151
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Farrell BM, Gerth F, Yang CHR, Yeh JTH. A synthetic KLHL20 ligand to validate CUL3 KLHL20 as a potent E3 ligase for targeted protein degradation. Genes Dev 2022; 36:1031-1042. [PMID: 36328355 PMCID: PMC9732910 DOI: 10.1101/gad.349717.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/31/2022] [Indexed: 11/06/2022]
Abstract
Targeted protein degradation (TPD) has risen as a promising therapeutic modality. Leveraging the catalytic nature of the ubiquitin-proteasome enzymatic machinery, TPD exhibits higher potency to eliminate disease-causing target proteins such as oncogenic transcription factors that may otherwise be difficult to abrogate by conventional inhibitors. However, there are challenges that remain. Currently, nearly all degraders engage CUL4CRBN or CUL2VHL as the E3 ligase for target ubiquitination. While their immediate efficacies are evident, the narrowed E3 ligase options make TPD vulnerable to potential drug resistance. In addition, E3 ligases show differential tissue expression and have intrinsic limitations in accessing varying types of disease-relevant targets. As the success of TPD is closely associated with the ability of E3 ligases to efficiently polyubiquitinate the target of interest, the long-term outlook of TPD drug development will depend on whether E3 ligases such as CUL4CRBN and CUL2VHL are accessible to the targets of interest. To overcome these potential caveats, a broad collection of actionable E3 ligases is required. Here, we designed a macrocyclic degrader engaging CUL3KLHL20 for targeting BET proteins and validated CUL3KLHL20 as an E3 ligase system suitable for TPD. This work thus contributes to the expansion of usable E3 ligases for potential drug development.
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Affiliation(s)
- Brian M Farrell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Fabian Gerth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Cheng-Hao R Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Johannes T-H Yeh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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152
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A Comprehensive Review of BET-targeting PROTACs for Cancer Therapy. Bioorg Med Chem 2022; 73:117033. [DOI: 10.1016/j.bmc.2022.117033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/11/2022] [Accepted: 09/22/2022] [Indexed: 11/23/2022]
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153
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Fang Y, Wang J, Zhao M, Zheng Q, Ren C, Wang Y, Zhang J. Progress and Challenges in Targeted Protein Degradation for Neurodegenerative Disease Therapy. J Med Chem 2022; 65:11454-11477. [PMID: 36006861 DOI: 10.1021/acs.jmedchem.2c00844] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Neurodegenerative diseases (NDs) are currently incurable diseases that cause progressive degeneration of nerve cells. Many of the disease-causing proteins of NDs are "undruggable" for traditional small-molecule inhibitors (SMIs). None of the compounds that attenuated the amyloid-β (Aβ) accumulation process have entered clinical practice, and many phase III clinical trials of SMIs for Alzheimer's disease (AD) have failed. In recent years, emerging targeted protein degradation (TPD) technologies such as proteolysis-targeting chimeras (PROTACs), lysosome-targeting chimaeras (LYTACs), and autophagy-targeting chimeras (AUTACs) with TPD-assistive technologies such as click-formed proteolysis-targeting chimeras (CLIPTACs) and deubiquitinase-targeting chimera (DUBTAC) have developed rapidly. In vitro and in vivo experiments have also confirmed that TPD technology can target the degradation of ND pathogenic proteins, bringing hope for the treatment of NDs. Herein, we review the latest TPD technologies, introduce their targets and technical characteristics, and discuss the emerging TPD technologies with potential in ND research, with the hope of providing a new perspective for the development of TPD technology in the NDs field.
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Affiliation(s)
- Yingxu Fang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Min Zhao
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Tianfu Jincheng Laboratory, Chengdu 610041, Sichuan, China
| | - Qinwen Zheng
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu 611130, Sichuan, China
| | - Yuxi Wang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Tianfu Jincheng Laboratory, Chengdu 610041, Sichuan, China
| | - Jifa Zhang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Tianfu Jincheng Laboratory, Chengdu 610041, Sichuan, China
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154
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Němec V, Schwalm MP, Müller S, Knapp S. PROTAC degraders as chemical probes for studying target biology and target validation. Chem Soc Rev 2022; 51:7971-7993. [PMID: 36004812 DOI: 10.1039/d2cs00478j] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule degraders such as PROTACs (PROteolysis TArgeting Chimeras) have emerged as new promising pharmacological modalities and the first PROTAC drug candidates are now studied clinically. The catalytic properties of PROTACs, acting as chemical degraders of a protein of interest (POI), represent an attractive new strategy for drug development. The development and characterization of PROTACs requires an array of additional assay systems that track the degradation pathway leading ultimately to degradation of the POI, identifying critical steps for PROTAC optimization. In addition to their exciting translational potential, PROTACs represent versatile chemical tools that considerably expanded our chemical biology toolbox and significantly enlarged the proteome that can be modulated by small molecules. Similar to conventional chemical probes, PROTACs used as chemical probes in target validation require comprehensive characterization. As a consequence, PROTAC-specific quality criteria should be defined by the chemical biology community. These criteria need to comprise additional or alternative parameters compared to those for conventional occupancy-driven chemical probes, such as the maximum level of target degradation (Dmax), confirmation of a proteasome dependent degradation mechanism and, importantly, also kinetic parameters of POI degradation. The kinetic aspects are particularly relevant for PROTACs that harbor covalent binding moieties. Here, we review recent progress in the development of assay systems for PROTAC characterization and suggest a set of criteria for PROTACs as high quality chemical probes.
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Affiliation(s)
- Václav Němec
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany. .,Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany
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155
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Payne NC, Maksoud S, Tannous BA, Mazitschek R. A direct high-throughput protein quantification strategy facilitates discovery and characterization of a celastrol-derived BRD4 degrader. Cell Chem Biol 2022; 29:1333-1340.e5. [PMID: 35649410 PMCID: PMC9391279 DOI: 10.1016/j.chembiol.2022.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/03/2022] [Accepted: 05/10/2022] [Indexed: 12/31/2022]
Abstract
We describe a generalizable time-resolved Förster resonance energy transfer (TR-FRET)-based platform to profile the cellular action of heterobifunctional degraders (or proteolysis-targeting chimeras [PROTACs]) that is capable of both accurately quantifying protein levels in whole-cell lysates in less than 1 h and measuring small-molecule target engagement to endogenous proteins, here specifically for human bromodomain-containing protein 4 (BRD4). The detection mix consists of a single primary antibody targeting the protein of interest, a luminescent donor-labeled anti-species nanobody, and a fluorescent acceptor ligand. Importantly, our strategy can readily be applied to other targets of interest and will greatly facilitate the cell-based profiling of small-molecule inhibitors and PROTACs in a high-throughput format with unmodified cell lines. We furthermore validate our platform in the characterization of celastrol, a p-quinone methide-containing pentacyclic triterpenoid, as a broad cysteine-targeting E3 ubiquitin ligase warhead for potent and efficient targeted protein degradation.
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Affiliation(s)
- N Connor Payne
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Semer Maksoud
- Experimental Therapeutics and Molecular Imaging Unit, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Bakhos A Tannous
- Experimental Therapeutics and Molecular Imaging Unit, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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156
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Cao C, He M, Wang L, He Y, Rao Y. Chemistries of bifunctional PROTAC degraders. Chem Soc Rev 2022; 51:7066-7114. [PMID: 35916511 DOI: 10.1039/d2cs00220e] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) technology is a novel and promising therapeutic strategy using small molecules to induce ubiquitin-dependent degradation of proteins. It has received extensive attention from both academia and industry as it can potentially access previously inaccessible targets. However, the design and optimization of PROTACs present big challenges for researchers, and the general strategy for its development and optimization is a lot of trial and error based on experience. This review highlights the important advances in this rapidly growing field and critical limitations of the traditional trial-and-error approach to developing PROTACs by analyzing numerous representative examples of PROTACs development. We summarize and analyze the general principles and strategies for PROTACs design and optimization from the perspective of chemical structure design, and propose potential future pathways to facilitate the development of PROTACs.
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Affiliation(s)
- Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 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.
| | - Liguo Wang
- 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.
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 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.
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157
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Zhu CL, Luo X, Tian T, Rao Z, Wang H, Zhou Z, Mi T, Chen D, Xu Y, Wu Y, Che J, Zhou Y, Li J, Dong X. Structure-based rational design enables efficient discovery of a new selective and potent AKT PROTAC degrader. Eur J Med Chem 2022; 238:114459. [DOI: 10.1016/j.ejmech.2022.114459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/13/2022]
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158
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Yamamoto J, Ito T, Yamaguchi Y, Handa H. Discovery of CRBN as a target of thalidomide: a breakthrough for progress in the development of protein degraders. Chem Soc Rev 2022; 51:6234-6250. [PMID: 35796627 DOI: 10.1039/d2cs00116k] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Progress in strategies aimed at breaking down therapeutic target proteins has led to a paradigm shift in drug discovery. Thalidomide and its derivatives are the only protein degraders currently used in clinical practice. Our understanding of the molecular mechanism of action of thalidomide and its derivatives has advanced dramatically since the identification of cereblon (CRBN) as their direct target. The binding of thalidomide derivatives to CRBN, a substrate recognition receptor for Cullin 4 RING E3 ubiquitin ligase (CRL4), induces the recruitment of non-native substrates to CRL4CRBN and their subsequent degradation. This discovery was a breakthrough in the current rapid development of protein-degrading agents because clarification of the mechanism of action of thalidomide derivatives has demonstrated the clinical value of these compounds. This review provides an overview of the mechanism of action of thalidomide and its derivatives and describes perspectives for protein degraders.
