1
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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2
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Zhu Y, Zhang Y, Zhang Q, Ma A, Zhang Y, Wang C, Gao P, Guo Q, Xia F, Tang H, Xu C, Wang J. Gambogic acid suppresses the pentose phosphate pathway by covalently inhibiting 6PGD protein in cancer cells. Chem Commun (Camb) 2022; 58:9030-9033. [PMID: 35876000 DOI: 10.1039/d2cc03069a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Whether or not the anticancer activity of gambogic acid is achieved via regulating the cellular metabolic process remains unclear. Here we report that gambogic acid suppresses the pentose phosphate pathway (PPP) by covalently inhibiting the 6-phosphogluconate dehydrogenase (6PGD) protein. This study elucidates the mechanism of action of gambogic acid from the perspective of metabolic reprogramming regulation in cancer cells.
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Affiliation(s)
- Yinhua Zhu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ying Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qianyu Zhang
- Pharmaceutical College, Henan University, Kaifeng, 475004, China.
| | - Ang Ma
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ying Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Chen Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Peng Gao
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qiuyan Guo
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Fei Xia
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Huan Tang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Chengchao Xu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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3
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Jiang J, Liu Y, Yang S, Peng H, Liu J, Cheng YX, Li N. Photoaffinity-Based Chemical Proteomics Reveals 7-Oxocallitrisic Acid Targets CPT1A to Trigger Lipogenesis Inhibition. ACS Med Chem Lett 2021; 12:1905-1911. [PMID: 34917253 DOI: 10.1021/acsmedchemlett.1c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/28/2021] [Indexed: 11/29/2022] Open
Abstract
One of the natural terpenoids isolated from Resina Commiphora, 7-oxocallitrisic acid (7-OCA), has lipid metabolism regulatory activity. To uncover its lipogenesis inhibition mechanism, we developed a photoaffinity and clickable probe based on the 7-OCA scaffold and performed chemical proteomics to profile its potential cellular targets. It was found that 7-OCA could directly interact with carnitine palmitoyl transferase 1A (CPT1A) to promote its activity to reduce lipid accumulation. The present work reveals our understanding of the mode of lipid mebabolism regulation by abietic acids and provides new clues for antiobesity drug development with CPT1A as a main target.
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Affiliation(s)
- Jianbing Jiang
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Ying Liu
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Shuxin Yang
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huipai Peng
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiawang Liu
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yong-Xian Cheng
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Nan Li
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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4
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Wang MR, Huang LF, Guo C, Yang J, Dong S, Tang JJ, Gao JM. Identification of NLRP3 as a covalent target of 1,6-O,O-diacetylbritannilactone against neuroinflammation by quantitative thiol reactivity profiling (QTRP). Bioorg Chem 2021; 119:105536. [PMID: 34894577 DOI: 10.1016/j.bioorg.2021.105536] [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: 10/18/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
Abstract
Neuroinflammation plays a key etiological role in the progressive neuronal damage of neurodegenerative diseases. Our phenotypic-based screening discovered 1,6-O,O-diacetylbritannilactone (OABL, 1) from Inula britannica exhibited the potential anti-neuroinflammatory activity as well as a favorable blood-brain barrier penetration. 1 and its active derivative Br-OABL (2) with insert of Br at the C-14 position both modulated TLR4/NF-kB/MAPK pathways. However, proteome-wide identification of 1 binding proteins remains unclear. Here, we employed an adapted isoTOP-ABPP, quantitative thiol reactivity profiling (QTRP) approach, to identify and quantify thiol reactivity binding proteins in murine microglia BV-2 cells. We screened out 15 proteins co-targeted by 1 and 2, which are involved in cellular response to oxidative stress and negative regulation NF-κB transcription factor in biological processes. In site-specific profiling, NLRP3 was identified as a covalent target of 1 and 2 for the first time, and the Cys483 of NLRP3 NACHT domain was identified as one active-site of NLRP3 cysteine residues that can be covalently modified by the α-methylene-γ-lactone moiety. Furthermore, NLRP3 was validated to be directly binded by 1 and 2 by cellular thermo shift assay (CETSA) and activity-based protein profiling (ABPP), and NLRP3 functions were also verified by small interfering RNA approach. Notably, OABL treatment (i.p., 20 mg/kg/day) for 21 days reduced inflammation in 5XFAD mice brain. Together, we applied the QTRP to uncover the binding proteins of OABL in BV-2 cells, among which NLRP3 was revealed as a new covalent target of 1 and 2 against neuroinflammation.
