1
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Scott DC, Dharuman S, Griffith E, Chai SC, Ronnebaum J, King MT, Tangallapally R, Lee C, Gee CT, Yang L, Li Y, Loudon VC, Lee HW, Ochoada J, Miller DJ, Jayasinghe T, Paulo JA, Elledge SJ, Harper JW, Chen T, Lee RE, Schulman BA. Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2. Nat Commun 2024; 15:8829. [PMID: 39396041 PMCID: PMC11470957 DOI: 10.1038/s41467-024-52966-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 09/27/2024] [Indexed: 10/14/2024] Open
Abstract
PROTAC® (proteolysis-targeting chimera) molecules induce proximity between an E3 ligase and protein-of-interest (POI) to target the POI for ubiquitin-mediated degradation. Cooperative E3-PROTAC-POI complexes have potential to achieve neo-substrate selectivity beyond that established by POI binding to the ligand alone. Here, we extend the collection of ubiquitin ligases employable for cooperative ternary complex formation to include the C-degron E3 KLHDC2. Ligands were identified that engage the C-degron binding site in KLHDC2, subjected to structure-based improvement, and linked to JQ1 for BET-family neo-substrate recruitment. Consideration of the exit vector emanating from the ligand engaged in KLHDC2's U-shaped degron-binding pocket enabled generation of SJ46421, which drives formation of a remarkably cooperative, paralog-selective ternary complex with BRD3BD2. Meanwhile, screening pro-drug variants enabled surmounting cell permeability limitations imposed by acidic moieties resembling the KLHDC2-binding C-degron. Selectivity for BRD3 compared to other BET-family members is further manifested in ubiquitylation in vitro, and prodrug version SJ46420-mediated degradation in cells. Selectivity is also achieved for the ubiquitin ligase, overcoming E3 auto-inhibition to engage KLHDC2, but not the related KLHDC1, KLHDC3, or KLHDC10 E3s. In sum, our study establishes neo-substrate-specific targeted protein degradation via KLHDC2, and provides a framework for developing selective PROTAC protein degraders employing C-degron E3 ligases.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suresh Dharuman
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jarrid Ronnebaum
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Moeko T King
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Rajendra Tangallapally
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chan Lee
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Victoria C Loudon
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ha Won Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason Ochoada
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Thilina Jayasinghe
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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2
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Chagaleti BK, B SK, G V A, Rajagopal R, Alfarhan A, Arockiaraj J, Muthu Kumaradoss K, Karthick Raja Namasivayam S. Targeting cyclin-dependent kinase 2 CDK2: Insights from molecular docking and dynamics simulation - A systematic computational approach to discover novel cancer therapeutics. Comput Biol Chem 2024; 112:108134. [PMID: 38964206 DOI: 10.1016/j.compbiolchem.2024.108134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024]
Abstract
Global public health is confronted with significant challenges due to the prevalence of cancer and the emergence of treatment resistance. This work focuses on the identification of cyclin-dependent kinase 2 (CDK2) through a systematic computational approach to discover novel cancer therapeutics. A ligand-based pharmacophore model was initially developed using a training set of seven potent CDK2 inhibitors. The obtained most robust model was characterized by three features: one donor (|Don|) and two acceptors (|Acc|). Screening this model against the ZINC database resulted in identifying 108 hits, which underwent further molecular docking studies. The docking results indicated binding affinity, with energy values ranging from -6.59 kcal mol⁻¹ to -7.40 kcal mol⁻¹ compared to the standard Roscovitine. The top 10 compounds (Z1-Z10) selected from the docking data were further screened for ADMET profiling, ensuring their compliance with pharmacokinetic and toxicological criteria. The top 3 compounds (Z1-Z3) chosen from the docking were subjected to Density Functional Theory (DFT) studies. They revealed significant variations in electronic properties, providing insights into the reactivity, stability, and polarity of these compounds. Molecular dynamics simulations confirmed the stability of the ligand-protein complexes, with acceptable RMSD and RMSF values. Specifically, compound Z1 demonstrated stability, around 2.4 Å, and maintained throughout the 100 ns simulation period with minimal conformational changes, stable RMSD, and consistent protein-ligand interactions.
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Affiliation(s)
- Bharath Kumar Chagaleti
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Shantha Kumar B
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Anjana G V
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Rajakrishnan Rajagopal
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box No. 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed Alfarhan
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box No. 2455, Riyadh 11451, Saudi Arabia
| | - Jesu Arockiaraj
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India.
| | - Kathiravan Muthu Kumaradoss
- Dr. APJ Kalam Research Lab, Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India.
| | - S Karthick Raja Namasivayam
- Centre for Applied Research, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, Tamil Nadu 602105, India.