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Affiliation(s)
- Junichi Yamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takumi Ito
- Institute of Medical Science, Tokyo Medical University, Shinjuku, Tokyo 160-8402, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroshi Handa
- Center for Future Medical Research, Tokyo Medical University, Shinjuku, Tokyo 160-8402, Japan.
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159
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Accelerating PROTAC drug discovery: Establishing a relationship between ubiquitination and target protein degradation. Biochem Biophys Res Commun 2022; 628:68-75. [DOI: 10.1016/j.bbrc.2022.08.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/08/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022]
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160
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Lin Z, Woo CM. Methods to characterize and discover molecular degraders in cells. Chem Soc Rev 2022; 51:7115-7137. [PMID: 35899832 DOI: 10.1039/d2cs00261b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cells use many post-translational modifications (PTMs) to tailor proteins and transduce cellular signals. Recent years have witnessed the rapid growth of small molecule and enzymatic strategies to purposely manipulate one particular PTM, ubiquitination, on desired target proteins in cells. These approaches typically act by induced proximity between an E3 ligase and a target protein resulting in ubiquitination and degradation of the substrate in cells. In this review, we cover recent approaches to study molecular degraders and discover their induced substrates in vitro and in live cells. Methods that have been adapted and applied to the development of molecular degraders are described, including global proteomics, affinity-purification, chemical proteomics and enzymatic strategies. Extension of these strategies to edit additional PTMs in cells is also discussed. This review is intended to assist researchers who are interested in editing PTMs with new modalities to select suitable method(s) and guide their studies.
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Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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161
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Sasso J, Tenchov R, Wang D, Johnson LS, Wang X, Zhou QA. Molecular Glues: The Adhesive Connecting Targeted Protein Degradation to the Clinic. Biochemistry 2022; 62:601-623. [PMID: 35856839 PMCID: PMC9910052 DOI: 10.1021/acs.biochem.2c00245] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Targeted protein degradation is a rapidly exploding drug discovery strategy that uses small molecules to recruit disease-causing proteins for rapid destruction mainly via the ubiquitin-proteasome pathway. It shows great potential for treating diseases such as cancer and infectious, inflammatory, and neurodegenerative diseases, especially for those with "undruggable" pathogenic protein targets. With the recent rise of the "molecular glue" type of protein degraders, which tighten and simplify the connection of an E3 ligase with a disease-causing protein for ubiquitination and subsequent degradation, new therapies for unmet medical needs are being designed and developed. Here we use data from the CAS Content Collection and the publication landscape of recent research on targeted protein degraders to provide insights into these molecules, with a special focus on molecular glues. We also outline the advantages of the molecular glues and summarize the advances in drug discovery practices for molecular glue degraders. We further provide a thorough review of drug candidates in targeted protein degradation through E3 ligase recruitment. Finally, we highlight the progression of molecular glues in drug discovery pipelines and their targeted diseases. Overall, our paper provides a comprehensive reference to support the future development of molecular glues in medicine.
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162
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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: 21] [Impact Index Per Article: 10.5] [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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163
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Hendrick CE, Jorgensen JR, Chaudhry C, Strambeanu II, Brazeau JF, Schiffer J, Shi Z, Venable JD, Wolkenberg SE. Direct-to-Biology Accelerates PROTAC Synthesis and the Evaluation of Linker Effects on Permeability and Degradation. ACS Med Chem Lett 2022; 13:1182-1190. [PMID: 35859867 PMCID: PMC9290060 DOI: 10.1021/acsmedchemlett.2c00124] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A platform to accelerate optimization of proteolysis targeting chimeras (PROTACs) has been developed using a direct-to-biology (D2B) approach with a focus on linker effects. A large number of linker analogs-with varying length, polarity, and rigidity-were rapidly prepared and characterized in four cell-based assays by streamlining time-consuming steps in synthesis and purification. The expansive dataset informs on linker structure-activity relationships (SAR) for in-cell E3 ligase target engagement, degradation, permeability, and cell toxicity. Unexpected aspects of linker SAR was discovered, consistent with literature reports on "linkerology", and the method dramatically speeds up empirical optimization. Physicochemical property trends emerged, and the platform has the potential to rapidly expand training sets for more complex prediction models. In-depth validation studies were carried out and confirm the D2B platform is a valuable tool to accelerate PROTAC design-make-test cycles.
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Affiliation(s)
- Charles E. Hendrick
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jeff R. Jorgensen
- Discovery
Technology and Molecular Pharmacology, Therapeutics Discovery, Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Charu Chaudhry
- Discovery
Technology and Molecular Pharmacology, Therapeutics Discovery, Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Iulia I. Strambeanu
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jean-Francois Brazeau
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Jamie Schiffer
- Computational
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Zhicai Shi
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jennifer D. Venable
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Scott E. Wolkenberg
- Discovery
Chemistry, Therapeutics Discovery, Janssen
Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
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164
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Design, Synthesis and Biological Characterization of Histone Deacetylase 8 (HDAC8) Proteolysis Targeting Chimeras (PROTACs) with Anti-Neuroblastoma Activity. Int J Mol Sci 2022; 23:ijms23147535. [PMID: 35886887 PMCID: PMC9322761 DOI: 10.3390/ijms23147535] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/07/2023] Open
Abstract
In addition to involvement in epigenetic gene regulation, histone deacetylases (HDACs) regulate multiple cellular processes through mediating the activity of non-histone protein substrates. The knockdown of HDAC8 isozyme is associated with the inhibition of cell proliferation and apoptosis enhancement in several cancer cell lines. As shown in several studies, HDAC8 can be considered a potential target in the treatment of cancer forms such as childhood neuroblastoma. The present work describes the development of proteolysis targeting chimeras (PROTACs) of HDAC8 based on substituted benzhydroxamic acids previously reported as potent and selective HDAC8 inhibitors. Within this study, we investigated the HDAC8-degrading profiles of the synthesized PROTACs and their effect on the proliferation of neuroblastoma cells. The combination of in vitro screening and cellular testing demonstrated selective HDAC8 PROTACs that show anti-neuroblastoma activity in cells.
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165
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Xu H, Kurohara T, Takano R, Yokoo H, Shibata N, Ohoka N, Inoue T, Naito M, Demizu Y. Development of Rapid and Facile Solid-Phase Synthesis of PROTACs via a Variety of Binding Styles. ChemistryOpen 2022; 11:e202200131. [PMID: 35822913 PMCID: PMC9278092 DOI: 10.1002/open.202200131] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Optimizing linker design is important for ensuring efficient degradation activity of proteolysis-targeting chimeras (PROTACs). Therefore, developing a straightforward synthetic approach that combines the protein-of-interest ligand (POI ligand) and the ligand for E3 ubiquitin ligase (E3 ligand) in various binding styles through a linker is essential for rapid PROTAC syntheses. Herein, a solid-phase approach for convenient PROTAC synthesis is presented. We designed azide intermediates with different linker lengths to which the E3 ligand, pomalidomide, is attached and performed facile PROTACs synthesis by forming triazole, amide, and urea bonds from the intermediates.
