1
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Setia N, Almuqdadi HTA, Abid M. Journey of Von Hippel-Lindau (VHL) E3 ligase in PROTACs design: From VHL ligands to VHL-based degraders. Eur J Med Chem 2024; 265:116041. [PMID: 38199162 DOI: 10.1016/j.ejmech.2023.116041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The scientific community has shown considerable interest in proteolysis-targeting chimeras (PROTACs) in the last decade, indicating their remarkable potential as a means of achieving targeted protein degradation (TPD). Not only are PROTACs seen as valuable tools in molecular biology but their emergence as a modality for drug discovery has also garnered significant attention. PROTACs bind to E3 ligases and target proteins through respective ligands connected via a linker to induce proteasome-mediated protein degradation. The discovery of small molecule ligands for E3 ligases has led to the prevalent use of various E3 ligases in PROTAC design. Furthermore, the incorporation of different types of linkers has proven beneficial in enhancing the efficacy of PROTACs. By far more than 3300 PROTACs have been reported in the literature. Notably, Von Hippel-Lindau (VHL)-based PROTACs have surfaced as a propitious strategy for targeting proteins, even encompassing those that were previously considered non-druggable. VHL is extensively utilized as an E3 ligase in the advancement of PROTACs owing to its widespread expression in various tissues and well-documented binders. Here, we review the discovery of VHL ligands, the types of linkers employed to develop VHL-based PROTACs, and their subsequent modulation to design advanced non-conventional degraders to target various disease-causing proteins. Furthermore, we provide an overview of other E3 ligases recruited in the field of PROTAC technology.
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Affiliation(s)
- Nisha Setia
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | | | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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2
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Ouyang M, Feng Y, Chen H, Liu Y, Tan C, Tan Y. Recent Advances in Optically Controlled PROTAC. Bioengineering (Basel) 2023; 10:1368. [PMID: 38135959 PMCID: PMC10740939 DOI: 10.3390/bioengineering10121368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Proteolysis-targeting chimera (PROTAC) technology is a groundbreaking therapeutic approach with significant clinical potential for degrading disease-inducing proteins within targeted cells. However, challenges related to insufficient target selectivity raise concerns about PROTAC toxicity toward normal cells. To address this issue, researchers are modifying PROTACs using various approaches to enhance their target specificity. This review highlights innovative optically controlled PROTACs as anti-cancer therapies currently used in clinical practice and explores the challenges associated with their efficacy and safety. The development of optically controlled PROTACs holds the potential to significantly expand the clinical applicability of PROTAC-based technology within the realm of drug discovery.
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Affiliation(s)
- Muzi Ouyang
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (M.O.); (Y.F.); (H.C.); (Y.L.); (C.T.)
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ying Feng
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (M.O.); (Y.F.); (H.C.); (Y.L.); (C.T.)
| | - Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (M.O.); (Y.F.); (H.C.); (Y.L.); (C.T.)
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yanping Liu
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (M.O.); (Y.F.); (H.C.); (Y.L.); (C.T.)
| | - Chunyan Tan
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (M.O.); (Y.F.); (H.C.); (Y.L.); (C.T.)
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (M.O.); (Y.F.); (H.C.); (Y.L.); (C.T.)
- Department of Chemistry, Tsinghua University, Beijing 100084, China
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3
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Zheng H, Li G, Min J, Xu X, Huang W. Lysosome and related protein degradation technologies. Drug Discov Today 2023; 28:103767. [PMID: 37708931 DOI: 10.1016/j.drudis.2023.103767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Recently, targeted protein degradation technologies based on lysosomal pathways have been developed. Lysosome-based targeted protein degradation technology has a broad range of substrates and the potential to degrade intracellular and extracellular proteins, protein aggregates, damaged organelles and non-protein molecules. Thus, they hold great promise for drug R&D. This study has focused on the biogenesis of lysosomes, their basic functions, lysosome-associated diseases and targeted protein degradation technologies through the lysosomal pathway. In addition, we thoroughly examine the potential applications and limitations of this technology and engage in insightful discussions on potential avenues for future research. Our primary objective is to foster preclinical research on this technology and facilitate its successful clinical implementation.
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Affiliation(s)
- Hongmei Zheng
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Gangjian Li
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Jingli Min
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Xiangwei Xu
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Wenhai Huang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China.
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4
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Wang Z, Tan M, Su W, Huang W, Zhang J, Jia F, Cao G, Liu X, Song H, Ran H, Nie G, Wang H. Persistent Degradation of HER2 Protein by Hybrid nanoPROTAC for Programmed Cell Death. J Med Chem 2023; 66:6263-6273. [PMID: 37092695 DOI: 10.1021/acs.jmedchem.3c00013] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Proteolysis-targeting chimera (PROTAC) has emerged as a promising strategy for degrading proteins of interest. Peptide-based PROTACs offer several advantages over small-molecule-based PROTACs, such as high specificity, low toxicity, and large protein-protein interaction surfaces. However, peptide-based PROTACs have several intrinsic shortcomings that strongly limit their application including poor cell permeability and low stability and potency. Herein, we designed a nanosized hybrid PROTAC (GNCTACs) to target and degrade human epidermal growth factor receptor 2 (HER2) in tumor cells. Gold nanoclusters (GNCs) were utilized to connect HER2-targeting peptides and cereblon (CRBN)-targeting ligands. GNCTACs could overcome the intrinsic barriers of peptide-based PROTACs, efficiently delivering HER2-targeting peptides in the cytoplasm and protecting them from degradation. Furthermore, a fasting-mimicking diet was applied to enhance the cellular uptake and proteasome activity. Consequently, more than 95% of HER2 in SKBR3 cells was degraded by GNCTACs, and the degradation lasted for at least 72 h, showing a catalytic-like reaction.
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Affiliation(s)
- Zhihang Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mixiao Tan
- The Second Affiliated Hospital of Chongqing Medical University & Chongqing Key Laboratory of Ultrasound Molecular Imaging, Chongqing 400010, China
| | - Wen Su
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Wenping Huang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhao Jia
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Cao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xinyang Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Haohao Song
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Haitao Ran
- The Second Affiliated Hospital of Chongqing Medical University & Chongqing Key Laboratory of Ultrasound Molecular Imaging, Chongqing 400010, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hai Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Sobhia ME, Kumar H, Kumari S. Bifunctional robots inducing targeted protein degradation. Eur J Med Chem 2023; 255:115384. [PMID: 37119667 DOI: 10.1016/j.ejmech.2023.115384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/01/2023]
Abstract
The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) and E3-ligase, which induce the ubiquitination of POI. These molecules are based on event-driven pharmacology and are applicable in different conditions such as oncology, antiviral, neurodegenerative disease, acne etc., offering tremendous scope to researchers. In this review, primarily, we attempted to compile the recent works available in the literature on PROTACs for various targeted proteins. We summarized the design and development strategies with a focus on molecular information of protein residues and linker design. Rationalization of the ternary complex formation using Artificial Intelligence including machine & deep learning models and traditionally followed computational tools are also included in this study. Moreover, details describing the optimization of PROTACs chemistry and pharmacokinetic properties are added. Advanced PROTAC designs and targeting complex proteins, is summed up to cover the wide spectrum.
