1
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [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: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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2
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Cho N, Naito M. Synthesis of SNIPERs against BCR-ABL with kinase inhibitors and a method to evaluate their growth inhibitory activity derived from BCR-ABL degradation. Methods Enzymol 2023; 681:41-60. [PMID: 36764763 DOI: 10.1016/bs.mie.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Specific and nongenetic IAP-dependent Protein Erasers (SNIPERs) are a kind of PROTACs recruiting IAP ubiquitin ligases to induce degradation of target proteins. We have developed a series of SNIPERs against BCR-ABL oncogenic kinases by employing kinase inhibitors as target ligands. Some of these SNIPERs show potent activities to degrade BCR-ABL protein and inhibit CML cell growth. However, since SNIPERs also inhibit kinase activity, it takes some ingenuity to show that degradation of BCR-ABL plays a significant role on growth inhibitory activity. Here we describe protocols for synthesizing SNIPERs against BCR-ABL oncogenic kinase that contain kinase inhibitors as target ligands, and methods for evaluating the growth inhibitory activity against cancer cells, especially focusing on a method to discriminate the significance of protein degradation from that of kinase inhibition.
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Affiliation(s)
- Nobuo Cho
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Mikihiko Naito
- Social Cooperation Program of Targeted Protein Degradation, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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3
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Jia X, Han X. Targeting androgen receptor degradation with PROTACs from bench to bedside. Biomed Pharmacother 2023; 158:114112. [PMID: 36508999 DOI: 10.1016/j.biopha.2022.114112] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Inhibition of androgen receptor (AR) has been extensively investigated to treat prostate cancer. Resistance mechanisms such as increased levels of androgen production, increased AR gene, enhancer expression and AR point mutations always reduce the clinical efficacy. Design and discovery of small-molecule PROTAC AR degraders have been pursued as a new therapeutic strategy to overcome common resistance mechanisms developed during prostate cancer treatment. In the last two decades, potent and efficacious PROTAC AR degraders have been gotten rapid development and several such compounds have been advanced into preclinical phase and phase I/II trials for the treatment of human prostate cancers. Especially, the first PROTAC to enter the clinic, ARV-110, has shown good clinical effects in patients with mCRPC. This fully demonstrates the high clinical value of PROTAC strategy in treatment of human diseases. Here, we summarized the recent advances in the development of these potential clinical-stage PROTAC AR degraders.
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Affiliation(s)
- Xiaojuan Jia
- The 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xin Han
- The 2nd Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.; Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310029, China..
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4
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Advances in AR-targeting chimeras: a case study of proteolysis-targeting chimeras from bench to bedside. Future Med Chem 2022; 14:1471-1489. [PMID: 36214138 DOI: 10.4155/fmc-2022-0147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Proteolysis-targeting chimera (PROTAC) is an emerging revolutionary technology that promotes degradation of target proteins by proteolysis. AR-targeting PROTACs marked many milestones in the history of PROTAC development. In this review, the author discusses the development of AR-targeting PROTACs over the last two decades. Also included in this focused review are medicinal chemistry strategies, pharmacokinetic profiles and clinical development. Taking AR targeting PROTACs for case study, this review provides a target specific overview of how PROTAC technology has advanced from a revolutionary concept and achieved proof of concept leading to drug candidates that benefit patients.
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5
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Li J, Cai Z, Li XW, Zhuang C. Natural Product-Inspired Targeted Protein Degraders: Advances and Perspectives. J Med Chem 2022; 65:13533-13560. [PMID: 36205223 DOI: 10.1021/acs.jmedchem.2c01223] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeted protein degradation (TPD), a promising therapeutic strategy in drug discovery, has great potential to regulate the endogenous degradation of undruggable targets with small molecules. As vital resources that provide diverse structural templates for drug discovery, natural products (NPs) are a rising and robust arsenal for the development of therapeutic TPD. The first proof-of-concept study of proteolysis-targeting chimeras (PROTACs) was a natural polyketide ovalicin-derived degrader; since then, NPs have shown great potential to promote TPD technology. The use of NP-inspired targeted protein degraders has been confirmed to be a promising strategy to treat many human conditions, including cancer, inflammation, and nonalcoholic fatty liver disease. Nevertheless, the development of NP-inspired degraders is challenging, and the field is currently in its infancy. In this review, we summarize the bioactivities and mechanisms of NP-inspired degraders and discuss the associated challenges and future opportunities in this field.
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Affiliation(s)
- Jiao Li
- Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Zhenyu Cai
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xu-Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China.,Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
| | - Chunlin Zhuang
- Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,School of Pharmacy, Second Military Medical University, Shanghai 200433, China
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6
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Lee J, Lee Y, Jung YM, Park JH, Yoo HS, Park J. Discovery of E3 Ligase Ligands for Target Protein Degradation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196515. [PMID: 36235052 PMCID: PMC9573645 DOI: 10.3390/molecules27196515] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022]
Abstract
Target protein degradation has emerged as a promising strategy for the discovery of novel therapeutics during the last decade. Proteolysis-targeting chimera (PROTAC) harnesses a cellular ubiquitin-dependent proteolysis system for the efficient degradation of a protein of interest. PROTAC consists of a target protein ligand and an E3 ligase ligand so that it enables the target protein degradation owing to the induced proximity with ubiquitin ligases. Although a great number of PROTACs has been developed so far using previously reported ligands of proteins for their degradation, E3 ligase ligands have been mostly limited to either CRBN or VHL ligands. Those PROTACs showed their limitation due to the cell type specific expression of E3 ligases and recently reported resistance toward PROTACs with CRBN ligands or VHL ligands. To overcome these hurdles, the discovery of various E3 ligase ligands has been spotlighted to improve the current PROTAC technology. This review focuses on currently reported E3 ligase ligands and their application in the development of PROTACs.
