1
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Martinelli P, Schaaf O, Mantoulidis A, Martin LJ, Fuchs JE, Bader G, Gollner A, Wolkerstorfer B, Rogers C, Balıkçı E, Lipp JJ, Mischerikow N, Doebel S, Gerstberger T, Sommergruber W, Huber KVM, Böttcher J. Discovery of a Chemical Probe to Study Implications of BPTF Bromodomain Inhibition in Cellular and in vivo Experiments. ChemMedChem 2023; 18:e202200686. [PMID: 36649575 DOI: 10.1002/cmdc.202200686] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
The bromodomain and PHD-finger containing transcription factor (BPTF) is part of the nucleosome remodeling factor (NURF) complex and has been implicated in multiple cancer types. Here, we report the discovery of a potent and selective chemical probe targeting the bromodomain of BPTF with an attractive pharmacokinetic profile enabling cellular and in vivo experiments in mice. Microarray-based transcriptomics in presence of the probe in two lung cancer cell lines revealed only minor effects on the transcriptome. Profiling against a panel of cancer cell lines revealed that the antiproliferative effect does not correlate with BPTF dependency score in depletion screens. Both observations and the multi-domain architecture of BPTF suggest that depleting the protein by proteolysis targeting chimeras (PROTACs) could be a promising strategy to target cancer cell proliferation. We envision that the presented chemical probe and the related negative control will enable the research community to further explore scientific hypotheses with respect to BPTF bromodomain inhibition.
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Affiliation(s)
- Paola Martinelli
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Otmar Schaaf
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Andreas Mantoulidis
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Laetitia J Martin
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Andreas Gollner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Bernhard Wolkerstorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Catherine Rogers
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
| | - Esra Balıkçı
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
| | - Jesse J Lipp
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Nikolai Mischerikow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Sandra Doebel
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Wolfgang Sommergruber
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Kilian V M Huber
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, Oxford, UK
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120, Vienna, Austria
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2
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Bröker J, Waterson AG, Smethurst C, Kessler D, Böttcher J, Mayer M, Gmaschitz G, Phan J, Little A, Abbott JR, Sun Q, Gmachl M, Rudolph D, Arnhof H, Rumpel K, Savarese F, Gerstberger T, Mischerikow N, Treu M, Herdeis L, Wunberg T, Gollner A, Weinstabl H, Mantoulidis A, Krämer O, McConnell DB, W. Fesik S. Fragment Optimization of Reversible Binding to the Switch II Pocket on KRAS Leads to a Potent, In Vivo Active KRAS G12C Inhibitor. J Med Chem 2022; 65:14614-14629. [PMID: 36300829 PMCID: PMC9661478 DOI: 10.1021/acs.jmedchem.2c01120] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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Activating mutations
in KRAS are the most frequent oncogenic alterations
in cancer. The oncogenic hotspot position 12, located at the lip of
the switch II pocket, offers a covalent attachment point for KRASG12C inhibitors. To date, KRASG12C inhibitors have
been discovered by first covalently binding to the cysteine at position
12 and then optimizing pocket binding. We report on the discovery
of the in vivo active KRASG12C inhibitor BI-0474 using
a different approach, in which small molecules that bind reversibly
to the switch II pocket were identified and then optimized for non-covalent
binding using structure-based design. Finally, the Michael acceptor
containing warhead was attached. Our approach offers not only an alternative
approach to discovering KRASG12C inhibitors but also provides
a starting point for the discovery of inhibitors against other oncogenic
KRAS mutants.
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Affiliation(s)
- Joachim Bröker
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Alex G. Waterson
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Chris Smethurst
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Gerhard Gmaschitz
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Andrew Little
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Jason R. Abbott
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Qi Sun
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Michael Gmachl
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Dorothea Rudolph
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Heribert Arnhof
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Fabio Savarese
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Nikolai Mischerikow
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Matthias Treu
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Lorenz Herdeis
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Tobias Wunberg
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Andreas Gollner
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Harald Weinstabl
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Andreas Mantoulidis
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Oliver Krämer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Darryl B. McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
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3
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Kofink C, Trainor N, Mair B, Wöhrle S, Wurm M, Mischerikow N, Roy MJ, Bader G, Greb P, Garavel G, Diers E, McLennan R, Whitworth C, Vetma V, Rumpel K, Scharnweber M, Fuchs JE, Gerstberger T, Cui Y, Gremel G, Chetta P, Hopf S, Budano N, Rinnenthal J, Gmaschitz G, Mayer M, Koegl M, Ciulli A, Weinstabl H, Farnaby W. A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo. Nat Commun 2022; 13:5969. [PMID: 36216795 PMCID: PMC9551036 DOI: 10.1038/s41467-022-33430-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [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: 03/02/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022] Open
Abstract
Targeted protein degradation offers an alternative modality to classical inhibition and holds the promise of addressing previously undruggable targets to provide novel therapeutic options for patients. Heterobifunctional molecules co-recruit a target protein and an E3 ligase, resulting in ubiquitylation and proteosome-dependent degradation of the target. In the clinic, the oral route of administration is the option of choice but has only been achieved so far by CRBN- recruiting bifunctional degrader molecules. We aimed to achieve orally bioavailable molecules that selectively degrade the BAF Chromatin Remodelling complex ATPase SMARCA2 over its closely related paralogue SMARCA4, to allow in vivo evaluation of the synthetic lethality concept of SMARCA2 dependency in SMARCA4-deficient cancers. Here we outline structure- and property-guided approaches that led to orally bioavailable VHL-recruiting degraders. Our tool compound, ACBI2, shows selective degradation of SMARCA2 over SMARCA4 in ex vivo human whole blood assays and in vivo efficacy in SMARCA4-deficient cancer models. This study demonstrates the feasibility for broadening the E3 ligase and physicochemical space that can be utilised for achieving oral efficacy with bifunctional molecules. Protein degraders are an emerging drug modality; however, their properties lie beyond typical drug-like space. Here the authors report optimisation via structure-based exit vector and linker design towards the VHL-recruiting PROTAC ACBI2, an orally bioavailable and selective degrader of SMARCA2.
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Affiliation(s)
| | - Nicole Trainor
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.,ACRF Chemical Biology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Melanie Wurm
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Michael J Roy
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.,ACRF Chemical Biology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Emelyne Diers
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ross McLennan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Claire Whitworth
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vesna Vetma
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Yunhai Cui
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | | | - Paolo Chetta
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Stefan Hopf
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Nicole Budano
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - William Farnaby
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
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4
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Wilding B, Scharn D, Böse D, Baum A, Santoro V, Chetta P, Schnitzer R, Botesteanu DA, Reiser C, Kornigg S, Knesl P, Hörmann A, Köferle A, Corcokovic M, Lieb S, Scholz G, Bruchhaus J, Spina M, Balla J, Peric-Simov B, Zimmer J, Mitzner S, Fett TN, Beran A, Lamarre L, Gerstberger T, Gerlach D, Bauer M, Bergner A, Schlattl A, Bader G, Treu M, Engelhardt H, Zahn S, Fuchs JE, Zuber J, Ettmayer P, Pearson M, Petronczki M, Kraut N, McConnell DB, Solca F, Neumüller RA. Discovery of potent and selective HER2 inhibitors with efficacy against HER2 exon 20 insertion-driven tumors, which preserve wild-type EGFR signaling. Nat Cancer 2022; 3:821-836. [PMID: 35883003 DOI: 10.1038/s43018-022-00412-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Oncogenic alterations in human epidermal growth factor receptor 2 (HER2) occur in approximately 2% of patients with non-small cell lung cancer and predominantly affect the tyrosine kinase domain and cluster in exon 20 of the ERBB2 gene. Most clinical-grade tyrosine kinase inhibitors are limited by either insufficient selectivity against wild-type (WT) epidermal growth factor receptor (EGFR), which is a major cause of dose-limiting toxicity or by potency against HER2 exon 20 mutant variants. Here we report the discovery of covalent tyrosine kinase inhibitors that potently inhibit HER2 exon 20 mutants while sparing WT EGFR, which reduce tumor cell survival and proliferation in vitro and result in regressions in preclinical xenograft models of HER2 exon 20 mutant non-small cell lung cancer, concomitant with inhibition of downstream HER2 signaling. Our results suggest that HER2 exon 20 insertion-driven tumors can be effectively treated by a potent and highly selective HER2 inhibitor while sparing WT EGFR, paving the way for clinical translation.
