1
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He T, Wen C, Yang G, Yang X. Targeted Protein Degradation: Principles, Strategies, and Applications. Adv Biol (Weinh) 2023; 7:e2300083. [PMID: 37518856 DOI: 10.1002/adbi.202300083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/11/2023] [Indexed: 08/01/2023]
Abstract
Protein degradation is a general process to maintain cell homeostasis. The intracellular protein quality control system mainly includes the ubiquitin-proteasome system and the lysosome pathway. Inspired by the physiological process, strategies to degrade specific proteins have developed, which emerge as potent and effective tools in biological research and drug discovery. This review focuses on recent advances in targeted protein degradation techniques, summarizing the principles, advantages, and challenges. Moreover, the potential applications and future direction in biological science and clinics are also discussed.
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Affiliation(s)
- Ting He
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Chenxi Wen
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Guodong Yang
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Xuekang Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
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2
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Xie S, Zhu J, Li J, Zhan F, Yao H, Xu J, Xu S. Small-Molecule Hydrophobic Tagging: A Promising Strategy of Druglike Technology for Targeted Protein Degradation. J Med Chem 2023; 66:10917-10933. [PMID: 37535706 DOI: 10.1021/acs.jmedchem.3c00736] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Targeted protein degradation (TPD) technologies have catalyzed a paradigm shift in therapeutic strategies and offer innovative avenues for drug design. Hydrophobic tags (HyTs) are bifunctional TPD molecules consisting of a ″lipophilic small-molecule tags″ group and a small-molecule ligand for the target protein. Despite the vast potential of HyTs, they have received relatively limited attention as a promising frontier. Leveraging their lower molecular weight and reduced numbers of hydrogen bond donors/acceptors (HBDs/HBAs) in comparison with proteolysis-targeting chimeras (PROTACs), HyTs present a compelling approach for enhancing druglike properties. In this Perspective, we explore the diverse range of HyT structures and their corresponding degradation mechanisms, thereby illuminating their broad applicability in targeting a diverse array of proteins, including previously elusive targets. Moreover, we scrutinize the challenges and opportunities entailed in developing this technology as a viable and fruitful strategy for drug discovery.
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Affiliation(s)
- Shaowen Xie
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Jingjie Zhu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Junda Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Feiyan Zhan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Hong Yao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Jinyi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Shengtao Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
- Department of Hepatobiliary Surgery, The First People's Hospital of Kunshan, Suzhou 215300, China
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3
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Liu Q, Fong B, Yoo S, Unruh JR, Guo F, Yu Z, Chen J, Si K, Li R, Zhou C. Nascent mitochondrial proteins initiate the localized condensation of cytosolic protein aggregates on the mitochondrial surface. Proc Natl Acad Sci U S A 2023; 120:e2300475120. [PMID: 37494397 PMCID: PMC10401023 DOI: 10.1073/pnas.2300475120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Eukaryotes organize cellular contents into membrane-bound organelles and membrane-less condensates, for example, protein aggregates. An unsolved question is why the ubiquitously distributed proteins throughout the cytosol give rise to spatially localized protein aggregates on the organellar surface, like mitochondria. We report that the mitochondrial import receptor Tom70 is involved in the localized condensation of protein aggregates in budding yeast and human cells. This is because misfolded cytosolic proteins do not autonomously aggregate in vivo; instead, they are recruited to the condensation sites initiated by Tom70's substrates (nascent mitochondrial proteins) on the organellar membrane using multivalent hydrophobic interactions. Knocking out Tom70 partially impairs, while overexpressing Tom70 increases the formation and association between cytosolic protein aggregates and mitochondria. In addition, ectopic targeting Tom70 and its substrates to the vacuole surface is able to redirect the localized aggregation from mitochondria to the vacuolar surface. Although other redundant mechanisms may exist, this nascent mitochondrial proteins-based initiation of protein aggregation likely explains the localized condensation of otherwise ubiquitously distributed molecules on the mitochondria. Disrupting the mitochondrial association of aggregates impairs their asymmetric retention during mitosis and reduces the mitochondrial import of misfolded proteins, suggesting a proteostasis role of the organelle-condensate interactions.
