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Reza R, Morshed N, Samdani MN, Reza MS. Pharmacophore mapping approach to find anti-cancer phytochemicals with metformin-like activities against transforming growth factor (TGF)-beta receptor I kinase: An in silico study. PLoS One 2023; 18:e0288208. [PMID: 37943796 PMCID: PMC10635513 DOI: 10.1371/journal.pone.0288208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/21/2023] [Indexed: 11/12/2023] Open
Abstract
The most frequently prescribed first-line treatment for type II diabetes mellitus is metformin. Recent reports asserted that this diabetes medication can also shield users from cancer. Metformin induces cell cycle arrest in cancer cells. However, the exact mechanism by which this occurs in the cancer system is yet to be elucidated. Here, we investigated the impact of metformin on cell cycle arrest in cancer cells utilizing transforming growth factor (TGF)-beta pathway. TGF-ß pathway has significant effect on cell progression and growth. In order to gain an insight on the underlying molecular mechanism of metformin's effect on TGF beta receptor 1 kinase, molecular docking was performed. Metformin was predicted to interact with transforming growth factor (TGF)-beta receptor I kinase based on molecular docking and molecular dynamics simulations. Furthermore, pharmacophore was generated for metformin-TGF-ßR1 complex to hunt for novel compounds having similar pharmacophore as metformin with enhanced anti-cancer potentials. Virtual screening with 29,000 natural compounds from NPASS database was conducted separately for the generated pharmacophores in Ligandscout® software. Pharmacophore mapping showed 60 lead compounds for metformin-TGF-ßR1 complex. Molecular docking, molecular dynamics simulation for 100 ns and ADMET analysis were performed on these compounds. Compounds with CID 72473, 10316977 and 45140078 showed promising binding affinities and formed stable complexes during dynamics simulation with aforementioned protein and thus have potentiality to be developed into anti-cancer medicaments.
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Affiliation(s)
- Rumman Reza
- Department of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Niaz Morshed
- Department of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | | | - Md. Selim Reza
- Department of Pharmaceutical Technology, University of Dhaka, Dhaka, Bangladesh
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Peng Y, Tang L, Li Y, Song J, Liu H, Wang P, Zhong Z, Yang Y, Wang S, Chen L, Zhang J, Zhang S, Wang Z, Li M, Liang L, Liu J. Comprehensive proteomic analysis reveals dynamic phospho-profiling in human early erythropoiesis. Br J Haematol 2022; 199:427-442. [PMID: 35974424 DOI: 10.1111/bjh.18407] [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: 02/16/2022] [Revised: 07/25/2022] [Accepted: 08/03/2022] [Indexed: 12/01/2022]
Abstract
Normal early erythropoiesis depends on the precise regulation of protein expression and phosphorylation modification. Dysregulation of protein levels or modification contributes to erythroid disorders. To date, the dynamics of protein phosphorylation profiling across human erythroid development is not fully understood. Here, we characterized quantitative proteomic and phosphoproteomic profiling by tandem mass-tagging technology. We systemically built phospho-expression profiling and expression clusters of 11 414 phosphopeptides for human early erythropoiesis. The standardization methods for multitier integrative analyses revealed multiple functional modules of phosphoproteins (e.g., regulation of the G2/M transition) and active phosphorylated signalling (e.g., cell cycle-related pathways). Our further analysis revealed that CDK family members were the main kinases that phosphorylate substrates in erythroid progenitors and identified that CDK9 played an important role in the proliferation of erythroid progenitors. Collectively, our phosphoproteomic profiling, integrative network analysis and functional studies define landscapes of the phosphoproteome and reveal signalling pathways that are involved in human early erythropoiesis. This study will serve as a valuable resource for further investigations of phosphatase and kinase functions in human erythropoiesis and erythroid-related diseases.
