1
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Zografou-Barredo NA, Hallatt AJ, Goujon-Ricci J, Cano C. A beginner's guide to current synthetic linker strategies towards VHL-recruiting PROTACs. Bioorg Med Chem 2023; 88-89:117334. [PMID: 37224698 DOI: 10.1016/j.bmc.2023.117334] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/05/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023]
Abstract
Over the last two decades, proteolysis targeting chimeras (PROTACs) have been revolutionary in drug development rendering targeted protein degradation (TPD) as an emerging therapeutic modality. These heterobifunctional molecules are comprised of three units: a ligand for the protein of interest (POI), a ligand for an E3 ubiquitin ligase, and a linker that tethers the two motifs together. Von Hippel-Lindau (VHL) is one of the most widely employed E3 ligases in PROTACs development due to its prevalent expression across tissue types and well-characterised ligands. Linker composition and length has proven to play an important role in determining the physicochemical properties and spatial orientation of the POI-PROTAC-E3 ternary complex, thus influencing the bioactivity of degraders. Numerous articles and reports have been published showcasing the medicinal chemistry aspects of the linker design, but few have focused on the chemistry around tethering linkers to E3 ligase ligands. In this review, we focus on the current synthetic linker strategies employed in the assembly of VHL-recruiting PROTACs. We aim to cover a range of fundamental chemistries used to incorporate linkers of varying length, composition and functionality.
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Affiliation(s)
- Nikol A Zografou-Barredo
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Alex J Hallatt
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Jennyfer Goujon-Ricci
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Céline Cano
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
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2
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Hu Z, Crews CM. Recent Developments in PROTAC-Mediated Protein Degradation: From Bench to Clinic. Chembiochem 2022; 23:e202100270. [PMID: 34494353 PMCID: PMC9395155 DOI: 10.1002/cbic.202100270] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/02/2021] [Indexed: 01/21/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs), an emerging paradigm-shifting technology, hijacks the ubiquitin-proteasome system for targeted protein degradation. PROTACs induce ternary complexes between an E3 ligase and POI, and this induced proximity leads to polyUb chain formation on substrates and eventual proteasomal-mediated POI degradation. PROTACs have shown great therapeutic potential by degrading many disease-causing proteins, such as the androgen receptor and BRD4. The PROTAC technology has advanced significantly in the last two decades, with the repertoire of PROTAC targets increased tremendously. Herein, we describe recent developments of PROTAC technology, focusing on mechanistic and kinetic studies, pharmacokinetic study, spatiotemporal control of PROTACs, covalent PROTACs, resistance to PROTACs, and new E3 ligands.
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Affiliation(s)
- Zhenyi Hu
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511, USA
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06511, USA
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3
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Powell CE, Du G, Bushman JW, He Z, Zhang T, Fischer ES, Gray NS. Selective degradation-inducing probes for studying cereblon (CRBN) biology. RSC Med Chem 2021; 12:1381-1390. [PMID: 34458741 PMCID: PMC8372211 DOI: 10.1039/d0md00382d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Targeted protein degradation represents a rapidly growing area in drug discovery and development. Moreover, small molecules that induce the targeted degradation of a given protein also represent an important addition to the chemical probes toolbox as these compounds can achieve selective protein knockdown, thus providing an approach that is orthogonal to genetic knockdowns. In order to develop degradation-inducing chemical probes for studying cereblon (CRBN) biology, we generated six CRBN-CRBN (homo-PROTAC) degraders and six CRBN-VHL (hetero-PROTAC) degraders. From these compounds we identified two potent and selective CRBN degraders (ZXH-4-130 and ZXH-4-137), both of which are CRBN-VHL compounds. We characterized these lead degraders by quantitative proteomics in five cell lines (MM1.S, Kelly, SK-N-DZ, HEK293T, and MOLT-4) and observed high selectivity for CRBN in all cell lines. Furthermore, we directly compared our compounds to current lead CRBN degraders and demonstrated how these probes can be used as chemical knockdown reagents for studying CRBN-dependent processes. Overall, our work provides a roadmap for thorough degrader characterization by combination western and proteomic analysis, as illustrated by the identification of ZXH-4-130 and ZXH-4-137 as CRBN-knockdown tool compounds suitable for cell-based studies.