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Affiliation(s)
| | | | | | - Anke Baum
- Boehringer Ingelheim RCV, Vienna, Austria
| | | | | | | | | | | | | | - Petr Knesl
- Boehringer Ingelheim RCV, Vienna, Austria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gerd Bader
- Boehringer Ingelheim RCV, Vienna, Austria
| | | | | | | | | | - Johannes Zuber
- Institute of Molecular Pathology (IMP), Vienna, Austria
- Medical University of Vienna, Vienna, Austria
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5
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Neumüller RA, Wilding B, Scharn D, Böse D, Santoro V, Gerlach D, Ettmayer P, Gerstberger T, Fuchs J, Treu M, Zahn S, Baum A, Chetta P, Pearson M, McConnell DB, Kraut N, Solca F. Abstract 1472: Novel EGFR WT sparing, HER2 selective inhibitors for the treatment of HER2 exon 20 insertion driven tumors address a clear unmet medical need. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Activating mutations in ERBB2 receptors are tractable oncogenes in 2-3% of NSCLC patients for whom no approved targeted therapies are available. In this indication, oncogenic mutations in HER2 predominantly affect the tyrosine kinase domain and cluster in exon 20 of the ERBB2 gene. We initiated a drug discovery program aiming at discovering novel HER2 selective inhibitors sparing EGFR WT activity. Focus was set on the most frequent HER2 mutation (ERBB2 A775 insYVMA), which is least sensitive to current compounds tested in clinical trials. Here, we report the identification and pharmacological characterization of novel selective HER2 exon 20 mutation TKIs that differ from currently tested TKIs such as poziotinib, TAK-788 or BDTX-189. We could demonstrate that selective inhibition of oncogenic HER2 signaling abrogates oncogenic signaling in in vitro models. Cell survival and proliferation was reduced, which translated into tumor regressions in preclinical CRISPR engineered xenotransplantation models of HER2 exon 20 mutants. The in vivo efficacy was confirmed in patient-derived tumor models. Our results suggest that HER2 exon 20 insertions can be effectively treated by a potent and highly selective HER2 inhibitor that spares EGFR wild type. These findings warrant the upcoming clinical testing in HER2 mutant NSCLC patients in order to effectively treat this aggressive type of cancer.
Citation Format: Ralph A. Neumüller, Birgit Wilding, Dirk Scharn, Dietrich Böse, Valeria Santoro, Daniel Gerlach, Peter Ettmayer, Thomas Gerstberger, Julian Fuchs, Matthias Treu, Stephan Zahn, Anke Baum, Paolo Chetta, Mark Pearson, Darryl B. McConnell, Norbert Kraut, Flavio Solca. Novel EGFR WT sparing, HER2 selective inhibitors for the treatment of HER2 exon 20 insertion driven tumors address a clear unmet medical need [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1472.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Anke Baum
- Boehringer Ingelheim, Vienna, Austria
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6
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Ramharter J, Kessler D, Ettmayer P, Hofmann MH, Gerstberger T, Gmachl M, Wunberg T, Kofink C, Sanderson M, Arnhof H, Bader G, Rumpel K, Zöphel A, Schnitzer R, Böttcher J, O'Connell JC, Mendes RL, Richard D, Pototschnig N, Weiner I, Hela W, Hauer K, Haering D, Lamarre L, Wolkerstorfer B, Salamon C, Werni P, Munico-Martinez S, Meyer R, Kennedy MD, Kraut N, McConnell DB. One Atom Makes All the Difference: Getting a Foot in the Door between SOS1 and KRAS. J Med Chem 2021; 64:6569-6580. [PMID: 33719426 DOI: 10.1021/acs.jmedchem.0c01949] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
KRAS, the most common oncogenic driver in human cancers, is controlled and signals primarily through protein-protein interactions (PPIs). The interaction between KRAS and SOS1, crucial for the activation of KRAS, is a typical, challenging PPI with a large contact surface area and high affinity. Here, we report that the addition of only one atom placed between Y884SOS1 and A73KRAS is sufficient to convert SOS1 activators into SOS1 inhibitors. We also disclose the discovery of BI-3406. Combination with the upstream EGFR inhibitor afatinib shows in vivo efficacy against KRASG13D mutant colorectal tumor cells, demonstrating the utility of BI-3406 to probe SOS1 biology. These findings challenge the dogma that large molecules are required to disrupt challenging PPIs. Instead, a "foot in the door" approach, whereby single atoms or small functional groups placed between key PPI interactions, can lead to potent inhibitors even for challenging PPIs such as SOS1-KRAS.
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Affiliation(s)
- Juergen Ramharter
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Marco H Hofmann
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Michael Gmachl
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Tobias Wunberg
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Christiane Kofink
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Michael Sanderson
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Heribert Arnhof
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Andreas Zöphel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Renate Schnitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Jonathan C O'Connell
- Forma Therapeutics, 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Rachel L Mendes
- Forma Therapeutics, 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - David Richard
- Forma Therapeutics, 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Nikolai Pototschnig
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Irene Weiner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Wolfgang Hela
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Katja Hauer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Daniela Haering
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Lyne Lamarre
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Bernhard Wolkerstorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Christian Salamon
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Patrick Werni
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Silvia Munico-Martinez
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Reiner Meyer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Matthew D Kennedy
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
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7
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Hofmann MH, Gmachl M, Ramharter J, Savarese F, Gerlach D, Marszalek JR, Sanderson MP, Kessler D, Trapani F, Arnhof H, Rumpel K, Botesteanu DA, Ettmayer P, Gerstberger T, Kofink C, Wunberg T, Zoephel A, Fu SC, Teh JL, Böttcher J, Pototschnig N, Schachinger F, Schipany K, Lieb S, Vellano CP, O'Connell JC, Mendes RL, Moll J, Petronczki M, Heffernan TP, Pearson M, McConnell DB, Kraut N. BI-3406, a Potent and Selective SOS1-KRAS Interaction Inhibitor, Is Effective in KRAS-Driven Cancers through Combined MEK Inhibition. Cancer Discov 2020; 11:142-157. [PMID: 32816843 DOI: 10.1158/2159-8290.cd-20-0142] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/14/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022]
Abstract
KRAS is the most frequently mutated driver of pancreatic, colorectal, and non-small cell lung cancers. Direct KRAS blockade has proved challenging, and inhibition of a key downstream effector pathway, the RAF-MEK-ERK cascade, has shown limited success because of activation of feedback networks that keep the pathway in check. We hypothesized that inhibiting SOS1, a KRAS activator and important feedback node, represents an effective approach to treat KRAS-driven cancers. We report the discovery of a highly potent, selective, and orally bioavailable small-molecule SOS1 inhibitor, BI-3406, that binds to the catalytic domain of SOS1, thereby preventing the interaction with KRAS. BI-3406 reduces formation of GTP-loaded RAS and limits cellular proliferation of a broad range of KRAS-driven cancers. Importantly, BI-3406 attenuates feedback reactivation induced by MEK inhibitors and thereby enhances sensitivity of KRAS-dependent cancers to MEK inhibition. Combined SOS1 and MEK inhibition represents a novel and effective therapeutic concept to address KRAS-driven tumors. SIGNIFICANCE: To date, there are no effective targeted pan-KRAS therapies. In-depth characterization of BI-3406 activity and identification of MEK inhibitors as effective combination partners provide an attractive therapeutic concept for the majority of KRAS-mutant cancers, including those fueled by the most prevalent mutant KRAS oncoproteins, G12D, G12V, G12C, and G13D.See related commentary by Zhao et al., p. 17.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
| | | | | | | | | | - Joseph R Marszalek
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | | | | | - Szu-Chin Fu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jessica L Teh
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Christopher P Vellano
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jurgen Moll
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Timothy P Heffernan
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.