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Affiliation(s)
- Qingqing Liu
- Buck Institute for Research on Aging, Novato, CA94945
| | - Benjamin Fong
- Buck Institute for Research on Aging, Novato, CA94945
| | - Seungmin Yoo
- Buck Institute for Research on Aging, Novato, CA94945
| | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Jingjing Chen
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, MO64110
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS66160
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD21218
- Mechanobiology Institute and Department of Biological Science, National University of Singapore, Singapore117411, Singapore
| | - Chuankai Zhou
- Buck Institute for Research on Aging, Novato, CA94945
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4
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Sansbury SE, Serebrenik YV, Lapidot T, Burslem GM, Shalem O. Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548611. [PMID: 37503003 PMCID: PMC10370017 DOI: 10.1101/2023.07.13.548611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
System-level understanding of proteome organization and function requires methods for direct visualization and manipulation of proteins at scale. We developed an approach enabled by high-throughput gene tagging for the generation and analysis of complex cell pools with endogenously tagged proteins. Proteins are tagged with HaloTag to enable visualization or direct perturbation. Fluorescent labeling followed by in situ sequencing and deep learning-based image analysis identifies the localization pattern of each tag, providing a bird's-eye-view of cellular organization. Next, we use a hydrophobic HaloTag ligand to misfold tagged proteins, inducing spatially restricted proteotoxic stress that is read out by single cell RNA sequencing. By integrating optical and perturbation data, we map compartment-specific responses to protein misfolding, revealing inter-compartment organization and direct crosstalk, and assigning proteostasis functions to uncharacterized genes. Altogether, we present a powerful and efficient method for large-scale studies of proteome dynamics, function, and homeostasis.
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5
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Targeted Protein Unfolding at the Golgi Apparatus. Methods Mol Biol 2022; 2557:645-659. [PMID: 36512243 DOI: 10.1007/978-1-0716-2639-9_39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Maintaining protein homeostasis (proteostasis) is vital to cellular and organismal health. How the Golgi apparatus, the central protein maturation and sorting station in the cell, manages misfolded proteins to maintain proteostasis is still poorly understood. Here we present a strategy for targeted protein unfolding at the Golgi that enables studying Golgi-related protein quality control and stress-signaling pathways. Targeted protein unfolding is induced by small molecule-based chemical biology approaches-hydrophobic tagging and the use of a destabilization domain. Imaging studies allow visualizing quality control (QC) phenotypes, such as the formation of QC carriers and Golgi-to-endoplasmic reticulum trafficking, and correlating these phenotypes with other trafficking processes.
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6
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Design, Synthesis and Biological Characterization of Histone Deacetylase 8 (HDAC8) Proteolysis Targeting Chimeras (PROTACs) with Anti-Neuroblastoma Activity. Int J Mol Sci 2022; 23:ijms23147535. [PMID: 35886887 PMCID: PMC9322761 DOI: 10.3390/ijms23147535] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/07/2023] Open
Abstract
In addition to involvement in epigenetic gene regulation, histone deacetylases (HDACs) regulate multiple cellular processes through mediating the activity of non-histone protein substrates. The knockdown of HDAC8 isozyme is associated with the inhibition of cell proliferation and apoptosis enhancement in several cancer cell lines. As shown in several studies, HDAC8 can be considered a potential target in the treatment of cancer forms such as childhood neuroblastoma. The present work describes the development of proteolysis targeting chimeras (PROTACs) of HDAC8 based on substituted benzhydroxamic acids previously reported as potent and selective HDAC8 inhibitors. Within this study, we investigated the HDAC8-degrading profiles of the synthesized PROTACs and their effect on the proliferation of neuroblastoma cells. The combination of in vitro screening and cellular testing demonstrated selective HDAC8 PROTACs that show anti-neuroblastoma activity in cells.
