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Cao N, Guo R, Song P, Wang S, Liu G, Shi J, Wang L, Li M, Zuo X, Yang X, Fan C, Li M, Zhang Y. DNA Framework-Programmed Nanoscale Enzyme Assemblies. NANO LETTERS 2024; 24:4682-4690. [PMID: 38563501 DOI: 10.1021/acs.nanolett.4c01137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Multienzyme assemblies mediated by multivalent interaction play a crucial role in cellular processes. However, the three-dimensional (3D) programming of an enzyme complex with defined enzyme activity in vitro remains unexplored, primarily owing to limitations in precisely controlling the spatial topological configuration. Herein, we introduce a nanoscale 3D enzyme assembly using a tetrahedral DNA framework (TDF), enabling the replication of spatial topological configuration and maintenance of an identical edge-to-edge distance akin to natural enzymes. Our results demonstrate that 3D nanoscale enzyme assemblies in both two-enzyme systems (glucose oxidase (GOx)/horseradish peroxidase (HRP)) and three-enzyme systems (amylglucosidase (AGO)/GOx/HRP) lead to enhanced cascade catalytic activity compared to the low-dimensional structure, resulting in ∼5.9- and ∼7.7-fold enhancements over homogeneous diffusional mixtures of free enzymes, respectively. Furthermore, we demonstrate the enzyme assemblies for the detection of the metabolism biomarkers creatinine and creatine, achieving a low limit of detection, high sensitivity, and broad detection range.
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Affiliation(s)
- Nan Cao
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruiyan Guo
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Ping Song
- State Key Laboratory of Oncogenes and Related Genes School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shaopeng Wang
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Gang Liu
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Min Li
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiurong Yang
- Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yueyue Zhang
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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Disrupting the phase separation of KAT8-IRF1 diminishes PD-L1 expression and promotes antitumor immunity. NATURE CANCER 2023; 4:382-400. [PMID: 36894639 PMCID: PMC10042735 DOI: 10.1038/s43018-023-00522-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/02/2023] [Indexed: 03/11/2023]
Abstract
Immunotherapies targeting the PD-1/PD-L1 axis have become first-line treatments in multiple cancers. However, only a limited subset of individuals achieves durable benefits because of the elusive mechanisms regulating PD-1/PD-L1. Here, we report that in cells exposed to interferon-γ (IFNγ), KAT8 undergoes phase separation with induced IRF1 and forms biomolecular condensates to upregulate PD-L1. Multivalency from both the specific and promiscuous interactions between IRF1 and KAT8 is required for condensate formation. KAT8-IRF1 condensation promotes IRF1 K78 acetylation and binding to the CD247 (PD-L1) promoter and further enriches the transcription apparatus to promote transcription of PD-L1 mRNA. Based on the mechanism of KAT8-IRF1 condensate formation, we identified the 2142-R8 blocking peptide, which disrupts KAT8-IRF1 condensate formation and consequently inhibits PD-L1 expression and enhances antitumor immunity in vitro and in vivo. Our findings reveal a key role of KAT8-IRF1 condensates in PD-L1 regulation and provide a competitive peptide to enhance antitumor immune responses.
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Li Y, Xing Z, Wang S, Wang Y, Wang Z, Dong L. Disruption of biofilms in periodontal disease through the induction of phase transition by cationic dextrans. Acta Biomater 2023; 158:759-768. [PMID: 36638945 DOI: 10.1016/j.actbio.2023.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Biofilm of oral pathogenic microorganisms induced by their multiplication and coaggregation would lead to periodontitis. In biofilms, the extracellular polymeric substances (EPS) as a protective shield encapsulates the individual bacteria, protecting them against attack. To alleviate periodontal disease, disrupting the EPS of pathogenic bacteria is crucial and challenging. Based on the sufficient capacity of disorganizing EPS of our designed cationic dextrans, we hypothesized that these polymers could be competent in relieving periodontitis. We validated that cationic dextrans could induce the phase transition of EPS in biofilms, especially the Porphyromonas gingivalis (P. gingivalis), a keystone periodontal pathogen, thus effectively destroying biofilm in vitro. More importantly, satisfactory in vivo treatment was achieved in a rat periodontal disease model. In summary, the study exploited a practical and effective strategy to treat periodontitis with cationic dextrans' powerful biofilm-controlling potential. STATEMENT OF SIGNIFICANCE: Periodontal disease is closely related to dental plaque biofilms on the tooth surface. The biofilm forms gel structures and shields the bacteria underneath, thus protecting oral pathogens from traditional anti-bacterial reagents. Due to limited penetration into gel, the efficacy of these reagents in biofilm elimination is restricted. Our designed cationic dextran could wipe out the coverage of gel-like EPS to disperse encapsulated bacteria. Such superior capacity endowed them with satisfactory effect in disrupting biofilm. Notably, in a rat periodontitis model, cationic dextrans dramatically suppressed alveolar bone loss and alleviated periodontal inflammation by controlling dental plaque. Given the increasing global concerns about periodontal disease, it's worth expanding the application of cationic dextrans both scientifically and clinically.
