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Yao X, Mao J, Zhang H, Xiao Y, Wang Y, Liu H. Development of novel N-aryl-2,4-bithiazole-2-amine-based CYP1B1 degraders for reversing drug resistance. Eur J Med Chem 2024; 272:116488. [PMID: 38733885 DOI: 10.1016/j.ejmech.2024.116488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
Extrahepatic cytochrome P450 1B1 (CYP1B1), which is highly expressed in non-small cell lung cancer, is an attractive target for cancer prevention, therapy, and overcoming drug resistance. Historically, CYP1B1 inhibition has been the primary therapeutic approach for treating CYP1B1-related malignancies, but its success has been limited. This study introduced CYP1B1 degradation as an alternative strategy to counter drug resistance and metastasis in CYP1B1-overexpressing non-small cell lung cancer A549/Taxol cells via a PROTAC strategy. Our investigation revealed that the identification of the potent CYP1B1 degrader PV2, achieving DC50 values of 1.0 nM and inducing >90 % CYP1B1 degradation at concentrations as low as 10 nM in A549/Taxol cells. Importantly, PV2 enhanced the sensitivity of the A549/Taxol subline to Taxol, possibly due to its stronger inhibitory effects on P-gp through CYP1B1 degradation. Additionally, compared to the CYP1B1 inhibitor A1, PV2 effectively suppressed the migration and invasion of A549/Taxol cells by inhibiting the FAK/SRC and EMT pathways. These findings hold promise for a novel therapy targeting advanced CYP1B1+ non-small cell lung cancer.
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Affiliation(s)
- Xiaoxuan Yao
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, Liaoning, PR China
| | - Jianping Mao
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, Liaoning, PR China
| | - Haoyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, Liaoning, PR China
| | - Yi Xiao
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, Liaoning, PR China
| | - Yongjun Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, Liaoning, PR China.
| | - Hongzhuo Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, Liaoning, PR China.
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2
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Zhang Y, Ming A, Wang J, Chen W, Fang Z. PROTACs targeting androgen receptor signaling: potential therapeutic agents for castration-resistant prostate cancer. Pharmacol Res 2024; 205:107234. [PMID: 38815882 DOI: 10.1016/j.phrs.2024.107234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
After the initial androgen deprivation therapy (ADT), part of the prostate cancer may continuously deteriorate into castration-resistant prostate cancer (CRPC). The majority of patients suffer from the localized illness at primary diagnosis that could rapidly assault other organs. This disease stage is referred as metastatic castration-resistant prostate cancer (mCRPC). Surgery and radiation are still the treatment of CRPC, but have some adverse effects such as urinary symptoms and sexual dysfunction. Hormonal castration therapy interfering androgen receptor (AR) signaling pathway is indispensable for most advanced prostate cancer patients, and the first- and second-generation of novel AR inhibitors could effectively cure hormone sensitive prostate cancer (HSPC). However, the resistance to these chemical agents is inevitable many of patients may experience relapses. The resistance to AR inhibitor mainly involves AR mutation, splice variant formation and amplification, which indicates the important role in CRPC. Proteolysis-targeting chimera (PROTAC), a potent technique to degrade targeted protein, has recently undergone extensive development as a biological tool and therapeutic drug. This technique has the potential to become the next generation of antitumor therapeutics as it could overcome the shortcomings of conventional small molecule inhibitors. In this review, we summarize the molecular mechanisms on PROTACs targeting AR signaling for CRPC, hoping to provide insights into drug development and clinical medication.
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Affiliation(s)
- Yulu Zhang
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China; Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, China
| | - Annan Ming
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China; Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, China
| | - Junyan Wang
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China
| | | | - Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, China.
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3
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Wu KY, Hung TI, Chang CEA. PROTAC-induced Protein Functional Dynamics in Targeted Protein Degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592590. [PMID: 38746111 PMCID: PMC11092786 DOI: 10.1101/2024.05.05.592590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are small molecules that induce target protein degradation via the ubiquitin-proteasome system. PROTACs recruit the target protein and E3 ligase; a critical first step is forming a ternary complex. However, while the formation a ternary complex is crucial, it may not always guarantee successful protein degradation. The dynamics of the PROTAC-induced degradation complex play a key role in ubiquitination and subsequent degradation. In this study, we computationally modelled protein complex structures and dynamics associated with a series of PROTACs featuring different linkers to investigate why these PROTACs, all of which formed ternary complexes with Cereblon (CRBN) E3 ligase and the target protein bromodomain-containing protein 4 (BRD4 BD1 ), exhibited varying degrees of degradation potency. We constructed the degradation machinery complexes with Culling-Ring Ligase 4A (CRL4A) E3 ligase scaffolds. Through atomistic molecular dynamics simulations, we illustrated how PROTAC-dependent protein dynamics facilitate the arrangement of surface lysine residues of BRD4 BD1 into the catalytic pocket of E2/ubiquitin for ubiquitination. Despite featuring identical warheads in this PROTAC series, the linkers were found to affect the residue-interaction networks, and thus governing the essential motions of the entire degradation machine for ubiquitination. These findings offer a dynamic perspective on ligand-induced protein degradation, providing insights to guide future PROTAC design endeavors.
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4
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Kuemper S, Cairns AG, Birchall K, Yao Z, Large JM. Targeted protein degradation in CNS disorders: a promising route to novel therapeutics? Front Mol Neurosci 2024; 17:1370509. [PMID: 38685916 PMCID: PMC11057381 DOI: 10.3389/fnmol.2024.1370509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Targeted protein degradation (TPD) is a rapidly expanding field, with various PROTACs (proteolysis-targeting chimeras) in clinical trials and molecular glues such as immunomodulatory imide drugs (IMiDs) already well established in the treatment of certain blood cancers. Many current approaches are focused on oncology targets, leaving numerous potential applications underexplored. Targeting proteins for degradation offers a novel therapeutic route for targets whose inhibition remains challenging, such as protein aggregates in neurodegenerative diseases. This mini review focuses on the prospect of utilizing TPD for neurodegenerative disease targets, particularly PROTAC and molecular glue formats and opportunities for novel CNS E3 ligases. Some key challenges of utilizing such modalities including molecular design of degrader molecules, drug delivery and blood brain barrier penetrance will be discussed.
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Affiliation(s)
- Sandra Kuemper
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, United Kingdom
| | - Andrew G. Cairns
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, United Kingdom
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5
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Hu Z, Chen PH, Li W, Krone M, Zheng S, Saarbach J, Velasco IU, Hines J, Liu Y, Crews CM. EGFR targeting PhosTACs as a dual inhibitory approach reveals differential downstream signaling. SCIENCE ADVANCES 2024; 10:eadj7251. [PMID: 38536914 PMCID: PMC10971414 DOI: 10.1126/sciadv.adj7251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 02/22/2024] [Indexed: 04/05/2024]
Abstract
We recently developed a heterobifunctional approach [phosphorylation targeting chimeras (PhosTACs)] to achieve the targeted protein dephosphorylation (TPDephos). Here, we envisioned combining the inhibitory effects of receptor tyrosine kinase inhibitors (RTKIs) and the active dephosphorylation by phosphatases to achieve dual inhibition of kinases. We report an example of tyrosine phosphatase-based TPDephos and the effective epidermal growth factor receptor (EGFR) tyrosine dephosphorylation. We also used phosphoproteomic approaches to study the signaling transductions affected by PhosTAC-related molecules at the proteome-wide level. This work demonstrated the differential signaling pathways inhibited by PhosTAC compared with the TKI, gefitinib. Moreover, a covalent PhosTAC selective for mutated EGFR was developed and showed its inhibitory potential for dysregulated EGFR. Last, EGFR PhosTACs, consistent with EGFR dephosphorylation profiles, induced apoptosis and inhibited cancer cell viability during prolonged PhosTAC treatment. PhosTACs showcased their potential of modulating RTKs activity, expanding the scope of bifunctional molecule utility.
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Affiliation(s)
- Zhenyi Hu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Po-Han Chen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Mackenzie Krone
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Sijin Zheng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Jacques Saarbach
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ines Urquizo Velasco
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - John Hines
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
- Department of Pharmacology, Yale University, New Haven, CT 06511, USA
- Yale University School of Medicine, New Haven, CT 06511, USA
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6
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Lee YB, Rhee HW. Spray-type modifications: an emerging paradigm in post-translational modifications. Trends Biochem Sci 2024; 49:208-223. [PMID: 38443288 DOI: 10.1016/j.tibs.2024.01.008] [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: 10/01/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 03/07/2024]
Abstract
A post-translational modification (PTM) occurs when a nucleophilic residue (e.g., lysine of a target protein) attacks electrophilic substrate molecules (e.g., acyl-AMP), involving writer enzymes or even occurring spontaneously. Traditionally, this phenomenon was thought to be sequence specific; however, recent research suggests that PTMs can also occur in a non-sequence-specific manner confined to a specific location in a cell. In this Opinion, we compile the accumulated evidence of spray-type PTMs and propose a mechanism for this phenomenon based on the exposure level of reactive electrophilic substrate molecules at the active site of the PTM writers. Overall, a spray-type PTM conceptual framework is useful for comprehending the promiscuous PTM writer events that cannot be adequately explained by the traditional concept of sequence-dependent PTM events.