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Affiliation(s)
- Min-Ran Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Lan-Fang Huang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Cong Guo
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Shuai Dong
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, Hainan, China
| | - Jiang-Jiang Tang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China.
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China.
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5
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Li G, Peng X, Guo Y, Gong S, Cao S, Qiu F. Currently Available Strategies for Target Identification of Bioactive Natural Products. Front Chem 2021; 9:761609. [PMID: 34660543 PMCID: PMC8515416 DOI: 10.3389/fchem.2021.761609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
In recent years, biologically active natural products have gradually become important agents in the field of drug research and development because of their wide availability and variety. However, the target sites of many natural products are yet to be identified, which is a setback in the pharmaceutical industry and has seriously hindered the translation of research findings of these natural products as viable candidates for new drug exploitation. This review systematically describes the commonly used strategies for target identification via the application of probe and non-probe approaches. The merits and demerits of each method were summarized using recent examples, with the goal of comparing currently available methods and selecting the optimum techniques for identifying the targets of bioactive natural products.
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Affiliation(s)
- Gen Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuling Peng
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yajing Guo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shaoxuan Gong
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shijie Cao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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6
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Bhukta S, Gopinath P, Dandela R. Target identification of anticancer natural products using a chemical proteomics approach. RSC Adv 2021; 11:27950-27964. [PMID: 35480761 PMCID: PMC9038044 DOI: 10.1039/d1ra04283a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
In recent years, there has been a strong demand worldwide for the identification and development of potential anticancer drugs based on natural products. Natural products have been explored for their diverse biological and therapeutic applications from ancient time. In order to enhance the efficacy and selectivity and to minimize the undesired side effects of anti cancer natural products (ANPs), it is essential to understand their target proteins and their mechanistic pathway. Chemical proteomics is one of the most powerful tools to connect ANP target identification and quantification where labeling and non-labeling based approaches have been used. Herein, we have discussed the various strategies to systemically develop selective ANP based chemical probes to characterise their specific and non-specific target proteins using a chemical proteomic approach in various cancer cell lysates.
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Affiliation(s)
- Swadhapriya Bhukta
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology Indianoil Odisha Campus, Samantpuri Bhubaneswar 751013 India
| | - Pushparathinam Gopinath
- Department of Chemistry, SRM-Institute of Science and Technology Kattankulathur 603203 Chennai Tamilnadu India
| | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology Indianoil Odisha Campus, Samantpuri Bhubaneswar 751013 India
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7
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Zhao M, Yao L, Zhang X, Wang L, Tu P, Zeng K. Global identification of the cellular targets for a multi-molecule system by a photochemically-induced coupling reaction. Chem Commun (Camb) 2021; 57:3449-3452. [PMID: 33870345 DOI: 10.1039/d1cc00392e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Current target identification strategies mainly focus on single compounds. However, no practical experimental methodologies have been developed for multi-molecule systems. Herein, we established a cellular target identification technology for a multi-molecule system by preparing 4,4'-dihydroxybenzophenone (DHBP)-bound Fe3O4 nanoparticles (NPs) with photochemically induced crosslinking capacity. DHBP-bound NPs reacted with the chemicals from the medicinal plant extract as a multi-molecule system under ultraviolet radiation by forming carbon-carbon bonds, thus generating extract-crosslinked NPs for capturing target proteins from cell lysates. The technology, which is named the Zhao-Yao (ZY) strategy, may promote the comprehensive interpretation of the pharmacological mechanism of multi-molecule systems via the global identification of cellular targets.
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Affiliation(s)
- Meimei Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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8
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Song K, Nho CW, Ha IJ, Kim YS. Cellular Target Proteome in Breast Cancer Cells of an Oplopane Sesquiterpenoid Isolated from Tussilago farfara. JOURNAL OF NATURAL PRODUCTS 2020; 83:2559-2566. [PMID: 32881525 DOI: 10.1021/acs.jnatprod.0c00043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tussilago farfara is a traditional herbal medicine used to treat coughs, bronchitis, and asthma. Its bioactive compounds include sesquiterpenoids with anti-inflammatory, antiproliferative, neuroprotective, and other effects. Biochemical studies have highlighted the mechanisms of action, but the investigations of related molecular pathways have not specified direct molecular targets. Therefore, this study profiled cellular target proteins of a sesquiterpenoid isolated from T. farfara using quantitative chemical proteomics in MDA-MB-231 and MCF-7 human breast cancer cells. Compound 8, 7β-(3'-ethyl-cis-crotonoyloxy)-1α-(2'-methyl butyryloxy)-3,14-dehydro-Z-notonipetranone, exhibited potent antiproliferative activity based on its α,β-unsaturated carbonyl moiety, and its potential cellular target proteins were identified using a compound 8-based clickable probe. Among >200 identified proteins, 17 showed enrichment ratios of >3 in both cell lines, while recombinant 14-3-3 protein zeta and peroxiredoxin-1 were verified using isothermic calorimetry and their alkylation sites. Considering the interaction between the α,β-unsaturated carbonyl moiety of compound 8 and cysteine residues of the proteins, peptides containing Cys25 and Cys94 of 14-3-3 protein zeta and Cys83 of peroxiredoxin-1 were significantly reduced by this sesquiterpene ester. Although the results did not elucidate the effects of compound 8 in breast cancer cells, identification of potential target proteins contributes to enhanced understanding of its antiproliferative and anti-inflammatory effects.
