1
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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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2
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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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3
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Smalley J, Cowley SM, Hodgkinson JT. MDM2 Antagonist Idasanutlin Reduces HDAC1/2 Abundance and Corepressor Partners but Not HDAC3. ACS Med Chem Lett 2024; 15:93-98. [PMID: 38229760 PMCID: PMC10788946 DOI: 10.1021/acsmedchemlett.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/18/2024] Open
Abstract
Histone deacetylases 1-3 (HDAC1, HDAC2, and HDAC3) and their associated corepressor complexes play important roles in regulating chromatin structure and gene transcription. HDAC enzymes are also validated drug targets for oncology and offer promise toward new drugs for neurodegenerative diseases and cardiovascular diseases. We synthesized four novel heterobifunctional molecules designed to recruit the mouse double minute 2 homologue (MDM2) E3 ligase to degrade HDAC1-3 utilizing the MDM2 inhibitor idasanutlin, known as proteolysis targeting chimeras (PROTACs). Idasanutlin inhibits the MDM2-P53 protein-protein interaction and is in clinical trials. Although two MDM2-recruiting heterobifunctional molecules reduced HDAC1 and HDAC2 abundance with complete selectivity over HDAC3 and reduced HDAC1/2 corepressor components LSD1 and SIN3A, we were surprised to observe that idasanutlin alone was also capable of this effect. This finding suggests an association between the MDM2 E3 ligase and HDAC1/2 corepressor complexes, which could be important for designing future dual/bifunctional HDAC- and MDM2-targeting therapeutics, such as PROTACs.
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Affiliation(s)
- Joshua
P. Smalley
- Leicester
Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Shaun M. Cowley
- Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, United Kingdom
| | - James T. Hodgkinson
- Leicester
Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
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4
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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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5
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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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6
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Zhang Y, Remillard D, Onubogu U, Karakyriakou B, Asiaban JN, Ramos AR, Bowland K, Bishop TR, Barta PA, Nance S, Durbin AD, Ott CJ, Janiszewska M, Cravatt BF, Erb MA. Collateral lethality between HDAC1 and HDAC2 exploits cancer-specific NuRD complex vulnerabilities. Nat Struct Mol Biol 2023; 30:1160-1171. [PMID: 37488358 PMCID: PMC10529074 DOI: 10.1038/s41594-023-01041-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/22/2023] [Indexed: 07/26/2023]
Abstract
Transcriptional co-regulators have been widely pursued as targets for disrupting oncogenic gene regulatory programs. However, many proteins in this target class are universally essential for cell survival, which limits their therapeutic window. Here we unveil a genetic interaction between histone deacetylase 1 (HDAC1) and HDAC2, wherein each paralog is synthetically lethal with hemizygous deletion of the other. This collateral synthetic lethality is caused by recurrent chromosomal deletions that occur in diverse solid and hematological malignancies, including neuroblastoma and multiple myeloma. Using genetic disruption or dTAG-mediated degradation, we show that targeting HDAC2 suppresses the growth of HDAC1-deficient neuroblastoma in vitro and in vivo. Mechanistically, we find that targeted degradation of HDAC2 in these cells prompts the degradation of several members of the nucleosome remodeling and deacetylase (NuRD) complex, leading to diminished chromatin accessibility at HDAC2-NuRD-bound sites of the genome and impaired control of enhancer-associated transcription. Furthermore, we reveal that several of the degraded NuRD complex subunits are dependencies in neuroblastoma and multiple myeloma, providing motivation to develop paralog-selective HDAC1 or HDAC2 degraders that could leverage HDAC1/2 synthetic lethality to target NuRD vulnerabilities. Altogether, we identify HDAC1/2 collateral synthetic lethality as a potential therapeutic target and reveal an unexplored mechanism for targeting NuRD-associated cancer dependencies.
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Affiliation(s)
- Yuxiang Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - David Remillard
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ugoma Onubogu
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Joshua N Asiaban
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Anissa R Ramos
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Kirsten Bowland
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Timothy R Bishop
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Paige A Barta
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Stephanie Nance
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam D Durbin
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Michalina Janiszewska
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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7
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Ayinde O, Sharpe C, Stahl E, Tokarski RJ, Lerma JR, Muthusamy N, Byrd JC, Fuchs JR. Examination of the Impact of Triazole Position within Linkers on Solubility and Lipophilicity of a CDK9 Degrader Series. ACS Med Chem Lett 2023; 14:936-942. [PMID: 37465296 PMCID: PMC10351057 DOI: 10.1021/acsmedchemlett.3c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/02/2023] [Indexed: 07/20/2023] Open
Abstract
Optimization of degrader properties is often a challenge due to their beyond-rule-of-5 nature. Given the paucity of known E3 ligases and the often-limited choice of ligands with varied chemical structures for a given protein target, degrader linkers represent the best position within the chimeric molecules to modify their overall physicochemical properties. In this work, a series of AT7519-based CDK9 degraders was assembled using click chemistry, facilitating the tuning of aqueous solubility and lipophilicity while retaining their linker type and molecular weight. Using chromatographic logD and kinetic solubility experiments, we show that degraders with similar chemical constitution but varied position of the embedded triazole demonstrate different lipophilicity and aqueous solubility properties. Overall, this work highlights the impact of triazole placement on linker composition through application of click chemistry for degrader synthesis and its ability to be used to promote the achievement of favorable physicochemical properties.