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Affiliation(s)
- Yun-Bin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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7
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Lawer A, Schulz L, Sawyer R, Liu X. Harmony of Protein Tags and Chimeric Molecules Empowers Targeted Protein Ubiquitination and Beyond. Cells 2024; 13:426. [PMID: 38474390 DOI: 10.3390/cells13050426] [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: 01/26/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Post-translational modifications (PTMs) are crucial mechanisms that underlie the intricacies of biological systems and disease mechanisms. This review focuses on the latest advancements in the design of heterobifunctional small molecules that hijack PTM machineries for target-specific modifications in living systems. A key innovation in this field is the development of proteolysis-targeting chimeras (PROTACs), which promote the ubiquitination of target proteins for proteasomal degradation. The past decade has seen several adaptations of the PROTAC concept to facilitate targeted (de)phosphorylation and acetylation. Protein fusion tags have been particularly vital in these proof-of-concept studies, aiding in the investigation of the functional roles of post-translationally modified proteins linked to diseases. This overview delves into protein-tagging strategies that enable the targeted modulation of ubiquitination, phosphorylation, and acetylation, emphasizing the synergies and challenges of integrating heterobifunctional molecules with protein tags in PTM research. Despite significant progress, many PTMs remain to be explored, and protein tag-assisted PTM-inducing chimeras will continue to play an important role in understanding the fundamental roles of protein PTMs and in exploring the therapeutic potential of manipulating protein modifications, particularly for targets not yet addressed by existing drugs.
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Affiliation(s)
- Aggie Lawer
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
| | - Luke Schulz
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Renata Sawyer
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
| | - Xuyu Liu
- School of Chemistry, Faculty of Science, The University of Sydney, Camperdown, NSW 2050, Australia
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia
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8
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Setia N, Almuqdadi HTA, Abid M. Journey of Von Hippel-Lindau (VHL) E3 ligase in PROTACs design: From VHL ligands to VHL-based degraders. Eur J Med Chem 2024; 265:116041. [PMID: 38199162 DOI: 10.1016/j.ejmech.2023.116041] [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: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The scientific community has shown considerable interest in proteolysis-targeting chimeras (PROTACs) in the last decade, indicating their remarkable potential as a means of achieving targeted protein degradation (TPD). Not only are PROTACs seen as valuable tools in molecular biology but their emergence as a modality for drug discovery has also garnered significant attention. PROTACs bind to E3 ligases and target proteins through respective ligands connected via a linker to induce proteasome-mediated protein degradation. The discovery of small molecule ligands for E3 ligases has led to the prevalent use of various E3 ligases in PROTAC design. Furthermore, the incorporation of different types of linkers has proven beneficial in enhancing the efficacy of PROTACs. By far more than 3300 PROTACs have been reported in the literature. Notably, Von Hippel-Lindau (VHL)-based PROTACs have surfaced as a propitious strategy for targeting proteins, even encompassing those that were previously considered non-druggable. VHL is extensively utilized as an E3 ligase in the advancement of PROTACs owing to its widespread expression in various tissues and well-documented binders. Here, we review the discovery of VHL ligands, the types of linkers employed to develop VHL-based PROTACs, and their subsequent modulation to design advanced non-conventional degraders to target various disease-causing proteins. Furthermore, we provide an overview of other E3 ligases recruited in the field of PROTAC technology.
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Affiliation(s)
- Nisha Setia
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | | | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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9
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Ma Q, Ye S, Liu H, Zhao Y, Mao Y, Zhang W. HMGA2 promotes cancer metastasis by regulating epithelial-mesenchymal transition. Front Oncol 2024; 14:1320887. [PMID: 38361784 PMCID: PMC10867147 DOI: 10.3389/fonc.2024.1320887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a complex physiological process that transforms polarized epithelial cells into moving mesenchymal cells. Dysfunction of EMT promotes the invasion and metastasis of cancer. The architectural transcription factor high mobility group AT-hook 2 (HMGA2) is highly overexpressed in various types of cancer (e.g., colorectal cancer, liver cancer, breast cancer, uterine leiomyomas) and significantly correlated with poor survival rates. Evidence indicated that HMGA2 overexpression markedly decreased the expression of epithelial marker E-cadherin (CDH1) and increased that of vimentin (VIM), Snail, N-cadherin (CDH2), and zinc finger E-box binding homeobox 1 (ZEB1) by targeting the transforming growth factor beta/SMAD (TGFβ/SMAD), mitogen-activated protein kinase (MAPK), and WNT/beta-catenin (WNT/β-catenin) signaling pathways. Furthermore, a new class of non-coding RNAs (miRNAs, circular RNAs, and long non-coding RNAs) plays an essential role in the process of HMGA2-induced metastasis and invasion of cancer by accelerating the EMT process. In this review, we discuss alterations in the expression of HMGA2 in various types of cancer. Furthermore, we highlight the role of HMGA2-induced EMT in promoting tumor growth, migration, and invasion. More importantly, we discuss extensively the mechanism through which HMGA2 regulates the EMT process and invasion in most cancers, including signaling pathways and the interacting RNA signaling axis. Thus, the elucidation of molecular mechanisms that underlie the effects of HMGA2 on cancer invasion and patient survival by mediating EMT may offer new therapeutic methods for preventing cancer progression.
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Affiliation(s)
- Qing Ma
- General Practice Ward/International Medical Center Ward, General Practice Medical Center, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Sisi Ye
- General Practice Ward/International Medical Center Ward, General Practice Medical Center, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Hong Liu
- General Practice Ward/International Medical Center Ward, General Practice Medical Center, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Yu Zhao
- General Practice Ward/International Medical Center Ward, General Practice Medical Center, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Yan Mao
- General Practice Ward/International Medical Center Ward, General Practice Medical Center, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Wei Zhang
- Emergency Department of West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
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10
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Hasan M, Panda D, Mann G, Brik A. De novo Semi-Synthetic Platform for Monitoring Protein degradation in Live Cells. Chembiochem 2024; 25:e202300731. [PMID: 38031893 DOI: 10.1002/cbic.202300731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/01/2023]
Abstract
We designed a platform for monitoring the degradation of exogenous proteins in live cells. We engineered a semi-synthetic platform, which consists of Enhanced Green Fluorescent Protein tagged with SpyCatcher to enable its conjugation to a SpyTag peptide bearing a Von Hippel-Lindau E3 ligand, which was delivered to live cells to promote its degradation. This platform lays the ground for studying the degradation of endogenous proteins equipped with SpyTag and for tracking the degradation of post-translationally modified proteins in live cells.
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Affiliation(s)
- Mahdi Hasan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Deepanjan Panda
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Guy Mann
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
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11
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Wang H, Chen M, Zhang X, Xie S, Qin J, Li J. Peptide-based PROTACs: Current Challenges and Future Perspectives. Curr Med Chem 2024; 31:208-222. [PMID: 36718000 DOI: 10.2174/0929867330666230130121822] [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: 08/11/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 02/01/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) are an attractive means to target previously undruggable or drug-resistant mutant proteins. While small molecule-based PROTACs are stable and can cross cell membranes, there is limited availability of suitable small molecule warheads capable of recruiting proteins to an E3 ubiquitin ligase for degradation. With advances in structural biology and in silico protein structure prediction, it is now becoming easier to define highly selective peptides suitable for PROTAC design. As a result, peptide-based PROTACs are becoming a feasible proposition for targeting previously "undruggable" proteins not amenable to small molecule inhibition. In this review, we summarize recent progress in the design and application of peptide-based PROTACs as well as several practical approaches for obtaining candidate peptides for PROTACs. We also discuss the major hurdles preventing the translation of peptide-based PROTACs from bench to bedside, such as their delivery and bioavailability, with the aim of stimulating discussion about how best to accelerate the clinical development of peptide- based PROTACs in the near future.
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Affiliation(s)
- Huidan Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Miao Chen
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Xiaoyuan Zhang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Songbo Xie
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Jie Qin
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Jingrui Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
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12
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Wang ZQ, Zhang ZC, Wu YY, Pi YN, Lou SH, Liu TB, Lou G, Yang C. Bromodomain and extraterminal (BET) proteins: biological functions, diseases, and targeted therapy. Signal Transduct Target Ther 2023; 8:420. [PMID: 37926722 PMCID: PMC10625992 DOI: 10.1038/s41392-023-01647-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/23/2023] [Accepted: 09/12/2023] [Indexed: 11/07/2023] Open
Abstract
BET proteins, which influence gene expression and contribute to the development of cancer, are epigenetic interpreters. Thus, BET inhibitors represent a novel form of epigenetic anticancer treatment. Although preliminary clinical trials have shown the anticancer potential of BET inhibitors, it appears that these drugs have limited effectiveness when used alone. Therefore, given the limited monotherapeutic activity of BET inhibitors, their use in combination with other drugs warrants attention, including the meaningful variations in pharmacodynamic activity among chosen drug combinations. In this paper, we review the function of BET proteins, the preclinical justification for BET protein targeting in cancer, recent advances in small-molecule BET inhibitors, and preliminary clinical trial findings. We elucidate BET inhibitor resistance mechanisms, shed light on the associated adverse events, investigate the potential of combining these inhibitors with diverse therapeutic agents, present a comprehensive compilation of synergistic treatments involving BET inhibitors, and provide an outlook on their future prospects as potent antitumor agents. We conclude by suggesting that combining BET inhibitors with other anticancer drugs and innovative next-generation agents holds great potential for advancing the effective targeting of BET proteins as a promising anticancer strategy.