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3
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Huang HT, Lumpkin RJ, Tsai RW, Su S, Zhao X, Xiong Y, Chen J, Mageed N, Donovan KA, Fischer ES, Sellers WR. Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates. Nat Chem Biol 2024; 20:1227-1236. [PMID: 38514884 DOI: 10.1038/s41589-024-01590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Protein ubiquitylation controls diverse processes within eukaryotic cells, including protein degradation, and is often dysregulated in disease. Moreover, small-molecule degraders that redirect ubiquitylation activities toward disease targets are an emerging and promising therapeutic class. Over 600 E3 ubiquitin ligases are expressed in humans, but their substrates remain largely elusive, necessitating the development of new methods for their discovery. Here we report the development of E3-substrate tagging by ubiquitin biotinylation (E-STUB), a ubiquitin-specific proximity labeling method that biotinylates ubiquitylated substrates in proximity to an E3 ligase of interest. E-STUB accurately identifies the direct ubiquitylated targets of protein degraders, including collateral targets and ubiquitylation events that do not lead to substrate degradation. It also detects known substrates of E3 ligase CRBN and VHL with high specificity. With the ability to elucidate proximal ubiquitylation events, E-STUB may facilitate the development of proximity-inducing therapeutics and act as a generalizable method for E3-substrate mapping.
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Affiliation(s)
- Hai-Tsang Huang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan W Tsai
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Shuyao Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xu Zhao
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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4
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Lin H, Riching K, Lai MP, Lu D, Cheng R, Qi X, Wang J. Lysineless HiBiT and NanoLuc Tagging Systems as Alternative Tools for Monitoring Targeted Protein Degradation. ACS Med Chem Lett 2024; 15:1367-1375. [PMID: 39140070 PMCID: PMC11318018 DOI: 10.1021/acsmedchemlett.4c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024] Open
Abstract
Target protein degradation (TPD) has emerged as a revolutionary approach in drug discovery, leveraging the cell's intrinsic machinery to selectively degrade disease-associated proteins. Nanoluciferase (nLuc) fusion proteins and the NanoBiT technology offer two robust and sensitive screening platforms to monitor the subtle changes in protein abundance induced by TPD molecules. Despite these advantages, concerns have arisen regarding potential degradation artifacts introduced by tagging systems due to the presence of lysine residues on them, prompting the development of alternative tools. In this study, we introduce HiBiT-RR and nLucK0, variants devoid of lysine residues, to mitigate such artifacts. Our findings demonstrate that HiBiT-RR maintains a similar sensitivity and binding affinity with the original HiBiT. Moreover, the comparison between nLucWT and nLucK0 constructs reveals variations in degradation patterns induced by certain TPD molecules, emphasizing the importance of choosing appropriate tagging systems to ensure the reliability of experimental outcomes in studying protein degradation processes.
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Affiliation(s)
- Hanfeng Lin
- The
Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center
for NextGen Therapeutics, Baylor College
of Medicine, Houston, Texas 77030, United
States
| | - Kristin Riching
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - May Poh Lai
- Malvern
Panalytical Inc., 2400
Computer Drive, Westborough, Massachusetts 01581, United States
| | - Dong Lu
- The
Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ran Cheng
- The
Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center
for NextGen Therapeutics, Baylor College
of Medicine, Houston, Texas 77030, United
States
| | - Xiaoli Qi
- The
Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center
for NextGen Therapeutics, Baylor College
of Medicine, Houston, Texas 77030, United
States
| | - Jin Wang
- The
Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Department
of Molecular and Cellular Biology, Baylor
College of Medicine, Houston, Texas 77030, United States
- Center
for NextGen Therapeutics, Baylor College
of Medicine, Houston, Texas 77030, United
States
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5
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Sobierajski T, Małolepsza J, Pichlak M, Gendaszewska-Darmach E, Błażewska KM. The impact of E3 ligase choice on PROTAC effectiveness in protein kinase degradation. Drug Discov Today 2024; 29:104032. [PMID: 38789027 DOI: 10.1016/j.drudis.2024.104032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Proteolysis targeting chimera (PROTACs) provide a novel therapeutic approach that is revolutionizing drug discovery. The success of PROTACs largely depends on the combination of their three fragments: E3 ligase ligand, linker and protein of interest (POI)-targeting ligand. We summarize the pivotal significance of the precise combination of the E3 ligase ligand with the POI-recruiting warhead, which is crucial for the successful execution of cellular processes and achieving the desired outcomes. Therefore, the key to our selection was the use of at least two ligands recruiting two different ligases. This approach enables a direct comparison of the impacts of the specific ligases on target degradation.
