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Gao J, Jiang X, Lei S, Cheng W, Lai Y, Li M, Yang L, Liu P, Chen XH, Huang M, Yu H, Xu H, Xu Z. A region-confined PROTAC nanoplatform for spatiotemporally tunable protein degradation and enhanced cancer therapy. Nat Commun 2024; 15:6608. [PMID: 39098906 PMCID: PMC11298519 DOI: 10.1038/s41467-024-50735-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 07/17/2024] [Indexed: 08/06/2024] Open
Abstract
The antitumor performance of PROteolysis-TArgeting Chimeras (PROTACs) is limited by its insufficient tumor specificity and poor pharmacokinetics. These disadvantages are further compounded by tumor heterogeneity, especially the presence of cancer stem-like cells, which drive tumor growth and relapse. Herein, we design a region-confined PROTAC nanoplatform that integrates both reactive oxygen species (ROS)-activatable and hypoxia-responsive PROTAC prodrugs for the precise manipulation of bromodomain and extraterminal protein 4 expression and tumor eradication. These PROTAC nanoparticles selectively accumulate within and penetrate deep into tumors via response to matrix metalloproteinase-2. Photoactivity is then reactivated in response to the acidic intracellular milieu and the PROTAC is discharged due to the ROS generated via photodynamic therapy specifically within the normoxic microenvironment. Moreover, the latent hypoxia-responsive PROTAC prodrug is restored in hypoxic cancer stem-like cells overexpressing nitroreductase. Here, we show the ability of region-confined PROTAC nanoplatform to effectively degrade BRD4 in both normoxic and hypoxic environments, markedly hindering tumor progression in breast and head-neck tumor models.
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Affiliation(s)
- Jing Gao
- State Key Laboratory of Chemical Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Department of Ultrasound, Zhongshan Hospital, Institute of Ultrasound in Medicine and Engineering, Fudan University, Shanghai, 200032, China
- Department of Medical Ultrasound and Center of Minimally Invasive Treatment for Tumor, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Xingyu Jiang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Shumin Lei
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Wenhao Cheng
- State Key Laboratory of Chemical Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yi Lai
- State Key Laboratory of Chemical Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min Li
- State Key Laboratory of Chemical Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lei Yang
- State Key Laboratory of Chemical Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Peifeng Liu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min Huang
- Division of Antitumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Haijun Yu
- State Key Laboratory of Chemical Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Huixiong Xu
- Department of Ultrasound, Zhongshan Hospital, Institute of Ultrasound in Medicine and Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhiai Xu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China.
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2
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Ma J, Fang L, Sun Z, Li M, Fan T, Xiang G, Ma X. Folate-PEG-PROTAC Micelles for Enhancing Tumor-Specific Targeting Proteolysis In Vivo. Adv Healthc Mater 2024; 13:e2400109. [PMID: 38676445 DOI: 10.1002/adhm.202400109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/01/2024] [Indexed: 04/28/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) technology is rapidly developed as a novel and selective medicinal strategy for the degradation of cellular proteins in cancer therapy. However, the applications of PROTACs as heterobifunctional molecules are largely limited by high molecular weight, low bioavailability, poor permeability, insufficient targeting, and low efficacy in vivo. Herein, self-assembling micelles of FA-PEG-PROTAC are designed for cancer cell selective targeting and reductive-response proteolysis in tumor-bearing mice. FA-PEG-PROTAC is prepared by conjugating folic acid (FA)-PEG with EGFR-targeting PROTAC via a disulfide bond. The FA-PEG-PROTAC micelles, formed by self-assembling, are demonstrated to significantly improve tumor targeting efficacy and exhibit excellent anti-tumor efficacy in the mouse xenograft model compared to the traditional PROTACs. The strategy of applying self-assembled FA-PEG-PROTAC micelles in tumor therapy can not only improve targeted proteolysis efficiency but also broaden applications in the development of PROTAC-based drugs.
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Affiliation(s)
- Junhui Ma
- Department of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lei Fang
- Department of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhengjun Sun
- Department of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Meijing Li
- Department of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ting Fan
- Department of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Guangya Xiang
- Department of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Pharmacy, Tongren Polytechnic College, Tongren, 554300, China
- Institute of the Higher Education Edible and Medicinal Fungi Engineering Research Center, Tongren, 554300, China
| | - Xiang Ma
- Department of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Pharmacy, Tongren Polytechnic College, Tongren, 554300, China
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3
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Zou ZF, Yang L, Nie HJ, Gao J, Lei SM, Lai Y, Zhang F, Wagner E, Yu HJ, Chen XH, Xu ZA. Tumor-targeted PROTAC prodrug nanoplatform enables precise protein degradation and combination cancer therapy. Acta Pharmacol Sin 2024; 45:1740-1751. [PMID: 38609561 PMCID: PMC11272941 DOI: 10.1038/s41401-024-01266-z] [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: 12/23/2023] [Accepted: 03/12/2024] [Indexed: 04/14/2024] Open
Abstract
Proteolysis targeting chimeras (PROTACs) have emerged as revolutionary anticancer therapeutics that degrade disease-causing proteins. However, the anticancer performance of PROTACs is often impaired by their insufficient bioavailability, unsatisfactory tumor specificity and ability to induce acquired drug resistance. Herein, we propose a polymer-conjugated PROTAC prodrug platform for the tumor-targeted delivery of the most prevalent von Hippel-Lindau (VHL)- and cereblon (CRBN)-based PROTACs, as well as for the precise codelivery of a degrader and conventional small-molecule drugs. The self-assembling PROTAC prodrug nanoparticles (NPs) can specifically target and be activated inside tumor cells to release the free PROTAC for precise protein degradation. The PROTAC prodrug NPs caused more efficient regression of MDA-MB-231 breast tumors in a mouse model by degrading bromodomain-containing protein 4 (BRD4) or cyclin-dependent kinase 9 (CDK9) with decreased systemic toxicity. In addition, we demonstrated that the PROTAC prodrug NPs can serve as a versatile platform for the codelivery of a PROTAC and chemotherapeutics for enhanced anticancer efficiency and combination benefits. This study paves the way for utilizing tumor-targeted protein degradation for precise anticancer therapy and the effective combination treatment of complex diseases.
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Affiliation(s)
- Zhi-Feng Zou
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lei Yang
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Hui-Jun Nie
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jing Gao
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Shu-Min Lei
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yi Lai
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Fan Zhang
- Department of Chemistry, Fudan University, Shanghai, 20043, China
| | - Ernst Wagner
- Department of Pharmacy, Ludwig-Maximilians-Universität, 81377, München, Germany
| | - Hai-Jun Yu
- State Key Laboratory of Chemistry Biology & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Xiao-Hua Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Zhi-Ai Xu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China.
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4
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Abbas A, Ye F. Computational methods and key considerations for in silico design of proteolysis targeting chimera (PROTACs). Int J Biol Macromol 2024:134293. [PMID: 39084437 DOI: 10.1016/j.ijbiomac.2024.134293] [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: 05/29/2024] [Revised: 07/19/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs), as heterobifunctional molecules, have garnered significant attention for their ability to target previously undruggable proteins. Due to the challenges in obtaining crystal structures of PROTAC molecules in the ternary complex, a plethora of computational tools have been developed to aid in PROTAC design. These computational tools can be broadly classified into artificial intelligence (AI)-based or non-AI-based methods. This review aims to provide a comprehensive overview of the latest computational methods for the PROTAC design process, covering both AI and non-AI approaches, from protein selection to ternary complex modeling and prediction. Key considerations for in silico PROTAC design are discussed, along with additional considerations for deploying AI-based models. These considerations are intended to guide subsequent model development in the PROTAC design process. Finally, future directions and recommendations are provided.
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Affiliation(s)
- Amr Abbas
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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5
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Liu F, Chen J, Li K, Li H, Zhu Y, Zhai Y, Lu B, Fan Y, Liu Z, Chen X, Jia X, Dong Z, Liu K. Ubiquitination and deubiquitination in cancer: from mechanisms to novel therapeutic approaches. Mol Cancer 2024; 23:148. [PMID: 39048965 PMCID: PMC11270804 DOI: 10.1186/s12943-024-02046-3] [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: 04/17/2024] [Accepted: 06/15/2024] [Indexed: 07/27/2024] Open
Abstract
Ubiquitination, a pivotal posttranslational modification of proteins, plays a fundamental role in regulating protein stability. The dysregulation of ubiquitinating and deubiquitinating enzymes is a common feature in various cancers, underscoring the imperative to investigate ubiquitin ligases and deubiquitinases (DUBs) for insights into oncogenic processes and the development of therapeutic interventions. In this review, we discuss the contributions of the ubiquitin-proteasome system (UPS) in all hallmarks of cancer and progress in drug discovery. We delve into the multiple functions of the UPS in oncology, including its regulation of multiple cancer-associated pathways, its role in metabolic reprogramming, its engagement with tumor immune responses, its function in phenotypic plasticity and polymorphic microbiomes, and other essential cellular functions. Furthermore, we provide a comprehensive overview of novel anticancer strategies that leverage the UPS, including the development and application of proteolysis targeting chimeras (PROTACs) and molecular glues.
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Affiliation(s)
- Fangfang Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Jingyu Chen
- Department of Pediatric Medicine, School of Third Clinical Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Kai Li
- Department of Clinical Medicine, School of First Clinical Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Haochen Li
- Department of Clinical Medicine, School of First Clinical Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yiyi Zhu
- Department of Clinical Medicine, School of First Clinical Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yubo Zhai
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Bingbing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yanle Fan
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Ziyue Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Xiaojie Chen
- School of Basic Medicine, Henan University of Science and Technology, Luoyang, China
| | - Xuechao Jia
- Henan International Joint Laboratory of TCM Syndrome and Prescription in Signaling, Traditional Chinese Medicine (Zhong Jing) School, Henan University of Chinese Medicine, Zhengzhou, Henan, China.
| | - Zigang Dong
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.
| | - Kangdong Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.
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6
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Xiao Y, Yuan Y, Liu Y, Lin Z, Zheng G, Zhou D, Lv D. Targeted Protein Degradation: Current and Emerging Approaches for E3 Ligase Deconvolution. J Med Chem 2024; 67:11580-11596. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Targeted protein degradation (TPD), including the use of proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) to degrade proteins, is an emerging strategy to develop novel therapies for cancer and beyond. PROTACs or MGDs function by inducing the proximity between an E3 ligase and a protein of interest (POI), leading to ubiquitination and consequent proteasomal degradation of the POI. Notably, one major issue in TPD is the lack of ligandable E3 ligases, as current studies predominantly use CUL4CRBN and CUL2VHL. The TPD community is seeking to expand the landscape of ligandable E3 ligases, but most discoveries rely on phenotypic screens or serendipity, necessitating systematic target deconvolution. Here, we examine and discuss both current and emerging E3 ligase deconvolution approaches for degraders discovered from phenotypic screens or monovalent glue chemistry campaigns, highlighting future prospects for identifying more ligandable E3 ligases.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
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Liu Y, Wang H, Ding M, Yao W, Wang K, Ullah I, Bulatov E, Yuan Y. Ultrasound-Activated PROTAC Prodrugs Overcome Immunosuppression to Actuate Efficient Deep-Tissue Sono-Immunotherapy in Orthotopic Pancreatic Tumor Mouse Models. NANO LETTERS 2024; 24:8741-8751. [PMID: 38953486 DOI: 10.1021/acs.nanolett.4c02287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The degradation of oncoproteins mediated by proteolysis-targeting chimera (PROTAC) has emerged as a potent strategy in cancer therapy. However, the clinical application of PROTACs is hampered by challenges such as poor water solubility and off-target adverse effects. Herein, we present an ultrasound (US)-activatable PROTAC prodrug termed NPCe6+PRO for actuating efficient sono-immunotherapy in a spatiotemporally controllable manner. Specifically, US irradiation, which exhibits deep-tissue penetration capability, results in Ce6-mediated generation of ROS, facilitating sonodynamic therapy (SDT) and inducing immunogenic cell death (ICD). Simultaneously, the generated ROS cleaves the thioketal (TK) linker through a ROS-responsive mechanism, realizing the on-demand activation of the PROTAC prodrug in deep tissues. This prodrug activation results in the degradation of the target protein BRD4, while simultaneously reversing the upregulation of PD-L1 expression associated with the SDT process. In the orthotopic mouse model of pancreatic tumors, NPCe6+PRO effectively suppressed tumor growth in conjunction with US stimulation.