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Affiliation(s)
- Hanqiao Xu
- National Institute of Health Sciences3-25-26 TonomachiKawasakiKanagawa210-9501Japan
- Graduate School of Medical Life ScienceYokohama City University 1-7-29YokohamaKanagawa230-0045Japan
| | - Takashi Kurohara
- National Institute of Health Sciences3-25-26 TonomachiKawasakiKanagawa210-9501Japan
| | - Reina Takano
- National Institute of Health Sciences3-25-26 TonomachiKawasakiKanagawa210-9501Japan
- Graduate School of Medical Life ScienceYokohama City University 1-7-29YokohamaKanagawa230-0045Japan
| | - Hidetomo Yokoo
- National Institute of Health Sciences3-25-26 TonomachiKawasakiKanagawa210-9501Japan
- Medical ChemistryGraduate School of Medical ScienceKyoto Prefectural University of MedicineKyoto606-0823Japan
| | - Norihito Shibata
- National Institute of Health Sciences3-25-26 TonomachiKawasakiKanagawa210-9501Japan
| | - Nobumichi Ohoka
- National Institute of Health Sciences3-25-26 TonomachiKawasakiKanagawa210-9501Japan
| | - Takao Inoue
- National Institute of Health Sciences3-25-26 TonomachiKawasakiKanagawa210-9501Japan
| | - Mikihiko Naito
- Laboratory of Targeted Protein DegradationGraduate School of Pharmaceutical SciencesThe University of TokyoTokyo113-0033Japan
| | - Yosuke Demizu
- National Institute of Health Sciences3-25-26 TonomachiKawasakiKanagawa210-9501Japan
- Graduate School of Medical Life ScienceYokohama City University 1-7-29YokohamaKanagawa230-0045Japan
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166
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Domostegui A, Nieto-Barrado L, Perez-Lopez C, Mayor-Ruiz C. Chasing molecular glue degraders: screening approaches. Chem Soc Rev 2022; 51:5498-5517. [PMID: 35723413 DOI: 10.1039/d2cs00197g] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein-protein interactions (PPIs) govern all biological processes. Some small molecules modulate PPIs through induced protein proximity. In particular, molecular glue degraders are monovalent compounds that orchestrate interactions between a target protein and an E3 ubiquitin ligase, prompting the proteasomal degradation of the former. This and other pharmacological strategies of targeted protein degradation (e.g. proteolysis-targeting chimeras - PROTACs) overcome some limitations of traditional occupancy-based therapeutics. Here, we provide an overview of the "molecular glue" concept, with a special focus on natural and synthetic inducers of proximity to E3s. We then briefly highlight the serendipitous discoveries of some clinical and preclinical molecular glue degraders, and discuss the first examples of intentional discoveries. Specifically, we outline the different screening strategies reported in this rapidly evolving arena and our thoughts on future perspectives. By mastering the ability to influence PPIs, molecular glue degraders can induce the degradation of unligandable proteins, thus providing an exciting path forward to broaden the targetable proteome.
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Affiliation(s)
- Ana Domostegui
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Luis Nieto-Barrado
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Carles Perez-Lopez
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Cristina Mayor-Ruiz
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
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167
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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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168
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Gopalsamy A. Selectivity through Targeted Protein Degradation (TPD). J Med Chem 2022; 65:8113-8126. [PMID: 35658428 DOI: 10.1021/acs.jmedchem.2c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeted protein degradation has become a reliable tool in the medicinal chemist's toolbox, as seen with rapid progression of PROTACs (proteolysis targeting chimeras) to clinic. Degraders have unique advantages to target proteins with no functional consequence or scaffolding function to achieve the desired phenotype. In some cases, selectivity was achieved among closely related targets. While the prospective design of degraders to achieve selectivity remains empirical, this Miniperspective analyzes some reported examples to gather key factors that are hypothesized to contribute to selectivity. Ternary complex conformation to access key lysine residues stands out as a potential key contributor. However, protein and E3 ligase expression levels, differential tissue expression, resynthesis rate, ubiquitination rate, and the stability of the ternary complex formed all have the potential to play a significant role. With continued progress in ternary structure determination along with several predictive modeling methods, a rational approach to achieve degradation and selectivity is tantalizingly close.
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Affiliation(s)
- Ariamala Gopalsamy
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
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169
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Pu C, Tong Y, Liu Y, Lan S, Wang S, Yan G, Zhang H, Luo D, Ma X, Yu S, Huang Q, Deng R, Li R. Selective degradation of PARP2 by PROTACs via recruiting DCAF16 for triple-negative breast cancer. Eur J Med Chem 2022; 236:114321. [DOI: 10.1016/j.ejmech.2022.114321] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 02/07/2023]
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170
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Guenette RG, Yang SW, Min J, Pei B, Potts PR. Target and tissue selectivity of PROTAC degraders. Chem Soc Rev 2022; 51:5740-5756. [PMID: 35587208 DOI: 10.1039/d2cs00200k] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Targeted protein degradation (TPD) strategies have revolutionized how scientists tackle challenging protein targets deemed undruggable with traditional small molecule inhibitors. Many promising campaigns to inhibit proteins have failed due to factors surrounding inhibition selectivity and targeting of compounds to specific tissues and cell types. One of the major improvements that PROTAC (proteolysis targeting chimera) and molecular glue technology can exert is highly selective control of target inhibition. Multiple studies have shown that PROTACs can gain selectivity for their protein targets beyond that of their parent ligands via optimization of linker length and stabilization of ternary complexes. Due to the bifunctional nature of PROTACs, the tissue selective nature of E3 ligases can be exploited to uncover novel targeting mechanisms. In this review, we provide critical analysis of the recent progress towards making selective PROTAC molecules and new PROTAC technologies that will continue to push the boundaries of achieving selectivity. These efforts have wide implications in the future of treating disease as they will broaden the possible targets that can be addressed by small molecules, like undruggable proteins or broadly active targets that would benefit from degradation in specific tissue types.
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Affiliation(s)
| | - Seung Wook Yang
- Induced Proximity Platform, Amgen, Thousand Oaks, CA 91320, USA.
| | - Jaeki Min
- Induced Proximity Platform, Amgen, Thousand Oaks, CA 91320, USA.
| | - Baikang Pei
- Genome Analysis Unit, Amgen, Thousand Oaks, CA 91320, USA
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171
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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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172
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Nitsch L, Jensen P, Yoon H, Koeppel J, Burman SSR, Fischer ES, Scholl C, Fröhling S, Słabicki M. BTB BCL6 dimers as building blocks for reversible drug-induced protein oligomerization. CELL REPORTS METHODS 2022; 2:100193. [PMID: 35497498 PMCID: PMC9046236 DOI: 10.1016/j.crmeth.2022.100193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/17/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022]
Abstract
Here, we characterize the BTB domain of the transcription factor BCL6 (BTBBCL6) as a small-molecule-controlled, reversible oligomerization switch, which oligomerizes upon BI-3802 treatment and de-oligomerizes upon addition of BI-3812. We show that the magnitude of oligomerization can be controlled in vitro by BI-3802 concentration and exposure time. In cellular models, exposure to BI-3802/BI-3812 can drive multiple cycles of foci formation consisting of BTBBCL6 fused to EGFP, which are not degraded due to the lack of a degron. We generated an epidermal growth factor receptor (EGFR)-BTBBCL6 fusion. Treatment with BI-3802, as an ON switch, induced EGFR-BTBBCL6 phosphorylation and activation of downstream effectors, which could in part be reversed by the addition of BI-3812, as an OFF switch. Finally, BI-3802-induced oligomerization of the EGFR-BTBBCL6 fusion enhanced proliferation of an EGF-dependent cell line in absence of EGF. These results demonstrate the successful application of small-molecule-induced, reversible oligomerization as a switch for synthetic biology.
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Affiliation(s)
- Lena Nitsch
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Patrizia Jensen
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Hojong Yoon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Koeppel
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shourya Sonkar Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric Sebastian Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Mikołaj Słabicki
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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173
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García Jiménez D, Rossi Sebastiano M, Vallaro M, Mileo V, Pizzirani D, Moretti E, Ermondi G, Caron G. Designing Soluble PROTACs: Strategies and Preliminary Guidelines. J Med Chem 2022; 65:12639-12649. [PMID: 35469399 PMCID: PMC9574862 DOI: 10.1021/acs.jmedchem.2c00201] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Solubility optimization is a crucial step to obtaining oral PROTACs. Here we measured the thermodynamic solubilities (log S) of 21 commercial PROTACs. Next, we measured BRlogD and log kwIAM (lipophilicity), EPSA, and Δ log kwIAM (polarity) and showed that lipophilicity plays a major role in governing log S, but a contribution of polarity cannot be neglected. Two-/three-dimensional descriptors calculated on conformers arising from conformational sampling and steered molecular dynamics failed in modeling solubility. Infographic tools were used to identify a privileged region of soluble PROTACs in a chemical space defined by BRlogD, log kwIAM and topological polar surface area, while machine learning provided a log S classification model. Finally, for three pairs of PROTACs we measured the solubility, lipophilicity, and polarity of the building blocks and identified the limits of estimating PROTAC solubility from the synthetic components. Overall, this paper provides promising guidelines for optimizing PROTAC solubility in early drug discovery programs.