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Affiliation(s)
- M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India.
| | - Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India
| | - Sonia Kumari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India
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6
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Li X, Liu Q, Xie X, Peng C, Pang Q, Liu B, Han B. Application of Novel Degraders Employing Autophagy for Expediting Medicinal Research. J Med Chem 2023; 66:1700-1711. [PMID: 36716420 DOI: 10.1021/acs.jmedchem.2c01712] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Targeted protein degradation (TPD) technology is based on a unique pharmacological mechanism that has profoundly revolutionized medicinal research by overcoming limitations associated with traditional small-molecule drugs. Autophagy, a mechanism for intracellular waste disposal and recovery, is an important biological process in medicinal research. Recently, studies have demonstrated that several emerging autophagic degraders can treat human diseases. Herein we summarize the progress in medicinal research on autophagic degraders, including autophagosome-tethering compounds (ATTEC), autophagy-targeting chimeras (AUTAC), and AUTOphagy-TArgeting chimeras (AUTOTAC), for treating human diseases. These autophagic degraders exhibit excellent potential for treating neurodegenerative diseases. Our research on autophagic degraders provides a new avenue for medicinal research on TPD via autophagy.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qian Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qiwen Pang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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7
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Ding Y, Xing D, Fei Y, Lu B. Emerging degrader technologies engaging lysosomal pathways. Chem Soc Rev 2022; 51:8832-8876. [PMID: 36218065 PMCID: PMC9620493 DOI: 10.1039/d2cs00624c] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Indexed: 08/24/2023]
Abstract
Targeted protein degradation (TPD) provides unprecedented opportunities for drug discovery. While the proteolysis-targeting chimera (PROTAC) technology has already entered clinical trials and changed the landscape of small-molecule drugs, new degrader technologies harnessing alternative degradation machineries, especially lysosomal pathways, have emerged and broadened the spectrum of degradable targets. We have recently proposed the concept of autophagy-tethering compounds (ATTECs) that hijack the autophagy protein microtubule-associated protein 1A/1B light chain 3 (LC3) for targeted degradation. Other groups also reported degrader technologies engaging lysosomal pathways through different mechanisms including AUTACs, AUTOTACs, LYTACs and MoDE-As. In this review, we analyse and discuss ATTECs along with other lysosomal-relevant degrader technologies. Finally, we will briefly summarize the current status of these degrader technologies and envision possible future studies.
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Affiliation(s)
- Yu Ding
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
| | - Dong Xing
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
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8
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Recent Advances in PROTACs for Drug Targeted Protein Research. Int J Mol Sci 2022; 23:ijms231810328. [PMID: 36142231 PMCID: PMC9499226 DOI: 10.3390/ijms231810328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 01/30/2023] Open
Abstract
Proteolysis-targeting chimera (PROTAC) is a heterobifunctional molecule. Typically, PROTAC consists of two terminals which are the ligand of the protein of interest (POI) and the specific ligand of E3 ubiquitin ligase, respectively, via a suitable linker. PROTAC degradation of the target protein is performed through the ubiquitin–proteasome system (UPS). The general process is that PROTAC binds to the target protein and E3 ligase to form a ternary complex and label the target protein with ubiquitination. The ubiquitinated protein is recognized and degraded by the proteasome in the cell. At present, PROTAC, as a new type of drug, has been developed to degrade a variety of cancer target proteins and other disease target proteins, and has shown good curative effects on a variety of diseases. For example, PROTACs targeting AR, BR, BTK, Tau, IRAK4, and other proteins have shown unprecedented clinical efficacy in cancers, neurodegenerative diseases, inflammations, and other fields. Recently, PROTAC has entered a phase of rapid development, opening a new field for biomedical research and development. This paper reviews the various fields of targeted protein degradation by PROTAC in recent years and summarizes and prospects the hot targets and indications of PROTAC.
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9
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Anwar Z, Ali MS, Galvano A, Perez A, La Mantia M, Bukhari I, Swiatczak B. PROTACs: The Future of Leukemia Therapeutics. Front Cell Dev Biol 2022; 10:851087. [PMID: 36120561 PMCID: PMC9479449 DOI: 10.3389/fcell.2022.851087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
The fight to find effective, long-lasting treatments for cancer has led many researchers to consider protein degrading entities. Recent developments in PROteolysis TArgeting Chimeras (PROTACs) have signified their potential as possible cancer therapies. PROTACs are small molecule, protein degraders that function by hijacking the built-in Ubiquitin-Proteasome pathway. This review mainly focuses on the general design and functioning of PROTACs as well as current advancements in the development of PROTACs as anticancer therapies. Particular emphasis is given to PROTACs designed against various types of Leukemia/Blood malignancies.
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Affiliation(s)
- Zubair Anwar
- Department of Surgical, Oncological, and Oral Sciences, Section of Medical Oncology, Uiniversity of Palermo, Palermo, Italy
- *Correspondence: Zubair Anwar, ; Bartlomiej Swiatczak,
| | - Muhammad Shahzad Ali
- Department of Clinical and Biological Sciences, University of Turin, San Luigi Hospital, Turin, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological, and Oral Sciences, Section of Medical Oncology, Uiniversity of Palermo, Palermo, Italy
| | - Alessandro Perez
- Department of Surgical, Oncological, and Oral Sciences, Section of Medical Oncology, Uiniversity of Palermo, Palermo, Italy
| | - Maria La Mantia
- Department of Surgical, Oncological, and Oral Sciences, Section of Medical Oncology, Uiniversity of Palermo, Palermo, Italy
| | - Ihtisham Bukhari
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, Hefei, China
- *Correspondence: Zubair Anwar, ; Bartlomiej Swiatczak,
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10
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Memon H, Patel BM. PROTACs: Novel approach for cancer breakdown by breaking proteins. Life Sci 2022; 300:120577. [PMID: 35487303 DOI: 10.1016/j.lfs.2022.120577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/21/2021] [Accepted: 04/20/2022] [Indexed: 11/19/2022]
Abstract
Ubiquitination defects have been reported in various diseases, including neurodegenerative diseases, metabolic disorders and cancer. Balance between degradation and synthesis of the proteins to treat cancer can be managed by designing a chimeric molecule, known as Proteolysis Targeting Chimeric molecule (Lee, Kim et al. 2021). Proteolysis-targeting chimeras (PROTACs) acts as a tool for conducting therapeutic intervention. It eradicates or reduces the proteins that are responsible for causing diseases. Each PROTAC contains a target warhead, an E3 ligand and a linker. E3 ligases are recruited by these bifunctional molecules, and the Ubiquitin (Ub) Proteasome System (UPS) is used to target the degradation of specific proteins. As compared to inhibition, this degradation offers several advantages in the drug resistance, selectivity, and potency. Thus, numerous small molecule PROTACs are identified so far. In this review, the development of PROTACs, historical milestones, the biological mechanism, advantages and recent progress, and role of PROTAC in prostate cancer, breast cancer, non-hodgkin lymphoma, multiple myeloma, and malignant peripheral nerve sheath tumors are summarized.
