1
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Tin G, Cigler M, Hinterndorfer M, Dong KD, Imrichova H, Gygi SP, Winter GE. Discovery of a DCAF11-dependent cyanoacrylamide-containing covalent degrader of BET-proteins. Bioorg Med Chem Lett 2024; 107:129779. [PMID: 38729317 DOI: 10.1016/j.bmcl.2024.129779] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Targeted protein degradation is mediated by small molecules that induce or stabilize protein-protein interactions between targets and the ubiquitin-proteasome machinery. Currently, there remains a need to expand the repertoire of viable E3 ligases available for hijacking. Notably, covalent chemistry has been employed to engage a handful of E3 ligases, including DCAF11. Here, we disclose a covalent PROTAC that enables DCAF11-dependent degradation, featuring a cyanoacrylamide warhead. Our findings underscore DCAF11 as an interesting candidate with a capacity to accommodate diverse electrophilic chemistries compatible with targeted protein degradation.
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Affiliation(s)
- Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kevin D Dong
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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2
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Offensperger F, Tin G, Duran-Frigola M, Hahn E, Dobner S, Ende CWA, Strohbach JW, Rukavina A, Brennsteiner V, Ogilvie K, Marella N, Kladnik K, Ciuffa R, Majmudar JD, Field SD, Bensimon A, Ferrari L, Ferrada E, Ng A, Zhang Z, Degliesposti G, Boeszoermenyi A, Martens S, Stanton R, Müller AC, Hannich JT, Hepworth D, Superti-Furga G, Kubicek S, Schenone M, Winter GE. Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells. Science 2024; 384:eadk5864. [PMID: 38662832 DOI: 10.1126/science.adk5864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024]
Abstract
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advanced fragment-based ligand discovery toward cellular systems, but throughput limitations have stymied the scalable identification of fragment-protein interactions. We report proteome-wide maps of protein-binding propensity for 407 structurally diverse small-molecule fragments. We verified that identified interactions can be advanced to active chemical probes of E3 ubiquitin ligases, transporters, and kinases. Integrating machine learning binary classifiers further enabled interpretable predictions of fragment behavior in cells. The resulting resource of fragment-protein interactions and predictive models will help to elucidate principles of molecular recognition and expedite ligand discovery efforts for hitherto undrugged proteins.
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Affiliation(s)
- Fabian Offensperger
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Miquel Duran-Frigola
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Ersilia Open Source Initiative, Cambridge CB1 3DE, UK
| | - Elisa Hahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Andrea Rukavina
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincenth Brennsteiner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Kevin Ogilvie
- Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Nara Marella
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katharina Kladnik
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Rodolfo Ciuffa
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Luca Ferrari
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Evandro Ferrada
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Amanda Ng
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Zhechun Zhang
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - Gianluca Degliesposti
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Robert Stanton
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - André C Müller
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Georg E Winter
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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3
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Barbosa BMG, Sfyaki A, Rafael S, José-Duran F, Pous J, Sánchez-Zarzalejo C, Perez-Lopez C, Vilanova M, Cigler M, Gay M, Vilaseca M, Winter GE, Riera A, Mayor-Ruiz C. Discovery and Mechanistic Elucidation of NQO1-Bioactivatable Small Molecules That Overcome Resistance to Degraders. Angew Chem Int Ed Engl 2024; 63:e202316730. [PMID: 38153885 DOI: 10.1002/anie.202316730] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
Degraders hold the promise to efficiently inactivate previously intractable disease-relevant targets. Unlike traditional inhibitors, degraders act substoichiometrically and rely on the hijacked proteolysis machinery, which can also act as an entry point for resistance. To fully harness the potential of targeted protein degradation, it is crucial to comprehend resistance mechanisms and formulate effective strategies to overcome them. We conducted a chemical screening to identify synthetic lethal vulnerabilities of cancer cells that exhibit widespread resistance to degraders. Comparative profiling followed by tailored optimization delivered the small molecule RBS-10, which shows preferential cytotoxicity against cells pan-resistant to degraders. Multiomics deconvolution of the mechanism of action revealed that RBS-10 acts as a prodrug bioactivated by the oxidoreductase enzyme NQO1, which is highly overexpressed in our resistance models. Collectively, our work informs on NQO1 as an actionable vulnerability to overcome resistance to degraders and as a biomarker to selectively exploit bioactivatable prodrugs in cancer.
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Affiliation(s)
- Bárbara M G Barbosa
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Aikaterini Sfyaki
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Sergi Rafael
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Ferran José-Duran
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Carolina Sánchez-Zarzalejo
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Carles Perez-Lopez
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Mar Vilanova
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Marko Cigler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090, Vienna, Austria
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Georg E Winter
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090, Vienna, Austria
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Secció Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
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4
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Hsia O, Hinterndorfer M, Cowan AD, Iso K, Ishida T, Sundaramoorthy R, Nakasone MA, Imrichova H, Schätz C, Rukavina A, Husnjak K, Wegner M, Correa-Sáez A, Craigon C, Casement R, Maniaci C, Testa A, Kaulich M, Dikic I, Winter GE, Ciulli A. Targeted protein degradation via intramolecular bivalent glues. Nature 2024; 627:204-211. [PMID: 38383787 PMCID: PMC10917667 DOI: 10.1038/s41586-024-07089-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Targeted protein degradation is a pharmacological modality that is based on the induced proximity of an E3 ubiquitin ligase and a target protein to promote target ubiquitination and proteasomal degradation. This has been achieved either via proteolysis-targeting chimeras (PROTACs)-bifunctional compounds composed of two separate moieties that individually bind the target and E3 ligase, or via molecular glues that monovalently bind either the ligase or the target1-4. Here, using orthogonal genetic screening, biophysical characterization and structural reconstitution, we investigate the mechanism of action of bifunctional degraders of BRD2 and BRD4, termed intramolecular bivalent glues (IBGs), and find that instead of connecting target and ligase in trans as PROTACs do, they simultaneously engage and connect two adjacent domains of the target protein in cis. This conformational change 'glues' BRD4 to the E3 ligases DCAF11 or DCAF16, leveraging intrinsic target-ligase affinities that do not translate to BRD4 degradation in the absence of compound. Structural insights into the ternary BRD4-IBG1-DCAF16 complex guided the rational design of improved degraders of low picomolar potency. We thus introduce a new modality in targeted protein degradation, which works by bridging protein domains in cis to enhance surface complementarity with E3 ligases for productive ubiquitination and degradation.
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Affiliation(s)
- Oliver Hsia
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Kentaro Iso
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Tsukuba Research Laboratory, Eisai Co., Ibaraki, Japan
| | - Tasuku Ishida
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Tsukuba Research Laboratory, Eisai Co., Ibaraki, Japan
| | | | - Mark A Nakasone
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Caroline Schätz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Koraljka Husnjak
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alejandro Correa-Sáez
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Conner Craigon
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ryan Casement
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chiara Maniaci
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrea Testa
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Amphista Therapeutics, Cambridge, UK
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
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5
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Kozicka Z, Suchyta DJ, Focht V, Kempf G, Petzold G, Jentzsch M, Zou C, Di Genua C, Donovan KA, Coomar S, Cigler M, Mayor-Ruiz C, Schmid-Burgk JL, Häussinger D, Winter GE, Fischer ES, Słabicki M, Gillingham D, Ebert BL, Thomä NH. Design principles for cyclin K molecular glue degraders. Nat Chem Biol 2024; 20:93-102. [PMID: 37679459 PMCID: PMC10746543 DOI: 10.1038/s41589-023-01409-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/01/2022] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.
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Affiliation(s)
- Zuzanna Kozicka
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Biology, University of Basel, Basel, Switzerland
| | - Dakota J Suchyta
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Vivian Focht
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Petzold
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Monte Rosa Therapeutics, Basel, Switzerland
| | - Marius Jentzsch
- Institute of Clinical Chemistry and Clinical Pharmacology, University and University Hospital Bonn, Bonn, Germany
| | - Charles Zou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Yale University, New Haven, CT, USA
| | - Cristina Di Genua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- VantAI, New York, NY, USA
| | - Katherine A Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Seemon Coomar
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- IRB Barcelona-Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jonathan L Schmid-Burgk
- Institute of Clinical Chemistry and Clinical Pharmacology, University and University Hospital Bonn, Bonn, Germany
| | | | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikołaj Słabicki
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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6
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Winter GE, Mayor-Ruiz C. Proximity-inducing pharmacology. Nat Chem Biol 2024; 20:13-14. [PMID: 37978259 DOI: 10.1038/s41589-023-01492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Affiliation(s)
- Georg E Winter
- Research Center for Molecular Medicine (CeMM), Austrian Academy of Sciences, Vienna, Austria.
