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Zhou L, Na J, Liu X, Wu P. Chromophore-Assisted Light Inactivation for Protein Degradation and Its Application in Biomedicine. Bioengineering (Basel) 2024; 11:651. [PMID: 39061733 PMCID: PMC11273424 DOI: 10.3390/bioengineering11070651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
The functional investigation of proteins holds immense significance in unraveling physiological and pathological mechanisms of organisms as well as advancing the development of novel pharmaceuticals in biomedicine. However, the study of cellular protein function using conventional genetic manipulation methods may yield unpredictable outcomes and erroneous conclusions. Therefore, precise modulation of protein activity within cells holds immense significance in the realm of biomedical research. Chromophore-assisted light inactivation (CALI) is a technique that labels photosensitizers onto target proteins and induces the production of reactive oxygen species through light control to achieve precise inactivation of target proteins. Based on the type and characteristics of photosensitizers, different excitation light sources and labeling methods are selected. For instance, KillerRed forms a fusion protein with the target protein through genetic engineering for labeling and inactivates the target protein via light activation. CALI is presently predominantly employed in diverse biomedical domains encompassing investigations into protein functionality and interaction, intercellular signal transduction research, as well as cancer exploration and therapy. With the continuous advancement of CALI technology, it is anticipated to emerge as a formidable instrument in the realm of life sciences, yielding more captivating outcomes for fundamental life sciences and precise disease diagnosis and treatment.
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Affiliation(s)
- Lvjia Zhou
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China; (L.Z.); (J.N.)
| | - Jintong Na
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China; (L.Z.); (J.N.)
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China; (L.Z.); (J.N.)
| | - Pan Wu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China; (L.Z.); (J.N.)
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
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Gao J, Yang L, Lei S, Zhou F, Nie H, Peng B, Xu T, Chen X, Yang X, Sheng C, Rao Y, Pu K, Jin J, Xu Z, Yu H. Stimuli-activatable PROTACs for precise protein degradation and cancer therapy. Sci Bull (Beijing) 2023; 68:1069-1085. [PMID: 37169612 DOI: 10.1016/j.scib.2023.04.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/28/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
The proteolysis targeting chimeras (PROTACs) approach has attracted extensive attention in the past decade, which represents an emerging therapeutic modality with the potential to tackle disease-causing proteins that are historically challengeable for conventional small molecular inhibitors. PROTAC harnesses the endogenic E3 ubiquitin ligase to degrade protein of interest (POI) via ubiquitin-proteasome system in a cycle-catalytic manner. The event-driven pharmacology of PROTAC is poised to pursue those targets that are conventionally undruggable, which enormously extends the space of drug development. Furthermore, PROTAC has the potential to address drug resistance of small molecular inhibitors by degrading the whole POI. Nevertheless, PROTACs display high-efficiency and always-on properties to degrade POI, they may cause severe side effects due to an "on-target but off-tissue" protein degradation profile at the undesirable tissues and cells. Given that, the stimuli-activatable PROTAC prodrugs have been recently exploited to confine precise protein degradation of the favorable targets, which may conquer the adverse effects of PROTAC due to uncontrollable protein degradation. Herein, we summarized the cutting-edge advances of the stimuli-activatable PROTAC prodrugs. We also overviewed the progress of PROTAC prodrug-based nanomedicine to improve PROTAC delivery to the tumors and precise POI degradation in the targeted cells.
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Affiliation(s)
- Jing Gao
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lei Yang
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shumin Lei
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Feng Zhou
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huijun Nie
- Center of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bo Peng
- Information Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tianfeng Xu
- Center of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaohua Chen
- Center of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiaobao Yang
- Gluetacs Therapeutics (Shanghai) Co., Ltd. Shanghai 201306, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Yu Rao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Kanyi Pu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York NY 10029, USA
| | - Zhiai Xu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
| | - Haijun Yu
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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Xie B, Xu B, Xin L, Wei Y, Guo X, Dong C. Discovery of estrogen receptor α targeting caged hypoxia-responsive PROTACs with an inherent bicyclic skeleton for breast cancer treatment. Bioorg Chem 2023; 137:106590. [PMID: 37163809 DOI: 10.1016/j.bioorg.2023.106590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/12/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023]
Abstract
In view of the potential off-target effects of antitumor drugs, including proteolysis targeting chimera (PROTAC), certain toxic effects may be caused in normal tissues. Herein, based on the characteristics of the tumor microenvironment, we reported the first estrogen receptor α (ERα) targeting hypoxia-responsive PROTACs in order to improve their safety in breast cancer treatment by introducing two hypoxia-activated groups, nitroimidazole and nitrobenzene, into the ER ligand or E3 ligand of an active PROTAC, which has certain cytotoxicity in normal cells. Bioactivity studies showed that these hypoxia-responsive PROTACs exhibited excellent hypoxic responsiveness and ERα degradation activity under hypoxic conditions, and thus improved the toxic effects of the active PROTAC in normal cells. It is expected that our caged compounds provide a new strategy for precise functional control of PROTAC drugs for breast cancer treatment.
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Affiliation(s)
- Baohua Xie
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Bin Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Lilan Xin
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yizhou Wei
- Wuhan Britain-China School, Wuhan 430030, China
| | - Xinyi Guo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Chune Dong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Wuhan University, Wuhan 430071, China.