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Affiliation(s)
- Jaeseok Lee
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
| | - Youngjun Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Young Mee Jung
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
| | - Ju Hyun Park
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Hyuk Sang Yoo
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: ; Tel.: +82-33-250-8482
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7
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Wang C, Zhang Y, Shi L, Yang S, Chang J, Zhong Y, Li Q, Xing D. Recent advances in IAP-based PROTACs (SNIPERs) as potential therapeutic agents. J Enzyme Inhib Med Chem 2022; 37:1437-1453. [PMID: 35589670 PMCID: PMC9122363 DOI: 10.1080/14756366.2022.2074414] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proteolytic targeting chimaeras (PROTACs) have been developed as an effective technology for targeted protein degradation. PROTACs are heterobifunctional molecules that can trigger the polyubiquitination of proteins of interest (POIs) by recruiting the ubiquitin-proteasome system, thereby inhibiting the intracellular level of POIs. To date, a variety of small-molecule PROTACs (CRBN, VHL, IAP, and MDM2-based PROTACs) have been developed. IAP-based PROTACs, also known as specific and nongenetic IAP-dependent protein erasers (SNIPERs), are used to degrade the target proteins closely related to diseases. Their structures consist of three parts, including target protein ligand, E3 ligase ligand, and the linker between them. So far, many SNIPERs have been extensively studied worldwide and have performed well in multiple diseases, especially cancer. In this review, we will present the most relevant advances in the field of SNIPERs and provide our perspective on the opportunities and challenges for SNIPERs to become therapeutic agents.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Lingyu Shi
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Shanbo Yang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Jing Chang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Yingjie Zhong
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Qian Li
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China.,School of Life Sciences, Tsinghua University, Beijing, China
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8
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Li X, Pu W, Zheng Q, Ai M, Chen S, Peng Y. Proteolysis-targeting chimeras (PROTACs) in cancer therapy. Mol Cancer 2022; 21:99. [PMID: 35410300 PMCID: PMC8996410 DOI: 10.1186/s12943-021-01434-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/21/2021] [Indexed: 12/18/2022] Open
Abstract
AbstractProteolysis-targeting chimeras (PROTACs) are engineered techniques for targeted protein degradation. A bifunctional PROTAC molecule with two covalently-linked ligands recruits target protein and E3 ubiquitin ligase together to trigger proteasomal degradation of target protein by the ubiquitin-proteasome system. PROTAC has emerged as a promising approach for targeted therapy in various diseases, particularly in cancers. In this review, we introduce the principle and development of PROTAC technology, as well as the advantages of PROTACs over traditional anti-cancer therapies. Moreover, we summarize the application of PROTACs in targeting critical oncoproteins, provide the guidelines for the molecular design of PROTACs and discuss the challenges in the targeted degradation by PROTACs.
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9
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Sosič I, Bricelj A, Steinebach C. E3 ligase ligand chemistries: from building blocks to protein degraders. Chem Soc Rev 2022; 51:3487-3534. [PMID: 35393989 DOI: 10.1039/d2cs00148a] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, proteolysis-targeting chimeras (PROTACs), capable of achieving targeted protein degradation, have proven their great therapeutic potential and usefulness as molecular biology tools. These heterobifunctional compounds are comprised of a protein-targeting ligand, an appropriate linker, and a ligand binding to the E3 ligase of choice. A successful PROTAC induces the formation of a ternary complex, leading to the E3 ligase-mediated ubiquitination of the targeted protein and its proteasomal degradation. In over 20 years since the concept was first demonstrated, the field has grown substantially, mainly due to the advancements in the discovery of non-peptidic E3 ligase ligands. Development of small-molecule E3 binders with favourable physicochemical profiles aided the design of PROTACs, which are known for breaking the rules of established guidelines for discovering small molecules. Synthetic accessibility of the ligands and numerous successful applications led to the prevalent use of cereblon and von Hippel-Lindau as the hijacked E3 ligase. However, the pool of over 600 human E3 ligases is full of untapped potential, which is why expanding the artillery of E3 ligands could contribute to broadening the scope of targeted protein degradation. In this comprehensive review, we focus on the chemistry aspect of the PROTAC design process by providing an overview of liganded E3 ligases, their chemistries, appropriate derivatisation, and synthetic approaches towards their incorporation into heterobifunctional degraders. By covering syntheses of both established and underexploited E3 ligases, this review can serve as a chemistry blueprint for PROTAC researchers during their future ventures into the complex field of targeted protein degradation.
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Affiliation(s)
- Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Aleša Bricelj
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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10
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Zhong Y, Chi F, Wu H, Liu Y, Xie Z, Huang W, Shi W, Qian H. Emerging targeted protein degradation tools for innovative drug discovery: From classical PROTACs to the novel and beyond. Eur J Med Chem 2022; 231:114142. [DOI: 10.1016/j.ejmech.2022.114142] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/22/2022]
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11
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Bricelj A, Steinebach C, Kuchta R, Gütschow M, Sosič I. E3 Ligase Ligands in Successful PROTACs: An Overview of Syntheses and Linker Attachment Points. Front Chem 2021; 9:707317. [PMID: 34291038 PMCID: PMC8287636 DOI: 10.3389/fchem.2021.707317] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/04/2021] [Indexed: 12/16/2022] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) have received tremendous attention as a new and exciting class of therapeutic agents that promise to significantly impact drug discovery. These bifunctional molecules consist of a target binding unit, a linker, and an E3 ligase binding moiety. The chemically-induced formation of ternary complexes leads to ubiquitination and proteasomal degradation of target proteins. Among the plethora of E3 ligases, only a few have been utilized for the novel PROTAC technology. However, extensive knowledge on the preparation of E3 ligands and their utilization for PROTACs has already been acquired. This review provides an in-depth analysis of synthetic entries to functionalized ligands for the most relevant E3 ligase ligands, i.e. CRBN, VHL, IAP, and MDM2. Less commonly used E3 ligase and their ligands are also presented. We compare different preparative routes to E3 ligands with respect to feasibility and productivity. A particular focus was set on the chemistry of the linker attachment by discussing the synthetic opportunities to connect the E3 ligand at an appropriate exit vector with a linker to assemble the final PROTAC. This comprehensive review includes many facets involved in the synthesis of such complex molecules and is expected to serve as a compendium to support future synthetic attempts towards PROTACs.
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Affiliation(s)
- Aleša Bricelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | | | - Robert Kuchta
- Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | | | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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12
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Tomoshige S, Ishikawa M. In vivo synthetic chemistry of proteolysis targeting chimeras (PROTACs). Bioorg Med Chem 2021; 41:116221. [PMID: 34034148 DOI: 10.1016/j.bmc.2021.116221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 11/29/2022]
Abstract
Chemical knockdown of therapeutic targets using proteolysis targeting chimeras (PROTACs) is a rapidly developing field in drug discovery, but PROTACs are bifunctional molecules that generally show poor bioavailability due to their relatively high molecular weight. Recent developments aimed at the development of next-generation PROTACs include the in vivo synthesis of PROTAC molecules, and the exploitation of PROTACs as chemical tools for in vivo synthesis of ubiquitinated proteins. This short review covers recent advances in these areas and discusses the prospects for in vivo synthetic PROTAC technology.
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Affiliation(s)
- Shusuke Tomoshige
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Minoru Ishikawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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13
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Mukhamejanova Z, Tong Y, Xiang Q, Xu F, Pang J. Recent Advances in the Design and Development of Anticancer Molecules based on PROTAC Technology. Curr Med Chem 2021; 28:1304-1327. [PMID: 32164504 DOI: 10.2174/0929867327666200312112412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 11/22/2022]
Abstract
PROTAC (Proteolysis Targeting Chimera) degraders based on protein knockdown technology are now suggested as a novel option for the treatment of various diseases. Over the last couple of years, the application of PROTAC technology has spread in a wide range of disorders, and plenty of PROTAC molecules with high potency have been reported. Mostly developing for anticancer therapy, these molecules showed high selectivities to target proteins, the ability to significantly induce degradation of oncoproteins, good in vitro and in vivo results. In this review, we summarized the recent development of PROTAC technology in the anticancer therapy field, including molecular design, types of targeted proteins, in vitro and in vivo results. Additionally, we also discuss the prospects and challenges for the application of candidates based on PROTAC strategy in clinical trials.