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Affiliation(s)
- Yuanliang Peng
- Department of Hematology, The Second Xiangya Hospital of Central South University, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Li Tang
- School of Information Science and Engineering, Central South University, Changsha, China
| | - Yanan Li
- Department of Hematology, The Second Xiangya Hospital of Central South University, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Jianhui Song
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Hong Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Pan Wang
- Department of Hematology, The Second Xiangya Hospital of Central South University, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Zhizhou Zhong
- School of Information Science and Engineering, Central South University, Changsha, China
| | - Yifei Yang
- School of Information Science and Engineering, Central South University, Changsha, China
| | - Shihui Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Lixiang Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ji Zhang
- Department of Clinical Laboratory, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong, China
| | - Shijie Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zi Wang
- Department of Hematology, The Second Xiangya Hospital of Central South University, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Min Li
- School of Information Science and Engineering, Central South University, Changsha, China
| | - Long Liang
- Department of Hematology, The Second Xiangya Hospital of Central South University, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Jing Liu
- Department of Hematology, The Second Xiangya Hospital of Central South University, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
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A function for ataxia telangiectasia and Rad3-related (ATR) kinase in cytokinetic abscission. iScience 2022; 25:104536. [PMID: 35754741 PMCID: PMC9213759 DOI: 10.1016/j.isci.2022.104536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/23/2022] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Abscission, the final stage of cytokinesis, occurs when the cytoplasmic canal connecting two emerging daughter cells is severed either side of a large proteinaceous structure, the midbody. Here, we expand the functions of ATR to include a cell-cycle-specific role in abscission, which is required for genome stability. All previously characterized roles for ATR depend upon its recruitment to replication protein A (RPA)-coated single-stranded DNA (ssDNA). However, we establish that in each cell cycle ATR, as well as ATRIP, localize to the midbody specifically during late cytokinesis and independently of RPA or detectable ssDNA. Rather, midbody localization and ATR-dependent regulation of abscission requires the known abscission regulator-charged multivesicular body protein 4C (CHMP4C). Intriguingly, this regulation is also dependent upon the CDC7 kinase and the known ATR activator ETAA1. We propose that in addition to its known RPA-ssDNA-dependent functions, ATR has further functions in preventing premature abscission. ATR localises non-canonically to the midbody during late cytokinesis Absence of ATR function results in faster abscission and increased binucleates CDC7 kinase and the ESCRT protein, CHMP4C are required for ATR midbody localisation ATR functions upstream of known abscission regulators, CHMP4B and ANCHR
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Abstract
KDM5 family members (A, B, C and D) that demethylate H3K4me3 have been shown to be involved in human cancers. Here we performed screening for KDM5A inhibitors from chemical libraries using the AlphaScreen method and identified a battery of screening hits that inhibited recombinant KDM5A. These compounds were further subjected to cell-based screening using a reporter gene that responded to KDM5A inhibition and 6 compounds were obtained as candidate inhibitors. When further confirmation of their inhibition activity on cellular KDM5A was made by immunostaining H3K4me3 in KDM5A-overexpressing cells, ryuvidine clearly repressed H3K4me3 demethylation. Ryuvidine prevented generation of gefitinib-tolerant human small-cell lung cancer PC9 cells and also inhibited the growth of the drug-tolerant cells at concentrations that did not affect the growth of parental PC9 cells. Ryuvidine inhibited not only KDM5A but also recombinant KDM5B and C; KDM5B was the most sensitive to the inhibitor. These results warrant that ryuvidine may serve as a lead compound for KDM5 targeted therapeutics.
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Post-Translational Modifications of the Mini-Chromosome Maintenance Proteins in DNA Replication. Genes (Basel) 2019; 10:genes10050331. [PMID: 31052337 PMCID: PMC6563057 DOI: 10.3390/genes10050331] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
The eukaryotic mini-chromosome maintenance (MCM) complex, composed of MCM proteins 2-7, is the core component of the replisome that acts as the DNA replicative helicase to unwind duplex DNA and initiate DNA replication. MCM10 tightly binds the cell division control protein 45 homolog (CDC45)/MCM2-7/ DNA replication complex Go-Ichi-Ni-San (GINS) (CMG) complex that stimulates CMG helicase activity. The MCM8-MCM9 complex may have a non-essential role in activating the pre-replicative complex in the gap 1 (G1) phase by recruiting cell division cycle 6 (CDC6) to the origin recognition complex (ORC). Each MCM subunit has a distinct function achieved by differential post-translational modifications (PTMs) in both DNA replication process and response to replication stress. Such PTMs include phosphorylation, ubiquitination, small ubiquitin-like modifier (SUMO)ylation, O-N-acetyl-D-glucosamine (GlcNAc)ylation, and acetylation. These PTMs have an important role in controlling replication progress and genome stability. Because MCM proteins are associated with various human diseases, they are regarded as potential targets for therapeutic development. In this review, we summarize the different PTMs of the MCM proteins, their involvement in DNA replication and disease development, and the potential therapeutic implications.
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Fei L, Xu H. Role of MCM2-7 protein phosphorylation in human cancer cells. Cell Biosci 2018; 8:43. [PMID: 30062004 PMCID: PMC6056998 DOI: 10.1186/s13578-018-0242-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 01/12/2023] Open
Abstract
A heterohexameric complex composed of minichromosome maintenance protein 2–7 (MCM2–7), which acts as a key replicative enzyme in eukaryotes, is crucial for initiating DNA synthesis only once per cell cycle. The MCM complex remains inactive through the G1 phase, until the S phase, when it is activated to initiate replication. During the transition from the G1 to S phase, the MCM undergoes multisite phosphorylation, an important change that promotes subsequent assembly of other replisome members. Phosphorylation is crucial for the regulation of MCM activity and function. MCMs can be phosphorylated by multiple kinases and these phosphorylation events are involved not only in DNA replication but also cell cycle progression and checkpoint response. Dysfunctional phosphorylation of MCMs appears to correlate with the occurrence and development of cancers. In this review, we summarize the currently available data regarding the regulatory mechanisms and functional consequences of MCM phosphorylation and seek the probability that protein kinase inhibitor can be used therapeutically to target MCM phosphorylation in cancer.