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Affiliation(s)
- Ye Liu
- School of Medicine, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Haiyang Wang
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 511442, People's Republic of China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Mengchao Ding
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 511442, People's Republic of China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Wang Yao
- School of Medicine, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Kewei Wang
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 511442, People's Republic of China
| | - Ihsan Ullah
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 511442, People's Republic of China
| | - Emil Bulatov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Youyong Yuan
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 511442, People's Republic of China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, People's Republic of China
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8
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Reboud-Ravaux M. [Protein induced proximity and targeted degradations by new degraders: concepts, developments, challenges for clinical applications]. Biol Aujourdhui 2024; 218:41-54. [PMID: 39007776 DOI: 10.1051/jbio/2024007] [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: 04/10/2024] [Indexed: 07/16/2024]
Abstract
The review is focused on recent drug discovery advances based on targeted protein degradation strategies. This new area of research has exploded leading to the development of potential drugs useful in a large variety of human diseases. They first target disease relevant proteins difficult to counteract with other classical strategies and extend now to aggregates, organelles, nucleic acids or lipidic droplets. These degraders engaged either the ubiquitin-proteasome system for PROTACs and molecular glues (first generation), or the lysosomal system via endosome-lysosome degradation (LYTACs) and autophagy-lysosome degradation (ATTEC, AUTAC, AUTOTAC) (following generations of degraders). PROTACs have expanded from the orthodox heterobifunctional ones to new derivatives such as homo-PROTACs, pro-PROTACs, CLIPTACs, HaloPROTACs, PHOTOTACs, Bac-PROTACs, AbTACs, ARN-PROTACs. The small molecular-weight molecular glues induce the formation of new ternary complexes which implicate the targeted protein and an ubiquitin ligase E3 allowing the protein ubiquinitation followed by its proteasomal degradation. Lysosomal degraders (LYTAC, ATTEC, AUTAC, AUTOTAC) specifically recognize extracellular and membrane proteins or dysfunctional organelles and transport them into lysosomes where they are degraded. They overcome the limitations observed with proteasomal degradations induced by PROTAC and molecular glues and demonstrate their potential to treat human diseases, especially neurodegenerative ones. Pharmaceutical companies are engaged at the world level to develop these new potential drugs targeting cancers, immuno-inflammatory and neurodegenerative diseases as well as a variety of other ones. Efficiency and risks for these novel therapeutic strategies are discussed.
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Affiliation(s)
- Michèle Reboud-Ravaux
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, 7 quai Saint-Bernard, 75252 Paris, France
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9
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Zhao H. Structural Basis of Conformational Dynamics in the PROTAC-Induced Protein Degradation. ChemMedChem 2024; 19:e202400171. [PMID: 38655701 DOI: 10.1002/cmdc.202400171] [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: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Pronounced conformational dynamics is unveiled upon analyzing multiple crystal structures of the same proteins recruited to the same E3 ligases by PROTACs, and yet, is largely permissive for targeted protein degradation due to the intrinsic mobility of E3 assemblies creating a large ubiquitylation zone. Mathematical modelling of ternary dynamics on ubiquitylation probability confirms the experimental finding that ternary complex rigidification need not correlate with enhanced protein degradation. Salt bridges are found to prevail in the PROTAC-induced ternary complexes, and may contribute to a positive cooperativity and prolonged half-life. The analysis highlights the importance of presenting lysines close to the active site of the E2 enzyme while constraining ternary dynamics in PROTAC design to achieve high degradation efficiency.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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10
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Kamaraj R, Ghosh S, Das S, Sen S, Kumar P, Majumdar M, Dasgupta R, Mukherjee S, Das S, Ghose I, Pavek P, Raja Karuppiah MP, Chuturgoon AA, Anand K. Targeted Protein Degradation (TPD) for Immunotherapy: Understanding Proteolysis Targeting Chimera-Driven Ubiquitin-Proteasome Interactions. Bioconjug Chem 2024. [PMID: 38990186 DOI: 10.1021/acs.bioconjchem.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Targeted protein degradation or TPD, is rapidly emerging as a treatment that utilizes small molecules to degrade proteins that cause diseases. TPD allows for the selective removal of disease-causing proteins, including proteasome-mediated degradation, lysosome-mediated degradation, and autophagy-mediated degradation. This approach has shown great promise in preclinical studies and is now being translated to treat numerous diseases, including neurodegenerative diseases, infectious diseases, and cancer. This review discusses the latest advances in TPD and its potential as a new chemical modality for immunotherapy, with a special focus on the innovative applications and cutting-edge research of PROTACs (Proteolysis TArgeting Chimeras) and their efficient translation from scientific discovery to technological achievements. Our review also addresses the significant obstacles and potential prospects in this domain, while also offering insights into the future of TPD for immunotherapeutic applications.
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Affiliation(s)
- Rajamanikkam Kamaraj
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Subhrojyoti Ghosh
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Souvadra Das
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, India
| | - Shinjini Sen
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, India
| | - Priyanka Kumar
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, India
| | - Madhurima Majumdar
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, India
| | - Renesa Dasgupta
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, India
| | - Sampurna Mukherjee
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, India
| | - Shrimanti Das
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, India
| | - Indrilla Ghose
- Department of Biotechnology, Heritage Institute of Technology, Kolkata 700107, India
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Muruga Poopathi Raja Karuppiah
- Department of Chemistry, School of Physical Sciences, Central University of Kerala, Tejaswini Hills, Periye, Kasaragod District, Kerala 671320, India
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Krishnan Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, Free State 9300, South Africa
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Chan A, Haley RM, Najar MA, Gonzalez-Martinez D, Bugaj LJ, Burslem GM, Mitchell MJ, Tsourkas A. Lipid-mediated intracellular delivery of recombinant bioPROTACs for the rapid degradation of undruggable proteins. Nat Commun 2024; 15:5808. [PMID: 38987546 PMCID: PMC11237011 DOI: 10.1038/s41467-024-50235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
Recently, targeted degradation has emerged as a powerful therapeutic modality. Relying on "event-driven" pharmacology, proteolysis targeting chimeras (PROTACs) can degrade targets and are superior to conventional inhibitors against undruggable proteins. Unfortunately, PROTAC discovery is limited by warhead scarcity and laborious optimization campaigns. To address these shortcomings, analogous protein-based heterobifunctional degraders, known as bioPROTACs, have been developed. Compared to small-molecule PROTACs, bioPROTACs have higher success rates and are subject to fewer design constraints. However, the membrane impermeability of proteins severely restricts bioPROTAC deployment as a generalized therapeutic modality. Here, we present an engineered bioPROTAC template able to complex with cationic and ionizable lipids via electrostatic interactions for cytosolic delivery. When delivered by biocompatible lipid nanoparticles, these modified bioPROTACs can rapidly degrade intracellular proteins, exhibiting near-complete elimination (up to 95% clearance) of targets within hours of treatment. Our bioPROTAC format can degrade proteins localized to various subcellular compartments including the mitochondria, nucleus, cytosol, and membrane. Moreover, substrate specificity can be easily reprogrammed, allowing modular design and targeting of clinically-relevant proteins such as Ras, Jnk, and Erk. In summary, this work introduces an inexpensive, flexible, and scalable platform for efficient intracellular degradation of proteins that may elude chemical inhibition.
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Affiliation(s)
- Alexander Chan
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca M Haley
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohd Altaf Najar
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Gonzalez-Martinez
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J Mitchell
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Zhang S, Nie S, Ma G, Shen M, Kong L, Zuo Z, Li Y. Identification of novel GSPT1 degraders by virtual screening and bioassay. Eur J Med Chem 2024; 273:116524. [PMID: 38795517 DOI: 10.1016/j.ejmech.2024.116524] [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: 04/08/2024] [Revised: 05/11/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
GSPT1 plays crucial physiological functions, such as terminating protein translation, overexpressed in various tumors. It is a promising anti-tumor target, but is also considered as an "undruggable" protein. Recent studies have found that a class of small molecules can degrade GSPT1 through the "molecular glue" mechanism with strong antitumor activity, which is expected to become a new therapy for hematological malignancies. Currently available GSPT1 degraders are mostly derived from the scaffold of immunomodulatory imide drug (IMiD), thus more active compounds with novel structure remain to be found. In this work, using computer-assisted multi-round virtual screening and bioassay, we identified a non-IMiD acylhydrazone compound, AN5782, which can reduce the protein level of GPST1 and obviously inhibit the proliferation of tumor cells. Some analogs were obtained by a substructure search of AN5782. The structure-activity relationship analysis revealed possible interactions between these compounds and CRBN-GSPT1. Further biological mechanistic studies showed that AN5777 decreased GSPT1 remarkably through the ubiquitin-proteasome system, and its effective cytotoxicity was CRBN- and GSPT1-dependent. Furthermore, AN5777 displayed good antiproliferative activities against U937 and OCI-AML-2 cells, and dose-dependently induced G1 phase arrest and apoptosis. The structure found in this work could be good start for antitumor drug development.
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Affiliation(s)
- Shuqun Zhang
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shiyun Nie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, China
| | - Guangchao Ma
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, China
| | - Meiling Shen
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingmei Kong
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, China
| | - Zhili Zuo
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yan Li
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, China.
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13
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Nie DY, Tabor JR, Li J, Kutera M, St-Germain J, Hanley RP, Wolf E, Paulakonis E, Kenney TMG, Duan S, Shrestha S, Owens DDG, Maitland MER, Pon A, Szewczyk M, Lamberto AJ, Menes M, Li F, Penn LZ, Barsyte-Lovejoy D, Brown NG, Barsotti AM, Stamford AW, Collins JL, Wilson DJ, Raught B, Licht JD, James LI, Arrowsmith CH. Recruitment of FBXO22 for targeted degradation of NSD2. Nat Chem Biol 2024:10.1038/s41589-024-01660-y. [PMID: 38965384 DOI: 10.1038/s41589-024-01660-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/31/2024] [Indexed: 07/06/2024]
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy that would benefit from new chemical entities with which to recruit a wider variety of ubiquitin E3 ligases to target proteins for proteasomal degradation. Here we describe a TPD strategy involving the recruitment of FBXO22 to induce degradation of the histone methyltransferase and oncogene NSD2. UNC8732 facilitates FBXO22-mediated degradation of NSD2 in acute lymphoblastic leukemia cells harboring the NSD2 gain-of-function mutation p.E1099K, resulting in growth suppression, apoptosis and reversal of drug resistance. The primary amine of UNC8732 is metabolized to an aldehyde species, which engages C326 of FBXO22 to recruit the SCFFBXO22 Cullin complex. We further demonstrate that a previously reported alkyl amine-containing degrader targeting XIAP is similarly dependent on SCFFBXO22. Overall, we present a potent NSD2 degrader for the exploration of NSD2 disease phenotypes and a new FBXO22-recruitment strategy for TPD.