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8
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Hofmann MH, Mani R, Engelhardt H, Impagnatiello MA, Carotta S, Kerenyi M, Lorenzo-Herrero S, Böttcher J, Scharn D, Arnhof H, Zoephel A, Schnitzer R, Gerstberger T, Sanderson MP, Rajgolikar G, Goswami S, Vasu S, Ettmayer P, Gonzalez S, Pearson M, McConnell DB, Kraut N, Muthusamy N, Moll J. Selective and Potent CDK8/19 Inhibitors Enhance NK-Cell Activity and Promote Tumor Surveillance. Mol Cancer Ther 2020; 19:1018-1030. [PMID: 32024684 DOI: 10.1158/1535-7163.mct-19-0789] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/18/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cells play a pivotal role in controlling cancer. Multiple extracellular receptors and internal signaling nodes tightly regulate NK activation. Cyclin-dependent kinases of the mediator complex (CDK8 and CDK19) were described as a signaling intermediates in NK cells. Here, we report for the first time the development and use of CDK8/19 inhibitors to suppress phosphorylation of STAT1S727 in NK cells and to augment the production of the cytolytic molecules perforin and granzyme B (GZMB). Functionally, this resulted in enhanced NK-cell-mediated lysis of primary leukemia cells. Treatment with the CDK8/19 inhibitor BI-1347 increased the response rate and survival of mice bearing melanoma and breast cancer xenografts. In addition, CDK8/19 inhibition augmented the antitumoral activity of anti-PD-1 antibody and SMAC mimetic therapy, both agents that promote T-cell-mediated antitumor immunity. Treatment with the SMAC mimetic compound BI-8382 resulted in an increased number of NK cells infiltrating EMT6 tumors. Combination of the CDK8/19 inhibitor BI-1347, which augments the amount of degranulation enzymes, with the SMAC mimetic BI-8382 resulted in increased survival of mice carrying the EMT6 breast cancer model. The observed survival benefit was dependent on an intermittent treatment schedule of BI-1347, suggesting the importance of circumventing a hyporesponsive state of NK cells. These results suggest that CDK8/19 inhibitors can be combined with modulators of the adaptive immune system to inhibit the growth of solid tumors, independent of their activity on cancer cells, but rather through promoting NK-cell function.
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Affiliation(s)
| | - Rajeswaran Mani
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | | | | | - Marc Kerenyi
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Seila Lorenzo-Herrero
- Department of Functional Biology, Universidad de Oviedo, Instituto de Investigación Biosanitaria del Principado de Asturias (IISPA), IUOPA, Oviedo, Spain
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Dirk Scharn
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | | | - Girish Rajgolikar
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Swagata Goswami
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Sumithira Vasu
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | - Segundo Gonzalez
- Department of Functional Biology, Universidad de Oviedo, Instituto de Investigación Biosanitaria del Principado de Asturias (IISPA), IUOPA, Oviedo, Spain
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Natarajan Muthusamy
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Jürgen Moll
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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9
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Hofmann MH, Gmachl M, Ramharter J, Savarese F, Gerlach D, Marszalek JR, Sanderson MP, Trapani F, Kessler D, Rumpel K, Botesteanu DA, Ettmayer P, Arnhof H, Gerstberger T, Kofink C, Wunberg T, Fu SC, Teh J, Vellano CP, O’Connell JC, Mendes RL, Moll J, Heffernan TP, Pearson M, McConnell DB, Kraut N. Abstract PL06-01: Discovery of BI-3406: A potent and selective SOS1::KRAS inhibitor opens a new approach for treating KRAS-driven tumors. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-pl06-01] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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
KRAS is the most frequently mutated oncogene with high prevalence in pancreatic, colorectal, and non-small cell lung tumors. KRAS signaling is tightly regulated and various factors, including negative feedback pathways have limited the clinical efficacy of inhibitors of downstream MAPK signaling in the KRAS mutant context. Here we report the discovery of BI-3406 and demonstrate it is a highly potent and selective, orally bioavailable SOS1::KRAS inhibitor which binds to the catalytic domain of the guanine nucleotide exchange factor (GEF) SOS1 thereby preventing the interaction with KRAS-GDP. BI-3406 does not block the interaction of KRAS with SOS2 but elicits activity on a broad panel of KRAS oncogenic variants, including all major G12 and G13 oncoproteins. In KRAS-dependent cancers, BI-3406 potently reduces the formation of GTP-loaded KRAS, and inhibits MAPK pathway signaling. Down-modulation of this signaling cascade by BI-3406 in KRAS G12 or G13 mutant cells effectively limits cell proliferation. As a monotherapy, BI-3406 modulates signaling, as assessed by p-ERK and target genes, and displays marked anti-tumor efficacy in KRAS mutant xenografts. Due to BI-3406 blocking the negative feedback relief induced by MAPK inhibition, it has the potential to sensitize KRAS-dependent cancers to MEK inhibitor treatment. Combination with MEK inhibition leads to profound pathway blockade and tumor regressions in vivo. The combination of SOS1 and MEK inhibition is a potential therapy for the majority of KRAS-driven cancers including those fuelled by the most prevalent KRAS mutant oncoproteins. Furthermore, the pharmacological properties of BI-3406 and close analogues hold the promise of a significant treatment benefit in a broad patient population that is currently lacking precision medicine options. A Phase 1 clinical trial is in preparation for patients with advanced KRAS-mutated cancers to evaluate safety, tolerability, pharmacokinetic and pharmacodynamic properties, and preliminary efficacy of BI 1701963, a SOS1::KRAS inhibitor closely related to BI-3406.
