51
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D'Amico F, Mukhopadhyay R, Ovaa H, Mulder MPC. Targeting TRIM Proteins: A Quest towards Drugging an Emerging Protein Class. Chembiochem 2021; 22:2011-2031. [PMID: 33482040 PMCID: PMC8251876 DOI: 10.1002/cbic.202000787] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/22/2021] [Indexed: 02/06/2023]
Abstract
The ubiquitylation machinery regulates several fundamental biological processes from protein homeostasis to a wide variety of cellular signaling pathways. As a consequence, its dysregulation is linked to diseases including cancer, neurodegeneration, and autoimmunity. With this review, we aim to highlight the therapeutic potential of targeting E3 ligases, with a special focus on an emerging class of RING ligases, named tri-partite motif (TRIM) proteins, whose role as targets for drug development is currently gaining pharmaceutical attention. TRIM proteins exert their catalytic activity as scaffolds involved in many protein-protein interactions, whose multidomains and adapter-like nature make their druggability very challenging. Herein, we give an overview of the current understanding of this class of single polypeptide RING E3 ligases and discuss potential targeting options.
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Affiliation(s)
- Francesca D'Amico
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Rishov Mukhopadhyay
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Monique P. C. Mulder
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
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52
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Qi SM, Dong J, Xu ZY, Cheng XD, Zhang WD, Qin JJ. PROTAC: An Effective Targeted Protein Degradation Strategy for Cancer Therapy. Front Pharmacol 2021; 12:692574. [PMID: 34025443 PMCID: PMC8138175 DOI: 10.3389/fphar.2021.692574] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 01/09/2023] Open
Abstract
Proteolysis targeting chimeric (PROTAC) technology is an effective endogenous protein degradation tool developed in recent years that can ubiquitinate the target proteins through the ubiquitin-proteasome system (UPS) to achieve an effect on tumor growth. A number of literature studies on PROTAC technology have proved an insight into the feasibility of PROTAC technology to degrade target proteins. Additionally, the first oral PROTACs (ARV-110 and ARV-471) have shown encouraging results in clinical trials for prostate and breast cancer treatment, which inspires a greater enthusiasm for PROTAC research. Here we focus on the structures and mechanisms of PROTACs and describe several classes of effective PROTAC degraders based on E3 ligases.
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Affiliation(s)
- Si-Min Qi
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinyun Dong
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Zhi-Yuan Xu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xiang-Dong Cheng
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Wei-Dong Zhang
- School of Pharmacy, Naval Medical University, Shanghai, China
| | - Jiang-Jiang Qin
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China.,The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
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53
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Morgan JJ, Crawford LJ. The Ubiquitin Proteasome System in Genome Stability and Cancer. Cancers (Basel) 2021; 13:2235. [PMID: 34066546 PMCID: PMC8125356 DOI: 10.3390/cancers13092235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/18/2023] Open
Abstract
Faithful DNA replication during cellular division is essential to maintain genome stability and cells have developed a sophisticated network of regulatory systems to ensure its integrity. Disruption of these control mechanisms can lead to loss of genomic stability, a key hallmark of cancer. Ubiquitination is one of the most abundant regulatory post-translational modifications and plays a pivotal role in controlling replication progression, repair of DNA and genome stability. Dysregulation of the ubiquitin proteasome system (UPS) can contribute to the initiation and progression of neoplastic transformation. In this review we provide an overview of the UPS and summarize its involvement in replication and replicative stress, along with DNA damage repair. Finally, we discuss how the UPS presents as an emerging source for novel therapeutic interventions aimed at targeting genomic instability, which could be utilized in the treatment and management of cancer.
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Affiliation(s)
| | - Lisa J. Crawford
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7BL, UK;
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54
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Mukhamejanova Z, Tong Y, Xiang Q, Xu F, Pang J. Recent Advances in the Design and Development of Anticancer Molecules based on PROTAC Technology. Curr Med Chem 2021; 28:1304-1327. [PMID: 32164504 DOI: 10.2174/0929867327666200312112412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 11/22/2022]
Abstract
PROTAC (Proteolysis Targeting Chimera) degraders based on protein knockdown technology are now suggested as a novel option for the treatment of various diseases. Over the last couple of years, the application of PROTAC technology has spread in a wide range of disorders, and plenty of PROTAC molecules with high potency have been reported. Mostly developing for anticancer therapy, these molecules showed high selectivities to target proteins, the ability to significantly induce degradation of oncoproteins, good in vitro and in vivo results. In this review, we summarized the recent development of PROTAC technology in the anticancer therapy field, including molecular design, types of targeted proteins, in vitro and in vivo results. Additionally, we also discuss the prospects and challenges for the application of candidates based on PROTAC strategy in clinical trials.
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Affiliation(s)
| | - Yichen Tong
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qi Xiang
- Institute of Biomedicine & Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jiyan Pang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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55
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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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56
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Hughes GR, Dudey AP, Hemmings AM, Chantry A. Frontiers in PROTACs. Drug Discov Today 2021; 26:2377-2383. [PMID: 33872800 DOI: 10.1016/j.drudis.2021.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
Targeting protein-protein interactions (PPI) is a key focus in the development of new and emerging small-molecule therapeutics. Shallow interacting surfaces can render PPI targeting notoriously difficult. This leaves many therapeutically captivating targets 'undruggable'. Despite these challenges, there has been extraordinary progress circumventing this issue by hijacking the ubiquitin proteasome system (UPS) to target selected substrates for destruction using target-based degradation (TBD) strategies, including bifunctional molecules known as proteolysis-targeting chimeras (PROTACs). In this review, we discuss some of the most recent innovative concepts emerging from PROTAC research and related technologies.