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Affiliation(s)
- Kwangho Song
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
- Korean Medicine Clinical Trial Center, Kyung Hee University Korean Medicine Hospital, Seoul 02447, South Korea
| | - Chu Won Nho
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung Institute of Natural Products, Gangneung, Gangwon-do 25451, South Korea
| | - In Jin Ha
- Korean Medicine Clinical Trial Center, Kyung Hee University Korean Medicine Hospital, Seoul 02447, South Korea
- Department of Clinical Korean Medicine, Graduate School, Kyung Hee University, Seoul 02447, South Korea
| | - Yeong Shik Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
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9
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Combined Omics Approach Identifies Gambogic Acid and Related Xanthones as Covalent Inhibitors of the Serine Palmitoyltransferase Complex. Cell Chem Biol 2020; 27:586-597.e12. [DOI: 10.1016/j.chembiol.2020.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/19/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023]
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10
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Xu Y, Deng Z, Shi Y, Chen X, Xu J, Zhong S, Xiao Y, Wong NK, Zhou Y. Molecular Imaging and In Situ Quantitative Profiling of Fatty Acid Synthase with a Chemical Probe. Anal Chem 2020; 92:4419-4426. [PMID: 32053360 DOI: 10.1021/acs.analchem.9b05327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cancer cells rely on fatty acid synthase (FASN), a key enzyme for de novo biosynthesis of long chain fatty acids, to sustain their proliferative potential and drive invasion. Unfortunately, conventional FASN assays are technically inadequate for discerning otherwise elusive FASN activity in complex biological milieux, which has hindered progress in the functional study of FASN and development of its inhibitors. Here, we describe a chemical probe with unprecedented selectivity and sensitivity for the labeling of active FASN in living cells, thus demonstrating a new analytical modality for visualizing endogenous FASN activity and exploring opportunities for drug discovery.
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Affiliation(s)
- Yue Xu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Zhangshuang Deng
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, 443002, China
| | - Yue Shi
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Xin Chen
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingyuan Xu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Suyun Zhong
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Nai-Kei Wong
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Yiqing Zhou
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China.,CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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11
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Nguyen A, Ando H, Böttger R, DurgaRao Viswanadham KK, Rouhollahi E, Ishida T, Li SD. Utilization of click chemistry to study the effect of poly(ethylene)glycol molecular weight on the self-assembly of PEGylated gambogic acid nanoparticles for the treatment of rheumatoid arthritis. Biomater Sci 2020; 8:4626-4637. [DOI: 10.1039/d0bm00711k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Click chemistry was used to study the effect of varied PEG molecular weights on the self-assembly of PEG-gambogic acid (GA) conjugates into nanoparticles.