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7
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Zhong Y, Chi F, Wu H, Liu Y, Xie Z, Huang W, Shi W, Qian H. Emerging targeted protein degradation tools for innovative drug discovery: From classical PROTACs to the novel and beyond. Eur J Med Chem 2022; 231:114142. [DOI: 10.1016/j.ejmech.2022.114142] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/22/2022]
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8
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Yang YL, Li S, Zhang FG, Ma JA. N-Iodosuccinimide-Promoted [3 + 2] Annulation Reaction of Aryldiazonium Salts with Guanidines To Construct Aminotetrazoles. Org Lett 2021; 23:8894-8898. [PMID: 34748357 DOI: 10.1021/acs.orglett.1c03395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A N-iodosuccinimide (NIS)-promoted [3 + 2] annulation reaction of aryldiazonium salts with guanidines has been developed for the construction of previously elusive 2-aryl-5-amino-2H-tetrazoles. This transformation takes advantage of readily available starting materials, proceeds under metal-free, mild, and robust conditions, and holds broad functional group compatibility. The utility of this protocol is further manifested via coupling, annulation, deamination, and denitrogenation derivatizations.
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Affiliation(s)
- Yi-Lin Yang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. of China
| | - Shen Li
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. of China
| | - Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. of China
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), and Tianjin Collaborative Innovation Center of Chemical Science & Engineering, Tianjin University, Tianjin 300072, P. R. of China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, P. R. of China
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9
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Asawa Y, Nishida K, Kawai K, Domae K, Ban HS, Kitazaki A, Asami H, Kohno JY, Okada S, Tokuma H, Sakano D, Kume S, Tanaka M, Nakamura H. Carborane as an Alternative Efficient Hydrophobic Tag for Protein Degradation. Bioconjug Chem 2021; 32:2377-2385. [PMID: 34699716 DOI: 10.1021/acs.bioconjchem.1c00431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carboranes 1 and 2 were designed and synthesized for hydrophobic tag (HyT)-induced degradation of HaloTag fusion proteins. The levels of the hemagglutinin (HA)-HaloTag2-green fluorescent protein (EGFP) stably expressed in Flp-In 293 cells were significantly reduced by HyT13, HyT55, and carboranes 1 and 2, with expression levels of 49, 79, 43, and 65%, respectively, indicating that carborane is an alternative novel hydrophobic tag (HyT) for protein degradation under an intracellular environment. To clarify the mechanism of HyT-induced proteolysis, bovine serum albumin (BSA) was chosen as an extracellular protein and modified with maleimide-conjugated m-carborane (MIC). The measurement of the ζ-potentials and the lysine residue modification with fluorescein isothiocyanate (FITC) of BSA-MIC conjugates suggested that the conjugation of carborane induced the exposure of lysine residues on BSA, resulting in the degradation via ubiquitin E3 ligase-related proteasome pathways in the cell.
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Affiliation(s)
- Yasunobu Asawa
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kei Nishida
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazuki Kawai
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kiyotaka Domae
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hyun Seung Ban
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Akihiro Kitazaki
- Department of Chemistry, Facility of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Hiroya Asami
- Department of Chemistry, Facility of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Jun-Ya Kohno
- Department of Chemistry, Facility of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Satoshi Okada
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Hiraku Tokuma
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Daisuke Sakano
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Shoen Kume
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hiroyuki Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
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10
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Zhang R, Huang C, Xiao X, Zhou J. Improving Strategies in the Development of Protein-Downregulation-Based Antiandrogens. ChemMedChem 2021; 16:2021-2033. [PMID: 33554455 DOI: 10.1002/cmdc.202100033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Indexed: 12/20/2022]
Abstract
The androgen receptor (AR) plays a crucial role in the occurrence and development of prostate cancer (PCa), and its signaling pathway remains active in castration-resistant prostate cancer (CRPC) patients. The resistance against antiandrogen drugs in current clinical use is a major challenge for the treatment of PCa, and thus the development of new generations of antiandrogens is under high demand. Recently, strategies for downregulating the AR have attracted significant attention, given its potential in the discovery and development of new antiandrogens, including G-quadruplex stabilizers, ROR-γ inhibitors, AR-targeting proteolysis targeting chimeras (PROTACs), and other selective AR degraders (SARDs), which are able to overcome current resistance mechanisms such as acquired AR mutations, the expression of AR variable splices, or overexpression of AR. This review summarizes the various strategies for downregulating the AR protein, at either the mRNA or protein level, thus providing new ideas for the development of promising antiandrogen drugs.