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Affiliation(s)
- Gregory R Hughes
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK; Department of Chemistry, King's College London, SE1 1DB, UK
| | - Ashley P Dudey
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Andrew M Hemmings
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK; School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
| | - Andrew Chantry
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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57
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Qi Z, Yang G, Deng T, Wang J, Zhou H, Popov SA, Shults EE, Wang C. Design and linkage optimization of ursane-thalidomide-based PROTACs and identification of their targeted-degradation properties to MDM2 protein. Bioorg Chem 2021; 111:104901. [PMID: 33878647 DOI: 10.1016/j.bioorg.2021.104901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/08/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
Ursolic acid (UA) is an accessible triterpenoid, widely applied in the design and synthesis of antitumor compounds. However, the mechanism of its anti-tumor effect is still unclear. To verify the molecular mechanism of its biological activity, based on the bifunctional activity of ubiquitination and subsequent proteasomal degradation of the target protein of the proteolysis-targeting chimeras (PROTACs) strategy, here we report the design, synthesis and cellular activity of six UA PROTAC hydrochloride compounds 1A-1F, in which UA acts as the binding ligand of the PROTAC and is linked to thalidomide (E3 ligand) through a series of synthetic linkers. The results revealed that compound 1B, connected with a POE-3 (3-Polyoxyether) possessed remarkable in vitro antitumor activity (with the IC50 value of 0.23 ~ 0.39 μM against A549, Huh7, HepG2). WB results demonstrated that the administration of compound 1B induced significant degradation of MDM2 (only 25% to that of SM1), and promoted the expression of P21 and PUMA proteins, and thus inhibited the proliferation (77.67% of 1B vs 60.37% of CON in G1 phase) and promoted the apoptosis (26.74% of 1B vs 3.35% of CON) of A549 cells. This work demonstrated proof of designing the efficient target protein degradation by UA PROTACs with the POE linkers. In addition, we confirmed that UA possess the characteristic of targeted-binding the protein of murine double minute-2 protein (MDM2). This will lay a foundation for the comprehensive utilization of forest natural compound UA.
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Affiliation(s)
- Zhiwen Qi
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forest, Nanjing 210042, Jiangsu, PR China.
| | - Guliang Yang
- National Engineering Laboratory for Rice and By-products Processing, Food Science and Engineering College, Central South University of Forestry and Technology, Changsha 410004, Hunan, PR China.
| | - Tao Deng
- Institute of Tropical Medicine & the Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 501405, PR China
| | - Jianmin Wang
- School of Computer Science and Engineering, Hunan University, Changsha 410012, PR China
| | - Hao Zhou
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forest, Nanjing 210042, Jiangsu, PR China
| | - Sergey A Popov
- Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev ave. 9, Novosibirsk 630090, Russia
| | - Elvira E Shults
- Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev ave. 9, Novosibirsk 630090, Russia
| | - Chengzhang Wang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forest, Nanjing 210042, Jiangsu, PR China.
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58
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Ishida T, Ciulli A. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:484-502. [PMID: 33143537 PMCID: PMC8013866 DOI: 10.1177/2472555220965528] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Bifunctional degrader molecules, also called proteolysis-targeting chimeras (PROTACs), are a new modality of chemical tools and potential therapeutics to understand and treat human disease. A required PROTAC component is a ligand binding to an E3 ubiquitin ligase, which is then joined to another ligand binding to a protein to be degraded via the ubiquitin-proteasome system. The advent of nonpeptidic small-molecule E3 ligase ligands, notably for von Hippel-Lindau (VHL) and cereblon (CRBN), revolutionized the field and ushered in the design of drug-like PROTACs with potent and selective degradation activity. A first wave of PROTAC drugs are now undergoing clinical development in cancer, and the field is seeking to extend the repertoire of chemistries that allow hijacking new E3 ligases to improve the scope of targeted protein degradation.Here, we briefly review how traditional E3 ligase ligands were discovered, and then outline approaches and ligands that have been recently used to discover new E3 ligases for PROTACs. We will then take an outlook at current and future strategies undertaken that invoke either target-based screening or phenotypic-based approaches, including the use of DNA-encoded libraries (DELs), display technologies and cyclic peptides, smaller molecular glue degraders, and covalent warhead ligands. These approaches are ripe for expanding the chemical space of PROTACs and usher in the advent of other emerging bifunctional modalities of proximity-based pharmacology.
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Affiliation(s)
- Tasuku Ishida
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
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59
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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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60
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Hanafi M, Chen X, Neamati N. Discovery of a Napabucasin PROTAC as an Effective Degrader of the E3 Ligase ZFP91. J Med Chem 2021; 64:1626-1648. [PMID: 33506674 DOI: 10.1021/acs.jmedchem.0c01897] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Napabucasin, undergoing multiple clinical trials, was reported to inhibit the signal transducer and transcription factor 3 (STAT3). To better elucidate its mechanism of action, we designed a napabucasin-based proteolysis targeting chimera (PROTAC), XD2-149 that resulted in inhibition of STAT3 signaling in pancreatic cancer cell lines without inducing proteasome-dependent degradation of STAT3. Proteomics analysis of XD2-149 revealed the downregulation of the E3 ubiquitin-protein ligase ZFP91. XD2-149 degrades ZFP91 with DC50 values in the nanomolar range. The cytotoxicity of XD2-149 was significantly, but not fully, reduced with ZFP91 knockdown providing evidence for its multi-targeted mechanism of action. The NQO1 inhibitor, dicoumarol, rescued the cytotoxicity of XD2-149 but not ZFP91 degradation, suggesting that the NQO1-induced cell death is independent of ZFP91. ZFP91 plays a role in tumorigenesis and is involved in multiple oncogenic pathways including NF-κB and HIF-1α.