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona Institute of Technology (BIST), Barcelona, Spain.
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7
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Ng A, Offensperger F, Cisneros JA, Scholes NS, Malik M, Villanti L, Rukavina A, Ferrada E, Hannich JT, Koren A, Kubicek S, Superti-Furga G, Winter GE. Discovery of Molecular Glue Degraders via Isogenic Morphological Profiling. ACS Chem Biol 2023; 18:2464-2473. [PMID: 38098458 PMCID: PMC10764104 DOI: 10.1021/acschembio.3c00598] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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] [Received: 09/26/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
Molecular glue degraders (MGDs) are small molecules that degrade proteins of interest via the ubiquitin-proteasome system. While MGDs were historically discovered serendipitously, approaches for MGD discovery now include cell-viability-based drug screens or data mining of public transcriptomics and drug response datasets. These approaches, however, have target spaces restricted to the essential proteins. Here we develop a high-throughput workflow for MGD discovery that also reaches the nonessential proteome. This workflow begins with the rapid synthesis of a compound library by sulfur(VI) fluoride exchange chemistry coupled to a morphological profiling assay in isogenic cell lines that vary in levels of the E3 ligase CRBN. By comparing the morphological changes induced by compound treatment across the isogenic cell lines, we were able to identify FL2-14 as a CRBN-dependent MGD targeting the nonessential protein GSPT2. We envision that this workflow would contribute to the discovery and characterization of MGDs that target a wider range of proteins.
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Affiliation(s)
- Amanda Ng
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Fabian Offensperger
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Jose A. Cisneros
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Natalie S. Scholes
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Monika Malik
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Ludovica Villanti
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Andrea Rukavina
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Evandro Ferrada
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - J. Thomas Hannich
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Anna Koren
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
- Center
for Physiology and Pharmacology, Medical
University of Vienna, 1090 Vienna, Austria
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
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8
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Xue G, Xie J, Hinterndorfer M, Cigler M, Dötsch L, Imrichova H, Lampe P, Cheng X, Adariani SR, Winter GE, Waldmann H. Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype. Nat Commun 2023; 14:7908. [PMID: 38036533 PMCID: PMC10689823 DOI: 10.1038/s41467-023-43657-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/20/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Targeted proteasomal and autophagic protein degradation, often employing bifunctional modalities, is a new paradigm for modulation of protein function. In an attempt to explore protein degradation by means of autophagy we combine arylidene-indolinones reported to bind the autophagy-related LC3B-protein and ligands of the PDEδ lipoprotein chaperone, the BRD2/3/4-bromodomain containing proteins and the BTK- and BLK kinases. Unexpectedly, the resulting bifunctional degraders do not induce protein degradation by means of macroautophagy, but instead direct their targets to the ubiquitin-proteasome system. Target and mechanism identification reveal that the arylidene-indolinones covalently bind DCAF11, a substrate receptor in the CUL4A/B-RBX1-DDB1-DCAF11 E3 ligase. The tempered α, β-unsaturated indolinone electrophiles define a drug-like DCAF11-ligand class that enables exploration of this E3 ligase in chemical biology and medicinal chemistry programs. The arylidene-indolinone scaffold frequently occurs in natural products which raises the question whether E3 ligand classes can be found more widely among natural products and related compounds.
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Affiliation(s)
- Gang Xue
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jianing Xie
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lara Dötsch
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Xiufen Cheng
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Soheila Rezaei Adariani
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
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9
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Dvorak V, Casiraghi A, Colas C, Koren A, Tomek T, Offensperger F, Rukavina A, Tin G, Hahn E, Dobner S, Frommelt F, Boeszoermenyi A, Bernada V, Hannich JT, Ecker GF, Winter GE, Kubicek S, Superti-Furga G. Paralog-dependent isogenic cell assay cascade generates highly selective SLC16A3 inhibitors. Cell Chem Biol 2023; 30:953-964.e9. [PMID: 37516113 PMCID: PMC10437005 DOI: 10.1016/j.chembiol.2023.06.029] [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: 01/27/2023] [Revised: 05/02/2023] [Accepted: 06/30/2023] [Indexed: 07/31/2023]
Abstract
Despite being considered druggable and attractive therapeutic targets, most of the solute carrier (SLC) membrane transporters remain pharmacologically underexploited. One of the reasons for this is a lack of reliable chemical screening assays, made difficult by functional redundancies among SLCs. In this study we leveraged synthetic lethality between the lactate transporters SLC16A1 and SLC16A3 in a screening strategy that we call paralog-dependent isogenic cell assay (PARADISO). The system involves five isogenic cell lines, each dependent on various paralog genes for survival/fitness, arranged in a screening cascade tuned for the identification of SLC16A3 inhibitors. We screened a diversity-oriented library of ∼90,000 compounds and further developed our hits into slCeMM1, a paralog-selective and potent SLC16A3 inhibitor. By implementing chemoproteomics, we showed that slCeMM1 is selective also at the proteome-wide level, thus fulfilling an important criterion for chemical probes. This study represents a framework for the development of specific cell-based drug discovery assays.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andrea Casiraghi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Claire Colas
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fabian Offensperger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Viktoriia Bernada
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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10
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Enders L, Siklos M, Borggräfe J, Gaussmann S, Koren A, Malik M, Tomek T, Schuster M, Reiniš J, Hahn E, Rukavina A, Reicher A, Casteels T, Bock C, Winter GE, Hannich JT, Sattler M, Kubicek S. Pharmacological perturbation of the phase-separating protein SMNDC1. Nat Commun 2023; 14:4504. [PMID: 37587144 PMCID: PMC10432564 DOI: 10.1038/s41467-023-40124-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 10/19/2022] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
SMNDC1 is a Tudor domain protein that recognizes di-methylated arginines and controls gene expression as an essential splicing factor. Here, we study the specific contributions of the SMNDC1 Tudor domain to protein-protein interactions, subcellular localization, and molecular function. To perturb the protein function in cells, we develop small molecule inhibitors targeting the dimethylarginine binding pocket of the SMNDC1 Tudor domain. We find that SMNDC1 localizes to phase-separated membraneless organelles that partially overlap with nuclear speckles. This condensation behavior is driven by the unstructured C-terminal region of SMNDC1, depends on RNA interaction and can be recapitulated in vitro. Inhibitors of the protein's Tudor domain drastically alter protein-protein interactions and subcellular localization, causing splicing changes for SMNDC1-dependent genes. These compounds will enable further pharmacological studies on the role of SMNDC1 in the regulation of nuclear condensates, gene regulation and cell identity.
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Affiliation(s)
- Lennart Enders
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Jan Borggräfe
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Stefan Gaussmann
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Monika Malik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Jiří Reiniš
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andreas Reicher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Tamara Casteels
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
- Sloan Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währinger Straße 25a, 1090, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
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11
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Hanzl A, Casement R, Imrichova H, Hughes SJ, Barone E, Testa A, Bauer S, Wright J, Brand M, Ciulli A, Winter GE. Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders. Nat Chem Biol 2023; 19:323-333. [PMID: 36329119 PMCID: PMC7614256 DOI: 10.1038/s41589-022-01177-2] [Citation(s) in RCA: 28] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/20/2022] [Indexed: 11/06/2022]
Abstract
Targeted protein degradation is a novel pharmacology established by drugs that recruit target proteins to E3 ubiquitin ligases. Based on the structure of the degrader and the target, different E3 interfaces are critically involved, thus forming defined 'functional hotspots'. Understanding disruptive mutations in functional hotspots informs on the architecture of the assembly, and highlights residues susceptible to acquire resistance phenotypes. Here we employ haploid genetics to show that hotspot mutations cluster in substrate receptors of hijacked ligases, where mutation type and frequency correlate with gene essentiality. Intersection with deep mutational scanning revealed hotspots that are conserved or specific for chemically distinct degraders and targets. Biophysical and structural validation suggests that hotspot mutations frequently converge on altered ternary complex assembly. Moreover, we validated hotspots mutated in patients that relapse from degrader treatment. In sum, we present a fast and widely accessible methodology to characterize small-molecule degraders and associated resistance mechanisms.
