood Institute (NHLBI) (project number ZIA/Hl006223 to C.K.); and the National Institute of Allergy and Infectious Diseases (NIAID) (project number ZIA/AI001175 to M.S.L.). T. Frum is supported by T32DE007057. Funding for part of the work was provided by the University of Michigan Biological Scholars Program (to C.E.W.), LifeARC Charity (to S.K.), and CRUK KHP Centre (to S.K.).
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Affiliation(s)
- Bingyu Yan
- 1Department of Biochemistry, Purdue University
| | - Tilo Freiwald
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
- 3Complement and Inflammation Research Section, NHLBI, NIH
- 4Department of Nephrology, University Hospital Frankfurt, Goethe-University, Germany
| | - Daniel Chauss
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
| | - Luopin Wang
- 5Department of Computer Science, Purdue University
| | - Erin West
- 3Complement and Inflammation Research Section, NHLBI, NIH
| | - Carmen Mirabelli
- 6Department of Microbiology and Immunology, University of Michigan
| | | | | | | | | | | | | | | | - Tristan Frum
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
| | - Jason R. Spence
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
- 10Department of Cell and Developmental Biology, University of Michigan
| | - Jonathan Z. Sexton
- 7Department of Medicinal Chemistry, University of Michigan
- 9Department of Internal Medicine, Michigan Medicine at University of Michigan
| | - Konstantinos D. Alysandratos
- 11Center for Regenerative Medicine of Boston University and Boston Medical Center
- 12Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | - Darrell N. Kotton
- 11Center for Regenerative Medicine of Boston University and Boston Medical Center
- 12Pulmonary Center and Department of Medicine, Boston University School of Medicine
| | | | - Jack Bibby
- 3Complement and Inflammation Research Section, NHLBI, NIH
| | - Nathalie Niyonzima
- 14Center of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Norway
| | | | - Shahram Kordasti
- 16CRUK KHP Centre, Comprehensive Cancer Centre, King’s College London, United Kingdom
- 17Haematology Department, Guy’s Hospital, United Kingdom
| | - Didier Portilla
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
- 18Division of Nephrology and Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia
| | | | - Arian Laurence
- 19Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Michail S. Lionakis
- 20Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH
| | - Claudia Kemper
- 3Complement and Inflammation Research Section, NHLBI, NIH
- 21Institute for Systemic Inflammation Research, University of Lübeck, Germany
| | - Behdad Afzali
- 2Immunoregulation Section, Kidney Diseases Branch, NIDDK, NIH
| | - Majid Kazemian
- 1Department of Biochemistry, Purdue University
- 5Department of Computer Science, Purdue University
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9
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Fallon DJ, Lehmann S, Chung CW, Phillipou A, Eberl C, Fantom KGM, Zappacosta F, Patel VK, Bantscheff M, Schofield CJ, Tomkinson NCO, Bush JT. One-Step Synthesis of Photoaffinity Probes for Live-Cell MS-Based Proteomics. Chemistry 2021; 27:17880-17888. [PMID: 34328642 DOI: 10.1002/chem.202102036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 11/06/2022]
Abstract
We present a one-step Ugi reaction protocol for the expedient synthesis of photoaffinity probes for live-cell MS-based proteomics. The reaction couples an amine affinity function with commonly used photoreactive groups, and a variety of handle functionalities. Using this technology, a series of pan-BET (BET: bromodomain and extra-terminal domain) selective bromodomain photoaffinity probes were obtained by parallel synthesis. Studies on the effects of photoreactive group, linker length and irradiation wavelength on photocrosslinking efficiency provide valuable insights into photoaffinity probe design. Optimal probes were progressed to MS-based proteomics to capture the BET family of proteins from live cells and reveal their potential on- and off-target profiles.
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Affiliation(s)
- David J Fallon
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, Glasgow, G1 1XL, UK
| | - Stephanie Lehmann
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Alex Phillipou
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Christian Eberl
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Ken G M Fantom
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | | | | | - Marcus Bantscheff
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | | | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, Glasgow, G1 1XL, UK
| | - Jacob T Bush
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
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10
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Moorey AR, Cabanillas A, Batt SM, Ghidelli-Disse S, Urones B, Sanz O, Lelievre J, Bantscheff M, Cox LR, Besra GS. The multi-target aspect of an MmpL3 inhibitor: The BM212 series of compounds bind EthR2, a transcriptional regulator of ethionamide activation. Cell Surf 2021; 7:100068. [PMID: 34888432 PMCID: PMC8634040 DOI: 10.1016/j.tcsw.2021.100068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) ensures that drug discovery efforts remain at the forefront of TB research. There are multiple different experimental approaches that can be employed in the discovery of anti-TB agents. Notably, inhibitors of MmpL3 are numerous and structurally diverse in Mtb and have been discovered through the generation of spontaneous resistant mutants and subsequent whole genome sequencing studies. However, this approach is not always reliable and can lead to incorrect target assignment and requires orthogonal confirmatory approaches. In fact, many of these inhibitors have also been shown to act as multi-target agents, with secondary targets in Mtb, as well as in other non-MmpL3-containing pathogens. Herein, we have investigated further the cellular targets of the MmpL3-inhibitor BM212 and a number of BM212 analogues. To determine the alternative targets of BM212, which may have been masked by MmpL3 mutations, we have applied a combination of chemo-proteomic profiling using bead-immobilised BM212 derivatives and protein extracts, along with whole-cell and biochemical assays. The study identified EthR2 (Rv0078) as a protein that binds BM212 analogues. We further demonstrated binding of BM212 to EthR2 through an in vitro tryptophan fluorescence assay, which showed significant quenching of tryptophan fluorescence upon addition of BM212. Our studies have demonstrated the value of revisiting drugs with ambiguous targets, such as MmpL3, in an attempt to find alternative targets and the study of off-target effects to understand more precisely target engagement of new hits emerging from drug screening campaigns.
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Affiliation(s)
- Alice R Moorey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Alejandro Cabanillas
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | | | - Beatriz Urones
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Olalla Sanz
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Marcus Bantscheff
- Cellzome - a GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Liam R Cox
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
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11
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Rauscher B, Mueller WF, Clauder-Münster S, Jakob P, Islam MS, Sun H, Ghidelli-Disse S, Boesche M, Bantscheff M, Pflaumer H, Collier P, Haase B, Chen S, Hoffman R, Wang G, Benes V, Drewes G, Snyder M, Steinmetz LM. Patient-derived gene and protein expression signatures of NGLY1 deficiency. J Biochem 2021; 171:187-199. [PMID: 34878535 DOI: 10.1093/jb/mvab131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/13/2021] [Indexed: 11/14/2022] Open
Abstract
N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parents, residual and likely non-functional NGLY1 protein was detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosome biogenesis and mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cysteine ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.
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Affiliation(s)
- Benedikt Rauscher
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | | | - Sandra Clauder-Münster
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Petra Jakob
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - M Saiful Islam
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Han Sun
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Markus Boesche
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Hannah Pflaumer
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Paul Collier
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Bettina Haase
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rene Hoffman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Guangwen Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
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12
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Law RP, Nunes J, Chung C, Bantscheff M, Buda K, Dai H, Evans JP, Flinders A, Klimaszewska D, Lewis AJ, Muelbaier M, Scott‐Stevens P, Stacey P, Tame CJ, Watt GF, Zinn N, Queisser MA, Harling JD, Benowitz AB. Discovery and Characterisation of Highly Cooperative FAK‐Degrading PROTACs. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Robert P. Law
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Joao Nunes
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Chun‐wa Chung
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Marcus Bantscheff
- Cellzome GmbH, a GSK company Meyerhofstraße 1 69117 Heidelberg Germany
| | - Karol Buda
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Han Dai
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - John P. Evans
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Adam Flinders
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | | | - Antonia J. Lewis
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Marcel Muelbaier
- Cellzome GmbH, a GSK company Meyerhofstraße 1 69117 Heidelberg Germany
| | | | - Peter Stacey
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | | | - Gillian F. Watt
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Nico Zinn
- Cellzome GmbH, a GSK company Meyerhofstraße 1 69117 Heidelberg Germany
| | | | - John D. Harling
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
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13
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Law RP, Nunes J, Chung CW, Bantscheff M, Buda K, Dai H, Evans JP, Flinders A, Klimaszewska D, Lewis AJ, Muelbaier M, Scott-Stevens P, Stacey P, Tame CJ, Watt GF, Zinn N, Queisser MA, Harling JD, Benowitz AB. Discovery and Characterisation of Highly Cooperative FAK-Degrading PROTACs. Angew Chem Int Ed Engl 2021; 60:23327-23334. [PMID: 34416073 DOI: 10.1002/anie.202109237] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 11/08/2022]
Abstract
Focal adhesion kinase (FAK) is a key mediator of tumour progression and metastasis. To date, clinical trials of FAK inhibitors have reported disappointing efficacy for oncology indications. We report the design and characterisation of GSK215, a potent, selective, FAK-degrading Proteolysis Targeting Chimera (PROTAC) based on a binder for the VHL E3 ligase and the known FAK inhibitor VS-4718. X-ray crystallography revealed the molecular basis of the highly cooperative FAK-GSK215-VHL ternary complex, and GSK215 showed differentiated in-vitro pharmacology compared to VS-4718. In mice, a single dose of GSK215 induced rapid and prolonged FAK degradation, giving a long-lasting effect on FAK levels (≈96 h) and a marked PK/PD disconnect. This tool PROTAC molecule is expected to be useful for the study of FAK-degradation biology in vivo, and our results indicate that FAK degradation may be a differentiated clinical strategy versus FAK inhibition for the treatment of cancer.
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Affiliation(s)
- Robert P Law
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Joao Nunes
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Chun-Wa Chung
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Marcus Bantscheff
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Karol Buda
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Han Dai
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - John P Evans
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Adam Flinders
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Diana Klimaszewska
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Antonia J Lewis
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Marcel Muelbaier
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Paul Scott-Stevens
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Peter Stacey
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Christopher J Tame
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Gillian F Watt
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Nico Zinn
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Markus A Queisser
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - John D Harling
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Andrew B Benowitz
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
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14
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Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT. Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer 2021; 2:1002-1017. [PMID: 34790902 DOI: 10.1038/s43018-021-00249-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/27/2021] [Indexed: 05/22/2023]
Abstract
DNA methylation, a key epigenetic driver of transcriptional silencing, is universally dysregulated in cancer. Reversal of DNA methylation by hypomethylating agents, such as the cytidine analogs decitabine or azacytidine, has demonstrated clinical benefit in hematologic malignancies. These nucleoside analogs are incorporated into replicating DNA where they inhibit DNA cytosine methyltransferases DNMT1, DNMT3A and DNMT3B through irreversible covalent interactions. These agents induce notable toxicity to normal blood cells thus limiting their clinical doses. Herein we report the discovery of GSK3685032, a potent first-in-class DNMT1-selective inhibitor that was shown via crystallographic studies to compete with the active-site loop of DNMT1 for penetration into hemi-methylated DNA between two CpG base pairs. GSK3685032 induces robust loss of DNA methylation, transcriptional activation and cancer cell growth inhibition in vitro. Due to improved in vivo tolerability compared with decitabine, GSK3685032 yields superior tumor regression and survival mouse models of acute myeloid leukemia.