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Affiliation(s)
- Yurong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China
| | - Zhen Xing
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China
| | - Shaocong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China
| | - Yulian Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China
| | - Zhenzhen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China.
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210093, China; Wuxi Xishan NJU Institute of Applied Biotechnology, Anzhen Street, Xishan District, Wuxi 214101, China.
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Zheng Y, Gao C. Phase Separation: The Robust Modulator of Innate Antiviral Signaling and SARS-CoV-2 Infection. Pathogens 2023; 12:pathogens12020243. [PMID: 36839515 PMCID: PMC9962166 DOI: 10.3390/pathogens12020243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 has been a pandemic threat to human health and the worldwide economy, but efficient treatments are still lacking. Type I and III interferons are essential for controlling viral infection, indicating that antiviral innate immune signaling is critical for defense against viral infection. Phase separation, one of the basic molecular processes, governs multiple cellular activities, such as cancer progression, microbial infection, and signaling transduction. Notably, recent studies suggest that phase separation regulates antiviral signaling such as the RLR and cGAS-STING pathways. Moreover, proper phase separation of viral proteins is essential for viral replication and pathogenesis. These observations indicate that phase separation is a critical checkpoint for virus and host interaction. In this study, we summarize the recent advances concerning the regulation of antiviral innate immune signaling and SARS-CoV-2 infection by phase separation. Our review highlights the emerging notion that phase separation is the robust modulator of innate antiviral signaling and viral infection.
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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Nucleation of the destruction complex on the centrosome accelerates degradation of β-catenin and regulates Wnt signal transmission. Proc Natl Acad Sci U S A 2022; 119:e2204688119. [PMID: 36037369 PMCID: PMC9457612 DOI: 10.1073/pnas.2204688119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) governs a variety of mesoscale cellular processes. However, less is known about how cells utilize LLPS to drive cellular function. Here, we examined the destruction complex (DC), an organelle which controls Wnt signaling and whose components phase separate. Through a combination of advanced microscopy, CRISPR, computational modeling, and optogenetics, we find that the DC is nucleated by the centrosome and that this nucleation drives efficient signal transduction. Our work not only uncovers a biological function for LLPS but also highlights nucleation as a general method for controlling the function of intracellular condensates. Finally, our findings suggest a thermodynamic coupling between Wnt signal transduction and the cell cycle which could lead to insights into Wnt-driven cancers. Wnt signal transduction is controlled by the destruction complex (DC), a condensate comprising scaffold proteins and kinases that regulate β-catenin stability. Overexpressed DC scaffolds undergo liquid–liquid phase separation (LLPS), but DC mesoscale organization at endogenous expression levels and its role in β-catenin processing were previously unknown. Here, we find that DC LLPS is nucleated by the centrosome. Through a combination of CRISPR-engineered custom fluorescent tags, finite element simulations, and optogenetic tools that allow for manipulation of DC concentration and multivalency, we find that centrosomal nucleation drives processing of β-catenin by colocalizing DC components to a single reaction crucible. Enriching GSK3β partitioning on the centrosome controls β-catenin processing and prevents Wnt-driven embryonic stem cell differentiation to mesoderm. Our findings demonstrate the role of nucleators in controlling biomolecular condensates and suggest tight integration between Wnt signal transduction and the cell cycle.
