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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [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: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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2
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Cheng B, Pan W, Xiao Y, Ding Z, Zhou Y, Fei X, Liu J, Su Z, Peng X, Chen J. HDAC-targeting epigenetic modulators for cancer immunotherapy. Eur J Med Chem 2024; 265:116129. [PMID: 38211468 DOI: 10.1016/j.ejmech.2024.116129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
HDAC inhibitors, which can inhibit the activity of HDAC enzymes, have been extensively studied in tumor immunotherapy and have shown potential therapeutic effects in cancer immunotherapy. To date, numerous small molecule HDAC inhibitors have been identified, but many of them suffer from limited clinical efficacy and serious toxicity. Hence, HDAC inhibitor-based combination therapies, and other HDAC modulators (e.g. PROTAC degraders, dual-acting agents) have attracted great attention with significant advancements achieved in the past few years due to their superior efficacy compared to single-target HDAC inhibitors. In this review, we overviewed the recent progress on HDAC-based drug discovery with a focus on HDAC inhibitor-based drug combination therapy and other HDAC-targeting strategies (e.g. selective HDAC inhibitors, HDAC-based dual-target inhibitors, and PROTAC HDAC degraders) for cancer immunotherapy. In addition, we also summarized the reported co-crystal structures of HDAC inhibitors in complex with their target proteins and the binding interactions. Finally, the challenges and future directions for HDAC-based drug discovery in cancer immunotherapy are also discussed in detail.
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Affiliation(s)
- Binbin Cheng
- School of Medicine, Hubei Polytechnic University, Huangshi, 435003, PR China; Key Laboratory of Joint Diagnosis and Treatment of Chronic Liver Disease and Liver Cancer of Lishui, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui People's Hospital, Lishui, Zhejiang, 323000, PR China; Molecular Pharmacology Research Center, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Wei Pan
- CardioIogy Department, Geriatric Department, Foshan Women and Children Hospital, Foshan, Guangdong, 528000, PR China
| | - Yao Xiao
- Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan Wuchang Hospital, Wuchang, 430063, PR China
| | - Zongbao Ding
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, 519041, PR China
| | - Yingxing Zhou
- School of Medicine, Hubei Polytechnic University, Huangshi, 435003, PR China
| | - Xiaoting Fei
- School of Medicine, Hubei Polytechnic University, Huangshi, 435003, PR China
| | - Jin Liu
- School of Medicine, Hubei Polytechnic University, Huangshi, 435003, PR China
| | - Zhenhong Su
- School of Medicine, Hubei Polytechnic University, Huangshi, 435003, PR China.
| | - Xiaopeng Peng
- College of Pharmacy, Gannan Medical University, Ganzhou, 314000, PR China.
| | - Jianjun Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, PR China.
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3
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Peng X, Hu Z, Zeng L, Zhang M, Xu C, Lu B, Tao C, Chen W, Hou W, Cheng K, Bi H, Pan W, Chen J. Overview of epigenetic degraders based on PROTAC, molecular glue, and hydrophobic tagging technologies. Acta Pharm Sin B 2024; 14:533-578. [PMID: 38322348 PMCID: PMC10840439 DOI: 10.1016/j.apsb.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 02/08/2024] Open
Abstract
Epigenetic pathways play a critical role in the initiation, progression, and metastasis of cancer. Over the past few decades, significant progress has been made in the development of targeted epigenetic modulators (e.g., inhibitors). However, epigenetic inhibitors have faced multiple challenges, including limited clinical efficacy, toxicities, lack of subtype selectivity, and drug resistance. As a result, the design of new epigenetic modulators (e.g., degraders) such as PROTACs, molecular glue, and hydrophobic tagging (HyT) degraders has garnered significant attention from both academia and pharmaceutical industry, and numerous epigenetic degraders have been discovered in the past decade. In this review, we aim to provide an in-depth illustration of new degrading strategies (2017-2023) targeting epigenetic proteins for cancer therapy, focusing on the rational design, pharmacodynamics, pharmacokinetics, clinical status, and crystal structure information of these degraders. Importantly, we also provide deep insights into the potential challenges and corresponding remedies of this approach to drug design and development. Overall, we hope this review will offer a better mechanistic understanding and serve as a useful guide for the development of emerging epigenetic-targeting degraders.
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Affiliation(s)
- Xiaopeng Peng
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Zhihao Hu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Limei Zeng
- College of Basic Medicine, Gannan Medical University, Ganzhou 314000, China
| | - Meizhu Zhang
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Congcong Xu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Benyan Lu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Chengpeng Tao
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Weiming Chen
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Wen Hou
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huichang Bi
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wanyi Pan
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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4
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Dai XJ, Ji SK, Fu MJ, Liu GZ, Liu HM, Wang SP, Shen L, Wang N, Herdewijn P, Zheng YC, Wang SQ, Chen XB. Degraders in epigenetic therapy: PROTACs and beyond. Theranostics 2024; 14:1464-1499. [PMID: 38389844 PMCID: PMC10879860 DOI: 10.7150/thno.92526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/21/2024] [Indexed: 02/24/2024] Open
Abstract
Epigenetics refers to the reversible process through which changes in gene expression occur without changing the nucleotide sequence of DNA. The process is currently gaining prominence as a pivotal objective in the treatment of cancers and other ailments. Numerous drugs that target epigenetic mechanisms have obtained approval from the Food and Drug Administration (FDA) for the therapeutic intervention of diverse diseases; many have drawbacks, such as limited applicability, toxicity, and resistance. Since the discovery of the first proteolysis-targeting chimeras (PROTACs) in 2001, studies on targeted protein degradation (TPD)-encompassing PROTACs, molecular glue (MG), hydrophobic tagging (HyT), degradation TAG (dTAG), Trim-Away, a specific and non-genetic inhibitor of apoptosis protein (IAP)-dependent protein eraser (SNIPER), antibody-PROTACs (Ab-PROTACs), and other lysosome-based strategies-have achieved remarkable progress. In this review, we comprehensively highlight the small-molecule degraders beyond PROTACs that could achieve the degradation of epigenetic proteins (including bromodomain-containing protein-related targets, histone acetylation/deacetylation-related targets, histone methylation/demethylation related targets, and other epigenetic targets) via proteasomal or lysosomal pathways. The present difficulties and forthcoming prospects in this domain are also deliberated upon, which may be valuable for medicinal chemists when developing more potent, selective, and drug-like epigenetic drugs for clinical applications.
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Affiliation(s)
- Xing-Jie Dai
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shi-Kun Ji
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Meng-Jie Fu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Gao-Zhi Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shao-Peng Wang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liang Shen
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ning Wang
- The School of Chinese Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Piet Herdewijn
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000 Leuven, Belgium
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Sai-Qi Wang
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer & Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
| | - Xiao-Bing Chen
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer & Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
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5
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Xiong D, Zhang L, Sun ZJ. Targeting the epigenome to reinvigorate T cells for cancer immunotherapy. Mil Med Res 2023; 10:59. [PMID: 38044445 PMCID: PMC10694991 DOI: 10.1186/s40779-023-00496-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023] Open
Abstract
Cancer immunotherapy using immune-checkpoint inhibitors (ICIs) has revolutionized the field of cancer treatment; however, ICI efficacy is constrained by progressive dysfunction of CD8+ tumor-infiltrating lymphocytes (TILs), which is termed T cell exhaustion. This process is driven by diverse extrinsic factors across heterogeneous tumor immune microenvironment (TIME). Simultaneously, tumorigenesis entails robust reshaping of the epigenetic landscape, potentially instigating T cell exhaustion. In this review, we summarize the epigenetic mechanisms governing tumor microenvironmental cues leading to T cell exhaustion, and discuss therapeutic potential of targeting epigenetic regulators for immunotherapies. Finally, we outline conceptual and technical advances in developing potential treatment paradigms involving immunostimulatory agents and epigenetic therapies.
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Affiliation(s)
- Dian Xiong
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Lu Zhang
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China.
| | - Zhi-Jun Sun
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China.
- Department of Oral Maxillofacial-Head Neck Oncology, School and and Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
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6
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Pichlak M, Sobierajski T, Błażewska KM, Gendaszewska-Darmach E. Targeting reversible post-translational modifications with PROTACs: a focus on enzymes modifying protein lysine and arginine residues. J Enzyme Inhib Med Chem 2023; 38:2254012. [PMID: 37667522 PMCID: PMC10481767 DOI: 10.1080/14756366.2023.2254012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/17/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023] Open
Abstract
PROTACs represent an emerging field in medicinal chemistry, which has already led to the development of compounds that reached clinical studies. Posttranslational modifications contribute to the complexity of proteomes, with 2846 disease-associated sites. PROTAC field is very advanced in targeting kinases, while its use for enzymes mediating posttranslational modifications of the basic amino acid residues, started to be developed recently. Therefore, we bring together this less popular class of PROTACs, targeting lysine acetyltransferases/deacetylases, lysine and arginine methyltransferases, ADP-ribosyltransferases, E3 ligases, and ubiquitin-specific proteases. We put special emphasis on structural aspects of PROTAC elements to facilitate the lengthy experimental endeavours directed towards developing PROTACs. We will cover the period from the inception of the field, 2017, to April 2023.