Citation Format: Marco H Hofmann, Michael Gmachl, Jürgen Ramharter, Fabio Savarese, Daniel Gerlach, Joseph R Marszalek, Michael P Sanderson, Francesca Trapani, Dirk Kessler, Klaus Rumpel, Dana-Adriana Botesteanu, Peter Ettmayer, Heribert Arnhof, Thomas Gerstberger, Christiane Kofink, Tobias Wunberg, Szu-Chin Fu, Jessica Teh, Christopher P. Vellano, Jonathan C. O’Connell, Rachel L Mendes, Juergen Moll, Timothy P. Heffernan, Mark Pearson, Darryl B McConnell, Norbert Kraut. Discovery of BI-3406: A potent and selective SOS1::KRAS inhibitor opens a new approach for treating KRAS-driven tumors [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 PL06-01. doi:10.1158/1535-7163.TARG-19-PL06-01
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Szu-Chin Fu
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jessica Teh
- 2The University of Texas MD Anderson Cancer Center, Houston, TX
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10
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Engelhardt H, Böse D, Petronczki M, Scharn D, Bader G, Baum A, Bergner A, Chong E, Döbel S, Egger G, Engelhardt C, Ettmayer P, Fuchs JE, Gerstberger T, Gonnella N, Grimm A, Grondal E, Haddad N, Hopfgartner B, Kousek R, Krawiec M, Kriz M, Lamarre L, Leung J, Mayer M, Patel ND, Simov BP, Reeves JT, Schnitzer R, Schrenk A, Sharps B, Solca F, Stadtmüller H, Tan Z, Wunberg T, Zoephel A, McConnell DB. Start Selective and Rigidify: The Discovery Path toward a Next Generation of EGFR Tyrosine Kinase Inhibitors. J Med Chem 2019; 62:10272-10293. [PMID: 31689114 DOI: 10.1021/acs.jmedchem.9b01169] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [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
The epidermal growth factor receptor (EGFR), when carrying an activating mutation like del19 or L858R, acts as an oncogenic driver in a subset of lung tumors. While tumor responses to tyrosine kinase inhibitors (TKIs) are accompanied by marked tumor shrinkage, the response is usually not durable. Most patients relapse within two years of therapy often due to acquisition of an additional mutation in EGFR kinase domain that confers resistance to TKIs. Crucially, oncogenic EGFR harboring both resistance mutations, T790M and C797S, can no longer be inhibited by currently approved EGFR TKIs. Here, we describe the discovery of BI-4020, which is a noncovalent, wild-type EGFR sparing, macrocyclic TKI. BI-4020 potently inhibits the above-described EGFR variants and induces tumor regressions in a cross-resistant EGFRdel19 T790M C797S xenograft model. Key was the identification of a highly selective but moderately potent benzimidazole followed by complete rigidification of the molecule through macrocyclization.
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Affiliation(s)
- Harald Engelhardt
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Dietrich Böse
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Mark Petronczki
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Dirk Scharn
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Anke Baum
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Andreas Bergner
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Eugene Chong
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Sandra Döbel
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Georg Egger
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Christian Engelhardt
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Nina Gonnella
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Andreas Grimm
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Elisabeth Grondal
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Nizar Haddad
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Barbara Hopfgartner
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Roland Kousek
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Mariusz Krawiec
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Monika Kriz
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Lyne Lamarre
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Joyce Leung
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Nitinchandra D Patel
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Biljana Peric Simov
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Jonathan T Reeves
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Renate Schnitzer
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Andreas Schrenk
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Bernadette Sharps
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Flavio Solca
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Heinz Stadtmüller
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Zhulin Tan
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Tobias Wunberg
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Andreas Zoephel
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
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11
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Kessler D, Gmachl M, Mantoulidis A, Martin LJ, Zoephel A, Mayer M, Gollner A, Covini D, Fischer S, Gerstberger T, Gmaschitz T, Goodwin C, Greb P, Häring D, Hela W, Hoffmann J, Karolyi-Oezguer J, Knesl P, Kornigg S, Koegl M, Kousek R, Lamarre L, Moser F, Munico-Martinez S, Peinsipp C, Phan J, Rinnenthal J, Sai J, Salamon C, Scherbantin Y, Schipany K, Schnitzer R, Schrenk A, Sharps B, Siszler G, Sun Q, Waterson A, Wolkerstorfer B, Zeeb M, Pearson M, Fesik SW, McConnell DB. Drugging an undruggable pocket on KRAS. Proc Natl Acad Sci U S A 2019; 116:15823-15829. [PMID: 31332011 PMCID: PMC6689897 DOI: 10.1073/pnas.1904529116] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene. Although KRAS is an excellent drug discovery target for many cancers, and despite decades of research, no therapeutic agent directly targeting RAS has been clinically approved. Using structure-based drug design, we have discovered BI-2852 (1), a KRAS inhibitor that binds with nanomolar affinity to a pocket, thus far perceived to be "undruggable," between switch I and II on RAS; 1 is mechanistically distinct from covalent KRASG12C inhibitors because it binds to a different pocket present in both the active and inactive forms of KRAS. In doing so, it blocks all GEF, GAP, and effector interactions with KRAS, leading to inhibition of downstream signaling and an antiproliferative effect in the low micromolar range in KRAS mutant cells. These findings clearly demonstrate that this so-called switch I/II pocket is indeed druggable and provide the scientific community with a chemical probe that simultaneously targets the active and inactive forms of KRAS.
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Affiliation(s)
- Dirk Kessler
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Michael Gmachl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Mantoulidis
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Laetitia J Martin
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Zoephel
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Moriz Mayer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Gollner
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - David Covini
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Silke Fischer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Thomas Gerstberger
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Teresa Gmaschitz
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Craig Goodwin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Peter Greb
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Daniela Häring
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Wolfgang Hela
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Johann Hoffmann
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jale Karolyi-Oezguer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Petr Knesl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Stefan Kornigg
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Manfred Koegl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Roland Kousek
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Lyne Lamarre
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Franziska Moser
- Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, D-88397 Biberach an der Riss, Germany
| | - Silvia Munico-Martinez
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Christoph Peinsipp
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Jörg Rinnenthal
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Christian Salamon
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Yvonne Scherbantin
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Katharina Schipany
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Renate Schnitzer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Schrenk
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Bernadette Sharps
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Gabriella Siszler
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Qi Sun
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Alex Waterson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Bernhard Wolkerstorfer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Markus Zeeb
- Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, D-88397 Biberach an der Riss, Germany
| | - Mark Pearson
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria;
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12
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Weinstabl H, Treu M, Rinnenthal J, Zahn SK, Ettmayer P, Bader G, Dahmann G, Kessler D, Rumpel K, Mischerikow N, Savarese F, Gerstberger T, Mayer M, Zoephel A, Schnitzer R, Sommergruber W, Martinelli P, Arnhof H, Peric-Simov B, Hofbauer KS, Garavel G, Scherbantin Y, Mitzner S, Fett TN, Scholz G, Bruchhaus J, Burkard M, Kousek R, Ciftci T, Sharps B, Schrenk A, Harrer C, Haering D, Wolkerstorfer B, Zhang X, Lv X, Du A, Li D, Li Y, Quant J, Pearson M, McConnell DB. Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) Inhibitor BI-4924 Disrupts Serine Biosynthesis. J Med Chem 2019; 62:7976-7997. [DOI: 10.1021/acs.jmedchem.9b00718] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Harald Weinstabl