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Affiliation(s)
- Melissa B Pappalardi
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Kathryn Keenan
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Mark Cockerill
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
- These authors contributed equally: Mark Cockerill, Wendy A. Kellner
| | - Wendy A Kellner
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
- These authors contributed equally: Mark Cockerill, Wendy A. Kellner
| | - Alexandra Stowell
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Christian Sherk
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Kristen Wong
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Sarath Pathuri
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacques Briand
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Michael Steidel
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Philip Chapman
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Arthur Groy
- Future Pipeline Discovery, GlaxoSmithKline, Collegeville, PA, USA
| | - Ashley K Wiseman
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Charles F McHugh
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Nino Campobasso
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Alan P Graves
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Emma Fairweather
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Thilo Werner
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Ali Raoof
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Roger J Butlin
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Lourdes Rueda
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David T Fosbenner
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Cunyu Zhang
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Jessica L Handler
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Morris Muliaditan
- Drug Metabolism and Pharmacokinetics Modelling, GlaxoSmithKline, Stevenage, UK
| | - Makda Mebrahtu
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Jon-Paul Jaworski
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Dean E McNulty
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Charlotte Burt
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - H Christian Eberl
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Amy N Taylor
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Thau Ho
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Susan Merrihew
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Shawn W Foley
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Anna Rutkowska
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Mei Li
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Stuart P Romeril
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Kristin Goldberg
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher S Kershaw
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Marcus Bantscheff
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | | | - Elisabeth Minthorn
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Paola Grandi
- Cellzome GmbH, Functional Genomics, GlaxoSmithKline, Heidelberg, Germany
| | - Mehul Patel
- Medicinal Science & Technology, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Helai P Mohammad
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Rab K Prinjha
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Donald Ogilvie
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | | | - Dirk Heerding
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Stephen B Baylin
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Peter A Jones
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bryan W King
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Juan I Luengo
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Allan M Jordan
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Ian Waddell
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Alderley Park, Macclesfield, UK
| | - Ryan G Kruger
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
| | - Michael T McCabe
- Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA
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15
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Abstract
The thermal stability of proteins can be altered when they interact with small molecules, other biomolecules or are subject to post-translation modifications. Thus monitoring the thermal stability of proteins under various cellular perturbations can provide insights into protein function, as well as potentially determine drug targets and off-targets. Thermal proteome profiling is a highly multiplexed mass-spectrommetry method for monitoring the melting behaviour of thousands of proteins in a single experiment. In essence, thermal proteome profiling assumes that proteins denature upon heating and hence become insoluble. Thus, by tracking the relative solubility of proteins at sequentially increasing temperatures, one can report on the thermal stability of a protein. Standard thermodynamics predicts a sigmoidal relationship between temperature and relative solubility and this is the basis of current robust statistical procedures. However, current methods do not model deviations from this behaviour and they do not quantify uncertainty in the melting profiles. To overcome these challenges, we propose the application of Bayesian functional data analysis tools which allow complex temperature-solubility behaviours. Our methods have improved sensitivity over the state-of-the art, identify new drug-protein associations and have less restrictive assumptions than current approaches. Our methods allows for comprehensive analysis of proteins that deviate from the predicted sigmoid behaviour and we uncover potentially biphasic phenomena with a series of published datasets.
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Affiliation(s)
- Siqi Fang
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paul D W Kirk
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | | | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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16
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Ketley A, Wojciechowska M, Ghidelli-Disse S, Bamborough P, Ghosh TK, Morato ML, Sedehizadeh S, Malik NA, Tang Z, Powalowska P, Tanner M, Billeter-Clark R, Trueman RC, Geiszler PC, Agostini A, Othman O, Bösche M, Bantscheff M, Rüdiger M, Mossakowska DE, Drewry DH, Zuercher WJ, Thornton CA, Drewes G, Uings I, Hayes CJ, Brook JD. CDK12 inhibition reduces abnormalities in cells from patients with myotonic dystrophy and in a mouse model. Sci Transl Med 2021; 12:12/541/eaaz2415. [PMID: 32350131 DOI: 10.1126/scitranslmed.aaz2415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/16/2019] [Accepted: 02/25/2020] [Indexed: 12/17/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is an RNA-based disease with no current treatment. It is caused by a transcribed CTG repeat expansion within the 3' untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. Mutant repeat expansion transcripts remain in the nuclei of patients' cells, forming distinct microscopically detectable foci that contribute substantially to the pathophysiology of the condition. Here, we report small-molecule inhibitors that remove nuclear foci and have beneficial effects in the HSALR mouse model, reducing transgene expression, leading to improvements in myotonia, splicing, and centralized nuclei. Using chemoproteomics in combination with cell-based assays, we identify cyclin-dependent kinase 12 (CDK12) as a druggable target for this condition. CDK12 is a protein elevated in DM1 cell lines and patient muscle biopsies, and our results showed that its inhibition led to reduced expression of repeat expansion RNA. Some of the inhibitors identified in this study are currently the subject of clinical trials for other indications and provide valuable starting points for a drug development program in DM1.
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Affiliation(s)
- Ami Ketley
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Marzena Wojciechowska
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 61997 Heidelberg, Germany
| | - Paul Bamborough
- Computational and Modelling Sciences, GlaxoSmithKline, Medicines Research Centre, Hertfordshire SG1 2NY, UK
| | - Tushar K Ghosh
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Marta Lopez Morato
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Saam Sedehizadeh
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Naveed Altaf Malik
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Zhenzhi Tang
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642-0001, USA
| | - Paulina Powalowska
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.,School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Matthew Tanner
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642-0001, USA
| | - Rudolf Billeter-Clark
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Rebecca C Trueman
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Philippine C Geiszler
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Alessandra Agostini
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Othman Othman
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Markus Bösche
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 61997 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 61997 Heidelberg, Germany
| | - Martin Rüdiger
- Screening Profiling and Mechanistic Biology, GlaxoSmithKline, Medicines Research Centre, Hertfordshire SG1 2NY, UK
| | - Danuta E Mossakowska
- Discovery Partnerships with Academia, GlaxoSmithKline, Medicines Research Centre, Hertfordshire SG1 2NY, UK.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-348 Krakow, Poland
| | - David H Drewry
- Department of Chemical Biology, GlaxoSmithKline, Research Triangle Park, NC 27709-3398, USA
| | - William J Zuercher
- Department of Chemical Biology, GlaxoSmithKline, Research Triangle Park, NC 27709-3398, USA.,SGC Center for Chemical Biology, UNC, Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642-0001, USA
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 61997 Heidelberg, Germany
| | - Iain Uings
- Discovery Partnerships with Academia, GlaxoSmithKline, Medicines Research Centre, Hertfordshire SG1 2NY, UK
| | - Christopher J Hayes
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - J David Brook
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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17
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Werner T, Steidel M, Eberl HC, Bantscheff M. Affinity Enrichment Chemoproteomics for Target Deconvolution and Selectivity Profiling. Methods Mol Biol 2021; 2228:237-252. [PMID: 33950495 DOI: 10.1007/978-1-0716-1024-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
In order to understand the full mechanism of action of candidate drug molecules, it is critical to thoroughly characterize their interactions with endogenously expressed pharmacological targets and potentially undesired off-targets. Here we describe a chemoproteomics approach that is based on functionalized analogs of the compound of interest to affinity enrich target proteins from cell or tissue extracts. Experiments are designed as competition binding assays where free parental compound is spiked at a range of concentrations into the extracts to compete specific binders off the immobilized compound matrix. Quantification of matrix-bound proteins enables generation of dose-response curves and half-binding concentrations. In addition, the influence of the affinity matrix on the equilibrium is determined in rebinding experiments. TMT10 isobaric mass tags enable analyzing repeat binding and dose-dependent competition samples in a single mass spectrometry analysis run, thus enabling the efficient identification of targets, apparent dissociation constants, and selectivity of small molecules in a single experiment. The workflow is exemplified with the kinase inhibitor sunitinib.
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Affiliation(s)
- Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
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18
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Vershinin Z, Feldman M, Werner T, Weil LE, Kublanovsky M, Abaev-Schneiderman E, Sklarz M, Lam EYN, Alasad K, Picaud S, Rotblat B, McAdam RA, Chalifa-Caspi V, Bantscheff M, Chapman T, Lewis HD, Filippakopoulos P, Dawson MA, Grandi P, Prinjha RK, Levy D. BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation. Sci Adv 2021; 7:7/22/eabf5374. [PMID: 34039605 PMCID: PMC8153730 DOI: 10.1126/sciadv.abf5374] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/06/2021] [Indexed: 05/14/2023]
Abstract
The transcriptional coactivator BRD4 has a fundamental role in transcription regulation and thus became a promising epigenetic therapeutic candidate to target diverse pathologies. However, the regulation of BRD4 by posttranslational modifications has been largely unexplored. Here, we show that BRD4 is methylated on chromatin at lysine-99 by the protein lysine methyltransferase SETD6. BRD4 methylation negatively regulates the expression of genes that are involved in translation and inhibits total mRNA translation in cells. Mechanistically, we provide evidence that supports a model where BRD4 methylation by SETD6 does not have a direct role in the association with acetylated histone H4 at chromatin. However, this methylation specifically determines the recruitment of the transcription factor E2F1 to selected target genes that are involved in mRNA translation. Together, our findings reveal a previously unknown molecular mechanism for BRD4 methylation-dependent gene-specific targeting, which may serve as a new direction for the development of therapeutic applications.
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Affiliation(s)
- Zlata Vershinin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Thilo Werner
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Lital Estrella Weil
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Margarita Kublanovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Elina Abaev-Schneiderman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Menachem Sklarz
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Enid Y N Lam
- Sir Peter MacCallum Department of Oncology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Khawla Alasad
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Barak Rotblat
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel
| | - Ruth A McAdam
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Marcus Bantscheff
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Trevor Chapman
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Huw D Lewis
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology and Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Paola Grandi
- GSK Cellzome GmbH, Functional Genomics R&D, 69117 Heidelberg, Germany
| | - Rab K Prinjha
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel.
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
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19
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Yan B, Freiwald T, Chauss D, Wang L, West E, Mirabelli C, Zhang CJ, Nichols EM, Malik N, Gregory R, Bantscheff M, Ghidelli-Disse S, Kolev M, Frum T, Spence JR, Sexton JZ, Alysandratos KD, Kotton DN, Pittaluga S, Bibby J, Niyonzima N, Olson MR, Kordasti S, Portilla D, Wobus CE, Laurence A, Lionakis MS, Kemper C, Afzali B, Kazemian M. SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation. Sci Immunol 2021; 6:6/58/eabg0833. [PMID: 33827897 PMCID: PMC8139422 DOI: 10.1126/sciimmunol.abg0833] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/31/2021] [Indexed: 12/26/2022]
Abstract
Patients with coronavirus disease 2019 (COVID-19) present a wide range of acute clinical manifestations affecting the lungs, liver, kidneys and gut. Angiotensin converting enzyme (ACE) 2, the best-characterized entry receptor for the disease-causing virus SARS-CoV-2, is highly expressed in the aforementioned tissues. However, the pathways that underlie the disease are still poorly understood. Here, we unexpectedly found that the complement system was one of the intracellular pathways most highly induced by SARS-CoV-2 infection in lung epithelial cells. Infection of respiratory epithelial cells with SARS-CoV-2 generated activated complement component C3a and could be blocked by a cell-permeable inhibitor of complement factor B (CFBi), indicating the presence of an inducible cell-intrinsic C3 convertase in respiratory epithelial cells. Within cells of the bronchoalveolar lavage of patients, distinct signatures of complement activation in myeloid, lymphoid and epithelial cells tracked with disease severity. Genes induced by SARS-CoV-2 and the drugs that could normalize these genes both implicated the interferon-JAK1/2-STAT1 signaling system and NF-B as the main drivers of their expression. Ruxolitinib, a JAK1/2 inhibitor, normalized interferon signature genes and all complement gene transcripts induced by SARS-CoV-2 in lung epithelial cell lines, but did not affect NF-B-regulated genes. Ruxolitinib, alone or in combination with the antiviral remdesivir, inhibited C3a protein produced by infected cells. Together, we postulate that combination therapy with JAK inhibitors and drugs that normalize NF-B-signaling could potentially have clinical application for severe COVID-19.