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Affiliation(s)
- Marta Pichlak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland
| | - Tomasz Sobierajski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
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7
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Xiao Y, Hale S, Awasthee N, Meng C, Zhang X, Liu Y, Ding H, Huo Z, Lv D, Zhang W, He M, Zheng G, Liao D. HDAC3 and HDAC8 PROTAC dual degrader reveals roles of histone acetylation in gene regulation. Cell Chem Biol 2023; 30:1421-1435.e12. [PMID: 37572669 PMCID: PMC10802846 DOI: 10.1016/j.chembiol.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 05/19/2023] [Accepted: 07/22/2023] [Indexed: 08/14/2023]
Abstract
HDAC3 and HDAC8 have critical biological functions and represent highly sought-after therapeutic targets. Because histone deacetylases (HDACs) have a very conserved catalytic domain, developing isozyme-selective inhibitors remains challenging. HDAC3/8 also have deacetylase-independent activity, which cannot be blocked by conventional enzymatic inhibitors. Proteolysis-targeting chimeras (PROTACs) can selectively degrade a target enzyme, abolishing both enzymatic and scaffolding function. Here, we report a novel HDAC3/8 dual degrader YX968 that induces highly potent, rapid, and selective degradation of both HDAC3/8 without triggering pan-HDAC inhibitory effects. Unbiased quantitative proteomic experiments confirmed its high selectivity. HDAC3/8 degradation by YX968 does not induce histone hyperacetylation and broad transcriptomic perturbation. Thus, histone hyperacetylation may be a major factor for altering transcription. YX968 promotes apoptosis and kills cancer cells with a high potency in vitro. YX968 thus represents a new probe for dissecting the complex biological functions of HDAC3/8.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Seth Hale
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nikee Awasthee
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Chengcheng Meng
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Haocheng Ding
- Department of Biostatistics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
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Chen S, Zheng Y, Liang B, Yin Y, Yao J, Wang Q, Liu Y, Neamati N. The application of PROTAC in HDAC. Eur J Med Chem 2023; 260:115746. [PMID: 37607440 DOI: 10.1016/j.ejmech.2023.115746] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023]
Abstract
Inducing protein degradation by proteolysis targeting chimera (PROTAC) has provided great opportunities for scientific research and industrial applications. Histone deacetylase (HDAC)-PROTAC has been widely developed since the first report of its ability to induce the degradation of SIRT2 in 2017. To date, ten of the eighteen HDACs (HDACs 1-8, HDAC10, and SIRT2) have been successfully targeted and degraded by HDAC-PROTACs. HDAC-PROTACs surpass traditional HDAC inhibitors in many aspects, such as higher selectivity, more potent antiproliferative activity, and the ability to disrupt the enzyme-independent functions of a multifunctional protein and overcome drug resistance. Rationally designing HDAC-PROTACs is a main challenge in development because slight variations in chemical structure can lead to drastic effects on the efficiency and selectivity of the degradation. In the future, HDAC-PROTACs can potentially be involved in clinical research with the support of the increased amount of in vivo data, pharmacokinetic evaluation, and pharmacological studies.
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Affiliation(s)
- Shaoting Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yuxiang Zheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Benji Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yudong Yin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Jian Yao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Quande Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Yanghan Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, United States.
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9
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Jia Q, Zhang Y, Liu F, Dong W, Zhu L, Wang F, Jiang JH. Cell-Specific Degradation of Histone Deacetylase Using Warhead-Caged Proteolysis Targeting Chimeras. Anal Chem 2023; 95:16474-16480. [PMID: 37903331 DOI: 10.1021/acs.analchem.3c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) have shifted the paradigm for drug development via target protein degradation. However, PROTACs may exhibit systemic toxicity to normal cells due to indiscriminate degradation and the utility of inhibitors as a warhead for protein targeting. Here, we propose a new strategy for developing activatable PROTACs for cell-specific degradation of histone deacetylase (HDAC) with minimal side effects via caging of the warhead. Molecular docking reveals that the hydroxyl group of the HDAC inhibitor is crucial for targeting. An enzyme-activatable PROTAC is designed by caging the hydroxyl group with the substrate for NAD(P)H: quinone oxidoreductase 1 (NQO1) overexpressed in cancer cells. We demonstrate that the caged PROTAC can be converted to its active form in response to NQO1. The enzyme-activatable PROTAC allows the efficient and specific degradation of HDAC6 and exerts antiproliferative activity in NQO1-positive cells. The generalizability of the design is further demonstrated by engineering a H2O2-responsive PROTAC for specific degradation of HDAC6 in cells with elevated H2O2. The strategy of caging the ligand for target proteins would afford a new dimension for developing activatable PROTACs with high specificity and minimal side effects.
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Affiliation(s)
- Qi Jia
- State Key Laboratory of Chemo/Bio-Sensing and Chemometric, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 P. R. China
| | - Yue Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometric, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 P. R. China
| | - Feng Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometric, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 P. R. China
| | - Wanrong Dong
- State Key Laboratory of Chemo/Bio-Sensing and Chemometric, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 P. R. China
| | - Lei Zhu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometric, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 P. R. China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometric, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometric, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 P. R. China
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10
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Bockstiegel J, Wurnig SL, Engelhardt J, Enns J, Hansen FK, Weindl G. Pharmacological inhibition of HDAC6 suppresses NLRP3 inflammasome-mediated IL-1β release. Biochem Pharmacol 2023; 215:115693. [PMID: 37481141 DOI: 10.1016/j.bcp.2023.115693] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
The nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome is an important regulator of inflammation and immune responses. Histone deacetylase 6 (HDAC6) has been implicated in the assembly and activation of the NLRP3 inflammasome in mouse cells, however, the role in human immune cells remains poorly understood. Here, we investigated the effect of HDAC6 deficiency on NLRP3-mediated interleukin (IL)-1β release using proteolysis targeting chimeras (PROTAC) technology. We designed an HDAC6 PROTAC (A6) composed of the pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA) and the E3 ligase ligand thalidomide and a control PROTAC (non-degrading control, nc-A6) that binds to HDAC6 but lacks the ability to induce HDAC6 degradation. A6 but not nc-A6 reduced HDAC6 levels in THP-1 macrophages without affecting cell viability. PROTAC A6 and nc-A6 significantly reduced the release of IL-1β in a concentration-dependent manner, suggesting that HDAC6 deficiency is not necessary for inhibition of NLRP3 inflammasome-mediated IL-1β release. We found that inhibition of the catalytic domain with HDAC inhibitor SAHA or the specific HDAC6 inhibitor tubastatin A is sufficient to reduce IL-1β release indicating that the enzymatic activity of HDAC6 is critical for NLRP3 inflammasome function. Mechanistically, the observed effects of HDAC6 inhibition on NLRP3-mediated inflammatory responses could be attributed to its interaction with Toll-like receptor (TLR) signaling. Tubastatin A did not affect IL-1β levels when added after TLR-mediated priming. Collectively, our findings indicate that HDAC6 inhibitors show potent anti-inflammatory activity and suppress IL-1β release by human macrophages, independent of NLRP3 assembly and activation.
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Affiliation(s)
- Judith Bockstiegel
- Pharmaceutical Institute, Pharmacology and Toxicology, University of Bonn, Gerhard-Domagk-Str. 3, 53121 Bonn, Germany
| | - Silas L Wurnig
- Pharmaceutical Institute, Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Jonas Engelhardt
- Pharmaceutical Institute, Pharmacology and Toxicology, University of Bonn, Gerhard-Domagk-Str. 3, 53121 Bonn, Germany
| | - Jana Enns
- Pharmaceutical Institute, Pharmacology and Toxicology, University of Bonn, Gerhard-Domagk-Str. 3, 53121 Bonn, Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Günther Weindl
- Pharmaceutical Institute, Pharmacology and Toxicology, University of Bonn, Gerhard-Domagk-Str. 3, 53121 Bonn, Germany.