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Affiliation(s)
- Chelsea E Powell
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School Boston Massachusetts 02115 USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston Massachusetts 02215 USA
| | - Guangyan Du
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School Boston Massachusetts 02115 USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston Massachusetts 02215 USA
| | - Jonathan W Bushman
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School Boston Massachusetts 02115 USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston Massachusetts 02215 USA
| | - Zhixiang He
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School Boston Massachusetts 02115 USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston Massachusetts 02215 USA
| | - Tinghu Zhang
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School Boston Massachusetts 02115 USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston Massachusetts 02215 USA
| | - Eric S Fischer
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School Boston Massachusetts 02115 USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston Massachusetts 02215 USA
| | - Nathanael S Gray
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School Boston Massachusetts 02115 USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston Massachusetts 02215 USA
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4
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Kim EJ. Advances in Strategies and Tools Available for Interrogation of Protein O-GlcNAcylation. Chembiochem 2021; 22:3010-3026. [PMID: 34101962 DOI: 10.1002/cbic.202100219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/08/2021] [Indexed: 11/08/2022]
Abstract
The attachment of a single O-linked β-N-acetylglucosamine (O-GlcNAc) to serine and threonine residues of numerous proteins in the nucleus, cytoplasm, and mitochondria is a reversible post-translational modification (PTM) and plays an important role as a regulator of various cellular processes in both healthy and disease states. Advances in strategies and tools that allow for the detection of dynamic O-GlcNAcylation on cellular proteins have helped to enhance our initial and ongoing understanding of its dynamic effects on cellular stimuli and given insights into its link to the pathogenesis of several chronic diseases. Furthermore, chemical genetic strategies and related tools have been successfully applied to a myriad of biological systems with a new level of spatiotemporal and molecular precision. These strategies have started to be used in studying and controlling O-GlcNAcylation both in vivo and in vitro. In this minireview, overviews of recent advances in molecular tools being applied to the detection and identification of O-GlcNAcylation on cellular proteins as well as on individual proteins are provided. In addition, chemical genetic strategies that have already been applied or are potentially usable in O-GlcNAc functional are also discussed.
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Affiliation(s)
- Eun Ju Kim
- Daegu University, Gyeongsan-Si, Gyeongsangbuk-do, Republic of Korea
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5
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Miao Y, Gao Q, Mao M, Zhang C, Yang L, Yang Y, Han D. Bispecific Aptamer Chimeras Enable Targeted Protein Degradation on Cell Membranes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yanyan Miao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Qianqian Gao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Menghan Mao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Chao Zhang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Liqun Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai 200433 China
| | - Da Han
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
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6
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Miao Y, Gao Q, Mao M, Zhang C, Yang L, Yang Y, Han D. Bispecific Aptamer Chimeras Enable Targeted Protein Degradation on Cell Membranes. Angew Chem Int Ed Engl 2021; 60:11267-11271. [PMID: 33634555 DOI: 10.1002/anie.202102170] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 12/12/2022]
Abstract
The ability to regulate membrane protein abundance offers great opportunities for developing therapeutic sites for various diseases. Herein, we describe a platform for the targeted degradation of membrane-associated proteins using bispecific aptamer chimeras that bind both the cell-surface lysosome-shuttling receptor (IGFIIR) and the targeted membrane-bound proteins of interest. We demonstrate that the aptamer chimeras can efficiently and quickly shuttle the therapeutically relevant membrane proteins of Met and PTK-7 to lysosomes and degrade them through the lysosomal protein degradation machinery. We anticipate that our method will provide a universal platform for the use of readily synthesized aptamer materials for biochemical research and potential therapeutics.
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Affiliation(s)
- Yanyan Miao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qianqian Gao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Menghan Mao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Chao Zhang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Liqun Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Da Han
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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7
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Tomoshige S, Ishikawa M. PROTACs and Other Chemical Protein Degradation Technologies for the Treatment of Neurodegenerative Disorders. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202004746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shusuke Tomoshige
- Graduate School of Life Sciences Tohoku University 2-1-1 Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Minoru Ishikawa
- Graduate School of Life Sciences Tohoku University 2-1-1 Katahira, Aoba-ku Sendai 980-8577 Japan
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8
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Tomoshige S, Ishikawa M. PROTACs and Other Chemical Protein Degradation Technologies for the Treatment of Neurodegenerative Disorders. Angew Chem Int Ed Engl 2020; 60:3346-3354. [PMID: 32410219 DOI: 10.1002/anie.202004746] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 02/03/2023]
Abstract
Neurodegenerative disorders (NDs) are a group of diseases that cause neural cell damage, leading to motility and/or cognitive dysfunctions. One of the causative agents is misfolded protein aggregates, which are considered as undruggable in terms of conventional tools, such as inhibitors and agonists/antagonists. Indeed, there is currently no FDA-approved drug for the causal treatment of NDs. However, emerging technologies for chemical protein degradation are opening up the possibility of selective elimination of target proteins through physiological protein degradation machineries, which do not depend on the functions of the target proteins. Here, we review recent efforts towards the treatment of NDs using chemical protein degradation technologies, and we briefly discuss the challenges and prospects.