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Matthias Treu
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Joerg Rinnenthal
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Stephan K. Zahn
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Georg Dahmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riß, Germany
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Nikolai Mischerikow
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Fabio Savarese
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Andreas Zoephel
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Renate Schnitzer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Wolfgang Sommergruber
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Paola Martinelli
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Heribert Arnhof
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Biljana Peric-Simov
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Karin S. Hofbauer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Géraldine Garavel
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Yvonne Scherbantin
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Sophie Mitzner
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Thomas N. Fett
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Guido Scholz
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Jens Bruchhaus
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Michelle Burkard
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Roland Kousek
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Tuncay Ciftci
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riß, Germany
| | - Bernadette Sharps
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Andreas Schrenk
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Christoph Harrer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Daniela Haering
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | | | - Xuechun Zhang
- Shanghai ChemPartner Co., LTD., No. 5 Building, 998 Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, China
| | - Xiaobing Lv
- Shanghai ChemPartner Co., LTD., No. 5 Building, 998 Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, China
| | - Alicia Du
- Shanghai ChemPartner Co., LTD., No. 5 Building, 998 Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, China
| | - Dongyang Li
- Shanghai ChemPartner Co., LTD., No. 5 Building, 998 Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, China
| | - Yali Li
- Shanghai ChemPartner Co., LTD., No. 5 Building, 998 Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, China
| | - Jens Quant
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Darryl B. McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, 1121 Vienna, Austria
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13
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Farnaby W, Koegl M, Roy MJ, Whitworth C, Diers E, Trainor N, Zollman D, Steurer S, Karolyi-Oezguer J, Riedmueller C, Gmaschitz T, Wachter J, Dank C, Galant M, Sharps B, Rumpel K, Traxler E, Gerstberger T, Schnitzer R, Petermann O, Greb P, Weinstabl H, Bader G, Zoephel A, Weiss-Puxbaum A, Ehrenhöfer-Wölfer K, Wöhrle S, Boehmelt G, Rinnenthal J, Arnhof H, Wiechens N, Wu MY, Owen-Hughes T, Ettmayer P, Pearson M, McConnell DB, Ciulli A. Publisher Correction: BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nat Chem Biol 2019; 15:846. [DOI: 10.1038/s41589-019-0329-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Farnaby W, Koegl M, Roy MJ, Whitworth C, Diers E, Trainor N, Zollman D, Steurer S, Karolyi-Oezguer J, Riedmueller C, Gmaschitz T, Wachter J, Dank C, Galant M, Sharps B, Rumpel K, Traxler E, Gerstberger T, Schnitzer R, Petermann O, Greb P, Weinstabl H, Bader G, Zoephel A, Weiss-Puxbaum A, Ehrenhöfer-Wölfer K, Wöhrle S, Boehmelt G, Rinnenthal J, Arnhof H, Wiechens N, Wu MY, Owen-Hughes T, Ettmayer P, Pearson M, McConnell DB, Ciulli A. BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nat Chem Biol 2019; 15:672-680. [PMID: 31178587 PMCID: PMC6600871 DOI: 10.1038/s41589-019-0294-6] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 04/16/2019] [Indexed: 12/22/2022]
Abstract
Targeting subunits of BAF/PBAF chromatin remodeling complexes has been proposed as an approach to exploit cancer vulnerabilities. Here we develop PROTAC degraders of the BAF ATPase subunits SMARCA2 and SMARCA4 using a bromodomain ligand and recruitment of the E3 ubiquitin ligase VHL. High-resolution ternary complex crystal structures and biophysical investigation guided rational and efficient optimization towards ACBI1, a potent and cooperative degrader of SMARCA2, SMARCA4 and PBRM1. ACBI1 induced antiproliferative effects and cell death caused by SMARCA2 depletion in SMARCA4 mutant cancer cells, and in acute myeloid leukemia cells dependent on SMARCA4 ATPase activity. These findings exemplify a successful biophysics- and structure-based PROTAC design approach to degrade high profile drug targets and pave the way towards new therapeutics for the treatment of tumors sensitive to the loss of BAF complex ATPases.
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Affiliation(s)
- William Farnaby
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Michael J Roy
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Claire Whitworth
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Emelyne Diers
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicole Trainor
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - David Zollman
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | | | | | | | | | | | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Nicola Wiechens
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Meng-Ying Wu
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.
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15
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Kerres N, Steurer S, Schlager S, Bader G, Caligiuri M, Dank C, Engen JR, Ettmayer P, Gerlach D, Gerstberger T, Han B, Iacob RE, Kessler D, Lancia DR, Moriz M, Mischerikow N, Rumpel K, Schnitzer R, Voss T, Zheng X, Zoephel A, Kraut N, McConnell D, Pearson M, Koegl M. Abstract 3354: Chemically induced degradation of the transcription factor BCL6. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3354] [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
The transcription factor BCL6 is a known driver of oncogenesis in lymphoid malignancies, including diffuse large B-cell lymphoma (DLBCL). Disruption of its interaction with transcriptional repressors interferes with the oncogenic effects of BCL6. We have used structure-based drug design to develop highly potent compounds that block this interaction. A subset of these inhibitors also cause rapid ubiquitylation and degradation of BCL6 in cells. These compounds display significantly stronger induction of expression of BCL6-repressed genes and antiproliferative effects than compounds that merely inhibited co-repressor interaction. The fact that the magnitude of effects elicited by this class of BCL6 degrading compounds greatly exceeds that of our equipotent non-degrading inhibitors offers exciting opportunities for the development of BCL6-based lymphoma therapeutics. To support further research, the most potent BCL6 degrading inhibitor is made freely available to the research community as an in vitro tool compound. Please see http://www.opnMe.com for further infos.
Citation Format: Nina Kerres, Steffen Steurer, Stefanie Schlager, Gerd Bader, Maureen Caligiuri, Christian Dank, John R. Engen, Peter Ettmayer, Daniel Gerlach, Thomas Gerstberger, Bingsong Han, Roxana E. Iacob, Dirk Kessler, David R. Lancia, Mayer Moriz, Nikolai Mischerikow, Klaus Rumpel, Renate Schnitzer, Tilman Voss, Xiaozhang Zheng, Andreas Zoephel, Norbert Kraut, Darryl McConnell, Mark Pearson, Manfred Koegl. Chemically induced degradation of the transcription factor BCL6 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3354.
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16
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Kerres N, Steurer S, Schlager S, Bader G, Berger H, Caligiuri M, Dank C, Engen JR, Ettmayer P, Fischerauer B, Flotzinger G, Gerlach D, Gerstberger T, Gmaschitz T, Greb P, Han B, Heyes E, Iacob RE, Kessler D, Kölle H, Lamarre L, Lancia DR, Lucas S, Mayer M, Mayr K, Mischerikow N, Mück K, Peinsipp C, Petermann O, Reiser U, Rudolph D, Rumpel K, Salomon C, Scharn D, Schnitzer R, Schrenk A, Schweifer N, Thompson D, Traxler E, Varecka R, Voss T, Weiss-Puxbaum A, Winkler S, Zheng X, Zoephel A, Kraut N, McConnell D, Pearson M, Koegl M. Chemically Induced Degradation of the Oncogenic Transcription Factor BCL6. Cell Rep 2018; 20:2860-2875. [PMID: 28930682 DOI: 10.1016/j.celrep.2017.08.081] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [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: 03/10/2017] [Revised: 06/29/2017] [Accepted: 08/24/2017] [Indexed: 01/08/2023] Open
Abstract
The transcription factor BCL6 is a known driver of oncogenesis in lymphoid malignancies, including diffuse large B cell lymphoma (DLBCL). Disruption of its interaction with transcriptional repressors interferes with the oncogenic effects of BCL6. We used a structure-based drug design to develop highly potent compounds that block this interaction. A subset of these inhibitors also causes rapid ubiquitylation and degradation of BCL6 in cells. These compounds display significantly stronger induction of expression of BCL6-repressed genes and anti-proliferative effects than compounds that merely inhibit co-repressor interactions. This work establishes the BTB domain as a highly druggable structure, paving the way for the use of other members of this protein family as drug targets. The magnitude of effects elicited by this class of BCL6-degrading compounds exceeds that of our equipotent non-degrading inhibitors, suggesting opportunities for the development of BCL6-based lymphoma therapeutics.
