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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; 35:1089-1115. [PMID: 38990186 PMCID: PMC11342303 DOI: 10.1021/acs.bioconjchem.4c00253] [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: 06/05/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [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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2
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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; 277:134293. [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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Li Y, Qu J, Jiang L, Peng X, Wu K, Chen M, Peng Y, Cao X. Application and challenges of nitrogen heterocycles in PROTAC linker. Eur J Med Chem 2024; 273:116520. [PMID: 38788299 DOI: 10.1016/j.ejmech.2024.116520] [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: 02/28/2024] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
The absence of effective active pockets makes traditional molecularly targeted drug strategies ineffective against 80 % of human disease-related proteins. The PROTAC technology effectively makes up for the deficiency of traditional molecular targeted drugs, which produces drug activity by degrading rather than inhibiting the target protein. The degradation of PROTAC is not only affected by POI ligand and E3 ligand, but by the selection of suitable linker which can play an important role in the efficiency and selectivity of the degradation. In the early exploring stage of the PROTAC, flexible chains were priorly applied as the linker of PROTAC. Although PROTAC with flexible chains as linkers sometimes perform well in vitro bioactivity evaluations, the introduction of lipophilic flexible chains reduces the hydrophilicity of these molecules, resulting in generally poor pharmacokinetic characteristics and pharmacological activities in vivo. In addition, recent reports have also shown that some PROTAC with flexible chains have some risks to causing hemolysis in vivo. Therefore, PROTAC with flexible chains show less druggability and large difficulty to entering the clinical trial stage. On the other hand, the application of nitrogen heterocycles in the design of PROTAC linkers has been widely reported in recent years. More and more reports have shown that the introduction of nitrogen heterocycles in the linker not only can effectively improves the metabolism of PROTAC in vivo, but also can enhance the degradation efficiency and selectivity of PROTAC. These PROTAC with nitrogen heterocycle linkers have attracted much attention of pharmaceutical chemists. The introduction of nitrogen heterocycles in the linker deserves priority consideration in the primary design of the PROTAC based on various druggabilities including pharmacokinetic characteristics and pharmacological activity. In this work, we summarized the optimization process and progress of nitrogen heterocyclic rings as the PROTAC linker in recent years. However, there were still limited understanding of how to discover, design and optimize PROTAC. For example, the selection of the types of nitrogen heterocycles and the optimization sites of this linker are challenges for researchers, choosing between four to six-membered nitrogen heterocycles, selecting from saturated to unsaturated ones, and even optimizing the length and extension angle of the linker. There is a truly need for theoretical explanation and elucidation of the PROTAC to guide the developing of more effective and valuable PROTAC.
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Affiliation(s)
- Yang Li
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Junfeng Qu
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Lizhi Jiang
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Xiaoyu Peng
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Kaiyue Wu
- Department of Pharmacy, Ezhou Central Hospital, Ezhou, Hubei, China
| | - Miaojia Chen
- Department of Pharmacy, The First People's Hospital, Pingjiang, Yueyang, Hunan, China
| | - Yuanyuan Peng
- School of Electrical and Automation Engineering, East China Jiaotong University, Nanchang, 330000, China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China.
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Hamamura K, Yoshida Y, Oyama K, Li J, Kawano S, Inoue K, Toyooka K, Yamadera M, Matsunaga N, Matsumura T, Aritake K. Hematopoietic Prostaglandin D Synthase Is Increased in Mast Cells and Pericytes in Autopsy Myocardial Specimens from Patients with Duchenne Muscular Dystrophy. Int J Mol Sci 2024; 25:1846. [PMID: 38339125 PMCID: PMC10855661 DOI: 10.3390/ijms25031846] [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: 12/28/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
The leading cause of death for patients with Duchenne muscular dystrophy (DMD), a progressive muscle disease, is heart failure. Prostaglandin (PG) D2, a physiologically active fatty acid, is synthesized from the precursor PGH2 by hematopoietic prostaglandin D synthase (HPGDS). Using a DMD animal model (mdx mice), we previously found that HPGDS expression is increased not only in injured muscle but also in the heart. Moreover, HPGDS inhibitors can slow the progression of muscle injury and cardiomyopathy. However, the location of HPGDS in the heart is still unknown. Thus, this study investigated HPGDS expression in autopsy myocardial samples from DMD patients. We confirmed the presence of fibrosis, a characteristic phenotype of DMD, in the autopsy myocardial sections. Additionally, HPGDS was expressed in mast cells, pericytes, and myeloid cells of the myocardial specimens but not in the myocardium. Compared with the non-DMD group, the DMD group showed increased HPGDS expression in mast cells and pericytes. Our findings confirm the possibility of using HPGDS inhibitor therapy to suppress PGD2 production to treat skeletal muscle disorders and cardiomyopathy. It thus provides significant insights for developing therapeutic drugs for DMD.