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Affiliation(s)
| | - Yichen Tong
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qi Xiang
- Institute of Biomedicine & Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jiyan Pang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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14
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Maneiro M, De Vita E, Conole D, Kounde CS, Zhang Q, Tate EW. PROTACs, molecular glues and bifunctionals from bench to bedside: Unlocking the clinical potential of catalytic drugs. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:67-190. [PMID: 34147206 DOI: 10.1016/bs.pmch.2021.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The vast majority of currently marketed drugs rely on small molecules with an 'occupancy-driven' mechanism of action (MOA). Therefore, the efficacy of these therapeutics depends on a high degree of target engagement, which often requires high dosages and enhanced drug exposure at the target site, thus increasing the risk of off-target toxicities (Churcher, 2018 [1]). Although small molecule drugs have been successfully used as treatments for decades, tackling a variety of disease-relevant targets with a defined binding site, many relevant therapeutic targets remain challenging to drug due, for example, to lack of well-defined binding pockets or large protein-protein interaction (PPI) interfaces which resist interference (Dang et al., 2017 [2]). In the quest for alternative therapeutic approaches to address different pathologies and achieve enhanced efficacy with reduced side effects, ligand-induced targeted protein degradation (TPD) has gained the attention of many research groups both in academia and in industry in the last two decades. This therapeutic modality represents a novel paradigm compared to conventional small-molecule inhibitors. To pursue this strategy, heterobifunctional small molecule degraders, termed PROteolysis TArgeting Chimeras (PROTACs) have been devised to artificially redirect a protein of interest (POI) to the cellular protein homeostasis machinery for proteasomal degradation (Chamberlain et al., 2019 [3]). In this chapter, the development of PROTACs will first be discussed providing a historical perspective in parallel to the experimental progress made to understand this novel therapeutic modality. Furthermore, common strategies for PROTAC design, including assays and troubleshooting tips will be provided for the reader, before presenting a compendium of all PROTAC targets reported in the literature to date. Due to the recent advancement of these molecules into clinical trials, consideration of pharmacokinetics and pharmacodynamic properties will be introduced, together with the biotech landscape that has developed from the success of PROTACs. Finally, an overview of subsequent strategies for targeted protein degradation will be presented, concluding with further scientific quests triggered by the invention of PROTACs.
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Affiliation(s)
- M Maneiro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - E De Vita
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - D Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - C S Kounde
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Q Zhang
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - E W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom.
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15
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Song R, Qiao W, He J, Huang J, Luo Y, Yang T. Proteases and Their Modulators in Cancer Therapy: Challenges and Opportunities. J Med Chem 2021; 64:2851-2877. [PMID: 33656892 DOI: 10.1021/acs.jmedchem.0c01640] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteostasis is the process of regulating intracellular proteins to maintain the balance of the cell proteome, which is crucial for cancer cell survival. Several proteases located in the cytoplasm, mitochondria, lysosome, and extracellular environment have been identified as potential antitumor targets because of their involvement in proteostasis. Although the discovery of small-molecule inhibitors targeting proteases faces particular challenges, rapid advances in chemical biology and structural biology, and the new technology of drug discovery have facilitated the development of promising protease modulators. In this review, the protein structure and function of important tumor-related proteases and their inhibitors are presented. We also provide a prospective on advances and the outlook of new drug strategies that target these proteases.
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Affiliation(s)
- Rao Song
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiasheng Huang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Laboratory of Human Disease and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China
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16
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Tomoshige S, Ishikawa M. PROTACs and Other Chemical Protein Degradation Technologies for the Treatment of Neurodegenerative Disorders. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202004746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shusuke Tomoshige
- Graduate School of Life Sciences Tohoku University 2-1-1 Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Minoru Ishikawa
- Graduate School of Life Sciences Tohoku University 2-1-1 Katahira, Aoba-ku Sendai 980-8577 Japan
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17
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Ma Z, Ji Y, Yu Y, Liang D. Specific non-genetic IAP-based protein erasers (SNIPERs) as a potential therapeutic strategy. Eur J Med Chem 2021; 216:113247. [PMID: 33652355 DOI: 10.1016/j.ejmech.2021.113247] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 12/29/2022]
Abstract
As a newly emerged technology, PROTAC (proteolysis targeting chimera) is a promising therapeutic strategy for varieties of diseases. Unlike small molecule inhibitors, PROTACs catalytically induce target proteins degradation, including currently "undruggable" target proteins. In addition, PROTACs can be a potentially successful strategy to overcome drug resistance. IAPs can inhibit apoptosis by inhibiting caspase, and also exhibits the activity of E3 ubiquitin ligase. Specific and nongenetic IAP-based protein erasers (SNIPERs) are hybrid molecules that designed based on IAPs, and used to degrade the target proteins closely associated with diseases. Their structures consist of three parts, including target protein ligand, E3 ligase ligand and the linker between them. SNIPERs (PROTACs) degrade diseases-associated proteins through human inherent ubiquitin-proteasome system. So far, many SNIPERs have been developed to treat diseases that difficult to handle by traditional methods, such as radiotherapy, chemotherapy and small molecule inhibitors, and showed promising prospects in application. In this paper, the recent advances of SNIPERs were summarized, and the chances and challenges associated with this area were also highlighted.
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Affiliation(s)
- Zonghui Ma
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China.
| | - Yu Ji
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China
| | - Yifan Yu
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China
| | - Dailin Liang
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China; Department of Medicinal Chemistry, China Pharmaceutical University, Tongjiaxiang 24, Nanjing, 210009, China
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18
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Abstract
Inducing degradation of undruggable target proteins by the use of chimeric small molecules, represented by proteolysis-targeting chimeras, is a promising strategy for drug development. We developed a series of chimeric molecules, termed "specific and nongenetic inhibitor of apoptosis protein (IAP)-dependent protein erasers" (SNIPERs) that recruit IAP ubiquitin ligases to induce degradation of target proteins. SNIPERs also induce degradation of some IAPs, including cIAP1 and XIAP, which are antiapoptotic proteins that are overexpressed in many cancers. Such protein degraders have unique properties that could be especially useful in cancer therapy. This chapter describes (1) the design and synthesis of SNIPER compounds, (2) the methods used for the detection of target protein degradation and ubiquitylation, and (3) the protocol to evaluate the antitumor activity of SNIPER.