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Affiliation(s)
- Anne Nguyen
- Faculty of Pharmaceutical Sciences
- University of British Columbia
- Vancouver
- Canada
| | - Hidenori Ando
- Department of Pharmacokinetics and Biopharmaceutics
- Subdivision of Biopharmaceutical Sciences
- Institute of Health Biosciences
- The University of Tokushima
- Tokushima
| | - Roland Böttger
- Faculty of Pharmaceutical Sciences
- University of British Columbia
- Vancouver
- Canada
| | | | - Elham Rouhollahi
- Faculty of Pharmaceutical Sciences
- University of British Columbia
- Vancouver
- Canada
| | - Tatsuhiro Ishida
- Department of Pharmacokinetics and Biopharmaceutics
- Subdivision of Biopharmaceutical Sciences
- Institute of Health Biosciences
- The University of Tokushima
- Tokushima
| | - Shyh-Dar Li
- Faculty of Pharmaceutical Sciences
- University of British Columbia
- Vancouver
- Canada
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12
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Franke R, Hinkelmann B, Fetz V, Stradal T, Sasse F, Klawonn F, Brönstrup M. xCELLanalyzer: A Framework for the Analysis of Cellular Impedance Measurements for Mode of Action Discovery. SLAS DISCOVERY 2019; 24:213-223. [PMID: 30681906 DOI: 10.1177/2472555218819459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mode of action (MoA) identification of bioactive compounds is very often a challenging and time-consuming task. We used a label-free kinetic profiling method based on an impedance readout to monitor the time-dependent cellular response profiles for the interaction of bioactive natural products and other small molecules with mammalian cells. Such approaches have been rarely used so far due to the lack of data mining tools to properly capture the characteristics of the impedance curves. We developed a data analysis pipeline for the xCELLigence Real-Time Cell Analysis detection platform to process the data, assess and score their reproducibility, and provide rank-based MoA predictions for a reference set of 60 bioactive compounds. The method can reveal additional, previously unknown targets, as exemplified by the identification of tubulin-destabilizing activities of the RNA synthesis inhibitor actinomycin D and the effects on DNA replication of vioprolide A. The data analysis pipeline is based on the statistical programming language R and is available to the scientific community through a GitHub repository.
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Affiliation(s)
- Raimo Franke
- 1 Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Bettina Hinkelmann
- 1 Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Verena Fetz
- 1 Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Theresia Stradal
- 2 Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Florenz Sasse
- 1 Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Frank Klawonn
- 3 Biostatistics Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.,4 Department of Computer Science, Ostfalia University, Wolfenbuettel, Germany
| | - Mark Brönstrup
- 1 Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,5 Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz Universität, Hannover, Germany
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13
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Li W, Zhou Y, Tang G, Wong NK, Yang M, Tan D, Xiao Y. Chemoproteomics Reveals the Antiproliferative Potential of Parkinson’s Disease Kinase Inhibitor LRRK2-IN-1 by Targeting PCNA Protein. Mol Pharm 2018; 15:3252-3259. [DOI: 10.1021/acs.molpharmaceut.8b00325] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Weichao Li
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guanghui Tang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Nai-Kei Wong
- State Key Discipline of Infection Diseases, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, Shenzhen University, Shenzhen 518112, China
| | - Mengquan Yang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dan Tan
- Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100039, China
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14
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Zhang Q, Zhang J, Gavathiotis E. ICBS 2017 in Shanghai-Illuminating Life with Chemical Innovation. ACS Chem Biol 2018; 13:1111-1122. [PMID: 29677443 PMCID: PMC6855916 DOI: 10.1021/acschembio.8b00220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Evripidis Gavathiotis
- Department of Biochemistry, Department of Medicine, Albert Einstein College of Medicine, New York 10461, United States
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15
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Chen L, Fu W, Zheng L, Wang Y, Liang G. Recent progress in the discovery of myeloid differentiation 2 (MD2) modulators for inflammatory diseases. Drug Discov Today 2018; 23:1187-1202. [PMID: 29330126 DOI: 10.1016/j.drudis.2018.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/09/2017] [Accepted: 01/04/2018] [Indexed: 02/07/2023]
Abstract
Myeloid differentiation protein 2 (MD2), together with Toll-like receptor 4 (TLR4), binds lipopolysaccharide (LPS) with high affinity, inducing the formation of the activated homodimer LPS-MD2-TLR4. MD2 directly recognizes the Lipid A domain of LPS, leading to the activation of downstream signaling of cytokine and chemokine production, and initiation of inflammatory and immune responses. However, excessive activation and potent host responses generate severe inflammatory syndromes such as acute sepsis and septic shock. MD2 is increasingly being considered as an attractive pharmacological target for the development of potent anti-inflammatory agents. In this Keynote review, we provide a comprehensive overview of the recent advances in the structure and biology of MD2, and present MD2 modulators as promising agents for anti-inflammatory intervention.
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Affiliation(s)
- Lingfeng Chen
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Weitao Fu
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Lulu Zheng
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yi Wang
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Guang Liang
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China.
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16
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Zhou Y, Li W, You W, Di Z, Wang M, Zhou H, Yuan S, Wong NK, Xiao Y. Discovery of Arabidopsis UGT73C1 as a steviol-catalyzing UDP-glycosyltransferase with chemical probes. Chem Commun (Camb) 2018; 54:7179-7182. [DOI: 10.1039/c7cc09951g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A strategy for rapidly mining biological parts from plants for synthetic biology utilizing natural product-derived chemical probes has been reported.