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11
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Patel U, Smalley JP, Hodgkinson JT. PROTAC chemical probes for histone deacetylase enzymes. RSC Chem Biol 2023; 4:623-634. [PMID: 37654508 PMCID: PMC10467623 DOI: 10.1039/d3cb00105a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/27/2023] [Indexed: 09/02/2023] Open
Abstract
Over the past three decades, we have witnessed the progression of small molecule chemical probes designed to inhibit the catalytic active site of histone deacetylase (HDAC) enzymes into FDA approved drugs. However, it is only in the past five years we have witnessed the emergence of proteolysis targeting chimeras (PROTACs) capable of promoting the proteasome mediated degradation of HDACs. This is a field still in its infancy, however given the current progress of PROTACs in clinical trials and the fact that FDA approved HDAC drugs are already in the clinic, there is significant potential in developing PROTACs to target HDACs as therapeutics. Beyond therapeutics, PROTACs also serve important applications as chemical probes to interrogate fundamental biology related to HDACs via their unique degradation mode of action. In this review, we highlight some of the key findings to date in the discovery of PROTACs targeting HDACs by HDAC class and HDAC isoenzyme, current gaps in PROTACs to target HDACs and future outlooks.
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Affiliation(s)
- Urvashi Patel
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester Leicester LE1 7RH UK
| | - Joshua P Smalley
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester Leicester LE1 7RH UK
| | - James T Hodgkinson
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester Leicester LE1 7RH UK
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12
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Li Y, Zeng ZW, Chen D, Gu ZC, Yan WL, Yue LY, Zhu RG, Zhao YL, Chen L, Zhao QJ, He B. Facilitated Drug Repurposing with Artemisinin-Derived PROTACs: Unveiling PCLAF as a Therapeutic Target. J Med Chem 2023; 66:11335-11350. [PMID: 37552639 DOI: 10.1021/acs.jmedchem.3c00824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Artemisinin, a prominent anti-malaria drug, is being investigated for its potential as a repurposed cancer treatment. However, its effectiveness in tumor cell lines remains limited, and its mechanism of action is unclear. To make more progress, the PROteolysis-TArgeting chimera (PROTAC) technique has been applied to design and synthesize novel artemisinin derivatives in this study. Among them, AD4, the most potent compound, exhibited an IC50 value of 50.6 nM in RS4;11 cells, over 12-fold better than that of its parent compound, SM1044. This was supported by prolonged survival of RS4;11-transplanted NOD/SCID mice. Meanwhile, AD4 effectively degraded PCLAF in RS4;11 cells and thus activated the p21/Rb axis to exert antitumor activity by directly targeting PCLAF. The discovery of AD4 highlights the great potential of using PROTACs to improve the efficacy of natural products, identify therapeutic targets, and facilitate drug repurposing. This opens a promising avenue for transforming other natural products into effective therapies.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Zi Wei Zeng
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Di Chen
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Zhi Cheng Gu
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Wan Li Yan
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Ling Yun Yue
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Ren Guang Zhu
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Yong Long Zhao
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Qing Jie Zhao
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal, Plants Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
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13
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Xie L, Xie L. Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning. PLoS Comput Biol 2023; 19:e1010974. [PMID: 37590332 PMCID: PMC10464998 DOI: 10.1371/journal.pcbi.1010974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/29/2023] [Accepted: 07/27/2023] [Indexed: 08/19/2023] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) are hetero-bifunctional molecules that induce the degradation of target proteins by recruiting an E3 ligase. PROTACs have the potential to inactivate disease-related genes that are considered undruggable by small molecules, making them a promising therapy for the treatment of incurable diseases. However, only a few hundred proteins have been experimentally tested for their amenability to PROTACs, and it remains unclear which other proteins in the entire human genome can be targeted by PROTACs. In this study, we have developed PrePROTAC, an interpretable machine learning model based on a transformer-based protein sequence descriptor and random forest classification. PrePROTAC predicts genome-wide targets that can be degraded by CRBN, one of the E3 ligases. In the benchmark studies, PrePROTAC achieved a ROC-AUC of 0.81, an average precision of 0.84, and over 40% sensitivity at a false positive rate of 0.05. When evaluated by an external test set which comprised proteins from different structural folds than those in the training set, the performance of PrePROTAC did not drop significantly, indicating its generalizability. Furthermore, we developed an embedding SHapley Additive exPlanations (eSHAP) method, which extends conventional SHAP analysis for original features to an embedding space through in silico mutagenesis. This method allowed us to identify key residues in the protein structure that play critical roles in PROTAC activity. The identified key residues were consistent with existing knowledge. Using PrePROTAC, we identified over 600 novel understudied proteins that are potentially degradable by CRBN and proposed PROTAC compounds for three novel drug targets associated with Alzheimer's disease.
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Affiliation(s)
- Li Xie
- Department of Computer Science, Hunter College, The City University of New York, New York City, New York, United States of America
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York City, New York, United States of America
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York City, New York, United States of America
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York City, New York, United States of America
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14
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Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that induce the ternary complex formation between a protein-of-interest (POI) and an E3 ligase, leading to targeted polyubiquitination and degradation of the POI. Particularly, PROTACs have the distinct advantage of targeting both canonical and noncanonical functions of epigenetic targets over traditional inhibitors, which typically target canonical functions only, resulting in greater therapeutic efficacy. In this review, we methodically analyze published PROTAC degraders of epigenetic writer, reader, and eraser proteins and their in vitro and in vivo effects. We highlight the mechanism of action of these degraders and their advantages in targeting both canonical and noncanonical functions of epigenetic targets in the context of cancer treatment. Furthermore, we present a future outlook for this exciting field. Overall, pharmacological degradation of epigenetic targets has emerged as an effective and attractive strategy to thwart cancer progression and growth.
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Affiliation(s)
- Md Kabir
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
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15
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Wang W, Liu Y, Xiong L, Sun D, Wang H, Song Z, Li Y, Li H, Chen L. Synthesis of Lathyrol PROTACs and Evaluation of Their Anti-Inflammatory Activities. JOURNAL OF NATURAL PRODUCTS 2023; 86:767-781. [PMID: 37002536 DOI: 10.1021/acs.jnatprod.2c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Lathyrol is a core scaffold structure of many lathyrane diterpenoids with potent anti-inflammatory activity isolated from Euphorbia lathyrism. It was chosen as a framework to design and synthesize a series of proteolysis targeting chimeras. A total of 15 derivatives were obtained. Compound 13 exhibited inhibitory activity on LPS-induced NO production in RAW264.7 cells (IC50 = 5.30 ± 1.23 μM) with low cytotoxicity. Furthermore, compound 13 significantly degraded v-maf musculoaponeurotic fibrosarcoma oncogene homologue F (MAFF) protein, a target of lathyrane diterpenoid, concentration- and time-dependently. The mechanism of action of 13 is related to activating the Keap1/Nrf2 pathway. It also inhibited the expression of NF-κB, blocked the nuclear translocation of NF-κB, and activated autophagy in LPS-induced RAW264.7 cells. Based on the results obtained, compound 13 might be a promising anti-inflammatory agent.