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19
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The Potential of Proteolytic Chimeras as Pharmacological Tools and Therapeutic Agents. Molecules 2020; 25:molecules25245956. [PMID: 33339292 PMCID: PMC7766482 DOI: 10.3390/molecules25245956] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
The induction of protein degradation in a highly selective and efficient way by means of druggable molecules is known as targeted protein degradation (TPD). TPD emerged in the literature as a revolutionary idea: a heterobifunctional chimera with the capacity of creating an interaction between a protein of interest (POI) and a E3 ubiquitin ligase will induce a process of events in the POI, including ubiquitination, targeting to the proteasome, proteolysis and functional silencing, acting as a sort of degradative knockdown. With this programmed protein degradation, toxic and disease-causing proteins could be depleted from cells with potentially effective low drug doses. The proof-of-principle validation of this hypothesis in many studies has made the TPD strategy become a new attractive paradigm for the development of therapies for the treatment of multiple unmet diseases. Indeed, since the initial protacs (Proteolysis targeting chimeras) were posited in the 2000s, the TPD field has expanded extraordinarily, developing innovative chemistry and exploiting multiple degradation approaches. In this article, we review the breakthroughs and recent novel concepts in this highly active discipline.
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20
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Development of a Bestatin-SAHA Hybrid with Dual Inhibitory Activity against APN and HDAC. Molecules 2020; 25:molecules25214991. [PMID: 33126591 PMCID: PMC7662900 DOI: 10.3390/molecules25214991] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 01/07/2023] Open
Abstract
With five histone deacetylase (HDAC) inhibitors approved for cancer treatment, proteolysis-targeting chimeras (PROTACs) for degradation of HDAC are emerging as an alternative strategy for HDAC-targeted therapeutic intervention. Herein, three bestatin-based hydroxamic acids (P1, P2 and P3) were designed, synthesized and biologically evaluated to see if they could work as HDAC degrader by recruiting cellular inhibitor of apoptosis protein 1 (cIAP1) E3 ubiquitin ligase. Among the three compounds, the bestatin-SAHA hybrid P1 exhibited comparable even more potent inhibitory activity against HDAC1, HDAC6 and HDAC8 relative to the approved HDAC inhibitor SAHA. It is worth noting that although P1 could not lead to intracellular HDAC degradation after 6 h of treatment, it could dramatically decrease the intracellular levels of HDAC1, HDAC6 and HDAC8 after 24 h of treatment. Intriguingly, the similar phenomenon was also observed in the HDAC inhibitor SAHA. Cotreatment with proteasome inhibitor bortezomib could not reverse the HDAC decreasing effects of P1 and SAHA, confirming that their HDAC decreasing effects were not due to protein degradation. Moreover, all three bestatin-based hydroxamic acids P1, P2 and P3 exhibited more potent aminopeptidase N (APN, CD13) inhibitory activities than the approved APN inhibitor bestatin, which translated to their superior anti-angiogenic activities. Taken together, a novel bestatin-SAHA hybrid was developed, which worked as a potent APN and HDAC dual inhibitor instead of a PROTAC.
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21
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Yamano K, Kikuchi R, Kojima W, Hayashida R, Koyano F, Kawawaki J, Shoda T, Demizu Y, Naito M, Tanaka K, Matsuda N. Critical role of mitochondrial ubiquitination and the OPTN-ATG9A axis in mitophagy. J Cell Biol 2020; 219:e201912144. [PMID: 32556086 PMCID: PMC7480101 DOI: 10.1083/jcb.201912144] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/02/2020] [Accepted: 05/14/2020] [Indexed: 01/24/2023] Open
Abstract
Damaged mitochondria are selectively eliminated in a process called mitophagy. Parkin and PINK1, proteins mutated in Parkinson's disease, amplify ubiquitin signals on damaged mitochondria with the subsequent activation of autophagic machinery. Autophagy adaptors are thought to link ubiquitinated mitochondria and autophagy through ATG8 protein binding. Here, we establish methods for inducing mitophagy by mitochondria-targeted ubiquitin chains and chemical-induced mitochondrial ubiquitination. Using these tools, we reveal that the ubiquitin signal is sufficient for mitophagy and that PINK1 and Parkin are unnecessary for autophagy activation per se. Furthermore, using phase-separated fluorescent foci, we show that the critical autophagy adaptor OPTN forms a complex with ATG9A vesicles. Disruption of OPTN-ATG9A interactions does not induce mitophagy. Therefore, in addition to binding ATG8 proteins, the critical autophagy adaptors also bind the autophagy core units that contribute to the formation of multivalent interactions in the de novo synthesis of autophagosomal membranes near ubiquitinated mitochondria.
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Affiliation(s)
- Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Reika Kikuchi
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Waka Kojima
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Ryota Hayashida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Fumika Koyano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Junko Kawawaki
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takuji Shoda
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa, Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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22
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Design and Applications of Bifunctional Small Molecules in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140534. [PMID: 32871274 DOI: 10.1016/j.bbapap.2020.140534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/17/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
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Tomoshige S, Ishikawa M. PROTACs and Other Chemical Protein Degradation Technologies for the Treatment of Neurodegenerative Disorders. Angew Chem Int Ed Engl 2020; 60:3346-3354. [PMID: 32410219 DOI: 10.1002/anie.202004746] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 02/03/2023]
Abstract
Neurodegenerative disorders (NDs) are a group of diseases that cause neural cell damage, leading to motility and/or cognitive dysfunctions. One of the causative agents is misfolded protein aggregates, which are considered as undruggable in terms of conventional tools, such as inhibitors and agonists/antagonists. Indeed, there is currently no FDA-approved drug for the causal treatment of NDs. However, emerging technologies for chemical protein degradation are opening up the possibility of selective elimination of target proteins through physiological protein degradation machineries, which do not depend on the functions of the target proteins. Here, we review recent efforts towards the treatment of NDs using chemical protein degradation technologies, and we briefly discuss the challenges and prospects.
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Affiliation(s)
- Shusuke Tomoshige
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Minoru Ishikawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
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24
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Lin X, Xiang H, Luo G. Targeting estrogen receptor α for degradation with PROTACs: A promising approach to overcome endocrine resistance. Eur J Med Chem 2020; 206:112689. [PMID: 32829249 DOI: 10.1016/j.ejmech.2020.112689] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
Abstract
Estrogen receptor alfa (ERα) is expressed in approximate 70% of breast cancer (BC) which is the most common malignancy in women worldwide. To date, the foremost intervention in the treatment of ER positive (ER+) BC is still the endocrine therapy. However, resistance to endocrine therapies remains a major hurdle in the long-term management of ER + BC. Although the mechanisms underlying endocrine resistance are complex, cumulative evidence revealed that ERα still plays a critical role in driving BC tumor cells to grow in resistance state. Fulvestrant, a selective estrogen receptor degrader (SERD), has moved to first line therapy for metastatic ER + BC, suggesting that removing ERα would be a useful strategy to overcome endocrine resistance. Proteolysis-Targeting Chimera (PROTAC) technology, an emerging paradigm for protein degradation, has the potential to eliminate both wild type and mutant ERα in breast cancer cells. Excitingly, ARV-471, an ERα-targeted PROTAC developed by Arvinas, has been in phase 1 clinical trials. In this review, we will summarize recent progress of ER-targeting PROTACs from publications and patents along with their therapeutic opportunities for the treatment of endocrine-resistant BC.