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Affiliation(s)
- David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John R Tabor
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jianping Li
- University of Florida Health Cancer Center, Gainesville, FL, USA
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maria Kutera
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ronan P Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- C4 Therapeutics, Watertown, MA, USA
| | - Esther Wolf
- Department of Chemistry, York University, Toronto, Ontario, Canada
| | - Ethan Paulakonis
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Tristan M G Kenney
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shili Duan
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Suman Shrestha
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Amphista Therapeutics, Cambridge, UK
| | | | - Ailing Pon
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Michael Menes
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas G Brown
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anthony M Barsotti
- Deerfield Discovery and Development, Deerfield Management, New York, NY, USA
| | - Andrew W Stamford
- Deerfield Discovery and Development, Deerfield Management, New York, NY, USA
| | - Jon L Collins
- Office of the Vice Chancellor for Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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14
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Bell LE, Bardelle C, Packer MJ, Kastl J, Holdgate GA, Davies G. Characterisation of high throughput screening outputs for small molecule degrader discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100162. [PMID: 38797285 DOI: 10.1016/j.slasd.2024.100162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
Targeted protein degradation is an important mechanism carried out by the cellular machinery, one that is gaining momentum as an exploitable strategy for the development of drug-like compounds. Molecules which are able to induce proximity between elusive therapeutic targets of interest and E3 ligases which subsequently leads to proteasomal degradation of the target are beginning to decrease the percentage of the human proteome described as undruggable. Therefore, having the ability to screen for, and understand the mechanism of, such molecules is becoming an increasingly attractive scientific focus. We have established a number of cascade experiments including cell-based assays and orthogonal triage steps to provide annotation to the selectivity and mechanism of action for compounds identified as putative degraders from a primary high throughput screen against a high value oncology target. We will describe our current position, using PROTACs as proof-of-concept, on the analysis of these novel outputs and highlight challenges encountered.
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Affiliation(s)
- Lillie E Bell
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Catherine Bardelle
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | | | - Johanna Kastl
- Assay.Works GmbH, Am Biopark 11, Regensburg, Germany
| | - Geoffrey A Holdgate
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK.
| | - Gareth Davies
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
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15
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Zhou Y, Zhou F, Xu S, Shi D, Ding D, Wang S, Poongavanam V, Tang K, Liu X, Zhan P. Hydrophobic tagging of small molecules: an overview of the literature and future outlook. Expert Opin Drug Discov 2024; 19:799-813. [PMID: 38825802 DOI: 10.1080/17460441.2024.2360416] [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: 01/04/2024] [Accepted: 05/23/2024] [Indexed: 06/04/2024]
Abstract
INTRODUCTION Hydrophobic tagging (HyT) technology presents a distinct therapeutic strategy diverging from conventional small molecule drugs, providing an innovative approach to drug design. This review aims to provide an overview of the HyT literature and future outlook to offer guidance for drug design. AREAS COVERED In this review, the authors introduce the composition, mechanisms and advantages of HyT technology, as well as summarize the detailed applications of HyT technology in anti-cancer, neurodegenerative diseases (NDs), autoimmune disorders, cardiovascular diseases (CVDs), and other fields. Furthermore, this review discusses key aspects of the future development of HyT molecules. EXPERT OPINION HyT emerges as a highly promising targeted protein degradation (TPD) strategy, following the successful development of proteolysis targeting chimeras (PROTAC) and molecular glue. Based on exploring new avenues, modification of the HyT molecule itself potentially enhances the technology. Improved synthetic pathways and emphasis on pharmacokinetic (PK) properties will facilitate the development of HyT. Furthermore, elucidating the biochemical basis by which the compound's hydrophobic moiety recruits the protein homeostasis network will enable the development of more precise assays that can guide the optimization of the linker and hydrophobic moiety.
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Affiliation(s)
- Yang Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Fan Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Dazhou Shi
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Shuo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | | | - Kai Tang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
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16
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Sobierajski T, Małolepsza J, Pichlak M, Gendaszewska-Darmach E, Błażewska KM. The impact of E3 ligase choice on PROTAC effectiveness in protein kinase degradation. Drug Discov Today 2024; 29:104032. [PMID: 38789027 DOI: 10.1016/j.drudis.2024.104032] [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: 02/02/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Proteolysis targeting chimera (PROTACs) provide a novel therapeutic approach that is revolutionizing drug discovery. The success of PROTACs largely depends on the combination of their three fragments: E3 ligase ligand, linker and protein of interest (POI)-targeting ligand. We summarize the pivotal significance of the precise combination of the E3 ligase ligand with the POI-recruiting warhead, which is crucial for the successful execution of cellular processes and achieving the desired outcomes. Therefore, the key to our selection was the use of at least two ligands recruiting two different ligases. This approach enables a direct comparison of the impacts of the specific ligases on target degradation.
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Affiliation(s)
- Tomasz Sobierajski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Joanna Małolepsza
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Marta Pichlak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland
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17
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Chang X, Qu F, Li C, Zhang J, Zhang Y, Xie Y, Fan Z, Bian J, Wang J, Li Z, Xu X. Development and therapeutic potential of GSPT1 molecular glue degraders: A medicinal chemistry perspective. Med Res Rev 2024; 44:1727-1767. [PMID: 38314926 DOI: 10.1002/med.22024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/18/2023] [Accepted: 01/21/2024] [Indexed: 02/07/2024]
Abstract
Unprecedented therapeutic targeting of previously undruggable proteins has now been achieved by molecular-glue-mediated proximity-induced degradation. As a small GTPase, G1 to S phase transition 1 (GSPT1) interacts with eRF1, the translation termination factor, to facilitate the process of translation termination. Studied demonstrated that GSPT1 plays a vital role in the acute myeloid leukemia (AML) and MYC-driven lung cancer. Thus, molecular glue (MG) degraders targeting GSPT1 is a novel and promising approach for treating AML and MYC-driven cancers. In this Perspective, we briefly summarize the structural and functional aspects of GSPT1, highlighting the latest advances and challenges in MG degraders, as well as some representative patents. The structure-activity relationships, mechanism of action and pharmacokinetic features of MG degraders are emphasized to provide a comprehensive compendium on the rational design of GSPT1 MG degraders. We hope to provide an updated overview, and design guide for strategies targeting GSPT1 for the treatment of cancer.
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Affiliation(s)
- Xiujin Chang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fangui Qu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Chunxiao Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jingtian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yanqing Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yuanyuan Xie
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhongpeng Fan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jinlei Bian
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jubo Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhiyu Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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18
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Wang Y, Yang G, Zhang X, Bai R, Yuan D, Gao D, He Q, Yuan Y, Zhang X, Kou J, Zheng L, Huang Y, Tang Z, Bao Y, Song X, Zhao Y. Antitumor Effect of Anti-c-Myc Aptamer-Based PROTAC for Degradation of the c-Myc Protein. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309639. [PMID: 38682443 PMCID: PMC11234457 DOI: 10.1002/advs.202309639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/04/2024] [Indexed: 05/01/2024]
Abstract
Targeting "undruggable" targets with intrinsically disordered structures is of great significance for the treatment of disease. The transcription factor c-Myc controls global gene expression and is an attractive therapeutic target for multiple types of cancers. However, due to the lack of defined ligand binding pockets, targeted c-Myc have thus far been unsuccessful. Herein, to address the dilemma of lacking ligands, an efficient and high throughput aptamer screening strategy is established, named polystyrene microwell plate-based systematic evolution of ligands by exponential enrichment (microwell-SELEX), and identify the specific aptamer (MA9C1) against c-Myc. The multifunctional aptamer-based Proteolysis Targeting Chimeras (PROTAC) for proteolysis of the c-Myc (ProMyc) is developed using the aptamer MA9C1 as the ligand. ProMyc not only significantly degrades c-Myc by the ubiquitin-proteasome system, but also reduces the Max protein, synergistically inhibiting c-Myc transcriptional activity. Combination of the artificial cyclization and anti-PD-L1 aptamer (PA1)-based delivery system, circular PA1-ProMyc chimeras achieve tumor regression in the xenograft tumor model, laying a solid foundation for the development of efficacious c-Myc degrader for the clinic. Therefore, this aptamer-based degrader provides an invaluable potential degrader in drug discovery and anti-tumor therapy, offering a promising degrader to overcome the challenge of targeting intractable targets.
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Affiliation(s)
- Yuchun Wang
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun, 130024, P. R. China
| | - Gang Yang
- College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Xinyu Zhang
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun, 130024, P. R. China
| | - Ruoling Bai
- College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Deyu Yuan
- College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Denghui Gao
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun, 130024, P. R. China
| | - Qianyu He
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun, 130024, P. R. China
| | - Yi Yuan
- Natural Products Research Centre, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, 610041, P. R. China
| | - Xinghe Zhang
- lncTAC Bio., Chengdu, Sichuan, 610200, P. R. China
| | | | - Lihua Zheng
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun, 130024, P. R. China
| | - Yanxin Huang
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun, 130024, P. R. China
| | - Zhuo Tang
- Natural Products Research Centre, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, 610041, P. R. China
| | - Yongli Bao
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun, 130024, P. R. China
| | - Xu Song
- College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
| | - Yongyun Zhao
- National Engineering Laboratory for Druggable Gene and Protein Screening, College of Life Science, Northeast Normal University, Changchun, 130024, P. R. China
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19
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Mukerjee N, Maitra S, Ghosh A, Alexiou A, Thorat ND. Exosome-mediated PROTAC delivery for treatment of RNA viral infections and zoonosis. Drug Discov Today 2024; 29:104044. [PMID: 38796097 DOI: 10.1016/j.drudis.2024.104044] [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: 03/10/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
The increase in diseases caused by RNA viruses, such as influenza, severe acute respiratory syndrome-coronavirus (SARS-CoV), Middle East respiratory syndrome (MERS), and Ebola, presents a growing global health challenge as well as the threat of zoonosis. Traditional antiviral treatments are often undermined by fast-mutating viruses, drug resistance, and newly emerging pathogens. Here, we explore proteolysis-targeting chimeras (PROTACs), a novel protein degradation machinery that has the potential to reshape the way in which RNA viral infections can be managed. PROTACs excel at specifically degrading pathogenic proteins, offering a targeted and efficient antiviral strategy. We also investigate the potential of exosome-based diagnostic technologies, which harness cell-derived nanovesicles for non-invasive sampling and early viral infection detection. Addressing the challenge of PROTAC delivery, we introduce a groundbreaking strategy utilizing exosomes to deliver PROTACs with improved precision and as a targeted delivery vehicle. Integrating these innovative strategies provides a novel approach to combat RNA zoonotic viral diseases, paving the way for a new era in antiviral therapy.
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Affiliation(s)
- Nobendu Mukerjee
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India.
| | - Swastika Maitra
- Department of Microbiology, Adamas University, Barasat, Kolkata 700126, India
| | - Arabinda Ghosh
- Department of Molecular Biology and Bioinformatics, Tripura University (A Central University), Suryamaninagar 799022, Tripura, India.
| | | | - Nanasaheb D Thorat
- Department of Physics and Bernal Institute, University of Limerick, Castletroy V94T9PX, Ireland; Limerick Digital Cancer Research Centre (LDCRC) University of Limerick, Castletroy V94T9PX, Ireland.