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Affiliation(s)
- Wang Wang
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
- Luoyang Key Laboratory of Organic Functional Molecules, College of Food and Drug, Luoyang Normal University, Luoyang 471934, China
| | - Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Liangliang Xiong
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Dejuan Sun
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hui Wang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhuorui Song
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yutong Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hua Li
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lixia Chen
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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16
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Wang C, Zhang Y, Deng J, Liang B, Xing D. Developments of PROTACs technology in immune-related diseases. Eur J Med Chem 2023; 249:115127. [PMID: 36724631 DOI: 10.1016/j.ejmech.2023.115127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023]
Abstract
Traditional chemotherapy and immunotherapy are primary disease-treatment strategies. However, they face numerous challenges, including limited therapeutic benefits, off-target effects, serious adverse effects, drug resistance, long half-life time, poor oral bioavailability, and drugging undruggable proteins. Proteolytic targeted chimeras (PROTACs) were suggested to solve these problems. PROTACs are heterogeneous functional molecules linked by a chemical linker and contain a binding ligand for the protein of interest and a recruiting ligand for the E3 ligand. The binding of a PROTAC to a target protein brings the E3 ligand enzyme into proximity, initiating polyubiquitination of the target protein, followed by protease-mediated degradation. To date, PROTACs against dozens of immunological targets have been successfully developed, many of which have been clinically validated drug targets, and several have entered clinical trials for immune-related diseases. This article reviews the role of PROTACs-mediated degradation of critical proteins in immune disorders and cancer immunotherapy. Chemical structures, cellular and in vivo activities, and pharmacodynamics of these PROTACs are summarized. Lastly, we also discuss the prospects and potential limitations that PROTACs face.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Junwen Deng
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China
| | - Bing Liang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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17
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Xie L, Xie L. Elucidation of Genome-wide Understudied Proteins targeted by PROTAC-induced degradation using Interpretable Machine Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529828. [PMID: 36865212 PMCID: PMC9980153 DOI: 10.1101/2023.02.23.529828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) are hetero-bifunctional molecules. They induce the degradation of a target protein by recruiting an E3 ligase to the target. The PROTAC can inactivate disease-related genes that are considered as understudied, thus has a great potential to be a new type of therapy for the treatment of incurable diseases. However, only hundreds of proteins have been experimentally tested if they are amenable to the PROTACs. It remains elusive what other proteins can be targeted by the PROTAC in the entire human genome. For the first time, we have developed an interpretable machine learning model PrePROTAC, which is based on a transformer-based protein sequence descriptor and random forest classification to predict genome-wide PROTAC-induced targets degradable by CRBN, one of the E3 ligases. In the benchmark studies, PrePROTAC achieved ROC-AUC of 0.81, PR-AUC of 0.84, and over 40% sensitivity at a false positive rate of 0.05, respectively. Furthermore, we developed an embedding SHapley Additive exPlanations (eSHAP) method to identify positions in the protein structure, which play key roles in the PROTAC activity. The key residues identified were consistent with our existing knowledge. We applied PrePROTAC to identify more than 600 novel understudied proteins that are potentially degradable by CRBN, and proposed PROTAC compounds for three novel drug targets associated with Alzheimer's disease. Author Summary Many human diseases remain incurable because disease-causing genes cannot by selectively and effectively targeted by small molecules. Proteolysis-targeting chimera (PROTAC), an organic compound that binds to both a target and a degradation-mediating E3 ligase, has emerged as a promising approach to selectively target disease-driving genes that are not druggable by small molecules. Nevertheless, not all of proteins can be accommodated by E3 ligases, and be effectively degraded. Knowledge on the degradability of a protein will be crucial for the design of PROTACs. However, only hundreds of proteins have been experimentally tested if they are amenable to the PROTACs. It remains elusive what other proteins can be targeted by the PROTAC in the entire human genome. In this paper, we propose an intepretable machine learning model PrePROTAC that takes advantage of powerful protein language modeling. PrePROTAC achieves high accuracy when evaluated by an external dataset which comes from different gene families from the proteins in the training data, suggesting the generalizability of PrePROTAC. We apply PrePROTAC to the human genome, and identify more than 600 understudied proteins that are potentially responsive to the PROTAC. Furthermore, we design three PROTAC compounds for novel drug targets associated with Alzheimer's disease.
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Affiliation(s)
- Li Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, 10065, USA
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, 10065, USA
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, USA
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10021, USA
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18
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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19
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Targeting histone deacetylases for cancer therapy: Trends and challenges. Acta Pharm Sin B 2023. [DOI: 10.1016/j.apsb.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
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20
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Huang J, Zhang J, Xu W, Wu Q, Zeng R, Liu Z, Tao W, Chen Q, Wang Y, Zhu WG. Structure-Based Discovery of Selective Histone Deacetylase 8 Degraders with Potent Anticancer Activity. J Med Chem 2023; 66:1186-1209. [PMID: 36516047 DOI: 10.1021/acs.jmedchem.2c00739] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inducing protein degradation by proteolysis targeting chimeras has gained tremendous momentum as a promising novel therapeutic strategy. Here, we report the design, synthesis, and biological characterization of highly potent proteolysis targeting chimeric small molecules targeting the epigenetic regulator histone deacetylase 8 (HDAC8). We developed potent and effective HDAC8 degraders, as exemplified by SZUH280 (16e), which effectively induced HDAC8 protein degradation and inhibited cancer cell growth even at low micromolar concentrations. Our preliminary mechanistic studies revealed that SZUH280 hampers DNA damage repair in cancer cells, promoting cellular radiosensitization. In mice, a single SZUH280 dose induced rapid and prolonged HDAC8 protein degradation in xenograft tumor tissues. Moreover, SZUH280 alone or in combination with irradiation resulted in long-lasting tumor regression in an A549 tumor mouse model. Our findings qualify a new chemical tool for HDAC8 knockdown and may lead to the development of a new class of cancer therapeutics.
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Affiliation(s)
- Jinbo Huang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, and International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China.,Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China.,Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Jun Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, and International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China.,Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China.,Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Wenchao Xu
- Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Qiong Wu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, and International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China.,Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China.,Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Rongsheng Zeng
- Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen 518055, China
| | - Zhichao Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, and International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China.,Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China.,Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Wenhui Tao
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, and International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China.,Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China.,Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Qian Chen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, and International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China.,Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China.,Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
| | - Yongqing Wang
- Division of Rheumatology and Immunology, University of Toledo Medical Center, 3120 Glendale Avenue, Toledo 43614, Ohio, United States
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, and International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518055, China.,Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen 518055, China.,Shenzhen Bay Laboratory, Shenzhen University School of Medicine, Shenzhen 518055, China.,Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen 518055, China.,Health Science Centre School of Basic Medical Sciences, Shenzhen University, Shenzhen 518055, China
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21
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Liu X, Wang A, Shi Y, Dai M, Liu M, Cai HB. PROTACs in Epigenetic Cancer Therapy: Current Status and Future Opportunities. Molecules 2023; 28:molecules28031217. [PMID: 36770884 PMCID: PMC9919707 DOI: 10.3390/molecules28031217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023] Open
Abstract
The epigenetic regulation of gene functions has been proven to be strongly associated with the development and progression of cancer. Reprogramming the cancer epigenome landscape is one of the most promising target therapies in both treatments and in reversing drug resistance. Proteolytic targeted chimeras (PROTACs) are an emerging therapeutic modality for selective degradation via the native ubiquitin-proteasome system. Rapid advances in PROTACs have facilitated the exploration of targeting epigenetic proteins, a lot of PROTAC degraders have already been designed in the field of epigenetic cancer therapy, and PROTACs targeting epigenetic proteins can better exploit target druggability and improve the mechanistic understanding of the epigenetic regulation of cancer. Thus, this review focuses on the progress made in the development of PROTAC degraders and PROTAC drugs targeting epigenetics in cancer and discusses challenges and future opportunities for the field.
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Affiliation(s)
- Xuelian Liu
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Anjin Wang
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Yuying Shi
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
| | - Mengyuan Dai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
- Correspondence: (M.D.); (H.-B.C.)
| | - Miao Liu
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hong-Bing Cai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Cancer Clinical Study Center, Wuhan 430071, China
- Correspondence: (M.D.); (H.-B.C.)
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22
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Zhao HY, Xin M, Zhang SQ. Progress of small molecules for targeted protein degradation: PROTACs and other technologies. Drug Dev Res 2023; 84:337-394. [PMID: 36606428 DOI: 10.1002/ddr.22026] [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: 09/11/2022] [Revised: 12/01/2022] [Accepted: 12/17/2022] [Indexed: 01/07/2023]
Abstract
Recent years have witnessed the rapid development of targeted protein degradation (TPD), especially proteolysis targeting chimeras. These degraders have manifested many advantages over small molecule inhibitors. To date, a huge number of degraders have been excavated against over 70 disease-related targets. In particular, degraders against estrogen receptor and androgen receptor have crowded into phase II clinical trial. TPD technologies largely expand the scope of druggable targets, and provide powerful tools for addressing intractable problems that can not be tackled by traditional small molecule inhibitors. In this review, we mainly focus on the structures and biological activities of small molecule degraders as well as the elucidation of mechanisms of emerging TPD technologies. We also propose the challenges that exist in the TPD field at present.
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Affiliation(s)
- Hong-Yi Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - San-Qi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
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23
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Sinatra L, Yang J, Schliehe-Diecks J, Dienstbier N, Vogt M, Gebing P, Bachmann LM, Sönnichsen M, Lenz T, Stühler K, Schöler A, Borkhardt A, Bhatia S, Hansen FK. Solid-Phase Synthesis of Cereblon-Recruiting Selective Histone Deacetylase 6 Degraders (HDAC6 PROTACs) with Antileukemic Activity. J Med Chem 2022; 65:16860-16878. [PMID: 36473103 DOI: 10.1021/acs.jmedchem.2c01659] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this work, we utilized the proteolysis targeting chimera (PROTAC) technology to achieve the chemical knock-down of histone deacetylase 6 (HDAC6). Two series of cereblon-recruiting PROTACs were synthesized via a solid-phase parallel synthesis approach, which allowed the rapid preparation of two HDAC6 degrader mini libraries. The PROTACs were either based on an unselective vorinostat-like HDAC ligand or derived from a selective HDAC6 inhibitor. Notably, both PROTAC series demonstrated selective degradation of HDAC6 in leukemia cell lines. The best degraders from each series (denoted A6 and B4) were capable of degrading HDAC6 via ternary complex formation and the ubiquitin-proteasome pathway, with DC50 values of 3.5 and 19.4 nM, respectively. PROTAC A6 demonstrated promising antiproliferative activity via inducing apoptosis in myeloid leukemia cell lines. These findings highlight the potential of this series of degraders as effective pharmacological tools for the targeted degradation of HDAC6.