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Affiliation(s)
- Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Tilo Freiwald
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.,Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA.,Department of Nephrology, University Hospital Frankfurt, Goethe-University, Frankfurt, Germany
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Erin West
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Charles J Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | | | - Tristan Frum
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 1702118, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 1702118, USA.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD, USA
| | - Jack Bibby
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nathalie Niyonzima
- Center of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Matthew R Olson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shahram Kordasti
- CRUK-KHP Centre, Comprehensive Cancer Centre, King's College London, London, UK.,Haematology Department, Guy's Hospital, London, UK
| | - Didier Portilla
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.,Division of Nephrology and the Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, VA, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Arian Laurence
- Nuffield Department of Medicine, University of Oxford, UK
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Claudia Kemper
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA. .,Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA. .,Department of Computer Science, Purdue University, West Lafayette, IN, USA
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20
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Balestra AC, Koussis K, Klages N, Howell SA, Flynn HR, Bantscheff M, Pasquarello C, Perrin AJ, Brusini L, Arboit P, Sanz O, Castaño LPB, Withers-Martinez C, Hainard A, Ghidelli-Disse S, Snijders AP, Baker DA, Blackman MJ, Brochet M. Ca 2+ signals critical for egress and gametogenesis in malaria parasites depend on a multipass membrane protein that interacts with PKG. Sci Adv 2021; 7:7/13/eabe5396. [PMID: 33762339 PMCID: PMC7990342 DOI: 10.1126/sciadv.abe5396] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Calcium signaling regulated by the cGMP-dependent protein kinase (PKG) controls key life cycle transitions in the malaria parasite. However, how calcium is mobilized from intracellular stores in the absence of canonical calcium channels in Plasmodium is unknown. Here, we identify a multipass membrane protein, ICM1, with homology to transporters and calcium channels that is tightly associated with PKG in both asexual blood stages and transmission stages. Phosphoproteomic analyses reveal multiple ICM1 phosphorylation events dependent on PKG activity. Stage-specific depletion of Plasmodium berghei ICM1 prevents gametogenesis due to a block in intracellular calcium mobilization, while conditional loss of Plasmodium falciparum ICM1 is detrimental for the parasite resulting in severely reduced calcium mobilization, defective egress, and lack of invasion. Our findings suggest that ICM1 is a key missing link in transducing PKG-dependent signals and provide previously unknown insights into atypical calcium homeostasis in malaria parasites essential for pathology and disease transmission.
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Affiliation(s)
- Aurélia C Balestra
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Konstantinos Koussis
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Natacha Klages
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Steven A Howell
- Mass Spectrometry Proteomics Platform, The Francis Crick Institute, London, UK
| | - Helen R Flynn
- Mass Spectrometry Proteomics Platform, The Francis Crick Institute, London, UK
| | - Marcus Bantscheff
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, 69117 Heidelberg, Germany
| | - Carla Pasquarello
- Proteomics Core Facility, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Abigail J Perrin
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Lorenzo Brusini
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Patrizia Arboit
- Proteomics Core Facility, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Olalla Sanz
- Diseases of the Developing World Global Health Pharma Unit, GlaxoSmithKline, 28760 Tres Cantos, Spain
| | | | | | - Alexandre Hainard
- Proteomics Core Facility, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, 69117 Heidelberg, Germany
| | | | - David A Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Mathieu Brochet
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland.
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21
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Zinn N, Werner T, Doce C, Mathieson T, Boecker C, Sweetman G, Fufezan C, Bantscheff M. Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags. J Proteome Res 2021; 20:1792-1801. [PMID: 33621079 DOI: 10.1021/acs.jproteome.0c00900] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multiplexed quantitative proteomics enabled complex workflows to study the mechanisms by which small molecule drugs interact with the proteome such as thermal proteome profiling (TPP) or multiplexed proteome dynamics profiling (mPDP). TPP measures changes in protein thermal stability in response to drug treatment and thus informs on direct targets and downstream regulation events, while the mPDP approach enables the discovery of regulated protein synthesis and degradation events caused by small molecules and other perturbations. The isobaric mass tags available for multiplexed proteomics have thus far limited the efficiency and sensitivity by which such experiments could be performed. Here we evaluate a recent generation of 16-plex isobaric mass tags and demonstrate the sensitive and time efficient identification of Staurosporine targets in HepG2 cell extracts by recording full thermal denaturation/aggregation profiles of vehicle and compound treated samples in a single mass spectrometry experiment. In 2D-TPP experiments, isothermal titration over seven concentrations per temperature enabled comprehensive selectivity profiling of Staurosporine with EC50 values for kinase targets tightly matching to the kinobeads gold standard assay. Finally, we demonstrate time and condition-based multiplexing of dynamic SILAC labeling experiments to delineate proteome-wide effects of the molecular glue Indisulam on synthesis and degradation rates.
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Affiliation(s)
- Nico Zinn
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Carola Doce
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Toby Mathieson
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Christine Boecker
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Gavain Sweetman
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Christian Fufezan
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, a GSK Company, Meyerhofstr. 1, 69117 Heidelberg, Germany
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22
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Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM. A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nat Commun 2020; 11:5783. [PMID: 33188197 PMCID: PMC7666118 DOI: 10.1038/s41467-020-19529-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. However, current data analysis strategies use preset thresholds that can lead to suboptimal sensitivity/specificity tradeoffs and limited comparability across datasets. Here, we present a method based on statistical hypothesis testing on curves, which provides control of the false discovery rate. We apply it to several datasets probing epigenetic drugs and a metabolite. This leads us to detect off-target drug engagement, including the finding that the HDAC8 inhibitor PCI-34051 and its analog BRD-3811 bind to and inhibit leucine aminopeptidase 3. An implementation is available as an R package from Bioconductor (https://bioconductor.org/packages/TPP2D). We hope that our method will facilitate prioritizing targets from thermal profiling experiments. 2D-thermal proteome profiling (2D-TPP) is a powerful assay for probing interactions of proteins with small molecules in their native context. Here the authors provide a statistical method for false discovery rate controlled analysis for 2D-TPP applications.
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Affiliation(s)
- Nils Kurzawa
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, 69120, Germany
| | - Isabelle Becher
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Sindhuja Sridharan
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, Heidelberg, 69120, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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23
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Mueller WF, Jakob P, Sun H, Clauder-Münster S, Ghidelli-Disse S, Ordonez D, Boesche M, Bantscheff M, Collier P, Haase B, Benes V, Paulsen M, Sehr P, Lewis J, Drewes G, Steinmetz LM. Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines. G3 (Bethesda) 2020; 10:1585-1597. [PMID: 32265286 PMCID: PMC7202010 DOI: 10.1534/g3.119.401031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/01/2020] [Indexed: 12/12/2022]
Abstract
N-Glycanase 1 (NGLY1) deficiency is an ultra-rare, complex and devastating neuromuscular disease. Patients display multi-organ symptoms including developmental delays, movement disorders, seizures, constipation and lack of tear production. NGLY1 is a deglycosylating protein involved in the degradation of misfolded proteins retrotranslocated from the endoplasmic reticulum (ER). NGLY1-deficient cells have been reported to exhibit decreased deglycosylation activity and an increased sensitivity to proteasome inhibitors. We show that the loss of NGLY1 causes substantial changes in the RNA and protein landscape of K562 cells and results in downregulation of proteasomal subunits, consistent with its processing of the transcription factor NFE2L1. We employed the CMap database to predict compounds that can modulate NGLY1 activity. Utilizing our robust K562 screening system, we demonstrate that the compound NVP-BEZ235 (Dactosilib) promotes degradation of NGLY1-dependent substrates, concurrent with increased autophagic flux, suggesting that stimulating autophagy may assist in clearing aberrant substrates during NGLY1 deficiency.
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Affiliation(s)
- William F Mueller
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Petra Jakob
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Han Sun
- Stanford University, CA, 94305
| | - Sandra Clauder-Münster
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Diana Ordonez
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Markus Boesche
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Paul Collier
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Bettina Haase
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Vladimir Benes
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Malte Paulsen
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Peter Sehr
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Joe Lewis
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Lars M Steinmetz
- European Molecular Biology Labs, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
- Stanford University, CA, 94305
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24
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Gilan O, Rioja I, Knezevic K, Bell MJ, Yeung MM, Harker NR, Lam EYN, Chung CW, Bamborough P, Petretich M, Urh M, Atkinson SJ, Bassil AK, Roberts EJ, Vassiliadis D, Burr ML, Preston AGS, Wellaway C, Werner T, Gray JR, Michon AM, Gobbetti T, Kumar V, Soden PE, Haynes A, Vappiani J, Tough DF, Taylor S, Dawson SJ, Bantscheff M, Lindon M, Drewes G, Demont EH, Daniels DL, Grandi P, Prinjha RK, Dawson MA. Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammation. Science 2020; 368:387-394. [PMID: 32193360 PMCID: PMC7610820 DOI: 10.1126/science.aaz8455] [Citation(s) in RCA: 234] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
The two tandem bromodomains of the BET (bromodomain and extraterminal domain) proteins enable chromatin binding to facilitate transcription. Drugs that inhibit both bromodomains equally have shown efficacy in certain malignant and inflammatory conditions. To explore the individual functional contributions of the first (BD1) and second (BD2) bromodomains in biology and therapy, we developed selective BD1 and BD2 inhibitors. We found that steady-state gene expression primarily requires BD1, whereas the rapid increase of gene expression induced by inflammatory stimuli requires both BD1 and BD2 of all BET proteins. BD1 inhibitors phenocopied the effects of pan-BET inhibitors in cancer models, whereas BD2 inhibitors were predominantly effective in models of inflammatory and autoimmune disease. These insights into the differential requirement of BD1 and BD2 for the maintenance and induction of gene expression may guide future BET-targeted therapies.
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Affiliation(s)
- Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Inmaculada Rioja
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Matthew J Bell
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Miriam M Yeung
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Nicola R Harker
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Chun-Wa Chung
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Paul Bamborough
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Massimo Petretich
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | | | - Stephen J Atkinson
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Anna K Bassil
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Emma J Roberts
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Dane Vassiliadis
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Marian L Burr
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Alex G S Preston
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | | | - Thilo Werner
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - James R Gray
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Anne-Marie Michon
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - Thomas Gobbetti
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Vinod Kumar
- Computational Biology, GlaxoSmithKline, Collegeville, PA, USA
| | - Peter E Soden
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Andrea Haynes
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Johanna Vappiani
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - David F Tough
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Simon Taylor
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Marcus Bantscheff
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - Matthew Lindon
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Gerard Drewes
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - Emmanuel H Demont
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | | | - Paola Grandi
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany
| | - Rab K Prinjha
- Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK.