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Affiliation(s)
- Zhi-Qiang Wang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Zhao-Cong Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Yu-Yang Wu
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ya-Nan Pi
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Sheng-Han Lou
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tian-Bo Liu
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Ge Lou
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China.
| | - Chang Yang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China.
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13
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Yang S, Zou LH, Li R, Jiang Y, Ren F, Shao A. Construction of Coumarin-Based Bioorthogonal Macromolecular Probes for Photoactivation. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37906696 DOI: 10.1021/acsami.3c10859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Photoactivatable fluorescence imaging is one of the most valuable methods for visualizing protein localization, trafficking, and interactions. Here, we designed four bioorthogonal fluorescent probes K1-K4 by installing photoactive cages and HaloTag ligands onto the different positions of the coumarin fluorophore. Although K1-K4 all exhibited rapid photostimulated responses in aqueous solution, only K3 was found to have an obvious aggregation-induced emission (AIE). Next, macromolecular fluorescent probes Kn=1/2/3/4_POIs were obtained by covalently attaching K1-K4 to HaloTag-fused proteins of interest (POIs). Kn=3/4_POIs exhibited a higher fluorescence increase than that of Kn=1/2_POIs upon photoactivation in both liquid and solid phases. Moreover, K3_GFP_Halo and K4_GFP_Halo presented the fluorescence resonance energy transfer (FRET) from photocleaved K3 and K4 to GFP in the protein complex. We further examined the fluorescence labeling ability of K1-K4 to intracellular IRE1_Halo protein and found that K3 and K4 containing the HaloTag ligand on the C4 position of coumarin could be retained in cells for long-term tracking of the IRE1_Halo protein. Hence, we established a platform of novel bioorthogonal fluorescent probes conjugating onto Halo-tagged POIs for rapid photoactivation in vitro and in cells.
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Affiliation(s)
- Shuke Yang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liang-Hua Zou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Runqi Li
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Yu Jiang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Fei Ren
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Andong Shao
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
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14
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Mostofian B, Martin HJ, Razavi A, Patel S, Allen B, Sherman W, Izaguirre JA. Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods. J Chem Inf Model 2023; 63:5408-5432. [PMID: 37602861 PMCID: PMC10498452 DOI: 10.1021/acs.jcim.3c00603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 08/22/2023]
Abstract
The therapeutic approach of targeted protein degradation (TPD) is gaining momentum due to its potentially superior effects compared with protein inhibition. Recent advancements in the biotech and pharmaceutical sectors have led to the development of compounds that are currently in human trials, with some showing promising clinical results. However, the use of computational tools in TPD is still limited, as it has distinct characteristics compared with traditional computational drug design methods. TPD involves creating a ternary structure (protein-degrader-ligase) responsible for the biological function, such as ubiquitination and subsequent proteasomal degradation, which depends on the spatial orientation of the protein of interest (POI) relative to E2-loaded ubiquitin. Modeling this structure necessitates a unique blend of tools initially developed for small molecules (e.g., docking) and biologics (e.g., protein-protein interaction modeling). Additionally, degrader molecules, particularly heterobifunctional degraders, are generally larger than conventional small molecule drugs, leading to challenges in determining drug-like properties like solubility and permeability. Furthermore, the catalytic nature of TPD makes occupancy-based modeling insufficient. TPD consists of multiple interconnected yet distinct steps, such as POI binding, E3 ligase binding, ternary structure interactions, ubiquitination, and degradation, along with traditional small molecule properties. A comprehensive set of tools is needed to address the dynamic nature of the induced proximity ternary complex and its implications for ubiquitination. In this Perspective, we discuss the current state of computational tools for TPD. We start by describing the series of steps involved in the degradation process and the experimental methods used to characterize them. Then, we delve into a detailed analysis of the computational tools employed in TPD. We also present an integrative approach that has proven successful for degrader design and its impact on project decisions. Finally, we examine the future prospects of computational methods in TPD and the areas with the greatest potential for impact.
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Affiliation(s)
- Barmak Mostofian
- OpenEye, Cadence Molecular Sciences, Boston, Massachusetts 02114 United States
| | - Holli-Joi Martin
- Laboratory
for Molecular Modeling, Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599 United States
| | - Asghar Razavi
- ENKO
Chem, Inc, Mystic, Connecticut 06355 United States
| | - Shivam Patel
- Psivant
Therapeutics, Boston, Massachusetts 02210 United States
| | - Bryce Allen
- Differentiated
Therapeutics, San Diego, California 92056 United States
| | - Woody Sherman
- Psivant
Therapeutics, Boston, Massachusetts 02210 United States
| | - Jesus A Izaguirre
- Differentiated
Therapeutics, San Diego, California 92056 United States
- Atommap
Corporation, New York, New York 10013 United States
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15
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Serebrenik YV, Mani D, Maujean T, Burslem GM, Shalem O. Pooled endogenous protein tagging and recruitment for scalable discovery of effectors for induced proximity therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548759. [PMID: 37503056 PMCID: PMC10369964 DOI: 10.1101/2023.07.13.548759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The field of induced proximity therapeutics is in its ascendancy but is limited by a lack of scalable tools to systematically explore effector-target protein pairs in an unbiased manner. Here, we combined Scalable POoled Targeting with a LIgandable Tag at Endogenous Sites (SPOTLITES) for the high-throughput tagging of endogenous proteins, with generic small molecule-based protein recruitment to screen for novel proximity-based effectors. We apply this methodology in two orthogonal screens for targeted protein degradation: the first using fluorescence to monitor target protein levels directly, and the second using a cellular growth phenotype that depends on the degradation of an essential protein. Our screens revealed a multitude of potential new effector proteins for degradation and converged on members of the CTLH complex which we demonstrate potently induce degradation. Altogether, we introduce a platform for pooled induction of endogenous protein-protein interactions that can be used to expand our toolset of effector proteins for targeted protein degradation and other forms of induced proximity.
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16
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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17
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Adams CM, Mitra R, Xiao Y, Michener P, Palazzo J, Chao A, Gour J, Cassel J, Salvino JM, Eischen CM. Targeted MDM2 Degradation Reveals a New Vulnerability for p53-Inactivated Triple-Negative Breast Cancer. Cancer Discov 2023; 13:1210-1229. [PMID: 36734633 PMCID: PMC10164114 DOI: 10.1158/2159-8290.cd-22-1131] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/29/2022] [Accepted: 01/31/2023] [Indexed: 02/04/2023]
Abstract
Triple-negative breast cancers (TNBC) frequently inactivate p53, increasing their aggressiveness and therapy resistance. We identified an unexpected protein vulnerability in p53-inactivated TNBC and designed a new PROteolysis TArgeting Chimera (PROTAC) to target it. Our PROTAC selectively targets MDM2 for proteasome-mediated degradation with high-affinity binding and VHL recruitment. MDM2 loss in p53 mutant/deleted TNBC cells in two-dimensional/three-dimensional culture and TNBC patient explants, including relapsed tumors, causes apoptosis while sparing normal cells. Our MDM2-PROTAC is stable in vivo, and treatment of TNBC xenograft-bearing mice demonstrates tumor on-target efficacy with no toxicity to normal cells, significantly extending survival. Transcriptomic analyses revealed upregulation of p53 family target genes. Investigations showed activation and a required role for TAp73 to mediate MDM2-PROTAC-induced apoptosis. Our data, challenging the current MDM2/p53 paradigm, show MDM2 is required for p53-inactivated TNBC cell survival, and PROTAC-targeted MDM2 degradation is an innovative potential therapeutic strategy for TNBC and superior to existing MDM2 inhibitors. SIGNIFICANCE p53-inactivated TNBC is an aggressive, therapy-resistant, and lethal breast cancer subtype. We designed a new compound targeting an unexpected vulnerability we identified in TNBC. Our MDM2-targeted degrader kills p53-inactivated TNBC cells, highlighting the requirement for MDM2 in TNBC cell survival and as a new therapeutic target for this disease. See related commentary by Peuget and Selivanova, p. 1043. This article is highlighted in the In This Issue feature, p. 1027.
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Affiliation(s)
- Clare M. Adams
- Department of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ramkrishna Mitra
- Department of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Peter Michener
- Department of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Juan Palazzo
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Allen Chao
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | | | - Christine M. Eischen
- Department of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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18
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Ji J, Ma S, Zhu Y, Zhao J, Tong Y, You Q, Jiang Z. ARE-PROTACs Enable Co-degradation of an Nrf2-MafG Heterodimer. J Med Chem 2023; 66:6070-6081. [PMID: 36892138 DOI: 10.1021/acs.jmedchem.2c01909] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Proteolysis-targeting chimera (PROTAC) technology has emerged as a potential strategy to degrade "undruggable" proteins in recent years. Nrf2, an aberrantly activated transcription factor in cancer, is generally considered undruggable as lacking active sites or allosteric pockets. Here, we constructed the chimeric molecule C2, which consists of an Nrf2-binding element and a CRBN ligand, as a first-in-class Nrf2 degrader. Surprisingly, C2 was found to selectively degrade an Nrf2-MafG heterodimer simultaneously via the ubiquitin-proteasome system. C2 impeded Nrf2-ARE transcriptional activity significantly and improved the sensitivity of NSCLC cells to ferroptosis and therapeutic drugs. The degradation character of ARE-PROTACs suggests that the PROTAC hijacking the transcription element of TFs could achieve co-degradation of the transcription complex.
