1
|
Yu S, Shi T, Li C, Xie C, Wang F, Liu X. Programming DNA Nanoassemblies into Polyvalent Lysosomal Degraders for Potent Degradation of Pathogenic Membrane Proteins. NANO LETTERS 2024. [PMID: 39225423 DOI: 10.1021/acs.nanolett.4c03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Lysosome-targeting chimera (LYTAC) shows great promise for protein-based therapeutics by targeted degradation of disease-associated membrane or extracellular proteins, yet its efficiency is constrained by the limited binding affinity between LYTAC reagents and designated proteins. Here, we established a programmable and multivalent LYTAC system by tandem assembly of DNA into a high-affinity protein degrader, a heterodimer aptamer nanostructure targeting both pathogenic membrane protein and lysosome-targeting receptor (insulin-like growth factor 2 receptor, IGF2R) with adjustable spatial distribution or organization pattern. The DNA-based multivalent LYTACs showed enhanced efficacy in removing immune-checkpoint protein programmable death-ligand 1 (PD-L1) and vascular endothelial growth factor receptor 2 (VEGFR2) in tumor cell membrane that respectively motivated a significant increase in T cell activity and a potent effect on cancer cell growth inhibition. With high programmability and versatility, this multivalent LYTAC system holds considerable promise for realizing protein therapeutics with enhanced activity.
Collapse
Affiliation(s)
- Shuyi Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Tianhui Shi
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Chenbiao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Chongyu Xie
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Beijing Life Science Academy, Beijing 102209, China
| |
Collapse
|
2
|
Zhu C, Wang W, Wang Y, Zhang W, Zhang Y, Li J. Targeted Extracellular Protein Degradation by Dendronized DNA Chimeras. ACS Chem Biol 2024; 19:654-659. [PMID: 38331720 DOI: 10.1021/acschembio.3c00645] [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: 02/10/2024]
Abstract
Extracellular soluble proteins are key agents in the development of various diseases. However, strategies to remove therapeutically relevant extracellular targets are still scarce. Here, we establish dendronized DNA chimera (DENTAC) as an efficient approach for targeted degradation of the extracellular protein of interest (ePOI). DENTAC consists of a DNA dendron against cell-surface scavenger receptors (SRs), a protein ligand, and a connecting linker, which harnesses SRs as a lysosome-trafficking receptor to mediate the lysosomal degradation of the ePOI. We interrogate and optimize structure-activity relationships of DENTAC. Using neutravidin as a model ePOI, we show that both branch number and DNA length in the DNA dendron are important determinants for efficient lysosomal delivery and degradation of the protein. We demonstrate three branches and 10 nucleotide-length polythymidine as the optimal DNA dendron components to construct DENTAC. We further exemplify the anticancer application of DENTAC by targeting matrix metalloproteinase-9 (MMP-9), where we find linker property as another factor important for DENTAC performance. We reveal that MMP-9-targeting DENTAC effectively restrain cancer cell proliferation, migration, and invasion. This study thus provides a potent strategy to delete extracellular proteins that are commonly difficult to target.
Collapse
Affiliation(s)
- Chenghong Zhu
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Weishan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Weijie Zhang
- Division of Breast Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| |
Collapse
|
3
|
Wang Q, Yang X, Yuan R, Shen A, Wang P, Li H, Zhang J, Tian C, Jiang Z, Li W, Dong S. A co-assembly platform engaging macrophage scavenger receptor A for lysosome-targeting protein degradation. Nat Commun 2024; 15:1663. [PMID: 38396109 PMCID: PMC10891067 DOI: 10.1038/s41467-024-46130-0] [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: 05/11/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Targeted degradation of proteins has emerged as a powerful method for modulating protein homeostasis. Identification of suitable degraders is essential for achieving effective protein degradation. Here, we present a non-covalent degrader construction strategy, based on a modular supramolecular co-assembly system consisting of two self-assembling peptide ligands that bind cell membrane receptors and the protein of interest simultaneously, resulting in targeted protein degradation. The developed lysosome-targeting co-assemblies (LYTACAs) can induce lysosomal degradation of extracellular protein IL-17A and membrane protein PD-L1 in several scavenger receptor A-expressing cell lines. The IL-17A-degrading co-assembly has been applied in an imiquimod-induced psoriasis mouse model, where it decreases IL-17A levels in the skin lesion and alleviates psoriasis-like inflammation. Extending to asialoglycoprotein receptor-related protein degradation, LYTACAs have demonstrated the versatility and potential in streamlining degraders for extracellular and membrane proteins.
Collapse
Affiliation(s)
- Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xingyue Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ruixin Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ao Shen
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Pushu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Haoting Li
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Jun Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Chao Tian
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhujun Jiang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Wenzhe Li
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China.
- Chemical Biology Center, Peking University, Beijing, China.