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Affiliation(s)
- Alexander Hanzl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ryan Casement
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dundee, UK
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Scott J Hughes
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dundee, UK
- Amphista Therapeutics Ltd., Newhouse, UK
| | - Eleonora Barone
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dundee, UK
- Amphista Therapeutics Ltd., Newhouse, UK
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Proxygen GmbH, Vienna, Austria
| | - Jane Wright
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dundee, UK
| | - Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Proxygen GmbH, Vienna, Austria
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dundee, UK.
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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12
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Abstract
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) promises to overcome some of these limitations. In brief, TPD is dependent on small molecules that induce the proximity between a protein of interest (POI) and an E3 ubiquitin ligase, causing ubiquitination and degradation of the POI. In this perspective, we want to reflect on current challenges in the field, and discuss how advances in multiomics profiling, artificial intelligence, and machine learning (AI/ML) will be vital in overcoming them. The presented roadmap is discussed in the context of small-molecule degraders but is equally applicable for other emerging proximity-inducing modalities.
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Affiliation(s)
- Miquel Duran-Frigola
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,Ersilia
Open Source Initiative, 28 Belgrave Road, CB1 3DE, Cambridge, United Kingdom,
| | - Marko Cigler
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,
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13
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Hanzl A, Barone E, Bauer S, Yue H, Nowak RP, Hahn E, Pankevich EV, Koren A, Kubicek S, Fischer ES, Winter GE. E3-Specific Degrader Discovery by Dynamic Tracing of Substrate Receptor Abundance. J Am Chem Soc 2023; 145:1176-1184. [PMID: 36602777 PMCID: PMC9853857 DOI: 10.1021/jacs.2c10784] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Indexed: 01/06/2023]
Abstract
Targeted protein degradation (TPD) is a new pharmacology based on small-molecule degraders that induce proximity between a protein of interest (POI) and an E3 ubiquitin ligase. Of the approximately 600 E3s encoded in the human genome, only around 2% can be co-opted with degraders. This underrepresentation is caused by a paucity of discovery approaches to identify degraders for defined E3s. This hampers a rational expansion of the druggable proteome and stymies critical advancements in the field, such as tissue- and cell-specific degradation. Here, we focus on dynamic NEDD8 conjugation, a post-translational, regulatory circuit that controls the activity of 250 cullin RING E3 ligases (CRLs). Leveraging this regulatory layer enabled us to develop a scalable assay to identify compounds that alter the interactome of an E3 of interest by tracing their abundance after pharmacologically induced auto-degradation. Initial validation studies are performed for CRBN and VHL, but proteomics studies indicate broad applicability for many CRLs. Among amenable ligases, we select CRLDCAF15 for a proof-of-concept screen, leading to the identification of a novel DCAF15-dependent molecular glue degrader inducing the degradation of RBM23 and RBM39. Together, this strategy empowers the scalable identification of degraders specific to a ligase of interest.
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Affiliation(s)
- Alexander Hanzl
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Eleonora Barone
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Sophie Bauer
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Hong Yue
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Radosław P. Nowak
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Elisa Hahn
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Eugenia V. Pankevich
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Anna Koren
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Eric S. Fischer
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
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14
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Schrempf A, Bernardo S, Arasa Verge EA, Ramirez Otero MA, Wilson J, Kirchhofer D, Timelthaler G, Ambros AM, Kaya A, Wieder M, Ecker GF, Winter GE, Costanzo V, Loizou JI. POLθ processes ssDNA gaps and promotes replication fork progression in BRCA1-deficient cells. Cell Rep 2022; 41:111716. [PMID: 36400033 DOI: 10.1016/j.celrep.2022.111716] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 03/18/2022] [Revised: 08/21/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
Polymerase theta (POLθ) is an error-prone DNA polymerase whose loss is synthetically lethal in cancer cells bearing breast cancer susceptibility proteins 1 and 2 (BRCA1/2) mutations. To investigate the basis of this genetic interaction, we utilized a small-molecule inhibitor targeting the POLθ polymerase domain. We found that POLθ processes single-stranded DNA (ssDNA) gaps that emerge in the absence of BRCA1, thus promoting unperturbed replication fork progression and survival of BRCA1 mutant cells. A genome-scale CRISPR-Cas9 knockout screen uncovered suppressors of the functional interaction between POLθ and BRCA1, including NBN, a component of the MRN complex, and cell-cycle regulators such as CDK6. While the MRN complex nucleolytically processes ssDNA gaps, CDK6 promotes cell-cycle progression, thereby exacerbating replication stress, a feature of BRCA1-deficient cells that lack POLθ activity. Thus, ssDNA gap formation, modulated by cell-cycle regulators and MRN complex activity, underlies the synthetic lethality between POLθ and BRCA1, an important insight for clinical trials with POLθ inhibitors.
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Affiliation(s)
- Anna Schrempf
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sara Bernardo
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Emili A Arasa Verge
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Miguel A Ramirez Otero
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Jordan Wilson
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Dominik Kirchhofer
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Gerald Timelthaler
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Anna M Ambros
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Atilla Kaya
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Marcus Wieder
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Georg E Winter
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Joanna I Loizou
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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15
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Peter B, Eisenwort G, Sadovnik I, Bauer K, Willmann M, Rülicke T, Berger D, Stefanzl G, Greiner G, Hoermann G, Keller A, Wolf D, Čulen M, Winter GE, Hoffmann T, Schiefer AI, Sperr WR, Zuber J, Mayer J, Valent P. BRD4 Degradation Blocks Expression of MYC and Multiple Forms of Stem Cell Resistance in Ph + Chronic Myeloid Leukemia. Am J Hematol 2022; 97:1215-1225. [PMID: 35794848 PMCID: PMC9546315 DOI: 10.1002/ajh.26650] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/23/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022]
Abstract
In most patients with chronic myeloid leukemia (CML) clonal cells can be kept under control by BCR::ABL1 tyrosine kinase inhibitors (TKI). However, overt resistance or intolerance against these TKI may occur. We identified the epigenetic reader BRD4 and its downstream‐effector MYC as growth regulators and therapeutic targets in CML cells. BRD4 and MYC were found to be expressed in primary CML cells, CD34+/CD38− leukemic stem cells (LSC), and in the CML cell lines KU812, K562, KCL22, and KCL22T315I. The BRD4‐targeting drug JQ1 was found to suppress proliferation in KU812 cells and primary leukemic cells in the majority of patients with chronic phase CML. In the blast phase of CML, JQ1 was less effective. However, the BRD4 degrader dBET6 was found to block proliferation and/or survival of primary CML cells in all patients tested, including blast phase CML and CML cells exhibiting the T315I variant of BCR::ABL1. Moreover, dBET6 was found to block MYC expression and to synergize with BCR::ABL1 TKI in inhibiting the proliferation in the JQ1‐resistant cell line K562. Furthermore, BRD4 degradation was found to overcome osteoblast‐induced TKI resistance of CML LSC in a co‐culture system and to block interferon‐gamma‐induced upregulation of the checkpoint antigen PD‐L1 in LSC. Finally, dBET6 was found to suppress the in vitro survival of CML LSC and their engraftment in NSG mice. Together, targeting of BRD4 and MYC through BET degradation sensitizes CML cells against BCR::ABL1 TKI and is a potent approach to overcome multiple forms of drug resistance in CML LSC.
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Affiliation(s)
- Barbara Peter
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
| | - Gregor Eisenwort
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
| | - Irina Sadovnik
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
| | - Karin Bauer
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
| | - Michael Willmann
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department for Companion Animals and Horses, University Clinic for Small Animals, Internal Medicine Small Animals, University of Veterinary Medicine Vienna, Austria
| | - Thomas Rülicke
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, Austria
| | - Daniela Berger
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
| | - Gabriele Stefanzl
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
| | - Georg Greiner
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Austria
| | - Gregor Hoermann
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Austria.,Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital Innsbruck, Innsbruck, Austria
| | - Alexandra Keller
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
| | - Dominik Wolf
- Department of Hematology and Oncology, Innsbruck Medical University, Innsbruck, Austria.,Department of Hematology, Oncology and Rheumatology, Center of Integrated Oncology Cologne Bonn, University Hospital of Bonn, Germany
| | - Martin Čulen
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Georg E Winter
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | | | - Wolfgang R Sperr
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Jiří Mayer
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Peter Valent
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Austria.,Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Austria
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16
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Müller S, Ackloo S, Al Chawaf A, Al-Lazikani B, Antolin A, Baell JB, Beck H, Beedie S, Betz UAK, Bezerra GA, Brennan PE, Brown D, Brown PJ, Bullock AN, Carter AJ, Chaikuad A, Chaineau M, Ciulli A, Collins I, Dreher J, Drewry D, Edfeldt K, Edwards AM, Egner U, Frye SV, Fuchs SM, Hall MD, Hartung IV, Hillisch A, Hitchcock SH, Homan E, Kannan N, Kiefer JR, Knapp S, Kostic M, Kubicek S, Leach AR, Lindemann S, Marsden BD, Matsui H, Meier JL, Merk D, Michel M, Morgan MR, Mueller-Fahrnow A, Owen DR, Perry BG, Rosenberg SH, Saikatendu KS, Schapira M, Scholten C, Sharma S, Simeonov A, Sundström M, Superti-Furga G, Todd MH, Tredup C, Vedadi M, von Delft F, Willson TM, Winter GE, Workman P, Arrowsmith CH. Target 2035 - update on the quest for a probe for every protein. RSC Med Chem 2022; 13:13-21. [PMID: 35211674 PMCID: PMC8792830 DOI: 10.1039/d1md00228g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/21/2021] [Indexed: 01/11/2023] Open
Abstract
Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome.