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Affiliation(s)
- Diego García Jiménez
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
| | - Valentina Mileo
- Global Research and Preclinical Development, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy.,Emerging Science & Technology Unit, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy
| | - Daniela Pizzirani
- Global Research and Preclinical Development, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy.,Emerging Science & Technology Unit, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy
| | - Elisa Moretti
- Global Research and Preclinical Development, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
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174
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Falcinelli SD, Peterson JJ, Turner AMW, Irlbeck D, Read J, Raines SL, James KS, Sutton C, Sanchez A, Emery A, Sampey G, Ferris R, Allard B, Ghofrani S, Kirchherr JL, Baker C, Kuruc JD, Gay CL, James LI, Wu G, Zuck P, Rioja I, Furze RC, Prinjha RK, Howell BJ, Swanstrom R, Browne EP, Strahl BD, Dunham RM, Archin NM, Margolis DM. Combined noncanonical NF-κB agonism and targeted BET bromodomain inhibition reverse HIV latency ex vivo. J Clin Invest 2022; 132:e157281. [PMID: 35426377 PMCID: PMC9012286 DOI: 10.1172/jci157281] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022] Open
Abstract
Latency reversal strategies for HIV cure using inhibitor of apoptosis protein (IAP) antagonists (IAPi) induce unprecedented levels of latent reservoir expression without immunotoxicity during suppressive antiretroviral therapy (ART). However, full targeting of the reservoir may require combinatorial approaches. A Jurkat latency model screen for IAPi combination partners demonstrated synergistic latency reversal with bromodomain (BD) and extraterminal domain protein inhibitors (BETi). Mechanistic investigations using CRISPR-CAS9 and single-cell RNA-Seq informed comprehensive ex vivo evaluations of IAPi plus pan-BET, bD-selective BET, or selective BET isoform targeting in CD4+ T cells from ART-suppressed donors. IAPi+BETi treatment resulted in striking induction of cell-associated HIV gag RNA, but lesser induction of fully elongated and tat-rev RNA compared with T cell activation-positive controls. IAPi+BETi resulted in HIV protein induction in bulk cultures of CD4+ T cells using an ultrasensitive p24 assay, but did not result in enhanced viral outgrowth frequency using a standard quantitative viral outgrowth assay. This study defines HIV transcriptional elongation and splicing as important barriers to latent HIV protein expression following latency reversal, delineates the roles of BET proteins and their BDs in HIV latency, and provides a rationale for exploration of IAPi+BETi in animal models of HIV latency.
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Affiliation(s)
- Shane D. Falcinelli
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Jackson J. Peterson
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Anne-Marie W. Turner
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - David Irlbeck
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, North Carolina, USA
| | - Jenna Read
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Samuel L.M. Raines
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Katherine S. James
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Cameron Sutton
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Anthony Sanchez
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Ann Emery
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Gavin Sampey
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Robert Ferris
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, North Carolina, USA
| | - Brigitte Allard
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Simon Ghofrani
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Jennifer L. Kirchherr
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Caroline Baker
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - JoAnn D. Kuruc
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - Cynthia L. Gay
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - Lindsey I. James
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Guoxin Wu
- Department of Infectious Disease, Merck & Co. Inc., Kenilworth, New Jersey, USA
| | - Paul Zuck
- Department of Infectious Disease, Merck & Co. Inc., Kenilworth, New Jersey, USA
| | - Inmaculada Rioja
- Immuno-Epigenetics, Immunology Research Unit, GSK Medicines Research Centre, Stevenage, United Kingdom
| | - Rebecca C. Furze
- Immuno-Epigenetics, Immunology Research Unit, GSK Medicines Research Centre, Stevenage, United Kingdom
| | - Rab K. Prinjha
- Immuno-Epigenetics, Immunology Research Unit, GSK Medicines Research Centre, Stevenage, United Kingdom
| | - Bonnie J. Howell
- Department of Infectious Disease, Merck & Co. Inc., Kenilworth, New Jersey, USA
| | - Ronald Swanstrom
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Edward P. Browne
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - Brian D. Strahl
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Richard M. Dunham
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, North Carolina, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
| | - David M. Margolis
- UNC HIV Cure Center, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, UNC, Chapel Hill, North Carolina, USA
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175
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Abstract
Targeted therapies have come to play an increasingly important role in cancer therapy over the past two decades. This success has been made possible in large part by technological advances in sequencing, which have greatly advanced our understanding of the mutational landscape of human cancer and the genetic drivers present in individual tumors. We are rapidly discovering a growing number of mutations that occur in targetable pathways, and thus tumor genetic testing has become an important component in the choice of appropriate therapies. Targeted therapy has dramatically transformed treatment outcomes and disease prognosis in some settings, whereas in other oncologic contexts, targeted approaches have yet to demonstrate considerable clinical efficacy. In this Review, we summarize the current knowledge of targetable mutations that occur in a range of cancers, including hematologic malignancies and solid tumors such as non-small cell lung cancer and breast cancer. We outline seminal examples of druggable mutations and targeting modalities and address the clinical and research challenges that must be overcome to maximize therapeutic benefit.
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Affiliation(s)
- Michael R. Waarts
- Gerstner Sloan Kettering Graduate Program in Biomedical Sciences
- Human Oncology and Pathogenesis Program
- Center for Hematologic Malignancies
- Center for Epigenetics Research, and
| | - Aaron J. Stonestrom
- Human Oncology and Pathogenesis Program
- Center for Hematologic Malignancies
- Center for Epigenetics Research, and
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Young C. Park
- Human Oncology and Pathogenesis Program
- Center for Hematologic Malignancies
- Center for Epigenetics Research, and
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program
- Center for Hematologic Malignancies
- Center for Epigenetics Research, and
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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176
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Liao J, Nie X, Unarta IC, Ericksen SS, Tang W. In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses. J Med Chem 2022; 65:6116-6132. [PMID: 35412837 DOI: 10.1021/acs.jmedchem.1c02155] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) are molecules that induce protein degradation via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The rational design of PROTACs requires accurate knowledge of the native configuration of the PROTAC-induced ternary complex. This study demonstrates that native and non-native ternary complex poses can be distinguished based on the pose occupancy time in MD, where native poses exhibit longer occupancy times at both room and higher temperatures. Candidate poses are generated by MD sampling and pre-ranked by classic MM/GBSA. A specific heating scheme is then applied to accelerate ternary pose departure, with the pose occupancy time and fraction being measured. This scoring identifies the native pose in all systems tested. Its success is partially attributed to the dynamic nature of pose departure analyses, which accounts for entropic effects typically neglected in the faster static scoring methods, while entropy plays a greater role in protein-protein than in protein-ligand systems.
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Affiliation(s)
- Junzhuo Liao
- 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
| | - Ilona Christy Unarta
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Spencer S Ericksen
- Drug Development Core, UW Carbone Cancer Center, School of Medicine and Public Health, 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 53706, United States.,Drug Development Core, UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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177
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Li X, Pu W, Zheng Q, Ai M, Chen S, Peng Y. Proteolysis-targeting chimeras (PROTACs) in cancer therapy. Mol Cancer 2022; 21:99. [PMID: 35410300 PMCID: PMC8996410 DOI: 10.1186/s12943-021-01434-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/21/2021] [Indexed: 12/18/2022] Open
Abstract
AbstractProteolysis-targeting chimeras (PROTACs) are engineered techniques for targeted protein degradation. A bifunctional PROTAC molecule with two covalently-linked ligands recruits target protein and E3 ubiquitin ligase together to trigger proteasomal degradation of target protein by the ubiquitin-proteasome system. PROTAC has emerged as a promising approach for targeted therapy in various diseases, particularly in cancers. In this review, we introduce the principle and development of PROTAC technology, as well as the advantages of PROTACs over traditional anti-cancer therapies. Moreover, we summarize the application of PROTACs in targeting critical oncoproteins, provide the guidelines for the molecular design of PROTACs and discuss the challenges in the targeted degradation by PROTACs.
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178
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Bai N, Riching KM, Makaju A, Wu H, Acker TM, Ou SC, Zhang Y, Shen X, Bulloch DN, Rui H, Gibson BW, Daniels DL, Urh M, Rock BM, Humphreys SC. Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs. J Biol Chem 2022; 298:101653. [PMID: 35101445 PMCID: PMC9019245 DOI: 10.1016/j.jbc.2022.101653] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are hetero-bifunctional small molecules that can simultaneously recruit target proteins and E3 ligases to form a ternary complex, promoting target protein ubiquitination and degradation via the Ubiquitin-Proteasome System (UPS). PROTACs have gained increasing attention in recent years due to certain advantages over traditional therapeutic modalities and enabling targeting of previously "undruggable" proteins. To better understand the mechanism of PROTAC-induced Target Protein Degradation (TPD), several computational approaches have recently been developed to study and predict ternary complex formation. However, mounting evidence suggests that ubiquitination can also be a rate-limiting step in PROTAC-induced TPD. Here, we propose a structure-based computational approach to predict target protein ubiquitination induced by cereblon (CRBN)-based PROTACs by leveraging available structural information of the CRL4A ligase complex (CRBN/DDB1/CUL4A/Rbx1/NEDD8/E2/Ub). We generated ternary complex ensembles with Rosetta, modeled multiple CRL4A ligase complex conformations, and predicted ubiquitination efficiency by separating the ternary ensemble into productive and unproductive complexes based on the proximity of the ubiquitin to accessible lysines on the target protein. We validated our CRL4A ligase complex models with published ternary complex structures and additionally employed our modeling workflow to predict ubiquitination efficiencies and sites of a series of cyclin-dependent kinases (CDKs) after treatment with TL12-186, a pan-kinase PROTAC. Our predictions are consistent with CDK ubiquitination and site-directed mutagenesis of specific CDK lysine residues as measured using a NanoBRET ubiquitination assay in HEK293 cells. This work structurally links PROTAC-induced ternary formation and ubiquitination, representing an important step toward prediction of target "degradability."