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
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25
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Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B. Meltome atlas-thermal proteome stability across the tree of life. Nat Methods 2020; 17:495-503. [PMID: 32284610 DOI: 10.1038/s41592-020-0801-4] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic proteins show a nonlinear relationship between the degree of disordered protein structure and thermal stability. The data indicate that evolutionary conservation of protein complexes is reflected by similar thermal stability of their proteins, and we show examples in which genomic alterations can affect thermal stability. Proteins of the respiratory chain were found to be very stable in many organisms, and human mitochondria showed close to normal respiration at 46 °C. We also noted cell-type-specific effects that can affect protein stability or the efficacy of drugs. This meltome atlas broadly defines the proteome amenable to thermal profiling in biology and drug discovery and can be explored online at http://meltomeatlas.proteomics.wzw.tum.de:5003/ and http://www.proteomicsdb.org.
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Affiliation(s)
- Anna Jarzab
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Nils Kurzawa
- Genome Biology Unit, EMBL, Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | | | - Matthias Moerch
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Niels Leijten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Yangyang Bian
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Eva Musiol
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | | | | | | | - Charlotte Daly
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Britta Spanier
- Chair of Nutritional Physiology, Technical University of Munich, Freising, Germany
| | - Angel Angelov
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Wolfgang Liebl
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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26
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Mares A, Miah AH, Smith IED, Rackham M, Thawani AR, Cryan J, Haile PA, Votta BJ, Beal AM, Capriotti C, Reilly MA, Fisher DT, Zinn N, Bantscheff M, MacDonald TT, Vossenkamper A, Dace P, Churcher I, Benowitz AB, Watt G, Denyer J, Scott-Stevens P, Harling JD. Extended pharmacodynamic responses observed upon PROTAC-mediated degradation of RIPK2. Commun Biol 2020; 3:140. [PMID: 32198438 PMCID: PMC7083851 DOI: 10.1038/s42003-020-0868-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Proteolysis-Targeting Chimeras (PROTACs) are heterobifunctional small-molecules that can promote the rapid and selective proteasome-mediated degradation of intracellular proteins through the recruitment of E3 ligase complexes to non-native protein substrates. The catalytic mechanism of action of PROTACs represents an exciting new modality in drug discovery that offers several potential advantages over traditional small-molecule inhibitors, including the potential to deliver pharmacodynamic (PD) efficacy which extends beyond the detectable pharmacokinetic (PK) presence of the PROTAC, driven by the synthesis rate of the protein. Herein we report the identification and development of PROTACs that selectively degrade Receptor-Interacting Serine/Threonine Protein Kinase 2 (RIPK2) and demonstrate in vivo degradation of endogenous RIPK2 in rats at low doses and extended PD that persists in the absence of detectable compound. This disconnect between PK and PD, when coupled with low nanomolar potency, offers the potential for low human doses and infrequent dosing regimens with PROTAC medicines. Mares et al. develop Proteolysis-Targeting Chimeras (PROTACs) that degrade its target RIPK2 in vivo at low doses for a prolonged period of time. This study suggests that PROTAC has a therapeutic potential that is superior to traditional RIPK2 small-molecule inhibitors.
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Affiliation(s)
- Alina Mares
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Afjal H Miah
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Ian E D Smith
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Mark Rackham
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Aditya R Thawani
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Jenni Cryan
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Pamela A Haile
- Innate Immunity Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - Bartholomew J Votta
- Innate Immunity Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - Allison M Beal
- Innate Immunity Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - Carol Capriotti
- Innate Immunity Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - Michael A Reilly
- Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - Don T Fisher
- Drug Design and Selection, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - Nico Zinn
- Cellzome, a GSK company, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome, a GSK company, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Thomas T MacDonald
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| | - Anna Vossenkamper
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| | - Phoebe Dace
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Ian Churcher
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Andrew B Benowitz
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Gillian Watt
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Jane Denyer
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Paul Scott-Stevens
- Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - John D Harling
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
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27
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Henley ZA, Amour A, Barton N, Bantscheff M, Bergamini G, Bertrand SM, Convery M, Down K, Dümpelfeld B, Edwards CD, Grandi P, Gore PM, Keeling S, Livia S, Mallett D, Maxwell A, Price M, Rau C, Reinhard FBM, Rowedder J, Rowland P, Taylor JA, Thomas DA, Hessel EM, Hamblin JN. Optimization of Orally Bioavailable PI3Kδ Inhibitors and Identification of Vps34 as a Key Selectivity Target. J Med Chem 2019; 63:638-655. [DOI: 10.1021/acs.jmedchem.9b01585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | - Birgit Dümpelfeld
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | | | - Mark Price
- In Vitro In Vivo Translation, GlaxoSmithKline R&D, David Jack Centre, Park Road, Ware SG12 0DP, U.K
| | - Christina Rau
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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28
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Childs D, Bach K, Franken H, Anders S, Kurzawa N, Bantscheff M, Savitski MM, Huber W. Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins. Mol Cell Proteomics 2019; 18:2506-2515. [PMID: 31582558 PMCID: PMC6885700 DOI: 10.1074/mcp.tir119.001481] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/01/2019] [Indexed: 12/19/2022] Open
Abstract
Detecting the targets of drugs and other molecules in intact cellular contexts is a major objective in drug discovery and in biology more broadly. Thermal proteome profiling (TPP) pursues this aim at proteome-wide scale by inferring target engagement from its effects on temperature-dependent protein denaturation. However, a key challenge of TPP is the statistical analysis of the measured melting curves with controlled false discovery rates at high proteome coverage and detection power. We present nonparametric analysis of response curves (NPARC), a statistical method for TPP based on functional data analysis and nonlinear regression. We evaluate NPARC on five independent TPP data sets and observe that it is able to detect subtle changes in any region of the melting curves, reliably detects the known targets, and outperforms a melting point-centric, single-parameter fitting approach in terms of specificity and sensitivity. NPARC can be combined with established analysis of variance (ANOVA) statistics and enables flexible, factorial experimental designs and replication levels. An open source software implementation of NPARC is provided.
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Affiliation(s)
- Dorothee Childs
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany; Cellzome GmbH, GlaxoSmithKline, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Karsten Bach
- Department of Pharmacology, University of Cambridge, CB2 1PD, Cambridge, UK; Cancer Research UK Cambridge Cancer Centre, CB2 0RE, Cambridge, UK
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Nils Kurzawa
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany.
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29
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Eberl HC, Werner T, Reinhard FB, Lehmann S, Thomson D, Chen P, Zhang C, Rau C, Muelbaier M, Drewes G, Drewry D, Bantscheff M. Chemical proteomics reveals target selectivity of clinical Jak inhibitors in human primary cells. Sci Rep 2019; 9:14159. [PMID: 31578349 PMCID: PMC6775116 DOI: 10.1038/s41598-019-50335-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Kinobeads are a set of promiscuous kinase inhibitors immobilized on sepharose beads for the comprehensive enrichment of endogenously expressed protein kinases from cell lines and tissues. These beads enable chemoproteomics profiling of kinase inhibitors of interest in dose-dependent competition studies in combination with quantitative mass spectrometry. We present improved bead matrices that capture more than 350 protein kinases and 15 lipid kinases from human cell lysates, respectively. A multiplexing strategy is suggested that enables determination of apparent dissociation constants in a single mass spectrometry experiment. Miniaturization of the procedure enabled determining the target selectivity of the clinical BCR-ABL inhibitor dasatinib in peripheral blood mononuclear cell (PBMC) lysates from individual donors. Profiling of a set of Jak kinase inhibitors revealed kinase off-targets from nearly all kinase families underpinning the need to profile kinase inhibitors against the kinome. Potently bound off-targets of clinical inhibitors suggest polypharmacology, e.g. through MRCK alpha and beta, which bind to decernotinib with nanomolar affinity.
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Affiliation(s)
- H Christian Eberl
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Thilo Werner
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Friedrich B Reinhard
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Stephanie Lehmann
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Douglas Thomson
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Peiling Chen
- GlaxoSmithKline, Upper Merion, 709 Swedeland Rd #1539, King of Prussia, PA, 19406, United States
| | - Cunyu Zhang
- GlaxoSmithKline, Upper Merion, 709 Swedeland Rd #1539, King of Prussia, PA, 19406, United States
| | - Christina Rau
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - David Drewry
- GlaxoSmithKline, Research Triangle Park, 5 Moore Drive, North Carolina, 27709, United States.,UNC Eshelman School of Pharmacy, Structural Genomics Consortium, University of North Carolina at Chapel Hill, 120 Mason Farm Rd, Chapel Hill, NC, 27599, United States
| | - Marcus Bantscheff
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117, Heidelberg, Germany.
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30
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Ramanjulu JM, Pesiridis GS, Yang J, Concha N, Singhaus R, Zhang SY, Tran JL, Moore P, Lehmann S, Eberl HC, Muelbaier M, Schneck JL, Clemens J, Adam M, Mehlmann J, Romano J, Morales A, Kang J, Leister L, Graybill TL, Charnley AK, Ye G, Nevins N, Behnia K, Wolf AI, Kasparcova V, Nurse K, Wang L, Puhl AC, Li Y, Klein M, Hopson CB, Guss J, Bantscheff M, Bergamini G, Reilly MA, Lian Y, Duffy KJ, Adams J, Foley KP, Gough PJ, Marquis RW, Smothers J, Hoos A, Bertin J. Author Correction: Design of amidobenzimidazole STING receptor agonists with systemic activity. Nature 2019; 570:E53. [PMID: 31142845 DOI: 10.1038/s41586-019-1265-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Change history: In this Letter, author Ana Puhl was inadvertently omitted; this error has been corrected online.An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Joshi M Ramanjulu
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA.
| | - G Scott Pesiridis
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Jingsong Yang
- Immuno-Oncology & Combinations DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Nestor Concha
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Robert Singhaus
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Shu-Yun Zhang
- Immuno-Oncology & Combinations DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Jean-Luc Tran
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Patrick Moore
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | | | | | | | - Jessica L Schneck
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Jim Clemens
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Michael Adam
- Immuno-Oncology & Combinations DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - John Mehlmann
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Joseph Romano
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Angel Morales
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - James Kang
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Lara Leister
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Todd L Graybill
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Adam K Charnley
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Guosen Ye
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Neysa Nevins
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Kamelia Behnia
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Amaya I Wolf
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Viera Kasparcova
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Kelvin Nurse
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Liping Wang
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Ana C Puhl
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Yue Li
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | - Michael Klein
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Jeffrey Guss
- Platform Technology & Science, GlaxoSmithKline, Collegeville, PA, USA
| | | | | | - Michael A Reilly
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Yiqian Lian
- Immuno-Oncology & Combinations DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Kevin J Duffy
- Immuno-Oncology & Combinations DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Jerry Adams
- Immuno-Oncology & Combinations DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Kevin P Foley
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Peter J Gough
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Robert W Marquis
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - James Smothers
- Immuno-Oncology & Combinations DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - Axel Hoos
- Immuno-Oncology & Combinations DPU, GlaxoSmithKline, Collegeville, PA, USA
| | - John Bertin
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, PA, USA
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31
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Thomson DW, Poeckel D, Zinn N, Rau C, Strohmer K, Wagner AJ, Graves AP, Perrin J, Bantscheff M, Duempelfeld B, Kasparcova V, Ramanjulu JM, Pesiridis GS, Muelbaier M, Bergamini G. Discovery of GSK8612, a Highly Selective and Potent TBK1 Inhibitor. ACS Med Chem Lett 2019; 10:780-785. [PMID: 31097999 DOI: 10.1021/acsmedchemlett.9b00027] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/11/2019] [Indexed: 02/06/2023] Open
Abstract
The serine/threonine protein kinase TBK1 (Tank-binding Kinase-1) is a noncanonical member of the IkB kinase (IKK) family. This kinase regulates signaling pathways in innate immunity, oncogenesis, energy homeostasis, autophagy, and neuroinflammation. Herein, we report the discovery and characterization of a novel potent and highly selective TBK1 inhibitor, GSK8612. In cellular assays, this small molecule inhibited toll-like receptor (TLR)3-induced interferon regulatory factor (IRF)3 phosphorylation in Ramos cells and type I interferon (IFN) secretion in primary human mononuclear cells. In THP1 cells, GSK8612 was able to inhibit secretion of interferon beta (IFNβ) in response to dsDNA and cGAMP, the natural ligand for STING. GSK8612 is a TBK1 small molecule inhibitor displaying an excellent selectivity profile and therefore represents an ideal probe to further dissect the biology of TBK1 in models of immunity, neuroinflammation, obesity, or cancer.