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Affiliation(s)
- Maha Hanafi
- Department of Medicinal Chemistry, College of Pharmacy and the Rogel Cancer Center, North Campus Research Complex, 1600 Huron Parkway, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Xinde Chen
- Department of Medicinal Chemistry, College of Pharmacy and the Rogel Cancer Center, North Campus Research Complex, 1600 Huron Parkway, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and the Rogel Cancer Center, North Campus Research Complex, 1600 Huron Parkway, University of Michigan, Ann Arbor, Michigan 48109, United States
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61
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Sinha A, Iyengar PV, ten Dijke P. E3 Ubiquitin Ligases: Key Regulators of TGFβ Signaling in Cancer Progression. Int J Mol Sci 2021; 22:E476. [PMID: 33418880 PMCID: PMC7825147 DOI: 10.3390/ijms22020476] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/25/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
Transforming growth factor β (TGFβ) is a secreted growth and differentiation factor that influences vital cellular processes like proliferation, adhesion, motility, and apoptosis. Regulation of the TGFβ signaling pathway is of key importance to maintain tissue homeostasis. Perturbation of this signaling pathway has been implicated in a plethora of diseases, including cancer. The effect of TGFβ is dependent on cellular context, and TGFβ can perform both anti- and pro-oncogenic roles. TGFβ acts by binding to specific cell surface TGFβ type I and type II transmembrane receptors that are endowed with serine/threonine kinase activity. Upon ligand-induced receptor phosphorylation, SMAD proteins and other intracellular effectors become activated and mediate biological responses. The levels, localization, and function of TGFβ signaling mediators, regulators, and effectors are highly dynamic and regulated by a myriad of post-translational modifications. One such crucial modification is ubiquitination. The ubiquitin modification is also a mechanism by which crosstalk with other signaling pathways is achieved. Crucial effector components of the ubiquitination cascade include the very diverse family of E3 ubiquitin ligases. This review summarizes the diverse roles of E3 ligases that act on TGFβ receptor and intracellular signaling components. E3 ligases regulate TGFβ signaling both positively and negatively by regulating degradation of receptors and various signaling intermediates. We also highlight the function of E3 ligases in connection with TGFβ's dual role during tumorigenesis. We conclude with a perspective on the emerging possibility of defining E3 ligases as drug targets and how they may be used to selectively target TGFβ-induced pro-oncogenic responses.
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Affiliation(s)
| | | | - Peter ten Dijke
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (A.S.); (P.V.I.)
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62
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Bemis TA, La Clair JJ, Burkart MD. Traceless Staudinger ligation enabled parallel synthesis of proteolysis targeting chimera linker variants. Chem Commun (Camb) 2021; 57:1026-1029. [PMID: 33406191 DOI: 10.1039/d0cc05395c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A parallel, one-pot assembly approach to proteolysis targeting chimeras (PROTACs) is demonstrated utilizing activated esters generated in situ, and traceless Staudinger ligation chemistry. The method described allows for rapid structure-activity relationship studies of PROTAC linker variants. Two previously studied systems, cereblon and BRD4 degraders, are examined as test cases for the synthetic method. The two related strategies to assemble PROTAC linker variants discussed can accommodate the chromotographic separations capabilities of labs of many sizes and incorporates commercially available degrader building blocks, thereby easing synthetic entry into PROTAC chemical space.
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Affiliation(s)
- Troy A Bemis
- Department of Chemistry and Biochemistry, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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63
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Fuchs O, Bokorova R. Preclinical Studies of PROTACs in Hematological Malignancies. Cardiovasc Hematol Disord Drug Targets 2021; 21:7-22. [PMID: 33687890 DOI: 10.2174/1871529x21666210308111546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/01/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Incorrectly expressed or mutated proteins associated with hematologic malignancies have been generally targeted by chemotherapy using small-molecule inhibitors or monoclonal antibodies. But the majority of these intracellular proteins are without active sites and antigens. PROTACs, proteolysis targeting chimeras, are bifunctional molecules designed to polyubiquitinate and degrade specific pathological proteins of interest (POIs) by hijacking the activity of E3-ubiquitin ligases for POI polyubiquitination and subsequent degradation by the proteasome. This strategy utilizes the ubiquitin-proteasome system for the degradation of specific proteins in the cell. In many cases, including hematologic malignancies, inducing protein degradation as a therapeutic strategy offers therapeutic benefits over classical enzyme inhibition connected with resistance to inhibitors. Limitations of small-molecule inhibitors are shown. PROTACs can polyubiquitinate and mark for degradation of "undruggable"proteins, e.g. transcription factor STAT3 and scaffold proteins. Today, this technology is used in preclinical studies in various hematologic malignancies, mainly for targeting drug-resistant bromodomain and extraterminal proteins and Bruton tyrosine kinase. Several mechanisms limiting selectivity and safety of PROTAC molecules function are also discussed.