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Affiliation(s)
- Rongyu Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, China.,Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, China
| | - Chenchao Huang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, China
| | - Xiaohui Xiao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, China.,Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, China.,Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, China
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11
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Kastl JM, Davies G, Godsman E, Holdgate GA. Small-Molecule Degraders beyond PROTACs-Challenges and Opportunities. SLAS DISCOVERY 2021; 26:524-533. [PMID: 33632029 DOI: 10.1177/2472555221991104] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Targeted protein degradation (TPD) is a recent strategy, utilizing the cell's proteostasis machinery to deplete specific proteins. This represents a paradigm shift in early drug discovery, away from occupancy-driven to event-driven mechanisms.Recent efforts have focused on the development of proteolysis-targeting chimeras (PROTACs). These heterobifunctional molecules combine a target-specific binding moiety linked to an E3 ligase ligand and trigger selective ubiquitination of the target protein, marking it for proteasomal degradation. While these molecules can be highly efficacious, they generally have unfavorable physicochemical properties due to their large size.In contrast, smaller molecules that induce degradation could represent an attractive, simple option to overcoming the limitations of both traditional modulators and PROTACs. These molecules may have a range of mechanisms: recruitment of an E3 ligase (molecular glues), introduction of hydrophobic areas, or inducing local unfolding, each of which triggers degradation.We recently completed a high-throughput screen of 111,000 compounds in a cellular HiBiT assay in an effort to identify such molecules. Preliminary analysis indicates that we have been able to identify alternative small-molecule degraders. We highlight methods for triage, characterization, selectivity, and mode of action. In summary, we believe that these types of small-molecule degraders, which may possibly have more acceptable physicochemical properties than the inherently larger heterobifunctional molecules, are an exciting approach for inducing TPD, and we illustrate that a general screening approach can be successful in identifying useful start points for developing such molecules.
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Affiliation(s)
- Johanna M Kastl
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Gareth Davies
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Eleanor Godsman
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Geoffrey A Holdgate
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
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12
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Long MJC. Time to Get Turned on by Chemical Biology. Chembiochem 2020; 22:814-817. [PMID: 33174365 DOI: 10.1002/cbic.202000497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/07/2020] [Indexed: 11/08/2022]
Abstract
The pressing need for innovation in drug discovery is spurring the emergence of drugs that turn on protein function, as opposed to shutting activity down. Several pharmacophores usher protein target gain-of-function, for instance: PROTACs promote protein target degradation; other drug candidates have been reported to function through dominant-negative inhibition of their target enzyme. Such classes of molecules are typically active at low target occupancy and display numerous advantages relative to canonical inhibitors, whose function is intrinsically tied to achieving, or exceeding a threshold occupancy. However, our ability to generally tap into gain-of-function processes through small molecule interventions is overall in its infancy. Herein, I outline how chemical biology is poised to help us bring this powerful idea to fruition. I further outline means through which gain-of-function events can be identified and harnessed.
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Affiliation(s)
- Marcus J C Long
- Départment de Biologie Moleculaire; Sciences II, 30 Quai Ernest-Ansermet, 1211, Genève 4, Switzerland
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13
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Wang Y, Jiang X, Feng F, Liu W, Sun H. Degradation of proteins by PROTACs and other strategies. Acta Pharm Sin B 2020; 10:207-238. [PMID: 32082969 PMCID: PMC7016280 DOI: 10.1016/j.apsb.2019.08.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Blocking the biological functions of scaffold proteins and aggregated proteins is a challenging goal. PROTAC proteolysis-targeting chimaera (PROTAC) technology may be the solution, considering its ability to selectively degrade target proteins. Recent progress in the PROTAC strategy include identification of the structure of the first ternary eutectic complex, extra-terminal domain-4-PROTAC-Von-Hippel-Lindau (BRD4-PROTAC-VHL), and PROTAC ARV-110 has entered clinical trials for the treatment of prostate cancer in 2019. These discoveries strongly proved the value of the PROTAC strategy. In this perspective, we summarized recent meaningful research of PROTAC, including the types of degradation proteins, preliminary biological data in vitro and in vivo, and new E3 ubiquitin ligases. Importantly, the molecular design, optimization strategy and clinical application of candidate molecules are highlighted in detail. Future perspectives for development of advanced PROTAC in medical fields have also been discussed systematically.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xueyang Jiang
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Feng
- Jiangsu Food and Pharmaceutical Science College, Huaian 223003, China
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
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14
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Hellerschmied D, Serebrenik YV, Shao L, Burslem GM, Crews CM. Protein folding state-dependent sorting at the Golgi apparatus. Mol Biol Cell 2019; 30:2296-2308. [PMID: 31166830 PMCID: PMC6743468 DOI: 10.1091/mbc.e19-01-0069] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In eukaryotic cells, organelle-specific protein quality control (PQC) is critical for maintaining cellular homeostasis. Despite the Golgi apparatus being the major protein processing and sorting site within the secretory pathway, how it contributes to PQC has remained largely unknown. Using different chemical biology-based protein unfolding systems, we reveal the segregation of unfolded proteins from folded proteins in the Golgi. Quality control (QC) substrates are subsequently exported in distinct carriers, which likely contain unfolded proteins as well as highly oligomerized cargo that mimic protein aggregates. At an additional sorting step, oligomerized proteins are committed to lysosomal degradation, while unfolded proteins localize to the endoplasmic reticulum (ER) and associate with chaperones. These results highlight the existence of checkpoints at which QC substrates are selected for Golgi export and lysosomal degradation. Our data also suggest that the steady-state ER localization of misfolded proteins, observed for several disease-causing mutants, may have different origins.