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Affiliation(s)
- Oluwatosin
R. Ayinde
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chia Sharpe
- Department
of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati Ohio 45267, United States
| | - Emily Stahl
- Division
of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Robert J. Tokarski
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - James R. Lerma
- Department
of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati Ohio 45267, United States
| | - Natarajan Muthusamy
- Division
of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- The
Ohio State University Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus Ohio 43210, United States
| | - John C. Byrd
- Department
of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati Ohio 45267, United States
- University
of Cincinnati Cancer Center, College of Medicine, University of Cincinnati, Cincinnati Ohio 45267, United States
| | - James R. Fuchs
- Division
of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- The
Ohio State University Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus Ohio 43210, United States
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8
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Han B, Wang M, Li J, Chen Q, Sun N, Yang X, Zhang Q. Perspectives and new aspects of histone deacetylase inhibitors in the therapy of CNS diseases. Eur J Med Chem 2023; 258:115613. [PMID: 37399711 DOI: 10.1016/j.ejmech.2023.115613] [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: 05/15/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
Many populations worldwide are suffering from central nervous system (CNS) diseases such as brain tumors, neurodegenerative diseases (Alzheimer's disease, Parkinson's disease and Huntington's disease) and stroke. There is a shortage of effective drugs for most CNS diseases. As one of the regulatory mechanisms of epigenetics, the particular role and therapeutic benefits of histone deacetylases (HDACs) in the CNS have been extensively studied. In recent years, HDACs have attracted increasing attention as potential drug targets for CNS diseases. In this review, we summarize the recent applications of representative histone deacetylases inhibitors (HDACis) in CNS diseases and discuss the challenges in developing HDACis with different structures and better blood-brain barrier (BBB) permeability, hoping to promote the development of more effective bioactive HDACis for the treatment of CNS diseases.
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Affiliation(s)
- Bo Han
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Mengfei Wang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Jiayi Li
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China; School of Chemistry & Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - Qiushi Chen
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China; School of Chemistry & Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - Niubing Sun
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China; School of Chemistry & Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - Xuezhi Yang
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Qingwei Zhang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, 201203, China.
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9
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Zografou-Barredo NA, Hallatt AJ, Goujon-Ricci J, Cano C. A beginner's guide to current synthetic linker strategies towards VHL-recruiting PROTACs. Bioorg Med Chem 2023; 88-89:117334. [PMID: 37224698 DOI: 10.1016/j.bmc.2023.117334] [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: 03/08/2023] [Revised: 05/05/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023]
Abstract
Over the last two decades, proteolysis targeting chimeras (PROTACs) have been revolutionary in drug development rendering targeted protein degradation (TPD) as an emerging therapeutic modality. These heterobifunctional molecules are comprised of three units: a ligand for the protein of interest (POI), a ligand for an E3 ubiquitin ligase, and a linker that tethers the two motifs together. Von Hippel-Lindau (VHL) is one of the most widely employed E3 ligases in PROTACs development due to its prevalent expression across tissue types and well-characterised ligands. Linker composition and length has proven to play an important role in determining the physicochemical properties and spatial orientation of the POI-PROTAC-E3 ternary complex, thus influencing the bioactivity of degraders. Numerous articles and reports have been published showcasing the medicinal chemistry aspects of the linker design, but few have focused on the chemistry around tethering linkers to E3 ligase ligands. In this review, we focus on the current synthetic linker strategies employed in the assembly of VHL-recruiting PROTACs. We aim to cover a range of fundamental chemistries used to incorporate linkers of varying length, composition and functionality.
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Affiliation(s)
- Nikol A Zografou-Barredo
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Alex J Hallatt
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Jennyfer Goujon-Ricci
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Céline Cano
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
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10
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Sobhia ME, Kumar H, Kumari S. Bifunctional robots inducing targeted protein degradation. Eur J Med Chem 2023; 255:115384. [PMID: 37119667 DOI: 10.1016/j.ejmech.2023.115384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/01/2023]
Abstract
The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) and E3-ligase, which induce the ubiquitination of POI. These molecules are based on event-driven pharmacology and are applicable in different conditions such as oncology, antiviral, neurodegenerative disease, acne etc., offering tremendous scope to researchers. In this review, primarily, we attempted to compile the recent works available in the literature on PROTACs for various targeted proteins. We summarized the design and development strategies with a focus on molecular information of protein residues and linker design. Rationalization of the ternary complex formation using Artificial Intelligence including machine & deep learning models and traditionally followed computational tools are also included in this study. Moreover, details describing the optimization of PROTACs chemistry and pharmacokinetic properties are added. Advanced PROTAC designs and targeting complex proteins, is summed up to cover the wide spectrum.
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Affiliation(s)
- M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India.
| | - Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India
| | - Sonia Kumari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India
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