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Affiliation(s)
- Tomasz Sobierajski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Joanna Małolepsza
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Marta Pichlak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland
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6
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Lin H, Riching K, Lai MP, Lu D, Cheng R, Qi X, Wang J. Lysineless HiBiT and NanoLuc Tagging Systems as Alternative Tools Monitoring Targeted Protein Degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594249. [PMID: 38798562 PMCID: PMC11118299 DOI: 10.1101/2024.05.14.594249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Target protein degradation (TPD) has emerged as a revolutionary approach in drug discovery, leveraging the cell's intrinsic machinery to selectively degrade disease-associated proteins. Proteolysis-Targeting Chimeras (PROTACs) exemplify this strategy, exploiting heterobifunctional molecules to induce ubiquitination and subsequent degradation of target proteins. The clinical advancement of PROTACs underscores their potential in therapeutic intervention, with numerous projects progressing through clinical stages. However, monitoring subtle changes in protein abundance induced by TPD molecules demands highly sensitive assays. Nano-luciferase (nLuc) fusion proteins, or the NanoBiT technology derived from it, offer a robust screening platform due to their high sensitivity and stability. Despite these advantages, concerns have arisen regarding potential degradation artifacts introduced by tagging systems due to the presence of lysine residues on them, prompting the development of alternative tools. In this study, we introduce HiBiT-RR and nLuc K0 , variants devoid of lysine residues, to mitigate such artifacts. Our findings demonstrate that HiBiT-RR maintains similar sensitivity and binding affinity with the original HiBiT. Moreover, the comparison between nLuc WT and nLuc K0 constructs reveals variations in degradation patterns induced by certain PROTAC molecules, emphasizing the importance of choosing appropriate tagging systems to ensure the reliability of experimental outcomes in studying protein degradation processes.
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7
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Vorderbruggen M, Velázquez-Martínez CA, Natarajan A, Karpf AR. PROTACs in Ovarian Cancer: Current Advancements and Future Perspectives. Int J Mol Sci 2024; 25:5067. [PMID: 38791105 PMCID: PMC11121112 DOI: 10.3390/ijms25105067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy. The majority of patients diagnosed with advanced ovarian cancer will relapse, at which point additional therapies can be administered but, for the most part, these are not curative. As such, a need exists for the development of novel therapeutic options for ovarian cancer patients. Research in the field of targeted protein degradation (TPD) through the use of proteolysis-targeting chimeras (PROTACs) has significantly increased in recent years. The ability of PROTACs to target proteins of interest (POI) for degradation, overcoming limitations such as the incomplete inhibition of POI function and the development of resistance seen with other inhibitors, is of particular interest in cancer research, including ovarian cancer research. This review provides a synopsis of PROTACs tested in ovarian cancer models and highlights PROTACs characterized in other types of cancers with potential high utility in ovarian cancer. Finally, we discuss methods that will help to enable the selective delivery of PROTACs to ovarian cancer and improve the pharmacodynamic properties of these agents.
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Affiliation(s)
- Makenzie Vorderbruggen
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | | | - Amarnath Natarajan
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Adam R. Karpf
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
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8
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Shah Zaib Saleem R, Schwalm MP, Knapp S. Expanding the ligand spaces for E3 ligases for the design of protein degraders. Bioorg Med Chem 2024; 105:117718. [PMID: 38621319 DOI: 10.1016/j.bmc.2024.117718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Targeted protein degradation (TPD) has recently emerged as an exciting new drug modality. However, the strategy of developing small molecule-based protein degraders has evolved over the past two decades and has now established molecular tags that are already in clinical use, as well as chimeric molecules, PROteolysis TArgeting Chimeras (PROTACs), based mainly on ligand systems developed for the two E3 ligases CRBN and VHL. The large size of the human E3 ligase family suggests that PROTACs can be developed by targeting a large diversity of E3 ligases, some of which have restricted expression patterns with the potential to design disease- or tissue-specific degraders. Indeed, many new E3 ligands have been published recently, confirming the druggability of E3 ligases. This review summarises recent data on E3 ligases and highlights the challenges in developing these molecules into efficient PROTACs rivalling the established degrader systems.
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Affiliation(s)
- Rahman Shah Zaib Saleem
- Department of Chemistry & Chemical Engineering, SBA School of Sciences & Engineering, LUMS, Pakistan
| | - 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; German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, 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) partner site Frankfurt/Mainz, Frankfurt, Germany.
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9
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Wang L, Yang Z, Li G, Liu Y, Ai C, Rao Y. Discovery of small molecule degraders for modulating cell cycle. Front Med 2023; 17:823-854. [PMID: 37935945 DOI: 10.1007/s11684-023-1027-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/16/2023] [Indexed: 11/09/2023]
Abstract
The cell cycle is a complex process that involves DNA replication, protein expression, and cell division. Dysregulation of the cell cycle is associated with various diseases. Cyclin-dependent kinases (CDKs) and their corresponding cyclins are major proteins that regulate the cell cycle. In contrast to inhibition, a new approach called proteolysis-targeting chimeras (PROTACs) and molecular glues can eliminate both enzymatic and scaffold functions of CDKs and cyclins, achieving targeted degradation. The field of PROTACs and molecular glues has developed rapidly in recent years. In this article, we aim to summarize the latest developments of CDKs and cyclin protein degraders. The selectivity, application, validation and the current state of each CDK degrader will be overviewed. Additionally, possible methods are discussed for the development of degraders for CDK members that still lack them. Overall, this article provides a comprehensive summary of the latest advancements in CDK and cyclin protein degraders, which will be helpful for researchers working on this topic.