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Affiliation(s)
- Humera Memon
- Institute of Pharmacy, Nirma University, Ahmedabad, India
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11
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Wang C, Zhang Y, Wu Y, Xing D. Developments of CRBN-based PROTACs as potential therapeutic agents. Eur J Med Chem 2021; 225:113749. [PMID: 34411892 DOI: 10.1016/j.ejmech.2021.113749] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022]
Abstract
Protease-targeted chimeras (PROTACs) are a new technology that is receiving much attention in the treatment of diseases. The mechanism is to inhibit protein function by hijacking the ubiquitin E3 ligase for protein degradation. Heterogeneous bifunctional PROTACs contain a ligand for recruiting E3 ligase, a linker, and another ligand to bind to the target protein for degradation. A variety of small-molecule PROTACs (CRBN, VHL, IAPs, MDM2, DCAF15, DCAF16, and RNF114-based PROTACs) have been identified so far. In particular, CRBN-based PROTACs (e.g., ARV-110 and ARV-471) have received more attention for their promising therapeutic intervention. To date, CRBN-based PRTOACs have been extensively explored worldwide and have excelled not only in cancer diseases but also in cardiovascular diseases, immune diseases, neurodegenerative diseases, and viral infections. In this review, we will provide a comprehensive update on the latest research progress in CRBN-based PRTOACs area. Following the criteria, such as disease area and drug target class, we will present the degradants in alphabetical order by target. We also provide our own perspective on the future prospects and potential challenges facing PROTACs.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Yudong Wu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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12
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Liu J, Peng Y, Wei W. Light-Controllable PROTACs for Temporospatial Control of Protein Degradation. Front Cell Dev Biol 2021; 9:678077. [PMID: 34350175 PMCID: PMC8326567 DOI: 10.3389/fcell.2021.678077] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/14/2021] [Indexed: 12/25/2022] Open
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) is an emerging and promising approach to target intracellular proteins for ubiquitination-mediated degradation, including those so-called undruggable protein targets, such as transcriptional factors and scaffold proteins. To date, plenty of PROTACs have been developed to degrade various disease-relevant proteins, such as estrogen receptor (ER), androgen receptor (AR), RTK, and CDKs. However, the on-target off-tissue and off-target effect is one of the major limitation that prevents the usage of PROTACs in clinic. To this end, we and several other groups have recently developed light-controllable PROTACs, as the representative for the third generation controllable PROTACs, by using either photo-caging or photo-switch approaches. In this review, we summarize the emerging light-controllable PROTACs and the prospective for other potential ways to achieve temporospatial control of PROTACs.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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13
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Wang C, Zhang Y, Xing D, Zhang R. PROTACs technology for targeting non-oncoproteins: Advances and perspectives. Bioorg Chem 2021; 114:105109. [PMID: 34175722 DOI: 10.1016/j.bioorg.2021.105109] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 12/18/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) have been developed to be an effective technology for targeted protein degradation. Each PROTAC contains three key components: a protein-of-interest (POI) ligand, an E3 ligase ligand, and a linker. These bifunctional molecules can hijack the intracellular inherent ubiquitin-proteasome system to degrade different POIs. With several advantages over other therapeutic strategies, PROTACs have set off a new upsurge of drug discovery in recent years. PRTOACs have been extensively explored worldwide and have excelled not only in cancer diseases but also in cardiovascular diseases, fatty liver disease, immune diseases, neurodegenerative diseases, and viral infections. In this review, we aim to summarize the rapid progress from 2010 to 2021 in PROTACs targeting various non-oncoproteins and elucidate the advantages of PROTACs technology. Finally, the potential challenges of this dynamic field are also discussed.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Cancer Institute, Qingdao 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao 266071, Shandong, China.
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Cancer Institute, Qingdao 266071, Shandong, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Renshuai Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Cancer Institute, Qingdao 266071, Shandong, China.
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Farrell K, Jarome TJ. Is PROTAC technology really a game changer for central nervous system drug discovery? Expert Opin Drug Discov 2021; 16:833-840. [PMID: 33870803 DOI: 10.1080/17460441.2021.1915979] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Central nervous system (CNS) diseases affect a large portion of the population, however, few therapeutic options are available. Furthermore, to date, clinical trials have been largely unsuccessful due to difficulty in targeting the undruggable, toxic proteins that underly many CNS disorders. PROteolysis Targeting Chimeras (PROTACs) are a rapidly emerging technology that has been proposed as a potential treatment option for various CNS diseases by hijacking the endogenous protein degradation process.Areas Covered: Herein, the authors discuss how the application of PROTACs may be beneficial in the treatment of major CNS diseases. They further discuss the main advantages and disadvantages of using PROTACs in the CNS, focusing on potential limitations such as their transient nature, localization, blood-brain barrier permeability and proteasome dysfunction.Expert opinion: It is evident that PROTACs have significant potential as a therapeutic tool for the treatment of CNS diseases and there is preliminary evidence suggesting that PROTACs could be successful in a clinical setting. Nevertheless, numerous limitations exist that must be overcome before this technology can be applied as a successful therapeutic for CNS disorders. Importantly, more in vivo studies are needed to determine the feasibility and effectiveness of using PROTACs in the brain.