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Affiliation(s)
- Laura Sinatra
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Jing Yang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany.,Department of Medicine, Yangzhou Polytechnic College, West Wenchang Road 458, Yangzhou, 225009, P.R. China
| | - Julian Schliehe-Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Niklas Dienstbier
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Melina Vogt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Philip Gebing
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Luisa M Bachmann
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Melf Sönnichsen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Thomas Lenz
- Molecular Proteomics Laboratory, Biological Medical Research Center, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Institute for Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Hein-rich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Andrea Schöler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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24
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Li D, Yu D, Li Y, Yang R. A bibliometric analysis of PROTAC from 2001 to 2021. Eur J Med Chem 2022; 244:114838. [DOI: 10.1016/j.ejmech.2022.114838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/30/2022]
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25
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Li Y, Lin S, Gu Z, Chen L, He B. Zinc-dependent deacetylases (HDACs) as potential targets for treating Alzheimer’s disease. Bioorg Med Chem Lett 2022; 76:129015. [DOI: 10.1016/j.bmcl.2022.129015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 09/29/2022] [Indexed: 11/30/2022]
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26
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Liu J, Peng Y, Inuzuka H, Wei W. Targeting micro-environmental pathways by PROTACs as a therapeutic strategy. Semin Cancer Biol 2022; 86:269-279. [PMID: 35798235 PMCID: PMC11000491 DOI: 10.1016/j.semcancer.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/01/2022] [Indexed: 10/31/2022]
Abstract
Tumor microenvironment (TME) composes of multiple cell types and non-cellular components, which supports the proliferation, metastasis and immune surveillance evasion of tumor cells, as well as accounts for the resistance to therapies. Therefore, therapeutic strategies using small molecule inhibitors (SMIs) and antibodies to block potential targets in TME are practical for cancer treatment. Targeted protein degradation using PROteolysis-TArgeting Chimera (PROTAC) technic has several advantages over traditional SMIs and antibodies, including overcoming drug resistance. Thus many PROTACs are currently under development for cancer treatment. In this review, we summarize the recent progress of PROTAC development that target TME pathways and propose the potential direction of future PROTAC technique to advance as novel cancer treatment options.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | - Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States.
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27
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Macabuag N, Esmieu W, Breccia P, Jarvis R, Blackaby W, Lazari O, Urbonas L, Eznarriaga M, Williams R, Strijbosch A, Van de Bospoort R, Matthews K, Clissold C, Ladduwahetty T, Vater H, Heaphy P, Stafford DG, Wang HJ, Mangette JE, McAllister G, Beaumont V, Vogt TF, Wilkinson HA, Doherty EM, Dominguez C. Developing HDAC4-Selective Protein Degraders To Investigate the Role of HDAC4 in Huntington's Disease Pathology. J Med Chem 2022; 65:12445-12459. [PMID: 36098485 PMCID: PMC9512014 DOI: 10.1021/acs.jmedchem.2c01149] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/30/2022]
Abstract
Huntington's disease (HD) is a lethal autosomal dominant neurodegenerative disorder resulting from a CAG repeat expansion in the huntingtin (HTT) gene. The product of translation of this gene is a highly aggregation-prone protein containing a polyglutamine tract >35 repeats (mHTT) that has been shown to colocalize with histone deacetylase 4 (HDAC4) in cytoplasmic inclusions in HD mouse models. Genetic reduction of HDAC4 in an HD mouse model resulted in delayed aggregation of mHTT, along with amelioration of neurological phenotypes and extended lifespan. To further investigate the role of HDAC4 in cellular models of HD, we have developed bifunctional degraders of the protein and report the first potent and selective degraders of HDAC4 that show an effect in multiple cell lines, including HD mouse model-derived cortical neurons. These degraders act via the ubiquitin-proteasomal pathway and selectively degrade HDAC4 over other class IIa HDAC isoforms (HDAC5, HDAC7, and HDAC9).
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Affiliation(s)
- Natsuko Macabuag
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - William Esmieu
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Perla Breccia
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Rebecca Jarvis
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Wesley Blackaby
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Ovadia Lazari
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Liudvikas Urbonas
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Maria Eznarriaga
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Rachel Williams
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | | | | | - Kim Matthews
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Cole Clissold
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Tammy Ladduwahetty
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Huw Vater
- Discovery
from Charles River, Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - Patrick Heaphy
- Curia, The Conventus Building, 1001 Main
Street, Buffalo, New York 14203, United States
| | - Douglas G. Stafford
- Curia, The Conventus Building, 1001 Main
Street, Buffalo, New York 14203, United States
| | - Hong-Jun Wang
- Curia, The Conventus Building, 1001 Main
Street, Buffalo, New York 14203, United States
| | - John E. Mangette
- Curia, The Conventus Building, 1001 Main
Street, Buffalo, New York 14203, United States
| | - George McAllister
- CHDI
Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Vahri Beaumont
- CHDI
Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Thomas F. Vogt
- CHDI
Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Hilary A. Wilkinson
- CHDI
Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Elizabeth M. Doherty
- CHDI
Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI
Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
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28
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Liu Z, Zhang Y, Xiang Y, Kang X. Small-Molecule PROTACs for Cancer Immunotherapy. Molecules 2022; 27:molecules27175439. [PMID: 36080223 PMCID: PMC9458232 DOI: 10.3390/molecules27175439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
Unsatisfactory physicochemical properties of macromolecular drugs seriously hinder their application in tumor immunotherapy. However, these problems can be effectively solved by small-molecule compounds. In the promising field of small-molecule drug development, proteolysis targeting chimera (PROTAC) offers a novel mode of action in the interactions between small molecules and therapeutic targets (mainly proteins). This revolutionary technology has shown considerable impact on several proteins related to tumor survival but is rarely exploited in proteins associated with immuno-oncology up until now. This review attempts to comprehensively summarize the well-studied and less-developed immunological targets available for PROTAC technology, as well as some targets to be explored, aiming to provide more options and opportunities for the development of small-molecule-based tumor immunotherapy. In addition, some novel directions that can magnify and broaden the protein degradation efficiency are mentioned to improve PROTAC design in the future.
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Affiliation(s)
| | | | | | - Xin Kang
- Correspondence: ; Tel.: +86-19138939183
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29
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Bakulina O, Sapegin A, Bunev AS, Krasavin M. Synthetic approaches to constructing proteolysis targeting chimeras (PROTACs). MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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30
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Sun Z, Deng B, Yang Z, Mai R, Huang J, Ma Z, Chen T, Chen J. Discovery of pomalidomide-based PROTACs for selective degradation of histone deacetylase 8. Eur J Med Chem 2022; 239:114544. [PMID: 35759908 DOI: 10.1016/j.ejmech.2022.114544] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/03/2022]
Abstract
Overexpression of histone deacetylase 8 (HDAC8) is associated with various diseases such as cancer. Thus, compounds that can modulate HDAC8 levels have therapeutic potential for these diseases. Based on the proteolysis targeting chimera (PROTAC) strategy, we designed and synthesized a series of HDAC8 degraders by tethering an HDAC6/8 dual inhibitor with pomalidomide (a cereblon ligand). Among them, compound ZQ-23 exhibited significant and selective degradation of HDAC8 with DC50 of 147 nM and Dmax of 93%, and exhibited no effects on HDAC1 and HDAC3. Interestingly, we found that the degradation of target protein started at ∼2 h after treatment with ZQ-23 and the maximal degradation effect was achieved at 10 h. The HDAC8 level was partially recovered within 24 h. In addition, ZQ-23 had no degrading effects on HDAC1 and HDAC3 at all concentrations, but could dose-dependently increase the levels of acetylated SMC-3 (HDAC8 substrate). Mechanism study demonstrated that ZQ-23 degraded HDAC8 through the ubiquitin-protease pathway, rather than lysosome system. Collectively, these results suggest that ZQ-23 represents a novel PROTAC-based HDAC8 degrader worthy of further investigation.
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Affiliation(s)
- Zhiqiang Sun
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
| | - Bulian Deng
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
| | - Zichao Yang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
| | - Ruiyao Mai
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
| | - Junli Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
| | - Zeli Ma
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ting Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jianjun Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China; Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China.
