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Bian Y, Alem D, Beato F, Hogenson TL, Yang X, Jiang K, Cai J, Ma WW, Fernandez-Zapico M, Tan AC, Lawrence NJ, Fleming JB, Yuan Y, Xie H. Development of SOS1 Inhibitor-Based Degraders to Target KRAS-Mutant Colorectal Cancer. J Med Chem 2022; 65:16432-16450. [PMID: 36459180 PMCID: PMC10113742 DOI: 10.1021/acs.jmedchem.2c01300] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Direct blockade of KRAS driver mutations in colorectal cancer (CRC) has been challenging. Targeting SOS1, a guanine nucleotide exchange factor, has arisen as an attractive approach for KRAS-mutant CRC. Here, we describe the development of novel SOS1 degraders and their activity in patient-derived CRC organoids (PDO). The design of these degraders as proteolysis-targeting chimera was based on the crystal structures of cereblon and SOS1. The synthesis used the 6- and 7-OH groups of a quinazoline core as anchor points to connect lenalidomide. Fifteen compounds were screened for SOS1 degradation. P7 was found to have up to 92% SOS1 degradation in both CRC cell lines and PDOs with excellent specificity. SOS1 degrader P7 demonstrated superior activity in inhibiting CRC PDO growth with an IC50 5 times lower than that of SOS1 inhibitor BI3406. In summary, we developed new SOS1 degraders and demonstrated SOS1 degradation as a feasible therapeutic strategy for KRAS-mutant CRC.
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Affiliation(s)
- Yujia Bian
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Diego Alem
- Department of Gastrointestinal Oncology, H Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, Florida 33612, United States
| | - Francisca Beato
- Department of Gastrointestinal Oncology, H Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, Florida 33612, United States
| | - Tara L Hogenson
- Schulze Center for Novel Therapeutics, Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Xinrui Yang
- Department of Gastrointestinal Oncology, H Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, Florida 33612, United States
| | - Kun Jiang
- Department of Pathology, H Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, Florida 33612, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 12111 USF Sweetgum Ln, Tampa, Florida 33620, United States
| | - Wen Wee Ma
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Martin Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Department of Oncology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Aik Choon Tan
- Department of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, Florida 33612, United States
| | - Nicholas J Lawrence
- Department of Drug Discovery, H Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, Florida 33612, United States
| | - Jason B Fleming
- Department of Gastrointestinal Oncology, H Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, Florida 33612, United States
| | - Yu Yuan
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Hao Xie
- Department of Gastrointestinal Oncology, H Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, Florida 33612, United States
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Lievens S, Van der Heyden J, Masschaele D, De Ceuninck L, Petta I, Gupta S, De Puysseleyr V, Vauthier V, Lemmens I, De Clercq DJH, Defever D, Vanderroost N, De Smet AS, Eyckerman S, Van Calenbergh S, Martens L, De Bosscher K, Libert C, Hill DE, Vidal M, Tavernier J. Proteome-scale Binary Interactomics in Human Cells. Mol Cell Proteomics 2016; 15:3624-3639. [PMID: 27803151 DOI: 10.1074/mcp.m116.061994] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/23/2016] [Indexed: 12/11/2022] Open
Abstract
Because proteins are the main mediators of most cellular processes they are also prime therapeutic targets. Identifying physical links among proteins and between drugs and their protein targets is essential in order to understand the mechanisms through which both proteins themselves and the molecules they are targeted with act. Thus, there is a strong need for sensitive methods that enable mapping out these biomolecular interactions. Here we present a robust and sensitive approach to screen proteome-scale collections of proteins for binding to proteins or small molecules using the well validated MAPPIT (Mammalian Protein-Protein Interaction Trap) and MASPIT (Mammalian Small Molecule-Protein Interaction Trap) assays. Using high-density reverse transfected cell microarrays, a close to proteome-wide collection of human ORF clones can be screened for interactors at high throughput. The versatility of the platform is demonstrated through several examples. With MAPPIT, we screened a 15k ORF library for binding partners of RNF41, an E3 ubiquitin protein ligase implicated in receptor sorting, identifying known and novel interacting proteins. The potential related to the fact that MAPPIT operates in living human cells is illustrated in a screen where the protein collection is scanned for interactions with the glucocorticoid receptor (GR) in its unliganded versus dexamethasone-induced activated state. Several proteins were identified the interaction of which is modulated upon ligand binding to the GR, including a number of previously reported GR interactors. Finally, the screening technology also enables detecting small molecule target proteins, which in many drug discovery programs represents an important hurdle. We show the efficiency of MASPIT-based target profiling through screening with tamoxifen, a first-line breast cancer drug, and reversine, an investigational drug with interesting dedifferentiation and antitumor activity. In both cases, cell microarray screens yielded known and new potential drug targets highlighting the utility of the technology beyond fundamental biology.
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Affiliation(s)
- Sam Lievens
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - José Van der Heyden
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Delphine Masschaele
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Leentje De Ceuninck
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Ioanna Petta
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium.,‖Inflammation Research Center, VIB, Ghent, Belgium.,**Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Surya Gupta
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Veronic De Puysseleyr
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Virginie Vauthier
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | | | - Dieter Defever
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Nele Vanderroost
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Anne-Sophie De Smet
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | | | - Lennart Martens
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium.,§Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Claude Libert
- ‖Inflammation Research Center, VIB, Ghent, Belgium.,**Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - David E Hill
- ‡‡Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,§§Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Marc Vidal
- ‡‡Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,§§Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Jan Tavernier
- From the ‡Medical Biotechnology Center, VIB, Ghent, Belgium; .,§Department of Biochemistry, Ghent University, Ghent, Belgium
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De Clercq DJH, Tavernier J, Lievens S, Van Calenbergh S. Chemical Dimerizers in Three-Hybrid Systems for Small Molecule-Target Protein Profiling. ACS Chem Biol 2016; 11:2075-90. [PMID: 27267544 DOI: 10.1021/acschembio.5b00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The identification of the molecular targets and mechanisms underpinning the beneficial or detrimental effects of small-molecule leads and drugs constitutes a crucial aspect of current drug discovery. Over the last two decades, three-hybrid (3H) systems have progressively taken an important position in the armamentarium of small molecule-target protein profiling technologies. Yet, a prerequisite for successful 3H analysis is the availability of appropriate chemical inducers of dimerization. Herein, we present a comprehensive and critical overview of the chemical dimerizers specifically applied in both yeast and mammalian three-hybrid systems for small molecule-target protein profiling within the broader scope of target deconvolution and drug discovery. Furthermore, examples and alternative suggestions for typical components of chemical dimerizers for 3H systems are discussed. As illustrated, more tools have become available that increase the sensitivity and efficiency of 3H-based screening platforms. Hence, it is anticipated that the great potential of 3H systems will further materialize in important contributions to drug discovery.
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Affiliation(s)
- Dries J. H. De Clercq
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sam Lievens
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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