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20
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Zhang C, Liu Y, Li G, Yang Z, Han C, Sun X, Sheng C, Ding K, Rao Y. Targeting the undruggables-the power of protein degraders. Sci Bull (Beijing) 2024; 69:1776-1797. [PMID: 38614856 DOI: 10.1016/j.scib.2024.03.056] [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: 01/27/2024] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Undruggable targets typically refer to a class of therapeutic targets that are difficult to target through conventional methods or have not yet been targeted, but are of great clinical significance. According to statistics, over 80% of disease-related pathogenic proteins cannot be targeted by current conventional treatment methods. In recent years, with the advancement of basic research and new technologies, the development of various new technologies and mechanisms has brought new perspectives to overcome challenging drug targets. Among them, targeted protein degradation technology is a breakthrough drug development strategy for challenging drug targets. This technology can specifically identify target proteins and directly degrade pathogenic target proteins by utilizing the inherent protein degradation pathways within cells. This new form of drug development includes various types such as proteolysis targeting chimera (PROTAC), molecular glue, lysosome-targeting Chimaera (LYTAC), autophagosome-tethering compound (ATTEC), autophagy-targeting chimera (AUTAC), autophagy-targeting chimera (AUTOTAC), degrader-antibody conjugate (DAC). This article systematically summarizes the application of targeted protein degradation technology in the development of degraders for challenging drug targets. Finally, the article looks forward to the future development direction and application prospects of targeted protein degradation technology.
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Affiliation(s)
- Chao Zhang
- Changping Laboratory, Beijing 102206, China
| | - Yongbo Liu
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Guangchen Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Zhouli Yang
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Chi Han
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiuyun Sun
- Changping Laboratory, Beijing 102206, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Ke Ding
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Yu Rao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Changping Laboratory, Beijing 102206, China.
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21
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Wang S, Wang J, Lu X, Liu M, Liu Y, Li M, Kong X, Wu L, Guan Q, Zhang W. Design, synthesis and biological evaluation of novel tubulin-targeting agents with a dual-mechanism for polymerization inhibition and protein degradation. Eur J Med Chem 2024; 272:116458. [PMID: 38703557 DOI: 10.1016/j.ejmech.2024.116458] [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: 03/03/2024] [Revised: 04/12/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
Microtubules are recognized as one of the most vital and attractive targets in anticancer therapy. The development of novel tubulin-targeting agents with a new action mechanism is imperative. Based on the hydrophobic tagging strategy, the molecular scaffold of tirbanibulin was selected as tubulin target-binding moiety, subsequent to which a series of target compounds were rationally designed by selecting various combinations of linkers and hydrophobic tags. A set of novel molecules were synthesized and most of them exhibited potent antiproliferative activity against tumor cells in vitro. The most active compound 14b inhibited polymerization of purified recombinant tubulin and induced degradation of α- and β-tubulin in MCF-7 cells. Notably, following treatment with compound 14b, an unexpected phenomenon of "microtubules fragmentation" was observed via immunofluorescence staining. Furthermore, compound 14b possessed antitumor activity in the 4T1 allograft models with TGI of 74.27 % without significant toxicity. In this work, we report the discovery of novel dual-mechanism tubulin-targeting agents.
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Affiliation(s)
- Sibo Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Jiahao Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Xiankun Lu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Meitong Liu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Yue Liu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Mi Li
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Xuejie Kong
- Department of Geratology, The First Affiliated Hospital, Chinese Medical University, Shenyang, 110001, China
| | - Lan Wu
- Department of Geratology, The First Affiliated Hospital, Chinese Medical University, Shenyang, 110001, China.
| | - Qi Guan
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China.
| | - Weige Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China.
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22
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Du Y, Shi S, Shu C, He Y, Xu W, Wu D, Tian Y, Kong M, He J, Xie W, Qiu Y, Xu Y, Zou Y, Zhu Q. Discovery of novel EGFR-PROTACs capable of degradation of multiple EGFR-mutated proteins. Eur J Med Chem 2024; 272:116489. [PMID: 38759458 DOI: 10.1016/j.ejmech.2024.116489] [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: 03/19/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
Although three generations of Epidermal growth factor receptor (EGFR) - TK inhibitors have been approved for the treatment of Non-small-cell lung cancers (NSCLC), their clinical application is still largely hindered by acquired drug resistance mediated new EGFR mutations and side effects. The Proteolysis targeting chimera (PROTAC) technology has the potential to overcome acquired resistance from mutant EGFR through a novel mechanism of action. In this study, we developed the candidate degrader IV-3 by structural modifications of the lead compound 13, which exhibited limited antiproliferative activity against HCC-827 cells. Compared to compound 13, IV-3 exhibited remarkable anti-proliferative activity against HCC-827 cells, NCI-H1975 cells, and NCI-H1975-TM cells (IC50 = 0.009 μM, 0.49 μM and 3.24 μM, respectively), as well as significantly inducing degradation of EGFR protein in these cell lines (DC50 = 17.93 nM, 0.25 μM and 0.63 μM, respectively). Further investigations confirmed that IV-3 exhibited superior anti-tumor activity in all xenograft tumor models through the degradation of mutant EGFR protein. Moreover, IV-3 showed no inhibitory activity against A431 and A549 cells expressing wild-type EGFR, thereby eliminating potential toxic side effects emerging from wild-type EGFR inhibition. Overall, our study provides promising insights into EGFR-PROTACs as a potential therapeutic strategy against EGFR-acquired mutation.
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Affiliation(s)
- Yu Du
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Shi Shi
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China; Jiangsu Lianhuan Pharmaceutical Co., Ltd, Yangzhou 225000, China
| | - Chen Shu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yezi He
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wangyang Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Daochen Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yushu Tian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Mingyang Kong
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Jiahuan He
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenhui Xie
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yijia Qiu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yungen Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China.
| | - Yi Zou
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China.
| | - Qihua Zhu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China.
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23
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Vicente ATS, Salvador JAR. PROteolysis-Targeting Chimeras (PROTACs) in leukemia: overview and future perspectives. MedComm (Beijing) 2024; 5:e575. [PMID: 38845697 PMCID: PMC11154823 DOI: 10.1002/mco2.575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 06/09/2024] Open
Abstract
Leukemia is a heterogeneous group of life-threatening malignant disorders of the hematopoietic system. Immunotherapy, radiotherapy, stem cell transplantation, targeted therapy, and chemotherapy are among the approved leukemia treatments. Unfortunately, therapeutic resistance, side effects, relapses, and long-term sequelae occur in a significant proportion of patients and severely compromise the treatment efficacy. The development of novel approaches to improve outcomes is therefore an unmet need. Recently, novel leukemia drug discovery strategies, including targeted protein degradation, have shown potential to advance the field of personalized medicine for leukemia patients. Specifically, PROteolysis-TArgeting Chimeras (PROTACs) are revolutionary compounds that allow the selective degradation of a protein by the ubiquitin-proteasome system. Developed against a wide range of cancer targets, they show promising potential in overcoming many of the drawbacks associated with conventional therapies. Following the exponential growth of antileukemic PROTACs, this article reviews PROTAC-mediated degradation of leukemia-associated targets. Chemical structures, in vitro and in vivo activities, pharmacokinetics, pharmacodynamics, and clinical trials of PROTACs are critically discussed. Furthermore, advantages, challenges, and future perspectives of PROTACs in leukemia are covered, in order to understand the potential that these novel compounds may have as future drugs for leukemia treatment.
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Affiliation(s)
- André T. S. Vicente
- Laboratory of Pharmaceutical ChemistryFaculty of PharmacyUniversity of CoimbraCoimbraPortugal
- Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical ChemistryFaculty of PharmacyUniversity of CoimbraCoimbraPortugal
- Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
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24
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Tian Y, Seifermann M, Bauer L, Luchena C, Wiedmann JJ, Schmidt S, Geisel A, Afonin S, Höpfner J, Brehm M, Liu X, Hopf C, Popova AA, Levkin PA. High-Throughput Miniaturized Synthesis of PROTAC-Like Molecules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307215. [PMID: 38258390 DOI: 10.1002/smll.202307215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/03/2024] [Indexed: 01/24/2024]
Abstract
The development of miniaturized high-throughput in situ screening platforms capable of handling the entire process of drug synthesis to final screening is essential for advancing drug discovery in the future. In this study, an approach based on combinatorial solid-phase synthesis, enabling the efficient synthesis of libraries of proteolysis targeting chimeras (PROTACs) in an array format is presented. This on-chip platform allows direct biological screening without the need for transfer steps. UV-induced release of target molecules into individual droplets facilitates further on-chip experimentation. Utilizing a mitogen-activated protein kinase kinases (MEK1/2) degrader as a template, a series of 132 novel PROTAC-like molecules is synthesized using solid-phase Ugi reaction. These compounds are further characterized using various methods, including matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) imaging, while consuming only a few milligrams of starting materials in total. Furthermore, the feasibility of culturing cancer cells on the modified spots and quantifying the effect of MEK suppression is demonstrated. The miniaturized synthesis platform lays a foundation for high-throughput in situ biological screening of potent PROTACs for potential anticancer activity and offers the potential for accelerating the drug discovery process by integrating miniaturized synthesis and biological steps on the same array.
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Affiliation(s)
- Ye Tian
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
- Department of Immunology, Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Provincial Key Laboratory of Infection & Immunology, School of Basic Medical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Maximilian Seifermann
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Liana Bauer
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Charlotte Luchena
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Janne J Wiedmann
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
| | - Alexander Geisel
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Julius Höpfner
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Marius Brehm
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 280, 69117, Heidelberg, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Theodor Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Anna A Popova
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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25
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Ji Y, Chen W, Wang X. Bromodomain and Extraterminal Domain Protein 2 in Multiple Human Diseases. J Pharmacol Exp Ther 2024; 389:277-288. [PMID: 38565308 DOI: 10.1124/jpet.123.002036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Bromodomain and extraterminal domain protein 2 (BRD2), a member of the bromodomain and extraterminal domain (BET) protein family, is a crucial epigenetic regulator with significant function in various diseases and cellular processes. The central function of BRD2 is modulating gene transcription by binding to acetylated lysine residues on histones and transcription factors. This review highlights key findings on BRD2 in recent years, emphasizing its roles in maintaining genomic stability, influencing chromatin spatial organization, and participating in transcriptional regulation. BRD2's diverse functions are underscored by its involvement in diseases such as malignant tumors, neurologic disorders, inflammatory conditions, metabolic diseases, and virus infection. Notably, the potential role of BRD2 as a diagnostic marker and therapeutic target is discussed in the context of various diseases. Although pan inhibitors targeting the BET family have shown promise in preclinical studies, a critical need exists for the development of highly selective BRD2 inhibitors. In conclusion, this review offers insights into the multifaceted nature of BRD2 and calls for continued research to unravel its intricate mechanisms and harness its therapeutic potential. SIGNIFICANCE STATEMENT: BRD2 is involved in the occurrence and development of diseases through maintaining genomic stability, influencing chromatin spatial organization, and participating in transcriptional regulation. Targeting BRD2 through protein degradation-targeting complexes technology is emerging as a promising therapeutic approach for malignant cancer and inflammatory diseases.
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Affiliation(s)
- Yikang Ji
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
| | - Wantao Chen
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
| | - Xu Wang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
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26
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Owens DDG, Maitland MER, Khalili Yazdi A, Song X, Reber V, Schwalm MP, Machado RAC, Bauer N, Wang X, Szewczyk MM, Dong C, Dong A, Loppnau P, Calabrese MF, Dowling MS, Lee J, Montgomery JI, O'Connell TN, Subramanyam C, Wang F, Adamson EC, Schapira M, Gstaiger M, Knapp S, Vedadi M, Min J, Lajoie GA, Barsyte-Lovejoy D, Owen DR, Schild-Poulter C, Arrowsmith CH. A chemical probe to modulate human GID4 Pro/N-degron interactions. Nat Chem Biol 2024:10.1038/s41589-024-01618-0. [PMID: 38773330 DOI: 10.1038/s41589-024-01618-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
The C-terminal to LisH (CTLH) complex is a ubiquitin ligase complex that recognizes substrates with Pro/N-degrons via its substrate receptor Glucose-Induced Degradation 4 (GID4), but its function and substrates in humans remain unclear. Here, we report PFI-7, a potent, selective and cell-active chemical probe that antagonizes Pro/N-degron binding to human GID4. Use of PFI-7 in proximity-dependent biotinylation and quantitative proteomics enabled the identification of GID4 interactors and GID4-regulated proteins. GID4 interactors are enriched for nucleolar proteins, including the Pro/N-degron-containing RNA helicases DDX21 and DDX50. We also identified a distinct subset of proteins whose cellular levels are regulated by GID4 including HMGCS1, a Pro/N-degron-containing metabolic enzyme. These data reveal human GID4 Pro/N-degron targets regulated through a combination of degradative and nondegradative functions. Going forward, PFI-7 will be a valuable research tool for investigating CTLH complex biology and facilitating development of targeted protein degradation strategies that highjack CTLH E3 ligase activity.