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Affiliation(s)
| | | | - Lin Shao
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520
| | | | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology.,Department of Chemistry, Yale University, New Haven, CT 06511.,Department of Pharmacology, Yale University, New Haven, CT 06511
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15
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Gao N, Huang YP, Chu TT, Li QQ, Zhou B, Chen YX, Zhao YF, Li YM. TDP-43 specific reduction induced by Di-hydrophobic tags conjugated peptides. Bioorg Chem 2019; 84:254-259. [DOI: 10.1016/j.bioorg.2018.11.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/18/2018] [Accepted: 11/24/2018] [Indexed: 12/14/2022]
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16
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Serebrenik YV, Hellerschmied D, Toure M, López-Giráldez F, Brookner D, Crews CM. Targeted protein unfolding uncovers a Golgi-specific transcriptional stress response. Mol Biol Cell 2018; 29:1284-1298. [PMID: 29851555 PMCID: PMC5994893 DOI: 10.1091/mbc.e17-11-0693] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/26/2018] [Accepted: 03/30/2018] [Indexed: 12/12/2022] Open
Abstract
In eukaryotic cells, organelle-specific stress-response mechanisms are vital for maintaining cellular homeostasis. The Golgi apparatus, an essential organelle of the secretory system, is the major site of protein modification and sorting within a cell and functions as a platform for spatially regulated signaling. Golgi homeostasis mechanisms that regulate organelle structure and ensure precise processing and localization of protein substrates remain poorly understood. Using a chemical biology strategy to induce protein unfolding, we uncover a Golgi-specific transcriptional response. An RNA-sequencing profile of this stress response compared with the current state-of-the-art Golgi stressors, nigericin and xyloside, demonstrates the enhanced precision of Golgi targeting achieved with our system. The data set further reveals previously uncharacterized genes that we find to be essential for Golgi structural integrity. These findings highlight the Golgi's ability to sense misfolded proteins and establish new aspects of Golgi autoregulation.
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Affiliation(s)
- Yevgeniy V. Serebrenik
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| | - Doris Hellerschmied
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| | - Momar Toure
- Department of Chemistry, Yale University, New Haven, CT 06511
| | | | - Dennis Brookner
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
| | - Craig M. Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- Department of Chemistry, Yale University, New Haven, CT 06511
- Department of Pharmacology, Yale University, New Haven, CT 06511
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17
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Affiliation(s)
- George M. Burslem
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
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18
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Abstract
Small-molecule drug discovery has traditionally focused on occupancy of a binding site that directly affects protein function, and this approach typically precludes targeting proteins that lack such amenable sites. Furthermore, high systemic drug exposures may be needed to maintain sufficient target inhibition in vivo, increasing the risk of undesirable off-target effects. Induced protein degradation is an alternative approach that is event-driven: upon drug binding, the target protein is tagged for elimination. Emerging technologies based on proteolysis-targeting chimaeras (PROTACs) that exploit cellular quality control machinery to selectively degrade target proteins are attracting considerable attention in the pharmaceutical industry owing to the advantages they could offer over traditional small-molecule strategies. These advantages include the potential to reduce systemic drug exposure, the ability to counteract increased target protein expression that often accompanies inhibition of protein function and the potential ability to target proteins that are not currently therapeutically tractable, such as transcription factors, scaffolding and regulatory proteins.