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Affiliation(s)
- Ota Fuchs
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Radka Bokorova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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Li C, Zhao J, Sun W. microRNA-222-Mediated VHL Downregulation Facilitates Retinoblastoma Chemoresistance by Increasing HIF1α Expression. Invest Ophthalmol Vis Sci 2021; 61:9. [PMID: 32756923 PMCID: PMC7441340 DOI: 10.1167/iovs.61.10.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Purpose Retinoblastoma (RB) is the most common primary intraocular tumor in children. Chemoresistance is the major obstacle for treatment of these tumors. This study aims to determine whether or not downregulating microRNA-222 (miR-222) could serve as a potential therapeutic target for preventing chemoresistance in RB treatment. Methods Differentially expressed miR-222 in RB samples and its downstream target genes were predicted using bioinformatics methods. The expression of miR-222 was altered by mimic or inhibitor to examine its role in RB cell in response to the chemotherapeutic agent vincristine (VCR). Further bioinformatic analysis predicted involvement of the stability of hypoxia-inducible factor 1α (HIF1α) protein in regulation of the von Hippel–Lindau (VHL) tumor suppressor, followed by characterization of the effect of VHL on the ubiquitin–proteasome degradation of HIF1α. Next, VHL or HIF1α was overexpressed to determine their effects on RB cell activities after VCR treatment. In vivo assays were performed on nude mice to further verify the in vitro results. Results miR-222 is highly expressed in RB tissues and cells and was found to facilitate resistance of RB cells to VCR. Of note, miR-222 specifically bound to and negatively regulated VHL. VHL could inhibit the stability of HIF1α and promote the degradation of ubiquitin–proteasome, thus reducing HIF1α expression to attenuate VCR resistance in RB cells. Moreover, inhibition of miR-222 in combination with VCR suppressed tumor formation in nude mice. Conclusions miR-222 promotes the expression of HIF1α by targeting VHL, thus accelerating the resistance of RB cells to the chemotherapeutic agent VCR.
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Affiliation(s)
- Chunzhi Li
- Department of Pharmacy, Linyi People's Hospital, Linyi, China
| | - Jun Zhao
- Department of Ophthalmology, Linyi People's Hospital, Linyi, China
| | - Weiying Sun
- Department of Pharmacy, Linyi People's Hospital, Linyi, China
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65
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Heim C, Maiwald S, Steinebach C, Collins MK, Strope J, Chau CH, Figg WD, Gütschow M, Hartmann MD. On the correlation of cereblon binding, fluorination and antiangiogenic properties of immunomodulatory drugs. Biochem Biophys Res Commun 2021; 534:67-72. [PMID: 33310190 PMCID: PMC7815984 DOI: 10.1016/j.bbrc.2020.11.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 11/26/2022]
Abstract
Cereblon (CRBN), the substrate receptor of an E3 ubiquitin ligase complex, is a target of thalidomide and thalidomide-derived immunomodulatory drugs (IMiDs). The binding of these IMiDs to CRBN alters the substrate specificity of the ligase, thereby mediating multiple effects that are exploited in cancer therapy. However, to date, it is not clear which other possible targets might be involved in the efficacy of IMiDs. One especially prominent effect of a number of thalidomide analogs is their ability to inhibit angiogenesis, which is typically enhanced in fluorinated analogs. So far, the involvement of CRBN in antiangiogenic effects is under debate. Here, starting from a systematic set of thalidomide analogs and employing a quantitative in vitro CRBN-binding assay, we study the correlation of fluorination, CRBN binding and antiangiogenic effects. We clearly identify fluorination to correlate both with CRBN binding affinity and with antiangiogenic effects, but do not find a correlation between the latter two phenomena, indicating that the main target for the antiangiogenic effects of thalidomide analogs still remains to be identified.
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Affiliation(s)
- Christopher Heim
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Samuel Maiwald
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Matthew K Collins
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Strope
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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66
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Maiwald S, Heim C, Hernandez Alvarez B, Hartmann MD. Sweet and Blind Spots in E3 Ligase Ligand Space Revealed by a Thermophoresis-Based Assay. ACS Med Chem Lett 2020; 12:74-81. [PMID: 33488967 PMCID: PMC7812675 DOI: 10.1021/acsmedchemlett.0c00440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
![]()
Repurposing E3 ubiquitin ligases
for targeted protein degradation
via customized molecular glues or proteolysis-targeting chimeras (PROTACs)
is an increasingly important therapeutic modality. Currently, a major
limitation in the design of suitable molecular glues and PROTACs is
our fragmentary understanding of E3 ligases and their ligand space.
We here describe a quantitative assay for the discovery and characterization
of E3 ligase ligands that is based on the thermophoretic behavior
of a custom reporter ligand. Thereby, it is orthogonal to commonly
employed fluorescence-based assays and less affected by the optical
properties of test compounds. It can be employed for the high-throughput
screening of compound libraries for a given ligase but also for hit
validation, which we demonstrate with the identification of unexpected
well-binders and non-binders, yielding new insights into the ligand
space of cereblon (CRBN).
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Affiliation(s)
- Samuel Maiwald
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Christopher Heim
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Birte Hernandez Alvarez
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Marcus D. Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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67
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Tomaselli D, Mautone N, Mai A, Rotili D. Recent advances in epigenetic proteolysis targeting chimeras (Epi-PROTACs). Eur J Med Chem 2020; 207:112750. [DOI: 10.1016/j.ejmech.2020.112750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 01/03/2023]
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68
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Yokoo H, Ohoka N, Naito M, Demizu Y. Design and synthesis of peptide-based chimeric molecules to induce degradation of the estrogen and androgen receptors. Bioorg Med Chem 2020; 28:115595. [PMID: 32631565 DOI: 10.1016/j.bmc.2020.115595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 01/12/2023]
Abstract
Peptide-based inducers of estrogen receptor (ER) α and androgen receptor (AR) degradations via the ubiquitin-proteasome system (UPS) were developed. The designated inducers were composed of two biologically active scaffolds: the helical peptide PERM3, which is an LXXLL-like mimic of the coactivator SRC-1, and various small molecules (MV1, LCL161, VH032, and POM) that bind to E3 ligases (IAPs, VHL, and cereblon, respectively), to induce ubiquitylation of nuclear receptors that bind to SRC-1. All of the synthesized chimeric E3 ligand-containing molecules induced the UPS-mediated degradation of ERα and AR. The PERM3 peptide was applicable for the development of the ERα and AR degraders using these E3 ligands.