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Affiliation(s)
- Jianai Ji
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Sinan Ma
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Zhu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Jinglong Zhao
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yuanyuan Tong
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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19
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Li M, Zhi Y, Liu B, Yao Q. Advancing Strategies for Proteolysis-Targeting Chimera Design. J Med Chem 2023; 66:2308-2329. [PMID: 36788245 DOI: 10.1021/acs.jmedchem.2c01555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) have shown great therapeutic potential by degrading various disease-causing proteins, particularly those related to tumors. Therefore, the introduction of PROTACs has ushered in a new chapter of antitumor drug development, marked by significant advances over recent years. Herein, we describe recent developments in PROTAC technology, focusing on design strategy, development workflow, and future outlooks. We also discuss potential opportunities and challenges for PROTAC research.
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Affiliation(s)
- Minglei Li
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Ying Zhi
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Bo Liu
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Qingqiang Yao
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
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20
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Guenette RG, Potts PR. High throughput E3 ligase degron binding assays for novel PROTAC ligand discovery. Methods Enzymol 2023; 681:23-39. [PMID: 36764759 DOI: 10.1016/bs.mie.2022.08.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The discovery of new small molecule ligands for E3 ligases will enable the creation of novel proteolysis targeting chimeras (PROTACs) and molecular glues to tackle traditionally undruggable proteins. Diversifying both the chemical matter for each E3 ligase and the type of ligases will be important to fully capture the potential of these targeted protein degradation modalities. A key step in this process is to establish an integrated screening platform for the rapid identification and optimization of small molecule ligands for E3 ligases. Here, we provide a method to evaluate E3 ligase ligands using AlphaScreen technology. AlphaScreen allows for the evaluation of a wide array of molecular interactions and is utilized extensively in small molecule screening campaigns. This bead-based proximity technology offers facile development for interactions across a wide range of affinities and can be adapted to interrogate E3 ligase-degron interactions. In this protocol, we demonstrate the development of AlphaScreen for E3 ligase ligand competition assays toward the discovery of new ligands for E3 ligases.
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Affiliation(s)
- Robert G Guenette
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA, United States
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA, United States.
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21
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Palomba T, Baroni M, Cross S, Cruciani G, Siragusa L. ELIOT: A platform to navigate the E3 pocketome and aid the design of new PROTACs. Chem Biol Drug Des 2023; 101:69-86. [PMID: 35857806 DOI: 10.1111/cbdd.14123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 12/15/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) are novel therapeutics for the treatment of human disease. They exploit the enormous potential of the E3 ligases, a class of proteins that mark a target protein for degradation via the ubiquitin-proteasome system. Despite the existence of several E3 ligase-related databases, the choice of the functioning ligase is limited to only 1.6% of those available, probably due to the fragmentary understanding of their structures and their known ligands; in fact, none of the existing databases report detailed studies covering their 3D structure or their pockets. Here, we report ELIOT (E3 LIgase pocketOme navigaTor), an accurate and complete platform containing the E3 ligase pocketome to enable navigation and selection of new E3 ligases and new ligands for the design of new PROTACs. All E3 ligase pockets were characterized with innovative 3D descriptors including their PROTAC-ability score, and similarity analyses between E3 pockets are presented. Tissue specificity and their degree of involvement in patients with specific cancer types are also annotated for each E3 ligase, enabling appropriate selection for the design of a PROTAC with improved specificity. All data are available at https://eliot.moldiscovery.com.
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Affiliation(s)
- Tommaso Palomba
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia, Italy
| | - Massimo Baroni
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK
| | - Simon Cross
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK
| | - Gabriele Cruciani
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia, Italy
| | - Lydia Siragusa
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK.,Molecular Horizon Srl, Bettona, Italy
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22
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Yu X, Wang J. Quantitative measurement of PROTAC intracellular accumulation. Methods Enzymol 2022; 681:189-214. [PMID: 36764757 PMCID: PMC11102804 DOI: 10.1016/bs.mie.2022.11.001] [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] [Indexed: 12/23/2022]
Abstract
In recent years, Proteolysis Targeting Chimera (PROTAC) technology has emerged as one of the most promising approaches to remove disease-associated proteins by utilizing cells' own destruction machinery. To achieve successful degradation of a protein of interest (POI), the heterobifunctional PROTAC molecules must penetrate into the cells first, followed by target engagement and formation of the POI-PROTAC-E3 ligase complex. Based on this understanding, the assessment of cell permeability and in cell target engagement are of great importance to evaluate the efficacy of PROTAC candidates. PROTAC molecules can be classified as non-covalent and covalent, and covalent PROTACs can be further divided into irreversible and reversible covalent. Here, we present a high-throughput assay to prioritize different types of BTK PROTACs by measuring their intracellular accumulation quantitatively, using kinase binding assays and the NanoBRET target engagement platform.
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Affiliation(s)
- Xin Yu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States.
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23
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PROTACs: Current Trends in Protein Degradation by Proteolysis-Targeting Chimeras. BioDrugs 2022; 36:609-623. [PMID: 36098871 DOI: 10.1007/s40259-022-00551-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2022] [Indexed: 11/02/2022]
Abstract
In the recent past, proteolysis-targeting chimera (PROTAC) technology has received enormous attention for its ability to overcome the limitations of protein inhibitors and its capability to target undruggable proteins. The PROTAC molecule consists of three components, a ubiquitin E3 ligase ligand, a linker, and a target protein ligand. The application of this technology is rapidly gaining momentum, especially in cancer therapy. In this review, we first look at the history of degraders, followed by a section on the ubiquitin proteasome system (UPS) and E3 ligases used in PROTAC development. PROTACs are dependent on the UPS for degradation of target proteins. We further discuss the scope and design of degraders and mitigation strategies for overcoming the hook effect seen with degraders. As PROTACs do not follow Lipinski's 'Rule of 5', these molecules face drug metabolism and pharmacokinetic challenges. A detailed section on absorption, distribution, metabolism, and excretion of degraders is provided wherein we discuss methodologies and strategies to surmount the challenges faced by these molecules. For understanding PROTAC-mediated degradation, the characterization and measurement of protein levels in cells is important. Currently used techniques and recent advancements in assessment tools for degraders are discussed. Furthermore, we examine the challenges and emerging technologies that need to be focused on in order to competently develop potent degraders. Many companies are working in this area of emerging new modality and a few PROTACs have already entered clinical trials; the details of the trials are included in this review.
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24
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Qin L, Dai H, Wang J. Key Considerations in Targeted Protein Degradation Drug Discovery and Development. Front Chem 2022; 10:934337. [PMID: 35978859 PMCID: PMC9376879 DOI: 10.3389/fchem.2022.934337] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Targeting proteins’ enzymatic functions with small molecule inhibitors, as well as functions of receptor proteins with small-molecule agonists and antagonists, were the major forms of small-molecule drug development. These small-molecule modulators are based on a conventional occupancy-driven pharmacological approach. For proteome space traditionally considered undruggable by small-molecule modulators, such as enzymes with scaffolding functions, transcription factors, and proteins that lack well-defined binding pockets for small molecules, targeted protein degraders offer the opportunity to drug the proteome with an event-driven pharmacological approach. A degrader molecule, either PROTAC or molecular glue, brings the protein of interest (POI) and E3 ubiquitin ligase in close proximity and engages the ubiquitin-proteasome system (UPS), the cellular waste disposal system for the degradation of the POI. For the development of targeted protein degraders to meet therapeutic needs, several aspects will be considered, namely, the selective degradation of disease-causing proteins, the oral bioavailability of degraders beyond Lipinski’s rule of five (bRo5) scope, demands of new E3 ubiquitin ligases and molecular glue degraders, and drug resistance of the new drug modality. This review will illustrate several under-discussed key considerations in targeted protein degradation drug discovery and development: 1) the contributing factors for the selectivity of PROTAC molecules and the design of PROTACs to selectively degrade synergistic pathological proteins; 2) assay development in combination with a multi-omics approach for the identification of new E3 ligases and their corresponding ligands, as well as molecular glue degraders; 3) a molecular design to improve the oral bioavailability of bRo5 PROTACs, and 4) drug resistance of degraders.