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Affiliation(s)
- Liguo Wang
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Zhouli Yang
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Guangchen Li
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yongbo Liu
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Chao Ai
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, China.
| | - Yu Rao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China.
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10
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Mostofian B, Martin HJ, Razavi A, Patel S, Allen B, Sherman W, Izaguirre JA. Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods. J Chem Inf Model 2023; 63:5408-5432. [PMID: 37602861 PMCID: PMC10498452 DOI: 10.1021/acs.jcim.3c00603] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 08/22/2023]
Abstract
The therapeutic approach of targeted protein degradation (TPD) is gaining momentum due to its potentially superior effects compared with protein inhibition. Recent advancements in the biotech and pharmaceutical sectors have led to the development of compounds that are currently in human trials, with some showing promising clinical results. However, the use of computational tools in TPD is still limited, as it has distinct characteristics compared with traditional computational drug design methods. TPD involves creating a ternary structure (protein-degrader-ligase) responsible for the biological function, such as ubiquitination and subsequent proteasomal degradation, which depends on the spatial orientation of the protein of interest (POI) relative to E2-loaded ubiquitin. Modeling this structure necessitates a unique blend of tools initially developed for small molecules (e.g., docking) and biologics (e.g., protein-protein interaction modeling). Additionally, degrader molecules, particularly heterobifunctional degraders, are generally larger than conventional small molecule drugs, leading to challenges in determining drug-like properties like solubility and permeability. Furthermore, the catalytic nature of TPD makes occupancy-based modeling insufficient. TPD consists of multiple interconnected yet distinct steps, such as POI binding, E3 ligase binding, ternary structure interactions, ubiquitination, and degradation, along with traditional small molecule properties. A comprehensive set of tools is needed to address the dynamic nature of the induced proximity ternary complex and its implications for ubiquitination. In this Perspective, we discuss the current state of computational tools for TPD. We start by describing the series of steps involved in the degradation process and the experimental methods used to characterize them. Then, we delve into a detailed analysis of the computational tools employed in TPD. We also present an integrative approach that has proven successful for degrader design and its impact on project decisions. Finally, we examine the future prospects of computational methods in TPD and the areas with the greatest potential for impact.
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Affiliation(s)
- Barmak Mostofian
- OpenEye, Cadence Molecular Sciences, Boston, Massachusetts 02114 United States
| | - Holli-Joi Martin
- Laboratory
for Molecular Modeling, Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599 United States
| | - Asghar Razavi
- ENKO
Chem, Inc, Mystic, Connecticut 06355 United States
| | - Shivam Patel
- Psivant
Therapeutics, Boston, Massachusetts 02210 United States
| | - Bryce Allen
- Differentiated
Therapeutics, San Diego, California 92056 United States
| | - Woody Sherman
- Psivant
Therapeutics, Boston, Massachusetts 02210 United States
| | - Jesus A Izaguirre
- Differentiated
Therapeutics, San Diego, California 92056 United States
- Atommap
Corporation, New York, New York 10013 United States
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11
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Rathje OH, Perryman L, Payne RJ, Hamprecht DW. PROTACs Targeting MLKL Protect Cells from Necroptosis. J Med Chem 2023; 66:11216-11236. [PMID: 37535857 DOI: 10.1021/acs.jmedchem.3c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Mixed Lineage Kinase domain-Like pseudokinase (MLKL) is implicated in a broad range of diseases due to its role as the ultimate effector of necroptosis and has therefore emerged as an attractive drug target. Here, we describe the development of PROteolysis TArgeting Chimeras (PROTACs) as a novel approach to knock down MLKL through chemical means. A series of candidate degraders were synthesized from a high-affinity pyrazole carboxamide-based MLKL ligand leading to the identification of a PROTAC molecule that effectively degraded MLKL and completely abrogated cell death in a TSZ model of necroptosis. By leveraging the innate ability of these PROTACs to degrade MLKL in a dose-dependent manner, the quantitative relationship between MLKL levels and necroptosis was interrogated. This work demonstrates the feasibility of targeting MLKL using a PROTAC approach and provides a powerful tool to further our understanding of the role of MLKL within the necroptotic pathway.