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Affiliation(s)
- Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Matthew E R Maitland
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | | | - Xiaosheng Song
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Viviane Reber
- Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Raquel A C Machado
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Nicolas Bauer
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Xu Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | | | - Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Jisun Lee
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | | | | | | | - Feng Wang
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Ella C Adamson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Gilles A Lajoie
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Dafydd R Owen
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Caroline Schild-Poulter
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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27
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Palazzotti D, Sguilla M, Manfroni G, Cecchetti V, Astolfi A, Barreca ML. Small Molecule Drugs Targeting Viral Polymerases. Pharmaceuticals (Basel) 2024; 17:661. [PMID: 38794231 PMCID: PMC11124969 DOI: 10.3390/ph17050661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Small molecules that specifically target viral polymerases-crucial enzymes governing viral genome transcription and replication-play a pivotal role in combating viral infections. Presently, approved polymerase inhibitors cover nine human viruses, spanning both DNA and RNA viruses. This review provides a comprehensive analysis of these licensed drugs, encompassing nucleoside/nucleotide inhibitors (NIs), non-nucleoside inhibitors (NNIs), and mutagenic agents. For each compound, we describe the specific targeted virus and related polymerase enzyme, the mechanism of action, and the relevant bioactivity data. This wealth of information serves as a valuable resource for researchers actively engaged in antiviral drug discovery efforts, offering a complete overview of established strategies as well as insights for shaping the development of next-generation antiviral therapeutics.
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Affiliation(s)
| | | | | | | | | | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy; (D.P.); (M.S.); (G.M.); (V.C.); (A.A.)
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28
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Liu TT, Wang Q, Zhou Y, Ye B, Liu T, Yan L, Fan J, Xu J, Zhou Y, Xia Z, Deng X. Discovery of a Meisoindigo-Derived PROTAC as the ATM Degrader: Revolutionizing Colorectal Cancer Therapy via Synthetic Lethality with ATR Inhibitors. J Med Chem 2024; 67:7620-7634. [PMID: 38634707 DOI: 10.1021/acs.jmedchem.4c00454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Meisoindigo (Mei) has long been recognized in chronic myeloid leukemia (CML) treatment. To elucidate its molecular target and mechanisms, we embarked on designing and synthesizing a series of Mei-derived PROTACs. Through this endeavor, VHL-type PROTAC 9b was identified to be highly cytotoxic against SW620, SW480, and K562 cells. Employing DiaPASEF-based quantitative proteomic analysis, in combination with extensive validation assays, we unveiled that 9b potently and selectively degraded ATM across SW620 and SW480 cells in a ubiquitin-proteasome-dependent manner. 9b-induced selective ATM degradation prompted DNA damage response cascades, thereby leading to the cell cycle arrest and cell apoptosis. This pioneering discovery renders the advent of ATM degradation for anti-cancer therapy. Notably, 9b-induced ATM degradation synergistically enhanced the efficacy of ATR inhibitor AZD6738 both in vitro and in vivo. This work establishes the synthetic lethality-inducing properties of ATR inhibitors in the ATM-deficient context, thereby providing new avenues to innovative therapies for colorectal cancer.
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Affiliation(s)
- Ting-Ting Liu
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Qing Wang
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Yuxing Zhou
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Baixin Ye
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 311106, China
| | - Tingting Liu
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Linyang Yan
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Jinbao Fan
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Jiahao Xu
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Yingjun Zhou
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
| | - Zanxian Xia
- School of Life Sciences, Central South University, Changsha, Hunan 410013, China
| | - Xu Deng
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan 410013, China
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29
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Chen X, Crawford MC, Xiong Y, Shaik AB, Suazo KF, Penkalapati MS, Williams JH, Andressen T, Swenson RE, Meier JL. Paralogue-selective degradation of the lysine acetyltransferase EP300. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592353. [PMID: 38746397 PMCID: PMC11092752 DOI: 10.1101/2024.05.03.592353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The transcriptional coactivators EP300 and CREBBP are critical regulators of gene expression that share high sequence identity but exhibit non-redundant functions in basal and pathological contexts. Here, we report the development of a bifunctional small molecule, MC-1, capable of selectively degrading EP300 over CREBBP. Using a potent aminopyridine-based inhibitor of the EP300/CREBBP catalytic domain in combination with a VHL ligand, we demonstrate that MC-1 preferentially degrades EP300 in a proteasome-dependent manner. Mechanistic studies reveal that selective degradation cannot be predicted solely by target engagement or ternary complex formation, suggesting additional factors govern paralogue-specific degradation. MC-1 inhibits cell proliferation in a subset of cancer cell lines and provides a new tool to investigate the non-catalytic functions of EP300 and CREBBP. Our findings expand the repertoire of EP300/CREBBP-targeting chemical probes and offer insights into the determinants of selective degradation of highly homologous proteins.
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Affiliation(s)
- Xuemin Chen
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | | | - Ying Xiong
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Anver Basha Shaik
- Chemistry and Synthesis Center, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Kiall F. Suazo
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA
| | | | | | - Thorkell Andressen
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, USA
| | - Rolf E. Swenson
- Chemistry and Synthesis Center, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Jordan L. Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
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30
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Shah Zaib Saleem R, Schwalm MP, Knapp S. Expanding the ligand spaces for E3 ligases for the design of protein degraders. Bioorg Med Chem 2024; 105:117718. [PMID: 38621319 DOI: 10.1016/j.bmc.2024.117718] [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: 01/24/2024] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Targeted protein degradation (TPD) has recently emerged as an exciting new drug modality. However, the strategy of developing small molecule-based protein degraders has evolved over the past two decades and has now established molecular tags that are already in clinical use, as well as chimeric molecules, PROteolysis TArgeting Chimeras (PROTACs), based mainly on ligand systems developed for the two E3 ligases CRBN and VHL. The large size of the human E3 ligase family suggests that PROTACs can be developed by targeting a large diversity of E3 ligases, some of which have restricted expression patterns with the potential to design disease- or tissue-specific degraders. Indeed, many new E3 ligands have been published recently, confirming the druggability of E3 ligases. This review summarises recent data on E3 ligases and highlights the challenges in developing these molecules into efficient PROTACs rivalling the established degrader systems.
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Affiliation(s)
- Rahman Shah Zaib Saleem
- Department of Chemistry & Chemical Engineering, SBA School of Sciences & Engineering, LUMS, Pakistan
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.
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31
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Ghonim MA, Ju J, Pyakurel K, Ibba SV, Abouzeid MM, Rady HF, Matsuyama S, Del Valle L, Boulares AH. Unconventional activation of PRKDC by TNF-α: deciphering its crucial role in Th1-mediated inflammation beyond DNA repair as part of the DNA-PK complex. J Inflamm (Lond) 2024; 21:14. [PMID: 38689261 PMCID: PMC11059672 DOI: 10.1186/s12950-024-00386-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND The DNA-dependent protein kinase (DNA-PK) complex comprises a catalytic (PRKDC) and two requisite DNA-binding (Ku70/Ku80) subunits. The role of the complex in repairing double-stranded DNA breaks (DSBs) is established, but its role in inflammation, as a complex or individual subunits, remains elusive. While only ~ 1% of PRKDC is necessary for DNA repair, we reported that partial inhibition blocks asthma in mice without causing SCID. METHODS We investigated the central role of PRKDC in inflammation and its potential association with DNA repair. We also elucidated the relationship between inflammatory cytokines (e.g., TNF-α) and PRKDC by analyzing its connections to inflammatory kinases. Human cell lines, primary human endothelial cells, and mouse fibroblasts were used to conduct the in vitro studies. For animal studies, LPS- and oxazolone-induced mouse models of acute lung injury (ALI) and delayed-type hypersensitivity (DHT) were used. Wild-type, PRKDC+/-, or Ku70+/- mice used in this study. RESULTS A ~ 50% reduction in PRKDC markedly blocked TNF-α-induced expression of inflammatory factors (e.g., ICAM-1/VCAM-1). PRKDC regulates Th1-mediated inflammation, such as DHT and ALI, and its role is highly sensitive to inhibition achieved by gene heterozygosity or pharmacologically. In endothelial or epithelial cells, TNF-α promoted rapid PRKDC phosphorylation in a fashion resembling that induced by, but independent of, DSBs. Ku70 heterozygosity exerted little to no effect on ALI in mice, and whatever effect it had was associated with a specific increase in MCP-1 in the lungs and systemically. While Ku70 knockout blocked VP-16-induced PRKDC phosphorylation, it did not prevent TNF-α - induced phosphorylation of the kinase, suggesting Ku70 dispensability. Immunoprecipitation studies revealed that PRKDC transiently interacts with p38MAPK. Inhibition of p38MAPK blocked TNF-α-induced PRKDC phosphorylation. Direct phosphorylation of PRKDC by p38MAPK was demonstrated using a cell-free system. CONCLUSIONS This study presents compelling evidence that PRKDC functions independently of the DNA-PK complex, emphasizing its central role in Th1-mediated inflammation. The distinct functionality of PRKDC as an individual enzyme, its remarkable sensitivity to inhibition, and its phosphorylation by p38MAPK offer promising therapeutic opportunities to mitigate inflammation while sparing DNA repair processes. These findings expand our understanding of PRKDC biology and open new avenues for targeted anti-inflammatory interventions.
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Affiliation(s)
- Mohamed A Ghonim
- The Stanley S. Scott Cancer Center, LSU Health Sciences Center-New Orleans, 1700 Tulane Ave, New Orleans, LA, 70112, USA
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Jihang Ju
- The Stanley S. Scott Cancer Center, LSU Health Sciences Center-New Orleans, 1700 Tulane Ave, New Orleans, LA, 70112, USA
| | - Kusma Pyakurel
- The Stanley S. Scott Cancer Center, LSU Health Sciences Center-New Orleans, 1700 Tulane Ave, New Orleans, LA, 70112, USA
| | - Salome V Ibba
- The Stanley S. Scott Cancer Center, LSU Health Sciences Center-New Orleans, 1700 Tulane Ave, New Orleans, LA, 70112, USA
| | - Mai M Abouzeid
- The Stanley S. Scott Cancer Center, LSU Health Sciences Center-New Orleans, 1700 Tulane Ave, New Orleans, LA, 70112, USA
| | - Hamada F Rady
- The Stanley S. Scott Cancer Center, LSU Health Sciences Center-New Orleans, 1700 Tulane Ave, New Orleans, LA, 70112, USA
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Shigemi Matsuyama
- Department of Ophthalmology and Visual Science; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Luis Del Valle
- The Stanley S. Scott Cancer Center, LSU Health Sciences Center-New Orleans, 1700 Tulane Ave, New Orleans, LA, 70112, USA
| | - A Hamid Boulares
- The Stanley S. Scott Cancer Center, LSU Health Sciences Center-New Orleans, 1700 Tulane Ave, New Orleans, LA, 70112, USA.