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Affiliation(s)
- Xin Lin
- State Key Laboratory of Natural Medicines, Jiangsu 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
| | - Hua Xiang
- State Key Laboratory of Natural Medicines, Jiangsu 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.
| | - Guoshun Luo
- State Key Laboratory of Natural Medicines, Jiangsu 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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25
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Chen Y, Jin J. The application of ubiquitin ligases in the PROTAC drug design. Acta Biochim Biophys Sin (Shanghai) 2020; 52:776-790. [PMID: 32506133 DOI: 10.1093/abbs/gmaa053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
Protein ubiquitylation plays important roles in many biological activities. Protein ubiquitylation is a unique process that is mainly controlled by ubiquitin ligases. The ubiquitin-proteasome system (UPS) is the main process to degrade short-lived and unwanted proteins in eukaryotes. Many components in the UPS are attractive drug targets. Recent studies indicated that ubiquitin ligases can be employed as tools in proteolysis-targeting chimeras (PROTACs) for drug discovery. In this review article, we will discuss the recent progress of the application of ubiquitin ligases in the PROTAC drug design. We will also discuss advantages and existing problems of PROTACs. Moreover, we will propose a few principles for selecting ubiquitin ligases in PROTAC applications.
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Affiliation(s)
- Yilin Chen
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
| | - Jianping Jin
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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26
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Ishikawa M, Hashimoto Y. Degradation of Disease Related Proteins in Living Cells by Small Molecules. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Selective Degradation of Target Proteins by Chimeric Small-Molecular Drugs, PROTACs and SNIPERs. Pharmaceuticals (Basel) 2020; 13:ph13040074. [PMID: 32326273 PMCID: PMC7243126 DOI: 10.3390/ph13040074] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 12/16/2022] Open
Abstract
New therapeutic modalities are needed to address the problem of pathological but undruggable proteins. One possible approach is the induction of protein degradation by chimeric drugs composed of a ubiquitin ligase (E3) ligand coupled to a ligand for the target protein. This article reviews chimeric drugs that decrease the level of specific proteins such as proteolysis targeting chimeric molecules (PROTACs) and specific and nongenetic inhibitor of apoptosis protein (IAP)-dependent protein erasers (SNIPERs), which target proteins for proteasome-mediated degradation. We cover strategies for increasing the degradation activity induced by small molecules, and their scope for application to undruggable proteins.
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Wang Y, Jiang X, Feng F, Liu W, Sun H. Degradation of proteins by PROTACs and other strategies. Acta Pharm Sin B 2020; 10:207-238. [PMID: 32082969 PMCID: PMC7016280 DOI: 10.1016/j.apsb.2019.08.001] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Blocking the biological functions of scaffold proteins and aggregated proteins is a challenging goal. PROTAC proteolysis-targeting chimaera (PROTAC) technology may be the solution, considering its ability to selectively degrade target proteins. Recent progress in the PROTAC strategy include identification of the structure of the first ternary eutectic complex, extra-terminal domain-4-PROTAC-Von-Hippel-Lindau (BRD4-PROTAC-VHL), and PROTAC ARV-110 has entered clinical trials for the treatment of prostate cancer in 2019. These discoveries strongly proved the value of the PROTAC strategy. In this perspective, we summarized recent meaningful research of PROTAC, including the types of degradation proteins, preliminary biological data in vitro and in vivo, and new E3 ubiquitin ligases. Importantly, the molecular design, optimization strategy and clinical application of candidate molecules are highlighted in detail. Future perspectives for development of advanced PROTAC in medical fields have also been discussed systematically.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xueyang Jiang
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Feng
- Jiangsu Food and Pharmaceutical Science College, Huaian 223003, China
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
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29
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Verma R, Mohl D, Deshaies RJ. Harnessing the Power of Proteolysis for Targeted Protein Inactivation. Mol Cell 2020; 77:446-460. [PMID: 32004468 DOI: 10.1016/j.molcel.2020.01.010] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/26/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022]
Abstract
Two decades into the twenty-first century, a confluence of breakthrough technologies wielded at the molecular level is presenting biologists with unique opportunities to unravel the complexities of the cellular world. CRISPR/Cas9 allows gene knock-outs, knock-ins, and single-base editing at chromosomal loci. RNA-based tools such as siRNA, antisense oligos, and morpholinos can be used to silence expression of specific genes. Meanwhile, protein knockdown tools that draw inspiration from natural regulatory mechanisms and facilitate elimination of native or degron-tagged proteins from cells are rapidly emerging. The acute and reversible reduction in protein levels enabled by these methods allows for precise determination of loss-of-function phenotypes free from secondary effects or compensatory adaptation that can confound nucleic-acid-based methods that involve slow depletion or permanent loss of a protein. In this Review, we summarize the ingenious ways biologists have exploited natural mechanisms for protein degradation to direct the elimination of specific proteins at will. This has led to advancements not only in basic research but also in the therapeutic space with the introduction of PROTACs into clinical trials for cancer patients.
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Affiliation(s)
- Rati Verma
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, CA 91320, USA.
| | - Dane Mohl
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
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30
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Itoh Y. Drug Discovery Researches on Modulators of Lysine-Modifying Enzymes Based on Strategic Chemistry Approaches. Chem Pharm Bull (Tokyo) 2020; 68:34-45. [DOI: 10.1248/cpb.c19-00741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine
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31
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Abstract
Proteolysis-targeting chimeras (PROTACs) have received much attention for their promising therapeutic intervention in recent years. These molecules, with the mechanism of simultaneous recruitment of target protein and an E3 ligase, can trigger the cellular ubiquitin–proteasome system to degrade the target proteins. This article systematically introduces the mechanism of small-molecule PROTACs, and summarized the research progress of small-molecule PROTACs. The prospect for further application and the problems to be solved are also discussed.
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32
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Konstantinidou M, Li J, Zhang B, Wang Z, Shaabani S, Ter Brake F, Essa K, Dömling A. PROTACs- a game-changing technology. Expert Opin Drug Discov 2019; 14:1255-1268. [PMID: 31538491 PMCID: PMC7008130 DOI: 10.1080/17460441.2019.1659242] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Introduction: Proteolysis – targeting chimeras (PROTACs) have emerged as a new modality with the potential to revolutionize drug discovery. PROTACs are heterobifunctional molecules comprising of a ligand targeting a protein of interest, a ligand targeting an E3 ligase and a connecting linker. The aim is instead of inhibiting the target to induce its proteasomal degradation. Areas covered: PROTACs, due to their bifunctional design, possess properties that differentiate them from classical inhibitors. A structural analysis, based on published crystal aspects, kinetic features and aspects of selectivity are discussed. Specific types such as homoPROTACs, PROTACs targeting Tau protein and the first PROTACs recently entering clinical trials are examined. Expert opinion: PROTACs have shown remarkable biological responses in challenging targets, including an unprecedented selectivity over protein family members and even efficacy starting from weak or unspecific binders. Moreover, PROTACs are standing out from classical pharmacology by inducing the degradation of the target protein and not merely its inhibition. However, there are also challenges in the field, such as the rational structure optimization, the evolution of computational tools, limited structural data and the greatly anticipated clinical data. Despite the remaining hurdles, PROTACs are expected to soon become a new therapeutic category of drugs.