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Affiliation(s)
- Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Wenjing You
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Zhengao Di
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Mingli Wang
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Haiyan Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Switzerland
| | - Nai-Kei Wong
- State Key Discipline of Infection Diseases
- Shenzhen Third People's Hospital
- The Second Affiliated Hospital
- Shenzhen University
- Shenzhen 518112
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
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17
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Li X, Wu Y, Wang Y, You Q, Zhang X. 'Click Chemistry' Synthesis of Novel Natural Product-Like Caged Xanthones Bearing a 1,2,3-Triazole Moiety with Improved Druglike Properties as Orally Active Antitumor Agents. Molecules 2017; 22:molecules22111834. [PMID: 29077076 PMCID: PMC6150271 DOI: 10.3390/molecules22111834] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 10/26/2017] [Accepted: 10/26/2017] [Indexed: 11/16/2022] Open
Abstract
DDO-6101, a natural-product-like caged xanthone discovered previously in our laboratory based on the pharmacophoric scaffold of the Garcinia natural product gambogic acid (GA), shows potent cytotoxicity in vitro, but poor efficacy in vivo due to its poor druglike properties. In order to improve the druglike properties and in vivo antitumor potency, a novel series of ten triazole-bearing caged xanthone derivatives of DDO-6101 has been efficiently synthesized by 'click chemistry' and evaluated for their in vitro antitumor activity and druglike properties. Most of the target compounds have sustained cytotoxicity against A549, HepG2, HCT116, and U2OS cancer cells and possess improved aqueous solubility, as well as permeability. Notably, these caged xanthones are also active towards taxol-resistant or cisplatin-resistant A549 cancer cells. Taking both the in vitro activities and druglike properties into consideration, compound 8g has been advanced into in vivo efficacy experiments. The results reveal that 8g (named as DDO-6318), both by intravenous or per os administration, are much more potent than the lead DDO-6101 in A549-transplanted mice models and it could be a promising antitumor candidate for further evaluation.
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Affiliation(s)
- Xiang Li
- Jiangsu Key Laboratory of Drug Design and Optimization, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing 211198, China.
| | - Yue Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China.
| | - Yanyan Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China.
| | - Qidong You
- Jiangsu Key Laboratory of Drug Design and Optimization, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 21009, China.
| | - Xiaojin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
- Department of Organic Chemistry, China Pharmaceutical University, Nanjing 211198, China.
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18
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Tian C, Sun R, Liu K, Fu L, Liu X, Zhou W, Yang Y, Yang J. Multiplexed Thiol Reactivity Profiling for Target Discovery of Electrophilic Natural Products. Cell Chem Biol 2017; 24:1416-1427.e5. [PMID: 28988947 DOI: 10.1016/j.chembiol.2017.08.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/06/2017] [Accepted: 08/30/2017] [Indexed: 02/09/2023]
Abstract
Electrophilic groups, such as Michael acceptors, expoxides, are common motifs in natural products (NPs). Electrophilic NPs can act through covalent modification of cysteinyl thiols on functional proteins, and exhibit potent cytotoxicity and anti-inflammatory/cancer activities. Here we describe a new chemoproteomic strategy, termed multiplexed thiol reactivity profiling (MTRP), and its use in target discovery of electrophilic NPs. We demonstrate the utility of MTRP by identifying cellular targets of gambogic acid, an electrophilic NP that is currently under evaluation in clinical trials as anticancer agent. Moreover, MTRP enables simultaneous comparison of seven structurally diversified α,β-unsaturated γ-lactones, which provides insights into the relative proteomic reactivity and target preference of diverse structural scaffolds coupled to a common electrophilic motif and reveals various potential druggable targets with liganded cysteines. We anticipate that this new method for thiol reactivity profiling in a multiplexed manner will find broad application in redox biology and drug discovery.
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Affiliation(s)
- Caiping Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Rui Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China; State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Keke Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China
| | - Xiaoyu Liu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Wanqi Zhou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Yong Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences - Beijing, Beijing 102206, China.
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19
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Zhou Y, Di Z, Li X, Shan Y, Li W, Zhang H, Xiao Y. Chemical proteomics reveal CD147 as a functional target of pseudolaric acid B in human cancer cells. Chem Commun (Camb) 2017; 53:8671-8674. [DOI: 10.1039/c7cc04345g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudolaric acid B targets CD147 in human cancer cells.
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Affiliation(s)
- Yiqing Zhou
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Zhengao Di
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Xiaoming Li
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Yuanhong Shan
- Core Facility Centre of the Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
| | - Haibing Zhang
- Institute for Nutritional Sciences
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology
- CAS Center for Excellence in Molecular Plant Sciences
- Institute of Plant Physiology and Ecology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
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