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Affiliation(s)
- Nina Kerres
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Helmut Berger
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Christian Dank
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | - Daniel Gerlach
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Heike Kölle
- Boehringer Ingelheim, MedChem, Structural Research, Birkendorfer Str. 65, 88397 Biberach, Germany
| | - Lyne Lamarre
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Simon Lucas
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Katharina Mayr
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Katja Mück
- Boehringer Ingelheim, MedChem, Structural Research, Birkendorfer Str. 65, 88397 Biberach, Germany
| | | | | | - Ulrich Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Carina Salomon
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Dirk Scharn
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | | | - Diane Thompson
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Roland Varecka
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Tilman Voss
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Sandra Winkler
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria.
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17
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Gerlach D, Tontsch-Grunt U, Baum A, Popow J, Scharn D, Hofmann MH, Engelhardt H, Kaya O, Beck J, Schweifer N, Gerstberger T, Zuber J, Savarese F, Kraut N. The novel BET bromodomain inhibitor BI 894999 represses super-enhancer-associated transcription and synergizes with CDK9 inhibition in AML. Oncogene 2018; 37:2687-2701. [PMID: 29491412 PMCID: PMC5955861 DOI: 10.1038/s41388-018-0150-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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: 07/21/2017] [Revised: 11/22/2017] [Accepted: 12/30/2017] [Indexed: 01/12/2023]
Abstract
Bromodomain and extra-terminal (BET) protein inhibitors have been reported as treatment options for acute myeloid leukemia (AML) in preclinical models and are currently being evaluated in clinical trials. This work presents a novel potent and selective BET inhibitor (BI 894999), which has recently entered clinical trials (NCT02516553). In preclinical studies, this compound is highly active in AML cell lines, primary patient samples, and xenografts. HEXIM1 is described as an excellent pharmacodynamic biomarker for target engagement in tumors as well as in blood. Mechanistic studies show that BI 894999 targets super-enhancer-regulated oncogenes and other lineage-specific factors, which are involved in the maintenance of the disease state. BI 894999 is active as monotherapy in AML xenografts, and in addition leads to strongly enhanced antitumor effects in combination with CDK9 inhibitors. This treatment combination results in a marked decrease of global p-Ser2 RNA polymerase II levels and leads to rapid induction of apoptosis in vitro and in vivo. Together, these data provide a strong rationale for the clinical evaluation of BI 894999 in AML.
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Affiliation(s)
- Daniel Gerlach
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | | | - Anke Baum
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Dirk Scharn
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Marco H Hofmann
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | | | - Onur Kaya
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | - Janina Beck
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria
| | | | | | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria.,Medical University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Fabio Savarese
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria.
| | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, 1120, Vienna, Austria.
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18
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Kerres N, Steurer S, Schlager S, Bader G, Berger H, Blake S, Caligiuri M, Engen J, Ettmayer P, Gerstberger T, Gerlach D, Jacob R, Lucas S, Mayer M, Nikolai M, Klaus R, Dirk S, Renate S, Voss T, Andreas Z, Kraut N, McConnell D, Mark P, Koegl M. Abstract 1525: Chemically induced degradation of the oncogenic transcription factor BCL6. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1525] [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
The transcription factor BCL6 is a known driver of oncogenesis in lymphoid malignancies, including diffuse large B-cell lymphoma (DLBCL). It is a DNA-binding protein that represses gene transcription through the recruitment of co-repressor proteins via its BTB domain. Disruption of the interaction of BCL6 with co-repressor proteins interferes with the physiological and oncogenic functions of BCL6. We have used structure-based drug desgin to develop potent compounds that block this interaction with half maximal inhibitory concentration values (IC50s) below 3 nM. In addition to inhibiting co-repressor binding, a subset of the identified inhibitors also caused rapid disappearance of BCL6 protein in cells. This effect was mediated by compound-induced multi-ubiquitylation of BCL6 and degradation by the proteasome and was dependent on the presence of a functional DNA binding domain on BCL6. Compounds that induced BCL6 degradation displayed significantly stronger induction of expression of BCL6-repressed genes than compounds that merely inhibited co-repressor interaction. BCL6-degrading inhibitors had anti-proliferative effects in several DLBCL cell lines, while non-degrading BCL6 inhibitors only had minor effects on proliferation. The fact that the magnitude of effects elicited by this novel class of BCL6 degrading compounds greatly exceeds that of our equipotent classical co-repressor interaction inhibitors offers exciting new opportunities for the development of BCL6-based lymphoma therapeutics.
Citation Format: Nina Kerres, Steffen Steurer, Stefanie Schlager, Gerd Bader, Helmut Berger, Sophia Blake, Maureen Caligiuri, John Engen, Peter Ettmayer, Thomas Gerstberger, Daniel Gerlach, Roxana Jacob, Simon Lucas, Moriz Mayer, Mischerikow Nikolai, Rumpel Klaus, Scharn Dirk, Schnitzer Renate, Tilman Voss, Zoephel Andreas, Norbert Kraut, Darryl McConnell, Pearson Mark, Manfred Koegl. Chemically induced degradation of the oncogenic transcription factor BCL6 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1525. doi:10.1158/1538-7445.AM2017-1525
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Affiliation(s)
- Nina Kerres
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Gerd Bader
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Helmut Berger
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Sophia Blake
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | | | | | - Simon Lucas
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Moriz Mayer
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Rumpel Klaus
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Scharn Dirk
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Tilman Voss
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Norbert Kraut
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Pearson Mark
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Manfred Koegl
- 1Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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19
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Gollner A, Rudolph D, Arnhof H, Bauer M, Blake SM, Boehmelt G, Cockroft XL, Dahmann G, Ettmayer P, Gerstberger T, Karolyi-Oezguer J, Kessler D, Kofink C, Ramharter J, Rinnenthal J, Savchenko A, Schnitzer R, Weinstabl H, Weyer-Czernilofsky U, Wunberg T, McConnell DB. Discovery of Novel Spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-one Compounds as Chemically Stable and Orally Active Inhibitors of the MDM2-p53 Interaction. J Med Chem 2016; 59:10147-10162. [PMID: 27775892 DOI: 10.1021/acs.jmedchem.6b00900] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Scaffold modification based on Wang's pioneering MDM2-p53 inhibitors led to novel, chemically stable spiro-oxindole compounds bearing a spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-one scaffold that are not prone to epimerization as observed for the initial spiro[3H-indole-3,3'-pyrrolidin]-2(1H)-one scaffold. Further structure-based optimization inspired by natural product architectures led to a complex fused ring system ideally suited to bind to the MDM2 protein and to interrupt its protein-protein interaction (PPI) with TP53. The compounds are highly selective and show in vivo efficacy in a SJSA-1 xenograft model even when given as a single dose as demonstrated for 4-[(3S,3'S,3'aS,5'R,6'aS)-6-chloro-3'-(3-chloro-2-fluorophenyl)-1'-(cyclopropylmethyl)-2-oxo-1,2,3',3'a,4',5',6',6'a-octahydro-1'H-spiro[indole-3,2'-pyrrolo[3,2-b]pyrrole]-5'-yl]benzoic acid (BI-0252).