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Affiliation(s)
- Nan Bai
- Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA.
| | - Kristin M Riching
- Research and Development Department, Promega Corporation, Madison, Wisconsin, USA.
| | - Aman Makaju
- Discovery Attribute Science, Amgen Research, South San Francisco, California, USA
| | - Hao Wu
- Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA
| | - Timothy M Acker
- Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA
| | - Shu-Ching Ou
- Discovery Attribute Science, Amgen Research, Thousand Oaks, California, USA
| | - Yaru Zhang
- Oncology, Amgen Research, Thousand Oaks, California, USA
| | - Xiaomeng Shen
- Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA
| | - Daryl N Bulloch
- Discovery Attribute Science, Amgen Research, South San Francisco, California, USA
| | - Huan Rui
- Discovery Attribute Science, Amgen Research, Thousand Oaks, California, USA
| | - Bradford W Gibson
- Discovery Attribute Science, Amgen Research, South San Francisco, California, USA
| | - Danette L Daniels
- Research and Development Department, Promega Corporation, Madison, Wisconsin, USA
| | - Marjeta Urh
- Research and Development Department, Promega Corporation, Madison, Wisconsin, USA
| | - Brooke M Rock
- Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA
| | - Sara C Humphreys
- Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California, USA.
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179
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Chen J, He H, Wei A, Li Y, Cheng G, Qin H, Zhong H, Liu H, Geng M, Shen A, Hu Y. Adjusted degradation of BRD4 S and BRD4 L based on fine structural modifications of the pyrrolopyridone scaffold. Eur J Med Chem 2022; 236:114259. [PMID: 35395439 DOI: 10.1016/j.ejmech.2022.114259] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/07/2022] [Accepted: 03/03/2022] [Indexed: 11/25/2022]
Abstract
Novel pyrrolopyridone BET degraders were designed and synthesized based on the binding mode between the pyrrolopyridone BET inhibitor with the BRD4 protein. The potent degraders on MV-4-11 cells were discovered through structure-activity relationship study. Modification of warhead on pyrrolopyridone BET degraders significantly regulates BRD4 isoform (long and short) protein degradation, which induces differential cell cycle arrest and apoptosis on MV-4-11 cells. Docking study revealed that the fine structural modification of BET degraders may bind with the BD domain of BRD4 protein to engage various surface areas that bind with CRBN.
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Affiliation(s)
- Jingjing Chen
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, 1 Xiangshanzhi Road, Hangzhou, 310024, China
| | - Huixin He
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 110039, China
| | - Aihuan Wei
- State Key Laboratory of Drug Research, Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai, 201203, China
| | - Yalei Li
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Gang Cheng
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 548, Binwen Road, Binjiang District, Hangzhou, 310053, China
| | - Hui Qin
- State Key Laboratory of Drug Research, Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 110039, China
| | - Hanyue Zhong
- State Key Laboratory of Drug Research, Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 110039, China
| | - Hongchun Liu
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Meiyu Geng
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, 1 Xiangshanzhi Road, Hangzhou, 310024, China; Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 110039, China
| | - Aijun Shen
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 110039, China.
| | - Youhong Hu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, 1 Xiangshanzhi Road, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 110039, China.
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180
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Qi J, Ouyang Z. Targeting CDK4/6 for Anticancer Therapy. Biomedicines 2022; 10:685. [PMID: 35327487 PMCID: PMC8945444 DOI: 10.3390/biomedicines10030685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/26/2022] Open
Abstract
Cyclin-dependent kinase 4/6 (CDK4/6) are key regulators of the cell cycle and are deemed as critical therapeutic targets of multiple cancers. Various approaches have been applied to silence CDK4/6 at different levels, i.e., CRISPR to knock out at the DNA level, siRNA to inhibit translation, and drugs that target the protein of interest. Here we summarize the current status in this field, highlighting the mechanisms of small molecular inhibitors treatment and drug resistance. We describe approaches to combat drug resistance, including combination therapy and PROTACs drugs that degrade the kinases. Finally, critical issues and perspectives in the field are outlined.
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Affiliation(s)
- Jiating Qi
- The Second Clinical College, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China;
| | - Zhuqing Ouyang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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181
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Silva MC, Nandi G, Donovan KA, Cai Q, Berry BC, Nowak RP, Fischer ES, Gray NS, Ferguson FM, Haggarty SJ. Discovery and Optimization of Tau Targeted Protein Degraders Enabled by Patient Induced Pluripotent Stem Cells-Derived Neuronal Models of Tauopathy. Front Cell Neurosci 2022; 16:801179. [PMID: 35317195 PMCID: PMC8934437 DOI: 10.3389/fncel.2022.801179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/26/2022] [Indexed: 12/21/2022] Open
Abstract
Accumulation of misfolded, aggregating proteins concurrent with disease onset and progression is a hallmark of neurodegenerative proteinopathies. An important class of these are tauopathies, such as frontotemporal dementia (FTD) and Alzheimer’s disease (AD), associated with accumulation of aberrant forms of tau protein in the brain. Pathological tau undergoes abnormal post-translational modifications, misfolding, oligomerization and changes in solubility, cellular redistribution, and spreading. Development and testing of experimental therapeutics that target these pathological tau conformers requires use of cellular models that recapitulate neuronal endogenous, non-heterologous tau expression under genomic and physiological contexts relevant to disease. In this study, we employed FTD-patient induced pluripotent stem cells (iPSC)-derived neurons, expressing a tau variant or mutation, as primary models for driving a medicinal chemistry campaign around tau targeting degrader series. Our screening goal was to establish structure-activity relationships (SAR) for the different chemical series to identify the molecular composition that most efficiently led to tau degradation in human FTD ex vivo neurons. We describe the identification of the lead compound QC-01-175 and follow-up optimization strategies for this molecule. We present three final lead molecules with tau degradation activity in mutant neurons, which establishes potential disease relevance and will drive future studies on specificity and pharmacological properties.
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Affiliation(s)
- M. Catarina Silva
- Chemical Neurobiology Laboratory, Department of Neurology and Psychiatry, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Neurology, Harvard Medical School, Boston, MA, United States
| | - Ghata Nandi
- Chemical Neurobiology Laboratory, Department of Neurology and Psychiatry, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Quan Cai
- Department of Neurology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Bethany C. Berry
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Radoslaw P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Nathanael S. Gray
- Department of Neurology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Fleur M. Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- *Correspondence: Fleur M. Ferguson,
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Department of Neurology and Psychiatry, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Neurology, Harvard Medical School, Boston, MA, United States
- Stephen J. Haggarty,
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182
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Carroll EC, Marqusee S. Site-specific ubiquitination: Deconstructing the degradation tag. Curr Opin Struct Biol 2022; 73:102345. [PMID: 35247748 DOI: 10.1016/j.sbi.2022.102345] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/28/2021] [Accepted: 01/17/2022] [Indexed: 02/04/2023]
Abstract
Ubiquitin is a small eukaryotic protein so named for its cellular abundance and originally recognized for its role as the posttranslational modification (PTM) "tag" condemning substrates to degradation by the 26S proteasome. Since its discovery in the 1970s, protein ubiquitination has also been identified as a key regulatory feature in dozens of non-degradative cellular processes. This myriad of roles illustrates the versatility of ubiquitin as a PTM; however, understanding the cellular and molecular factors that enable discrimination between degradative versus non-degradative ubiquitination events has been a persistent challenge. Here, we discuss recent advances in uncovering how site-specificity - the exact residue that gets modified - modulates distinct protein fates and cellular outcomes with an emphasis on how ubiquitination site specificity regulates proteasomal degradation. We explore recent advances in structural biology, biophysics, and cell biology that have enabled a broader understanding of the role of ubiquitination in altering the dynamics of the target protein, including implications for the design of targeted protein degradation therapeutics.
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Affiliation(s)
- Emma C Carroll
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, 94038, USA.
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA; QB3 Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, 94720, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.
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183
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Abstract
Targeted protein degradation (TPD) is an emerging therapeutic modality with the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules. In the 20 years since the concept of a proteolysis-targeting chimera (PROTAC) molecule harnessing the ubiquitin-proteasome system to degrade a target protein was reported, TPD has moved from academia to industry, where numerous companies have disclosed programmes in preclinical and early clinical development. With clinical proof-of-concept for PROTAC molecules against two well-established cancer targets provided in 2020, the field is poised to pursue targets that were previously considered 'undruggable'. In this Review, we summarize the first two decades of PROTAC discovery and assess the current landscape, with a focus on industry activity. We then discuss key areas for the future of TPD, including establishing the target classes for which TPD is most suitable, expanding the use of ubiquitin ligases to enable precision medicine and extending the modality beyond oncology.