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Affiliation(s)
- Hidetomo Yokoo
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan; Graduate School of Medical Health Sciences, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Nobumichi Ohoka
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Mikihiko Naito
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Yosuke Demizu
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan; Graduate School of Medical Health Sciences, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan.
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69
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Chen Y, Jin J. The application of ubiquitin ligases in the PROTAC drug design. Acta Biochim Biophys Sin (Shanghai) 2020; 52:776-790. [PMID: 32506133 DOI: 10.1093/abbs/gmaa053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
Protein ubiquitylation plays important roles in many biological activities. Protein ubiquitylation is a unique process that is mainly controlled by ubiquitin ligases. The ubiquitin-proteasome system (UPS) is the main process to degrade short-lived and unwanted proteins in eukaryotes. Many components in the UPS are attractive drug targets. Recent studies indicated that ubiquitin ligases can be employed as tools in proteolysis-targeting chimeras (PROTACs) for drug discovery. In this review article, we will discuss the recent progress of the application of ubiquitin ligases in the PROTAC drug design. We will also discuss advantages and existing problems of PROTACs. Moreover, we will propose a few principles for selecting ubiquitin ligases in PROTAC applications.
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Affiliation(s)
- Yilin Chen
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
| | - Jianping Jin
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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70
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Khan S, He Y, Zhang X, Yuan Y, Pu S, Kong Q, Zheng G, Zhou D. PROteolysis TArgeting Chimeras (PROTACs) as emerging anticancer therapeutics. Oncogene 2020; 39:4909-4924. [PMID: 32475992 PMCID: PMC7319888 DOI: 10.1038/s41388-020-1336-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/21/2022]
Abstract
Using PROteolysis TArgeting Chimeras (PROTACs) to degrade proteins that are important for tumorigenesis has emerged as a potential therapeutic strategy for cancer. PROTACs are heterobifunctional molecules consisting of one ligand for binding to a protein of interest (POI) and another to an E3 ubiquitin (E3) ligase, connected via a linker. PROTACs recruit the E3 ligase to the POI and cause proximity-induced ubiquitination and degradation of the POI by the ubiquitin proteasome system (UPS). PROTACs have been developed to degrade a variety of cancer targets with unprecedented efficacy against a multitude of tumor types. To date, most of the PROTACs developed have utilized ligands to recruit E3 ligases that are ubiquitously expressed in both tumor and normal tissues. These PROTACs can cause on-target toxicities if the POIs are not tumor-specific. Therefore, identifying and recruiting the E3 ligases that are enriched in tumors with minimal expression in normal tissues holds the potential to develop tumor-specific/selective PROTACs. In this review, we will discuss the potential of PROTACs to become anticancer therapeutics, chemical and bioinformatics approaches for PROTAC design, and safety concerns with a special focus on the development of tumor-specific/selective PROTACs. In addition, the identification of tumor types in terms of solid versus hematological malignancies that can be best targeted with PROTAC approach will be briefly discussed.
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Affiliation(s)
- Sajid Khan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Yonghan He
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Shaoyan Pu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Qingpeng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
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71
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Yang K, Wu H, Zhang Z, Leisten ED, Nie X, Liu B, Wen Z, Zhang J, Cunningham MD, Tang W. Development of Selective Histone Deacetylase 6 (HDAC6) Degraders Recruiting Von Hippel-Lindau (VHL) E3 Ubiquitin Ligase. ACS Med Chem Lett 2020; 11:575-581. [PMID: 32292566 DOI: 10.1021/acsmedchemlett.0c00046] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022] Open
Abstract
Histone deacetylase 6 (HDAC6) is involved in multiple cellular processes such as aggresome formation, protein stability, and cell motility. Numerous HDAC6-selective inhibitors have been developed as cellular chemical tools to elucidate the function of HDAC6. Since HDAC6 has multiple domains that cannot be studied by HDAC6-selective inhibitors, CRISPR-CAS9 and siRNA/shRNA have been employed to elucidate the nonenzymatic functions of HDAC6. However, these genetic methods have many limitations. Proteolysis targeting chimera (PROTAC) is an emerging technology for the development of small molecules that can quickly remove the entire protein in cells. We previously developed multifunctional HDAC6 degraders that can recruit cereblon (CRBN) E3 ubiquitin ligase. These HDAC6 degraders can degrade not only HDAC6 but also neo-substrates of CRBN. They are excellent candidates for the development of anticancer therapeutics, but the multifunctional nature of the CRBN-based HDAC6 degraders has limited their utility as specific chemical probes for the study of HDAC6-related cellular pathways. Herein we report the development of the first cell-permeable HDAC6-selective degraders employing Von Hippel-Lindau (VHL) E3 ubiquitin ligase, which does not have any known neo-substrates. The DC50's of the most potent compound 3j are 7.1 nM and 4.3 nM in human MM1S and mouse 4935 cell lines, respectively. The D max's of 3j in these two cell lines are 90% and 57%, respectively.