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Affiliation(s)
- Liena Qin
- Insilico Medicine Ltd., Shanghai, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
| | - Han Dai
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- International Magnetobiology Frontier Research Center, Hefei, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
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25
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Riching KM, Caine EA, Urh M, Daniels DL. The importance of cellular degradation kinetics for understanding mechanisms in targeted protein degradation. Chem Soc Rev 2022; 51:6210-6221. [PMID: 35792307 DOI: 10.1039/d2cs00339b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted protein degradation has exploded over the past several years due to preclinical and early clinical therapeutic success of numerous compounds, and the emergence of new degradation modalities, which has broadened the definition of what a degrader is. The most characterized and well-studied small molecule degraders are molecular glues and proteolysis targeting chimeras (PROTACs). These degraders induce a ternary complex between a target protein, degrader, and E3 ligase component, resulting in ubiquitination and subsequent degradation of the target protein via the ubiquitin proteasomal system (UPS). This event-driven process requires success at all steps through a complex cascade of events. As more systems, degraders, and targets are tested, it has become increasingly clear that achieving degradation is only the first critical milestone in a degrader development program. Rather highly efficacious degraders require a combination of multiple optimized parameters: rapid degradation, high potency, high maximal degradation (Dmax), and sustained loss of target without re-dosing. Success to meet these more rigorous goals depends upon the ability to characterize and understand the dynamic cellular degradation profiles and relate them to the underlying mechanism for any given target treated with a specific concentration of degrader. From this starting point, optimization and fine tuning of multiple kinetic parameters such as how fast degradation occurs (the rate), how much of the target is degraded (the extent), and how long the target remains degraded (the duration) can be performed. In this review we explore the diversity of cellular kinetic degradation profiles which can arise after molecular glue and PROTAC treatment and the potential implications of these varying responses. As the overall degradation kinetics are a sum of individual mechanistic steps, each with their own kinetic contributions, we discuss the ways in which changes at any one of these steps could potentially influence the resultant kinetic degradation profiles. Looking forward, we address the importance in characterizing the kinetics of target protein loss in the early stages of degrader design and how this will enable more rapid discovery of therapeutic agents to elicit desired phenotypic outcomes.
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Affiliation(s)
- Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
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26
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Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules consisting of one ligand that binds to a protein of interest (POI) and another that can recruit an E3 ubiquitin ligase. The chemically-induced proximity between the POI and E3 ligase results in ubiquitination and subsequent degradation of the POI by the ubiquitin-proteasome system (UPS). The event-driven mechanism of action (MOA) of PROTACs offers several advantages compared to traditional occupancy-driven small molecule inhibitors, such as a catalytic nature, reduced dosing and dosing frequency, a more potent and longer-lasting effect, an added layer of selectivity to reduce potential toxicity, efficacy in the face of drug-resistance mechanisms, targeting nonenzymatic functions, and expanded target space. Here, we highlight important milestones and briefly discuss lessons learned about targeted protein degradation (TPD) in recent years and conjecture on the efforts still needed to expand the toolbox for PROTAC discovery to ultimately provide promising therapeutics.
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Affiliation(s)
- Ke Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA.
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA. .,Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA.,Department of Pharmacology, Yale University, New Haven, Connecticut 06511, USA
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Sahoo S, Padhy AA, Kumari V, Mishra P. Role of Ubiquitin-Proteasome and Autophagy-Lysosome Pathways in α-Synuclein Aggregate Clearance. Mol Neurobiol 2022; 59:5379-5407. [PMID: 35699874 DOI: 10.1007/s12035-022-02897-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/21/2022] [Indexed: 11/26/2022]
Abstract
Synuclein aggregation in neuronal cells is the primary underlying cause of synucleinopathies. Changes in gene expression patterns, structural modifications, and altered interactions with other cellular proteins often trigger aggregation of α-synuclein, which accumulates as oligomers or fibrils in Lewy bodies. Although fibrillar forms of α-synuclein are primarily considered pathological, recent studies have revealed that even the intermediate states of aggregates are neurotoxic, complicating the development of therapeutic interventions. Autophagy and ubiquitin-proteasome pathways play a significant role in maintaining the soluble levels of α-synuclein inside cells; however, the heterogeneous nature of the aggregates presents a significant bottleneck to its degradation by these cellular pathways. With studies focused on identifying the proteins that modulate synuclein aggregation and clearance, detailed mechanistic insights are emerging about the individual and synergistic effects of these degradation pathways in regulating soluble α-synuclein levels. In this article, we discuss the impact of α-synuclein aggregation on autophagy-lysosome and ubiquitin-proteasome pathways and the therapeutic strategies that target various aspects of synuclein aggregation or degradation via these pathways. Additionally, we also highlight the natural and synthetic compounds that have shown promise in alleviating the cellular damage caused due to synuclein aggregation.
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Affiliation(s)
- Subhashree Sahoo
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Amrita Arpita Padhy
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Varsha Kumari
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Parul Mishra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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28
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Targeted protein degraders march towards the clinic for neurodegenerative diseases. Ageing Res Rev 2022; 78:101616. [PMID: 35378298 DOI: 10.1016/j.arr.2022.101616] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/26/2022] [Accepted: 03/30/2022] [Indexed: 12/28/2022]
Abstract
Protein degraders are emerging as potent therapeutic tools to address neurological disorders and many complex diseases. It offered several key advantages, including the doses, drug resistance, and side effects over traditional occupancy-based inhibitors. Translation of chemical degraders into a clinical therapy for neurodegenerative disorders has a well-documented knowledge and resource gap. Researchers strive to develop clinical candidates employing chemical degraders' technologies, including hydrophobic tagging, molecular glues, proteolysis targeting chimeras (PROTACs), specific and nongenetic Inhibitor of Apoptosis Protein (IAP)-dependent protein erasers (SNIPERs), autophagy targeted chimeras, and autophagosome-tethered compounds for targeted degradation of pathological markers in neurodegenerative disease. Herein, we examined the present state of chemical-mediated targeted protein degradation in the quest for medications to treat neurodegenerative diseases. We further identified targeted degraders under clinical development for neurodegenerative diseases summarizing pertinent discoveries guiding the future of degradation therapeutics. We also addressed the necessary pharmacological interventions needed to achieve unprecedented therapeutic efficacy and its associated challenges.
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Xu Z, Liu X, Ma X, Zou W, Chen Q, Chen F, Deng X, Liang J, Dong C, Lan K, Wu S, Zhou HB. Discovery of oseltamivir-based novel PROTACs as degraders targeting neuraminidase to combat H1N1 influenza virus. CELL INSIGHT 2022; 1:100030. [PMID: 37193052 PMCID: PMC10120310 DOI: 10.1016/j.cellin.2022.100030] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 05/16/2023]
Abstract
Annual and sporadic influenza outbreaks pose a great threat to human health and the economy worldwide. Moreover, the frequent mutation of influenza viruses caused by antigen drift complicates the application of antiviral therapeutics. As such, there is an urgent need for novel antiviral agents to tackle the problem of insufficient efficacy of licensed drugs. Inspired by the success of the newly emerged PROTACs (PROteolysis TArgeting Chimeras) strategy, we report herein the design and synthesis of novel PROTAC molecules based on an oseltamivir scaffold to combat severe annual influenza outbreaks. Among these, several compounds showed good anti-H1N1 activity and efficient influenza neuraminidase (NA) degradation activity. The best compound, 8e, effectively induced influenza NA degradation in a dose-dependent manner and relied on the ubiquitin-proteasome pathway. Moreover, Compound 8e exhibited potent antiviral activity toward both wild-type H1N1 virus and an oseltamivir-resistant strain (H1N1, H274Y). A molecular docking study demonstrated that Compound 8e had good hydrogen-bonding and hydrophobic interactions with both the active sites of NA and Von Hippel-Lindau (VHL) proteins, which could effectively drive the favorable interaction of these two proteins. Thus, as the first report of a successful anti-influenza PROTAC, this proof of concept will greatly widen the application range of the PROTAC technique to antiviral drug discovery.
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Affiliation(s)
- Zhichao Xu
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xinjin Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaoyu Ma
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Wenting Zou
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Qi Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Feifei Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaofei Deng
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Jinsen Liang
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Chune Dong
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hai-Bing Zhou
- State Key Laboratory of Virology, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
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Abstract
AbstractThe druggable genome is limited by structural features that can be targeted by small molecules in disease-relevant proteins. While orthosteric and allosteric protein modulators have been well studied, they are limited to antagonistic/agonistic functions. This approach to protein modulation leaves many disease-relevant proteins as undruggable targets. Recently, protein-protein interaction modulation has emerged as a promising therapeutic field for previously undruggable protein targets. Molecular glues and heterobifunctional degraders such as PROTACs can facilitate protein interactions and bring the proteasome into proximity to induce targeted protein degradation. In this review, we discuss the function and rational design of molecular glues, heterobifunctional degraders, and hydrophobic tag degraders. We also review historic and novel molecular glues and targets and discuss the challenges and opportunities in this new therapeutic field.