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Affiliation(s)
- Oliver H Rathje
- Pharmaxis Ltd., 20 Rodborough Road, Frenchs Forest, NSW 2086, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lara Perryman
- Pharmaxis Ltd., 20 Rodborough Road, Frenchs Forest, NSW 2086, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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12
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O'Brien Laramy MN, Luthra S, Brown MF, Bartlett DW. Delivering on the promise of protein degraders. Nat Rev Drug Discov 2023; 22:410-427. [PMID: 36810917 DOI: 10.1038/s41573-023-00652-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 02/23/2023]
Abstract
Over the past 3 years, the first bivalent protein degraders intentionally designed for targeted protein degradation (TPD) have advanced to clinical trials, with an initial focus on established targets. Most of these clinical candidates are designed for oral administration, and many discovery efforts appear to be similarly focused. As we look towards the future, we propose that an oral-centric discovery paradigm will overly constrain the chemical designs that are considered and limit the potential to drug novel targets. In this Perspective, we summarize the current state of the bivalent degrader modality and propose three categories of degrader designs, based on their likely route of administration and requirement for drug delivery technologies. We then describe a vision for how parenteral drug delivery, implemented early in research and supported by pharmacokinetic-pharmacodynamic modelling, can enable exploration of a broader drug design space, expand the scope of accessible targets and deliver on the promise of protein degraders as a therapeutic modality.
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Affiliation(s)
| | - Suman Luthra
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., Boston, MA, USA
| | - Matthew F Brown
- Discovery Sciences, Worldwide Research, Development, and Medical, Pfizer Inc., Groton, CT, USA
| | - Derek W Bartlett
- Pharmacokinetics, Dynamics, & Metabolism, Worldwide Research, Development, and Medical, Pfizer Inc., San Diego, CA, USA
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13
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Hope I, Endicott JA, Watt JE. Emerging approaches to CDK inhibitor development, a structural perspective. RSC Chem Biol 2023; 4:146-164. [PMID: 36794018 PMCID: PMC9906319 DOI: 10.1039/d2cb00201a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Aberrant activity of the cyclin-dependent kinase family is frequently noted in a number of diseases identifying them as potential targets for drug development. However, current CDK inhibitors lack specificity owing to the high sequence and structural conservation of the ATP binding cleft across family members, highlighting the necessity of finding novel modes of CDK inhibition. The wealth of structural information regarding CDK assemblies and inhibitor complexes derived from X-ray crystallographic studies has been recently complemented through the use of cryo-electron microscopy. These recent advances have provided insights into the functional roles and regulatory mechanisms of CDKs and their interaction partners. This review explores the conformational malleability of the CDK subunit, the importance of SLiM recognition sites in CDK complexes, the progress made in chemically induced CDK degradation and how these studies can contribute to CDK inhibitor design. Additionally, fragment-based drug discovery can be utilised to identify small molecules that bind to allosteric sites on the CDK surface employing interactions which mimic those of native protein-protein interactions. These recent structural advances in CDK inhibitor mechanisms and in chemical probes which do not occupy the orthosteric ATP binding site can provide important insights for targeted CDK therapies.
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Affiliation(s)
- Ian Hope
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jane A Endicott
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jessica E Watt
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
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14
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Zhao HY, Xin M, Zhang SQ. Progress of small molecules for targeted protein degradation: PROTACs and other technologies. Drug Dev Res 2023; 84:337-394. [PMID: 36606428 DOI: 10.1002/ddr.22026] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/01/2022] [Accepted: 12/17/2022] [Indexed: 01/07/2023]
Abstract
Recent years have witnessed the rapid development of targeted protein degradation (TPD), especially proteolysis targeting chimeras. These degraders have manifested many advantages over small molecule inhibitors. To date, a huge number of degraders have been excavated against over 70 disease-related targets. In particular, degraders against estrogen receptor and androgen receptor have crowded into phase II clinical trial. TPD technologies largely expand the scope of druggable targets, and provide powerful tools for addressing intractable problems that can not be tackled by traditional small molecule inhibitors. In this review, we mainly focus on the structures and biological activities of small molecule degraders as well as the elucidation of mechanisms of emerging TPD technologies. We also propose the challenges that exist in the TPD field at present.
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Affiliation(s)
- Hong-Yi Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Minhang Xin
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - San-Qi Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
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15
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D'costa M, Bothe A, Das S, Udhaya Kumar S, Gnanasambandan R, George Priya Doss C. CDK regulators—Cell cycle progression or apoptosis—Scenarios in normal cells and cancerous cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:125-177. [PMID: 37061330 DOI: 10.1016/bs.apcsb.2022.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Serine/threonine kinases called cyclin-dependent kinases (CDKs) interact with cyclins and CDK inhibitors (CKIs) to control the catalytic activity. CDKs are essential controllers of RNA transcription and cell cycle advancement. The ubiquitous overactivity of the cell cycle CDKs is caused by a number of genetic and epigenetic processes in human cancer, and their suppression can result in both cell cycle arrest and apoptosis. This review focused on CDKs, describing their kinase activity, their role in phosphorylation inhibition, and CDK inhibitory proteins (CIP/KIP, INK 4, RPIC). We next compared the role of different CDKs, mainly p21, p27, p57, p16, p15, p18, and p19, in the cell cycle and apoptosis in cancer cells with respect to normal cells. The current work also draws attention to the use of CDKIs as therapeutics, overcoming the pharmacokinetic barriers of pan-CDK inhibitors, analyze new chemical classes that are effective at attacking the CDKs that control the cell cycle (cdk4/6 or cdk2). It also discusses CDKI's drawbacks and its combination therapy against cancer patients. These findings collectively demonstrate the complexity of cancer cell cycles and the need for targeted therapeutic intervention. In order to slow the progression of the disease or enhance clinical outcomes, new medicines may be discovered by researching the relationship between cell death and cell proliferation.