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Shih PY, Fang YL, Shankar S, Lee SP, Hu HT, Chen H, Wang TF, Hsia KC, Hsueh YP. Phase separation and zinc-induced transition modulate synaptic distribution and association of autism-linked CTTNBP2 and SHANK3. Nat Commun 2022; 13:2664. [PMID: 35562389 PMCID: PMC9106668 DOI: 10.1038/s41467-022-30353-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/26/2022] [Indexed: 11/09/2022] Open
Abstract
Many synaptic proteins form biological condensates via liquid-liquid phase separation (LLPS). Synaptopathy, a key feature of autism spectrum disorders (ASD), is likely relevant to the impaired phase separation and/or transition of ASD-linked synaptic proteins. Here, we report that LLPS and zinc-induced liquid-to-gel phase transition regulate the synaptic distribution and protein-protein interaction of cortactin-binding protein 2 (CTTNBP2), an ASD-linked protein. CTTNBP2 forms self-assembled condensates through its C-terminal intrinsically disordered region and facilitates SHANK3 co-condensation at dendritic spines. Zinc binds the N-terminal coiled-coil region of CTTNBP2, promoting higher-order assemblies. Consequently, it leads to reduce CTTNBP2 mobility and enhance the stability and synaptic retention of CTTNBP2 condensates. Moreover, ASD-linked mutations alter condensate formation and synaptic retention of CTTNBP2 and impair mouse social behaviors, which are all ameliorated by zinc supplementation. Our study suggests the relevance of condensate formation and zinc-induced phase transition to the synaptic distribution and function of ASD-linked proteins. Autism impacts synapses. This study reports that autism-linked mutations of CTTNBP2 regulate phase separation to control synaptic enrichment of that protein. A zinc-induced liquid-to-gel transition improves synaptic retention of CTTNBP2 and SHANK3.
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Affiliation(s)
- Pu-Yun Shih
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Department of Neurology, University of California San Francisco, San Francisco, USA
| | - Yu-Lun Fang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Department and Graduate Institute of Biochemistry, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Sahana Shankar
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Molecular and Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Sue-Ping Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsiao-Tang Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsin Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Undergraduate Program in Neuroscience, John Hopkins University, Baltimore, USA
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Molecular and Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Kuo-Chiang Hsia
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC. .,Molecular and Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC.
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC. .,Molecular and Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC.
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Wang Z, Zhai Z, Chen C, Tian X, Xing Z, Xing P, Yang Y, Zhang J, Wang C, Dong L. Air pollution particles hijack peroxidasin to disrupt immunosurveillance and promote lung cancer. eLife 2022; 11:e75345. [PMID: 35437145 PMCID: PMC9054135 DOI: 10.7554/elife.75345] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Although fine particulate matter (FPM) in air pollutants and tobacco smoke is recognized as a strong carcinogen and global threat to public health, its biological mechanism for inducing lung cancer remains unclear. Here, by investigating FPM's bioactivities in lung carcinoma mice models, we discover that these particles promote lung tumor progression by inducing aberrant thickening of tissue matrix and hampering migration of antitumor immunocytes. Upon inhalation into lung tissue, these FPM particles abundantly adsorb peroxidasin (PXDN) - an enzyme mediating type IV collagen (Col IV) crosslinking - onto their surface. The adsorbed PXDN exerts abnormally high activity to crosslink Col IV via increasing the formation of sulfilimine bonds at the NC1 domain, leading to an overly dense matrix in the lung tissue. This disordered structure decreases the mobility of cytotoxic CD8+ T lymphocytes into the lung and consequently impairs the local immune surveillance, enabling the flourishing of nascent tumor cells. Meanwhile, inhibiting the activity of PXDN abolishes the tumor-promoting effect of FPM, indicating the key impact of aberrant PXDN activity on the tumorigenic process. In summary, our finding elucidates a new mechanism for FPM-induced lung tumorigenesis and identifies PXDN as a potential target for treatment or prevention of the FPM-relevant biological risks.
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Affiliation(s)
- Zhenzhen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of MacauMacauChina
| | - Ziyu Zhai
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Chunyu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Xuejiao Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Zhen Xing
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Panfei Xing
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of MacauMacauChina
| | - Yushun Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of MacauMacauChina
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
- Chemistry and Biomedicine Innovative Center, Nanjing UniversityNanjingChina
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