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Affiliation(s)
- Kengo Hamamura
- Laboratory of Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Daiichi University of Pharmacy, Fukuoka 815-8511, Japan;
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan; (Y.Y.); (J.L.); (S.K.); (N.M.)
| | - Yuya Yoshida
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan; (Y.Y.); (J.L.); (S.K.); (N.M.)
| | - Kosuke Oyama
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan;
| | - Junhao Li
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan; (Y.Y.); (J.L.); (S.K.); (N.M.)
| | - Shimpei Kawano
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan; (Y.Y.); (J.L.); (S.K.); (N.M.)
| | - Kimiko Inoue
- Department of Neurology and Rehabilitation Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toneyama 5-1-1, Toyonaka 560-8552, Japan;
| | - Keiko Toyooka
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toneyama 5-1-1, Toyonaka 560-8552, Japan; (K.T.); (T.M.)
| | - Misaki Yamadera
- Department of Clinical Research, National Hospital Organization Osaka Toneyama Medical Center, Toneyama 5-1-1, Toyonaka 560-8552, Japan;
| | - Naoya Matsunaga
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan; (Y.Y.); (J.L.); (S.K.); (N.M.)
| | - Tsuyoshi Matsumura
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toneyama 5-1-1, Toyonaka 560-8552, Japan; (K.T.); (T.M.)
| | - Kosuke Aritake
- Laboratory of Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Daiichi University of Pharmacy, Fukuoka 815-8511, Japan;
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5
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Yokoo H, Shibata N, Demizu Y. In Silico Design, Synthesis, and Evaluation of PROTAC Against Hematopoietic Prostaglandin D Synthase. Methods Mol Biol 2024; 2780:345-359. [PMID: 38987477 DOI: 10.1007/978-1-0716-3985-6_18] [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] [Indexed: 07/12/2024]
Abstract
Chemical protein knockdown technology using proteolysis-targeting chimeras (PROTACs) to hijack the endogenous ubiquitin-proteasome system is a powerful strategy to degrade disease-related proteins. This chapter describes in silico design of a hematopoietic prostaglandin D synthase (H-PGDS) degrader, PROTAC(H-PGDS), using a docking simulation of the ternary complex of H-PGDS/PROTAC/E3 ligase as well as the synthesis of the designed PROTAC(H-PGDS)s and evaluation of their H-PGDS degradation activity.
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Affiliation(s)
- Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences, Kawasaki-shi, Kanagawa, Japan
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Sakyo-ku, Kyoto, Japan
| | - Norihito Shibata
- Division of Biochemistry, National Institute of Health Sciences, Kawasaki-shi, Kanagawa, Japan.
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Kawasaki-shi, Kanagawa, Japan.
- Graduate School of Medical Life Science, Yokohama City University, Yokohama-shi, Kanagawa, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Kita-ku, Okayama, Japan.
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6
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Danishuddin, Jamal MS, Song KS, Lee KW, Kim JJ, Park YM. Revolutionizing Drug Targeting Strategies: Integrating Artificial Intelligence and Structure-Based Methods in PROTAC Development. Pharmaceuticals (Basel) 2023; 16:1649. [PMID: 38139776 PMCID: PMC10747325 DOI: 10.3390/ph16121649] [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: 10/24/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
PROteolysis TArgeting Chimera (PROTAC) is an emerging technology in chemical biology and drug discovery. This technique facilitates the complete removal of the target proteins that are "undruggable" or challenging to target through chemical molecules via the Ubiquitin-Proteasome System (UPS). PROTACs have been widely explored and outperformed not only in cancer but also in other diseases. During the past few decades, several academic institutes and pharma companies have poured more efforts into PROTAC-related technologies, setting the stage for several major degrader trial readouts in clinical phases. Despite their promising results, the formation of robust ternary orientation, off-target activity, poor permeability, and binding affinity are some of the limitations that hinder their development. Recent advancements in computational technologies have facilitated progress in the development of PROTACs. Researchers have been able to utilize these technologies to explore a wider range of E3 ligases and optimize linkers, thereby gaining a better understanding of the effectiveness and safety of PROTACs in clinical settings. In this review, we briefly explore the computational strategies reported to date for the formation of PROTAC components and discuss the key challenges and opportunities for further research in this area.