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Affiliation(s)
- Maria D'costa
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Anusha Bothe
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Soumik Das
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - R Gnanasambandan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
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16
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Liu Z, Hu M, Yang Y, Du C, Zhou H, Liu C, Chen Y, Fan L, Ma H, Gong Y, Xie Y. An overview of PROTACs: a promising drug discovery paradigm. MOLECULAR BIOMEDICINE 2022; 3:46. [PMID: 36536188 PMCID: PMC9763089 DOI: 10.1186/s43556-022-00112-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Proteolysis targeting chimeras (PROTACs) technology has emerged as a novel therapeutic paradigm in recent years. PROTACs are heterobifunctional molecules that degrade target proteins by hijacking the ubiquitin-proteasome system. Currently, about 20-25% of all protein targets are being studied, and most works focus on their enzymatic functions. Unlike small molecules, PROTACs inhibit the whole biological function of the target protein by binding to the target protein and inducing subsequent proteasomal degradation. PROTACs compensate for limitations that transcription factors, nuclear proteins, and other scaffolding proteins are difficult to handle with traditional small-molecule inhibitors. Currently, PROTACs have successfully degraded diverse proteins, such as BTK, BRD4, AR, ER, STAT3, IRAK4, tau, etc. And ARV-110 and ARV-471 exhibited excellent efficacy in clinical II trials. However, what targets are appropriate for PROTAC technology to achieve better benefits than small-molecule inhibitors are not fully understood. And how to rationally design an efficient PROTACs and optimize it to be orally effective poses big challenges for researchers. In this review, we summarize the features of PROTAC technology, analyze the detail of general principles for designing efficient PROTACs, and discuss the typical application of PROTACs targeting different protein categories. In addition, we also introduce the progress of relevant clinical trial results of representative PROTACs and assess the challenges and limitations that PROTACs may face. Collectively, our studies provide references for further application of PROTACs.
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Affiliation(s)
- Zi Liu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Mingxing Hu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yu Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Chenghao Du
- grid.42505.360000 0001 2156 6853Department of Biological Sciences, USC Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, 90089 USA
| | - Haoxuan Zhou
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Chengyali Liu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yuanwei Chen
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Lei Fan
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Hongqun Ma
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Youling Gong
- grid.13291.380000 0001 0807 1581Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yongmei Xie
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
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17
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Hill-Payne B, Dilones S, Burslem G. The importance of controls in targeted protein degradation: Determining mechanism. Methods Enzymol 2022; 681:215-240. [PMID: 36764758 DOI: 10.1016/bs.mie.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Targeted protein degradation has emerged as a useful approach for both basic biological investigations and therapeutic development. However, it can provide confounding results if not properly controlled. In this manuscript, we discuss the importance of proper controls and provide a detailed protocol for their application to proteolysis targeting chimera mediated degradation.
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Affiliation(s)
- Brianna Hill-Payne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sebastian Dilones
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - George Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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18
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PROTACs: Current Trends in Protein Degradation by Proteolysis-Targeting Chimeras. BioDrugs 2022; 36:609-623. [PMID: 36098871 DOI: 10.1007/s40259-022-00551-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2022] [Indexed: 11/02/2022]
Abstract
In the recent past, proteolysis-targeting chimera (PROTAC) technology has received enormous attention for its ability to overcome the limitations of protein inhibitors and its capability to target undruggable proteins. The PROTAC molecule consists of three components, a ubiquitin E3 ligase ligand, a linker, and a target protein ligand. The application of this technology is rapidly gaining momentum, especially in cancer therapy. In this review, we first look at the history of degraders, followed by a section on the ubiquitin proteasome system (UPS) and E3 ligases used in PROTAC development. PROTACs are dependent on the UPS for degradation of target proteins. We further discuss the scope and design of degraders and mitigation strategies for overcoming the hook effect seen with degraders. As PROTACs do not follow Lipinski's 'Rule of 5', these molecules face drug metabolism and pharmacokinetic challenges. A detailed section on absorption, distribution, metabolism, and excretion of degraders is provided wherein we discuss methodologies and strategies to surmount the challenges faced by these molecules. For understanding PROTAC-mediated degradation, the characterization and measurement of protein levels in cells is important. Currently used techniques and recent advancements in assessment tools for degraders are discussed. Furthermore, we examine the challenges and emerging technologies that need to be focused on in order to competently develop potent degraders. Many companies are working in this area of emerging new modality and a few PROTACs have already entered clinical trials; the details of the trials are included in this review.