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32
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Offensperger F, Tin G, Duran-Frigola M, Hahn E, Dobner S, Ende CWA, Strohbach JW, Rukavina A, Brennsteiner V, Ogilvie K, Marella N, Kladnik K, Ciuffa R, Majmudar JD, Field SD, Bensimon A, Ferrari L, Ferrada E, Ng A, Zhang Z, Degliesposti G, Boeszoermenyi A, Martens S, Stanton R, Müller AC, Hannich JT, Hepworth D, Superti-Furga G, Kubicek S, Schenone M, Winter GE. Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells. Science 2024; 384:eadk5864. [PMID: 38662832 DOI: 10.1126/science.adk5864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024]
Abstract
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advanced fragment-based ligand discovery toward cellular systems, but throughput limitations have stymied the scalable identification of fragment-protein interactions. We report proteome-wide maps of protein-binding propensity for 407 structurally diverse small-molecule fragments. We verified that identified interactions can be advanced to active chemical probes of E3 ubiquitin ligases, transporters, and kinases. Integrating machine learning binary classifiers further enabled interpretable predictions of fragment behavior in cells. The resulting resource of fragment-protein interactions and predictive models will help to elucidate principles of molecular recognition and expedite ligand discovery efforts for hitherto undrugged proteins.
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Affiliation(s)
- Fabian Offensperger
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Miquel Duran-Frigola
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Ersilia Open Source Initiative, Cambridge CB1 3DE, UK
| | - Elisa Hahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Andrea Rukavina
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincenth Brennsteiner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Kevin Ogilvie
- Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Nara Marella
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katharina Kladnik
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Rodolfo Ciuffa
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Luca Ferrari
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Evandro Ferrada
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Amanda Ng
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Zhechun Zhang
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - Gianluca Degliesposti
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Robert Stanton
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - André C Müller
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Georg E Winter
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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33
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Crook ZR, Sevilla GP, Young P, Girard EJ, Phi TD, Howard M, Price J, Olson JM, Nairn NW. CYpHER: Catalytic extracellular targeted protein degradation with high potency and durable effect. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581471. [PMID: 38712232 PMCID: PMC11071310 DOI: 10.1101/2024.02.21.581471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Many disease-causing proteins have multiple pathogenic mechanisms, and conventional inhibitors struggle to reliably disrupt more than one. Targeted protein degradation (TPD) can eliminate the protein, and thus all its functions, by directing a cell's protein turnover machinery towards it. Two established strategies either engage catalytic E3 ligases or drive uptake towards the endolysosomal pathway. Here we describe CYpHER (CatalYtic pH-dependent Endolysosomal delivery with Recycling) technology with potency and durability from a novel catalytic mechanism that shares the specificity and straightforward modular design of endolysosomal uptake. By bestowing pH-dependent release on the target engager and using the rapid-cycling transferrin receptor as the uptake receptor, CYpHER induces endolysosomal target delivery while re-using drug, potentially yielding increased potency and reduced off-target tissue exposure risks. The TfR-based approach allows targeting to tumors that overexpress this receptor and offers the potential for transport to the CNS. CYpHER function was demonstrated in vitro with EGFR and PD-L1, and in vivo with EGFR in a model of EGFR-driven non-small cell lung cancer.
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Affiliation(s)
- Zachary R. Crook
- Cyclera Therapeutics Inc, Seattle, WA 98115, USA. Present address of Z.R.C., G.P.S., and N.W.N
- Blaze Bioscience Inc., Seattle, WA 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Gregory P. Sevilla
- Cyclera Therapeutics Inc, Seattle, WA 98115, USA. Present address of Z.R.C., G.P.S., and N.W.N
- Blaze Bioscience Inc., Seattle, WA 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Emily J. Girard
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98105, USA. Present address of E.J.G. and J.M.O
| | | | | | - Jason Price
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98105, USA. Present address of E.J.G. and J.M.O
| | - James M. Olson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98105, USA. Present address of E.J.G. and J.M.O
| | - Natalie W. Nairn
- Cyclera Therapeutics Inc, Seattle, WA 98115, USA. Present address of Z.R.C., G.P.S., and N.W.N
- Blaze Bioscience Inc., Seattle, WA 98109, USA
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34
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Mslati H, Gentile F, Pandey M, Ban F, Cherkasov A. PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. J Chem Inf Model 2024; 64:3034-3046. [PMID: 38504115 DOI: 10.1021/acs.jcim.3c01878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than those of a small molecule drug, we explored a combination of computational chemistry and deep learning strategies to forecast PROTAC activity and enable automated design. A new method named PROTACable was developed for the de novo design of PROTACs, which includes a robust 3-D modeling workflow to model PROTAC ternary complexes using a library of E3 ligase and linker and an SE(3)-equivariant graph transformer network to predict the activity of newly designed PROTACs. PROTACable is available at https://github.com/giaguaro/PROTACable/.
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Affiliation(s)
- Hazem Mslati
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Francesco Gentile
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1N 6N5, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
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35
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Hu J, Xu H, Wu T, Zhang C, Shen H, Dong R, Hu Q, Xiang Q, Chai S, Luo G, Chen X, Huang Y, Zhao X, Peng C, Wu X, Lin B, Zhang Y, Xu Y. Discovery of Highly Potent and Efficient CBP/p300 Degraders with Strong In Vivo Antitumor Activity. J Med Chem 2024. [PMID: 38649304 DOI: 10.1021/acs.jmedchem.3c02195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The transcriptional coactivator cAMP response element binding protein (CREB)-binding protein (CBP) and its homologue p300 have emerged as attractive therapeutic targets for human cancers such as acute myeloid leukemia (AML). Herein, we report the design, synthesis, and biological evaluation of a series of cereblon (CRBN)-recruiting CBP/p300 proteolysis targeting chimeras (PROTACs) based on the inhibitor CCS1477. The representative compounds 14g (XYD190) and 14h (XYD198) potently inhibited the growth of AML cells with low nanomolar IC50 values and effectively degraded CBP and p300 proteins in a concentration- and time-dependent manner. Mechanistic studies confirmed that 14g and 14h can selectively bind to CBP/p300 bromodomains and induce CBP and p300 degradation in bromodomain family proteins in a CRBN- and proteasome-dependent manner. 14g and 14h displayed remarkable antitumor efficacy in the MV4;11 xenograft model (TGI = 88% and 93%, respectively). Our findings demonstrated that 14g and 14h are useful lead compounds and deserve further optimization and activity evaluation for the treatment of human cancers.
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Affiliation(s)
- Jiankang Hu
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
- University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Hongrui Xu
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Tianbang Wu
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Cheng Zhang
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Hui Shen
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Ruibo Dong
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Qingqing Hu
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Qiuping Xiang
- Ningbo No. 2 Hospital, Ningbo, Zhejiang 315010, China
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang 315010, China
| | - Shuang Chai
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Guolong Luo
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Xiaoshan Chen
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
- University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Yumin Huang
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
- University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Xiaofan Zhao
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Chao Peng
- Jiangsu S&T Exchange Center with Foreign Countries, No. 175 Longpan Road, Nanjing 210042, China
| | - Xishan Wu
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Bin Lin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yan Zhang
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Yong Xu
- China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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Ma X, Yin J, Qiao L, Wan H, Liu X, Zhou Y, Wu J, Niu L, Wu M, Wang X, Ye H. A programmable targeted protein-degradation platform for versatile applications in mammalian cells and mice. Mol Cell 2024; 84:1585-1600.e7. [PMID: 38479385 DOI: 10.1016/j.molcel.2024.02.019] [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: 08/17/2023] [Revised: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 04/21/2024]
Abstract
Myriad physiological and pathogenic processes are governed by protein levels and modifications. Controlled protein activity perturbation is essential to studying protein function in cells and animals. Based on Trim-Away technology, we screened for truncation variants of E3 ubiquitinase Trim21 with elevated efficiency (ΔTrim21) and developed multiple ΔTrim21-based targeted protein-degradation systems (ΔTrim-TPD) that can be transfected into host cells. Three ΔTrim-TPD variants are developed to enable chemical and light-triggered programmable activation of TPD in cells and animals. Specifically, we used ΔTrim-TPD for (1) red-light-triggered inhibition of HSV-1 virus proliferation by degrading the packaging protein gD, (2) for chemical-triggered control of the activity of Cas9/dCas9 protein for gene editing, and (3) for blue-light-triggered degradation of two tumor-associated proteins for spatiotemporal inhibition of melanoma tumor growth in mice. Our study demonstrates that multiple ΔTrim21-based controllable TPD systems provide powerful tools for basic biology research and highlight their potential biomedical applications.
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Affiliation(s)
- Xiaoding Ma
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Longliang Qiao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Hang Wan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xingwan Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Wuhu Hospital, Health Science Center, East China Normal University, Wuhu City 241001, China
| | - Jiali Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Lingxue Niu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Min Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Centre, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
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Emert-Sedlak LA, Tice CM, Shi H, Alvarado JJ, Shu ST, Reitz AB, Smithgall TE. PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication. Cell Chem Biol 2024; 31:658-668.e14. [PMID: 38508197 PMCID: PMC11031313 DOI: 10.1016/j.chembiol.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/20/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
The HIV-1 Nef accessory factor enhances the viral life cycle in vivo, promotes immune escape of HIV-infected cells, and represents an attractive antiretroviral drug target. However, Nef lacks enzymatic activity and an active site, complicating traditional occupancy-based drug development. Here we describe the development of proteolysis targeting chimeras (PROTACs) for the targeted degradation of Nef. Nef-binding compounds, based on an existing hydroxypyrazole core, were coupled to ligands for ubiquitin E3 ligases via flexible linkers. The resulting bivalent PROTACs induced formation of a ternary complex between Nef and the cereblon E3 ubiquitin ligase thalidomide-binding domain in vitro and triggered Nef degradation in a T cell expression system. Nef-directed PROTACs efficiently rescued Nef-mediated MHC-I and CD4 downregulation in T cells and suppressed HIV-1 replication in donor PBMCs. Targeted degradation is anticipated to reverse all HIV-1 Nef functions and may help restore adaptive immune responses against HIV-1 reservoir cells in vivo.
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Affiliation(s)
- Lori A Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Colin M Tice
- Fox Chase Therapeutics Discovery, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Sherry T Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Allen B Reitz
- Fox Chase Therapeutics Discovery, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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Neigenfind P, Massaro L, Péter Á, Degnan AP, Emmanuel MA, Oderinde MS, He C, Peters D, El-Hayek Ewing T, Kawamata Y, Baran PS. Simplifying Access to Targeted Protein Degraders via Nickel Electrocatalytic Cross-Coupling. Angew Chem Int Ed Engl 2024; 63:e202319856. [PMID: 38354272 DOI: 10.1002/anie.202319856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/01/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
C-C linked glutarimide-containing structures with direct utility in the preparation of cereblon-based degraders (PROTACs, CELMoDs) can be assessed in a single step from inexpensive, commercial α-bromoglutarimide through a unique Brønsted-acid assisted Ni-electrocatalytic approach. The reaction tolerates a broad array of functional groups that are historically problematic and can be applied to the simplified synthesis of dozens of known compounds that have only been procured through laborious, wasteful, multi-step sequences. The reaction is scalable in both batch and flow and features a trivial procedure wherein the most time-consuming aspect of reaction setup is weighing out the starting materials.