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Affiliation(s)
- Shusuke Tomoshige
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Minoru Ishikawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
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9
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Field SD, Lee W, Dutra JK, Serneo FSF, Oyer J, Xu H, Johnson DS, am Ende CW, Seneviratne U. Fluorophosphonate‐Based Degrader Identifies Degradable Serine Hydrolases by Quantitative Proteomics. Chembiochem 2020; 21:2916-2920. [DOI: 10.1002/cbic.202000253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/25/2020] [Indexed: 01/26/2023]
Affiliation(s)
- S. Denise Field
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
| | - Wankyu Lee
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
| | - Jason K. Dutra
- Pfizer Worldwide Research and Development Eastern Point Road Groton CT 06340 USA
| | - Finley Scott F. Serneo
- Pfizer Worldwide Research and Development 10770 Science Center Drive San Diego CA 92121 USA
| | - Jon Oyer
- Pfizer Worldwide Research and Development 10770 Science Center Drive San Diego CA 92121 USA
| | - Hua Xu
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
| | - Douglas S. Johnson
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
| | | | - Uthpala Seneviratne
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
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10
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Sofja Kovalevskaja Prizes: D. Hellerschmied and J. P. Barham / Georg Manecke Prize: J. Thiele. Angew Chem Int Ed Engl 2019; 58:16355. [DOI: 10.1002/anie.201912504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Sofja‐Kovalevskaja‐Preise: D. Hellerschmied und J. P. Barham / Georg‐Manecke‐Preis: J. Thiele. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Zhang Z, Shokat KM. Bifunctional Small-Molecule Ligands of K-Ras Induce Its Association with Immunophilin Proteins. Angew Chem Int Ed Engl 2019; 58:16314-16319. [PMID: 31557383 PMCID: PMC6980260 DOI: 10.1002/anie.201910124] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Indexed: 12/20/2022]
Abstract
Here we report the design, synthesis, and characterization of bifunctional chemical ligands that induce the association of Ras with ubiquitously expressed immunophilin proteins such as FKBP12 and cyclophilin A. We show this approach is applicable to two distinct Ras ligand scaffolds, and that both the identity of the immunophilin ligand and the linker chemistry affect compound efficacy in biochemical and cellular contexts. These ligands bind to Ras in an immunophilin-dependent fashion and mediate the formation of tripartite complexes of Ras, immunophilin, and the ligand. The recruitment of cyclophilin A to GTP-bound Ras blocks its interaction with B-Raf in biochemical assays. Our study demonstrates the feasibility of ligand-induced association of Ras with intracellular proteins and suggests it as a promising therapeutic strategy for Ras-driven cancers.
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Affiliation(s)
- Ziyang Zhang
- Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94143, USA
| | - Kevan M Shokat
- Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94143, USA
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13
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Zhang Z, Shokat KM. Bifunctional Small‐Molecule Ligands of K‐Ras Induce Its Association with Immunophilin Proteins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ziyang Zhang
- Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California, San Francisco 600 16th Street San Francisco CA 94143 USA
| | - Kevan M. Shokat
- Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California, San Francisco 600 16th Street San Francisco CA 94143 USA
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14
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Long MJC, Hnedzko D, Kim BK, Aye Y. Breaking the Fourth Wall: Modulating Quaternary Associations for Protein Regulation and Drug Discovery. Chembiochem 2019; 20:1091-1104. [PMID: 30589188 PMCID: PMC6499692 DOI: 10.1002/cbic.201800716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions (PPIs) are an effective means to orchestrate intricate biological processes required to sustain life. Approximately 650 000 PPIs underlie the human interactome; thus underscoring its complexity and the manifold signaling outputs altered in response to changes in specific PPIs. This minireview illustrates the growing arsenal of PPI assemblies and offers insights into how these varied PPI regulatory modalities are relevant to customized drug discovery, with a focus on cancer. First, known and emerging PPIs and PPI-targeted drugs of both natural and synthetic origin are categorized. Building on these discussions, the merits of PPI-guided therapeutics over traditional drug design are discussed. Finally, a compare-and-contrast section for different PPI blockers, with gain-of-function PPI interventions, such as PROTACS, is provided.