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Affiliation(s)
- Andreas Gollner
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Dorothea Rudolph
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Heribert Arnhof
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Markus Bauer
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Sophia M Blake
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Guido Boehmelt
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Xiao-Ling Cockroft
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Georg Dahmann
- Boehringer Ingelheim Pharma GmbH & Co. KG , 88400 Biberach, Germany
| | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Jale Karolyi-Oezguer
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Christiane Kofink
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Juergen Ramharter
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Jörg Rinnenthal
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Alexander Savchenko
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Renate Schnitzer
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Harald Weinstabl
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | | | - Tobias Wunberg
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
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20
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Hohmann AF, Martin LJ, Minder J, Roe JS, Shi J, Steurer S, Bader G, McConnell D, Pearson M, Gerstberger T, Gottschamel T, Thompson D, Suzuki Y, Koegl M, Vakoc C. Abstract LB-206: A bromodomain-swap allele demonstrates that on-target chemical inhibition of BRD9 limits the proliferation of acute myeloid leukemia cells. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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
Recent studies have revealed vital roles of SWI/SNF complexes in leukemia and a variety of other cancers, making this chromatin remodeler a candidate drug target in human malignancy. Chemical modulation of SWI/SNF activity, however, remains to be achieved. Given the success of pharmacological bromodomain inhibition, we evaluated the role of bromodomain-carrying SWI/SNF subunits and identified Bromodomain-containing protein 9 (BRD9) as critical for the growth of Acute Myeloid Leukemia (AML). In AML cells, BRD9 binds the enhancer of the MYC proto-oncogene and sustains MYC transcription, rapid cell proliferation, as well as a block in differentiation. Based on these observations, we derived a small-molecule inhibitor of the BRD9 bromodomain, which partially displaces BRD9 from MYC enhancer elements and selectively suppresses the proliferation of mouse and human AML cell lines.
Given the known role of other bromodomains, namely those of BRD4, in leukemia growth, ruling out potential off-target activity of our BRD9 inhibitor was critical. Traditionally, bromodomain inhibitor selectivity is tested using in vitro binding assays that examine a subset of other bromodomains. To sample the entire space of potential off-target proteins, we sought an in-cell selectivity assay. To this end, we engineered a bromodomain-swap allele of BRD9, which retains functionality despite a radically altered bromodomain pocket. Expression of this allele in AML cells confers resistance to the anti-proliferative effects of our BRD9 inhibitor, thus establishing BRD9 as the relevant cellular target. Furthermore, we used an analogous domain-swap strategy to generate an inhibitor-resistant allele of EZH2.
Our study provides the first evidence for a role of BRD9 in cancer and further highlights a simple genetic strategy for constructing resistance alleles to demonstrate on-target activity of chemical probes in cells.
Citation Format: Anja F. Hohmann, Laetitia J. Martin, Jessica Minder, Jae-Seok Roe, Junwei Shi, Steffen Steurer, Gerd Bader, Darryl McConnell, Mark Pearson, Thomas Gerstberger, Teresa Gottschamel, Diane Thompson, Yutaka Suzuki, Manfred Koegl, Christopher Vakoc. A bromodomain-swap allele demonstrates that on-target chemical inhibition of BRD9 limits the proliferation of acute myeloid leukemia cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-206.
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Affiliation(s)
| | | | | | - Jae-Seok Roe
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Junwei Shi
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Gerd Bader
- 2Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Mark Pearson
- 2Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | - Manfred Koegl
- 2Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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21
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Hohmann AF, Martin LJ, Minder JL, Roe JS, Shi J, Steurer S, Bader G, McConnell D, Pearson M, Gerstberger T, Gottschamel T, Thompson D, Suzuki Y, Koegl M, Vakoc CR. Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition. Nat Chem Biol 2016; 12:672-9. [PMID: 27376689 PMCID: PMC4990482 DOI: 10.1038/nchembio.2115] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [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: 09/11/2015] [Accepted: 04/06/2016] [Indexed: 02/07/2023]
Abstract
Here we show that acute myeloid leukemia (AML) cells require the BRD9 subunit of the SWI-SNF chromatin-remodeling complex to sustain MYC transcription, rapid cell proliferation and a block in differentiation. Based on these observations, we derived small-molecule inhibitors of the BRD9 bromodomain that selectively suppress the proliferation of mouse and human AML cell lines. To establish these effects as on-target, we engineered a bromodomain-swap allele of BRD9 that retains functionality despite a radically altered bromodomain pocket. Expression of this allele in AML cells confers resistance to the antiproliferative effects of our compound series, thus establishing BRD9 as the relevant cellular target. Furthermore, we used an analogous domain-swap strategy to generate an inhibitor-resistant allele of EZH2. To our knowledge, our study provides the first evidence for a role of BRD9 in cancer and reveals a simple genetic strategy for constructing resistance alleles to demonstrate on-target activity of chemical probes in cells.
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Affiliation(s)
- Anja F Hohmann
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Laetitia J Martin
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Jessica L Minder
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Jae-Seok Roe
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Junwei Shi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York, USA
| | - Steffen Steurer
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Gerd Bader
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Darryl McConnell
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Teresa Gottschamel
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Diane Thompson
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, University of Tokyo, Kashiwa, Japan
| | - Manfred Koegl
- Boehringer Ingelheim Regional Center Vienna GmbH and Company KG, Vienna, Austria
| | - Christopher R Vakoc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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22
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Martin LJ, Koegl M, Bader G, Cockcroft XL, Fedorov O, Fiegen D, Gerstberger T, Hofmann MH, Hohmann AF, Kessler D, Knapp S, Knesl P, Kornigg S, Müller S, Nar H, Rogers C, Rumpel K, Schaaf O, Steurer S, Tallant C, Vakoc CR, Zeeb M, Zoephel A, Pearson M, Boehmelt G, McConnell D. Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor. J Med Chem 2016; 59:4462-75. [PMID: 26914985 PMCID: PMC4885110 DOI: 10.1021/acs.jmedchem.5b01865] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [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: 12/13/2022]
Abstract
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Components of the chromatin remodelling
switch/sucrose nonfermentable (SWI/SNF) complex are recurrently mutated
in tumors, suggesting that altering the activity of the complex plays
a role in oncogenesis. However, the role that the individual subunits
play in this process is not clear. We set out to develop an inhibitor
compound targeting the bromodomain of BRD9 in order to evaluate its
function within the SWI/SNF complex. Here, we present the discovery
and development of a potent and selective BRD9 bromodomain inhibitor
series based on a new pyridinone-like scaffold. Crystallographic information
on the inhibitors bound to BRD9 guided their development with respect
to potency for BRD9 and selectivity against BRD4. These compounds
modulate BRD9 bromodomain cellular function and display antitumor
activity in an AML xenograft model. Two chemical probes, BI-7273 (1) and BI-9564 (2), were
identified that should prove to be useful in further exploring BRD9
bromodomain biology in both in vitro and in vivo settings.