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Affiliation(s)
- Douglas W. Thomson
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Daniel Poeckel
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nico Zinn
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christina Rau
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Katrin Strohmer
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Anne J. Wagner
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alan P. Graves
- Data and Computational Sciences, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jessica Perrin
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Birgit Duempelfeld
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Viera Kasparcova
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Joshi M. Ramanjulu
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - G. Scott Pesiridis
- Pattern Recognition Receptor DPU, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Marcel Muelbaier
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
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32
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Grandi P, Bantscheff M. Advanced proteomics approaches to unravel protein homeostasis. Drug Discov Today Technol 2019; 31:99-108. [PMID: 31200865 DOI: 10.1016/j.ddtec.2019.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 05/22/2023]
Abstract
Quantitative proteomics methods are instrumental in measuring the interplay between protein synthesis and protein degradation in cells and tissues in different conditions and substantially contribute to the understanding of control mechanisms for protein homeostasis. Proteomics and chemoproteomics approaches enable the characterization of small molecule modifiers of protein degradation for therapeutic applications. Here, we review recent developments and applications of mass spectrometry-based (chemo-)proteomics methods for the study of cellular homeostasis.
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Affiliation(s)
- Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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33
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Tinworth CP, Lithgow H, Dittus L, Bassi ZI, Hughes SE, Muelbaier M, Dai H, Smith IED, Kerr WJ, Burley GA, Bantscheff M, Harling JD. PROTAC-Mediated Degradation of Bruton's Tyrosine Kinase Is Inhibited by Covalent Binding. ACS Chem Biol 2019; 14:342-347. [PMID: 30807093 DOI: 10.1021/acschembio.8b01094] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The impact of covalent binding on PROTAC-mediated degradation of BTK was investigated through the preparation of both covalent binding and reversible binding PROTACs derived from the covalent BTK inhibitor ibrutinib. It was determined that a covalent binding PROTAC inhibited BTK degradation despite evidence of target engagement, while BTK degradation was observed with a reversible binding PROTAC. These observations were consistently found when PROTACs that were able to recruit either IAP or cereblon E3 ligases were employed. Proteomics analysis determined that the use of a covalently bound PROTAC did not result in the degradation of covalently bound targets, while degradation was observed for some reversibly bound targets. This observation highlights the importance of catalysis for successful PROTAC-mediated degradation and highlights a potential caveat for the use of covalent target binders in PROTAC design.
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Affiliation(s)
- Christopher P Tinworth
- GSK Medicines Research Centre , Gunnels Wood Road , Stevenage SG1 2NY , U.K
- Department of Pure and Applied Chemistry, WestCHEM , University of Strathclyde , 295 Cathedral Street , Glasgow G1 1XL , U.K
| | - Hannah Lithgow
- GSK Medicines Research Centre , Gunnels Wood Road , Stevenage SG1 2NY , U.K
- Department of Pure and Applied Chemistry, WestCHEM , University of Strathclyde , 295 Cathedral Street , Glasgow G1 1XL , U.K
| | - Lars Dittus
- Cellzome GmbH, GlaxoSmithKline , Meyerhofstrasse 1 , D-69117 Heidelberg , Germany
| | - Zuni I Bassi
- GSK Medicines Research Centre , Gunnels Wood Road , Stevenage SG1 2NY , U.K
| | - Sophie E Hughes
- GSK Medicines Research Centre , Gunnels Wood Road , Stevenage SG1 2NY , U.K
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline , Meyerhofstrasse 1 , D-69117 Heidelberg , Germany
| | - Han Dai
- GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Ian E D Smith
- GSK Medicines Research Centre , Gunnels Wood Road , Stevenage SG1 2NY , U.K
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM , University of Strathclyde , 295 Cathedral Street , Glasgow G1 1XL , U.K
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, WestCHEM , University of Strathclyde , 295 Cathedral Street , Glasgow G1 1XL , U.K
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline , Meyerhofstrasse 1 , D-69117 Heidelberg , Germany
| | - John D Harling
- GSK Medicines Research Centre , Gunnels Wood Road , Stevenage SG1 2NY , U.K
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34
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Sridharan S, Kurzawa N, Werner T, Günthner I, Helm D, Huber W, Bantscheff M, Savitski MM. Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP. Nat Commun 2019; 10:1155. [PMID: 30858367 PMCID: PMC6411743 DOI: 10.1038/s41467-019-09107-y] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/22/2019] [Indexed: 02/03/2023] Open
Abstract
Adenosine triphosphate (ATP) plays fundamental roles in cellular biochemistry and was recently discovered to function as a biological hydrotrope. Here, we use mass spectrometry to interrogate ATP-mediated regulation of protein thermal stability and protein solubility on a proteome-wide scale. Thermal proteome profiling reveals high affinity interactions of ATP as a substrate and as an allosteric modulator that has widespread influence on protein complexes and their stability. Further, we develop a strategy for proteome-wide solubility profiling, and discover ATP-dependent solubilization of at least 25% of the insoluble proteome. ATP increases the solubility of positively charged, intrinsically disordered proteins, and their susceptibility for solubilization varies depending on their localization to different membrane-less organelles. Moreover, a few proteins, exhibit an ATP-dependent decrease in solubility, likely reflecting polymer formation. Our data provides a proteome-wide, quantitative insight into how ATP influences protein structure and solubility across the spectrum of physiologically relevant concentrations. ATP can function as a biological hydrotrope, but its global effects on protein solubility have not yet been characterized. Here, the authors quantify the effect of ATP on the thermal stability and solubility of the cellular proteome, providing insights into protein solubility regulation by ATP.
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Affiliation(s)
- Sindhuja Sridharan
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Candidate for joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, 69120, Heidelberg, Germany
| | - Thilo Werner
- Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Ina Günthner
- Cellzome, A GSK company, 69117, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | | | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
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35
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Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M. Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis. Cell 2018; 173:260-274.e25. [PMID: 29551266 PMCID: PMC5871718 DOI: 10.1016/j.cell.2018.02.030] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 12/01/2017] [Accepted: 02/09/2018] [Indexed: 02/07/2023]
Abstract
Protein degradation plays important roles in biological processes and is tightly regulated. Further, targeted proteolysis is an emerging research tool and therapeutic strategy. However, proteome-wide technologies to investigate the causes and consequences of protein degradation in biological systems are lacking. We developed “multiplexed proteome dynamics profiling” (mPDP), a mass-spectrometry-based approach combining dynamic-SILAC labeling with isobaric mass tagging for multiplexed analysis of protein degradation and synthesis. In three proof-of-concept studies, we uncover different responses induced by the bromodomain inhibitor JQ1 versus a JQ1 proteolysis targeting chimera; we elucidate distinct modes of action of estrogen receptor modulators; and we comprehensively classify HSP90 clients based on their requirement for HSP90 constitutively or during synthesis, demonstrating that constitutive HSP90 clients have lower thermal stability than non-clients, have higher affinity for the chaperone, vary between cell types, and change upon external stimuli. These findings highlight the potential of mPDP to identify dynamically controlled degradation mechanisms in cellular systems. Multiplexed proteome dynamics profiling, mPDP, measures changes in proteostasis JQ1-PROTAC degrades a key mRNA export factor and blocks protein synthesis Raloxifene induces TMEM97 degradation dysregulating cholesterol homeostasis Characterization of proteins dependent on HSP90 constitutively or during synthesis
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Affiliation(s)
- Mikhail M Savitski
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Nico Zinn
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Daniel Poeckel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Gade
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anne J Wagner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Katrin Strohmer
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephanie Melchert
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Massimo Petretich
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anna Rutkowska
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Johanna Vappiani
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Michael Steidel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gavain M Sweetman
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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36
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Paquet T, Le Manach C, Cabrera DG, Younis Y, Henrich PP, Abraham TS, Lee MCS, Basak R, Ghidelli-Disse S, Lafuente-Monasterio MJ, Bantscheff M, Ruecker A, Blagborough AM, Zakutansky SE, Zeeman AM, White KL, Shackleford DM, Mannila J, Morizzi J, Scheurer C, Angulo-Barturen I, Martínez MS, Ferrer S, Sanz LM, Gamo FJ, Reader J, Botha M, Dechering KJ, Sauerwein RW, Tungtaeng A, Vanachayangkul P, Lim CS, Burrows J, Witty MJ, Marsh KC, Bodenreider C, Rochford R, Solapure SM, Jiménez-Díaz MB, Wittlin S, Charman SA, Donini C, Campo B, Birkholtz LM, Hanson KK, Drewes G, Kocken CHM, Delves MJ, Leroy D, Fidock DA, Waterson D, Street LJ, Chibale K. Antimalarial efficacy of MMV390048, an inhibitor of Plasmodium phosphatidylinositol 4-kinase. Sci Transl Med 2018; 9:9/387/eaad9735. [PMID: 28446690 DOI: 10.1126/scitranslmed.aad9735] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 11/21/2016] [Indexed: 12/13/2022]
Abstract
As part of the global effort toward malaria eradication, phenotypic whole-cell screening revealed the 2-aminopyridine class of small molecules as a good starting point to develop new antimalarial drugs. Stemming from this series, we found that the derivative, MMV390048, lacked cross-resistance with current drugs used to treat malaria. This compound was efficacious against all Plasmodium life cycle stages, apart from late hypnozoites in the liver. Efficacy was shown in the humanized Plasmodium falciparum mouse model, and modest reductions in mouse-to-mouse transmission were achieved in the Plasmodium berghei mouse model. Experiments in monkeys revealed the ability of MMV390048 to be used for full chemoprotection. Although MMV390048 was not able to eliminate liver hypnozoites, it delayed relapse in a Plasmodium cynomolgi monkey model. Both genomic and chemoproteomic studies identified a kinase of the Plasmodium parasite, phosphatidylinositol 4-kinase, as the molecular target of MMV390048. The ability of MMV390048 to block all life cycle stages of the malaria parasite suggests that this compound should be further developed and may contribute to malaria control and eradication as part of a single-dose combination treatment.