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Affiliation(s)
- Ka Yang
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Hao Wu
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Zhongrui Zhang
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Eric D. Leisten
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Xueqing Nie
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Binkai Liu
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Zhi Wen
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Jing Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Michael D. Cunningham
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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72
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Steinebach C, Ng YLD, Sosič I, Lee CS, Chen S, Lindner S, Vu LP, Bricelj A, Haschemi R, Monschke M, Steinwarz E, Wagner KG, Bendas G, Luo J, Gütschow M, Krönke J. Systematic exploration of different E3 ubiquitin ligases: an approach towards potent and selective CDK6 degraders. Chem Sci 2020; 11:3474-3486. [PMID: 33133483 PMCID: PMC7552917 DOI: 10.1039/d0sc00167h] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/28/2020] [Indexed: 12/18/2022] Open
Abstract
Cyclin-dependent kinase 6 (CDK6) is an important regulator of the cell cycle. Together with CDK4, it phosphorylates and inactivates retinoblastoma (Rb) protein.
Cyclin-dependent kinase 6 (CDK6) is an important regulator of the cell cycle. Together with CDK4, it phosphorylates and inactivates retinoblastoma (Rb) protein. In tumour cells, CDK6 is frequently upregulated and CDK4/6 kinase inhibitors like palbociclib possess high activity in breast cancer and other malignancies. Besides its crucial catalytic function, kinase-independent roles of CDK6 have been described. Therefore, targeted degradation of CDK6 may be advantageous over kinase inhibition. Proteolysis targeting chimeras (PROTACs) structurally based on the cereblon (CRBN) ligand thalidomide have recently been described to degrade the targets CDK4/6. However, CRBN-based PROTACs have several limitations including the remaining activity of immunomodulatory drugs (IMiDs) on Ikaros transcription factors as well as CRBN inactivation as a resistance mechanism in cancer. Here, we systematically explored the chemical space of CDK4/6 PROTACs by addressing different E3 ligases and connecting their respective small-molecule binders via various linkers to palbociclib. The spectrum of CDK6-specific PROTACs was extended to von Hippel Lindau (VHL) and cellular inhibitor of apoptosis protein 1 (cIAP1) that are essential for most cancer cells and therefore less likely to be inactivated. Our VHL-based PROTAC series included compounds that were either specific for CDK6 or exhibited dual activity against CDK4 and CDK6. IAP-based PROTACs caused a combined degradation of CDK4/6 and IAPs resulting in synergistic effects on cancer cell growth. Our new degraders showed potent and long-lasting degrading activity in human and mouse cells and inhibited proliferation of several leukemia, myeloma and breast cancer cell lines. In conclusion, we show that VHL- and IAP-based PROTACs are an attractive approach for targeted degradation of CDK4/6 in cancer.
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Affiliation(s)
- Christian Steinebach
- Pharmaceutical Institute , Department of Pharmaceutical & Medicinal Chemistry , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany .
| | - Yuen Lam Dora Ng
- Department of Internal Medicine III , University Hospital Ulm , Albert-Einstein-Allee 23 , 89081 Ulm , Germany .
| | - Izidor Sosič
- Faculty of Pharmacy , University of Ljubljana , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia
| | - Chih-Shia Lee
- Laboratory of Cancer Biology and Genetics , Center for Cancer Research , National Cancer Institute , Bethesda , MD 20892 , USA
| | - Sirui Chen
- Department of Internal Medicine III , University Hospital Ulm , Albert-Einstein-Allee 23 , 89081 Ulm , Germany .
| | - Stefanie Lindner
- Department of Internal Medicine III , University Hospital Ulm , Albert-Einstein-Allee 23 , 89081 Ulm , Germany .
| | - Lan Phuong Vu
- Pharmaceutical Institute , Department of Pharmaceutical & Medicinal Chemistry , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany .
| | - Aleša Bricelj
- Faculty of Pharmacy , University of Ljubljana , Aškerčeva cesta 7 , 1000 Ljubljana , Slovenia
| | - Reza Haschemi
- Pharmaceutical Institute , Department of Pharmaceutical & Cell Biological Chemistry , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Marius Monschke
- Pharmaceutical Institute , Pharmaceutical Technology , University of Bonn , Gerhard-Domagk-Straße 3 , 53121 Bonn , Germany
| | - Elisabeth Steinwarz
- Pharmaceutical Institute , Department of Pharmaceutical & Cell Biological Chemistry , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Karl G Wagner
- Pharmaceutical Institute , Pharmaceutical Technology , University of Bonn , Gerhard-Domagk-Straße 3 , 53121 Bonn , Germany
| | - Gerd Bendas
- Pharmaceutical Institute , Department of Pharmaceutical & Cell Biological Chemistry , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics , Center for Cancer Research , National Cancer Institute , Bethesda , MD 20892 , USA
| | - Michael Gütschow
- Pharmaceutical Institute , Department of Pharmaceutical & Medicinal Chemistry , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany .
| | - Jan Krönke
- Department of Internal Medicine III , University Hospital Ulm , Albert-Einstein-Allee 23 , 89081 Ulm , Germany .
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Abstract
Protein ubiquitylation is essential for the maintenance of cellular homeostasis. E3 ubiquitin ligases are key components of the enzymatic machinery catalyzing the attachment of ubiquitin to substrate proteins. Consequently, enzymatic dysfunction has been associated with medical conditions including cancer, diabetes, and cardiovascular and neurodegenerative disorders. To safeguard substrate selection and ubiquitylation, the activity of E3 ligases is tightly regulated by post-translational modifications including phosphorylation, sumoylation, and ubiquitylation, as well as binding of alternative adaptor molecules and cofactors. Recent structural studies identified homotypic and heterotypic interactions between E3 ligases, adding another layer of control for rapid adaptation to changing environmental and physiological conditions. Here, we discuss the regulation of E3 ligase activity by combinatorial oligomerization and summarize examples of associated ubiquitylation pathways and mechanisms.