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Affiliation(s)
- Danishuddin
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | | | - Kyoung-Seob Song
- Department of Medical Science, Kosin University College of Medicine, 194 Wachi-ro, Yeongdo-gu, Busan 49104, Republic of Korea;
| | - Keun-Woo Lee
- Division of Life Science, Department of Bio & Medical Big-Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
- Angel i-Drug Design (AiDD), 33-3 Jinyangho-ro 44, Jinju 52650, Republic of Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Yeong-Min Park
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neugdong-ro, Gwangjin-gu, Seoul 05006, Republic of Korea
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7
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Bhole RP, Kute PR, Chikhale RV, Bonde CG, Pant A, Gurav SS. Unlocking the potential of PROTACs: A comprehensive review of protein degradation strategies in disease therapy. Bioorg Chem 2023; 139:106720. [PMID: 37480814 DOI: 10.1016/j.bioorg.2023.106720] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/24/2023]
Abstract
The technology known asPROTACs (PROteolysisTArgeting Chimeras) is a method of protein degradation. Utilising bifunctional small molecules, the ubiquitin-proteosome system (UPS) is used to induce the ubiquitination and degradation of target proteins. In addition to being novel chemical knockdown agents for biological studies that are catalytic, reversible, and rapid, PROTACs used in the treatment for disorders like cancer, immunological disorders, viral diseases, and neurological disorders. The protein degradation field has advanced quickly over the last two years, with a significant rise in research articles on the subject as well as a quick rise in smallmolecule degraders that are currently in or will soon enter the clinical stage. Other new degrading technologies, in addition to PROTAC and molecular glue technology, are also emerging rapidly. In this review article, we mainly focuses on various PROTAC molecules designed with special emphasis on targeted cellular pathways for different diseases i.e., cancer, Viral diseases Immune disorders, Neurodegenerative diseases, etc. We discussed about new technologies based on PROTACs such as Antibody PROTAC, Aptamers, Dual target, Folate caged, TF PROTAC, etc. Also, we listed out the PROTACs which are in clinical trials.
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Affiliation(s)
- Ritesh P Bhole
- Department of Pharmaceutical Chemistry, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India.
| | - Payal R Kute
- Department of Pharmaceutical Chemistry, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India
| | | | - C G Bonde
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management, SVKM's NMIMS, Shirpur Campus 425 405, India.
| | - Amit Pant
- School of Medicine Creighton University, Omaha, Neraska, USA.
| | - Shailendra S Gurav
- Department of Pharmacognosy, Goa College of Pharmacy, Panaji, Goa University, Goa 403001, India.
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Osawa H, Kurohara T, Ito T, Shibata N, Demizu Y. CRBN ligand expansion for Hematopoietic Prostaglandin D2 Synthase (H-PGDS) targeting PROTAC design and their in vitro ADME profiles. Bioorg Med Chem 2023; 84:117259. [PMID: 37018877 DOI: 10.1016/j.bmc.2023.117259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
An increasing number of research reports are describing modifications of the E3 ligand, in particular, cereblon (CRBN) ligands, to improve the chemical and metabolic stabilities as well as the physical properties of PROTACs. In this study, phenyl-glutarimide (PG) and 6-fluoropomalidomide (6-F-POM), recently used as CRBN ligands for PROTAC design, were applied to hematopoietic prostaglandin D2 synthase (H-PGDS)-targeted PROTACs. Both PROTAC-5 containing PG and PROTAC-6 containing 6-F-POM were found to have potent activities to induce H-PGDS degradation. Furthermore, we obtained in vitro ADME data on the newly designed PROTACS as well as our previously reported PROTACs(H-PGDS) series. Although all PROTACs(H-PGDS) are relatively stable toward metabolism, they had poor PAMPA values. Nevertheless, PROTAC-5 showed Papp values similar to TAS-205, which is in Phase 3 clinical trials, and is expected to be the key to improving the pharmacokinetics of PROTACs.