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Affiliation(s)
- Tanya Paquet
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Claire Le Manach
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | | | - Yassir Younis
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Philipp P Henrich
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Tara S Abraham
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, 1020 Locust Street, Suite 368, Philadelphia, PA 19107, USA
| | - Marcus C S Lee
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Rajshekhar Basak
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - María José Lafuente-Monasterio
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Marcus Bantscheff
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Andrea Ruecker
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | | | | | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, 2280 GH Rijswijk, Netherlands
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Janne Mannila
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia.,Admescope Ltd., Typpitie 1, 90620 Oulu, Finland
| | - Julia Morizzi
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Christian Scheurer
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Iñigo Angulo-Barturen
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - María Santos Martínez
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Santiago Ferrer
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Laura María Sanz
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Francisco Javier Gamo
- Malaria Disease Performance Unit, Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Janette Reader
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Mariette Botha
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Koen J Dechering
- TropIQ Health Sciences, Transistorweg 5, 6534 AT Nijmegen, Netherlands
| | - Robert W Sauerwein
- TropIQ Health Sciences, Transistorweg 5, 6534 AT Nijmegen, Netherlands.,Radboud University Medical Center, Department of Medical Microbiology, 6500 HB Nijmegen, Netherlands
| | - Anchalee Tungtaeng
- Department of Veterinary Medicine, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Pattaraporn Vanachayangkul
- Department of Immunology and Medicine, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Chek Shik Lim
- Novartis Institute for Tropical Diseases Pte. Ltd., 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore
| | - Jeremy Burrows
- Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Michael J Witty
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Kennan C Marsh
- AbbVie, 1 North Waukegan Road, North Chicago, IL 60064-6104, USA
| | - Christophe Bodenreider
- Novartis Institute for Tropical Diseases Pte. Ltd., 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore
| | - Rosemary Rochford
- Departments of Immunology and Microbiology and Environmental and Occupational Health, University of Colorado Denver, Aurora, CO 80045, USA
| | - Suresh M Solapure
- Nagarjuna Gardens, 60 Feet Road, Sahakaranagar, Bangalore 560092, India
| | - María Belén Jiménez-Díaz
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, 1020 Locust Street, Suite 368, Philadelphia, PA 19107, USA
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4003 Basel, Switzerland
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Cristina Donini
- Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Pretoria, South Africa
| | - Kirsten K Hanson
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Clemens H M Kocken
- Department of Parasitology, Biomedical Primate Research Centre, 2280 GH Rijswijk, Netherlands
| | - Michael J Delves
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Didier Leroy
- Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.,Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - David Waterson
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Medicines for Malaria Venture, International Center Cointrin, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Leslie J Street
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa. .,South African Medical Research Council Drug Discovery and Development Research Unit, and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
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37
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Dalton SE, Dittus L, Thomas DA, Convery MA, Nunes J, Bush JT, Evans JP, Werner T, Bantscheff M, Murphy JA, Campos S. Selectively Targeting the Kinome-Conserved Lysine of PI3Kδ as a General Approach to Covalent Kinase Inhibition. J Am Chem Soc 2018; 140:932-939. [DOI: 10.1021/jacs.7b08979] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Samuel E. Dalton
- Department
of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Lars Dittus
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Daniel A. Thomas
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Máire A. Convery
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Joao Nunes
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Jacob T. Bush
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - John P. Evans
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Thilo Werner
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - John A. Murphy
- Department
of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Sebastien Campos
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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38
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Dietrich S, Oleś M, Lu J, Sellner L, Anders S, Velten B, Wu B, Hüllein J, da Silva Liberio M, Walther T, Wagner L, Rabe S, Ghidelli-Disse S, Bantscheff M, Oleś AK, Słabicki M, Mock A, Oakes CC, Wang S, Oppermann S, Lukas M, Kim V, Sill M, Benner A, Jauch A, Sutton LA, Young E, Rosenquist R, Liu X, Jethwa A, Lee KS, Lewis J, Putzker K, Lutz C, Rossi D, Mokhir A, Oellerich T, Zirlik K, Herling M, Nguyen-Khac F, Plass C, Andersson E, Mustjoki S, von Kalle C, Ho AD, Hensel M, Dürig J, Ringshausen I, Zapatka M, Huber W, Zenz T. Drug-perturbation-based stratification of blood cancer. J Clin Invest 2018; 128:427-445. [PMID: 29227286 PMCID: PMC5749541 DOI: 10.1172/jci93801] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/31/2017] [Indexed: 12/11/2022] Open
Abstract
As new generations of targeted therapies emerge and tumor genome sequencing discovers increasingly comprehensive mutation repertoires, the functional relationships of mutations to tumor phenotypes remain largely unknown. Here, we measured ex vivo sensitivity of 246 blood cancers to 63 drugs alongside genome, transcriptome, and DNA methylome analysis to understand determinants of drug response. We assembled a primary blood cancer cell encyclopedia data set that revealed disease-specific sensitivities for each cancer. Within chronic lymphocytic leukemia (CLL), responses to 62% of drugs were associated with 2 or more mutations, and linked the B cell receptor (BCR) pathway to trisomy 12, an important driver of CLL. Based on drug responses, the disease could be organized into phenotypic subgroups characterized by exploitable dependencies on BCR, mTOR, or MEK signaling and associated with mutations, gene expression, and DNA methylation. Fourteen percent of CLLs were driven by mTOR signaling in a non-BCR-dependent manner. Multivariate modeling revealed immunoglobulin heavy chain variable gene (IGHV) mutation status and trisomy 12 as the most important modulators of response to kinase inhibitors in CLL. Ex vivo drug responses were associated with outcome. This study overcomes the perception that most mutations do not influence drug response of cancer, and points to an updated approach to understanding tumor biology, with implications for biomarker discovery and cancer care.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 12/metabolism
- Databases, Factual
- Female
- Hematologic Neoplasms/classification
- Hematologic Neoplasms/drug therapy
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/pathology
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/classification
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Models, Biological
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Signal Transduction
- Trisomy/genetics
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Affiliation(s)
- Sascha Dietrich
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Małgorzata Oleś
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Junyan Lu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Leopold Sellner
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Simon Anders
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Britta Velten
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Bian Wu
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Jennifer Hüllein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Michelle da Silva Liberio
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Tatjana Walther
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Lena Wagner
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Sophie Rabe
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | | | | | - Andrzej K. Oleś
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mikołaj Słabicki
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Andreas Mock
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Christopher C. Oakes
- Division of Hematology, Departments of Internal Medicine and Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Centre, Heidelberg, Germany
| | - Shihui Wang
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Sina Oppermann
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Marina Lukas
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Vladislav Kim
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Sill
- Division of Biostatistics, German Cancer Research Centre, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Centre, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Lesley Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Emma Young
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Xiyang Liu
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Alexander Jethwa
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Kwang Seok Lee
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, Heidelberg, Germany
| | - Kerstin Putzker
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, Heidelberg, Germany
| | - Christoph Lutz
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | - Davide Rossi
- Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy; Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Andriy Mokhir
- Friedrich-Alexander-University of Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Organic Chemistry II, Erlangen, Germany
| | - Thomas Oellerich
- Hematology/Oncology, Department of Medicine, Johann Wolfgang Goethe University, Frankfurt, Germany; Department of Haematology, Cambridge Institute of Medical Research, University of Cambridge, Cambridge, United Kingdom
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Katja Zirlik
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Hematology/Oncology, University Hospital Freiburg, Freiburg, Germany and Tumorzentrum ZeTuP Chur, Chur, Schweiz
| | - Marco Herling
- Department of Internal Medicine I, University Hospital Cologne, Cologne, Germany
| | - Florence Nguyen-Khac
- INSERM U1138, Université Pierre et Marie Curie-Paris and Service d’Hématologie Biologique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Centre, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Emma Andersson
- Hematology Research Unit Helsinki, University of Helsinki, Helsinki, Finland and Department of Hematology, Comprehensive Cancer Centre, Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki, Helsinki, Finland and Department of Hematology, Comprehensive Cancer Centre, Helsinki University Hospital, Helsinki, Finland
| | - Christof von Kalle
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Heidelberg Centre for Personalized Oncology, DKFZ-HIPO, DKFZ, Heidelberg, Germany
| | - Anthony D. Ho
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Jan Dürig
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Hematology, University Hospital Essen, Essen, Germany
| | - Ingo Ringshausen
- Department of Hematology, University of Cambridge, Cambridge, United Kingdom
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Centre, Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Thorsten Zenz
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, and Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Hematology, University of Zürich, Zürich, Switzerland
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39
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Dittus L, Werner T, Muelbaier M, Bantscheff M. Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors. ACS Chem Biol 2017; 12:2515-2521. [PMID: 28876896 DOI: 10.1021/acschembio.7b00617] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemoproteomics profiling of kinase inhibitors with kinobeads enables the assessment of inhibitor potency and selectivity for endogenously expressed protein kinases in cell lines and tissues. Using a small panel of targeted covalent inhibitors, we demonstrate the importance of measuring covalent target binding in live cells. We present a differential kinobeads profiling strategy for covalent kinase inhibitors where a compound is added either to live cells or to a cell extract that enables the comprehensive assessment of inhibitor selectivity for covalent and noncovalent targets. We found that Acalabrutinib, CC-292, and Ibrutinib potently and covalently bind TEC family kinases, but only Ibrutinib also potently binds to BLK. ZAK was identified as a submicromolar affinity Ibrutinib off-target due to covalent modification of Cys22. In contrast to Ibrutinib, 5Z-7-Oxozeaenol reacted with Cys150 next to the DFG loop, demonstrating an alternative route to covalent inactivation of this kinase, e.g., to inhibit canonical TGF-β dependent processes.