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Luo X, Archibeque I, Dellamaggiore K, Smither K, Homann O, Lipford JR, Mohl D. Profiling of diverse tumor types establishes the broad utility of VHL-based ProTaCs and triages candidate ubiquitin ligases. iScience 2022; 25:103985. [PMID: 35295813 PMCID: PMC8919295 DOI: 10.1016/j.isci.2022.103985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 11/01/2021] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
The success of small molecule therapeutics that promotes degradation of critical cancer targets has fueled an intense effort to mimic this activity with bispecific molecules called PROTACs (proteolysis targeting chimeras). The simultaneous binding of PROTACs to a ligase and target can induce proximity-driven ubiquitination and degradation. VHL and CRBN are the two best characterized PROTAC ligases, but the rules governing their cellular activities remain unclear. To establish these requirements and extend them to new ligases, we screened a panel of 56 cell lines with two potent PROTACs that utilized VHL, MZ1, or CRBN, dBET1 to induce degradation of BRD4. With notable exceptions, MZ1 was broadly active in the panel whereas dBET1 was frequently inactive. A search for predictive biomarkers of PROTAC activity found that expression and mutation of VHL and CRBN were themselves predictors of PROTAC activity in the cell line panel. Profiling of diverse tumor types establishes the broad utility of VHL-based PROTACs CRBN-dependent dBET1 activity is frequently suppressed in cancer cell lines Copy loss and mRNA expression predict the activity of VHL and CRBN-dependent PROTACs
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Affiliation(s)
- Xin Luo
- AMGEN Research, Amgen Inc, South San Francisco, CA 94080, USA
| | | | | | - Kate Smither
- AMGEN Research, Amgen Inc, Thousand Oaks, CA 91320, USA
| | - Oliver Homann
- AMGEN Research, Amgen Inc, South San Francisco, CA 94080, USA
| | | | - Dane Mohl
- AMGEN Research, Amgen Inc, Thousand Oaks, CA 91320, USA
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Shi S, Du Y, Huang L, Cui J, Niu J, Xu Y, Zhu Q. Discovery of novel potent covalent inhibitor-based EGFR degrader with excellent in vivo efficacy. Bioorg Chem 2022; 120:105605. [DOI: 10.1016/j.bioorg.2022.105605] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 01/22/2023]
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Yu X, Xu J, Shen Y, Cahuzac KM, Park KS, Dale B, Liu J, Parsons RE, Jin J. Discovery of Potent, Selective, and In Vivo Efficacious AKT Kinase Protein Degraders via Structure-Activity Relationship Studies. J Med Chem 2022; 65:3644-3666. [PMID: 35119851 PMCID: PMC8900464 DOI: 10.1021/acs.jmedchem.1c02165] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We recently reported a potent, selective, and in vivo efficacious AKT degrader, MS21, which is a von Hippel-Lindau (VHL)-recruiting proteolysis targeting chimera (PROTAC) based on the AKT inhibitor AZD5363. However, no structure-activity relationship (SAR) studies that resulted in this discovery have been reported. Herein, we present our SAR studies that led to the discovery of MS21, another VHL-recruiting AKT degrader, MS143 (compound 20) with similar potency as MS21, and a novel cereblon (CRBN)-recruiting PROTAC, MS5033 (compound 35). Compounds 20 and 35 induced rapid and robust AKT degradation in a concentration- and time-dependent manner via hijacking the ubiquitin-proteasome system. Compound 20 suppressed cell growth more effectively than AZD5363 in multiple cancer cell lines. Furthermore, 20 and 35 displayed good plasma exposure levels in mice and are suitable for in vivo efficacy studies. Lastly, compound 20 effectively suppressed tumor growth in vivo in a xenograft model without apparent toxicity.
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Affiliation(s)
| | | | - Yudao Shen
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kaitlyn M. Cahuzac
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kwang-su Park
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Brandon Dale
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jing Liu
- Corresponding Authors: Jing Liu – Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States; , Ramon E. Parsons – Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States; , Jian Jin – Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States;
| | - Ramon E. Parsons
- Corresponding Authors: Jing Liu – Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States; , Ramon E. Parsons – Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States; , Jian Jin – Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States;
| | - Jian Jin
- Corresponding Authors: Jing Liu – Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States; , Ramon E. Parsons – Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States; , Jian Jin – Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States;
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34
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Sibley CD, Schneekloth JS. Heterobifunctional molecules tackle targeted protein dephosphorylation. Trends Pharmacol Sci 2022; 43:263-265. [DOI: 10.1016/j.tips.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
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35
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Chen PH, Hu Z, An E, Okeke IO, Zheng S, Luo X, Gong A, Jaime-Figueroa S, Crews CM. Modulation of Phosphoprotein Activity by Phosphorylation Targeting Chimeras (PhosTACs). ACS Chem Biol 2021; 16:2808-2815. [PMID: 34780684 PMCID: PMC10437008 DOI: 10.1021/acschembio.1c00693] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protein phosphorylation, which regulates many critical aspects of cell biology, is dynamically governed by kinases and phosphatases. Many diseases are associated with dysregulated hyperphosphorylation of critical proteins, such as retinoblastoma protein in cancer. Although kinase inhibitors have been widely applied in the clinic, growing evidence of off-target effects and increasing drug resistance prompts the need to develop a new generation of drugs. Here, we propose a proof-of-concept study of phosphorylation targeting chimeras (PhosTACs). Similar to PROTACs in their ability to induce ternary complexes, PhosTACs focus on recruiting a Ser/Thr phosphatase to a phosphosubstrate to mediate its dephosphorylation. However, distinct from PROTACs, PhosTACs can uniquely provide target gain-of-function opportunities to manipulate protein activity. In this study, we applied a chemical biology approach to evaluate the feasibility of PhosTACs by recruiting the scaffold and catalytic subunits of the PP2A holoenzyme to protein substrates such as PDCD4 and FOXO3a for targeted protein dephosphorylation. For FOXO3a, this dephosphorylation resulted in the transcriptional activation of a FOXO3a-responsive reporter gene.
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Affiliation(s)
- Po-Han Chen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Zhenyi Hu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Elvira An
- Department of Pharmacology, Yale University, New Haven, Connecticut, 06511, United States
| | - Ifunanya Ozioma Okeke
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Sijin Zheng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
- Yale University School of Medicine, New Haven, Connecticut, 06511, United States
| | - Xuanmeng Luo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Angela Gong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Saul Jaime-Figueroa
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
| | - Craig M. Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06511, United States
- Department of Chemistry, Yale University, New Haven, Connecticut, 06511, United States
- Department of Pharmacology, Yale University, New Haven, Connecticut, 06511, United States
- Yale University School of Medicine, New Haven, Connecticut, 06511, United States
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36
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Grohmann C, Marapana DS, Ebert G. Targeted protein degradation at the host-pathogen interface. Mol Microbiol 2021; 117:670-681. [PMID: 34816514 DOI: 10.1111/mmi.14849] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022]
Abstract
Infectious diseases remain a major burden to global health. Despite the implementation of successful vaccination campaigns and efficient drugs, the increasing emergence of pathogenic vaccine or treatment resistance demands novel therapeutic strategies. The development of traditional therapies using small-molecule drugs is based on modulating protein function and activity through the occupation of active sites such as enzyme inhibition or ligand-receptor binding. These prerequisites result in the majority of host and pathogenic disease-relevant, nonenzymatic and structural proteins being labeled "undruggable." Targeted protein degradation (TPD) emerged as a powerful strategy to eliminate proteins of interest including those of the undruggable variety. Proteolysis-targeting chimeras (PROTACs) are rationally designed heterobifunctional small molecules that exploit the cellular ubiquitin-proteasome system to specifically mediate the highly selective and effective degradation of target proteins. PROTACs have shown remarkable results in the degradation of various cancer-associated proteins, and several candidates are already in clinical development. Significantly, PROTAC-mediated TPD holds great potential for targeting and modulating pathogenic proteins, especially in the face of increasing drug resistance to the best-in-class treatments. In this review, we discuss advances in the development of TPD in the context of targeting the host-pathogen interface and speculate on their potential use to combat viral, bacterial, and parasitic infection.
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Affiliation(s)
- Christoph Grohmann
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Danushka S Marapana
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Gregor Ebert
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
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37
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Li Y, Wang C, Xi HM, Li WT, Liu YJ, Feng S, Chu YJ, Wang YH. Chorionic villus-derived mesenchymal stem cells induce E3 ligase TRIM72 expression and regulate cell behaviors through ubiquitination of p53 in trophoblasts. FASEB J 2021; 35:e22005. [PMID: 34788479 DOI: 10.1096/fj.202100801r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/23/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022]
Abstract
Preeclampsia is a significant contributor for maternal or fetal morbidity and mortality, which is characterized by reduced invasion capacity of trophoblasts and is regulated by extracellular matrix (ECM). It is still under investigation whether chorionic villus-derived mesenchymal stem cells (CVMSC) could affect the functionality of trophoblasts. In this study, CVMSC-derived exosomes were isolated; their effect on trophoblasts was investigated based on the CCK8 assay, migration assay, and apoptosis detection. And the underlying mechanism of this effect was investigated using mRNA sequencing, western blot, co-immunoprecipitation, luciferase report assay, and ubiquitination assay. The results show that CVMSC-derived exosomes promote migration and proliferation of trophoblasts, and also reduce cell apoptosis. mRNA sequencing confirmed that after treatment of CVMSC-derived exosomes, Tripartite Motif Containing 72 (TRIM72) expression was upregulated and Tumor Protein P53 (P53) expression was downregulated, both significantly in trophoblasts. Subsequent study confirms that TRM72 can directly interact with P53 and promote P53 ubiquitination and proteasomal degradation, reducing apoptosis rate and elevating proliferation and migration in trophoblasts. Our study confirms that CVMSC-derived exosomes promote trophoblast migration and proliferation by upregulating TRIM72 expression, and subsequently advance P53 ubiquitination and proteasomal degradation.