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Affiliation(s)
- Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | | | - Bissan Al-Lazikani
- Department of Data Science, The Institute of Cancer Research London SM2 5NG UK
- CRUK ICR/Imperial Convergence Science Centre London SM2 5NG UK
| | - Albert Antolin
- Department of Data Science, The Institute of Cancer Research London SM2 5NG UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
- School of Pharmaceutical Sciences, Nanjing Tech University No. 30 South Puzhu Road Nanjing 211816 People's Republic of China
| | - Hartmut Beck
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | - Shaunna Beedie
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | | | - Gustavo Arruda Bezerra
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, University of Oxford Oxford OX3 7FZ UK
| | - David Brown
- Institut Recherches de Servier 125 Chemin de Ronde 78290 Croissy France
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | - Alex N Bullock
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Adrian J Carter
- Discovery Research, Boehringer Ingelheim 55216 Ingelheim am Rhein Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Mathilde Chaineau
- Early Drug Discovery Unit (EDDU), Montreal Neurological Institute-Hospital, McGill University Montreal QC Canada
| | - Alessio Ciulli
- School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee James Black Centre Dundee UK
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Jan Dreher
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | - David Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy Chapel Hill NC USA
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Kristina Edfeldt
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet Stockholm Sweden
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | - Ursula Egner
- Nuvisan Innovation Campus Berlin GmbH Müllerstraße 178 13353 Berlin Germany
| | - Stephen V Frye
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | | | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville Maryland 20850 USA
| | - Ingo V Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA Frankfurter Straße 250 64293 Darmstadt Germany
| | - Alexander Hillisch
- Research and Development, Bayer AG, Pharmaceuticals 42103 Wuppertal Germany
| | | | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology Karolinska Institutet Stockholm Sweden
| | - Natarajan Kannan
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia Athens GA USA
| | - James R Kiefer
- Genentech, Inc. 1 DNA Way South San Francisco California 94080 USA
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Milka Kostic
- Department of Cancer Biology and Chemical Biology Program, Dana-Farber Cancer Institute 450 Brookline Ave Boston MA 02215 USA
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Genome Campus, Hinxton Cambridgeshire CB10 1SD UK
| | - Sven Lindemann
- Strategic Innovation, Global R&D, Merck Healthcare KGaA Frankfurter Straße 250 64293 Darmstadt Germany
| | - Brian D Marsden
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford UK
| | - Hisanori Matsui
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited Fujisawa Kanagawa Japan
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD USA
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- LMU Munich, Department of Pharmacy, Chair of Pharmaceutical and Medicinal Chemistry 81377 Munich Germany
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology Karolinska Institutet Stockholm Sweden
| | - Maxwell R Morgan
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
| | | | - Dafydd R Owen
- Discovery Network Group, Pfizer Medicine Design Cambridge MA 02139 USA
| | - Benjamin G Perry
- Drugs for Neglected Diseases initiative 15 Chemin Camille Vidart Geneva 1202 Switzerland
| | | | - Kumar Singh Saikatendu
- Global Research Externalization, Takeda California, Inc. 9625 Towne Center Drive San Diego CA 92121 USA
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Cora Scholten
- Research and Development, Bayer AG, Pharmaceuticals 13353 Berlin Germany
| | - Sujata Sharma
- Structural & Protein Sciences, Discovery Sciences, Janssen Research & Development 1400 McKean Rd Spring House PA 19477 USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville Maryland 20850 USA
| | - Michael Sundström
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institutet Stockholm Sweden
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
- Center for Physiology and Pharmacology, Medical University of Vienna Vienna Austria
| | - Matthew H Todd
- School of Pharmacy, University College London London WC1N 1AX UK
| | - Claudia Tredup
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt Frankfurt 60438 Germany
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
- Diamond Light Source Ltd Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Department of Biochemistry, University of Johannesburg Auckland Park 2006 South Africa
- Research Complex at Harwell Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Timothy M Willson
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
| | - Paul Workman
- CRUK ICR/Imperial Convergence Science Centre London SM2 5NG UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London SM2 5NG UK
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Princess Margaret Cancer Centre Toronto Ontario M5G 1L7 Canada
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17
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Scholes NS, Mayor-Ruiz C, Winter GE. Identification and selectivity profiling of small-molecule degraders via multi-omics approaches. Cell Chem Biol 2021; 28:1048-1060. [PMID: 33811812 DOI: 10.1016/j.chembiol.2021.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 01/13/2021] [Revised: 02/18/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022]
Abstract
The therapeutic modality of targeted protein degradation promises to overcome limitations of traditional pharmacology. Small-molecule degraders recruit disease-causing proteins to E3 ubiquitin ligases, prompting their ubiquitination and degradation by the proteasome. The discovery, mechanistic elucidation, and selectivity profiling of novel degraders are often conducted in cellular systems. This highlights the need for unbiased multi-omics strategies that inform on the functionally involved components. Here, we review how proteomics and functional genomics can be integrated to identify and mechanistically understand degraders, their target selectivity as well as putative resistance mechanisms.
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Affiliation(s)
- Natalie S Scholes
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Cristina Mayor-Ruiz
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; IRB Barcelona - Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Georg E Winter
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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18
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Jaeger MG, Winter GE. Fast-acting chemical tools to delineate causality in transcriptional control. Mol Cell 2021; 81:1617-1630. [PMID: 33689749 DOI: 10.1016/j.molcel.2021.02.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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] [Received: 11/13/2020] [Revised: 01/20/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
Multi-dimensional omics profiling continues to illuminate the complexity of cellular processes. Because of difficult mechanistic interpretation of phenotypes induced by slow perturbation, fast experimental setups are increasingly used to dissect causal interactions directly in cells. Here we review a growing body of studies that leverage rapid pharmacological perturbation to delineate causality in gene control. When coupled with kinetically matched readouts, fast chemical genetic tools allow recording of primary phenotypes before confounding secondary effects manifest. The toolbox encompasses directly acting probes, such as active-site inhibitors and proteolysis-targeting chimeras, as well as strategies using genetic engineering to render target proteins chemically tractable, such as analog-sensitive and degron systems. We anticipate that extrapolation of these concepts to single-cell setups will further transform our mechanistic understanding of transcriptional control in the future. Importantly, the concept of leveraging speed to derive causality should be broadly applicable to many aspects of biological regulation.
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Affiliation(s)
- Martin G Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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19
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Kiely-Collins H, Winter GE, Bernardes GJL. The role of reversible and irreversible covalent chemistry in targeted protein degradation. Cell Chem Biol 2021; 28:952-968. [PMID: 33789091 DOI: 10.1016/j.chembiol.2021.03.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/30/2021] [Accepted: 03/09/2021] [Indexed: 12/15/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) that degrade disease-causing proteins by hijacking the endogenous ubiquitin-proteasome system have emerged as an exciting and transformative technology in both chemical biology and drug discovery. Currently, the majority of PROTACs use reversible non-covalent ligands for both the target protein of interest (POI) and E3 ligase. In this review, we explore the burgeoning role of reversible and irreversible covalent chemistry in targeted protein degradation. We highlight the key advantages of targeted covalent inhibitors, whether as the target POI or E3 ligase ligand, such as their ability to enhance the selectivity of PROTACs, enable access to more of the "undruggable" proteome and expand the repertoire of recruited E3 ligases.