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Affiliation(s)
| | | | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
- Department of Pharmacology, Yale University, New Haven, CT, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
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184
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Cowan AD, Ciulli A. Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory. Annu Rev Biochem 2022; 91:295-319. [PMID: 35320687 DOI: 10.1146/annurev-biochem-032620-104421] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methods to direct the degradation of protein targets with proximity-inducing molecules that coopt the cellular degradation machinery are advancing in leaps and bounds, and diverse modalities are emerging. The most used and well-studied approach is to hijack E3 ligases of the ubiquitin-proteasome system. E3 ligases use specific molecular recognition to determine which proteins in the cell are ubiquitinated and degraded. This review focuses on the structural determinants of E3 ligase recruitment of natural substrates and neo-substrates obtained through monovalent molecular glues and bivalent proteolysis-targeting chimeras. We use structures to illustrate the different types of substrate recognition and assess the basis for neo-protein-protein interactions in ternary complex structures. The emerging structural and mechanistic complexity is reflective of the diverse physiological roles of protein ubiquitination. This molecular insight is also guiding the application of structure-based design approaches to the development of new and existing degraders as chemical tools and therapeutics. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
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185
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Liu Z, Li Y, Chen H, Lai HT, Wang P, Wu SY, Wold EA, Leonard PG, Joseph S, Hu H, Chiang CM, Brasier AR, Tian B, Zhou J. Discovery, X-ray Crystallography, and Anti-inflammatory Activity of Bromodomain-containing Protein 4 (BRD4) BD1 Inhibitors Targeting a Distinct New Binding Site. J Med Chem 2022; 65:2388-2408. [PMID: 34982556 PMCID: PMC8989062 DOI: 10.1021/acs.jmedchem.1c01851] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bromodomain-containing protein 4 (BRD4) is an emerging epigenetic drug target for intractable inflammatory disorders. The lack of highly selective inhibitors among BRD4 family members has stalled the collective understanding of this critical system and the progress toward clinical development of effective therapeutics. Here we report the discovery of a potent BRD4 bromodomain 1 (BD1)-selective inhibitor ZL0590 (52) targeting a unique, previously unreported binding site, while exhibiting significant anti-inflammatory activities in vitro and in vivo. The X-ray crystal structural analysis of ZL0590 in complex with human BRD4 BD1 and the associated mutagenesis study illustrate a first-in-class nonacetylated lysine (KAc) binding site located at the helix αB and αC interface that contains important BRD4 residues (e.g., Glu151) not commonly shared among other family members and is spatially distinct from the classic KAc recognition pocket. This new finding facilitates further elucidation of the complex biology underpinning bromodomain specificity among BRD4 and its protein-protein interaction partners.
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Affiliation(s)
| | | | | | | | | | | | | | - Paul G Leonard
- Core for Biomolecular Structure and Function, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Sarah Joseph
- Core for Biomolecular Structure and Function, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | | | | | - Allan R Brasier
- Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison School of Medicine and Public Health, 4248 Health Sciences Learning Center, Madison, Wisconsin 53705, United States
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186
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Synthesis and Evaluation of RNase L-binding 2-aminothiophenes as anticancer agents. Bioorg Med Chem 2022; 58:116653. [DOI: 10.1016/j.bmc.2022.116653] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 01/08/2023]
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187
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Li W, Zhang J, Guo L, Wang Q. Importance of Three-Body Problems and Protein-Protein Interactions in Proteolysis-Targeting Chimera Modeling: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:523-532. [PMID: 35084845 DOI: 10.1021/acs.jcim.1c01150] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) are a class of bifunctional molecules that can induce the ubiquitin degradation of its target protein by hijacking the E3 ligase to form a target protein-PROTAC-E3 ligase ternary complex. Its underlying principle has inspired the development of a wide range of protein degraders that are similar to or beyond PROTACs in recent years. The formation of the ternary complexes is the key to the success of PROTAC-induced protein degradation. Nevertheless, the lack of effective ternary complex modeling techniques has limited the application of computer-aided drug discovery tools to this emerging and fast developing new land in drug industry. Thus, in this study, we explored the application of the more physically sound molecular dynamics simulation and the molecular mechanics combined with the generalized Born and surface area continuum solvation (MM/GBSA) method to solve the underlying three-body problem in PROTAC modeling. We first verified the accuracy of our approach using a series of known Brd4 BD2 degraders. The calculated binding energy showed a good correlation with the experimental Kd values. The modeling of a unique property, namely, the α value, for PROTACs was also first and accurately performed to our best knowledge. The results also demonstrated the importance of PROTAC-induced protein-protein interactions in its modeling, either qualitatively or quantitatively. Finally, by standing on the success of earlier docking-based approaches, our protocol was also applied as a rescoring function in pose prediction. The results showed a notable improvement in reranking the initial poses generated from a modified Rosetta method, which was reportedly one of the best among a handful of PROTAC modeling approaches available in this field. We hope this work could provide a practical protocol and more insights to study the binding and the design of PROTACs and other protein degraders.
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Affiliation(s)
- Wenqing Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Jiabin Zhang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Li Guo
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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188
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Hu Z, Crews CM. Recent Developments in PROTAC-Mediated Protein Degradation: From Bench to Clinic. Chembiochem 2022; 23:e202100270. [PMID: 34494353 PMCID: PMC9395155 DOI: 10.1002/cbic.202100270] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/02/2021] [Indexed: 01/21/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs), an emerging paradigm-shifting technology, hijacks the ubiquitin-proteasome system for targeted protein degradation. PROTACs induce ternary complexes between an E3 ligase and POI, and this induced proximity leads to polyUb chain formation on substrates and eventual proteasomal-mediated POI degradation. PROTACs have shown great therapeutic potential by degrading many disease-causing proteins, such as the androgen receptor and BRD4. The PROTAC technology has advanced significantly in the last two decades, with the repertoire of PROTAC targets increased tremendously. Herein, we describe recent developments of PROTAC technology, focusing on mechanistic and kinetic studies, pharmacokinetic study, spatiotemporal control of PROTACs, covalent PROTACs, resistance to PROTACs, and new E3 ligands.
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Affiliation(s)
- Zhenyi Hu
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511, USA
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06511, USA
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189
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Noncovalent CDK12/13 dual inhibitors-based PROTACs degrade CDK12-Cyclin K complex and induce synthetic lethality with PARP inhibitor. Eur J Med Chem 2022; 228:114012. [PMID: 34864331 DOI: 10.1016/j.ejmech.2021.114012] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) plays a crucial role in DNA-damage response gene transcription and has recently been validated as a promising target in cancer therapy. However, existing CDK12 inhibitors potently inhibit its closest isoform CDK13, which could cause potential toxicity. Therefore, the development of CDK12 inhibitors with isoform-selectivity against CDK13 continues to be a challenge. By taking advantage of the emerging PROteolysis-TArgeting Chimeras (PROTACs) approach, we have synthesized a potent PROTAC degrader PP-C8 based on the noncovalent dual inhibitors of CDK12/13 and demonstrated its specificity for CDK12 over CDK13. Notably, PP-C8 induces profound degradation of cyclin K simultaneously and downregulates the mRNA level of DNA-damage response genes. Global proteomics profiling revealed PP-C8 is highly selective toward CDK12-cyclin K complex. Importantly, PP-C8 demonstrates profound synergistic antiproliferative effects with PARP inhibitor in triple-negative breast cancer (TNBC). The potent and selective CDK12 PROTAC degrader developed in this study could potentially be used to treat CDK12-dependent cancers as combination therapy.
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190
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Lin Z, Amako Y, Kabir F, Flaxman HA, Budnik B, Woo CM. Development of Photolenalidomide for Cellular Target Identification. J Am Chem Soc 2022; 144:606-614. [PMID: 34978798 DOI: 10.1021/jacs.1c11920] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The thalidomide analogue lenalidomide (Len) is a clinical therapeutic that alters the substrate engagement of cereblon (CRBN), a substrate receptor for the CRL4 E3 ubiquitin ligase. Here, we report the development of photolenalidomide (pLen), a Len probe with a photoaffinity label and enrichment handle, designed for target identification by chemical proteomics. pLen preserves the substrate degradation profile, phenotypic antiproliferative and immunomodulatory properties of Len, and enhances interactions with the thalidomide-binding domain of CRBN, as revealed by binding site mapping and molecular modeling. Using pLen, we captured the known targets IKZF1 and CRBN from multiple myeloma MM.1S cells and further identified a new target, eukaryotic translation initiation factor 3 subunit i (eIF3i), from HEK293T cells. eIF3i is directly labeled by pLen and forms a ternary complex with CRBN in the presence of Len across several epithelial cell lines but is itself not ubiquitylated or degraded. These data point to the existence of a broader array of targets induced by ligands to CRBN that may or may not be degraded, which can be identified by the highly translatable application of pLen to additional biological systems.