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Abstract
Proteolysis-targeting chimeras (PROTACs) have shown great therapeutic potential by degrading various disease-causing proteins, particularly those related to tumors. Therefore, the introduction of PROTACs has ushered in a new chapter of antitumor drug development, marked by significant advances over recent years. Herein, we describe recent developments in PROTAC technology, focusing on design strategy, development workflow, and future outlooks. We also discuss potential opportunities and challenges for PROTAC research.
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Affiliation(s)
- Minglei Li
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Ying Zhi
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Bo Liu
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Qingqiang Yao
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
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Murakami Y, Osawa H, Kurohara T, Yanase Y, Ito T, Yokoo H, Shibata N, Naito M, Aritake K, Demizu Y. Structure-activity relationship study of PROTACs against hematopoietic prostaglandin D 2 synthase. RSC Med Chem 2022; 13:1495-1503. [PMID: 36561070 PMCID: PMC9749925 DOI: 10.1039/d2md00284a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/21/2022] [Indexed: 12/25/2022] Open
Abstract
Degradation of hematopoietic prostaglandin D2 synthase (H-PGDS) by proteolysis-targeting chimeras (PROTACs) is expected to be important in the treatment of allergic diseases and Duchenne's muscular dystrophy. We recently reported that PROTAC(H-PGDS)-7 (PROTAC1), which is composed of H-PGDS inhibitor (TFC-007) and cereblon (CRBN) E3 ligase ligand (pomalidomide), showed potent H-PGDS degradation activity. Here, we investigated the structure-activity relationships of PROTAC1, focusing on the C4- or C5-conjugation of pomalidomide, in addition, the H-PGDS ligand exchanging from TFC-007 with the biaryl ether to TAS-205 with the pyrrole. Three new PROTACs were evaluated for H-PGDS affinity, H-PGDS degrading activity, and inhibition of prostaglandin D2 production. All compounds showed high H-PGDS degrading activities, but PROTAC(H-PGDS)-4-TAS-205 (PROTAC3) was slightly less active than the other compounds. Molecular dynamics simulations suggested that the decrease in activity of PROTAC3 may be due to the lower stability of the CRBN-PROTAC-H-PGDS ternary complex.
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Affiliation(s)
- Yuki Murakami
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Yokohama Kanagawa 230-0045 Japan
| | - Hinata Osawa
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Division of Pharmaceutical Science of Okayama University 1-1-1 Tsushimanaka Kita 700-8530 Japan
| | - Takashi Kurohara
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki Kanagawa 210-9501 Japan
| | - Yuta Yanase
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Yokohama Kanagawa 230-0045 Japan
| | - Takahito Ito
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Yokohama Kanagawa 230-0045 Japan
| | - Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kyoto 606-0823 Japan
| | - Norihito Shibata
- Division of Biochemistry, National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki Kanagawa 210-9501 Japan
| | - Mikihiko Naito
- Laboratory of Targeted Protein Degradation, Graduate School of Pharmaceutical Sciences, The University of Tokyo Tokyo 113-0033 Japan
| | - Kosuke Aritake
- Laboratory of Chemical Pharmacology, Daiichi University of Pharmacy Fukuoka 815-8511 Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26, Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Yokohama Kanagawa 230-0045 Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Division of Pharmaceutical Science of Okayama University 1-1-1 Tsushimanaka Kita 700-8530 Japan
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11
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Ekins S. Al-novation: Finding New Uses for Artificial Intelligence Across Industries. GEN BIOTECHNOLOGY 2022; 1:444-446. [PMID: 36311442 PMCID: PMC9607920 DOI: 10.1089/genbio.2022.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
As we have seen throughout history, people and indeed companies can catalyze dramatic changes through invention and innovations. They can create new fields of science that did not exist before. In doing so, new technologies can reshape cities and create unintended consequences. We are now in a different era in which the development of artificial intelligence (AI) is both being rapidly applied in many areas of science and creating ethical challenges that need to be considered. AI may autonomously suggest innovations leading to a revolution in science and health care. What follows is a provocative brief opinion that looks at the future of how new technologies are developed through AI with all its attendant challenges.