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Affiliation(s)
- Hannah Kiely-Collins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Instituto de Medicina Molecular, Faculdade de Medicina de Universidad de Lisboa, Avenida Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
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20
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Mayor-Ruiz C, Bauer S, Brand M, Kozicka Z, Siklos M, Imrichova H, Kaltheuner IH, Hahn E, Seiler K, Koren A, Petzold G, Fellner M, Bock C, Müller AC, Zuber J, Geyer M, Thomä NH, Kubicek S, Winter GE. Rational discovery of molecular glue degraders via scalable chemical profiling. Nat Chem Biol 2020; 16:1199-1207. [PMID: 32747809 PMCID: PMC7116640 DOI: 10.1038/s41589-020-0594-x] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [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: 05/05/2020] [Accepted: 06/15/2020] [Indexed: 11/09/2022]
Abstract
Targeted protein degradation is a new therapeutic modality based on drugs that destabilize proteins by inducing their proximity to E3 ubiquitin ligases. Of particular interest are molecular glues that can degrade otherwise unligandable proteins by orchestrating direct interactions between target and ligase. However, their discovery has so far been serendipitous, thus hampering broad translational efforts. Here, we describe a scalable strategy toward glue degrader discovery that is based on chemical screening in hyponeddylated cells coupled to a multi-omics target deconvolution campaign. This approach led us to identify compounds that induce ubiquitination and degradation of cyclin K by prompting an interaction of CDK12-cyclin K with a CRL4B ligase complex. Notably, this interaction is independent of a dedicated substrate receptor, thus functionally segregating this mechanism from all described degraders. Collectively, our data outline a versatile and broadly applicable strategy to identify degraders with nonobvious mechanisms and thus empower future drug discovery efforts.
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Affiliation(s)
- Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Zuzanna Kozicka
- FMI Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kristina Seiler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg Petzold
- FMI Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michaela Fellner
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Nicolas H Thomä
- FMI Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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21
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Abstract
In this issue of Cell Chemical Biology, Li et al. (2020), Hsu et al. (2020), and Potjewyd et al. (2020) expand the target spectrum amenable to protein degradation by designing degraders of the cell cycle checkpoint kinase Wee1 and the polycomb repressive complex 2 (PRC2) via its regulatory EED subunit.
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Affiliation(s)
- Martin G Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090 Vienna, Austria.
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22
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Bensimon A, Pizzagalli MD, Kartnig F, Dvorak V, Essletzbichler P, Winter GE, Superti-Furga G. Targeted Degradation of SLC Transporters Reveals Amenability of Multi-Pass Transmembrane Proteins to Ligand-Induced Proteolysis. Cell Chem Biol 2020; 27:728-739.e9. [PMID: 32386596 PMCID: PMC7303955 DOI: 10.1016/j.chembiol.2020.04.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/21/2020] [Accepted: 04/03/2020] [Indexed: 01/05/2023]
Abstract
With more than 450 members, the solute carrier (SLC) group of proteins represents the largest class of transporters encoded in the human genome. Their several-pass transmembrane domain structure and hydrophobicity contribute to the orphan status of many SLCs, devoid of known cargos or chemical inhibitors. We report that SLC proteins belonging to different families and subcellular compartments are amenable to induced degradation by heterobifunctional ligands. Engineering endogenous alleles via the degradation tag (dTAG) technology enabled chemical control of abundance of the transporter protein, SLC38A2. Moreover, we report the design of d9A-2, a chimeric compound engaging several members of the SLC9 family and leading to their degradation. d9A-2 impairs cellular pH homeostasis and promotes cell death in a range of cancer cell lines. These findings open the era of SLC-targeting chimeric degraders and demonstrate potential access of multi-pass transmembrane proteins of different subcellular localizations to the chemically exploitable degradation machinery.
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Affiliation(s)
- Ariel Bensimon
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Mattia D Pizzagalli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Patrick Essletzbichler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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23
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Abstract
Traditional approaches in the development of small-molecule drugs typically aim to inhibit the biochemical activity of functional protein domains. In contrast, targeted protein degradation aims to reduce overall levels of disease-relevant proteins. Mechanistically, this can be achieved via chemical ligands that induce molecular proximity between an E3 ubiquitin ligase and a protein of interest, leading to ubiquitination and degradation of the protein of interest. This paradigm-shifting pharmacology promises to address several limitations inherent to conventional inhibitor design. Most notably, targeted protein degradation has the potential not only to expand the druggable proteome beyond the reach of traditional competitive inhibitors but also to develop therapeutic strategies of unmatched selectivity. This review briefly summarizes key challenges that remain to be addressed to deliver on these promises and to realize the full therapeutic potential of pharmacologic modulation of protein degradation pathways.
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Affiliation(s)
- Alexander Hanzl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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24
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Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G. Abstract A08: Genetic drug resistance screen identifies LZTR1 as regulator of RAS ubiquitination and signaling. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-a08] [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
Small-molecule tyrosine kinase inhibitor (TKI)-based treatment of chronic myeloid leukemia (CML), directed by the presence of the Philadelphia chromosome (Ph+) encoded BCR-ABL tyrosine kinase, is a paradigm of targeted cancer therapy. However, the development of TKI resistance limits the long-term success of these therapeutics. We used a genetic screening approach in the near-haploid CML cell line KBM-7 to identify six genes whose individual loss of function led to TKI drug resistance. We investigated in detail the role of the leucine zipper-like transcription regulator 1 (LZTR1) gene, as it was mechanistically enigmatic despite its involvement in many human developmental and oncologic diseases including glioblastoma, schwannomatosis and Noonan syndrome. We found that LZTR1 inactivation led to enhanced MAPK pathway activity and reduced TKI sensitivity of CML cells in a RAS-dependent way. LZTR1 missense mutations identified in human diseases failed to revert the loss-of-function phenotype. Knockdown of the LZTR1 orthologue CG3711 in Drosophila led to an increase in ectopic wing vein formation that could be rescued by impairment of RAS gene function, confirming the epistatic relationship and suggesting an evolutionary conserved role for LZTR1 in RAS regulation. Endogenous LZTR1 protein associated with the four main RAS isoforms KRAS4A, KRAS4B, NRAS and HRAS in proximity biotinylation proteomic and immunoprecipitation experiments in a manner that for KRAS required farnesylation and palmitoylation. Ectopic expression of LZTR1 along with all four RAS proteins led to their ubiquitination, compatible with the proposed role of LZTR1 as a cullin (CUL)-3 E3 ligase adaptor. Loss of LZTR1 led to reduced ubiquitination of endogenous KRAS and its increased abundance as well as enhanced localization at the plasma membrane. Together with the work on the role of LZTR1 in diseases driven by the dysregulation of RAS ubiquitination and signaling (Steklov, Pandolfi, Baietti et al., Anna Sablina lab, KU Leuven; see separate abstract), we propose that LZTR1 acts as a conserved regulator of RAS ubiquitination and MAPK pathway activation, providing a mechanistic explanation to its genetic involvement across a variety of human pathologies.
Citation Format: Johannes W. Bigenzahn, Giovanna M. Collu, Felix Kartnig, Melanie Pieraks, Gregory I. Vladimer, Leonhard X. Heinz, Vitaly Sedlyarov, Fiorella Schischlik, Astrid Fauster, Manuele Rebsamen, Katja Parapatics, Vincent A. Blomen, André C. Müller, Georg E. Winter, Robert Kralovics, Thijn R. Brummelkamp, Marek Mlodzik, Giulio Superti-Furga. Genetic drug resistance screen identifies LZTR1 as regulator of RAS ubiquitination and signaling [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A08.
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Affiliation(s)
| | | | - Felix Kartnig
- 1CeMM Center for Molecular Medicine, Vienna, Austria,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marek Mlodzik
- 2Icahn School of Medicine at Mount Sinai, New York, NY,
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25
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Mayor-Ruiz C, Jaeger MG, Bauer S, Brand M, Sin C, Hanzl A, Mueller AC, Menche J, Winter GE. Plasticity of the Cullin-RING Ligase Repertoire Shapes Sensitivity to Ligand-Induced Protein Degradation. Mol Cell 2020; 75:849-858.e8. [PMID: 31442425 DOI: 10.1016/j.molcel.2019.07.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [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: 04/02/2019] [Revised: 06/13/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
Inducing protein degradation via small molecules is a transformative therapeutic paradigm. Although structural requirements of target degradation are emerging, mechanisms determining the cellular response to small-molecule degraders remain poorly understood. To systematically delineate effectors required for targeted protein degradation, we applied genome-scale CRISPR/Cas9 screens for five drugs that hijack different substrate receptors (SRs) of cullin RING ligases (CRLs) to induce target proteolysis. We found that sensitivity to small-molecule degraders is dictated by shared and drug-specific modulator networks, including the COP9 signalosome and the SR exchange factor CAND1. Genetic or pharmacologic perturbation of these effectors impairs CRL plasticity and arrests a wide array of ligases in a constitutively active state. Resulting defects in CRL decommissioning prompt widespread CRL auto-degradation that confers resistance to multiple degraders. Collectively, our study informs on regulation and architecture of CRLs amenable for targeted protein degradation and outlines biomarkers and putative resistance mechanisms for upcoming clinical investigation.