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Affiliation(s)
| | - Craig M. Crews
- Departments of Molecular, Cellular & Developmental Biology; Chemistry; Pharmacology, Yale University, New Haven, CT 06511, USA
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19
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Shi Y, Long MJ, Rosenberg MM, Li S, Kobjack A, Lessans P, Coffey RT, Hedstrom L. Boc 3Arg-Linked Ligands Induce Degradation by Localizing Target Proteins to the 20S Proteasome. ACS Chem Biol 2016; 11:3328-3337. [PMID: 27704767 DOI: 10.1021/acschembio.6b00656] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Targeted protein degradation is a promising strategy for drug design and functional assessment. Several small molecule approaches have been developed that localize target proteins to ubiquitin ligases, inducing ubiquitination and subsequent degradation by the 26S proteasome. We discovered that the degradation of a target protein can also be induced by a recognition ligand linked to tert-butyl carbamate (Boc3)-protected arginine (B3A). Here, we show that this process requires the proteasome but does not involve ubiquitination of the target protein. B3A does not perturb the structure of the target protein; instead, a B3A-ligand stabilizes its target protein. B3A ligands stimulate activity of purified 20S proteasome, demonstrating that the tag binds directly to the 20S proteasome. Moreover, purified 20S proteasome is sufficient to degrade target proteins in the presence of their respective B3A-linked recognition ligands. These observations suggest a simple model for B3A-mediated degradation wherein the B3A tag localizes target proteins directly to the 20S proteasome. Thus, B3A ligands are the first example of a ubiquitin-free strategy for targeted protein degradation.
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Affiliation(s)
- Yuntao Shi
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Marcus J.C. Long
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Masha M. Rosenberg
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Shican Li
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Aimee Kobjack
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Philip Lessans
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Rory T. Coffey
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
| | - Lizbeth Hedstrom
- Graduate Program in Chemistry, ‡Graduate Program
in Biochemistry and Biophysics, §Department of Biology, ∥Graduate Program
in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, United States
- Department of Biochemistry, #Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States
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20
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Abstract
Protein homeostasis networks are highly regulated systems responsible for maintaining the health and productivity of cells. Whereas therapeutics have been developed to disrupt protein homeostasis, more recently identified techniques have been used to repurpose homeostatic networks to effect degradation of disease-relevant proteins. Here, we review recent advances in the use of small molecules to degrade proteins in a selective manner. First, we highlight all-small-molecule techniques with direct clinical application. Second, we describe techniques that may find broader acceptance in the biomedical research community that require little or no synthetic chemistry. In addition to serving as innovative research tools, these new approaches to control intracellular protein levels offer the potential to develop novel therapeutics targeting proteins that are not currently pharmaceutically vulnerable.
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Affiliation(s)
- Daniel P Bondeson
- Department of Molecular, Cellular, and Developmental Biology, Department of Chemistry, and Department of Pharmacology, Yale University, New Haven, Connecticut 06511;
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Department of Chemistry, and Department of Pharmacology, Yale University, New Haven, Connecticut 06511;
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21
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Efficient protein knockdown of HaloTag-fused proteins using hybrid molecules consisting of IAP antagonist and HaloTag ligand. Bioorg Med Chem 2016; 24:3144-8. [PMID: 27236416 DOI: 10.1016/j.bmc.2016.05.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 11/22/2022]
Abstract
We previously reported a protein knockdown system for HaloTag-fused proteins using hybrid small molecules consisting of alkyl chloride, which binds covalently to HaloTag, linked to BE04 (2), a bestatin (3) derivative with an affinity for cellular inhibitor of apoptosis protein 1 (cIAP1, a kind of ubiquitin ligase). This system addressed several limitations of prior protein knockdown technology, and was applied to degrade two HaloTag-fused proteins. However, the degradation activity of these hybrid small molecules was not potent. Therefore, we set out to improve this system. We report here the design, synthesis and biological evaluation of novel hybrid compounds 4a and 4b consisting of alkyl chloride linked to IAP antagonist MV1 (5). Compounds 4a and 4b were confirmed to reduce the levels of HaloTag-fused tumor necrosis factor α (HaloTag-TNFα), HaloTag-fused cell division control protein 42 (HaloTag-Cdc42), and unfused HaloTag protein in living cells more potently than did BE04-linked compound 1b. Analysis of the mode of action revealed that the reduction of HaloTag-TNFα is proteasome-dependent, and is also dependent on the linker structure between MV1 (5) and alkyl chloride. These compounds appear to induce ubiquitination at the HaloTag moiety of HaloTag-fused proteins. Our results indicate that these newly synthesized MV1-type hybrid compounds, 4a and 4b, are efficient tools for protein knockdown for HaloTag-fused proteins.