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Affiliation(s)
- Philipp Neigenfind
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, 92037, La Jolla, CA, United States
| | - Luca Massaro
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, 92037, La Jolla, CA, United States
- Department of Chemistry, KTH Royal Institute of Technology, Teknikringen 30, S-10044, Stockholm, Sweden
| | - Áron Péter
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, 92037, La Jolla, CA, United States
| | - Andrew P Degnan
- Small Molecule Drug Discovery, Bristol Myers Squibb Research & Early Development, Route 206 & Province Line Road, 08543, Princeton, NJ, United States
| | - Megan A Emmanuel
- Chemical Process Development, Bristol Myers Squibb, 1 Squibb Drive, 08901, New Brunswick, NJ, United States
| | - Martins S Oderinde
- Small Molecule Drug Discovery, Bristol Myers Squibb Research & Early Development, Route 206 & Province Line Road, 08543, Princeton, NJ, United States
| | - Chi He
- Small Molecule Drug Discovery, Bristol Myers Squibb Research & Early Development, 10300 Campus Point Drive, 92121, San Diego, CA, United States
| | - David Peters
- Small Molecule Drug Discovery, Bristol Myers Squibb Research & Early Development, 10300 Campus Point Drive, 92121, San Diego, CA, United States
| | - Tamara El-Hayek Ewing
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, 92037, La Jolla, CA, United States
| | - Yu Kawamata
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, 92037, La Jolla, CA, United States
| | - Phil S Baran
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, 92037, La Jolla, CA, United States
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39
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Rutherford KA, McManus KJ. PROTACs: Current and Future Potential as a Precision Medicine Strategy to Combat Cancer. Mol Cancer Ther 2024; 23:454-463. [PMID: 38205881 PMCID: PMC10985480 DOI: 10.1158/1535-7163.mct-23-0747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Proteolysis targeting chimeras (PROTAC) are an emerging precision medicine strategy, which targets key proteins for proteolytic degradation to ultimately induce cancer cell killing. These hetero-bifunctional molecules hijack the ubiquitin proteasome system to selectively add polyubiquitin chains onto a specific protein target to induce proteolytic degradation. Importantly, PROTACs have the capacity to target virtually any intracellular and transmembrane protein for degradation, including oncoproteins previously considered undruggable, which strategically positions PROTACs at the crossroads of multiple cancer research areas. In this review, we present normal functions of the ubiquitin regulation proteins and describe the application of PROTACs to improve the efficacy of current broad-spectrum therapeutics. We subsequently present the potential for PROTACs to exploit specific cancer vulnerabilities through synthetic genetic approaches, which may expedite the development, translation, and utility of novel synthetic genetic therapies in cancer. Finally, we describe the challenges associated with PROTACs and the ongoing efforts to overcome these issues to streamline clinical translation. Ultimately, these efforts may lead to their routine clinical use, which is expected to revolutionize cancer treatment strategies, delay familial cancer onset, and ultimately improve the lives and outcomes of those living with cancer.
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Affiliation(s)
- Kailee A. Rutherford
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciencs, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J. McManus
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciencs, University of Manitoba, Winnipeg, Manitoba, Canada
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Kim J, Byun I, Kim DY, Joh H, Kim HJ, Lee MJ. Targeted protein degradation directly engaging lysosomes or proteasomes. Chem Soc Rev 2024; 53:3253-3272. [PMID: 38369971 DOI: 10.1039/d3cs00344b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Targeted protein degradation (TPD) has been established as a viable alternative to attenuate the function of a specific protein of interest in both biological and clinical contexts. The unique TPD mode-of-action has allowed previously undruggable proteins to become feasible targets, expanding the landscape of "druggable" properties and "privileged" target proteins. As TPD continues to evolve, a range of innovative strategies, which do not depend on recruiting E3 ubiquitin ligases as in proteolysis-targeting chimeras (PROTACs), have emerged. Here, we present an overview of direct lysosome- and proteasome-engaging modalities and discuss their perspectives, advantages, and limitations. We outline the chemical composition, biochemical activity, and pharmaceutical characteristics of each degrader. These alternative TPD approaches not only complement the first generation of PROTACs for intracellular protein degradation but also offer unique strategies for targeting pathologic proteins located on the cell membrane and in the extracellular space.
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Affiliation(s)
- Jiseong Kim
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Do Young Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hyunhi Joh
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hak Joong Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Min Jae Lee
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Huang Y, Zhou X, Zhang Y, Xie M, Wang F, Qin J, Ye H, Zhang H, Zhang C, Hong J. A Nucleic Acid-Based LYTAC Plus Platform to Simultaneously Mediate Disease-Driven Protein Downregulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306248. [PMID: 38251411 PMCID: PMC10987141 DOI: 10.1002/advs.202306248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/13/2024] [Indexed: 01/23/2024]
Abstract
Protein degradation techniques, such as proteolysis-targeting chimeras (PROTACs) and lysosome-targeting chimeras (LYTACs), have emerged as promising therapeutic strategies for the treatment of diseases. However, the efficacy of current protein degradation methods still needs to be improved to address the complex mechanisms underlying diseases. Herein, a LYTAC Plus hydrogel engineered is proposed by nucleic acid self-assembly, which integrates a gene silencing motif into a LYTAC construct to enhance its therapeutic potential. As a proof-of-concept study, vascular endothelial growth factor receptor (VEGFR)-binding peptides and mannose-6 phosphate (M6P) moieties into a self-assembled nucleic acid hydrogel are introduced, enabling its LYTAC capability. Small interference RNAs (siRNAs) is then employed that target the angiopoietin-2 (ANG-2) gene as cross-linkers for hydrogel formation, giving the final LYTAC Plus hydrogel gene silencing ability. With dual functionalities, the LYTAC Plus hydrogel demonstrated effectiveness in simultaneously reducing the levels of VEGFR-2 and ANG-2 both in vitro and in vivo, as well as in improving therapeutic outcomes in treating neovascular age-related macular degeneration in a mouse model. As a general material platform, the LYTAC Plus hydrogel may possess great potential for the treatment of various diseases and warrant further investigation.
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Affiliation(s)
- Yangyang Huang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesShanghai Key Laboratory for Molecular Engineering of Chiral DrugsShanghai Jiao Tong UniversityShanghai200240P. R. China
| | - Xujiao Zhou
- Department of Ophthalmology and Vision ScienceShanghai Eye, Ear, Nose and Throat HospitalFudan UniversityShanghai200030P. R. China
| | - Yirou Zhang
- Department of Ophthalmology and Vision ScienceShanghai Eye, Ear, Nose and Throat HospitalFudan UniversityShanghai200030P. R. China
| | - Miao Xie
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesShanghai Key Laboratory for Molecular Engineering of Chiral DrugsShanghai Jiao Tong UniversityShanghai200240P. R. China
| | - Fujun Wang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesShanghai Key Laboratory for Molecular Engineering of Chiral DrugsShanghai Jiao Tong UniversityShanghai200240P. R. China
| | - Jingcan Qin
- Department of RadiologyChanghai HospitalNaval Medical UniversityShanghai200433P. R. China
| | - Han Ye
- Department of Ophthalmology and Vision ScienceShanghai Eye, Ear, Nose and Throat HospitalFudan UniversityShanghai200030P. R. China
| | - Hong Zhang
- Department of Ophthalmology and Vision ScienceShanghai Eye, Ear, Nose and Throat HospitalFudan UniversityShanghai200030P. R. China
- Department of Ophthalmologythe Affiliated Hospital of Guizhou Medical UniversityGuiyang550025P. R. China
| | - Chuan Zhang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesShanghai Key Laboratory for Molecular Engineering of Chiral DrugsShanghai Jiao Tong UniversityShanghai200240P. R. China
| | - Jiaxu Hong
- Department of Ophthalmology and Vision ScienceShanghai Eye, Ear, Nose and Throat HospitalFudan UniversityShanghai200030P. R. China
- Shanghai Engineering Research Center of Synthetic ImmunologyShanghai200032China
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Kaushik A, Parashar S, Ambasta RK, Kumar P. Ubiquitin E3 ligases assisted technologies in protein degradation: Sharing pathways in neurodegenerative disorders and cancer. Ageing Res Rev 2024; 96:102279. [PMID: 38521359 DOI: 10.1016/j.arr.2024.102279] [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: 01/10/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
E3 ligases, essential components of the ubiquitin-proteasome-mediated protein degradation system, play a critical role in cellular regulation. By covalently attaching ubiquitin (Ub) molecules to target proteins, these ligases mark them for degradation, influencing various bioprocesses. With over 600 E3 ligases identified, there is a growing realization of their potential as therapeutic candidates for addressing proteinopathies in cancer and neurodegenerative disorders (NDDs). Recent research has highlighted the need to delve deeper into the intricate roles of E3 ligases as nexus points in the pathogenesis of both cancer and NDDs. Their dysregulation is emerging as a common thread linking these seemingly disparate diseases, necessitating a comprehensive understanding of their molecular intricacies. Herein, we have discussed (i) the fundamental mechanisms through which different types of E3 ligases actively participate in selective protein degradation in cancer and NDDs, followed by an examination of common E3 ligases playing pivotal roles in both situations, emphasising common players. Moving to, (ii) the functional domains and motifs of E3 ligases involved in ubiquitination, we have explored their interactions with specific substrates in NDDs and cancer. Additionally, (iii) we have explored techniques like PROTAC, molecular glues, and other state-of-the-art methods for hijacking neurotoxic and oncoproteins. Lastly, (iv) we have provided insights into ongoing clinical trials, offering a glimpse into the evolving landscape of E3-based therapeutics for cancer and NDDs. Unravelling the intricate network of E3 ligase-mediated regulation holds the key to unlocking targeted therapies that address the specific molecular signatures of individual patients, heralding a new era in personalized medicines.
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Affiliation(s)
- Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University-Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India.
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43
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Xia X, Ni R. Designing Superselectivity in Linker-Mediated Multivalent Nanoparticle Adsorption. PHYSICAL REVIEW LETTERS 2024; 132:118202. [PMID: 38563948 DOI: 10.1103/physrevlett.132.118202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/09/2024] [Accepted: 02/22/2024] [Indexed: 04/04/2024]
Abstract
Using a statistical mechanical model and numerical simulations, we provide the design principle for the bridging strength (ξ) and linker density (ρ) dependent superselectivity in linker-mediated multivalent nanoparticle adsorption. When the bridges are insufficient, the formation of multiple bridges leads to both ξ- and ρ-dependent superselectivity. When the bridges are excessive, the system becomes insensitive to bridging strength due to entropy-induced self-saturation and shows a superselective desorption with respect to the linker density. Counterintuitively, lower linker density or stronger bridging strength enhances the superselectivity. These findings help the understanding of relevant biological processes and open up opportunities for applications in biosensing, drug delivery, and programmable self-assembly.
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Affiliation(s)
- Xiuyang Xia
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| | - Ran Ni
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
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Hu X, Li E, Zhou Y, You Q, Jiang Z. Casitas b cell lymphoma‑B (Cbl-b): A new therapeutic avenue for small-molecule immunotherapy. Bioorg Med Chem 2024; 102:117677. [PMID: 38457911 DOI: 10.1016/j.bmc.2024.117677] [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: 01/12/2024] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Immunotherapy has revolutionized the area of cancer treatment. Although most immunotherapies now are antibodies targeting membrane checkpoint molecules, there is an increasing demand for small-molecule drugs that address intracellular pathways. The E3 ubiquitin ligase Casitas B cell lymphoma‑b (Cbl-b) has been regarded as a promising intracellular immunotherapy target. Cbl-b regulates the downstream proteins of multiple membrane receptors and co-receptors, restricting the activation of the innate and adaptive immune system. Recently, Cbl-b inhibitors have been reported with promising effects on immune surveillance activation and anti-tumor efficacy. Several molecules have entered phase Ⅰ clinical trials. In this review, the biological rationale of Cbl-b as a promising target for cancer immunotherapy and the latest research progress of Cbl-b are summarized, with special emphasis on the allosteric small-molecule inhibitors of Cbl-b.