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31
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He M, Cao C, Ni Z, Liu Y, Song P, Hao S, He Y, Sun X, Rao Y. PROTACs: great opportunities for academia and industry (an update from 2020 to 2021). Signal Transduct Target Ther 2022; 7:181. [PMID: 35680848 PMCID: PMC9178337 DOI: 10.1038/s41392-022-00999-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
PROteolysis TArgeting Chimeras (PROTACs) technology is a new protein-degradation strategy that has emerged in recent years. It uses bifunctional small molecules to induce the ubiquitination and degradation of target proteins through the ubiquitin–proteasome system. PROTACs can not only be used as potential clinical treatments for diseases such as cancer, immune disorders, viral infections, and neurodegenerative diseases, but also provide unique chemical knockdown tools for biological research in a catalytic, reversible, and rapid manner. In 2019, our group published a review article “PROTACs: great opportunities for academia and industry” in the journal, summarizing the representative compounds of PROTACs reported before the end of 2019. In the past 2 years, the entire field of protein degradation has experienced rapid development, including not only a large increase in the number of research papers on protein-degradation technology but also a rapid increase in the number of small-molecule degraders that have entered the clinical and will enter the clinical stage. In addition to PROTAC and molecular glue technology, other new degradation technologies are also developing rapidly. In this article, we mainly summarize and review the representative PROTACs of related targets published in 2020–2021 to present to researchers the exciting developments in the field of protein degradation. The problems that need to be solved in this field will also be briefly introduced.
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Affiliation(s)
- Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China.,Tsinghua-Peking Center for Life Sciences, 100084, Beijing, P. R. China
| | - Zhihao Ni
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yongbo Liu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Peilu Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Shuang Hao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China. .,School of Pharmaceutical Sciences, Zhengzhou University, 450001, Zhengzhou, China.
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32
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Wu Y, Zhang J, Zhu X, Zhang Y. Developing PROteolysis TArgeting Chimeras (PROTACs) for hematologic malignancies. Cancer Lett 2022; 544:215808. [DOI: 10.1016/j.canlet.2022.215808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/01/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022]
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33
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Histone Deacetylases as Epigenetic Targets for Treating Parkinson’s Disease. Brain Sci 2022; 12:brainsci12050672. [PMID: 35625059 PMCID: PMC9140162 DOI: 10.3390/brainsci12050672] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
Parkinson’s disease (PD) is a chronic progressive neurodegenerative disease that is increasingly becoming a global threat to the health and life of the elderly worldwide. Although there are some drugs clinically available for treating PD, these treatments can only alleviate the symptoms of PD patients but cannot completely cure the disease. Therefore, exploring other potential mechanisms to develop more effective treatments that can modify the course of PD is still highly desirable. Over the last two decades, histone deacetylases, as an important group of epigenetic targets, have attracted much attention in drug discovery. This review focused on the current knowledge about histone deacetylases involved in PD pathophysiology and their inhibitors used in PD studies. Further perspectives related to small molecules that can inhibit or degrade histone deacetylases to treat PD were also discussed.
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34
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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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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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Ni B, Hou J. Promising therapeutic approaches for relapsed/refractory multiple myeloma. Hematology 2022; 27:343-352. [PMID: 35287555 DOI: 10.1080/16078454.2022.2045724] [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: 11/04/2022] Open
Abstract
OBJECTIVE Treatment strategies for relapsed/refractory MM are particularly complex. In particular, patients who are refractory to the three classes of therapies have limited therapeutic options and poor survival. Fortunately, promising treatments are emerging, but their incorporation into existing treatments still needs to be defined. We will describe the latest trends and emerging developments in the field of therapies for RRMM by analyzing the most recent clinical data and new technologies in drug development. METHODS Pubmed, Embase and Cochrane Library were searched to select eligible studies, the clinical data of new promising treatments were reviewed. The key results of the most recent clinical trial were summarized in Table. RESULTS A total of 13 studies were included in the final analysis involving anti-BCMA CAR T-cell therapy, Combined CAR T-cell therapy, antibody-drug conjugates, bispecific Ab therapy and CELMoDs. The key efficacy and side effects of treatments were summarized. CONCLUSIONS There is great promise for a set of next-generation of rescue therapies, including CAR T-cell therapy, bispecific antibodies, antibody-drug conjugates, and novel PROteolysis Targeting Chimeras. Emerging new treatments for MM provide more choices for relapsed/refractory multiple myeloma (RRMM). The optimal therapy for each patient should be based on disease-related factors, such as previous therapies, duration of response to prior drugs, clinical and biochemical features of relapse, and the relationship of patient comorbidities with known AE profiles of the different therapies.
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Affiliation(s)
- Beiwen Ni
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jian Hou
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Yang G, Zhong H, Xia X, Qi Z, Wang C, Li S. Potential application of proteolysis targeting chimera (PROTAC) modification technology in natural products for their targeted protein degradation. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2021.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Li D, Nie J, Han Y, Ni L. Epigenetic Mechanism and Therapeutic Implications of Atrial Fibrillation. Front Cardiovasc Med 2022; 8:763824. [PMID: 35127848 PMCID: PMC8815458 DOI: 10.3389/fcvm.2021.763824] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 12/28/2022] Open
Abstract
Atrial fibrillation (AF) is the most common arrhythmia attacking 1. 5–2.0% of general population worldwide. It has a significant impact on morbidity and mortality globally and its prevalence increases exponentially with age. Therapies like catheter ablation or conventional antiarrhythmic drugs have not provided effective solution to the recurrence for AF over the past decades. Over 100 genetic loci have been discovered to be associated with AF by Genome-wide association studies (GWAS) but none has led to a therapy. Recently potential involvement of epigenetics (DNA methylation, histone modification, and non-coding RNAs) in the initiation and maintenance of AF has partly emerged as proof-of-concept in the mechanism and management of AF. Here we reviewed the epigenetic features involved in AF pathophysiology and provided an update of their implications in AF therapy.
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Daśko M, de Pascual-Teresa B, Ortín I, Ramos A. HDAC Inhibitors: Innovative Strategies for Their Design and Applications. Molecules 2022; 27:molecules27030715. [PMID: 35163980 PMCID: PMC8837987 DOI: 10.3390/molecules27030715] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022] Open
Abstract
Histone deacetylases (HDACs) are a large family of epigenetic metalloenzymes that are involved in gene transcription and regulation, cell proliferation, differentiation, migration, and death, as well as angiogenesis. Particularly, disorders of the HDACs expression are linked to the development of many types of cancer and neurodegenerative diseases, making them interesting molecular targets for the design of new efficient drugs and imaging agents that facilitate an early diagnosis of these diseases. Thus, their selective inhibition or degradation are the basis for new therapies. This is supported by the fact that many HDAC inhibitors (HDACis) are currently under clinical research for cancer therapy, and the Food and Drug Administration (FDA) has already approved some of them. In this review, we will focus on the recent advances and latest discoveries of innovative strategies in the development and applications of compounds that demonstrate inhibitory or degradation activity against HDACs, such as PROteolysis-TArgeting Chimeras (PROTACs), tumor-targeted HDACis (e.g., folate conjugates and nanoparticles), and imaging probes (positron emission tomography (PET) and fluorescent ligands).
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Affiliation(s)
- Mateusz Daśko
- Department of Inorganic Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland;
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28925 Alcorcón, Spain;
| | - Beatriz de Pascual-Teresa
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28925 Alcorcón, Spain;
| | - Irene Ortín
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28925 Alcorcón, Spain;
- Correspondence: (I.O.); (A.R.)
| | - Ana Ramos
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28925 Alcorcón, Spain;
- Correspondence: (I.O.); (A.R.)
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Ruzic D, Djoković N, Srdić-Rajić T, Echeverria C, Nikolic K, Santibanez JF. Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention. Pharmaceutics 2022; 14:pharmaceutics14010209. [PMID: 35057104 PMCID: PMC8778744 DOI: 10.3390/pharmaceutics14010209] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
The dysregulation of gene expression is a critical event involved in all steps of tumorigenesis. Aberrant histone and non-histone acetylation modifications of gene expression due to the abnormal activation of histone deacetylases (HDAC) have been reported in hematologic and solid types of cancer. In this sense, the cancer-associated epigenetic alterations are promising targets for anticancer therapy and chemoprevention. HDAC inhibitors (HDACi) induce histone hyperacetylation within target proteins, altering cell cycle and proliferation, cell differentiation, and the regulation of cell death programs. Over the last three decades, an increasing number of synthetic and naturally derived compounds, such as dietary-derived products, have been demonstrated to act as HDACi and have provided biological and molecular insights with regard to the role of HDAC in cancer. The first part of this review is focused on the biological roles of the Zinc-dependent HDAC family in malignant diseases. Accordingly, the small-molecules and natural products such as HDACi are described in terms of cancer therapy and chemoprevention. Furthermore, structural considerations are included to improve the HDACi selectivity and combinatory potential with other specific targeting agents in bifunctional inhibitors and proteolysis targeting chimeras. Additionally, clinical trials that combine HDACi with current therapies are discussed, which may open new avenues in terms of the feasibility of HDACi’s future clinical applications in precision cancer therapies.