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Affiliation(s)
- Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
| | - Martin G Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Celine Sin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Alexander Hanzl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - André C Mueller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria.
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26
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Brand M, Winter GE. Abstract LB-A11: Quantitative and qualitative characterization of spontaneous resistance to targeted protein degradation. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-lb-a11] [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
Targeted protein degradation (TPD) by heterobifunctional small molecules commonly called PROTACs has recently emerged as a promising novel strategy in drug development. PROTACs hijack the endogenous cellular degradation machinery by recruiting E3 ubiquitin ligases to a protein of interest, resulting in its ubiquitination and degradation by the proteasome. The first two PROTACs have entered clinical investigation this year, but resistance mechanisms to this novel pharmacology are not yet thoroughly understood. Here, we set out to systematically quantify and characterize spontaneous resistance to TPD. For this, we made use of the well-characterized PROTACs dBET6 and ARV-771, that induce degradation of BET bromodomain proteins by recruitment of the E3 ligase CRBN or VHL, respectively. We estimated spontaneous resistance rates by exposing cells to lethal doses of drug and monitoring for the emergence of resistant clones. We detected important quantitative differences between the two PROTACs, with resistance rates to the VHL-based degrader ARV-771 being significantly lower than to dBET6. To characterize the mechanism of resistance, we implemented a customized hybrid-capture sequencing pipeline for known determinants of PROTAC sensitivity and applied it to drug-resistant cells, revealing several resistance-conferring mutations. Mapping of the mutations on crystal structures of the E3 ligase complexes highlighted their clustering at the drug binding pocket, as well as on important protein-protein interaction surfaces in the complex. The majority of identified mutations affected the hijiacked E3 ligase complex directly and not the general ubiquitination machinery, thereby not conferring cross-resistance to different PROTACS. This suggests combination treatment with degraders that exploit different E3 ligases as a viable strategy to limit emergence of PROTAC resistance.
Citation Format: Matthias Brand, Georg E. Winter. Quantitative and qualitative characterization of spontaneous resistance to targeted protein degradation [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr LB-A11. doi:10.1158/1535-7163.TARG-19-LB-A11
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Affiliation(s)
- Matthias Brand
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna
| | - Georg E. Winter
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna
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Mayor-Ruiz C, Winter GE. Identification and characterization of cancer vulnerabilities via targeted protein degradation. Drug Discov Today Technol 2019; 31:81-90. [PMID: 31200863 DOI: 10.1016/j.ddtec.2018.12.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Target(ed) protein degradation (TPD) is a novel paradigm in drug discovery and a promising therapeutic strategy. TPD is based on small-molecules that catalyze the degradation of proteins by re-directing the ubiquitination activity of ubiquitin E3 ligases. Its unique molecular pharmacology enables robust, selective and fast elimination of proteins in cellular assays and in vivo. In addition to possible clinical applications, TPD is also emerging as an attractive alternative to traditional pharmacologic or genetic perturbation strategies. Directly acting degraders, as well as chemical-genetics derivatives offer unique opportunities in the pre-clinical identification, characterization and mechanistic validation of therapeutic targets.
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Affiliation(s)
- Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Vienna, 1090, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Vienna, 1090, Austria.
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29
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Abstract
Small molecule-induced targeted protein degradation is a powerful approach for drug target validation given its selectivity, high kinetic resolution, dose dependency, and reversibility. Out of the several methods that have been reported so far, the 12 kDa degradation tag (dTAG) system has the advantage of hijacking a degradation machinery that is ubiquitously expressed in all human tissues. Therefore it is independent of expressing additional, exogenous factors and additionally permits target validation in vivo. Here, we describe the protocol for generation and validation of clones harboring knock-in of a selectable dTAG cassette at the endogenous locus of proteins of interest using the near-haploid cell line KBM7.
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Affiliation(s)
- Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G. LZTR1 is a regulator of RAS ubiquitination and signaling. Science 2018; 362:1171-1177. [PMID: 30442766 DOI: 10.1126/science.aap8210] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 06/26/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
In genetic screens aimed at understanding drug resistance mechanisms in chronic myeloid leukemia cells, inactivation of the cullin 3 adapter protein-encoding leucine zipper-like transcription regulator 1 (LZTR1) gene led to enhanced mitogen-activated protein kinase (MAPK) pathway activity and reduced sensitivity to tyrosine kinase inhibitors. Knockdown of the Drosophila LZTR1 ortholog CG3711 resulted in a Ras-dependent gain-of-function phenotype. Endogenous human LZTR1 associates with the main RAS isoforms. Inactivation of LZTR1 led to decreased ubiquitination and enhanced plasma membrane localization of endogenous KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog). We propose that LZTR1 acts as a conserved regulator of RAS ubiquitination and MAPK pathway activation. Because LZTR1 disease mutations failed to revert loss-of-function phenotypes, our findings provide a molecular rationale for LZTR1 involvement in a variety of inherited and acquired human disorders.
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Affiliation(s)
- Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giovanna M Collu
- Department of Cell, Developmental, and Regenerative Biology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Melanie Pieraks
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gregory I Vladimer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fiorella Schischlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Astrid Fauster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincent A Blomen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Thijn R Brummelkamp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.,Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.,Cancer Genomics Center (CGC.nl), Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Marek Mlodzik
- Department of Cell, Developmental, and Regenerative Biology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. .,Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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Zeid R, Lawlor MA, Poon E, Reyes JM, Fulciniti M, Lopez MA, Scott TG, Nabet B, Erb MA, Winter GE, Jacobson Z, Polaski DR, Karlin KL, Hirsch RA, Munshi NP, Westbrook TF, Chesler L, Lin CY, Bradner JE. Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma. Nat Genet 2018; 50:515-523. [PMID: 29379199 PMCID: PMC6310397 DOI: 10.1038/s41588-018-0044-9] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [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: 08/18/2017] [Accepted: 12/18/2017] [Indexed: 11/08/2022]
Abstract
Amplification of the locus encoding the oncogenic transcription factor MYCN is a defining feature of high-risk neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of MYCN perturbation in neuroblastoma. At oncogenic levels, MYCN associates with E-box binding motifs in an affinity-dependent manner, binding to strong canonical E-boxes at promoters and invading abundant weaker non-canonical E-boxes clustered at enhancers. Loss of MYCN leads to a global reduction in transcription, which is most pronounced at MYCN target genes with the greatest enhancer occupancy. These highly occupied MYCN target genes show tissue-specific expression and are linked to poor patient survival. The activity of genes with MYCN-occupied enhancers is dependent on the tissue-specific transcription factor TWIST1, which co-occupies enhancers with MYCN and is required for MYCN-dependent proliferation. These data implicate tissue-specific enhancers in defining often highly tumor-specific 'MYC target gene signatures' and identify disruption of the MYCN enhancer regulatory axis as a promising therapeutic strategy in neuroblastoma.
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Affiliation(s)
- Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew A Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Jaime M Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mariateresa Fulciniti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A Lopez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Behnam Nabet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael A Erb
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoe Jacobson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Donald R Polaski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen L Karlin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rachel A Hirsch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nikhil P Munshi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas F Westbrook
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Novartis Institute for Biomedical Research, Cambridge, MA, USA.
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Ishoey M, Chorn S, Singh N, Jaeger MG, Brand M, Paulk J, Bauer S, Erb MA, Parapatics K, Müller AC, Bennett KL, Ecker GF, Bradner JE, Winter GE. Translation Termination Factor GSPT1 Is a Phenotypically Relevant Off-Target of Heterobifunctional Phthalimide Degraders. ACS Chem Biol 2018; 13:553-560. [PMID: 29356495 DOI: 10.1021/acschembio.7b00969] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein degradation is an emerging therapeutic strategy with a unique molecular pharmacology that enables the disruption of all functions associated with a target. This is particularly relevant for proteins depending on molecular scaffolding, such as transcription factors or receptor tyrosine kinases (RTKs). To address tractability of multiple RTKs for chemical degradation by the E3 ligase CUL4-RBX1-DDB1-CRBN (CRL4CRBN), we synthesized a series of phthalimide degraders based on the promiscuous kinase inhibitors sunitinib and PHA665752. While both series failed to induce degradation of their consensus targets, individual molecules displayed pronounced efficacy in leukemia cell lines. Orthogonal target identification supported by molecular docking led us to identify the translation termination factor G1 to S phase transition 1 (GSPT1) as a converging off-target, resulting from inadvertent E3 ligase modulation. This research highlights the importance of monitoring degradation events that are independent of the respective targeting ligand as a unique feature of small-molecule degraders.