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Affiliation(s)
- Marcus J. C. Long
- 47 Pudding Gate, Bishop Burton, Beverley East Riding of Yorkshire, HU17 8QH, UK
| | - Dziyana Hnedzko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Bo Kyoung Kim
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
| | - Yimon Aye
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- 47 Pudding Gate, Bishop Burton, Beverley East Riding of Yorkshire, HU17 8QH, UK
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15
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Burslem G, Ottis P, Jaime-Figueroa S, Morgan A, Cromm P, Toure M, Crews C. Efficient Synthesis of Immunomodulatory Drug Analogues Enables Exploration of Structure-Degradation Relationships. ChemMedChem 2018; 13:1508-1512. [PMID: 29870139 PMCID: PMC6291207 DOI: 10.1002/cmdc.201800271] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/25/2018] [Indexed: 12/22/2022]
Abstract
The immunomodulatory drugs (IMiDs) thalidomide, pomalidomide, and lenalidomide have been approved for the treatment of multiple myeloma for many years. Recently, their use as E3 ligase recruiting elements for small-molecule-induced protein degradation has led to a resurgence in interest in IMiD synthesis and functionalization. Traditional IMiD synthesis follows a stepwise route with multiple purification steps. Herein we describe a novel one-pot synthesis without purification that provides rapid access to a multitude of IMiD analogues. Binding studies with the IMiD target protein cereblon (CRBN) reveals a narrow structure-activity relationship with only a few compounds showing sub-micromolar binding affinity in the range of pomalidomide and lenalidomide. However, anti-proliferative activity as well as Aiolos degradation could be identified for two IMiD analogues. This study provides useful insight into the structure-degradation relationships for molecules of this type as well as a rapid and robust method for IMiD synthesis.
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Affiliation(s)
- G.M. Burslem
- Department of Molecular, Cellular and Developmental BiologyYale University,219 Prospect Street, New Haven, CT, USA, ,
| | - P. Ottis
- Department of Molecular, Cellular and Developmental BiologyYale University,219 Prospect Street, New Haven, CT, USA, ,
| | - S. Jaime-Figueroa
- Department of Molecular, Cellular and Developmental BiologyYale University,219 Prospect Street, New Haven, CT, USA, ,
| | - A. Morgan
- Arvinas LLC, 5 Science Park, New Haven, CT, USA
| | - P.M. Cromm
- Department of Molecular, Cellular and Developmental BiologyYale University,219 Prospect Street, New Haven, CT, USA, ,
| | - M. Toure
- Department of Molecular, Cellular and Developmental BiologyYale University,219 Prospect Street, New Haven, CT, USA, ,
| | - C.M. Crews
- Department of Molecular, Cellular and Developmental BiologyYale University,219 Prospect Street, New Haven, CT, USA, ,
- Departments of Chemistry and Pharmacology, Yale University, New Haven, CT, USA
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16
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Powell CE, Gao Y, Tan L, Donovan KA, Nowak RP, Loehr A, Bahcall M, Fischer ES, Jänne PA, George RE, Gray NS. Chemically Induced Degradation of Anaplastic Lymphoma Kinase (ALK). J Med Chem 2018; 61:4249-4255. [PMID: 29660984 DOI: 10.1021/acs.jmedchem.7b01655] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present the development of the first small molecule degraders that can induce anaplastic lymphoma kinase (ALK) degradation, including in non-small-cell lung cancer (NSCLC), anaplastic large-cell lymphoma (ALCL), and neuroblastoma (NB) cell lines. These degraders were developed through conjugation of known pyrimidine-based ALK inhibitors, TAE684 or LDK378, and the cereblon ligand pomalidomide. We demonstrate that in some cell types degrader potency is compromised by expression of drug transporter ABCB1. In addition, proteomic profiling demonstrated that these compounds also promote the degradation of additional kinases including PTK2 (FAK), Aurora A, FER, and RPS6KA1 (RSK1).