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Affiliation(s)
- Yan Li
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chen Wang
- Department of Operating Room, Qingdao Municipal Hospital, Qingdao, China
| | - Hong-Min Xi
- Department of Neonatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wen-Ting Li
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ya-Jun Liu
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shan Feng
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yi-Jing Chu
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yi-Hao Wang
- Department of Pain Management, Qingdao Municipal Hospital, Qingdao, China
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Luo M, Li Z, Li S, Lee TY. A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction. BMC Bioinformatics 2021; 22:507. [PMID: 34663215 PMCID: PMC8524957 DOI: 10.1186/s12859-021-04435-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/04/2021] [Indexed: 01/01/2023] Open
Abstract
Background Ubiquitylation is an important post-translational modification of proteins that not only plays a central role in cellular coding, but is also closely associated with the development of a variety of diseases. The specific selection of substrate by ligase E3 is the key in ubiquitylation. As various high-throughput analytical techniques continue to be applied to the study of ubiquitylation, a large amount of ubiquitylation site data, and records of E3-substrate interactions continue to be generated. Biomedical literature is an important vehicle for information on E3-substrate interactions in ubiquitylation and related new discoveries, as well as an important channel for researchers to obtain such up to date data. The continuous explosion of ubiquitylation related literature poses a great challenge to researchers in acquiring and analyzing the information. Therefore, automatic annotation of these E3-substrate interaction sentences from the available literature is urgently needed. Results In this research, we proposed a model based on representation and attention mechanism based deep learning methods, to automatic annotate E3-substrate interaction sentences in biomedical literature. Focusing on the sentences with E3 protein inside, we applied several natural language processing methods and a Long Short-Term Memory (LSTM)-based deep learning classifier to train the model. Experimental results had proved the effectiveness of our proposed model. And also, the proposed attention mechanism deep learning method outperforms other statistical machine learning methods. We also created a manual corpus of E3-substrate interaction sentences, in which the E3 proteins and substrate proteins are also labeled, in order to construct our model. The corpus and model proposed by our research are definitely able to be very useful and valuable resource for advancement of ubiquitylation-related research. Conclusion Having the entire manual corpus of E3-substrate interaction sentences readily available in electronic form will greatly facilitate subsequent text mining and machine learning analyses. Automatic annotating ubiquitylation sentences stating E3 ligase-substrate interaction is significantly benefited from semantic representation and deep learning. The model enables rapid information accessing and can assist in further screening of key ubiquitylation ligase substrates for in-depth studies.
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Affiliation(s)
- Mengqi Luo
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhongyan Li
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Shangfu Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China
| | - Tzong-Yi Lee
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China. .,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 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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40
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Pinch BJ, Buckley DL, Gleim S, Brittain SM, Tandeske L, D'Alessandro PL, Hauseman ZJ, Lipps J, Xu L, Harvey EP, Schirle M, Sprague ER, Forrester WC, Dovala D, McGregor LM, Thoma CR. A strategy to assess the cellular activity of E3 ligase components against neo-substrates using electrophilic probes. Cell Chem Biol 2021; 29:57-66.e6. [PMID: 34499862 DOI: 10.1016/j.chembiol.2021.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 06/17/2021] [Accepted: 08/20/2021] [Indexed: 01/12/2023]
Abstract
While there are hundreds of predicted E3 ligases, characterizing their applications for targeted protein degradation has proved challenging. Here, we report a chemical biology approach to evaluate the ability of modified recombinant E3 ligase components to support neo-substrate degradation. Bypassing the need for specific E3 ligase binders, we use maleimide-thiol chemistry for covalent functionalization followed by E3 electroporation (COFFEE) in live cells. We demonstrate that electroporated recombinant von Hippel-Lindau (VHL) protein, covalently functionalized at its ligandable cysteine with JQ1 or dasatinib, induces degradation of BRD4 or tyrosine kinases, respectively. Furthermore, by applying COFFEE to SPSB2, a Cullin-RING ligase 5 receptor, as well as to SKP1, the adaptor protein for Cullin-RING ligase 1 F box (SCF) complexes, we validate this method as a powerful approach to define the activity of previously uncharacterized ubiquitin ligase components, and provide further evidence that not only E3 ligase receptors but also adaptors can be directly hijacked for neo-substrate degradation.
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Affiliation(s)
- Benika J Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Dennis L Buckley
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott M Brittain
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Laura Tandeske
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | | | | | - Jennifer Lipps
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Lei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Edward P Harvey
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | | | - Dustin Dovala
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA.
| | - Lynn M McGregor
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
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41
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Chen X, Htet ZM, López-Alfonzo E, Martin A, Walters KJ. Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies. FEBS J 2021; 288:5231-5251. [PMID: 33211406 PMCID: PMC8131406 DOI: 10.1111/febs.15638] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022]
Abstract
The 26S proteasome is responsible for regulated proteolysis in eukaryotic cells. Its substrates are diverse in structure, function, sequence length, and amino acid composition, and are targeted to the proteasome by post-translational modification with ubiquitin. Ubiquitination occurs through a complex enzymatic cascade and can also signal for other cellular events, unrelated to proteasome-catalyzed degradation. Like other post-translational protein modifications, ubiquitination is reversible, with ubiquitin chain hydrolysis catalyzed by the action of deubiquitinating enzymes (DUBs), ~ 90 of which exist in humans and allow for temporal events and dynamic ubiquitin-chain remodeling. DUBs have been known for decades to be an integral part of the proteasome, as deubiquitination is coupled to substrate unfolding and translocation into the internal degradation chamber. Moreover, the proteasome also binds several ubiquitinating enzymes and shuttle factors that recruit ubiquitinated substrates. The role of this intricate machinery and how ubiquitinated substrates interact with proteasomes remains an area of active investigation. Here, we review what has been learned about the mechanisms used by the proteasome to bind ubiquitinated substrates, substrate shuttle factors, ubiquitination machinery, and DUBs. We also discuss many open questions that require further study or the development of innovative approaches to be answered. Finally, we address the promise of expanded therapeutic targeting that could benefit from such new discoveries.
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Affiliation(s)
- Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
| | - Erika López-Alfonzo
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California at Berkeley, CA, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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42
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Rodriguez-Rivera FP, Levi SM. Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms. ACS CENTRAL SCIENCE 2021; 7:1117-1125. [PMID: 34345664 PMCID: PMC8323112 DOI: 10.1021/acscentsci.1c00389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Indexed: 06/13/2023]
Abstract
Diverging from traditional target inhibition, proteasomal protein degradation approaches have emerged as novel therapeutic modalities that embody distinct pharmacological profiles and can access previously undrugged targets. Small molecule degraders have the potential to catalytically destroy target proteins at substoichiometric concentrations, thus lowering administered doses and extending pharmacological effects. With this mechanistic premise, research efforts have advanced the development of small molecule degraders that benefit from stable and increased affinity ternary complexes. However, a holistic framework that evaluates different degradation modes from a catalytic perspective, including focusing on kinetically favored degradation mechanisms, is lacking. In this Outlook, we introduce the concept of an induced cooperativity spectrum as a unifying framework to mechanistically understand catalytic degradation profiles. This framework is bolstered by key examples of published molecular degraders extending from molecular glues to bivalent degraders. Critically, we discuss remaining challenges and future opportunities in drug discovery to rationally design and phenotypically screen for efficient degraders.
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Affiliation(s)
- Frances P. Rodriguez-Rivera
- Discovery
Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Samuel M. Levi
- Pfizer
Worldwide Research and Development, Pfizer,
Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
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43
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Massafra V, Tundo S, Dietzig A, Ducret A, Jost C, Klein C, Kontermann RE, Knoetgen H, Steegmaier M, Romagnani A, Nagel YA. Proteolysis-Targeting Chimeras Enhance T Cell Bispecific Antibody-Driven T Cell Activation and Effector Function through Increased MHC Class I Antigen Presentation in Cancer Cells. THE JOURNAL OF IMMUNOLOGY 2021; 207:493-504. [PMID: 34215653 DOI: 10.4049/jimmunol.2000252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022]
Abstract
The availability of Ags on the surface of tumor cells is crucial for the efficacy of cancer immunotherapeutic approaches using large molecules, such as T cell bispecific Abs (TCBs). Tumor Ags are processed through intracellular proteasomal protein degradation and are displayed as peptides on MHC class I (MHC I). Ag recognition through TCRs on the surface of CD8+ T cells can elicit a tumor-selective immune response. In this article, we show that proteolysis-targeting chimeras (PROTACs) that target bromo- and extraterminal domain proteins increase the abundance of the corresponding target-derived peptide Ags on MHC I in both liquid and solid tumor-derived human cell lines. This increase depends on the engagement of the E3 ligase to bromo- and extraterminal domain protein. Similarly, targeting of a doxycycline-inducible Wilms tumor 1 (WT1)-FKBP12F36V fusion protein, by a mutant-selective FKBP12F36V degrader, increases the presentation of WT1 Ags in human breast cancer cells. T cell-mediated response directed against cancer cells was tested on treatment with a TCR-like TCB, which was able to bridge human T cells to a WT1 peptide displayed on MHC I. FKBP12F36V degrader treatment increased the expression of early and late activation markers (CD69, CD25) in T cells; the secretion of granzyme β, IFN-γ, and TNF-α; and cancer cell killing in a tumor-T cell coculture model. This study supports harnessing targeted protein degradation in tumor cells, for modulation of T cell effector function, by investigating for the first time, to our knowledge, the potential of combining a degrader and a TCB in a cancer immunotherapy setting.