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Guedeney N, Cornu M, Schwalen F, Kieffer C, Voisin-Chiret AS. PROTAC technology: A new drug design for chemical biology with many challenges in drug discovery. Drug Discov Today 2023; 28:103395. [PMID: 36228895 DOI: 10.1016/j.drudis.2022.103395] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Target Protein Degradation TPD is a new avenue and revolutionary for therapeutics because redefining the principles of classical drug discovery and guided by event-based target activity rather than the occupancy-driven activity. Since the discovery of the first PROTAC in 2001, TPD represents a rapidly growing technology, with applications in both drug discovery and chemical biology. Over the last decade, many questions have been raised and today the knowledge gained by each team has elucidated a number of them, although there is still a long way to go. The objective of this work is to present the challenges that the PROTAC strategy has very recently addressed in drug design and discovery by presenting extremely recent results from the literature and to provide guidelines in the drug design of new PROTACs as successful therapeutic modality for medicinal chemists.
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Affiliation(s)
| | - Marie Cornu
- Normandie Univ, UNICAEN, CERMN, 14000 Caen, France
| | - Florian Schwalen
- Normandie Univ, UNICAEN, CERMN, 14000 Caen, France; Department of Pharmacy, Caen University Hospital, Caen 14000, France
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Recent Advances of Degradation Technologies Based on PROTAC Mechanism. Biomolecules 2022; 12:biom12091257. [PMID: 36139095 PMCID: PMC9496103 DOI: 10.3390/biom12091257] [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: 07/13/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
PROTAC (proteolysis-targeting chimeras), which selectively degrades target proteins, has become the most popular technology for drug development in recent years. Here, we introduce the history of PROTAC, and summarize the recent advances in novel types of degradation technologies based on the PROTAC mechanism, including TF-PROTAC, Light-controllable PROTAC, PhosphoTAC, LYTAC, AUTAC, ATTEC, CMA, RNA-PROTAC and RIBOTACs. In addition, the clinical progress, current challenges and future prospects of degradation technologies based on PROTAC mechanism are discussed.
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Shi S, Du Y, Zou Y, Niu J, Cai Z, Wang X, Qiu F, Ding Y, Yang G, Wu Y, Xu Y, Zhu Q. Rational Design for Nitroreductase (NTR)-Responsive Proteolysis Targeting Chimeras (PROTACs) Selectively Targeting Tumor Tissues. J Med Chem 2022; 65:5057-5071. [PMID: 35175763 DOI: 10.1021/acs.jmedchem.1c02221] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The catalytic properties of proteolysis targeting chimeras (PROTACs) may lead to uncontrolled off-tissue target degradation that causes potential toxicity, limiting their clinical applications. The precise control of this technology in a tissue-selective manner can minimize the potential toxicity. Hypoxia is a hallmark of most solid tumors, accompanied by elevated levels of nitroreductase (NTR). Based on this character, we presented a type of NTR-responsive PROTACs to selectively degrade proteins of interest (POI) in tumor tissues. Compound 17-1 was the first NTR-responsive PROTAC synthesized by incorporating the caging group on the Von Hippel-Lindau (VHL) E3 ubiquitin ligase ligand. It could be activated by NTR to release the active PROTAC 17 to efficiently degrade the EGFR protein and subsequently exert antitumor efficacy. Thus, a general strategy for the precise control of PROTAC to induce POI degradation in tumor tissues by NTR was established, which provided a generalizable platform for the development of NTR-controlled PROTACs to achieve selective degradation.
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Affiliation(s)
- Shi Shi
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yu Du
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Zou
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Jing Niu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Zeyu Cai
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaonan Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Feihuang Qiu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Ding
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Gengchen Yang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yunze Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yungen Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.,Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Qihua Zhu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.,Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
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Mukadum F, Nguyen Q, Adrion DM, Appleby G, Chen R, Dang H, Chang R, Garnett R, Lopez SA. Efficient Discovery of Visible Light-Activated Azoarene Photoswitches with Long Half-Lives Using Active Search. J Chem Inf Model 2021; 61:5524-5534. [PMID: 34752100 DOI: 10.1021/acs.jcim.1c00954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Photoswitches are molecules that undergo a reversible, structural isomerization after exposure to certain wavelengths of light. The dynamic control offered by molecular photoswitches is favorable for materials chemistry, photopharmacology, and catalysis applications. Ideal photoswitches absorb visible light and have long-lived metastable isomers. We used high-throughput virtual screening to predict the absorption maxima (λmax) of the E-isomer and half-life (t1/2) of the Z-isomer. However, computing the photophysical and kinetic stabilities with density functional theory of each entry of a virtual molecular library containing thousands or millions of molecules is prohibitively time-consuming. We applied active search, a machine-learning technique, to intelligently search a chemical search space of 255 991 photoswitches based on 29 known azoarenes and their derivatives. We iteratively trained the active search algorithm on whether a candidate absorbed visible light (λmax > 450 nm). Active search was found to triple the discovery rate compared to random search. Further, we projected 1962 photoswitches to 2D using the Uniform Manifold Approximation and Projection algorithm and found that λmax depends on the core, which is tunable by substituents. We then incorporated a second stage of screening to predict the stabilities of the Z-isomers for the top candidates of each core. We identified four ideal photoswitches that concurrently satisfy the following criteria: λmax > 450 nm and t1/2 > 2 h.These candidates had λmax and t1/2 range from 465 to 531 nm and hours to days, respectively.
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Affiliation(s)
- Fatemah Mukadum
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Quan Nguyen
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daniel M Adrion
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Gabriel Appleby
- Department of Computer Science, Tufts University, Medford, Massachusetts 02155, United States
| | - Rui Chen
- Department of Computer Science, Tufts University, Medford, Massachusetts 02155, United States
| | - Haley Dang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Remco Chang
- Department of Computer Science, Tufts University, Medford, Massachusetts 02155, United States
| | - Roman Garnett
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Steven A Lopez
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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