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Affiliation(s)
- Vishnu Balaji
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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74
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Wang Y, Jiang X, Feng F, Liu W, Sun H. Degradation of proteins by PROTACs and other strategies. Acta Pharm Sin B 2020; 10:207-238. [PMID: 32082969 PMCID: PMC7016280 DOI: 10.1016/j.apsb.2019.08.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Blocking the biological functions of scaffold proteins and aggregated proteins is a challenging goal. PROTAC proteolysis-targeting chimaera (PROTAC) technology may be the solution, considering its ability to selectively degrade target proteins. Recent progress in the PROTAC strategy include identification of the structure of the first ternary eutectic complex, extra-terminal domain-4-PROTAC-Von-Hippel-Lindau (BRD4-PROTAC-VHL), and PROTAC ARV-110 has entered clinical trials for the treatment of prostate cancer in 2019. These discoveries strongly proved the value of the PROTAC strategy. In this perspective, we summarized recent meaningful research of PROTAC, including the types of degradation proteins, preliminary biological data in vitro and in vivo, and new E3 ubiquitin ligases. Importantly, the molecular design, optimization strategy and clinical application of candidate molecules are highlighted in detail. Future perspectives for development of advanced PROTAC in medical fields have also been discussed systematically.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xueyang Jiang
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Feng
- Jiangsu Food and Pharmaceutical Science College, Huaian 223003, China
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
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75
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Foley CA, Potjewyd F, Lamb KN, James LI, Frye SV. Assessing the Cell Permeability of Bivalent Chemical Degraders Using the Chloroalkane Penetration Assay. ACS Chem Biol 2020; 15:290-295. [PMID: 31846298 DOI: 10.1021/acschembio.9b00972] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bivalent chemical degraders provide a catalytic route to selectively degrade disease-associated proteins. By linking target-specific ligands with E3 ubiquitin ligase recruiting ligands, these compounds facilitate targeted protein ubiquitination and degradation by the proteasome. Due to the complexity of this multistep mechanism, the development of effective degrader molecules remains a difficult, lengthy, and unpredictable process. Since degraders are large heterobifunctional molecules, the efficacy of these compounds may be limited by poor cell permeability, and an efficient and reliable method to quantify the cell permeability of these compounds is lacking. Herein, we demonstrate that by the addition of a chloroalkane tag on the BRD4 specific degrader, MZ1, cell permeability can be quantified via the chloroalkane penetration assay. By extending this analysis to individual components of the degrader molecule, we have obtained structure-permeability relationships that will be informative for future degrader development, particularly as degraders move into the clinic as potential therapeutics.
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Affiliation(s)
- Caroline A. Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frances Potjewyd
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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76
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Sun X, Gao H, Yang Y, He M, Wu Y, Song Y, Tong Y, Rao Y. PROTACs: great opportunities for academia and industry. Signal Transduct Target Ther 2019; 4:64. [PMID: 31885879 PMCID: PMC6927964 DOI: 10.1038/s41392-019-0101-6] [Citation(s) in RCA: 330] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/17/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
Although many kinds of therapies are applied in the clinic, drug-resistance is a major and unavoidable problem. Another disturbing statistic is the limited number of drug targets, which are presently only 20-25% of all protein targets that are currently being studied. Moreover, the focus of current explorations of targets are their enzymatic functions, which ignores the functions from their scaffold moiety. As a promising and appealing technology, PROteolysis TArgeting Chimeras (PROTACs) have attracted great attention both from academia and industry for finding available approaches to solve the above problems. PROTACs regulate protein function by degrading target proteins instead of inhibiting them, providing more sensitivity to drug-resistant targets and a greater chance to affect the nonenzymatic functions. PROTACs have been proven to show better selectivity compared to classic inhibitors. PROTACs can be described as a chemical knockdown approach with rapidity and reversibility, which presents new and different biology compared to other gene editing tools by avoiding misinterpretations that arise from potential genetic compensation and/or spontaneous mutations. PRTOACs have been widely explored throughout the world and have outperformed not only in cancer diseases, but also in immune disorders, viral infections and neurodegenerative diseases. Although PROTACs present a very promising and powerful approach for crossing the hurdles of present drug discovery and tool development in biology, more efforts are needed to gain to get deeper insight into the efficacy and safety of PROTACs in the clinic. More target binders and more E3 ligases applicable for developing PROTACs are waiting for exploration.
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Affiliation(s)
- Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Hongying Gao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Yiqing Yang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yue Wu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yugang Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yan Tong
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 China
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77
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Kim K, Lee DH, Park S, Jo SH, Ku B, Park SG, Park BC, Jeon YU, Ahn S, Kang CH, Hwang D, Chae S, Ha JD, Kim S, Hwang JY, Kim JH. Disordered region of cereblon is required for efficient degradation by proteolysis-targeting chimera. Sci Rep 2019; 9:19654. [PMID: 31873151 PMCID: PMC6928225 DOI: 10.1038/s41598-019-56177-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/06/2019] [Indexed: 01/21/2023] Open
Abstract
Proteolysis targeting chimeras (PROTACs) are an emerging strategy for promoting targeted protein degradation by inducing the proximity between targeted proteins and E3 ubiquitin ligases. Although successful degradation of numerous proteins by PROTACs has been demonstrated, the elements that determine the degradability of PROTAC-targeted proteins have not yet been explored. In this study, we developed von Hippel-Lindau-Cereblon (VHL-CRBN) heterodimerizing PROTACs that induce the degradation of CRBN, but not VHL. A quantitative proteomic analysis further revealed that VHL-CRBN heterodimerizing PROTACs induced the degradation of CRBN, but not the well-known immunomodulatory drug (IMiD) neo-substrates, IKAROS family zinc finger 1 (IKZF1) and -3 (IZKF3). Moreover, truncation of disordered regions of CRBN and the androgen receptor (AR) attenuated their PROTAC-induced degradation, and attachment of the disordered region to stable CRBN or AR facilitated PROTAC-induced degradation. Thus, these results suggest that the intrinsically disordered region of targeted proteins is essential for efficient proteolysis, providing a novel criterion for choosing degradable protein targets.