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Affiliation(s)
- Lars Dittus
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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40
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Affiliation(s)
- Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Hannes Hahne
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Mikhail Savitski
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Harald Marx
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Simone Lemeer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
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41
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Thomson DW, Wagner AJ, Bantscheff M, Benson RE, Dittus L, Duempelfeld B, Drewes G, Krause J, Moore JT, Mueller K, Poeckel D, Rau C, Salzer E, Shewchuk L, Hopf C, Emery JG, Muelbaier M. Discovery of a Highly Selective Tankyrase Inhibitor Displaying Growth Inhibition Effects against a Diverse Range of Tumor Derived Cell Lines. J Med Chem 2017; 60:5455-5471. [DOI: 10.1021/acs.jmedchem.7b00137] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Douglas W. Thomson
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Anne J. Wagner
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - R. Edward Benson
- GlaxoSmithKline, Research Triangle Park, 5 Moore Drive, North Carolina 27709, United States
| | - Lars Dittus
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Birgit Duempelfeld
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jana Krause
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - John T. Moore
- GlaxoSmithKline, Research Triangle Park, 5 Moore Drive, North Carolina 27709, United States
| | - Katrin Mueller
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Daniel Poeckel
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christina Rau
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Elsa Salzer
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lisa Shewchuk
- Protein, Cellular & Structural Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Upper Providence, Pennsylvania 19426, United States
| | - Carsten Hopf
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - John G. Emery
- Virtual
Proof of Concept DPU, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Marcel Muelbaier
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
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42
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Qin P, Arabacilar P, Bernard RE, Bao W, Olzinski AR, Guo Y, Lal H, Eisennagel SH, Platchek MC, Xie W, Del Rosario J, Nayal M, Lu Q, Roethke T, Schnackenberg CG, Wright F, Quaile MP, Halsey WS, Hughes AM, Sathe GM, Livi GP, Kirkpatrick RB, Qu XA, Rajpal DK, Faelth Savitski M, Bantscheff M, Joberty G, Bergamini G, Force TL, Gatto GJ, Hu E, Willette RN. Activation of the Amino Acid Response Pathway Blunts the Effects of Cardiac Stress. J Am Heart Assoc 2017; 6:JAHA.116.004453. [PMID: 28487390 PMCID: PMC5524058 DOI: 10.1161/jaha.116.004453] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND The amino acid response (AAR) is an evolutionarily conserved protective mechanism activated by amino acid deficiency through a key kinase, general control nonderepressible 2. In addition to mobilizing amino acids, the AAR broadly affects gene and protein expression in a variety of pathways and elicits antifibrotic, autophagic, and anti-inflammatory activities. However, little is known regarding its role in cardiac stress. Our aim was to investigate the effects of halofuginone, a prolyl-tRNA synthetase inhibitor, on the AAR pathway in cardiac fibroblasts, cardiomyocytes, and in mouse models of cardiac stress and failure. METHODS AND RESULTS Consistent with its ability to inhibit prolyl-tRNA synthetase, halofuginone elicited a general control nonderepressible 2-dependent activation of the AAR pathway in cardiac fibroblasts as evidenced by activation of known AAR target genes, broad regulation of the transcriptome and proteome, and reversal by l-proline supplementation. Halofuginone was examined in 3 mouse models of cardiac stress: angiotensin II/phenylephrine, transverse aortic constriction, and acute ischemia reperfusion injury. It activated the AAR pathway in the heart, improved survival, pulmonary congestion, left ventricle remodeling/fibrosis, and left ventricular function, and rescued ischemic myocardium. In human cardiac fibroblasts, halofuginone profoundly reduced collagen deposition in a general control nonderepressible 2-dependent manner and suppressed the extracellular matrix proteome. In human induced pluripotent stem cell-derived cardiomyocytes, halofuginone blocked gene expression associated with endothelin-1-mediated activation of pathologic hypertrophy and restored autophagy in a general control nonderepressible 2/eIF2α-dependent manner. CONCLUSIONS Halofuginone activated the AAR pathway in the heart and attenuated the structural and functional effects of cardiac stress.
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Affiliation(s)
- Pu Qin
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Pelin Arabacilar
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Roberta E Bernard
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Weike Bao
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Alan R Olzinski
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Yuanjun Guo
- Basic & Translational Research, School of Medicine, Vanderbilt University, Nashville, TN
| | - Hind Lal
- Basic & Translational Research, School of Medicine, Vanderbilt University, Nashville, TN
| | - Stephen H Eisennagel
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Michael C Platchek
- Target and Pathway Validation, Target Sciences, GlaxoSmithKline, King of Prussia, PA
| | - Wensheng Xie
- Target and Pathway Validation, Target Sciences, GlaxoSmithKline, King of Prussia, PA
| | - Julius Del Rosario
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Mohamad Nayal
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Quinn Lu
- Target and Pathway Validation, Target Sciences, GlaxoSmithKline, King of Prussia, PA
| | - Theresa Roethke
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Christine G Schnackenberg
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Fe Wright
- Preclinical and Translational Imaging, Platform Technology and Science, GlaxoSmithKline, King of Prussia, PA
| | - Michael P Quaile
- Preclinical and Translational Imaging, Platform Technology and Science, GlaxoSmithKline, King of Prussia, PA
| | - Wendy S Halsey
- Target and Pathway Validation, Target Sciences, GlaxoSmithKline, King of Prussia, PA
| | - Ashley M Hughes
- Target and Pathway Validation, Target Sciences, GlaxoSmithKline, King of Prussia, PA
| | - Ganesh M Sathe
- Target and Pathway Validation, Target Sciences, GlaxoSmithKline, King of Prussia, PA
| | - George P Livi
- Target and Pathway Validation, Target Sciences, GlaxoSmithKline, King of Prussia, PA
| | | | - Xiaoyan A Qu
- Computational Biology, Projects Clinical Platforms and Sciences, GlaxoSmithKline, King of Prussia, PA
| | - Deepak K Rajpal
- Computational Biology, Projects Clinical Platforms and Sciences, GlaxoSmithKline, King of Prussia, PA
| | | | | | - Gerard Joberty
- Cellzome GmbH, A GSK Company, GlaxoSmithKline, King of Prussia, PA
| | | | - Thomas L Force
- Basic & Translational Research, School of Medicine, Vanderbilt University, Nashville, TN
| | - Gregory J Gatto
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Erding Hu
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
| | - Robert N Willette
- Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapy Area GlaxoSmithKline, King of Prussia, PA
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Kalxdorf M, Gade S, Eberl HC, Bantscheff M. Monitoring Cell-surface N-Glycoproteome Dynamics by Quantitative Proteomics Reveals Mechanistic Insights into Macrophage Differentiation. Mol Cell Proteomics 2017; 16:770-785. [PMID: 28336715 DOI: 10.1074/mcp.m116.063859] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/17/2017] [Indexed: 11/06/2022] Open
Abstract
The plasma membrane proteome plays a crucial role in inter- and intracellular signaling, cell survival, and cell identity. As such, it is a prominent target for pharmacological intervention. The relatively low abundance of this subproteome in conjunction with challenging extractability and solubility still hampers its comprehensive analysis. Here, we combined a chemical glycoprotein-tagging strategy with mass spectrometry to enable comprehensive analysis of the cell-surface glycoproteome. To benchmark this workflow and to provide guidance for cell line selection for functional experiments, we generated an inventory of the N-linked cell-surface glycoproteomes of 15 standard laboratory human cell lines and three primary lymphocytic cell types. On average, about 900 plasma membrane and secreted proteins were identified per experiment, including more than 300 transporters and ion channels. Primary cells displayed distinct expression of surface markers and transporters underpinning the importance of carefully validating model cell lines selected for the study of cell surface-mediated processes. To monitor dynamic changes of the cell-surface proteome in a highly multiplexed experiment, we employed an isobaric mass tag-based chemical labeling strategy. This enabled the time-resolved analysis of plasma membrane protein presentation during differentiation of the monocytic suspension cell line THP-1 into macrophage-like adherent cells. Time-dependent changes observed in membrane protein presentation reflect functional remodeling during the phenotypic transition in three distinct phases: rapid surface presentation and secretion of proteins from intracellular pools concurrent with rapid internalization of no longer needed proteins and finally delayed presentation of newly synthesized macrophage markers. Perturbation of this process using marketed receptor tyrosine kinase inhibitors revealed dasatinib to severely compromise macrophage differentiation due to an off-target activity. This finding suggests that dynamic processes can be highly vulnerable to drug treatment and should be monitored more rigorously to identify adverse drug effects.
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Affiliation(s)
- Mathias Kalxdorf
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Gade
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - H Christian Eberl
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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44
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Flanagan JJ, Rossi AK, Anderoli M, Willard RR, Gordon D, Harling J, Churcher I, Smith I, Zinn N, Bantscheff M, Crews CM, Crew A, Coleman KG, Winkler JD, Qian Y. Abstract S4-03: Targeted and selective degradation of estrogen receptor (ER) alpha by PROTACs. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-s4-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
ERα-positive breast cancers comprise approximately 80% of all newly diagnosed cases. Current treatment approaches targeting ER signaling include antagonizing and/or downregulating ER or reducing estrogen levels. Faslodex (fulvestrant) is the only clinically-approved agent that is both a potent ER antagonist and downregulator but has limitations given its pharmacokinetics and route of administration. Over the past several years, targeted ER therapies have focused on developing selective estrogen receptor downregulators (SERDs, i.e, GDC-0810, GDC-0927, AZD9496, RAD1901). The mechanisms involved in ER downregulation by SERD binding are not completely understood, but evidence suggests that conformational changes in the receptor upon ligand binding combined with specific co-regulator interactions destabilize the receptor making it a target for passive proteasomal degradation. We hypothesized that the complex ER pharmacology required for SERD-based passive degradation might be different across various ER-positive cell lines and that targeted degradation of the receptor by actively recruiting the ubiquitin-proteasome machinery would provide a better approach for reducing ER levels. To test this hypothesis, we developed potent molecules directed against ER using our pioneering technology—proteolysis targeting chimeras (PROTACs). PROTACs are heterobifunctional molecules that actively recruit specific E3 ligases resulting in ubiquitylation and degradation of target proteins. When testing for ER degradation using several SERDs and ER PROTACs, we discovered that both fulvestrant and ER PROTACs provided robust degradation in all ER-positive lines (<1 nM 50% degradation; >90% reduction) whereas other SERDs did not degrade or only modestly degraded the receptor. Importantly, MCF-7 cells were uniquely sensitive to SERD-based degradation of ER compared to other cell lines. Subcutaneous administration of fulvestrant (1mpk) or ER PROTACs (10 mpk) reduced uterine ER alpha levels in immature rats (>65% reduction). PROTAC-mediated degradation of ER was also achieved in breast cancer xenografts. To further validate the PROTAC mechanism, incubation of ER-positive cells with ER PROTACs resulted in increased levels of poly-ubiquitylated ERα when compared to SERDs. Lastly, to demonstrate the specificity of PROTAC-mediated ERα degradation, we utilized a cellular expression proteomics-based approach to examine over 7,000 proteins. In this experiment, only ERα and several known proteins whose genes are regulated by ERα, were significantly reduced by PROTACs. It remains to be seen how the current class of investigational downregulators will perform in the clinic. More importantly, a better understanding of the therapeutic potential and benefit of degrading the receptor instead of inhibiting the receptor needs to be explored. To that end, we continue to develop and characterize novel ER PROTACs with the anticipation that targeted ERα degradation will provide a greater clinical benefit than receptor antagonism.
Citation Format: Flanagan JJ, Rossi AK, Anderoli M, Willard RR, Gordon D, Harling J, Churcher I, Smith I, Zinn N, Bantscheff M, Crews CM, Crew A, Coleman KG, Winkler JD, Qian Y. Targeted and selective degradation of estrogen receptor (ER) alpha by PROTACs [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S4-03.