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Affiliation(s)
- Chelsea E Powell
- Department of Biological Chemistry & Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Yang Gao
- Department of Pediatric Hematology and Oncology , Dana-Farber Cancer Institute and Children's Hospital Boston, Harvard Medical School , Boston , Massachusetts 02215 , United States
| | - Li Tan
- Department of Biological Chemistry & Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Katherine A Donovan
- Department of Biological Chemistry & Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Radosław P Nowak
- Department of Biological Chemistry & Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Amanda Loehr
- Department of Pediatric Hematology and Oncology , Dana-Farber Cancer Institute and Children's Hospital Boston, Harvard Medical School , Boston , Massachusetts 02215 , United States
| | | | - Eric S Fischer
- Department of Biological Chemistry & Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | | | - Rani E George
- Department of Pediatric Hematology and Oncology , Dana-Farber Cancer Institute and Children's Hospital Boston, Harvard Medical School , Boston , Massachusetts 02215 , United States
| | - Nathanael S Gray
- Department of Biological Chemistry & Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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17
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Madak JT, Cuthbertson CR, Chen W, Showalter HD, Neamati N. Design, Synthesis, and Characterization of Brequinar Conjugates as Probes to Study DHODH Inhibition. Chemistry 2017; 23:13875-13878. [DOI: 10.1002/chem.201702999] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Joseph T. Madak
- Department of Medicinal Chemistry, College of Pharmacy, and Translational Oncology Program; University of Michigan, North Campus Research Complex; 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Christine R. Cuthbertson
- Department of Medicinal Chemistry, College of Pharmacy, and Translational Oncology Program; University of Michigan, North Campus Research Complex; 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Wenmin Chen
- Department of Medicinal Chemistry, College of Pharmacy, and Translational Oncology Program; University of Michigan, North Campus Research Complex; 1600 Huron Parkway Ann Arbor MI 48109 USA
| | - Hollis D. Showalter
- Department of Medicinal Chemistry, College of Pharmacy; University of Michigan; 428 Church St. Ann Arbor MI 48109 USA
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, and Translational Oncology Program; University of Michigan, North Campus Research Complex; 1600 Huron Parkway Ann Arbor MI 48109 USA
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. New Modalities for Challenging Targets in Drug Discovery. Angew Chem Int Ed Engl 2017; 56:10294-10323. [PMID: 28186380 DOI: 10.1002/anie.201611914] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/31/2017] [Indexed: 12/11/2022]
Abstract
Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities". This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein-protein interactions and for biological processes at the center of cell regulation.
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Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Stéphanie M Guéret
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
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19
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. Neue Modalitäten für schwierige Zielstrukturen in der Wirkstoffentwicklung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611914] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Stéphanie M. Guéret
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
- Fakultät für Chemie and Chemische Biologie; Technische Universität Dortmund; Deutschland
| | - Tom N. Grossmann
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; Niederlande
| | - Alleyn T. Plowright
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
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20
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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21
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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22
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Remillard D, Buckley DL, Paulk J, Brien GL, Sonnett M, Seo HS, Dastjerdi S, Wühr M, Dhe-Paganon S, Armstrong SA, Bradner JE. Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl 2017; 56:5738-5743. [PMID: 28418626 DOI: 10.1002/anie.201611281] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/24/2017] [Indexed: 12/12/2022]
Abstract
The bromodomain-containing protein BRD9, a subunit of the human BAF (SWI/SNF) nucleosome remodeling complex, has emerged as an attractive therapeutic target in cancer. Despite the development of chemical probes targeting the BRD9 bromodomain, there is a limited understanding of BRD9 function beyond acetyl-lysine recognition. We have therefore created the first BRD9-directed chemical degraders, through iterative design and testing of heterobifunctional ligands that bridge the BRD9 bromodomain and the cereblon E3 ubiquitin ligase complex. Degraders of BRD9 exhibit markedly enhanced potency compared to parental ligands (10- to 100-fold). Parallel study of degraders with divergent BRD9-binding chemotypes in models of acute myeloid leukemia resolves bromodomain polypharmacology in this emerging drug class. Together, these findings reveal the tractability of non-BET bromodomain containing proteins to chemical degradation, and highlight lead compound dBRD9 as a tool for the study of BRD9.
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Affiliation(s)
- David Remillard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gerard L Brien
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew Sonnett
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shiva Dastjerdi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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23
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Remillard D, Buckley DL, Paulk J, Brien GL, Sonnett M, Seo HS, Dastjerdi S, Wühr M, Dhe-Paganon S, Armstrong SA, Bradner JE. Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- David Remillard
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Dennis L. Buckley
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Joshiawa Paulk
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Gerard L. Brien
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Matthew Sonnett
- Department of Systems Biology; Harvard Medical School; Boston MA USA
- Lewis-Sigler Institute for Integrative Genomics; Princeton University; Princeton NJ USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology; Dana-Farber Cancer Institute; Boston MA USA
| | - Shiva Dastjerdi
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics; Princeton University; Princeton NJ USA
- Department of Molecular Biology; Princeton University; Princeton NJ USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology; Dana-Farber Cancer Institute; Boston MA USA
| | - Scott A. Armstrong
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - James E. Bradner
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
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