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Affiliation(s)
- Kayla Farrell
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, VA, USA
| | - Timothy J Jarome
- Department of Animal and Poultry Science and the School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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Kaur R, Chaudhary G, Kaur A, Singh P, Longowal GD, Sapkale GP, Arora S. PROTACs: A Hope for Breast Cancer Patients? Anticancer Agents Med Chem 2021; 22:406-417. [PMID: 33687888 DOI: 10.2174/1871520621666210308100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Breast Cancer (BC) is the most widely recognized disease in women. A massive number of women are diagnosed with breast cancer and many lost their lives every year. Cancer is the subsequent driving reason for dying, giving rise to it one of the current medication's most prominent difficulties. OBJECTIVES The main objective of the study is to examine and explore novel therapy (PROTAC) and its effectiveness against breast cancer. METHODS The literature search was done across Medline, Cochrane, ScienceDirect, Wiley Online, Google Scholar, PubMed, Bentham Sciences from 2001 to 2020. The articles were collected; screened, segregated, and selected papers were included for writing the review article. RESULTS AND CONCLUSION A novel innovation emerged around two decades ago that has great potential to not only overcome the limitations but also can provide future direction for the treatment of many diseases which has presently not many therapeutic options available and regarded as incurable with traditional techniques; that innovation is called PROTAC (Proteolysis Targeting Chimera) and able to efficaciously ubiquitinate and debase cancer encouraging proteins by noncovalent interaction. PROTACs are constituted of two active regions isolated by a linker and equipped for eliminating explicit undesirable protein. It is empowering greater sensitivity to "drug-resistant targets" as well as a more prominent opportunity to influence non-enzymatic function. PROTACs have been demonstrated to show better target selectivity contrasted with traditional small-molecule inhibitors. So far, the most investigation into PROTACs possesses particularly concentrated on applications to cancer treatment including breast cancer, the treatment of different ailments may profit from this blossoming innovation.
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Affiliation(s)
- Rajwinder Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab. India
| | - Gaurav Chaudhary
- Chitkara College of Pharmacy, Chitkara University, Punjab. India
| | - Amritpal Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab. India
| | - Pargat Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab. India
| | | | - Gayatri P Sapkale
- Fortis Flt. Lt. Rajan Dhall Hospital, Aruna Asaf Ali Marg, Pocket 1, Sector B, Vasant Kunj, New Delhi-110070. India
| | - Sandeep Arora
- Chitkara College of Pharmacy, Chitkara University, Punjab. India
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Muddassir M, Soni K, Sangani CB, Alarifi A, Afzal M, Abduh NAY, Duan Y, Bhadja P. Bromodomain and BET family proteins as epigenetic targets in cancer therapy: their degradation, present drugs, and possible PROTACs. RSC Adv 2021; 11:612-636. [PMID: 35746919 PMCID: PMC9133982 DOI: 10.1039/d0ra07971e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/28/2020] [Indexed: 12/27/2022] Open
Abstract
Alteration in the pattern of epigenetic marking leads to cancer, neurological disorders, inflammatory problems etc. These changes are due to aberration in histone modification enzymes that function as readers, writers and erasers. Bromodomains (BDs) and BET proteins that recognize acetylation of chromatin regulate gene expression. To block the function of any of these BrDs and/or BET protein can be a controlling agent in disorders such as cancer. BrDs and BET proteins are now emerging as targets for new therapeutic development. Traditional drugs like enzyme inhibitors and protein–protein inhibitors have many limitations. Recently Proteolysis-Targeting Chimeras (PROTACs) have become an advanced tool in therapeutic intervention as they remove disease causing proteins. This review provides an overview of the development and mechanisms of PROTACs for BRD and BET protein regulation in cancer and advanced possibilities of genetic technologies in therapeutics. Alteration in the pattern of epigenetic marking leads to cancer, neurological disorders, inflammatory problems etc.![]()
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Affiliation(s)
- Mohd. Muddassir
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Kunjal Soni
- Shri Maneklal M. Patel Institute of Sciences and Research
- Kadi Sarva Vishwavidyalaya University
- Gandhinagar
- India
| | - Chetan B. Sangani
- Shri Maneklal M. Patel Institute of Sciences and Research
- Kadi Sarva Vishwavidyalaya University
- Gandhinagar
- India
| | - Abdullah Alarifi
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Mohd. Afzal
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Naaser A. Y. Abduh
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Yongtao Duan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases
- Zhengzhou Children's Hospital
- Zhengzhou University
- Zhengzhou 450018
- China
| | - Poonam Bhadja
- Arthropod Ecology and Biological Control Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Environment and Labour Safety
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Wu X, Luo Q, Liu Z. Ubiquitination and deubiquitination of MCL1 in cancer: deciphering chemoresistance mechanisms and providing potential therapeutic options. Cell Death Dis 2020; 11:556. [PMID: 32699213 PMCID: PMC7376237 DOI: 10.1038/s41419-020-02760-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
MCL1 is an important antiapoptotic member of the BCL-2 family that is distinguishable from other family members based on its relatively short half-life. Emerging studies have revealed the crucial role of MCL1 in the chemoresistance of cancer cells. The antiapoptotic function of MCL1 makes it a popular therapeutic target, although specific inhibitors have begun to emerge only recently. Notably, emerging studies have reported that several E3 ligases and deubiquitinases modulate MCL1 stability, providing an alternate means of targeting MCL1 activity. In addition, the emergence and development of proteolysis-targeting chimeras, the function of which is based on ubiquitination-mediated degradation, has shown great potential. In this review, we provide an overview of the studies investigating the ubiquitination and deubiquitination of MCL1, summarize the latest evidence regarding the development of therapeutic strategies targeting MCL1 in cancer treatment, and discuss the promising future of targeting MCL1 via the ubiquitin–proteasome system in clinical practice.
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Affiliation(s)
- Xiaowei Wu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Qingyu Luo
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
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18
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Li X, Song Y. Proteolysis-targeting chimera (PROTAC) for targeted protein degradation and cancer therapy. J Hematol Oncol 2020; 13:50. [PMID: 32404196 PMCID: PMC7218526 DOI: 10.1186/s13045-020-00885-3] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
Proteolysis-targeting chimera (PROTAC) has been developed to be a useful technology for targeted protein degradation. A bifunctional PROTAC molecule consists of a ligand (mostly small-molecule inhibitor) of the protein of interest (POI) and a covalently linked ligand of an E3 ubiquitin ligase (E3). Upon binding to the POI, the PROTAC can recruit E3 for POI ubiquitination, which is subjected to proteasome-mediated degradation. PROTAC complements nucleic acid-based gene knockdown/out technologies for targeted protein reduction and could mimic pharmacological protein inhibition. To date, PROTACs targeting ~ 50 proteins, many of which are clinically validated drug targets, have been successfully developed with several in clinical trials for cancer therapy. This article reviews PROTAC-mediated degradation of critical oncoproteins in cancer, particularly those in hematological malignancies. Chemical structures, cellular and in vivo activities, pharmacokinetics, and pharmacodynamics of these PROTACs are summarized. In addition, potential advantages, challenges, and perspectives of PROTAC technology in cancer therapy are discussed.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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Bao SM, Hu QH, Yang WT, Wang Y, Tong YP, Bao WD. Targeting Epidermal Growth Factor Receptor in Non-Small-Cell-Lung Cancer: Current State and Future Perspective. Anticancer Agents Med Chem 2020; 19:984-991. [PMID: 30868964 DOI: 10.2174/1871520619666190313161009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 12/20/2018] [Accepted: 03/01/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Lung cancer is one of the leading cause of cancer death worldwide, the most common histological type of lung cancer is non-small cell lung cancer (NSCLC), whose occurrence and development is closely related to the mutation and amplification of epidermal growth factor receptors (EGFR). Currently , a series of targeted drugs were developed on the inhibition of EGFR such as epidermal growth factor receptortyrosine kinase inhibitor EGFR-TKI and monoclonal antibody (McAb). OBJECTIVE We sought to summarizes the current drugs targeting Epidermal Growth Factor Receptor in nonsmall- cell-lung. METHODS We conducted a comprehensive review of the development and application of EGFR-TKI and McAb which targeted EGFR in NSCLC and compared the mechanisms of PROTAC with the traditional inhibitors. RESULTS The drugs targeted EGFR in NSCLC have been widely used in clinic practices. Compared to traditional chemotherapy, these drugs excel with their clear and specific targeting, better curative effects, and less toxic and side effects. However, the mechanism comes with some insurmountable weaknesses like serious toxic and other side effects, as well as proneness to producing drug resistance. CONCLUSION The emerging PROTAC (Proteolysis Targeting Chimera) technology has been successfully applied to selective degradation of multiple protein targets, including EGFR. It also highlights the potential and challenges of PROTAC therapy regarding future combination therapeutic options in NSCLC treatment.