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Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yuka Amako
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Farah Kabir
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Hope A Flaxman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource (MSPRL), Division of Science, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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191
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Weerakoon D, Carbajo RJ, De Maria L, Tyrchan C, Zhao H. Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex. J Chem Inf Model 2022; 62:340-349. [PMID: 35018781 DOI: 10.1021/acs.jcim.1c01036] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The conformational behavior of a small molecule free in solution is important to understand the free energy of binding to its target. This could be of special interest for proteolysis-targeting chimeras (PROTACs) due to their often flexible and lengthy linkers and the need to induce a ternary complex. Here, we report on the molecular dynamics (MD) simulations of two PROTACs, MZ1 and dBET6, revealing different linker conformational behaviors. The simulation of MZ1 in dimethyl sulfoxide (DMSO) agrees well with the nuclear magnetic resonance study, providing strong support for the relevance of our simulations. To further understand the role of linker plasticity in the formation of a ternary complex, the dissociation of the complex von Hippel-Lindau-MZ1-BRD4 is investigated in detail by steered simulations and is shown to follow a two-step pathway. Interestingly, both MZ1 and dBET6 display in water, a tendency toward an intramolecular lipophilic interaction between the two warheads. The hydrophobic contact of the two warheads would prevent them from binding to their respective proteins and might have an effect on the efficacy of induced cellular protein degradation. However, conformations featuring this hydrophobic contact of the two warheads are calculated to be marginally more favorable.
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Affiliation(s)
- Dhanushka Weerakoon
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Rodrigo J Carbajo
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United Kingdom
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
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192
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He S, Dong G, Cheng J, Wu Y, Sheng C. Strategies for designing proteolysis targeting chimaeras (PROTACs). Med Res Rev 2022; 42:1280-1342. [PMID: 35001407 DOI: 10.1002/med.21877] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022]
Abstract
Proteolysis targeting chimaeras (PROTACs) is a cutting edge and rapidly growing technique for new drug discovery and development. Currently, the largest challenge in the molecular design and drug development of PROTACs is efficient identification of potent and drug-like degraders. This review aims to comprehensively summarize and analyse state-of-the-art methods and strategies in the design of PROTACs. We provide a detailed illustration of the general principles and tactics for designing potent PROTACs, highlight representative case studies, and discuss the advantages and limitations of these strategies. Particularly, structure-based rational PROTAC design and emerging new types of PROTACs (e.g., homo-PROTACs, multitargeting PROTACs, photo-control PROTACs and PROTAC-based conjugates) will be focused on.
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Affiliation(s)
- Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Junfei Cheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Ying Wu
- School of Pharmacy, Second Military Medical University, Shanghai, China.,Department of Pharmacy, 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
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193
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Wang C, Zhang Y, Wang J, Xing D. VHL-based PROTACs as potential therapeutic agents: Recent progress and perspectives. Eur J Med Chem 2022; 227:113906. [PMID: 34656901 DOI: 10.1016/j.ejmech.2021.113906] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023]
Abstract
Proteolysis targeting chimeras (PROTACs), which hijack proteins of interest (POIs) and recruit E3 ligases for target degradation via the ubiquitin-proteasome pathway, are a novel drug discovery paradigm that has been widely used as biological tools and medicinal molecules with the potential of clinical application value. To date, a wide variety of small molecule PROTACs have been developed. Importantly, VHL-based PROTACs have emerged to be a promising approach for proteins, including those non-druggable ones, such as transcriptional factors and scaffold proteins. VHL-based PRTOACs have been developed for the treatment of diseases that are difficult to be dealt with by conventional methods, such as radiotherapy, chemotherapy, and small molecule inhibitors. In this review, the recent advances of VHL-based PRTOACs were summarized, and the chances and challenges associated with this area were also highlighted.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; School of Pharmacy, Qingdao University, Qingdao, 266021, Shandong, China.
| | - Jie Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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194
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Hu R, Wang WL, Yang YY, Hu XT, Wang QW, Zuo WQ, Xu Y, Feng Q, Wang NY. Identification of a selective BRD4 PROTAC with potent antiproliferative effects in AR-positive prostate cancer based on a dual BET/PLK1 inhibitor. Eur J Med Chem 2022; 227:113922. [PMID: 34700270 DOI: 10.1016/j.ejmech.2021.113922] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 02/05/2023]
Abstract
BRD4-targeted proteolysis targeting chimera (PROTAC) have exhibited promising in vitro and in vivo anticancer activity in a number of cancer models. However, the clinical development of current reported BRD4-PROTACs have stagnated, largely due to the safety risks caused by their poor degradation selectivity. In this study, we designed and synthesized a series of PROTACs based on our recently reported dual BET/PLK1 inhibitor WNY0824, which led to the discovery of an isoform-selective and potent BRD4-PROTAC 12a (WWL0245). WWL0245 exhibited excellent selective cytotoxicity in the BETi sensitive cancer cell lines, including AR-positive prostate cancer cell lines. It could also efficiently induce ubiquitin-proteasomal degradation of BRD4 in AR-positive prostate cancer cell lines, with sub-nanomolar half-maximal degrading concentration (DC50) and maximum degradation (Dmax) > 99%. Moreover, WWL0245 induced cell cycle arrest at the G0/G1 phase and apoptosis in AR-positive prostate cancer by downregulation of the protein levels of AR, PSA and c-Myc as well as transcriptionally suppressed AR-regulated genes. WWL0245 was thus expected to be developed as a promising drug candidate for AR-positive prostate cancer and a valuable tool compound to study the biological function of BRD4.
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Affiliation(s)
- Rong Hu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Wan-Li Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Ying-Yue Yang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Xia-Tong Hu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Qi-Wei Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, And Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Wei-Qiong Zuo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, And Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Ying Xu
- School of Chemical Engineering, Northwest University, No.229 North Taibai Road, Xi'an, Shaanxi, 710069, PR China
| | - Qiang Feng
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu, China.
| | - Ning-Yu Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
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195
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Inuzuka H, Liu J, Wei W, Rezaeian AH. PROTACs technology for treatment of Alzheimer's disease: Advances and perspectives. ACTA MATERIA MEDICA 2022; 1:24-41. [PMID: 35237768 PMCID: PMC8887676 DOI: 10.15212/amm-2021-0001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Neurodegenerative diseases (NDs) are characteristic with progression of neuron degeneration, resulting in dysfunction of cognition and mobility. Many neurodegenerative diseases are because of proteinopathies that results from unusual protein accumulations and aggregations. The aggregation of misfolded proteins like β-amyloid, α-synuclein, tau, and polyglutamates are hallmarked in Alzheimer's disease (AD), which are undruggable targets, and usually do not respond to conventional small-molecule agents. Therefore, developing novel technology and strategy for reducing the levels of protein aggregates would be critical for treatment of AD. Recently, the emerging proteolysis targeting chimeras (PRPTACs) technology has been significantly considered for artificial and selective degradation of aberrant target proteins. These engineered bifunctional molecules engage target proteins to be degraded by either the cellular degradation machinery in the ubiquitin-proteasome system (UPS) or via the autophagy-lysosome degradation pathway. Although the application of PROTACs technology is preferable than oligonucleotide and antibodies for treatment of NDs, many limitations such as their pharmacokinetic properties, tissue distribution and cell permeabilities, still need to be corrected. Herein, we review the recent advances in PROTACs technology with their limitation for pharmaceutical targeting of aberrant proteins involved in Alzheimer's diseases. We also review therapeutic potential of dysregulated signaling such as PI3K/AKT/mTOR axis for the management of AD.
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Affiliation(s)
- Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Corresponding author. Contact: ,
| | - Abdol-Hossein Rezaeian
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Corresponding author. Contact: ,
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196
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Brownsey DK, Rowley BC, Gorobets E, Mihara K, Maity R, Papatzimas JW, Gelfand BS, Hollenberg MD, Bahlis NJ, Derksen DJ. Identification of ligand linkage vectors for the development of p300/CBP degraders. RSC Med Chem 2022; 13:726-730. [PMID: 35814928 PMCID: PMC9215131 DOI: 10.1039/d1md00070e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/12/2022] [Indexed: 01/10/2023] Open
Abstract
To develop new degrader molecules from an existing protein ligand a linkage vector must be identified and then joined with a suitable E3 ligase without disrupting binding to the respective...