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Affiliation(s)
- Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina, USA
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12
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Němec V, Schwalm MP, Müller S, Knapp S. PROTAC degraders as chemical probes for studying target biology and target validation. Chem Soc Rev 2022; 51:7971-7993. [PMID: 36004812 DOI: 10.1039/d2cs00478j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule degraders such as PROTACs (PROteolysis TArgeting Chimeras) have emerged as new promising pharmacological modalities and the first PROTAC drug candidates are now studied clinically. The catalytic properties of PROTACs, acting as chemical degraders of a protein of interest (POI), represent an attractive new strategy for drug development. The development and characterization of PROTACs requires an array of additional assay systems that track the degradation pathway leading ultimately to degradation of the POI, identifying critical steps for PROTAC optimization. In addition to their exciting translational potential, PROTACs represent versatile chemical tools that considerably expanded our chemical biology toolbox and significantly enlarged the proteome that can be modulated by small molecules. Similar to conventional chemical probes, PROTACs used as chemical probes in target validation require comprehensive characterization. As a consequence, PROTAC-specific quality criteria should be defined by the chemical biology community. These criteria need to comprise additional or alternative parameters compared to those for conventional occupancy-driven chemical probes, such as the maximum level of target degradation (Dmax), confirmation of a proteasome dependent degradation mechanism and, importantly, also kinetic parameters of POI degradation. The kinetic aspects are particularly relevant for PROTACs that harbor covalent binding moieties. Here, we review recent progress in the development of assay systems for PROTAC characterization and suggest a set of criteria for PROTACs as high quality chemical probes.
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Affiliation(s)
- Václav Němec
- 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
| | - 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
| | - Susanne Müller
- 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
| | - 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)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany
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13
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Tian Y, Liu K, Liu R, Qiu Z, Xu Y, Wei W, Xu X, Wang J, Ding H, Li Z, Bian J. Discovery of Potent Small-Molecule USP8 Inhibitors for the Treatment of Breast Cancer through Regulating ERα Expression. J Med Chem 2022; 65:8914-8932. [PMID: 35786929 DOI: 10.1021/acs.jmedchem.2c00013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ubiquitin-specific protease 8 (USP8), belonging to the deubiquitinase family, has been implicated to be closely related to the occurrence of many malignant tumors, but only a few USP8-targeting inhibitors have been reported to date. In this study, we present virtual screening to discover novel hit candidates that inhibit the catalytic activity of USP8. Exploration of the structure-activity relationship led to the identification of compound DC-U4106, which binds to USP8 with a KD value of 4.7 μM and is selective over USP2 and USP7. Western blotting and immunoprecipitation showed that DC-U4106 could target the ubiquitin pathway and facilitate the degradation of ERα. In a xenograft tumor model, DC-U4106 also significantly inhibited tumor growth with minimal toxicity. Overall, our findings suggest that DC-U4106 is a promising drug candidate and targeting the USP8-ERα complex could be a new approach to treat ER-positive or drug-resistant breast cancer.
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Affiliation(s)
- Yucheng Tian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Kang Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Ruoyi Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Zhixia Qiu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Yifan Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Wei Wei
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Xi Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Jubo Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Material Medical, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai201203, China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
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14
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Xu H, Kurohara T, Takano R, Yokoo H, Shibata N, Ohoka N, Inoue T, Naito M, Demizu Y. Development of Rapid and Facile Solid-Phase Synthesis of PROTACs via a Variety of Binding Styles. Chemistry 2022; 11:e202200131. [PMID: 35822913 PMCID: PMC9278092 DOI: 10.1002/open.202200131] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/13/2022] [Indexed: 11/25/2022]
Abstract
Optimizing linker design is important for ensuring efficient degradation activity of proteolysis‐targeting chimeras (PROTACs). Therefore, developing a straightforward synthetic approach that combines the protein‐of‐interest ligand (POI ligand) and the ligand for E3 ubiquitin ligase (E3 ligand) in various binding styles through a linker is essential for rapid PROTAC syntheses. Herein, a solid‐phase approach for convenient PROTAC synthesis is presented. We designed azide intermediates with different linker lengths to which the E3 ligand, pomalidomide, is attached and performed facile PROTACs synthesis by forming triazole, amide, and urea bonds from the intermediates.