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Affiliation(s)
- Kidae Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Proteome Structural biology, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Dong Ho Lee
- Therapeutics & Biotechnology, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Sungryul Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Proteome Structural biology, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Seung-Hyun Jo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sung Goo Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Byoung Chul Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Proteome Structural biology, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Yeong Uk Jeon
- Therapeutics & Biotechnology, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Sunjoo Ahn
- Therapeutics & Biotechnology, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Chung Hyo Kang
- Bio & Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.,College of Pharmacy, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Daehee Hwang
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sehyun Chae
- Korea Brain Bank, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Jae Du Ha
- Therapeutics & Biotechnology, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Sunhong Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea. .,Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Jong Yeon Hwang
- Therapeutics & Biotechnology, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Jeong-Hoon Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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78
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Potjewyd F, Turner AMW, Beri J, Rectenwald JM, Norris-Drouin JL, Cholensky SH, Margolis DM, Pearce KH, Herring LE, James LI. Degradation of Polycomb Repressive Complex 2 with an EED-Targeted Bivalent Chemical Degrader. Cell Chem Biol 2019; 27:47-56.e15. [PMID: 31831267 DOI: 10.1016/j.chembiol.2019.11.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/04/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
Abstract
Protein degradation via the use of bivalent chemical degraders provides an alternative strategy to block protein function and assess the biological roles of putative drug targets. This approach capitalizes on the advantages of small-molecule inhibitors while moving beyond the restrictions of traditional pharmacology. Here, we report a chemical degrader (UNC6852) that targets polycomb repressive complex 2 (PRC2). UNC6852 contains an EED226-derived ligand and a ligand for VHL which bind to the WD40 aromatic cage of EED and CRL2VHL, respectively, to induce proteasomal degradation of PRC2 components, EED, EZH2, and SUZ12. Degradation of PRC2 with UNC6852 blocks the histone methyltransferase activity of EZH2, decreasing H3K27me3 levels in HeLa cells and diffuse large B cell lymphoma (DLBCL) cells containing EZH2 gain-of-function mutations. UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system.
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Affiliation(s)
- Frances Potjewyd
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anne-Marie W Turner
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua Beri
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Justin M Rectenwald
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jacqueline L Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie H Cholensky
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David M Margolis
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, School Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth H Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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79
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Konstantinidou M, Li J, Zhang B, Wang Z, Shaabani S, Ter Brake F, Essa K, Dömling A. PROTACs- a game-changing technology. Expert Opin Drug Discov 2019; 14:1255-1268. [PMID: 31538491 PMCID: PMC7008130 DOI: 10.1080/17460441.2019.1659242] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Introduction: Proteolysis – targeting chimeras (PROTACs) have emerged as a new modality with the potential to revolutionize drug discovery. PROTACs are heterobifunctional molecules comprising of a ligand targeting a protein of interest, a ligand targeting an E3 ligase and a connecting linker. The aim is instead of inhibiting the target to induce its proteasomal degradation. Areas covered: PROTACs, due to their bifunctional design, possess properties that differentiate them from classical inhibitors. A structural analysis, based on published crystal aspects, kinetic features and aspects of selectivity are discussed. Specific types such as homoPROTACs, PROTACs targeting Tau protein and the first PROTACs recently entering clinical trials are examined. Expert opinion: PROTACs have shown remarkable biological responses in challenging targets, including an unprecedented selectivity over protein family members and even efficacy starting from weak or unspecific binders. Moreover, PROTACs are standing out from classical pharmacology by inducing the degradation of the target protein and not merely its inhibition. However, there are also challenges in the field, such as the rational structure optimization, the evolution of computational tools, limited structural data and the greatly anticipated clinical data. Despite the remaining hurdles, PROTACs are expected to soon become a new therapeutic category of drugs.
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Affiliation(s)
| | - Jingyao Li
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Bidong Zhang
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Zefeng Wang
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Shabnam Shaabani
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Frans Ter Brake
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Khaled Essa
- Drug Design, University of Groningen , Groningen , The Netherlands
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80
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Maniaci C, Ciulli A. Bifunctional chemical probes inducing protein-protein interactions. Curr Opin Chem Biol 2019; 52:145-156. [PMID: 31419624 DOI: 10.1016/j.cbpa.2019.07.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/23/2019] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
Inducing biomolecular interactions with synthetic molecules to impact biological function is a concept of enormous appeal. Recent years have seen a resurgence of interest in designing bispecific molecules that serve as bridging agents to bring proteins together. Pioneering structural and biophysical investigation of ternary complexes formed by mono-functional and bifunctional ligands highlights that proximity-induced stabilization or de novo formation of protein-protein interactions is a common feature of their molecular recognition. In this review, we illustrate these concepts and advances with representative case studies, and highlight progress over the past three years, with particular focus on recruitment to E3 ubiquitin ligases by 'molecular glues' and chimeric dimerizers (PROTACs) for targeted protein degradation. This approach promises to significantly expand the range of tractable targets for chemical biology and therapeutic intervention.
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Affiliation(s)
- Chiara Maniaci
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, Scotland, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, Scotland, UK.
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