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Affiliation(s)
- Duncan K Brownsey
- Department of Chemistry, University of Calgary 2500 University Drive NW T2N 1N4 Calgary Alberta Canada
- Arnie Charbonneau Cancer Institute, University of Calgary 3280 Hospital Drive NW T2N 4Z6 Calgary Alberta Canada
| | - Ben C Rowley
- Department of Chemistry, University of Calgary 2500 University Drive NW T2N 1N4 Calgary Alberta Canada
- Arnie Charbonneau Cancer Institute, University of Calgary 3280 Hospital Drive NW T2N 4Z6 Calgary Alberta Canada
| | - Evgueni Gorobets
- Department of Chemistry, University of Calgary 2500 University Drive NW T2N 1N4 Calgary Alberta Canada
- Arnie Charbonneau Cancer Institute, University of Calgary 3280 Hospital Drive NW T2N 4Z6 Calgary Alberta Canada
| | - Koichiro Mihara
- Department of Physiology and Pharmacology, University of Calgary 3330 Hospital Drive NW T2N 4N1 Calgary Canada
| | - Ranjan Maity
- Arnie Charbonneau Cancer Institute, University of Calgary 3280 Hospital Drive NW T2N 4Z6 Calgary Alberta Canada
| | - James W Papatzimas
- Department of Chemistry, University of Calgary 2500 University Drive NW T2N 1N4 Calgary Alberta Canada
- Arnie Charbonneau Cancer Institute, University of Calgary 3280 Hospital Drive NW T2N 4Z6 Calgary Alberta Canada
| | - Benjamin S Gelfand
- Department of Chemistry, University of Calgary 2500 University Drive NW T2N 1N4 Calgary Alberta Canada
| | - Morley D Hollenberg
- Department of Physiology and Pharmacology, University of Calgary 3330 Hospital Drive NW T2N 4N1 Calgary Canada
| | - Nizar J Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary 3280 Hospital Drive NW T2N 4Z6 Calgary Alberta Canada
| | - Darren J Derksen
- Department of Chemistry, University of Calgary 2500 University Drive NW T2N 1N4 Calgary Alberta Canada
- Arnie Charbonneau Cancer Institute, University of Calgary 3280 Hospital Drive NW T2N 4Z6 Calgary Alberta Canada
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197
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Hati S, Zallocchi M, Hazlitt R, Li Y, Vijayakumar S, Min J, Rankovic Z, Lovas S, Zuo J. AZD5438-PROTAC: A selective CDK2 degrader that protects against cisplatin- and noise-induced hearing loss. Eur J Med Chem 2021; 226:113849. [PMID: 34560429 PMCID: PMC8608744 DOI: 10.1016/j.ejmech.2021.113849] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) is a potential therapeutic target for the treatment of hearing loss and cancer. Previously, we identified AZD5438 and AT7519-7 as potent inhibitors of CDK2, however, they also targeted additional kinases, leading to unwanted toxicities. Proteolysis Targeting Chimeras (PROTACs) are a new promising class of small molecules that can effectively direct specific proteins to proteasomal degradation. Herein we report the design, synthesis, and characterization of PROTACs of AT7519-7 and AZD5438 and the identification of PROTAC-8, an AZD5438-PROTAC, that exhibits selective, partial CDK2 degradation. Furthermore, PROTAC-8 protects against cisplatin ototoxicity and kainic acid excitotoxicity in zebrafish. Molecular dynamics simulations reveal the structural requirements for CDK2 degradation. Together, PROTAC-8 is among the first-in-class PROTACs with in vivo therapeutic activities and represents a new lead compound that can be further developed for better efficacy and selectivity for CDK2 degradation against hearing loss and cancer.
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Affiliation(s)
- Santanu Hati
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Marisa Zallocchi
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Robert Hazlitt
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuju Li
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Sarath Vijayakumar
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Jaeki Min
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Sándor Lovas
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA
| | - Jian Zuo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE, 68178, USA.
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198
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Wang C, Zhang Y, Wu Y, Xing D. Developments of CRBN-based PROTACs as potential therapeutic agents. Eur J Med Chem 2021; 225:113749. [PMID: 34411892 DOI: 10.1016/j.ejmech.2021.113749] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022]
Abstract
Protease-targeted chimeras (PROTACs) are a new technology that is receiving much attention in the treatment of diseases. The mechanism is to inhibit protein function by hijacking the ubiquitin E3 ligase for protein degradation. Heterogeneous bifunctional PROTACs contain a ligand for recruiting E3 ligase, a linker, and another ligand to bind to the target protein for degradation. A variety of small-molecule PROTACs (CRBN, VHL, IAPs, MDM2, DCAF15, DCAF16, and RNF114-based PROTACs) have been identified so far. In particular, CRBN-based PROTACs (e.g., ARV-110 and ARV-471) have received more attention for their promising therapeutic intervention. To date, CRBN-based PRTOACs have been extensively explored worldwide and have excelled not only in cancer diseases but also in cardiovascular diseases, immune diseases, neurodegenerative diseases, and viral infections. In this review, we will provide a comprehensive update on the latest research progress in CRBN-based PRTOACs area. Following the criteria, such as disease area and drug target class, we will present the degradants in alphabetical order by target. We also provide our own perspective on the future prospects and potential challenges facing PROTACs.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Yudong Wu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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199
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Eron SJ, Huang H, Agafonov RV, Fitzgerald ME, Patel J, Michael RE, Lee TD, Hart AA, Shaulsky J, Nasveschuk CG, Phillips AJ, Fisher SL, Good A. Structural Characterization of Degrader-Induced Ternary Complexes Using Hydrogen-Deuterium Exchange Mass Spectrometry and Computational Modeling: Implications for Structure-Based Design. ACS Chem Biol 2021; 16:2228-2243. [PMID: 34582690 DOI: 10.1021/acschembio.1c00376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The field of targeted protein degradation (TPD) has grown exponentially over the past decade with the goal of developing therapies that mark proteins for destruction leveraging the ubiquitin-proteasome system. One common approach to achieve TPD is to employ a heterobifunctional molecule, termed as a degrader, to recruit the protein target of interest to the E3 ligase machinery. The resultant generation of an intermediary ternary complex (target-degrader-ligase) is pivotal in the degradation process. Understanding the ternary complex geometry offers valuable insight into selectivity, catalytic efficiency, linker chemistry, and rational degrader design. In this study, we utilize hydrogen-deuterium exchange mass spectrometry (HDX-MS) to identify degrader-induced protein-protein interfaces. We then use these data in conjunction with constrained protein docking to build three-dimensional models of the ternary complex. The approach was used to characterize complex formation between the E3 ligase CRBN and the first bromodomain of BRD4, a prominent oncology target. We show marked differences in the ternary complexes formed in solution based on distinct patterns of deuterium uptake for two degraders, CFT-1297 and dBET6. CFT-1297, which exhibited positive cooperativity, altered the deuterium uptake profile revealing the degrader-induced protein-protein interface of the ternary complex. For CFT-1297, the ternary complexes generated by the highest scoring HDX-constrained docking models differ markedly from those observed in the published crystal structures. These results highlight the potential utility of HDX-MS to provide rapidly accessible structural insights into degrader-induced protein-protein interfaces in solution. They further suggest that degrader ternary complexes exhibit significant conformation flexibility and that biologically relevant complexes may well not exhibit the largest interaction surfaces between proteins. Taken together, the results indicate that methods capable of incorporating linker conformation uncertainty may prove an important component in degrader design moving forward. In addition, the development of scoring functions modified to handle interfaces with no evolved complementarity, for example, through consideration of high levels of water infiltration, may prove valuable. Furthermore, the use of crystal structures as validation tools for novel degrader methods needs to be considered with caution.
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Affiliation(s)
- Scott J. Eron
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Hongwei Huang
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Roman V. Agafonov
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Mark E. Fitzgerald
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Joe Patel
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Ryan E. Michael
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Tobie D. Lee
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Ashley A. Hart
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Jodi Shaulsky
- Dassault Systèmes BIOVIA, 5005 Wateridge Vista Dr, San Diego, California 92121, United States
| | | | - Andrew J. Phillips
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Stewart L. Fisher
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
| | - Andrew Good
- C4 Therapeutics, Inc., 490 Arsenal Way Suite 200, Watertown, Massachusetts 02472, United States
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200
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Targeted protein degraders from an oncologist point of view: The Holy Grail of cancer therapy? Crit Rev Oncol Hematol 2021; 169:103532. [PMID: 34800655 DOI: 10.1016/j.critrevonc.2021.103532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 01/18/2023] Open
Abstract
In the era of precision medicine, monoclonal antibodies and small molecule inhibitors are the mainstays of the biological therapy in patients with solid tumors. However, resistance to treatment and the "undruggability" of certain key oncogenic proteins emerged as major limitations and jeopardize the clinical benefit of modern therapeutic approaches. Targeted protein degraders are novel molecules entering the early phase of clinical development that exploit the intracellular ubiquitine-proteasome system to promote a specific degradation of target proteins. Since the peculiar mechanism of action, targeted protein degraders have the potential to limit and overcome resistance to treatment and to allow a full actionability of certain cancer drivers that are actually elusive targets. Here, we discuss the state-of-the-art and the open issues in the development of these emerging biological agents from a clinical perspective and with a focus on solid tumors.
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