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| |
Collapse
|
4
|
Wang Y, Zheng J, Long Y, Wu W, Zhu Y. Direct degradation and stabilization of proteins: New horizons in treatment of nonalcoholic steatohepatitis. Biochem Pharmacol 2024; 220:115989. [PMID: 38122854 DOI: 10.1016/j.bcp.2023.115989] [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: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is featured with excessive hepatic lipid accumulation and its global prevalence is soaring. Nonalcoholic steatohepatitis (NASH), the severe systemic inflammatory subtype of NAFLD, is tightly associated with metabolic comorbidities, and the hepatocytes manifest severe inflammation and ballooning. Currently the therapeutic options for treating NASH are limited. Potent small molecules specifically intervene with the signaling pathways that promote pathogenesis of NASH. Nevertheless they have obvious adverse effects and show long-term ineffectiveness in clinical trials. It poses the fundamental question to efficiently and safely inhibit the pathogenic processes. Targeted protein degradation (TPD) belongs to the direct degradation strategies and is a burgeoning strategy. It utilizes the small molecules to bind to the target proteins and recruit the endogenous proteasome, lysosome and autophagosome-mediated degradation machineries. They effectively and specifically degrade the target proteins. It has exhibited promising therapeutic effects in treatment of cancer, neurodegenerative diseases and other diseases in a catalytic manner at low doses. We critically discuss the principles of multiple direct degradation strategies, especially PROTAC and ATTEC. We extensively analyze their emerging application in degradation of excessive pathogenic proteins and lipid droplets, which promote the progression of NASH. Moreover, we discuss the opposite strategy that utilizes the small molecules to recruit deubiquinases to stabilize the NASH/MASH-suppressing proteins. Their advantages, limitations, as well as the solutions to address the limitations have been analyzed. In summary, the innovative direct degradation strategies provide new insights into design of next-generation therapeutics to combat NASH with optimal safety paradigm and efficiency.
Collapse
Affiliation(s)
- Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, PR China.
| | - Jianan Zheng
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
| | - Yun Long
- Department of Endocrinology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, PR China
| | - Wenyi Wu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
| | - Yutong Zhu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
| |
Collapse
|
5
|
Chen S, Cui J, Chen H, Yu B, Long S. Recent progress in degradation of membrane proteins by PROTACs and alternative targeted protein degradation techniques. Eur J Med Chem 2023; 262:115911. [PMID: 37924709 DOI: 10.1016/j.ejmech.2023.115911] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
Targeted protein degradation (TPD) is one of the key strategies of current targeted cancer therapy, and it can eliminate some of the root causes of cancer, and effectively avoid drug resistance caused by traditional drugs. Proteolysis targeting chimera (PROTAC) is a hot branch of the TPD strategy, and it has been shown to induce the degradation of target proteins by activating the inherent ubiquitin-proteasome system (UPS) in tumor cells. PROTACs have been developed for more than two decades, and some of them have been clinically evaluated. Although most of the proteins degraded by PROTACs are intracellular, degradation of some typical membrane proteins has also been reported, such as epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), programmed death ligand 1 (PD-L1), and G-protein-coupled receptor (GPCR). In addition, some other effective membrane protein-degrading strategies have also emerged, such as antibody-based PROTAC (AbTAC), lysosome targeting chimera (LYTAC), molecular glue, and nanoparticle-based PROTAC (Nano-PROTAC). Herein, we discussed the advantages, disadvantages and potential applications of several important membrane protein degradation techniques. These techniques that we have summarized are insightful in paving the way for future development of more general strategies for membrane protein degradation.
Collapse
Affiliation(s)
- Siyu Chen
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei, 430205, China
| | - Jingliang Cui
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei, 430205, China
| | - Haiyan Chen
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei, 430205, China
| | - Bo Yu
- Tongji Hospital, Department of Nuclear Medicine, Tongji Medical College, Huazhong University of Science & Technology, 1095 Jiefang Ave, Wuhan, 430030, China.
| | - Sihui Long
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei, 430205, China.
| |
Collapse
|
6
|
Chen X, Zhou Y, Zhao Y, Tang W. Targeted degradation of extracellular secreted and membrane proteins. Trends Pharmacol Sci 2023; 44:762-775. [PMID: 37758536 PMCID: PMC10591793 DOI: 10.1016/j.tips.2023.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023]
Abstract
Targeted protein degradation (TPD) involving chimeric molecules has emerged as one of the most promising therapeutic modalities in recent years. Among various reported TPD strategies, proteolysis-targeting chimeras (PROTACs) stand out as a significant breakthrough in small-molecule drug discovery and have garnered the most attention to date. However, PROTACs are mainly capable of depleting intracellular proteins. Given that many important therapeutic targets such as cytokines, growth factors, and numerous receptors are membrane proteins or secreted extracellularly, there is interest in the development of novel strategies to degrade these protein categories. We review advances in this emerging area and provide insights to enhance the development of novel TPDs targeting extracellular proteins.
Collapse
Affiliation(s)
- Xuankun Chen
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Yaxian Zhou
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Yuan Zhao
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Weiping Tang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| |
Collapse
|