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Affiliation(s)
- Shui-Ming Bao
- Department of biology, East China University of Technology, 418 Guanglan Road, Nan chang, Jiangxi province 330013, China
| | - Qing-Hui Hu
- Nanchang Five Elements Biology Technology Company Limited, Nanchang, Jiangxi, China
| | - Wen-Ting Yang
- Nanchang Five Elements Biology Technology Company Limited, Nanchang, Jiangxi, China
| | - Yao Wang
- Nanchang Five Elements Biology Technology Company Limited, Nanchang, Jiangxi, China
| | - Yin-Ping Tong
- Nanchang Five Elements Biology Technology Company Limited, Nanchang, Jiangxi, China
| | - Wen-Dai Bao
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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20
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Liu J, Ma J, Liu Y, Xia J, Li Y, Wang ZP, Wei W. PROTACs: A novel strategy for cancer therapy. Semin Cancer Biol 2020; 67:171-179. [PMID: 32058059 DOI: 10.1016/j.semcancer.2020.02.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/08/2020] [Accepted: 02/09/2020] [Indexed: 12/29/2022]
Abstract
Chemotherapeutic strategy has been widely used for treating malignance by targeting irregular expressed or mutant proteins with small molecular inhibitors (SMIs) or monoclonal antibodies (mAbs). However, most intracellular proteins lack of active sites or antigens where SMIs or mAbs bind with, and are called as non-druggable targets for a long time. From the first year of this century, PROteolysis-TArgeting Chimeras (PROTACs) has emerged to be a promising approach for proteins, including those non-druggable ones, such as transcriptional factors and scaffold proteins. The first generation of peptide-based PROTACs adopts β-TrCP and VHL as E3 ligases, but the cellular permeability and chemical stability issues restrict their clinical application. The second generation of small molecule-based PROTACs adopts MDM2, VHL, IAPs and Cereblon as E3 ligases have been tensely studied. To date, the targets of PROTACs including those overexpressed oncogenic proteins such as ER, AR and BRDs, disease-relevant fusion proteins such as NPM/EML4-ALK and BCR-ABL, cancer-driven mutant proteins such as EGFR, kinases such as CDKs and RTKs. The major disadvantage of PROTACs is the noncancer specificity and relative higher toxicity, due to its catalytic role. To overcome this, we and other have recently developed several similar light-controllable PROTACs, termed as the third generation controllable PROTACs. The degradation of targets by those PROTACs can be triggered by UVA or visible light, providing a tool box for further PROTACs design. Here in this review, we introduce the historical milestones and prospective for further PROTACs development in clinical use.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jia Ma
- Department of Biochemistry and Molecular Biology, Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Yi Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Jun Xia
- Department of Biochemistry and Molecular Biology, Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Yuyun Li
- Department of Clinical Laboratory Diagnostics, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Z Peter Wang
- Department of Biochemistry and Molecular Biology, Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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22
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Sun X, Gao H, Yang Y, He M, Wu Y, Song Y, Tong Y, Rao Y. PROTACs: great opportunities for academia and industry. Signal Transduct Target Ther 2019; 4:64. [PMID: 31885879 PMCID: PMC6927964 DOI: 10.1038/s41392-019-0101-6] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/17/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
Although many kinds of therapies are applied in the clinic, drug-resistance is a major and unavoidable problem. Another disturbing statistic is the limited number of drug targets, which are presently only 20-25% of all protein targets that are currently being studied. Moreover, the focus of current explorations of targets are their enzymatic functions, which ignores the functions from their scaffold moiety. As a promising and appealing technology, PROteolysis TArgeting Chimeras (PROTACs) have attracted great attention both from academia and industry for finding available approaches to solve the above problems. PROTACs regulate protein function by degrading target proteins instead of inhibiting them, providing more sensitivity to drug-resistant targets and a greater chance to affect the nonenzymatic functions. PROTACs have been proven to show better selectivity compared to classic inhibitors. PROTACs can be described as a chemical knockdown approach with rapidity and reversibility, which presents new and different biology compared to other gene editing tools by avoiding misinterpretations that arise from potential genetic compensation and/or spontaneous mutations. PRTOACs have been widely explored throughout the world and have outperformed not only in cancer diseases, but also in immune disorders, viral infections and neurodegenerative diseases. Although PROTACs present a very promising and powerful approach for crossing the hurdles of present drug discovery and tool development in biology, more efforts are needed to gain to get deeper insight into the efficacy and safety of PROTACs in the clinic. More target binders and more E3 ligases applicable for developing PROTACs are waiting for exploration.
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Affiliation(s)
- Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Hongying Gao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Yiqing Yang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yue Wu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yugang Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yan Tong
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 China
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Sun M, Veschi V, Bagchi S, Xu M, Mendoza A, Liu Z, Thiele CJ. Targeting the Chromosomal Passenger Complex Subunit INCENP Induces Polyploidization, Apoptosis, and Senescence in Neuroblastoma. Cancer Res 2019; 79:4937-4950. [PMID: 31416840 DOI: 10.1158/0008-5472.can-19-0695] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/03/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022]
Abstract
Chromosomal passenger complex (CPC) has been demonstrated to be a potential target of cancer therapy by inhibiting Aurora B or survivin in different types of cancer including neuroblastoma. However, chemical inhibition of either Aurora B or survivin does not target CPC specifically due to off-target effects or CPC-independent activities of these two components. In a previous chromatin-focused siRNA screen, we found that neuroblastoma cells were particularly vulnerable to loss of INCENP, a gene encoding a key scaffolding component of the CPC. In this study, INCENP was highly expressed by neuroblastoma cells, and its expression decreased following retinoic acid-induced neuroblastoma differentiation. Elevated levels of INCENP were significantly associated with poor prognosis in primary tumors of neuroblastoma patients with high-risk disease. Genetic silencing of INCENP reduced the growth of both MYCN-wild-type and MYCN-amplified neuroblastoma cell lines in vitro and decreased the growth of neuroblastoma xenografts in vivo, with significant increases in murine survival. Mechanistically, INCENP depletion suppressed neuroblastoma cell growth by inducing polyploidization, apoptosis, and senescence. In most neuroblastoma cell lines tested in vitro, apoptosis was the primary cell fate after INCENP silencing due to induction of DNA damage response and activation of the p53-p21 axis. These results confirm that CPC is a therapeutic target in neuroblastoma, and targeting INCENP is a novel way to disrupt the activity of CPC and inhibit tumor progression in neuroblastoma. SIGNIFICANCE: Dysregulation of INCENP contributes to neuroblastoma tumorigenesis and targeting INCENP presents a novel strategy to disrupt the activity of chromosomal passenger complex and inhibit neuroblastoma progression.