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Affiliation(s)
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | | | - Oleg Fedorov
- SGC, University of Oxford , Oxford OX3 7DQ, United Kingdom
| | - Dennis Fiegen
- Boehringer Ingelheim Pharma GmbH & Co KG , Biberach 88400, Germany
| | | | - Marco H Hofmann
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Anja F Hohmann
- Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, United States
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Stefan Knapp
- SGC, University of Oxford , Oxford OX3 7DQ, United Kingdom
| | - Petr Knesl
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Stefan Kornigg
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Susanne Müller
- SGC, University of Oxford , Oxford OX3 7DQ, United Kingdom
| | - Herbert Nar
- Boehringer Ingelheim Pharma GmbH & Co KG , Biberach 88400, Germany
| | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Otmar Schaaf
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Steffen Steurer
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | | | - Christopher R Vakoc
- Cold Spring Harbor Laboratory , Cold Spring Harbor, New York 11724, United States
| | - Markus Zeeb
- Boehringer Ingelheim Pharma GmbH & Co KG , Biberach 88400, Germany
| | - Andreas Zoephel
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
| | - Guido Boehmelt
- Boehringer Ingelheim RCV GmbH & Co KG , Vienna 1121, Austria
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23
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Braunwarth A, Fromont-Racine M, Legrain P, Bischoff FR, Gerstberger T, Hurt E, Kunzler M. Identification and characterization of a novel RanGTP-binding protein in the yeast Saccharomyces cerevisiae. J Biol Chem 2003; 278:15397-405. [PMID: 12578832 DOI: 10.1074/jbc.m210630200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The small Ras-like GTPase Ran plays an essential role in the transport of macromolecules in and out of the nucleus and has been implicated in spindle (1,2 ) and nuclear envelope formation (3,4 ) during mitosis in higher eukaryotes. We identified Saccharomyces cerevisiae open reading frame YGL164c encoding a novel RanGTP-binding protein, termed Yrb30p. The protein competes with yeast RanBP1 (Yrb1p) for binding to the GTP-bound form of yeast Ran (Gsp1p) and is, like Yrb1p, able to form trimeric complexes with RanGTP and some of the karyopherins. In contrast to Yrb1p, Yrb30p does not coactivate but inhibits RanGAP1(Rna1p)-mediated GTP hydrolysis on Ran, like the karyopherins. At steady state, Yrb30p localizes exclusively to the cytoplasm, but the presence of a functional nuclear export signal and the localization of truncated forms of Yrb30p suggest that the protein shuttles between nucleus and cytoplasm and is exported via two alternative pathways, dependent on the nuclear export receptor Xpo1p/Crm1p and on RanGTP binding. Whereas overproduction of the full-length protein and complete deletion of the open reading frame reveal no obvious phenotype, overproduction of C-terminally truncated forms of the protein inhibits yeast vegetative growth. Based on these results and the exclusive conservation of the protein in the fungal kingdom, we hypothesize that Yrb30p represents a novel modulator of the Ran GTPase switch related to fungal lifestyle.
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Affiliation(s)
- Andreas Braunwarth
- Biochemie-Zentrum Heidelberg, Ruprecht-Karls-Universität, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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24
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Panse VG, Küster B, Gerstberger T, Hurt E. Unconventional tethering of Ulp1 to the transport channel of the nuclear pore complex by karyopherins. Nat Cell Biol 2003; 5:21-7. [PMID: 12471376 DOI: 10.1038/ncb893] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [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: 06/25/2002] [Revised: 09/13/2002] [Accepted: 10/28/2002] [Indexed: 11/08/2022]
Abstract
The ubiquitin-like protein SUMO-1 (small ubiquitin-related modifier 1) is covalently attached to substrate proteins by ligases and cleaved by isopeptidases. Yeast has two SUMO-1-deconjugating enzymes, Ulp1 and Ulp2, which are located at nuclear pores and in the nucleoplasm, respectively. Here we show that the catalytic C-domain of Ulp1 must be excluded from the nucleoplasm for cell viability. This is achieved by the noncatalytic N-domain, which tethers Ulp1 to the nuclear pores. The bulk of cellular Ulp1 is not associated with nucleoporins but instead associates with three karyopherins (Pse1, Kap95 and Kap60), in a complex that is not dissociated by RanGTP in vitro. The Ulp1 N-domain has two distinct binding sites for Pse1 and Kap95/Kap60, both of which are required for anchoring to the nuclear pore complex. We propose that Ulp1 is tethered to the nuclear pores by a Ran-insensitive interaction with karyopherins associated with nucleoporins. This location could allow Ulp1 to remove SUMO-1 from sumoylated cargo proteins during their passage through the nuclear pore channel.
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25
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Künzler M, Gerstberger T, Stutz F, Bischoff FR, Hurt E. Yeast Ran-binding protein 1 (Yrb1) shuttles between the nucleus and cytoplasm and is exported from the nucleus via a CRM1 (XPO1)-dependent pathway. Mol Cell Biol 2000; 20:4295-308. [PMID: 10825193 PMCID: PMC85797 DOI: 10.1128/mcb.20.12.4295-4308.2000] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [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: 11/01/1999] [Accepted: 03/29/2000] [Indexed: 11/20/2022] Open
Abstract
The RanGTP-binding protein RanBP1, which is located in the cytoplasm, has been implicated in release of nuclear export complexes from the cytoplasmic side of the nuclear pore complex. Here we show that Yrb1 (the yeast homolog of RanBP1) shuttles between the nucleus and the cytoplasm. Nuclear import of Yrb1 is a facilitated process that requires a short basic sequence within the Ran-binding domain (RBD). By contrast, nuclear export of Yrb1 requires an intact RBD, which forms a ternary complex with the Xpo1 (Crm1) NES receptor in the presence of RanGTP. Nuclear export of Yrb1, however, is insensitive towards leptomycin B, suggesting a novel type of substrate recognition between Yrb1 and Xpo1. Taken together, these data suggest that ongoing nuclear import and export is an important feature of Yrb1 function in vivo.
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Affiliation(s)
- M Künzler
- Ruprecht-Karls-Universität Heidelberg, Biochemie-Zentrum Heidelberg (BZH), Germany
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26
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Krappmann S, Helmstaedt K, Gerstberger T, Eckert S, Hoffmann B, Hoppert M, Schnappauf G, Braus GH. The aroC gene of Aspergillus nidulans codes for a monofunctional, allosterically regulated chorismate mutase. J Biol Chem 1999; 274:22275-82. [PMID: 10428795 DOI: 10.1074/jbc.274.32.22275] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cDNA and the chromosomal locus of the aroC gene of Aspergillus nidulans were cloned and is the first representative of a filamentous fungal gene encoding chorismate mutase (EC 5.4.99.5), the enzyme at the first branch point of aromatic amino acid biosynthesis. The aroC gene complements the Saccharomyces cerevisiae aro7Delta as well as the A. nidulans aroC mutation. The gene consists of three exons interrupted by two short intron sequences. The expressed mRNA is 0.96 kilobases in length and aroC expression is not regulated on the transcriptional level under amino acid starvation conditions. aroC encodes a monofunctional polypeptide of 268 amino acids. Purification of this 30-kDa enzyme allowed determination of its kinetic parameters (k(cat) = 82 s(-1), n(H) = 1. 56, [S](0.5) = 2.3 mM), varying pH dependence of catalytic activity in different regulatory states, and an acidic pI value of 4.7. Tryptophan acts as heterotropic activator and tyrosine as negative acting, heterotropic feedback-inhibitor with a K(i) of 2.8 microM. Immunological data, homology modeling, as well as electron microscopy studies, indicate that this chorismate mutase has a dimeric structure like the S. cerevisiae enzyme. Site-directed mutagenesis of a crucial residue in loop220s (Asp(233)) revealed differences concerning the intramolecular signal transduction for allosteric regulation of enzymatic activity.
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Affiliation(s)
- S Krappmann
- Institute of Microbiology & Genetics, Georg-August-University, Grisebachstrasse 8, D-37077 Göttingen, Germany
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