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19
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Simpson LM, Glennie L, Brewer A, Zhao JF, Crooks J, Shpiro N, Sapkota GP. Target protein localization and its impact on PROTAC-mediated degradation. Cell Chem Biol 2022; 29:1482-1504.e7. [PMID: 36075213 DOI: 10.1016/j.chembiol.2022.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 12/21/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) bring a protein of interest (POI) into spatial proximity of an E3 ubiquitin ligase, promoting POI ubiquitylation and proteasomal degradation. PROTACs rely on endogenous cellular machinery to mediate POI degradation, therefore the subcellular location of the POI and access to the E3 ligase being recruited potentially impacts PROTAC efficacy. To interrogate whether the subcellular context of the POI influences PROTAC-mediated degradation, we expressed either Halo or FKBP12F36V (dTAG) constructs consisting of varying localization signals and tested the efficacy of their degradation by von Hippel-Lindau (VHL)- or cereblon (CRBN)-recruiting PROTACs targeting either Halo or dTAG. POIs were localized to the nucleus, cytoplasm, outer mitochondrial membrane, endoplasmic reticulum, Golgi, peroxisome or lysosome. Differentially localized Halo or FKBP12F36V proteins displayed varying levels of degradation using the same respective PROTACs, suggesting therefore that the subcellular context of the POI can influence the efficacy of PROTAC-mediated POI degradation.
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Affiliation(s)
- Luke M Simpson
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Lorraine Glennie
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Abigail Brewer
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jin-Feng Zhao
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jennifer Crooks
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Natalia Shpiro
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gopal P Sapkota
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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20
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Kurimchak AM, Herrera-Montávez C, Montserrat-Sangrà S, Araiza-Olivera D, Hu J, Neumann-Domer R, Kuruvilla M, Bellacosa A, Testa JR, Jin J, Duncan JS. The drug efflux pump MDR1 promotes intrinsic and acquired resistance to PROTACs in cancer cells. Sci Signal 2022; 15:eabn2707. [PMID: 36041010 PMCID: PMC9552188 DOI: 10.1126/scisignal.abn2707] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) are a promising new class of drugs that selectively degrade cellular proteins of interest. PROTACs that target oncogene products are avidly being explored for cancer therapies, and several are currently in clinical trials. Drug resistance is a substantial challenge in clinical oncology, and resistance to PROTACs has been reported in several cancer cell models. Here, using proteomic analysis, we found intrinsic and acquired resistance mechanisms to PROTACs in cancer cell lines mediated by greater abundance or production of the drug efflux pump MDR1. PROTAC-resistant cells were resensitized to PROTACs by genetic ablation of ABCB1 (which encodes MDR1) or by coadministration of MDR1 inhibitors. In MDR1-overexpressing colorectal cancer cells, degraders targeting either the kinases MEK1/2 or the oncogenic mutant GTPase KRASG12C synergized with the dual epidermal growth factor receptor (EGFR/ErbB)/MDR1 inhibitor lapatinib. Moreover, compared with single-agent therapies, combining MEK1/2 degraders with lapatinib improved growth inhibition of MDR1-overexpressing KRAS-mutant colorectal cancer xenografts in mice. Together, our findings suggest that concurrent blockade of MDR1 will likely be required with PROTACs to achieve durable protein degradation and therapeutic response in cancer.
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Affiliation(s)
- Alison M. Kurimchak
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Carlos Herrera-Montávez
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sara Montserrat-Sangrà
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Daniela Araiza-Olivera
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jianping Hu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York 10029, USA
| | - Ryan Neumann-Domer
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Mathew Kuruvilla
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA,Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA,Biomedical Sciences Graduate Program, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Alfonso Bellacosa
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA,Biomedical Sciences Graduate Program, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Joseph R. Testa
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York 10029, USA
| | - James S. Duncan
- Cancer Signaling & Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA,Correspondence:
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21
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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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22
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Tao AJ, Gadbois GE, Buczynski SA, Ferguson FM. Targeted protein degradation: Emerging concepts and protein state-specific targeting principles. Curr Opin Chem Biol 2022; 67:102114. [PMID: 35042023 PMCID: PMC9701552 DOI: 10.1016/j.cbpa.2021.102114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022]
Abstract
Targeted protein degraders are heterobifunctional small molecules that link a target ligand or bait to an E3-ligase binder via a chemical spacer. Upon entering the cell, these ligands trigger the formation of a ternary complex between the target protein, degrader and E3-ligase, which leads to target polyubiquitination and proteasomal degradation. In recent years, TPD has expanded rapidly as a field, becoming the modality of choice in drug discovery and chemical probe development. This has been driven by the unique pharmacology of these molecules, which allows for fast and reversible knockdown of the target protein. Recent studies have demonstrated that degraders with specificity for a defined subpopulation of a protein-of-interest can be developed, giving rise to the emerging concept of protein state-specific targeting. In this article, we review advances towards developing degraders that differentiate between target protein subpopulations based on their; activation state, oligomerization state, cellular localization state, and cell type.