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Affiliation(s)
- Ming Sun
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Veronica Veschi
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sukriti Bagchi
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Man Xu
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Arnulfo Mendoza
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Zhihui Liu
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Carol J Thiele
- Cell and Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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Xi M, Chen Y, Yang H, Xu H, Du K, Wu C, Xu Y, Deng L, Luo X, Yu L, Wu Y, Gao X, Cai T, Chen B, Shen R, Sun H. Small molecule PROTACs in targeted therapy: An emerging strategy to induce protein degradation. Eur J Med Chem 2019; 174:159-180. [PMID: 31035238 DOI: 10.1016/j.ejmech.2019.04.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/13/2019] [Accepted: 04/13/2019] [Indexed: 01/01/2023]
Abstract
Inhibitors and nucleic acid based techniques were two main approaches to interfere with protein signaling and respective cascade in the past. Until recently, a new class of small molecules named proteolysis-targeting chimeras (PROTACs) have emerged. Each contains a target warhead, a linker and an E3 ligand. These bifunctional molecules recruit E3 ligases and target specific proteins for degradation via the ubiquitin (Ub) proteasome system (UPS). The degradation provides several advantages over inhibition in potency, selectivity and drug resistance. Thus, a variety of small molecule PROTACs have been discovered so far. In this review, we summarize the biological mechanism, advantages and recent progress of PROTACs, trying to offer an outlook in development of drugs targeting degradation in future.
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Affiliation(s)
- Meiyang Xi
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yi Chen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Hongyu Yang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China
| | - Huiting Xu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Kui Du
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Chunlei Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yanfei Xu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Liping Deng
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiang Luo
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Lemao Yu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yonghua Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiaozhong Gao
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Tao Cai
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Bin Chen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Runpu Shen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China.
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China.
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Zou Y, Ma D, Wang Y. The PROTAC technology in drug development. Cell Biochem Funct 2019; 37:21-30. [PMID: 30604499 PMCID: PMC6590639 DOI: 10.1002/cbf.3369] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/28/2022]
Abstract
Currently, a new technology termed PROTAC, proteolysis targeting chimera, has been developed for inducing the protein degradation by a targeting molecule. This technology takes advantage of a moiety of targeted protein and a moiety of recognizing E3 ubiquitin ligase and produces a hybrid molecule to specifically knock down a targeted protein. During the first decade, three pedigreed groups worked on the development of this technology. To date, this technology has been extended by different groups, aiming to develop new drugs against different diseases including cancers. This review summarizes the contributions of the groups for the development of PROTAC. SIGNIFICANCE OF THE STUDY: This review summarized the development of the PROTAC technology for readers and also presented the author's opinions on the application of the technology in tumor therapy.
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Affiliation(s)
- Yutian Zou
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China.,Department of Science, Brookwood High School, Snellville, Georgia
| | - Danhui Ma
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Yinyin Wang
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China
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26
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Cheng J, Guo J, North BJ, Tao K, Zhou P, Wei W. The emerging role for Cullin 4 family of E3 ligases in tumorigenesis. Biochim Biophys Acta Rev Cancer 2018; 1871:138-159. [PMID: 30602127 DOI: 10.1016/j.bbcan.2018.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
As a member of the Cullin-RING ligase family, Cullin-RING ligase 4 (CRL4) has drawn much attention due to its broad regulatory roles under physiological and pathological conditions, especially in neoplastic events. Based on evidence from knockout and transgenic mouse models, human clinical data, and biochemical interactions, we summarize the distinct roles of the CRL4 E3 ligase complexes in tumorigenesis, which appears to be tissue- and context-dependent. Notably, targeting CRL4 has recently emerged as a noval anti-cancer strategy, including thalidomide and its derivatives that bind to the substrate recognition receptor cereblon (CRBN), and anticancer sulfonamides that target DCAF15 to suppress the neoplastic proliferation of multiple myeloma and colorectal cancers, respectively. To this end, PROTACs have been developed as a group of engineered bi-functional chemical glues that induce the ubiquitination-mediated degradation of substrates via recruiting E3 ligases, such as CRL4 (CRBN) and CRL2 (pVHL). We summarize the recent major advances in the CRL4 research field towards understanding its involvement in tumorigenesis and further discuss its clinical implications. The anti-tumor effects using the PROTAC approach to target the degradation of undruggable targets are also highlighted.
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Affiliation(s)
- Ji Cheng
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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Natsume T, Kanemaki MT. Conditional Degrons for Controlling Protein Expression at the Protein Level. Annu Rev Genet 2018; 51:83-102. [PMID: 29178817 DOI: 10.1146/annurev-genet-120116-024656] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
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Affiliation(s)
- Toyoaki Natsume
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
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28
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Li W, Gao C, Zhao L, Yuan Z, Chen Y, Jiang Y. Phthalimide conjugations for the degradation of oncogenic PI3K. Eur J Med Chem 2018; 151:237-247. [DOI: 10.1016/j.ejmech.2018.03.066] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 12/11/2022]
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29
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Akuffo AA, Alontaga AY, Metcalf R, Beatty MS, Becker A, McDaniel JM, Hesterberg RS, Goodheart WE, Gunawan S, Ayaz M, Yang Y, Karim MR, Orobello ME, Daniel K, Guida W, Yoder JA, Rajadhyaksha AM, Schönbrunn E, Lawrence HR, Lawrence NJ, Epling-Burnette PK. Ligand-mediated protein degradation reveals functional conservation among sequence variants of the CUL4-type E3 ligase substrate receptor cereblon. J Biol Chem 2018; 293:6187-6200. [PMID: 29449372 DOI: 10.1074/jbc.m117.816868] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/15/2018] [Indexed: 12/13/2022] Open
Abstract
Upon binding to thalidomide and other immunomodulatory drugs, the E3 ligase substrate receptor cereblon (CRBN) promotes proteosomal destruction by engaging the DDB1-CUL4A-Roc1-RBX1 E3 ubiquitin ligase in human cells but not in mouse cells, suggesting that sequence variations in CRBN may cause its inactivation. Therapeutically, CRBN engagers have the potential for broad applications in cancer and immune therapy by specifically reducing protein expression through targeted ubiquitin-mediated degradation. To examine the effects of defined sequence changes on CRBN's activity, we performed a comprehensive study using complementary theoretical, biophysical, and biological assays aimed at understanding CRBN's nonprimate sequence variations. With a series of recombinant thalidomide-binding domain (TBD) proteins, we show that CRBN sequence variants retain their drug-binding properties to both classical immunomodulatory drugs and dBET1, a chemical compound and targeting ligand designed to degrade bromodomain-containing 4 (BRD4) via a CRBN-dependent mechanism. We further show that dBET1 stimulates CRBN's E3 ubiquitin-conjugating function and degrades BRD4 in both mouse and human cells. This insight paves the way for studies of CRBN-dependent proteasome-targeting molecules in nonprimate models and provides a new understanding of CRBN's substrate-recruiting function.