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Affiliation(s)
| | - Jingyao Li
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Bidong Zhang
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Zefeng Wang
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Shabnam Shaabani
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Frans Ter Brake
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Khaled Essa
- Drug Design, University of Groningen , Groningen , The Netherlands
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33
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Nicke L, Horx P, Harms K, Geyer A. Directed C(sp 3)-H arylation of tryptophan: transformation of the directing group into an activated amide. Chem Sci 2019; 10:8634-8641. [PMID: 31803437 PMCID: PMC6844298 DOI: 10.1039/c9sc03440d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/03/2019] [Indexed: 12/18/2022] Open
Abstract
The aminoquinoline-directed C–H activation was used to synthezise unnatural tryptophans for solid phase peptide synthesis for the first time.
The 8-aminoquinoline (8AQ) directed C(sp3)–H functionalization was applied in the synthesis of β-arylated tryptophan derivatives. The laborious protecting group reorganization towards α-amino acids compatible for solid phase peptide synthesis (SPPS) was cut short by the transformation of the directing group into an activated amide, which was either used directly in peptide coupling or in the gram scale synthesis of storable Fmoc-protected amino acids for SPPS. In this work, directed C–H activation and nonplanar amide chemistry complement each other for the synthesis of hybrids between phenylalanine and tryptophan with restricted side chain mobility.
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Affiliation(s)
- Lennart Nicke
- Philipps-Universität Marburg , Fachbereich Chemie , Hans Meerwein Straße , 35032 Marburg , Germany .
| | - Philip Horx
- Philipps-Universität Marburg , Fachbereich Chemie , Hans Meerwein Straße , 35032 Marburg , Germany .
| | - Klaus Harms
- Philipps-Universität Marburg , Fachbereich Chemie , Hans Meerwein Straße , 35032 Marburg , Germany .
| | - Armin Geyer
- Philipps-Universität Marburg , Fachbereich Chemie , Hans Meerwein Straße , 35032 Marburg , Germany .
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34
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Röth S, Fulcher LJ, Sapkota GP. Advances in targeted degradation of endogenous proteins. Cell Mol Life Sci 2019; 76:2761-2777. [PMID: 31030225 PMCID: PMC6588652 DOI: 10.1007/s00018-019-03112-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/23/2019] [Accepted: 04/16/2019] [Indexed: 01/07/2023]
Abstract
Protein silencing is often employed as a means to aid investigations in protein function and is increasingly desired as a therapeutic approach. Several types of protein silencing methodologies have been developed, including targeting the encoding genes, transcripts, the process of translation or the protein directly. Despite these advances, most silencing systems suffer from limitations. Silencing protein expression through genetic ablation, for example by CRISPR/Cas9 genome editing, is irreversible, time consuming and not always feasible. Similarly, RNA interference approaches warrant prolonged treatments, can lead to incomplete protein depletion and are often associated with off-target effects. Targeted proteolysis has the potential to overcome some of these limitations. The field of targeted proteolysis has witnessed the emergence of many methodologies aimed at targeting specific proteins for degradation in a spatio-temporal manner. In this review, we provide an appraisal of the different targeted proteolytic systems and discuss their applications in understanding protein function, as well as their potential in therapeutics.
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Affiliation(s)
- Sascha Röth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Luke J Fulcher
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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35
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Shibata N, Ohoka N, Hattori T, Naito M. Development of a Potent Protein Degrader against Oncogenic BCR-ABL Protein. Chem Pharm Bull (Tokyo) 2019; 67:165-172. [PMID: 30827996 DOI: 10.1248/cpb.c18-00703] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chromosomal translocation occurs in some cancer cells, resulting in the expression of aberrant oncogenic fusion proteins that include BCR-ABL in chronic myelogenous leukemia (CML). Inhibitors of ABL tyrosine kinase, such as imatinib and dasatinib, exhibit remarkable therapeutic effects, although emergence of drug resistance hampers the therapy during long-term treatment. An alternative approach to treat CML is to downregulate expression of the BCR-ABL protein. Recently, we have devised a protein knockdown system by hybrid molecules named Specific and Nongenetic inhibitor of apoptosis protein [IAP]-dependent Protein Erasers (SNIPER). This system is designed to induce IAP-mediated ubiquitylation and proteasomal degradation of target proteins. In this review, we describe the development of SNIPER against BCR-ABL, and discuss the features and prospect for treatment of CML.
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Affiliation(s)
- Norihito Shibata
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
| | - Nobumichi Ohoka
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
| | - Takayuki Hattori
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
| | - Mikihiko Naito
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
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36
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Abstract
Proteolysis-targeting chimeras (PROTACs) are an emerging tool for therapeutic intervention by reducing or eliminating disease-causing proteins. PROTACs are bifunctional molecules that consist of a target protein ligand, a linker and an E3 ligase ligand, which mediate the polyubiquitination of the target protein, ultimately leading to the target protein degradation by the ubiquitin–proteasome pathway. We review some of the main PROTACs that have been reported recently and discuss their potential therapeutic benefits over classical enzyme inhibition. Future research is expected to focus on the delivery and bioavailability of PROTACs due to their high molecular weight (700–1000 Da).
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37
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Targeting the BIR Domains of Inhibitor of Apoptosis (IAP) Proteins in Cancer Treatment. Comput Struct Biotechnol J 2019; 17:142-150. [PMID: 30766663 PMCID: PMC6360406 DOI: 10.1016/j.csbj.2019.01.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 01/07/2023] Open
Abstract
Inhibitor of apoptosis (IAP) proteins are characterized by the presence of the conserved baculoviral IAP repeat (BIR) domain that is involved in protein-protein interactions. IAPs were initially thought to be mainly responsible for caspase inhibition, acting as negative regulators of apoptosis, but later works have shown that IAPs also control a plethora of other different cellular pathways. As X-linked IAP (XIAP), and other IAP, levels are often deregulated in cancer cells and have been shown to correlate with patients' prognosis, several approaches have been pursued to inhibit their activity in order to restore apoptosis. Many small molecules have been designed to target the BIR domains, the vast majority being inspired by the N-terminal tetrapeptide of Second Mitochondria-derived Activator of Caspases/Direct IAp Binding with Low pI (Smac/Diablo), which is the natural XIAP antagonist. These compounds are therefore usually referred to as Smac mimetics (SMs). Despite the fact that SMs were intended to specifically target XIAP, it has been shown that they also interact with cellular IAP-1 (cIAP1) and cIAP2, promoting their proteasome-dependent degradation. SMs have been tested in combination with several cytotoxic compounds and are now considered promising immune modulators which can be exploited in cancer therapy, especially in combination with immune checkpoint inhibitors. In this review, we give an overview of the structural hot-spots of BIRs, focusing on their fold and on the peculiar structural patches which characterize the diverse BIRs. These structures are exploited/exploitable for the development of specific and active IAP inhibitors.