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Affiliation(s)
- Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Nemanja Djoković
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Cesar Echeverria
- Facultad de Medicina, Universidad de Atacama, Copayapu 485, Copiapo 1531772, Chile;
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Juan F. Santibanez
- Group for Molecular Oncology, Institute for Medical Research, National Institute of the Republic of Serbia, University of Belgrade, Dr. Subotica 4, POB 102, 11129 Belgrade, Serbia
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 8370854, Chile
- Correspondence: ; Tel.: +381-11-2685-788; Fax: +381-11-2643-691
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Abstract
Proteolysis-targeting chimeras (PROTACs) are a powerful tool to hijack the endogenous ubiquitin-proteasome system (UPS) and to degrade the intracellular proteins of therapeutic importance. Recently, two heterobifunctional degraders targeting hormone receptors headed into Phase II clinical trials. Compared to traditional drug design and common modes of action, the PROTAC approach offers new opportunities for the drug research field. Histone deacetylase inhibitors (HDACi) are well-established drugs for the treatment of hematological malignancies. The integration of HDAC binding motifs in PROTACs explores the possibility of targeted, chemical HDAC degradation. This review provides an overview and a perspective about the key steps in the structure development of HDAC-PROTACs. In particular, the influence of the three canonical PROTAC elements on HDAC-PROTAC efficacy and selectivity are discussed, the HDACi, the linker and the E3 ligase ligand.
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Cao Z, Gu Z, Lin S, Chen D, Wang J, Zhao Y, Li Y, Liu T, Li Y, Wang Y, Lin H, He B. Attenuation of NLRP3 Inflammasome Activation by Indirubin-Derived PROTAC Targeting HDAC6. ACS Chem Biol 2021; 16:2746-2751. [PMID: 34860497 DOI: 10.1021/acschembio.1c00681] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylase 6 (HDAC6) is a potential therapeutic target for treating several diseases. A recent study revealed that HDAC6 is important for NLRP3 inflammasome activation, suggesting that targeting HDAC6 could be useful for treating many inflammatory disorders. Using the proteolysis targeting chimera (PROTAC) strategy, we herein report an HDAC6 degrader with low cytotoxicity by tethering a selective HDAC6 inhibitor derived from a natural product, indirubin, with pomalidomide, a CRBN E3 ligand. Our HDAC6 degrader efficiently and selectively decreased HDAC6 levels in several cell lines, including activated THP-1 cells. Application of this HDAC6 degrader attenuated NLRP3 inflammasome activation in LPS-induced mice, which for the first time demonstrates that HDAC6 PROTAC could be a novel strategy to treat NLRP3 inflammasome-associated diseases.
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Affiliation(s)
- Zhuoxian Cao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Zhicheng Gu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Shuxian Lin
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Di Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Jie Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Yonglong Zhao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Yan Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Ting Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Yongjun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Yi Wang
- College of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, School of Basic Medicine, Guizhou Medical University, Guiyang 550004, China
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Wang C, Zhang Y, Wu Y, Xing D. Developments of CRBN-based PROTACs as potential therapeutic agents. Eur J Med Chem 2021; 225:113749. [PMID: 34411892 DOI: 10.1016/j.ejmech.2021.113749] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022]
Abstract
Protease-targeted chimeras (PROTACs) are a new technology that is receiving much attention in the treatment of diseases. The mechanism is to inhibit protein function by hijacking the ubiquitin E3 ligase for protein degradation. Heterogeneous bifunctional PROTACs contain a ligand for recruiting E3 ligase, a linker, and another ligand to bind to the target protein for degradation. A variety of small-molecule PROTACs (CRBN, VHL, IAPs, MDM2, DCAF15, DCAF16, and RNF114-based PROTACs) have been identified so far. In particular, CRBN-based PROTACs (e.g., ARV-110 and ARV-471) have received more attention for their promising therapeutic intervention. To date, CRBN-based PRTOACs have been extensively explored worldwide and have excelled not only in cancer diseases but also in cardiovascular diseases, immune diseases, neurodegenerative diseases, and viral infections. In this review, we will provide a comprehensive update on the latest research progress in CRBN-based PRTOACs area. Following the criteria, such as disease area and drug target class, we will present the degradants in alphabetical order by target. We also provide our own perspective on the future prospects and potential challenges facing PROTACs.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Yudong Wu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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Shao L, Yang F, Su Y, Li W, Zhang J, Xu H, Huang B, Sun M, Mu Y, Zhang Y, Yu F. Design and Synthesis of Oleanolic Acid Trimers to Enhance Inhibition of Influenza Virus Entry. ACS Med Chem Lett 2021; 12:1759-1765. [PMID: 34795865 DOI: 10.1021/acsmedchemlett.1c00374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Influenza is a major threat to millions of people worldwide. Entry inhibitors are of particular interest for the development of novel therapeutic strategies for influenza. We have previously discovered oleanolic acid (OA) to be a mild influenza hemagglutinin (HA) inhibitor. In this work, inspired by the 3D structure of HA as a homotrimeric receptor, we designed and synthesized 15 OA trimers with different linkers and central region via the copper-catalyzed azide-alkyne cycloaddition reaction. All of the OA trimers were evaluated for their antiviral activities in vitro, and 12c, 12e, 13c, and 13d were observed to exhibit robust potency (IC50 in the submicromolar range) against influenza A/WSN/33 (H1N1) virus that was stronger than that observed with oseltamivir. In addition, these compounds also displayed strong biological activity against A/Hong Kong/4801/2014 and B/Sichuan/531/2018 (BV). The results of hemagglutination inhibition assays and surface plasmon resonance binding assays suggest that these OA trimers may interrupt the interaction between the HA protein of influenza virus and the host cell sialic acid receptor, thus blocking viral entry. These findings highlight the utility of multivalent OA conjugates to enhance the ligand-target interactions in anti-influenza virus drug design and are also helpful for studying antiviral drugs derived from natural products.
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Affiliation(s)
- Liang Shao
- Medical School of Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Fan Yang
- Medical School of Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yangqing Su
- Medical School of Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Weijia Li
- Medical School of Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Jihong Zhang
- Medical School of Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Huan Xu
- Institute of Chemical Biology, Shenzhen Bay Laboratories, Shenzhen, Guangdong 518132, China
| | - Boxuan Huang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518052, China
| | - Mengsi Sun
- Institute of Chemical Biology, Shenzhen Bay Laboratories, Shenzhen, Guangdong 518132, China
| | - Yu Mu
- Institute of Chemical Biology, Shenzhen Bay Laboratories, Shenzhen, Guangdong 518132, China
| | - Yuan Zhang
- Medical School of Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Fei Yu
- Medical School of Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Rana S, Mallareddy JR, Singh S, Boghean L, Natarajan A. Inhibitors, PROTACs and Molecular Glues as Diverse Therapeutic Modalities to Target Cyclin-Dependent Kinase. Cancers (Basel) 2021; 13:5506. [PMID: 34771669 PMCID: PMC8583118 DOI: 10.3390/cancers13215506] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/25/2022] Open
Abstract
The cyclin-dependent kinase (CDK) family of proteins play prominent roles in transcription, mRNA processing, and cell cycle regulation, making them attractive cancer targets. Palbociclib was the first FDA-approved CDK inhibitor that non-selectively targets the ATP binding sites of CDK4 and CDK6. In this review, we will briefly inventory CDK inhibitors that are either part of over 30 active clinical trials or recruiting patients. The lack of selectivity among CDKs and dose-limiting toxicities are major challenges associated with the development of CDK inhibitors. Proteolysis Targeting Chimeras (PROTACs) and Molecular Glues have emerged as alternative therapeutic modalities to target proteins. PROTACs and Molecular glues utilize the cellular protein degradation machinery to destroy the target protein. PROTACs are heterobifunctional molecules that form a ternary complex with the target protein and E3-ligase by making two distinct small molecule-protein interactions. On the other hand, Molecular glues function by converting the target protein into a "neo-substrate" for an E3 ligase. Unlike small molecule inhibitors, preclinical studies with CDK targeted PROTACs have exhibited improved CDK selectivity. Moreover, the efficacy of PROTACs and molecular glues are not tied to the dose of these molecular entities but to the formation of the ternary complex. Here, we provide an overview of PROTACs and molecular glues that modulate CDK function as emerging therapeutic modalities.