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Affiliation(s)
- Hanqiao Xu
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan.,Graduate School of Medical Life Science, Yokohama City University 1-7-29, Yokohama, Kanagawa, 230-0045, Japan
| | - Takashi Kurohara
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan
| | - Reina Takano
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan.,Graduate School of Medical Life Science, Yokohama City University 1-7-29, Yokohama, Kanagawa, 230-0045, Japan
| | - Hidetomo Yokoo
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan.,Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 606-0823, Japan
| | - Norihito Shibata
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan
| | - Nobumichi Ohoka
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takao Inoue
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan
| | - Mikihiko Naito
- Laboratory of Targeted Protein Degradation, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yosuke Demizu
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan.,Graduate School of Medical Life Science, Yokohama City University 1-7-29, Yokohama, Kanagawa, 230-0045, Japan
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15
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He M, Cao C, Ni Z, Liu Y, Song P, Hao S, He Y, Sun X, Rao Y. PROTACs: great opportunities for academia and industry (an update from 2020 to 2021). Signal Transduct Target Ther 2022; 7:181. [PMID: 35680848 PMCID: PMC9178337 DOI: 10.1038/s41392-022-00999-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
PROteolysis TArgeting Chimeras (PROTACs) technology is a new protein-degradation strategy that has emerged in recent years. It uses bifunctional small molecules to induce the ubiquitination and degradation of target proteins through the ubiquitin-proteasome system. PROTACs can not only be used as potential clinical treatments for diseases such as cancer, immune disorders, viral infections, and neurodegenerative diseases, but also provide unique chemical knockdown tools for biological research in a catalytic, reversible, and rapid manner. In 2019, our group published a review article "PROTACs: great opportunities for academia and industry" in the journal, summarizing the representative compounds of PROTACs reported before the end of 2019. In the past 2 years, the entire field of protein degradation has experienced rapid development, including not only a large increase in the number of research papers on protein-degradation technology but also a rapid increase in the number of small-molecule degraders that have entered the clinical and will enter the clinical stage. In addition to PROTAC and molecular glue technology, other new degradation technologies are also developing rapidly. In this article, we mainly summarize and review the representative PROTACs of related targets published in 2020-2021 to present to researchers the exciting developments in the field of protein degradation. The problems that need to be solved in this field will also be briefly introduced.
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Affiliation(s)
- Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, P. R. China
| | - Zhihao Ni
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yongbo Liu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Peilu Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Shuang Hao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China.
- School of Pharmaceutical Sciences, Zhengzhou University, 450001, Zhengzhou, China.
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16
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Naito M. Targeted Protein Degradation and Drug Discovery. J Biochem 2022; 172:61-69. [PMID: 35468190 DOI: 10.1093/jb/mvac041] [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: 02/02/2022] [Accepted: 04/19/2022] [Indexed: 11/12/2022] Open
Abstract
Targeted protein degradation attracts attention as a novel modality for drug discovery as well as for basic research. Various types of degrader molecules have been developed so far, which include PROTACs and SNIPERs, E3 modulators, hydrophobic tagging molecules, IAP antagonists, and deubiquitylase inhibitors. PROTACs and SNIPERs are chimeric degrader molecules consisting of a target ligand linked to another ligand that binds to an E3 ubiquitin ligase. In the cells, they recruit an E3 ligase to the target protein, thereby inducing ubiquitylation and proteasomal degradation of the target protein. Because of their modular structure, novel PROTACs and SNIPERs targeting proteins of your interest can be rationally developed by substituting target ligands. In this article, various compounds capable of inducing protein degradation were overviewed, including SNIPER compounds developed in our laboratory.
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Affiliation(s)
- Mikihiko Naito
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
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17
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Recent progress on small molecules targeting epigenetic complexes. Curr Opin Chem Biol 2022; 67:102130. [DOI: 10.1016/j.cbpa.2022.102130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 12/16/2022]
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