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Affiliation(s)
- Afua A Akuffo
- From the Department of Immunology.,the Cancer Biology Ph.D. Program, University of South Florida, Tampa, Florida 33612
| | | | | | | | | | | | - Rebecca S Hesterberg
- From the Department of Immunology.,the Cancer Biology Ph.D. Program, University of South Florida, Tampa, Florida 33612
| | | | - Steven Gunawan
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Muhammad Ayaz
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | | | - Md Rezaul Karim
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | | | | | | | - Jeffrey A Yoder
- the Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27607, and
| | - Anjali M Rajadhyaksha
- Pediatric Neurology, Pediatrics, Brain and Mind Research Institute, Graduate Program in Neuroscience, Weill Cornell Medicine, Molecular and Developmental Neuroscience Laboratory, New York, New York 10065
| | - Ernst Schönbrunn
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | | | - Nicholas J Lawrence
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
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30
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Lei H, Wang W, Wu Y. Targeting oncoproteins for degradation by small molecules in myeloid leukemia. Leuk Lymphoma 2017; 59:2297-2304. [DOI: 10.1080/10428194.2017.1403600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hu Lei
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Weiwei Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Yingli Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
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Abstract
Three decades after the discovery of prions as the cause of Creutzfeldt-Jakob disease and other transmissible spongiform encephalopathies, we are still nowhere close to finding an effective therapy. Numerous pharmacological interventions have attempted to target various stages of disease progression, yet none has significantly ameliorated the course of disease. We still lack a mechanistic understanding of how the prions damage the brain, and this situation results in a dearth of validated pharmacological targets. In this review, we discuss the attempts to interfere with the replication of prions and to enhance their clearance. We also trace some of the possibilities to identify novel targets that may arise with increasing insights into prion biology.
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Affiliation(s)
- Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, CH-8091 Zürich, Switzerland;
| | - Asvin K K Lakkaraju
- Institute of Neuropathology, University of Zurich, CH-8091 Zürich, Switzerland;
| | - Karl Frontzek
- Institute of Neuropathology, University of Zurich, CH-8091 Zürich, Switzerland;
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32
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Nguyen C, West GM, Geoghegan KF. Emerging Methods in Chemoproteomics with Relevance to Drug Discovery. Methods Mol Biol 2017; 1513:11-22. [PMID: 27807827 DOI: 10.1007/978-1-4939-6539-7_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A powerful interplay exists between the recognition of gene families, sensitive techniques in proteomics, and the interrogation of protein function using chemical probes. The most prominent methods, such as affinity capture, activity-based protein profiling and photoaffinity labeling, are extensively reviewed in the literature. Here we briefly review additional methods developed in the past 15 years. These include "stability proteomics" methods such as proteomically analyzed cellular thermal shift assays and the use of chemical oxidation as a probe of structure, the use of multiple bead-linked kinase inhibitors to analyze inhibitor specificities, and advances in the use of proteolysis-targeting chimeras for selective protein elimination.
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Affiliation(s)
- Chuong Nguyen
- Structural Biology and Biophysics, Pfizer Worldwide Research, Groton, CT, 06340, USA
| | - Graham M West
- Structural Biology and Biophysics, Pfizer Worldwide Research, Groton, CT, 06340, USA
| | - Kieran F Geoghegan
- Structural Biology and Biophysics, Pfizer Worldwide Research, Groton, CT, 06340, USA.
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The chimeric ubiquitin ligase SH2-U-box inhibits the growth of imatinib-sensitive and resistant CML by targeting the native and T315I-mutant BCR-ABL. Sci Rep 2016; 6:28352. [PMID: 27329306 PMCID: PMC4916441 DOI: 10.1038/srep28352] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/02/2016] [Indexed: 01/01/2023] Open
Abstract
Chronic myeloid leukemia (CML) is characterized by constitutively active fusion protein tyrosine kinase BCR-ABL. Although the tyrosine kinase inhibitor (TKI) against BCR-ABL, imatinib, is the first-line therapy for CML, acquired resistance almost inevitably emerges. The underlying mechanism are point mutations within the BCR-ABL gene, among which T315I is notorious because it resists to almost all currently available inhibitors. Here we took use of a previously generated chimeric ubiquitin ligase, SH2-U-box, in which SH2 from the adaptor protein Grb2 acts as a binding domain for activated BCR-ABL, while U-box from CHIP functions as an E3 ubiquitin ligase domain, so as to target the ubiquitination and degradation of both native and T315I-mutant BCR-ABL. As such, SH2-U-box significantly inhibited proliferation and induced apoptosis in CML cells harboring either the wild-type or T315I-mutant BCR-ABL (K562 or K562R), with BCR-ABL-dependent signaling pathways being repressed. Moreover, SH2-U-box worked in concert with imatinib in K562 cells. Importantly, SH2-U-box-carrying lentivirus could markedly suppress the growth of K562-xenografts in nude mice or K562R-xenografts in SCID mice, as well as that of primary CML cells. Collectively, by degrading the native and T315I-mutant BCR-ABL, the chimeric ubiquitin ligase SH2-U-box may serve as a potential therapy for both imatinib-sensitive and resistant CML.
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34
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Long MC, Poganik JR, Aye Y. On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry. J Am Chem Soc 2016; 138:3610-22. [PMID: 26907082 PMCID: PMC4805449 DOI: 10.1021/jacs.5b12608] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 11/28/2022]
Abstract
Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is "tethering"-a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein-protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: "multifunctional scaffolding" versus "on-demand targeting". By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms.