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Affiliation(s)
- Xiuqi Hu
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Erdong Li
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yangguo Zhou
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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Wang X, Xin L, Deng X, Dong C, Hu G, Zhou HB. Fluorescence theranostic PROTACs for real-time visualization of ERα degradation. Eur J Med Chem 2024; 267:116184. [PMID: 38320426 DOI: 10.1016/j.ejmech.2024.116184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/14/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
Proteolysis targeting chimera (PROTAC) technology, a groundbreaking strategy for degradation of pathogenic proteins by hijacking of the ubiquitin-proteasome-system has become a promising strategy in drug design. However, the real-time monitoring and visualization of protein degradation processes have been long-standing challenges in the realm of drug development. In this research, we sought to amalgamate the highly efficient protein-degrading capabilities of PROTAC technology with the visualization attributes of fluorescent probes, with the potential to pave the path for the design and development of a novel class of visual PROTACs. These novel PROTACs uniquely possess both fluorescence imaging and therapeutic characteristics, all with the goal of enabling real-time observations of protein degradation processes. Our approach involved the utilization of a high ER-targeting fluorescent probe, previously reported in our laboratory, which served as a warhead that specifically binds to the protein of interest (POI). Additionally, a VHL ligand for recruiting E3 ligase and linkers of various lengths were incorporated to synthesize a series of novel ER-inherent fluorescence PROTACs. Among them, compound A3 demonstrated remarkable efficiency in degrading ERα proteins (DC50 = 0.12 μM) and displaying exceptional anti-proliferative activity against MCF-7 cells (IC50 = 0.051 μM). Furthermore, it exhibited impressive fluorescence imaging performance, boasting an emission wavelength of up to 582 nm, a Stokes shift of 116 nm, and consistent optical properties. These attributes make it especially suitable for the real-time, in situ tracking of ERα protein degradation processes, thus may serve as a privileged visual theranostic PROTAC for ERα+ breast cancer. This study not only broadens the application spectrum of PROTAC technology but also introduces a novel approach for real-time visualization of protein degradation processes, ultimately enhancing the diagnostic and treatment efficacy of PROTACs.
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Affiliation(s)
- Xiaohua Wang
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China; College of Life Sciences, Wuchang University of Technology, Wuhan, Hubei Province, 430223, China
| | - Lilan Xin
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xiaofei Deng
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Chune Dong
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Guoyuan Hu
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
| | - Hai-Bing Zhou
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.
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46
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Wang L, Xiao Y, Luo Y, Master RP, Mo J, Kim MC, Liu Y, Maharjan CK, Patel UM, De U, Carelock ME, Tithi TI, Li X, Shaffer DR, Guertin KR, Zhuang H, Moser E, Smalley KS, Lv D, Zhou D, Zheng G, Zhang W. PROTAC-mediated NR4A1 degradation as a novel strategy for cancer immunotherapy. J Exp Med 2024; 221:e20231519. [PMID: 38334978 PMCID: PMC10857906 DOI: 10.1084/jem.20231519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/01/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
An effective cancer therapy requires killing cancer cells and targeting the tumor microenvironment (TME). Searching for molecules critical for multiple cell types in the TME, we identified NR4A1 as one such molecule that can maintain the immune suppressive TME. Here, we establish NR4A1 as a valid target for cancer immunotherapy and describe a first-of-its-kind proteolysis-targeting chimera (PROTAC, named NR-V04) against NR4A1. NR-V04 degrades NR4A1 within hours in vitro and exhibits long-lasting NR4A1 degradation in tumors with an excellent safety profile. NR-V04 inhibits and frequently eradicates established tumors. At the mechanistic level, NR-V04 induces the tumor-infiltrating (TI) B cells and effector memory CD8+ T (Tem) cells and reduces monocytic myeloid-derived suppressor cells (m-MDSC), all of which are known to be clinically relevant immune cell populations in human melanomas. Overall, NR-V04-mediated NR4A1 degradation holds promise for enhancing anticancer immune responses and offers a new avenue for treating various types of cancers such as melanoma.
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Affiliation(s)
- Lei Wang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Yuewan Luo
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Rohan P. Master
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jiao Mo
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Myung-Chul Kim
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- Veterinary Diagnostic Laboratory Medicine, College of Veterinary Medicine, Jeju National University, Jeju-si, South Korea
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Chandra K. Maharjan
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Urvi M. Patel
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Umasankar De
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Madison E. Carelock
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Tanzia Islam Tithi
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | | | | | | | - Haoyang Zhuang
- Rheumatology and Clinical Immunology, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Emily Moser
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Keiran S.M. Smalley
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology, Center of Innovative Drug Discovery, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology, Center of Innovative Drug Discovery, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
- University of Florida Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- University of Florida Health Cancer Center, University of Florida, Gainesville, FL, USA
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47
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O'Reilly S. S100A4 a classical DAMP as a therapeutic target in fibrosis. Matrix Biol 2024; 127:1-7. [PMID: 38219976 DOI: 10.1016/j.matbio.2024.01.002] [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: 11/07/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
Fibrosis regardless of aetiology is characterised by persistently activated myofibroblasts that are contractile and secrete excessive amounts of extracellular matrix molecules that leads to loss of organ function. Damage-Associated Molecular Patterns (DAMPs) are endogenous host-derived molecules that are released from cells dying or under stress that can be triggered by a variety of insults, either chemical or physical, leading to an inflammatory response. Among these DAMPs is S100A4, part of the S100 family of calcium binding proteins that participate in a variety of cellular processes. S100A4 was first described in context of cancer as a pro-metastatic factor. It is now appreciated that aside from its role in cancer promotion, S100A4 is intimately involved in tissue fibrosis. The extracellular form of S100A4 exerts its effects through multiple receptors including Toll-Like Receptor 4 and RAGE to evoke signalling cascades involving downstream mediators facilitating extracellular matrix deposition and myofibroblast generation and can play a role in persistent activation of myofibroblasts. S100A4 may be best understood as an amplifier of inflammatory and fibrotic processes. S100A4 appears critical in systemic sclerosis pathogenesis and blocking the extracellular form of S100A4 in vivo in various animal models of disease mitigates fibrosis and may even reverse established disease. This review appraises S100A4's position as a DAMP and its role in fibrotic conditions and highlight therapeutically targeting this protein to halt fibrosis, suggesting that it is a tractable target.
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Affiliation(s)
- Steven O'Reilly
- Biosciences, Durham University, South Road, Durham, United Kingdom.
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48
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Liang X, Ren H, Han F, Liang R, Zhao J, Liu H. The new direction of drug development: Degradation of undruggable targets through targeting chimera technology. Med Res Rev 2024; 44:632-685. [PMID: 37983964 DOI: 10.1002/med.21992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/13/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Imbalances in protein and noncoding RNA levels in vivo lead to the occurrence of many diseases. In addition to the use of small molecule inhibitors and agonists to restore these imbalances, recently emerged targeted degradation technologies provide a new direction for disease treatment. Targeted degradation technology directly degrades target proteins or RNA by utilizing the inherent degradation pathways, thereby eliminating the functions of pathogenic proteins (or RNA) to treat diseases. Compared with traditional therapies, targeted degradation technology which avoids the principle of traditional inhibitor occupation drive, has higher efficiency and selectivity, and widely expands the range of drug targets. It is one of the most promising and hottest areas for future drug development. Herein, we systematically introduced the in vivo degradation systems applied to degrader design: ubiquitin-proteasome system, lysosomal degradation system, and RNA degradation system. We summarized the development progress, structural characteristics, and limitations of novel chimeric design technologies based on different degradation systems. In addition, due to the lack of clear ligand-binding pockets, about 80% of disease-associated proteins cannot be effectively intervened with through traditional therapies. We deeply elucidated how to use targeted degradation technology to discover and design molecules for representative undruggable targets including transcription factors, small GTPases, and phosphatases. Overall, this review provides a comprehensive and systematic overview of targeted degradation technology-related research advances and a new guidance for the chimeric design of undruggable targets.
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Affiliation(s)
- Xuewu Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hairu Ren
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Fengyang Han
- School of Pharmacy, Fudan University, Shanghai, China
| | - Renwen Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jiayan Zhao
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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49
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Tang YD, Yu C, Cai XH. Novel technologies are turning a dream into reality: conditionally replicating viruses as vaccines. Trends Microbiol 2024; 32:292-301. [PMID: 37798168 DOI: 10.1016/j.tim.2023.09.002] [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: 07/18/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Conditionally replicating viruses (CRVs) are a type of virus with one or more essential gene functions that are impaired resulting in the disruption of viral genome replication, protein synthesis, or virus particle assembly. CRVs can replicate only if the deficient essential genes are supplied. CRVs are widely used in biomedical research, particularly as vaccines. Traditionally, CRVs are generated by creating complementary cell lines that provide the impaired genes. With the development of biotechnology, novel techniques have been invented to generate CRVs, such as targeted protein degradation (TPD) technologies and premature termination codon (PTC) read-through technologies. The advantages and disadvantages of these novel technologies are discussed. Finally, we provide perspectives on what challenges need to be overcome for CRVs to reach the market.
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Affiliation(s)
- Yan-Dong Tang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China.
| | - Changqing Yu
- Engineering Center of Agricultural Biosafety Assessment and Biotechnology, School of Advanced Agricultural Sciences, Yibin Vocational and Technical College, Yibin, China.
| | - Xue-Hui Cai
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, China.
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50
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Menendez JA, Cuyàs E, Encinar JA, Vander Steen T, Verdura S, Llop‐Hernández À, López J, Serrano‐Hervás E, Osuna S, Martin‐Castillo B, Lupu R. Fatty acid synthase (FASN) signalome: A molecular guide for precision oncology. Mol Oncol 2024; 18:479-516. [PMID: 38158755 PMCID: PMC10920094 DOI: 10.1002/1878-0261.13582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/27/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
The initial excitement generated more than two decades ago by the discovery of drugs targeting fatty acid synthase (FASN)-catalyzed de novo lipogenesis for cancer therapy was short-lived. However, the advent of the first clinical-grade FASN inhibitor (TVB-2640; denifanstat), which is currently being studied in various phase II trials, and the exciting advances in understanding the FASN signalome are fueling a renewed interest in FASN-targeted strategies for the treatment and prevention of cancer. Here, we provide a detailed overview of how FASN can drive phenotypic plasticity and cell fate decisions, mitochondrial regulation of cell death, immune escape and organ-specific metastatic potential. We then present a variety of FASN-targeted therapeutic approaches that address the major challenges facing FASN therapy. These include limitations of current FASN inhibitors and the lack of precision tools to maximize the therapeutic potential of FASN inhibitors in the clinic. Rethinking the role of FASN as a signal transducer in cancer pathogenesis may provide molecularly driven strategies to optimize FASN as a long-awaited target for cancer therapeutics.
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Affiliation(s)
- Javier A. Menendez
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Elisabet Cuyàs
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Jose Antonio Encinar
- Institute of Research, Development and Innovation in Biotechnology of Elche (IDiBE) and Molecular and Cell Biology Institute (IBMC)Miguel Hernández University (UMH)ElcheSpain
| | - Travis Vander Steen
- Division of Experimental Pathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
- Mayo Clinic Cancer CenterRochesterMNUSA
- Department of Biochemistry and Molecular Biology LaboratoryMayo Clinic LaboratoryRochesterMNUSA
| | - Sara Verdura
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Àngela Llop‐Hernández
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Júlia López
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Eila Serrano‐Hervás
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaGironaSpain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaGironaSpain
- ICREABarcelonaSpain
| | - Begoña Martin‐Castillo
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
- Unit of Clinical ResearchCatalan Institute of OncologyGironaSpain
| | - Ruth Lupu
- Division of Experimental Pathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
- Mayo Clinic Cancer CenterRochesterMNUSA
- Department of Biochemistry and Molecular Biology LaboratoryMayo Clinic LaboratoryRochesterMNUSA
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