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38
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Naito M, Ohoka N, Shibata N. SNIPERs-Hijacking IAP activity to induce protein degradation. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:35-42. [PMID: 31200857 DOI: 10.1016/j.ddtec.2018.12.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/11/2018] [Accepted: 12/18/2018] [Indexed: 12/28/2022]
Abstract
The induction of protein degradation by chimeric small molecules represented by proteolysis-targeting chimeras (PROTACs) is an emerging approach for novel drug development. We have developed a series of chimeric molecules termed specific and non-genetic inhibitor of apoptosis protein (IAP)-dependent protein erasers (SNIPERs) that recruit IAP ubiquitin ligases to effect targeted degradation. Unlike the chimeric molecules that recruit von Hippel-Lindau and cereblon ubiquitin ligases, SNIPERs induce simultaneous degradation of IAPs such as cIAP1 and XIAP along with the target proteins. Because cancer cells often overexpress IAPs-a mechanism involved in the resistance to cancer therapy-SNIPERs could be used to kill cancer cells efficiently.
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Affiliation(s)
- Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Japan.
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Japan
| | - Norihito Shibata
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Japan
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39
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Shibata N, Shimokawa K, Nagai K, Ohoka N, Hattori T, Miyamoto N, Ujikawa O, Sameshima T, Nara H, Cho N, Naito M. Pharmacological difference between degrader and inhibitor against oncogenic BCR-ABL kinase. Sci Rep 2018; 8:13549. [PMID: 30202081 PMCID: PMC6131351 DOI: 10.1038/s41598-018-31913-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023] Open
Abstract
Chronic myelogenous leukemia (CML) is characterized by the oncogenic fusion protein, BCR-ABL protein kinase, against which clinically useful inhibitors have been developed. An alternative approach to treat CML is to degrade the BCR-ABL protein. Recently, potent degraders against BCR-ABL have been developed by conjugating dasatinib to ligands for E3 ubiquitin ligases. Since the degraders contain the dasatinib moiety, they also inhibit BCR-ABL kinase activity, which complicates our understanding of the impact of BCR-ABL degradation by degraders in CML growth inhibition. To address this issue, we chose DAS-IAP, as a potent BCR-ABL degrader, and developed a structurally related inactive degrader, DAS-meIAP, which inhibits kinase activity but does not degrade the BCR-ABL protein. DAS-IAP showed slightly weaker activity than DAS-meIAP in inhibiting cell growth when CML cells were treated for 48 h. However, DAS-IAP showed sustained growth inhibition even when the drug was removed after short-term treatment, whereas CML cell growth rapidly resumed following removal of DAS-meIAP and dasatinib. Consistently, suppression of BCR-ABL levels and downstream kinase signaling were maintained after DAS-IAP removal, whereas kinase signaling rapidly recovered following removal of DAS-meIAP and dasatinib. These results indicate that BCR-ABL degrader shows more sustained inhibition of CML cell growth than ABL kinase inhibitor.
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Affiliation(s)
- Norihito Shibata
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kenichiro Shimokawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Katsunori Nagai
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan.,Axcelead Drug Discovery Partners, Inc., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-0012, Japan
| | - Nobumichi Ohoka
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takayuki Hattori
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Naoki Miyamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Osamu Ujikawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan.,Axcelead Drug Discovery Partners, Inc., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-0012, Japan
| | - Tomoya Sameshima
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroshi Nara
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan.,The Pharmaceutical Society of Japan, 2-12-15 Shibuya, Shibuya-ku, Tokyo, 150-0002, Japan
| | - Nobuo Cho
- Pharmaceutical Research Division, Takeda Pharmaceutical Co. Ltd., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan.,Drug Discovery Chemistry Platform Unit (Wako branch), RIKEN Center for Life Science Technologies, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mikihiko Naito
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.
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40
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Itoh Y. Chemical Protein Degradation Approach and its Application to Epigenetic Targets. CHEM REC 2018; 18:1681-1700. [PMID: 29893461 DOI: 10.1002/tcr.201800032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022]
Abstract
In addition to traditional drugs, such as enzyme inhibitors, receptor agonists/antagonists, and protein-protein interaction inhibitors as well as genetic technology, such as RNA interference and the CRISPR/Cas9 system, protein knockdown approaches using proteolysis-targeting chimeras (PROTACs) have attracted much attention. PROTACs, which induce selective degradation of their target protein via the ubiquitin-proteasome system, are useful for the down-regulation of various proteins, including disease-related proteins and epigenetic proteins. Recent reports have shown that chemical protein knockdown is possible not only in cells, but also in vivo and this approach is expected to be used as the therapeutic strategy for several diseases. Thus, this approach may be a significant technique to complement traditional drugs and genetic ablation and will be more widely used for drug discovery and chemical biology studies in the future. In this personal account, a history of chemical protein knockdown is introduced, and its features, recent progress in the epigenetics field, and future outlooks are discussed.
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Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
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41
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Targeted protein degradation and the enzymology of degraders. Curr Opin Chem Biol 2018; 44:47-55. [DOI: 10.1016/j.cbpa.2018.05.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
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42
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Coleman KG, Crews CM. Proteolysis-Targeting Chimeras: Harnessing the Ubiquitin-Proteasome System to Induce Degradation of Specific Target Proteins. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018. [DOI: 10.1146/annurev-cancerbio-030617-050430] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Craig M. Crews
- Department of Molecular, Cellular, and Developmental Biology; Department of Chemistry; and Department of Pharmacology, Yale University, New Haven, Connecticut 06511, USA
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43
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Itoh Y, Suzuki M. Design, synthesis, and biological evaluation of novel ubiquitin-activating enzyme inhibitors. Bioorg Med Chem Lett 2018; 28:2723-2727. [PMID: 29548576 DOI: 10.1016/j.bmcl.2018.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 01/22/2023]
Abstract
Ubiquitin-activating enzyme (E1), which catalyzes the activation of ubiquitin in the initial step of the ubiquitination cascade, is a potential therapeutic target in multiple myeloma and breast cancer treatment. However, only a few E1 inhibitors have been reported to date. Moreover, there has been little medicinal chemistry research on the three-dimensional structure of E1. Therefore, in the present study, we attempted to identify novel E1 inhibitors using structure-based drug design. Following the rational design, synthesis, and in vitro biological evaluation of several such compounds, we identified a reversible E1 inhibitor (4b). Compound 4b increased p53 levels in MCF-7 breast cancer cells and inhibited their growth. These findings suggest that reversible E1 inhibitors are potential anticancer agents.