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Affiliation(s)
- Marcus
J. C. Long
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Jesse R. Poganik
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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35
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Proteolysis targeting peptide (PROTAP) strategy for protein ubiquitination and degradation. Biochem Biophys Res Commun 2016; 470:936-40. [DOI: 10.1016/j.bbrc.2016.01.158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 01/25/2016] [Indexed: 11/21/2022]
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36
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Buckley DL, Raina K, Darricarrere N, Hines J, Gustafson JL, Smith IE, Miah AH, Harling JD, Crews CM. HaloPROTACS: Use of Small Molecule PROTACs to Induce Degradation of HaloTag Fusion Proteins. ACS Chem Biol 2015; 10:1831-7. [PMID: 26070106 DOI: 10.1021/acschembio.5b00442] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Small molecule-induced protein degradation is an attractive strategy for the development of chemical probes. One method for inducing targeted protein degradation involves the use of PROTACs, heterobifunctional molecules that can recruit specific E3 ligases to a desired protein of interest. PROTACs have been successfully used to degrade numerous proteins in cells, but the peptidic E3 ligase ligands used in previous PROTACs have hindered their development into more mature chemical probes or therapeutics. We report the design of a novel class of PROTACs that incorporate small molecule VHL ligands to successfully degrade HaloTag7 fusion proteins. These HaloPROTACs will inspire the development of future PROTACs with more drug-like properties. Additionally, these HaloPROTACs are useful chemical genetic tools, due to their ability to chemically knock down widely used HaloTag7 fusion proteins in a general fashion.
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Affiliation(s)
| | | | | | | | | | - Ian E. Smith
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
| | - Afjal H. Miah
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
| | - John D. Harling
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
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37
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Montrose K, Krissansen GW. Design of a PROTAC that antagonizes and destroys the cancer-forming X-protein of the hepatitis B virus. Biochem Biophys Res Commun 2014; 453:735-40. [PMID: 25305486 DOI: 10.1016/j.bbrc.2014.10.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 10/02/2014] [Indexed: 11/18/2022]
Abstract
The X-protein of the hepatitis B virus (HBV) is essential for virus infection and contributes to the development of HBV-induced hepatocellular carcinoma (HCC), a disease which causes more than one million deaths each year. Here we describe the design of a novel PROTAC (proteolysis targeting chimeric molecule) capable of simultaneously inducing the degradation of the X-protein, and antagonizing its function. The PROTAC was constructed by fusing the N-terminal oligomerization and C-terminal instability domains of the X-protein to each other, and rendering them cell-permeable by the inclusion of a polyarginine cell-penetrating peptide (CPP). It was predicted that the oligomerization domain would bind the X-protein, and that the instability domain would cause the X-protein to be targeted for proteasomal degradation. Addition of the PROTAC to HepG2 liver cancer cells, engineered to express full-length and C-terminally truncated forms of the X-protein, resulted in the degradation of both forms of the X-protein. A cell-permeable stand-alone form of the oligomerization domain was taken up by HepG2 cells, and acted as a dominant-negative inhibitor, causing inhibition of X-protein-induced apoptosis. In summary, the PROTAC described here induces the degradation of the X-protein, and antagonizes its function, and warrants investigation in a preclinical study for its ability to prevent or treat HBV infection and/or the development of HCC.
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Affiliation(s)
- Kristopher Montrose
- Department of Molecular Medicine & Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Geoffrey W Krissansen
- Department of Molecular Medicine & Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
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38
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Wang Q, Ru Y, Zhong D, Zhang J, Yao L, Li X. Engineered ubiquitin ligase PTB-U-box targets insulin/insulin-like growth factor receptor for degradation and coordinately inhibits cancer malignancy. Oncotarget 2014; 5:4945-58. [PMID: 24970814 PMCID: PMC4148113 DOI: 10.18632/oncotarget.2066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/05/2014] [Indexed: 12/27/2022] Open
Abstract
The type 1 insulin-like growth factor receptor (IGF-1R) is a promising target for cancer therapy with antibodies and small molecule tyrosine kinase inhibitors (TKIs) which have been actively tested clinically. Evidences have demonstrated that insulin receptor (IR), which is implicated in tumorigenesis, conveys resistance to IGF-1R targeted therapy. This provided the compelling rationale for co-targeting IGF-1R and IR. Herein we have developed an approach to simultaneously down-regulate IGF-1R and IR in protein levels. By generating and screening several engineered ubiquitin ligases, we have identified that, PTB-U-box, which is composed of an IGF-1R/IR-binding domain and a functional E3 ubiquitin ligase domain, binds activated IGF-1R/IR and targets their ubiquitination and degradation. When ectopically expressed in HepG2 and HeLa cells, PTB-U-box inhibits cell proliferation and invasion, increases chemo-sensitivity, as well as interrupts glucose metabolism. Finally, intratumoral injection of adenovirus carrying PTB-U-box dramatically retards the growth of HepG2 xenograft. Therefore, well-designed engineered ubiquitin ligase represents an effective therapeutic strategy for the treatment of the cancers with co-expressed IGF-1R/IR.
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Affiliation(s)
- Qinhao Wang
- State Key Laboratory of Cancer Biology, Departments of Biochemistry and Molecular Biology, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yi Ru
- State Key Laboratory of Cancer Biology, Departments of Biochemistry and Molecular Biology, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Daixing Zhong
- Department of Thoracic Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jing Zhang
- Experiment Teaching Center, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Libo Yao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xia Li
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, the Fourth Military Medical University, Xi’an, Shaanxi, China
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39
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Abstract
Small-molecule modulators of protein activity are increasingly being utilized as tools to examine the functional roles of proteins. Operating at the post-translational level, these molecules provide enhanced temporal and spatial control and mitigate the potential for compensatory responses in comparison with classical genetic approaches. Proteolysis targeting chimeric molecules, or PROTACs, are small molecules that inhibit the function of their target proteins by targeting them for degradation by the ubiquitin proteasome system. This chapter summarizes strategies for PROTAC preparation and characterization.
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40
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Abstract
The topic of the special series of reviews in this issue will be nanobiology and nanomedicine, with a focus on the impact of nanotechnology on children and their health; hence, the title of this collection and this introduction, Nanopediatrics: Enabling Personalized Medicine for Children. We will address what is meant when we discuss these nanodisciplines and why we developed a NanoPediatrics Program at University of California, Los Angeles. We will consider the implications of these nanodisciplines for individuals and society. The nature of research, diagnosis, and screening in nanomedicine and nanopediatrics will be illustrated by selected projects in nanodiagnostics and nanotherapeutics by our group and our collaborators, and the combined use of diagnostics and therapeutics in a single nanodevice referred to as "theranostics." We will conclude this introductory review with a summary of the reasons for developing the discipline of nanopediatrics.
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Affiliation(s)
- Edward R B McCabe
- Departments of Pediatrics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA.
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