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Affiliation(s)
- Sandeep Rana
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA;
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Lidia Boghean
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
- Pharmaceutical Sciences and University of Nebraska Medical Center, Omaha, NE 68198, USA
- Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Xiong Y, Donovan KA, Eleuteri NA, Kirmani N, Yue H, Razov A, Krupnick NM, Nowak RP, Fischer ES. Chemo-proteomics exploration of HDAC degradability by small molecule degraders. Cell Chem Biol 2021; 28:1514-1527.e4. [PMID: 34314730 PMCID: PMC9339248 DOI: 10.1016/j.chembiol.2021.07.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/01/2021] [Accepted: 06/29/2021] [Indexed: 12/25/2022]
Abstract
Targeted protein degradation refers to the use of small molecules that recruit a ubiquitin ligase to a target protein for ubiquitination and subsequent proteasome-dependent degradation. While degraders have been developed for many targets, key questions regarding degrader development and the consequences of acute pharmacological degradation remain, specifically for targets that exist in obligate multi-protein complexes. Here, we synthesize a pan-histone deacetylase (HDAC) degrader library for the chemo-proteomic exploration of acute degradation of a key class of chromatin-modifying enzymes. Using chemo-proteomics, we not only map the degradability of the zinc-dependent HDAC family identifying leads for targeting HDACs 1-8 and 10 but also explore important aspects of degrading epigenetic enzymes. We discover cell line-driven target specificity and that HDAC degradation often results in collateral loss of HDAC-containing repressive complexes. These findings potentially offer a new mechanism toward controlling chromatin structure, and our resource will facilitate accelerated degrader design and development for HDACs.
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Affiliation(s)
- Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas A Eleuteri
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nadia Kirmani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Razov
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Noah M Krupnick
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Rodrigues DA, Roe A, Griffith D, Chonghaile TN. Advances in the Design and Development of PROTAC-mediated HDAC degradation. Curr Top Med Chem 2021; 22:408-424. [PMID: 34649488 DOI: 10.2174/1568026621666211015092047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023]
Abstract
Due to developments in modern chemistry, previously undruggable targets are becoming druggable thanks to selective degradation using the ubiquitin-proteasomal degradation system. PROteolysis TArgeting Chimeras (PROTACs) are heterobifunctional molecules designed specifically to degrade target proteins (protein of interest, POI). They are of significant interest to industry and academia as they are highly specific and can target previously undruggable target proteins from transcription factors to enzymes. More than 15 degraders are expected to be evaluated in clinical trials by the end of 2021. Herein, we describe recent advances in the design and development of PROTAC-mediated degradation of histone deacetylases (HDACs). PROTAC-mediated degradation of HDACs can offer some significant advantages over direct inhibition, such as the use of substoichiometric doses and the potential to disrupt enzyme-independent HDAC function. Herein, we discuss the potential implications of the degradation of HDACs with HDAC knockout studies and the selection of HDAC inhibitors and E3 ligase ligands for the design of the PROTACs. The potential utility of HDAC PROTACs in various disease pathologies from cancer to inflammation to neurodegeneration is driving the interest in this field.
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Affiliation(s)
- Daniel Alencar Rodrigues
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin. Ireland
| | - Andrew Roe
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin. Ireland
| | - Darren Griffith
- Department of Chemistry, Royal College of Surgeons in Ireland, Dublin. Ireland
| | - Tríona Ní Chonghaile
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin. Ireland
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Liu P, Xiao J, Wang Y, Song X, Huang L, Ren Z, Kitazato K, Wang Y. Posttranslational modification and beyond: interplay between histone deacetylase 6 and heat-shock protein 90. Mol Med 2021; 27:110. [PMID: 34530730 PMCID: PMC8444394 DOI: 10.1186/s10020-021-00375-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/07/2021] [Indexed: 12/17/2022] Open
Abstract
Posttranslational modification (PTM) and regulation of protein stability are crucial to various biological processes. Histone deacetylase 6 (HDAC6), a unique histone deacetylase with two functional catalytic domains (DD1 and DD2) and a ZnF-UBP domain (ubiquitin binding domain, BUZ), regulates a number of biological processes, including gene expression, cell motility, immune response, and the degradation of misfolded proteins. In addition to the deacetylation of histones, other nonhistone proteins have been identified as substrates for HDAC6. Hsp90, a molecular chaperone that is a critical modulator of cell signaling, is one of the lysine deacetylase substrates of HDAC6. Intriguingly, as one of the best-characterized regulators of Hsp90 acetylation, HDAC6 is the client protein of Hsp90. In addition to regulating Hsp90 at the post-translational modification level, HDAC6 also regulates Hsp90 at the gene transcription level. HDAC6 mainly regulates the Hsp90-HSF1 complex through the ZnF-UBP domain, thereby promoting the HSF1 entry into the nucleus and activating gene transcription. The mutual interaction between HDAC6 and Hsp90 plays an important role in the regulation of protein stability, cell migration, apoptosis and other functions. Plenty of of studies have indicated that blocking HDAC6/Hsp90 has a vital regulatory role in multifarious diseases, mainly in cancers. Therefore, developing inhibitors or drugs against HDAC6/Hsp90 becomes a promising development direction. Herein, we review the current knowledge on molecular regulatory mechanisms based on the interaction of HDAC6 and Hsp90 and inhibition of HDAC6 and/or Hsp90 in oncogenesis and progression, antiviral and immune-related diseases and other vital biological processes.
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Affiliation(s)
- Ping Liu
- College of Life Science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou, China
| | - Ji Xiao
- College of Life Science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou, China
| | - Yiliang Wang
- College of Life Science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou, China
| | - Xiaowei Song
- College of Life Science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou, China
| | - Lianzhou Huang
- College of Life Science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| | - Zhe Ren
- College of Life Science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou, China
| | - Kaio Kitazato
- Department of Clinical Research Pharmacy, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
| | - Yifei Wang
- College of Life Science and Technology, Guangzhou Jinan Biomedicine Research and Development Center, Jinan University, Guangzhou, China.
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Márquez-Cantudo L, Ramos A, Coderch C, de Pascual-Teresa B. Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation. Molecules 2021; 26:molecules26185606. [PMID: 34577077 PMCID: PMC8467390 DOI: 10.3390/molecules26185606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022] Open
Abstract
Protein degradation by the Ubiquitin-Proteasome System is one of the main mechanisms of the regulation of cellular proteostasis, and the E3 ligases are the key effectors for the protein recognition and degradation. Many E3 ligases have key roles in cell cycle regulation, acting as checkpoints and checkpoint regulators. One of the many important proteins involved in the regulation of the cell cycle are the members of the Histone Deacetylase (HDAC) family. The importance of zinc dependent HDACs in the regulation of chromatin packing and, therefore, gene expression, has made them targets for the design and synthesis of HDAC inhibitors. However, achieving potency and selectivity has proven to be a challenge due to the homology between the zinc dependent HDACs. PROteolysis TArgeting Chimaera (PROTAC) design has been demonstrated to be a useful strategy to inhibit and selectively degrade protein targets. In this review, we attempt to summarize the E3 ligases that naturally ubiquitinate HDACs, analyze their structure, and list the known ligands that can bind to these E3 ligases and be used for PROTAC design, as well as the already described HDAC-targeted PROTACs.
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50
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Liu J, Peng Y, Wei W. Light-Controllable PROTACs for Temporospatial Control of Protein Degradation. Front Cell Dev Biol 2021; 9:678077. [PMID: 34350175 PMCID: PMC8326567 DOI: 10.3389/fcell.2021.678077] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/14/2021] [Indexed: 12/25/2022] Open
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) is an emerging and promising approach to target intracellular proteins for ubiquitination-mediated degradation, including those so-called undruggable protein targets, such as transcriptional factors and scaffold proteins. To date, plenty of PROTACs have been developed to degrade various disease-relevant proteins, such as estrogen receptor (ER), androgen receptor (AR), RTK, and CDKs. However, the on-target off-tissue and off-target effect is one of the major limitation that prevents the usage of PROTACs in clinic. To this end, we and several other groups have recently developed light-controllable PROTACs, as the representative for the third generation controllable PROTACs, by using either photo-caging or photo-switch approaches. In this review, we summarize the emerging light-controllable PROTACs and the prospective for other potential ways to achieve temporospatial control of PROTACs.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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