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22
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Discovery of Novel Haloalkane Dehalogenase Inhibitors. Appl Environ Microbiol 2016; 82:1958-1965. [PMID: 26773086 DOI: 10.1128/aem.03916-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/12/2016] [Indexed: 12/27/2022] Open
Abstract
Haloalkane dehalogenases (HLDs) have recently been discovered in a number of bacteria, including symbionts and pathogens of both plants and humans. However, the biological roles of HLDs in these organisms are unclear. The development of efficient HLD inhibitors serving as molecular probes to explore their function would represent an important step toward a better understanding of these interesting enzymes. Here we report the identification of inhibitors for this enzyme family using two different approaches. The first builds on the structures of the enzymes' known substrates and led to the discovery of less potent nonspecific HLD inhibitors. The second approach involved the virtual screening of 150,000 potential inhibitors against the crystal structure of an HLD from the human pathogen Mycobacterium tuberculosis H37Rv. The best inhibitor exhibited high specificity for the target structure, with an inhibition constant of 3 μM and a molecular architecture that clearly differs from those of all known HLD substrates. The new inhibitors will be used to study the natural functions of HLDs in bacteria, to probe their mechanisms, and to achieve their stabilization.
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23
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Toure M, Crews CM. Niedermolekulare PROTACs: neue Wege zum Abbau von Proteinen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507978] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Momar Toure
- Departments of Chemistry; Molecular, Cellular & Developmental Biology; Pharmacology; Yale University; New Haven CT 06511 USA
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental Biology; Pharmacology; Yale University; New Haven CT 06511 USA
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24
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Toure M, Crews CM. Small-Molecule PROTACS: New Approaches to Protein Degradation. Angew Chem Int Ed Engl 2016; 55:1966-73. [DOI: 10.1002/anie.201507978] [Citation(s) in RCA: 379] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Momar Toure
- Departments of Chemistry; Molecular, Cellular & Developmental Biology, Pharmacology; Yale University; New Haven CT 06511 USA
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental Biology, Pharmacology; Yale University; New Haven CT 06511 USA
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25
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Gustafson JL, Neklesa TK, Cox CS, Roth AG, Buckley DL, Tae HS, Sundberg TB, Stagg DB, Hines J, McDonnell DP, Norris JD, Crews CM. Small-Molecule-Mediated Degradation of the Androgen Receptor through Hydrophobic Tagging. Angew Chem Int Ed Engl 2015; 54:9659-62. [PMID: 26083457 PMCID: PMC4547777 DOI: 10.1002/anie.201503720] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Indexed: 11/07/2022]
Abstract
Androgen receptor (AR)-dependent transcription is a major driver of prostate tumor cell proliferation. Consequently, it is the target of several antitumor chemotherapeutic agents, including the AR antagonist MDV3100/enzalutamide. Recent studies have shown that a single AR mutation (F876L) converts MDV3100 action from an antagonist to an agonist. Here we describe the generation of a novel class of selective androgen receptor degraders (SARDs) to address this resistance mechanism. Molecules containing hydrophobic degrons linked to small-molecule AR ligands induce AR degradation, reduce expression of AR target genes and inhibit proliferation in androgen-dependent prostate cancer cell lines. These results suggest that selective AR degradation may be an effective therapeutic prostate tumor strategy in the context of AR mutations that confer resistance to second-generation AR antagonists.
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Affiliation(s)
- Jeffrey L Gustafson
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Taavi K Neklesa
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Carly S Cox
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Anke G Roth
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Dennis L Buckley
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Hyun Seop Tae
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Thomas B Sundberg
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - D Blake Stagg
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710 (USA)
| | - John Hines
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Donald P McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710 (USA)
| | - John D Norris
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710 (USA)
| | - Craig M Crews
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA).
