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Schröder M, Renatus M, Liang X, Meili F, Zoller T, Ferrand S, Gauter F, Li X, Sigoillot F, Gleim S, Stachyra TM, Thomas JR, Begue D, Khoshouei M, Lefeuvre P, Andraos-Rey R, Chung B, Ma R, Pinch B, Hofmann A, Schirle M, Schmiedeberg N, Imbach P, Gorses D, Calkins K, Bauer-Probst B, Maschlej M, Niederst M, Maher R, Henault M, Alford J, Ahrne E, Tordella L, Hollingworth G, Thomä NH, Vulpetti A, Radimerski T, Holzer P, Carbonneau S, Thoma CR. DCAF1-based PROTACs with activity against clinically validated targets overcoming intrinsic- and acquired-degrader resistance. Nat Commun 2024; 15:275. [PMID: 38177131 PMCID: PMC10766610 DOI: 10.1038/s41467-023-44237-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Targeted protein degradation (TPD) mediates protein level through small molecule induced redirection of E3 ligases to ubiquitinate neo-substrates and mark them for proteasomal degradation. TPD has recently emerged as a key modality in drug discovery. So far only a few ligases have been utilized for TPD. Interestingly, the workhorse ligase CRBN has been observed to be downregulated in settings of resistance to immunomodulatory inhibitory drugs (IMiDs). Here we show that the essential E3 ligase receptor DCAF1 can be harnessed for TPD utilizing a selective, non-covalent DCAF1 binder. We confirm that this binder can be functionalized into an efficient DCAF1-BRD9 PROTAC. Chemical and genetic rescue experiments validate specific degradation via the CRL4DCAF1 E3 ligase. Additionally, a dasatinib-based DCAF1 PROTAC successfully degrades cytosolic and membrane-bound tyrosine kinases. A potent and selective DCAF1-BTK-PROTAC (DBt-10) degrades BTK in cells with acquired resistance to CRBN-BTK-PROTACs while the DCAF1-BRD9 PROTAC (DBr-1) provides an alternative strategy to tackle intrinsic resistance to VHL-degrader, highlighting DCAF1-PROTACS as a promising strategy to overcome ligase mediated resistance in clinical settings.
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Affiliation(s)
- Martin Schröder
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Basel, Switzerland
- Ridgeline Discovery, Basel, Switzerland
| | - Xiaoyou Liang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Fabian Meili
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Francois Gauter
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Xiaoyan Li
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Damien Begue
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Peggy Lefeuvre
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - BoYee Chung
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Renate Ma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Benika Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Andreas Hofmann
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Patricia Imbach
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Delphine Gorses
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Keith Calkins
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Matt Niederst
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rob Maher
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John Alford
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erik Ahrne
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Luca Tordella
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anna Vulpetti
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thomas Radimerski
- Novartis Institutes for BioMedical Research, Basel, Switzerland
- Ridgeline Discovery, Basel, Switzerland
| | - Philipp Holzer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Seth Carbonneau
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
- Ridgeline Discovery, Basel, Switzerland.
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Vulpetti A, Holzer P, Schmiedeberg N, Imbach-Weese P, Pissot-Soldermann C, Hollingworth GJ, Radimerski T, Thoma CR, Stachyra TM, Wojtynek M, Maschlej M, Chau S, Schuffenhauer A, Fernández C, Schröder M, Renatus M. Discovery of New Binders for DCAF1, an Emerging Ligase Target in the Targeted Protein Degradation Field. ACS Med Chem Lett 2023; 14:949-954. [PMID: 37465299 PMCID: PMC10350940 DOI: 10.1021/acsmedchemlett.3c00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/31/2023] [Indexed: 07/20/2023] Open
Abstract
In this study, we describe the rapid identification of potent binders for the WD40 repeat domain (WDR) of DCAF1. This was achieved by two rounds of iterative focused screening of a small set of compounds selected on the basis of internal WDR domain knowledge followed by hit expansion. Subsequent structure-based design led to nanomolar potency binders with a clear exit vector enabling DCAF1-based bifunctional degrader exploration.
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Affiliation(s)
- Anna Vulpetti
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Philipp Holzer
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Niko Schmiedeberg
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Patricia Imbach-Weese
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Carole Pissot-Soldermann
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Gregory J. Hollingworth
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Thomas Radimerski
- Oncology
Drug Discovery, Novartis Institutes for
BioMedical Research, Basel 4002, Switzerland
| | - Claudio R. Thoma
- Oncology
Drug Discovery, Novartis Institutes for
BioMedical Research, Basel 4002, Switzerland
| | - Therese-Marie Stachyra
- Oncology
Drug Discovery, Novartis Institutes for
BioMedical Research, Basel 4002, Switzerland
| | - Matthias Wojtynek
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Magdalena Maschlej
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Suzanne Chau
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Ansgar Schuffenhauer
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - César Fernández
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Martin Schröder
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Martin Renatus
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
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