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Vetma V, Perez LC, Eliaš J, Stingu A, Kombara A, Gmaschitz T, Braun N, Ciftci T, Dahmann G, Diers E, Gerstberger T, Greb P, Kidd G, Kofink C, Puoti I, Spiteri V, Trainor N, Weinstabl H, Westermaier Y, Whitworth C, Ciulli A, Farnaby W, McAulay K, Frost AB, Chessum N, Koegl M. Confounding Factors in Targeted Degradation of Short-Lived Proteins. ACS Chem Biol 2024; 19:1484-1494. [PMID: 38958654 DOI: 10.1021/acschembio.4c00152] [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: 07/04/2024]
Abstract
Targeted protein degradation has recently emerged as a novel option in drug discovery. Natural protein half-life is expected to affect the efficacy of degrading agents, but to what extent it influences target protein degradation has not been systematically explored. Using simple mathematical modeling of protein degradation, we find that the natural half-life of a target protein has a dramatic effect on the level of protein degradation induced by a degrader agent which can pose significant hurdles to screening efforts. Moreover, we show that upon screening for degraders of short-lived proteins, agents that stall protein synthesis, such as GSPT1 degraders and generally cytotoxic compounds, deceptively appear as protein-degrading agents. This is exemplified by the disappearance of short-lived proteins such as MCL1 and MDM2 upon GSPT1 degradation and upon treatment with cytotoxic agents such as doxorubicin. These findings have implications for target selection as well as for the type of control experiments required to conclude that a novel agent works as a bona fide targeted protein degrader.
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Affiliation(s)
- Vesna Vetma
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Laura Casares Perez
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Ján Eliaš
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Andrea Stingu
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Anju Kombara
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Nina Braun
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Tuncay Ciftci
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Georg Dahmann
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Emelyne Diers
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Giorgia Kidd
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | - Ilaria Puoti
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Valentina Spiteri
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Nicole Trainor
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | | | - Claire Whitworth
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - William Farnaby
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Kirsten McAulay
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Aileen B Frost
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Nicola Chessum
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
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Marcellino BK, Yang X, Kaniskan HÜ, Brady C, Chen H, Chen K, Qiu X, Clementelli C, Herschbein L, Li Z, Elghaity-beckley S, Arandela J, Kelly B, Hoffman R, Liu J, Xiong Y, Jin J, Shih AH. An MDM2 degrader for treatment of acute leukemias. Leukemia 2023; 37:370-378. [PMID: 36309559 PMCID: PMC9899314 DOI: 10.1038/s41375-022-01735-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 02/06/2023]
Abstract
In acute myeloid leukemia (AML), p53 tumor suppressor activity can be reduced due to enhanced expression of MDM2 which promotes the degradation of p53. In TP53 wild-type malignancies, therapy with small molecule antagonists of MDM2 results in antileukemic activity. Current treatment strategies, however, have been limited by poor tolerability and incomplete clinical activity. We have developed a proteolysis-targeting chimera (PROTAC) MS3227 that targets MDM2 by recruiting the E3 ligase Von Hippel-Lindau, resulting in proteasome-dependent degradation of MDM2. In WT TP53 leukemia cell lines, MS3227 led to activation of p53 targets p21, PUMA, and MDM2 and resulted in cell-cycle arrest, apoptosis, and decreased viability. The catalytic PROTAC MS3227 led to more potent activation when compared to a stoichiometric inhibitor, in part by dampening the negative feedback mechanism in the p53 - MDM2 circuit. The effectiveness of MS3227 was also observed in primary patient specimens with selectivity towards leukemic blasts. The addition of MS3227 enhanced the activity of other anti-leukemic agents including azacytidine, cytarabine, and venetoclax. In particular, MS3227 treatment was shown to downregulate MCL-1, a known mediator of resistance to venetoclax. A PROTAC-based approach may provide a means of improving MDM2 inhibition to gain greater therapeutic potential in AML.
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Affiliation(s)
- Bridget K. Marcellino
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - Xiaobao Yang
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences, and Neuroscience, Tisch Cancer Institute (TCI) Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, NY
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences, and Neuroscience, Tisch Cancer Institute (TCI) Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, NY
| | - Claudia Brady
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - He Chen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences, and Neuroscience, Tisch Cancer Institute (TCI) Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, NY
| | - Karie Chen
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - Xing Qiu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences, and Neuroscience, Tisch Cancer Institute (TCI) Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, NY
| | - Cara Clementelli
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - Lauren Herschbein
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - Zhijun Li
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sebastian Elghaity-beckley
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - Joann Arandela
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - Brianna Kelly
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - Ronald Hoffman
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences, and Neuroscience, Tisch Cancer Institute (TCI) Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, NY
| | - Yue Xiong
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Cullgen Inc., San Diego, CA, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences, and Neuroscience, Tisch Cancer Institute (TCI) Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, NY, USA.
| | - Alan H. Shih
- Department of Medicine, Division of Hematology Oncology and Tisch Cancer Institute (TCI), Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY,Corresponding authors, AHS (), JJ (), and YX ()
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3
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Koroleva OA, Dutikova YV, Trubnikov AV, Zenov FA, Manasova EV, Shtil AA, Kurkin AV. PROTAC: targeted drug strategy. Principles and limitations. Russ Chem Bull 2022; 71:2310-2334. [PMID: 36569659 PMCID: PMC9762658 DOI: 10.1007/s11172-022-3659-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 12/23/2022]
Abstract
The PROTAC (PROteolysis TArgeting Chimera) technology is a method of targeting intracellular proteins previously considered undruggable. This technology utilizes the ubiquitin-proteasome system in cells to specifically degrade target proteins, thereby offering significant advantages over conventional small-molecule inhibitors of the enzymatic function. Preclinical and preliminary clinical trials of PROTAC-based compounds (degraders) are presented. The review considers the general principles of the design of degraders. Advances and challenges of the PROTAC technology are discussed.
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Affiliation(s)
- O. A. Koroleva
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - Yu. V. Dutikova
- Patent & Law Firm “A. Zalesov and Partners”, Build. 9, 2 ul. Marshala Rybalko, 123060 Moscow, Russian Federation
| | - A. V. Trubnikov
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - F. A. Zenov
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - E. V. Manasova
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - A. A. Shtil
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Build. 15, 24 Kashirskoe shosse, 115478 Moscow, Russian Federation
| | - A. V. Kurkin
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
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