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Affiliation(s)
- Mette Ishoey
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Someth Chorn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Natesh Singh
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Martin G. Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Michael A. Erb
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
| | - Gerhard F. Ecker
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - James E. Bradner
- Department of Medical Oncology, Dana−Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Georg E. Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Science, Lazarettgasse 14, AKH Bt. 25.3, 1090 Vienna, Austria
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Moser SC, Voerman JSA, Buckley DL, Winter GE, Schliehe C. Acute Pharmacologic Degradation of a Stable Antigen Enhances Its Direct Presentation on MHC Class I Molecules. Front Immunol 2018; 8:1920. [PMID: 29358938 PMCID: PMC5766668 DOI: 10.3389/fimmu.2017.01920] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 09/25/2017] [Accepted: 12/14/2017] [Indexed: 12/23/2022] Open
Abstract
Bifunctional degraders, also referred to as proteolysis-targeting chimeras (PROTACs), are a recently developed class of small molecules. They were designed to specifically target endogenous proteins for ubiquitin/proteasome-dependent degradation and to thereby interfere with pathological mechanisms of diseases, including cancer. In this study, we hypothesized that this process of acute pharmacologic protein degradation might increase the direct MHC class I presentation of degraded targets. By studying this question, we contribute to an ongoing discussion about the origin of peptides feeding the MHC class I presentation pathway. Two scenarios have been postulated: peptides can either be derived from homeostatic turnover of mature proteins and/or from short-lived defective ribosomal products (DRiPs), but currently, it is still unclear to what ratio and efficiency both pathways contribute to the overall MHC class I presentation. We therefore generated the intrinsically stable model antigen GFP-S8L-F12 that was susceptible to acute pharmacologic degradation via the previously described degradation tag (dTAG) system. Using different murine cell lines, we show here that the bifunctional molecule dTAG-7 induced rapid proteasome-dependent degradation of GFP-S8L-F12 and simultaneously increased its direct presentation on MHC class I molecules. Using the same model in a doxycycline-inducible setting, we could further show that stable, mature antigen was the major source of peptides presented, thereby excluding a dominant role of DRiPs in our system. This study is, to our knowledge, the first to investigate targeted pharmacologic protein degradation in the context of antigen presentation and our data point toward future applications by strategically combining therapies using bifunctional degraders with their stimulating effect on direct MHC class I presentation.
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Affiliation(s)
- Sarah C Moser
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jane S A Voerman
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Dennis L Buckley
- Department for Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christopher Schliehe
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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Huang HT, Seo HS, Zhang T, Wang Y, Jiang B, Li Q, Buckley DL, Nabet B, Roberts JM, Paulk J, Dastjerdi S, Winter GE, McLauchlan H, Moran J, Bradner JE, Eck MJ, Dhe-Paganon S, Zhao JJ, Gray NS. MELK is not necessary for the proliferation of basal-like breast cancer cells. eLife 2017; 6. [PMID: 28926338 PMCID: PMC5605198 DOI: 10.7554/elife.26693] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [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: 03/09/2017] [Accepted: 08/18/2017] [Indexed: 01/22/2023] Open
Abstract
Thorough preclinical target validation is essential for the success of drug discovery efforts. In this study, we combined chemical and genetic perturbants, including the development of a novel selective maternal embryonic leucine zipper kinase (MELK) inhibitor HTH-01-091, CRISPR/Cas9-mediated MELK knockout, a novel chemical-induced protein degradation strategy, RNA interference and CRISPR interference to validate MELK as a therapeutic target in basal-like breast cancers (BBC). In common culture conditions, we found that small molecule inhibition, genetic deletion, or acute depletion of MELK did not significantly affect cellular growth. This discrepancy to previous findings illuminated selectivity issues of the widely used MELK inhibitor OTSSP167, and potential off-target effects of MELK-targeting short hairpins. The different genetic and chemical tools developed here allow for the identification and validation of any causal roles MELK may play in cancer biology, which will be required to guide future MELK drug discovery efforts. Furthermore, our study provides a general framework for preclinical target validation.
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Affiliation(s)
- Hai-Tsang Huang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Yubao Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Qing Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Behnam Nabet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Shiva Dastjerdi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Hilary McLauchlan
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States.,Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Jean J Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
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Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, di Iulio J, Souza A, Ott CJ, Roberts JM, Zeid R, Scott TG, Paulk J, Lachance K, Olson CM, Dastjerdi S, Bauer S, Lin CY, Gray NS, Kelliher MA, Churchman LS, Bradner JE. BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment. Mol Cell 2017; 67:5-18.e19. [PMID: 28673542 DOI: 10.1016/j.molcel.2017.06.004] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [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: 12/06/2016] [Revised: 03/14/2017] [Accepted: 06/02/2017] [Indexed: 12/19/2022]
Abstract
Processive elongation of RNA Polymerase II from a proximal promoter paused state is a rate-limiting event in human gene control. A small number of regulatory factors influence transcription elongation on a global scale. Prior research using small-molecule BET bromodomain inhibitors, such as JQ1, linked BRD4 to context-specific elongation at a limited number of genes associated with massive enhancer regions. Here, the mechanistic characterization of an optimized chemical degrader of BET bromodomain proteins, dBET6, led to the unexpected identification of BET proteins as master regulators of global transcription elongation. In contrast to the selective effect of bromodomain inhibition on transcription, BET degradation prompts a collapse of global elongation that phenocopies CDK9 inhibition. Notably, BRD4 loss does not directly affect CDK9 localization. These studies, performed in translational models of T cell leukemia, establish a mechanism-based rationale for the development of BET bromodomain degradation as cancer therapy.
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Affiliation(s)
- Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andreas Mayer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michael A Erb
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sarah Vittori
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jaime M Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Julia di Iulio
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Souza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kate Lachance
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Calla M Olson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Shiva Dastjerdi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
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37
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Winter GE, Buckley DL, Bradner JE. Abstract IA31: Phthalimide conjugation as a strategy for targeted protein degradation. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.pmccavuln16-ia31] [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
Ligand-induced target protein destabilization is an efficacious therapeutic strategy in cancer, but discovery in this field has historically been serendipitous given the lack of rational design principles. Building on the molecular logic of immunomodulatory drugs (“IMiDs”), we innovated a facile chemical solution for targeted protein degradation using bifunctional small molecules capable of recruiting the E3 ligase cereblon (CRBN). These bifunctional molecules induce immediate, and complete proteasomal degradation of their target proteins and thus represent a novel class of small molecule therapeutics with an entirely uncharted and unique molecular pharmacology.
Focusing our initial efforts on degraders of the BET family of proteins, we observed that they exhibit superior efficacy than BET inhibitors through unknown mechanisms. In order to dissect and mechanistically explain that differential molecular pharmacology, we used optimized small-molecule degraders and kinetic measures of chromatin structure and function to unveil an unrecognized, essential role for BRD4 in global control of transcriptional pause-release. Targeted BET degradation nucleates a collapse in the transcriptional core regulatory circuitry and thus enabled us to exploit transcriptional addictions in T-Cell acute lymphoblastic leukemia (T-ALL) that were intractable using competitive BET bromodomain inhibitors.
Citation Format: Georg E. Winter, Dennis L. Buckley, James E. Bradner. Phthalimide conjugation as a strategy for targeted protein degradation. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr IA31.