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26
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Gustafson JL, Neklesa TK, Cox CS, Roth AG, Buckley DL, Tae HS, Sundberg TB, Stagg DB, Hines J, McDonnell DP, Norris JD, Crews CM. Small-Molecule-Mediated Degradation of the Androgen Receptor through Hydrophobic Tagging. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503720] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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27
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Daniel L, Buryska T, Prokop Z, Damborsky J, Brezovsky J. Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using in Silico Screening. J Chem Inf Model 2014; 55:54-62. [DOI: 10.1021/ci500486y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Lukas Daniel
- Loschmidt
Laboratories, Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Tomas Buryska
- Loschmidt
Laboratories, Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt
Laboratories, Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
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28
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Raina K, Noblin DJ, Serebrenik YV, Adams A, Zhao C, Crews CM. Targeted protein destabilization reveals an estrogen-mediated ER stress response. Nat Chem Biol 2014; 10:957-62. [PMID: 25242550 PMCID: PMC4324732 DOI: 10.1038/nchembio.1638] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/14/2014] [Indexed: 12/16/2022]
Abstract
Accumulation of unfolded proteins within the endoplasmic reticulum (ER) of eukaryotic cells leads to an unfolded protein response (UPR) that either restores homeostasis or commits the cells to apoptosis. Tools traditionally used to study the UPR are proapoptotic and thus confound analysis of long-term cellular responses to ER stress. Here, we describe an ER-localized HaloTag (ERHT) protein that can be conditionally destabilized using a small-molecule hydrophobic tag (HyT36). Treatment of ERHT-expressing cells with HyT36 induces acute, resolvable ER stress that results in transient UPR activation without induction of apoptosis. Transcriptome analysis of late-stage responses to this UPR stimulus reveals a link between UPR activity and estrogen signaling.
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Affiliation(s)
- Kanak Raina
- 1] Department of Chemistry, Yale University New Haven, Connecticut, USA. [2]
| | - Devin J Noblin
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, Connecticut, USA. [2]
| | - Yevgeniy V Serebrenik
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, Connecticut, USA
| | - Alison Adams
- Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, Connecticut, USA
| | - Connie Zhao
- Molecular Biophysics and Biochemistry, Yale University New Haven, Connecticut, USA
| | - Craig M Crews
- 1] Department of Chemistry, Yale University New Haven, Connecticut, USA. [2] Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, Connecticut, USA. [3] Department of Pharmacology, Yale University New Haven, Connecticut, USA
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29
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Buckley DL, Crews CM. Small-molecule control of intracellular protein levels through modulation of the ubiquitin proteasome system. Angew Chem Int Ed Engl 2014; 53:2312-30. [PMID: 24459094 PMCID: PMC4348030 DOI: 10.1002/anie.201307761] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 12/25/2022]
Abstract
Traditionally, biological probes and drugs have targeted the activities of proteins (such as enzymes and receptors) that can be readily controlled by small molecules. The remaining majority of the proteome has been deemed "undruggable". By using small-molecule modulators of the ubiquitin proteasome, protein levels, rather than protein activity, can be targeted instead, thus increasing the number of druggable targets. Whereas targeting of the proteasome itself can lead to a global increase in protein levels, the targeting of other components of the UPS (e.g., the E3 ubiquitin ligases) can lead to an increase in protein levels in a more targeted fashion. Alternatively, multiple strategies for inducing protein degradation with small-molecule probes are emerging. With the ability to induce and inhibit the degradation of targeted proteins, small-molecule modulators of the UPS have the potential to significantly expand the druggable portion of the proteome beyond traditional targets, such as enzymes and receptors.
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Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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30
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Buckley DL, Crews CM. Steuerung der intrazellulären Proteinmenge durch niedermolekulare Modulatoren des Ubiquitin-Proteasom-Systems. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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31
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Auld D, Davis MI, Lea W, Parker C, Simeonov A. Literature Search and Review. Assay Drug Dev Technol 2013. [DOI: 10.1089/adt.2013.1109.lr] [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] Open
Affiliation(s)
- Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | | | - Christian Parker
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
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