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Affiliation(s)
- Vittoria Massafra
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Sofia Tundo
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Aline Dietzig
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Axel Ducret
- Pharmaceutical Sciences-Biomarkers, Bioinformatics, and Omics, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Christian Jost
- Cancer Immunotherapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Zurich, F. Hoffmann-La Roche Ltd., Schlieren, Switzerland
| | - Christian Klein
- Cancer Immunotherapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Zurich, F. Hoffmann-La Roche Ltd., Schlieren, Switzerland
| | - Roland E Kontermann
- Institute of Cell Biology and Immunology, Stuttgart University, Stuttgart, Germany
| | - Hendrik Knoetgen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland; and
| | - Martin Steegmaier
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, F. Hoffmann-La Roche Ltd., Penzberg, Germany
| | - Andrea Romagnani
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Yvonne A Nagel
- Molecular Targeted Therapy-Discovery Oncology, Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland;
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44
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Chain reactions: molecular mechanisms of RBR ubiquitin ligases. Biochem Soc Trans 2021; 48:1737-1750. [PMID: 32677670 PMCID: PMC7458406 DOI: 10.1042/bst20200237] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Ubiquitination is a fundamental post-translational modification that regulates almost all aspects of cellular signalling and is ultimately catalysed by the action of E3 ubiquitin ligases. The RING-between-RING (RBR) family of E3 ligases encompasses 14 distinct human enzymes that are defined by a unique domain organisation and catalytic mechanism. Detailed characterisation of several RBR ligase family members in the last decade has revealed common structural and mechanistic features. At the same time these studies have highlighted critical differences with respect to autoinhibition, activation and catalysis. Importantly, the majority of RBR E3 ligases remain poorly studied, and thus the extent of diversity within the family remains unknown. In this mini-review we outline the current understanding of the RBR E3 mechanism, structure and regulation with a particular focus on recent findings and developments that will shape the field in coming years.
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45
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Cresser-Brown JO, Marsh GP, Maple HJ. Reviewing the toolbox for degrader development in oncology. Curr Opin Pharmacol 2021; 59:43-51. [PMID: 34058637 DOI: 10.1016/j.coph.2021.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022]
Abstract
The field of targeted protein degradation encompasses a growing number of modalities that achieve potent and selective knockdown of target proteins at the post-translational level. Among the most clinically advanced are bifunctional small-molecule degraders, also referred to as PROteolysis Targeting Chimeras, Degronimids, SNIPERs, or uSMITEs. Although applicable to many disease indications, oncology stands to be the first to benefit from this promising therapeutic approach, with the first investigational new drugs (INDs) filed in 2019 and a proliferation of research specifically focused on harnessing degraders for cancer treatment. In this review, we consider the toolbox of guidelines, reagents, and technologies that has evolved alongside the field to support degrader research and development.
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Affiliation(s)
- Joel O Cresser-Brown
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK
| | - Graham P Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK
| | - Hannah J Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK.
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46
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Song YQ, Wu C, Wu KJ, Han QB, Miao XM, Ma DL, Leung CH. Ubiquitination Regulators Discovered by Virtual Screening for the Treatment of Cancer. Front Cell Dev Biol 2021; 9:665646. [PMID: 34055799 PMCID: PMC8149734 DOI: 10.3389/fcell.2021.665646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/15/2021] [Indexed: 12/03/2022] Open
Abstract
The ubiquitin-proteasome system oversees cellular protein degradation in order to regulate various critical processes, such as cell cycle control and DNA repair. Ubiquitination can serve as a marker for mutation, chemical damage, transcriptional or translational errors, and heat-induced denaturation. However, aberrant ubiquitination and degradation of tumor suppressor proteins may result in the growth and metastasis of cancer. Hence, targeting the ubiquitination cascade reaction has become a potential strategy for treating malignant diseases. Meanwhile, computer-aided methods have become widely accepted as fast and efficient techniques for early stage drug discovery. This review summarizes ubiquitination regulators that have been discovered via virtual screening and their applications for cancer treatment.
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Affiliation(s)
- Ying-Qi Song
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Ke-Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Quan-Bin Han
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Xiang-Min Miao
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
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47
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Kannt A, Đikić I. Expanding the arsenal of E3 ubiquitin ligases for proximity-induced protein degradation. Cell Chem Biol 2021; 28:1014-1031. [PMID: 33945791 DOI: 10.1016/j.chembiol.2021.04.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Efficacy and selectivity of molecules inducing protein degradation depend on their affinity to the target protein but also on the type of E3 ubiquitin ligase that is recruited to trigger proteasomal degradation. While tremendous progress has been made on the former, the latter-the arsenal of E3 ligases that can be hijacked for targeted protein degradation-is still largely unexplored. Only about 2% of the more than 600 E3 ligases have been utilized to date. Exploiting additional E3 ligases that are, for example, selectively expressed in specific tissues or cells, or regulated under certain conditions, can considerably broaden the applicability of molecular degraders as a therapeutic modality. Here, we provide an overview of major classes of E3 ligases, review the enzymes that have been exploited for induced protein degradation and approaches used to identify or design E3 ligands, and highlight challenges and opportunities for targeting new E3 ligases.
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Affiliation(s)
- Aimo Kannt
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Clinical Pharmacology, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ivan Đikić
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
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48
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Alabi SB, Crews CM. Major advances in targeted protein degradation: PROTACs, LYTACs, and MADTACs. J Biol Chem 2021; 296:100647. [PMID: 33839157 PMCID: PMC8131913 DOI: 10.1016/j.jbc.2021.100647] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Of late, targeted protein degradation (TPD) has surfaced as a novel and innovative chemical tool and therapeutic modality. By co-opting protein degradation pathways, TPD facilitates complete removal of the protein molecules from within or outside the cell. While the pioneering Proteolysis-Targeting Chimera (PROTAC) technology and molecular glues hijack the ubiquitin-proteasome system, newer modalities co-opt autophagy or the endo-lysosomal pathway. Using this mechanism, TPD is posited to largely expand the druggable space far beyond small-molecule inhibitors. In this review, we discuss the major advances in TPD, highlight our current understanding, and explore outstanding questions in the field.
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Affiliation(s)
- Shanique B Alabi
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA
| | - Craig M Crews
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA; Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA; Department of Chemistry, Yale University, New Haven, Connecticut, USA.
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49
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Kiely-Collins H, Winter GE, Bernardes GJL. The role of reversible and irreversible covalent chemistry in targeted protein degradation. Cell Chem Biol 2021; 28:952-968. [PMID: 33789091 DOI: 10.1016/j.chembiol.2021.03.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/30/2021] [Accepted: 03/09/2021] [Indexed: 12/15/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) that degrade disease-causing proteins by hijacking the endogenous ubiquitin-proteasome system have emerged as an exciting and transformative technology in both chemical biology and drug discovery. Currently, the majority of PROTACs use reversible non-covalent ligands for both the target protein of interest (POI) and E3 ligase. In this review, we explore the burgeoning role of reversible and irreversible covalent chemistry in targeted protein degradation. We highlight the key advantages of targeted covalent inhibitors, whether as the target POI or E3 ligase ligand, such as their ability to enhance the selectivity of PROTACs, enable access to more of the "undruggable" proteome and expand the repertoire of recruited E3 ligases.
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Affiliation(s)
- Hannah Kiely-Collins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Instituto de Medicina Molecular, Faculdade de Medicina de Universidad de Lisboa, Avenida Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
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50
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Maneiro M, De Vita E, Conole D, Kounde CS, Zhang Q, Tate EW. PROTACs, molecular glues and bifunctionals from bench to bedside: Unlocking the clinical potential of catalytic drugs. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:67-190. [PMID: 34147206 DOI: 10.1016/bs.pmch.2021.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The vast majority of currently marketed drugs rely on small molecules with an 'occupancy-driven' mechanism of action (MOA). Therefore, the efficacy of these therapeutics depends on a high degree of target engagement, which often requires high dosages and enhanced drug exposure at the target site, thus increasing the risk of off-target toxicities (Churcher, 2018 [1]). Although small molecule drugs have been successfully used as treatments for decades, tackling a variety of disease-relevant targets with a defined binding site, many relevant therapeutic targets remain challenging to drug due, for example, to lack of well-defined binding pockets or large protein-protein interaction (PPI) interfaces which resist interference (Dang et al., 2017 [2]). In the quest for alternative therapeutic approaches to address different pathologies and achieve enhanced efficacy with reduced side effects, ligand-induced targeted protein degradation (TPD) has gained the attention of many research groups both in academia and in industry in the last two decades. This therapeutic modality represents a novel paradigm compared to conventional small-molecule inhibitors. To pursue this strategy, heterobifunctional small molecule degraders, termed PROteolysis TArgeting Chimeras (PROTACs) have been devised to artificially redirect a protein of interest (POI) to the cellular protein homeostasis machinery for proteasomal degradation (Chamberlain et al., 2019 [3]). In this chapter, the development of PROTACs will first be discussed providing a historical perspective in parallel to the experimental progress made to understand this novel therapeutic modality. Furthermore, common strategies for PROTAC design, including assays and troubleshooting tips will be provided for the reader, before presenting a compendium of all PROTAC targets reported in the literature to date. Due to the recent advancement of these molecules into clinical trials, consideration of pharmacokinetics and pharmacodynamic properties will be introduced, together with the biotech landscape that has developed from the success of PROTACs. Finally, an overview of subsequent strategies for targeted protein degradation will be presented, concluding with further scientific quests triggered by the invention of PROTACs.
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Affiliation(s)
- M Maneiro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - E De Vita
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - D Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - C S Kounde
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Q Zhang
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - E W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom.
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