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Wu Q, Madany P, Akech J, Dobson JR, Douthwright S, Browne G, Colby JL, Winter GE, Bradner JE, Pratap J, Sluder G, Bhargava R, Chiosea SI, van Wijnen AJ, Stein JL, Stein GS, Lian JB, Nickerson JA, Imbalzano AN. The SWI/SNF ATPases Are Required for Triple Negative Breast Cancer Cell Proliferation. J Cell Physiol 2015; 230:2683-94. [PMID: 25808524 DOI: 10.1002/jcp.24991] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/18/2015] [Indexed: 12/30/2022]
Abstract
The Brahma (BRM) and Brahma-related Gene 1 (BRG1) ATPases are highly conserved homologs that catalyze the chromatin remodeling functions of the multi-subunit human SWI/SNF chromatin remodeling enzymes in a mutually exclusive manner. SWI/SNF enzyme subunits are mutated or missing in many cancer types, but are overexpressed without apparent mutation in other cancers. Here, we report that both BRG1 and BRM are overexpressed in most primary breast cancers independent of the tumor's receptor status. Knockdown of either ATPase in a triple negative breast cancer cell line reduced tumor formation in vivo and cell proliferation in vitro. Fewer cells in S phase and an extended cell cycle progression time were observed without any indication of apoptosis, senescence, or alterations in migration or attachment properties. Combined knockdown of BRM and BRG1 showed additive effects in the reduction of cell proliferation and time required for completion of cell cycle, suggesting that these enzymes promote cell cycle progression through independent mechanisms. Knockout of BRG1 or BRM using CRISPR/Cas9 technology resulted in the loss of viability, consistent with a requirement for both enzymes in triple negative breast cancer cells.
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Affiliation(s)
- Qiong Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Pasil Madany
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jacqueline Akech
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jason R Dobson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Department of Computer Science, Brown University, Providence, Rhode Island
| | - Stephen Douthwright
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Gillian Browne
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Biochemistry and Vermont Cancer Center for Basic and Translational Research, University of Vermont College of Medicine, Burlington, Vermont
| | - Jennifer L Colby
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jitesh Pratap
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Anatomy and Cell Biology, Rush University, Chicago, Illinois
| | - Greenfield Sluder
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Rohit Bhargava
- Department of Pathology, Magee-Womens Hospital, Pittsburgh, Pennsylvania
| | - Simion I Chiosea
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Andre J van Wijnen
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
- Departments of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Janet L Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Biochemistry and Vermont Cancer Center for Basic and Translational Research, University of Vermont College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Biochemistry and Vermont Cancer Center for Basic and Translational Research, University of Vermont College of Medicine, Burlington, Vermont
| | - Jane B Lian
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Biochemistry and Vermont Cancer Center for Basic and Translational Research, University of Vermont College of Medicine, Burlington, Vermont
- Department of Orthopedics and Physical Rehabilitation, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
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Dixon SJ, Winter GE, Musavi LS, Lee ED, Snijder B, Rebsamen M, Superti-Furga G, Stockwell BR. Human Haploid Cell Genetics Reveals Roles for Lipid Metabolism Genes in Nonapoptotic Cell Death. ACS Chem Biol 2015; 10:1604-9. [PMID: 25965523 PMCID: PMC4509420 DOI: 10.1021/acschembio.5b00245] [Citation(s) in RCA: 572] [Impact Index Per Article: 63.6] [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] [Indexed: 02/07/2023]
Abstract
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Little is known about the regulation
of nonapoptotic cell death.
Using massive insertional mutagenesis of haploid KBM7 cells we identified
nine genes involved in small-molecule-induced nonapoptotic cell death,
including mediators of fatty acid metabolism (ACSL4) and lipid remodeling (LPCAT3) in ferroptosis.
One novel compound, CIL56, triggered cell death dependent upon the
rate-limiting de novo lipid synthetic enzyme ACC1.
These results provide insight into the genetic regulation of cell
death and highlight the central role of lipid metabolism in nonapoptotic
cell death.
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Affiliation(s)
- Scott J. Dixon
- Department
of Biology, Stanford University, 337 Campus Drive, Stanford, California 94305, United States
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | | | | | - Berend Snijder
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Manuele Rebsamen
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
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Winter GE, Buckley DL, Paulk J, Roberts JM, Souza A, Dhe-Paganon S, Bradner JE. DRUG DEVELOPMENT. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 2015; 348:1376-81. [PMID: 25999370 DOI: 10.1126/science.aab1433] [Citation(s) in RCA: 1084] [Impact Index Per Article: 120.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/06/2015] [Indexed: 01/23/2023]
Abstract
The development of effective pharmacological inhibitors of multidomain scaffold proteins, notably transcription factors, is a particularly challenging problem. In part, this is because many small-molecule antagonists disrupt the activity of only one domain in the target protein. We devised a chemical strategy that promotes ligand-dependent target protein degradation using as an example the transcriptional coactivator BRD4, a protein critical for cancer cell growth and survival. We appended a competitive antagonist of BET bromodomains to a phthalimide moiety to hijack the cereblon E3 ubiquitin ligase complex. The resultant compound, dBET1, induced highly selective cereblon-dependent BET protein degradation in vitro and in vivo and delayed leukemia progression in mice. A second series of probes resulted in selective degradation of the cytosolic protein FKBP12. This chemical strategy for controlling target protein stability may have implications for therapeutically targeting previously intractable proteins.
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Affiliation(s)
- Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Amanda Souza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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Winter GE, Radic B, Mayor-Ruiz C, Blomen VA, Trefzer C, Kandasamy RK, Huber KVM, Gridling M, Chen D, Klampfl T, Kralovics R, Kubicek S, Fernandez-Capetillo O, Brummelkamp TR, Superti-Furga G. The solute carrier SLC35F2 enables YM155-mediated DNA damage toxicity. Nat Chem Biol 2014; 10:768-773. [PMID: 25064833 DOI: 10.1038/nchembio.1590] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/19/2014] [Indexed: 01/09/2023]
Abstract
Genotoxic chemotherapy is the most common cancer treatment strategy. However, its untargeted generic DNA-damaging nature and associated systemic cytotoxicity greatly limit its therapeutic applications. Here, we used a haploid genetic screen in human cells to discover an absolute dependency of the clinically evaluated anticancer compound YM155 on solute carrier family member 35 F2 (SLC35F2), an uncharacterized member of the solute carrier protein family that is highly expressed in a variety of human cancers. YM155 generated DNA damage through intercalation, which was contingent on the expression of SLC35F2 and its drug-importing activity. SLC35F2 expression and YM155 sensitivity correlated across a panel of cancer cell lines, and targeted genome editing verified SLC35F2 as the main determinant of YM155-mediated DNA damage toxicity in vitro and in vivo. These findings suggest a new route to targeted DNA damage by exploiting tumor and patient-specific import of YM155.
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Affiliation(s)
- Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Branka Radic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Vincent A Blomen
- Division of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Claudia Trefzer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Richard K Kandasamy
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Kilian V M Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Manuela Gridling
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Doris Chen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Thorsten Klampfl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | | | - Thijn R Brummelkamp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria.,Division of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
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Borgdorff V, Rix U, Winter GE, Gridling M, Müller AC, Breitwieser FP, Wagner C, Colinge J, Bennett KL, Superti-Furga G, Wagner SN. A chemical biology approach identifies AMPK as a modulator of melanoma oncogene MITF. Oncogene 2013; 33:2531-9. [DOI: 10.1038/onc.2013.185] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 01/29/2013] [Accepted: 04/12/2013] [Indexed: 12/12/2022]
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Winter GE, Rix U, Lissat A, Stukalov A, Müllner MK, Bennett KL, Colinge J, Nijman SM, Kubicek S, Kovar H, Kontny U, Superti-Furga G. An Integrated Chemical Biology Approach Identifies Specific Vulnerability of Ewing's Sarcoma to Combined Inhibition of Aurora Kinases A and B. Mol Cancer Ther 2011; 10:1846-56. [DOI: 10.1158/1535-7163.mct-11-0100] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Ubaida Mohien C, Hartler J, Breitwieser F, Rix U, Remsing Rix L, Winter GE, Thallinger GG, Bennett KL, Superti-Furga G, Trajanoski Z, Colinge J. MASPECTRAS 2: An integration and analysis platform for proteomic data. Proteomics 2010; 10:2719-22. [PMID: 20455215 DOI: 10.1002/pmic.201000075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
MASPECTRAS 2 is a freely available platform for integrating MS protein identifications with information from the major bioinformatics databases (ontologies, domains, literature, etc.). It assists researchers in understanding their data and publishing through sample comparisons, targeted queries, summaries, and exports in multiple formats such as PRIDE XML (Jones et al., Nucleic Acids Res. 2008, 36, D878-D883). MASPECTRAS 2 also comprises mechanisms to facilitate its integration in a high-throughput infrastructure. We illustrate application of MASPECTRAS 2 with unpublished tyrosine kinase inhibitor drug proteomics profiles in cancerous cells.
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Winter GE. ALCHEMY AND THE ALCHEMISTS. Bull Med Libr Assoc 1933; 21:79-88. [PMID: 16016137 PMCID: PMC234292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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