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Affiliation(s)
- JJ Flanagan
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - AK Rossi
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - M Anderoli
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - RR Willard
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - D Gordon
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - J Harling
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - I Churcher
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - I Smith
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - N Zinn
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - M Bantscheff
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - CM Crews
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - A Crew
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - KG Coleman
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - JD Winkler
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
| | - Y Qian
- Arvinas LLC, New Haven, CT; GSK Medicines Research Centre, Stevenage, United Kingdom; Yale University, New Haven, CT
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Frost J, Galdeano C, Soares P, Gadd MS, Grzes KM, Ellis L, Epemolu O, Shimamura S, Bantscheff M, Grandi P, Read KD, Cantrell DA, Rocha S, Ciulli A. Potent and selective chemical probe of hypoxic signalling downstream of HIF-α hydroxylation via VHL inhibition. Nat Commun 2016; 7:13312. [PMID: 27811928 PMCID: PMC5097156 DOI: 10.1038/ncomms13312] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
Chemical strategies to using small molecules to stimulate hypoxia inducible factors (HIFs) activity and trigger a hypoxic response under normoxic conditions, such as iron chelators and inhibitors of prolyl hydroxylase domain (PHD) enzymes, have broad-spectrum activities and off-target effects. Here we disclose VH298, a potent VHL inhibitor that stabilizes HIF-α and elicits a hypoxic response via a different mechanism, that is the blockade of the VHL:HIF-α protein–protein interaction downstream of HIF-α hydroxylation by PHD enzymes. We show that VH298 engages with high affinity and specificity with VHL as its only major cellular target, leading to selective on-target accumulation of hydroxylated HIF-α in a concentration- and time-dependent fashion in different cell lines, with subsequent upregulation of HIF-target genes at both mRNA and protein levels. VH298 represents a high-quality chemical probe of the HIF signalling cascade and an attractive starting point to the development of potential new therapeutics targeting hypoxia signalling. Small molecule probes used to trigger hypoxic response by activating hypoxia inducible factors (HIFs) often lack specificity. Here the authors report a potent small molecule inhibitor that induces hypoxic response by blocking VHL:HIF interactions, providing a selective route to probe hypoxic signalling.
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Affiliation(s)
- Julianty Frost
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Carles Galdeano
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Pedro Soares
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Morgan S Gadd
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Katarzyna M Grzes
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Lucy Ellis
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Ola Epemolu
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | | | | | - Paola Grandi
- Cellzome GmbH, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kevin D Read
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Doreen A Cantrell
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Sonia Rocha
- Center for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
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46
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Becher I, Werner T, Doce C, Zaal EA, Tögel I, Khan CA, Rueger A, Muelbaier M, Salzer E, Berkers CR, Fitzpatrick PF, Bantscheff M, Savitski MM. Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat. Nat Chem Biol 2016; 12:908-910. [DOI: 10.1038/nchembio.2185] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/20/2016] [Indexed: 02/07/2023]
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47
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Rutkowska A, Thomson DW, Vappiani J, Werner T, Mueller KM, Dittus L, Krause J, Muelbaier M, Bergamini G, Bantscheff M. A Modular Probe Strategy for Drug Localization, Target Identification and Target Occupancy Measurement on Single Cell Level. ACS Chem Biol 2016; 11:2541-50. [PMID: 27384741 DOI: 10.1021/acschembio.6b00346] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Late stage failures of candidate drug molecules are frequently caused by off-target effects or inefficient target engagement in vivo. In order to address these fundamental challenges in drug discovery, we developed a modular probe strategy based on bioorthogonal chemistry that enables the attachment of multiple reporters to the same probe in cell extracts and live cells. In a systematic evaluation, we identified the inverse electron demand Diels-Alder reaction between trans-cyclooctene labeled probe molecules and tetrazine-tagged reporters to be the most efficient bioorthogonal reaction for this strategy. Bioorthogonal biotinylation of the probe allows the identification of drug targets in a chemoproteomics competition binding assay using quantitative mass spectrometry. Attachment of a fluorescent reporter enables monitoring of spatial localization of probes as well as drug-target colocalization studies. Finally, direct target occupancy of unlabeled drugs can be determined at single cell resolution by competitive binding with fluorescently labeled probe molecules. The feasibility of the modular probe strategy is demonstrated with noncovalent PARP inhibitors.
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Affiliation(s)
- Anna Rutkowska
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Douglas W. Thomson
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Johanna Vappiani
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Katrin M. Mueller
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Lars Dittus
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Jana Krause
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse
1, D- 69117 Heidelberg, Germany
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Abrahams KA, Chung CW, Ghidelli-Disse S, Rullas J, Rebollo-López MJ, Gurcha SS, Cox JAG, Mendoza A, Jiménez-Navarro E, Martínez-Martínez MS, Neu M, Shillings A, Homes P, Argyrou A, Casanueva R, Loman NJ, Moynihan PJ, Lelièvre J, Selenski C, Axtman M, Kremer L, Bantscheff M, Angulo-Barturen I, Izquierdo MC, Cammack NC, Drewes G, Ballell L, Barros D, Besra GS, Bates RH. Identification of KasA as the cellular target of an anti-tubercular scaffold. Nat Commun 2016; 7:12581. [PMID: 27581223 PMCID: PMC5025758 DOI: 10.1038/ncomms12581] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/14/2016] [Indexed: 12/12/2022] Open
Abstract
Phenotypic screens for bactericidal compounds are starting to yield promising hits against tuberculosis. In this regard, whole-genome sequencing of spontaneous resistant mutants generated against an indazole sulfonamide (GSK3011724A) identifies several specific single-nucleotide polymorphisms in the essential Mycobacterium tuberculosis β-ketoacyl synthase (kas) A gene. Here, this genomic-based target assignment is confirmed by biochemical assays, chemical proteomics and structural resolution of a KasA-GSK3011724A complex by X-ray crystallography. Finally, M. tuberculosis GSK3011724A-resistant mutants increase the in vitro minimum inhibitory concentration and the in vivo 99% effective dose in mice, establishing in vitro and in vivo target engagement. Surprisingly, the lack of target engagement of the related β-ketoacyl synthases (FabH and KasB) suggests a different mode of inhibition when compared with other Kas inhibitors of fatty acid biosynthesis in bacteria. These results clearly identify KasA as the biological target of GSK3011724A and validate this enzyme for further drug discovery efforts against tuberculosis. Screens for bactericidal compounds have resulted in promising anti-tubercular hits. Here, the authors analyse in detail the target of an indazole sulfonamide (GSK3011724A), and find that it has a different mode of inhibition compared to other Kas inhibitors of fatty acid biosynthesis in bacteria.
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Affiliation(s)
- Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Chun-Wa Chung
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Joaquín Rullas
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - María José Rebollo-López
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Sudagar S Gurcha
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jonathan A G Cox
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alfonso Mendoza
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Elena Jiménez-Navarro
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | | | - Margarete Neu
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Paul Homes
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Ruth Casanueva
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Patrick J Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joël Lelièvre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Carolyn Selenski
- GlaxoSmithKline, 709 Swedeland Road, PO Box 1539, King of Prussia, Pennsylvania 19406-0939, USA
| | - Matthew Axtman
- GlaxoSmithKline, 709 Swedeland Road, PO Box 1539, King of Prussia, Pennsylvania 19406-0939, USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique FRE 3689, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé, Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France.,INSERM, CPBS, 34293 Montpellier, France
| | - Marcus Bantscheff
- Cellzome-a GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Iñigo Angulo-Barturen
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Mónica Cacho Izquierdo
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Nicholas C Cammack
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Gerard Drewes
- Cellzome-a GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Lluis Ballell
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - David Barros
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert H Bates
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
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49
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Joberty G, Boesche M, Brown JA, Eberhard D, Garton NS, Humphreys PG, Mathieson T, Muelbaier M, Ramsden NG, Reader V, Rueger A, Sheppard RJ, Westaway SM, Bantscheff M, Lee K, Wilson DM, Prinjha RK, Drewes G. Interrogating the Druggability of the 2-Oxoglutarate-Dependent Dioxygenase Target Class by Chemical Proteomics. ACS Chem Biol 2016; 11:2002-10. [PMID: 27197014 DOI: 10.1021/acschembio.6b00080] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The 2-oxoglutarate-dependent dioxygenase target class comprises around 60 enzymes including several subfamilies with relevance to human disease, such as the prolyl hydroxylases and the Jumonji-type lysine demethylases. Current drug discovery approaches are largely based on small molecule inhibitors targeting the iron/2-oxoglutarate cofactor binding site. We have devised a chemoproteomics approach based on a combination of unselective active-site ligands tethered to beads, enabling affinity capturing of around 40 different dioxygenase enzymes from human cells. Mass-spectrometry-based quantification of bead-bound enzymes using a free-ligand competition-binding format enabled the comprehensive determination of affinities for the cosubstrate 2-oxoglutarate and for oncometabolites such as 2-hydroxyglutarate. We also profiled a set of representative drug-like inhibitor compounds. The results indicate that intracellular competition by endogenous cofactors and high active site similarity present substantial challenges for drug discovery for this target class.
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Affiliation(s)
- Gérard Joberty
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Markus Boesche
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Jack A. Brown
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Dirk Eberhard
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Neil S. Garton
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Philip G. Humphreys
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Toby Mathieson
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Nigel G. Ramsden
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Valérie Reader
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Anne Rueger
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Robert J. Sheppard
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Susan M. Westaway
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
| | - Kevin Lee
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - David M. Wilson
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Rab K. Prinjha
- Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline company, Meyerhofstrasse 1, Heidelberg, Germany
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Klaeger S, Gohlke B, Perrin J, Gupta V, Heinzlmeir S, Helm D, Qiao H, Bergamini G, Handa H, Savitski MM, Bantscheff M, Médard G, Preissner R, Kuster B. Chemical Proteomics Reveals Ferrochelatase as a Common Off-target of Kinase Inhibitors. ACS Chem Biol 2016; 11:1245-54. [PMID: 26863403 DOI: 10.1021/acschembio.5b01063] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many protein kinases are valid drug targets in oncology because they are key components of signal transduction pathways. The number of clinical kinase inhibitors is on the rise, but these molecules often exhibit polypharmacology, potentially eliciting desired and toxic effects. Therefore, a comprehensive assessment of a compound's target space is desirable for a better understanding of its biological effects. The enzyme ferrochelatase (FECH) catalyzes the conversion of protoporphyrin IX into heme and was recently found to be an off-target of the BRAF inhibitor Vemurafenib, likely explaining the phototoxicity associated with this drug in melanoma patients. This raises the question of whether FECH binding is a more general feature of kinase inhibitors. To address this, we applied a chemical proteomics approach using kinobeads to evaluate 226 clinical kinase inhibitors for their ability to bind FECH. Surprisingly, low or submicromolar FECH binding was detected for 29 of all compounds tested and isothermal dose response measurements confirmed target engagement in cells. We also show that Vemurafenib, Linsitinib, Neratinib, and MK-2461 reduce heme levels in K562 cells, verifying that drug binding leads to a loss of FECH activity. Further biochemical and docking experiments identified the protoporphyrin pocket in FECH as one major drug binding site. Since the genetic loss of FECH activity leads to photosensitivity in humans, our data strongly suggest that FECH inhibition by kinase inhibitors is the molecular mechanism triggering photosensitivity in patients. We therefore suggest that a FECH assay should generally be part of the preclinical molecular toxicology package for the development of kinase inhibitors.
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Affiliation(s)
- Susan Klaeger
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bjoern Gohlke
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Structural
Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
| | | | - Vipul Gupta
- Department
of Nanoparticle Translational Research, Tokyo Medical University, Tokyo, Japan
| | - Stephanie Heinzlmeir
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Helm
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Huichao Qiao
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | | | - Hiroshi Handa
- Department
of Nanoparticle Translational Research, Tokyo Medical University, Tokyo, Japan
| | | | | | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Robert Preissner
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Structural
Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), Berlin, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bavarian
Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
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