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Affiliation(s)
- Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.
| | - Miki Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
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44
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Gu S, Cui D, Chen X, Xiong X, Zhao Y. PROTACs: An Emerging Targeting Technique for Protein Degradation in Drug Discovery. Bioessays 2018; 40:e1700247. [PMID: 29473971 DOI: 10.1002/bies.201700247] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 01/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Shanshan Gu
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
| | - Danrui Cui
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
| | - Xiaoyu Chen
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
| | - Xiufang Xiong
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
| | - Yongchao Zhao
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
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45
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Degradation of huntingtin mediated by a hybrid molecule composed of IAP antagonist linked to phenyldiazenyl benzothiazole derivative. Bioorg Med Chem Lett 2018; 28:707-710. [PMID: 29366651 DOI: 10.1016/j.bmcl.2018.01.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/06/2018] [Accepted: 01/11/2018] [Indexed: 01/28/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by aggregation of mutant huntingtin (mHtt), and removal of mHtt is expected as a potential therapeutic option. We previously reported protein knockdown of Htt by using hybrid small molecules (Htt degraders) consisting of BE04, a ligand of ubiquitin ligase (E3), linked to probes for protein aggregates. Here, in order to examine the effect of changing the ligand, we synthesized a similar Htt degrader utilizing MV1, an antagonist of the inhibitor of apoptosis protein (IAP) family (a subgroup of ubiquitin E3 ligases), which is expected to have a higher affinity and specificity for IAP, as compared with BE04. The MV1-based hybrid successfully induced interaction between Htt aggregates and IAP, and reduced mHtt levels in living cells. Its mode of action was confirmed to be the same as that of the BE04-based hybrid. However, although the affinity of MV1 for IAP is greater than that of BE04, the efficacy of Htt degradation by the MV1-based molecule was lower, suggesting that linker length between the ligand and probe might be an important determinant of efficacy.
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46
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Affiliation(s)
- George M. Burslem
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
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47
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Shibata N, Nagai K, Morita Y, Ujikawa O, Ohoka N, Hattori T, Koyama R, Sano O, Imaeda Y, Nara H, Cho N, Naito M. Development of Protein Degradation Inducers of Androgen Receptor by Conjugation of Androgen Receptor Ligands and Inhibitor of Apoptosis Protein Ligands. J Med Chem 2017; 61:543-575. [DOI: 10.1021/acs.jmedchem.7b00168] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Norihito Shibata
- Divisions
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Katsunori Nagai
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Yoko Morita
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Osamu Ujikawa
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Nobumichi Ohoka
- Divisions
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Takayuki Hattori
- Divisions
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Ryokichi Koyama
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Osamu Sano
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Yasuhiro Imaeda
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Hiroshi Nara
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Nobuo Cho
- Pharmaceutical
Research Division, Takeda Pharmaceutical Co. Ltd., 26-1, Muraoka-Higashi
2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Mikihiko Naito
- Divisions
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
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48
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Abstract
Traditional pharmaceutical drug discovery is almost exclusively focused on directly controlling protein activity to cure diseases. Modulators of protein activity, especially inhibitors, are developed and applied at high concentration to achieve maximal effects. Thereby, reduced bioavailability and off-target effects can hamper compound efficacy. Nucleic acid-based strategies that control protein function by affecting expression have emerged as an alternative. However, metabolic stability and broad bioavailability represent development hurdles that remain to be overcome for these approaches. More recently, utilizing the cell's own protein destruction machinery for selective degradation of essential drivers of human disorders has opened up a new and exciting area of drug discovery. Small-molecule-induced proteolysis of selected substrates offers the potential of reaching beyond the limitations of the current pharmaceutical paradigm to expand the druggable target space.
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Affiliation(s)
- Philipp M Cromm
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA.
| | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Pharmacology, Yale University, New Haven, CT 06511, USA.
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49
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Shibata N, Miyamoto N, Nagai K, Shimokawa K, Sameshima T, Ohoka N, Hattori T, Imaeda Y, Nara H, Cho N, Naito M. Development of protein degradation inducers of oncogenic BCR-ABL protein by conjugation of ABL kinase inhibitors and IAP ligands. Cancer Sci 2017; 108:1657-1666. [PMID: 28556300 PMCID: PMC5543464 DOI: 10.1111/cas.13284] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/16/2017] [Accepted: 05/19/2017] [Indexed: 12/28/2022] Open
Abstract
Chromosomal translocation occurs in some cancer cells, which results in the expression of aberrant oncogenic fusion proteins that include BCR‐ABL in chronic myelogenous leukemia (CML). Inhibitors of ABL tyrosine kinase, such as imatinib and dasatinib, exhibit remarkable therapeutic effects, although emergence of drug resistance hampers the therapy during long‐term treatment. An alternative approach to treat CML is to downregulate the BCR‐ABL protein. We have devised a protein knockdown system by hybrid molecules named Specific and Non‐genetic inhibitor of apoptosis protein [IAP]‐dependent Protein Erasers (SNIPER), which is designed to induce IAP‐mediated ubiquitylation and proteasomal degradation of target proteins, and a couple of SNIPER(ABL) against BCR‐ABL protein have been developed recently. In this study, we tested various combinations of ABL inhibitors and IAP ligands, and the linker was optimized for protein knockdown activity of SNIPER(ABL). The resulting SNIPER(ABL)‐39, in which dasatinib is conjugated to an IAP ligand LCL161 derivative by polyethylene glycol (PEG) × 3 linker, shows a potent activity to degrade the BCR‐ABL protein. Mechanistic analysis suggested that both cellular inhibitor of apoptosis protein 1 (cIAP1) and X‐linked inhibitor of apoptosis protein (XIAP) play a role in the degradation of BCR‐ABL protein. Consistent with the degradation of BCR‐ABL protein, the SNIPER(ABL)‐39 inhibited the phosphorylation of signal transducer and activator of transcription 5 (STAT5) and Crk like proto‐oncogene (CrkL), and suppressed the growth of BCR‐ABL‐positive CML cells. These results suggest that SNIPER(ABL)‐39 could be a candidate for a degradation‐based novel anti‐cancer drug against BCR‐ABL‐positive CML.
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Affiliation(s)
- Norihito Shibata
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, Japan
| | - Naoki Miyamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Katsunori Nagai
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | | | - Tomoya Sameshima
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, Japan
| | - Takayuki Hattori
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, Japan
| | - Yasuhiro Imaeda
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Hiroshi Nara
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Nobuo Cho
- Pharmaceutical Research Division, Takeda Pharmaceutical, Kanagawa, Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, Japan
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50
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Okitsu K, Hattori T, Misawa T, Shoda T, Kurihara M, Naito M, Demizu Y. Development of a Small Hybrid Molecule That Mediates Degradation of His-Tag Fused Proteins. J Med Chem 2017; 61:576-582. [DOI: 10.1021/acs.jmedchem.7b00413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Koyo Okitsu
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
- Graduate
School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takayuki Hattori
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Takashi Misawa
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Takuji Shoda
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Masaaki Kurihara
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Mikihiko Naito
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute of Health Sciences, 1-18-1,
Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| |
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