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23
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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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24
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Borowczak J, Szczerbowski K, Ahmadi N, Szylberg Ł. CDK9 inhibitors in multiple myeloma: a review of progress and perspectives. Med Oncol 2022; 39:39. [PMID: 35092513 PMCID: PMC8800928 DOI: 10.1007/s12032-021-01636-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/21/2021] [Indexed: 12/05/2022]
Abstract
Currently, multiple myeloma is not yet considered a curable disease. Despite the recent advances in therapy, the average patient lifespan is still unsatisfactory. Recently, CDK9 inhibitors emerged as a suitable agent to overcome resistance and prolong survival in patients with poor diagnoses. Downregulation of c-MYC, XIAP, Mcl-1 and restoration of p53 tumor-suppressive functions seems to play a key role in achieving clinical response. The applicability of the first generation of CDK9 inhibitors was limited due to relatively high toxicity, but the introduction of novel, highly selective drugs, seems to reduce the effects of off-target inhibition. CDK9 inhibitors were able to induce dose-dependent cytotoxicity in Doxorubicin-resistant, Lenalidomide-resistant and Bortezomib-resistant cell lines. They seem to be effective in cell lines with unfavorable prognostic factors, such as p53 deletion, t(4; 14) and t(14; 16). In preclinical trials, the application of CDK9 inhibitors led to tumor cells apoptosis, tumor growth inhibition and tumor mass reduction. Synergistic effects between CDK9 inhibitors and either Venetoclax, Bortezomib, Lenalidomide or Erlotinib have been proven and are awaiting verification in clinical trials. Although conclusions should be drawn with due care, obtained reports suggest that including CDK9 inhibitors into the current drug regimen may turn out to be beneficial, especially in poor prognosis patients.
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Affiliation(s)
- Jędrzej Borowczak
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.
| | - Krzysztof Szczerbowski
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Navid Ahmadi
- Department of Cardiothoracic Surgery, Royal Papworth Hospital, Cambridge, UK
| | - Łukasz Szylberg
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
- Department of Tumor Pathology and Pathomorphology, Oncology Centre-Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
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25
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Abstract
Proteolysis-targeting chimeras are a new modality of chemical tools and potential therapeutics involving the induction of protein degradation. Cyclin-dependent kinase (CDK) protein, which is involved in cycles and transcription cycles, participates in regulation of the cell cycle, transcription and splicing. Proteolysis-targeting chimeras targeting CDKs show several advantages over traditional CDK small-molecule inhibitors in potency, selectivity and drug resistance. In addition, the discovery of molecule glues promotes the development of CDK degraders. Herein, the authors describe the existing CDK degraders and focus on the discussion of the structural characteristics and design of these degraders.
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26
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Rodriguez-Rivera FP, Levi SM. Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms. ACS CENTRAL SCIENCE 2021; 7:1117-1125. [PMID: 34345664 PMCID: PMC8323112 DOI: 10.1021/acscentsci.1c00389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Indexed: 06/13/2023]
Abstract
Diverging from traditional target inhibition, proteasomal protein degradation approaches have emerged as novel therapeutic modalities that embody distinct pharmacological profiles and can access previously undrugged targets. Small molecule degraders have the potential to catalytically destroy target proteins at substoichiometric concentrations, thus lowering administered doses and extending pharmacological effects. With this mechanistic premise, research efforts have advanced the development of small molecule degraders that benefit from stable and increased affinity ternary complexes. However, a holistic framework that evaluates different degradation modes from a catalytic perspective, including focusing on kinetically favored degradation mechanisms, is lacking. In this Outlook, we introduce the concept of an induced cooperativity spectrum as a unifying framework to mechanistically understand catalytic degradation profiles. This framework is bolstered by key examples of published molecular degraders extending from molecular glues to bivalent degraders. Critically, we discuss remaining challenges and future opportunities in drug discovery to rationally design and phenotypically screen for efficient degraders.
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Affiliation(s)
- Frances P. Rodriguez-Rivera
- Discovery
Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Samuel M. Levi
- Pfizer
Worldwide Research and Development, Pfizer,
Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
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27
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Castaldi MP, Fisher SL. Advances in Protein Degradation. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:471-473. [PMID: 33780295 DOI: 10.1177/24725552211001823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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