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Affiliation(s)
- Liangru Fei
- Department of Pathology, College of Basic Medical Sciences and the First Affiliated Hospital, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122 Liaoning Province People's Republic of China
| | - Hongtao Xu
- Department of Pathology, College of Basic Medical Sciences and the First Affiliated Hospital, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122 Liaoning Province People's Republic of China
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Rainey MD, Quachthithu H, Gaboriau D, Santocanale C. DNA Replication Dynamics and Cellular Responses to ATP Competitive CDC7 Kinase Inhibitors. ACS Chem Biol 2017; 12:1893-1902. [PMID: 28560864 DOI: 10.1021/acschembio.7b00117] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The CDC7 kinase, by phosphorylating the MCM DNA helicase, is a key switch for DNA replication initiation. ATP competitive CDC7 inhibitors are being developed as potential anticancer agents; however how human cells respond to the selective pharmacological inhibition of this kinase is controversial and not understood. Here we have characterized the mode of action of the two widely used CDC7 inhibitors, PHA-767491 and XL-413, which have become important tool compounds to explore the kinase's cellular functions. We have used a chemical genetics approach to further characterize pharmacological CDC7 inhibition and CRISPR/CAS9 technology to assess the requirement for kinase activity for cell proliferation. We show that, in human breast cells, CDC7 is essential and that CDC7 kinase activity is formally required for proliferation. However, full and sustained inhibition of the kinase, which is required to block the cell-cycle progression with ATP competitor compounds, is problematic to achieve. We establish that MCM2 phosphorylation is highly sensitive to CDC7 inhibition and, as a biomarker, it lacks in dynamic range since it is easily lost at concentrations of inhibitors that only mildly affect DNA synthesis. Furthermore, we find that the cellular effects of selective CDC7 inhibitors can be altered by the concomitant inhibition of cell-cycle and transcriptional CDKs. This work shows that DNA replication and cell proliferation can occur with reduced CDC7 activity for at least 5 days and that the bulk of DNA synthesis is not tightly coupled to MCM2 phosphorylation and provides guidance for the development of next generation CDC7 inhibitors.
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Affiliation(s)
- Michael D. Rainey
- Centre for Chromosome Biology,
School of Natural Sciences, National University of Ireland Galway H91 TK33, Ireland
| | - Huong Quachthithu
- Centre for Chromosome Biology,
School of Natural Sciences, National University of Ireland Galway H91 TK33, Ireland
| | - David Gaboriau
- Centre for Chromosome Biology,
School of Natural Sciences, National University of Ireland Galway H91 TK33, Ireland
| | - Corrado Santocanale
- Centre for Chromosome Biology,
School of Natural Sciences, National University of Ireland Galway H91 TK33, Ireland
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Hiraga SI, Ly T, Garzón J, Hořejší Z, Ohkubo YN, Endo A, Obuse C, Boulton SJ, Lamond AI, Donaldson AD. Human RIF1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation. EMBO Rep 2017; 18:403-419. [PMID: 28077461 PMCID: PMC5331243 DOI: 10.15252/embr.201641983] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 11/08/2016] [Accepted: 12/05/2016] [Indexed: 01/13/2023] Open
Abstract
The human RIF1 protein controls DNA replication, but the molecular mechanism is largely unknown. Here, we demonstrate that human RIF1 negatively regulates DNA replication by forming a complex with protein phosphatase 1 (PP1) that limits phosphorylation-mediated activation of the MCM replicative helicase. We identify specific residues on four MCM helicase subunits that show hyperphosphorylation upon RIF1 depletion, with the regulatory N-terminal domain of MCM4 being particularly strongly affected. In addition to this role in limiting origin activation, we discover an unexpected new role for human RIF1-PP1 in mediating efficient origin licensing. Specifically, during the G1 phase of the cell cycle, RIF1-PP1 protects the origin-binding ORC1 protein from untimely phosphorylation and consequent degradation by the proteasome. Depletion of RIF1 or inhibition of PP1 destabilizes ORC1, thereby reducing origin licensing. Consistent with reduced origin licensing, RIF1-depleted cells exhibit increased spacing between active origins. Human RIF1 therefore acts as a PP1-targeting subunit that regulates DNA replication positively by stimulating the origin licensing step, and then negatively by counteracting replication origin activation.
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Affiliation(s)
- Shin-Ichiro Hiraga
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK
| | - Tony Ly
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Javier Garzón
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK
| | - Zuzana Hořejší
- The Francis Crick Institute, Clare Hall Laboratories, South Mimms, UK
| | - Yoshi-Nobu Ohkubo
- Graduate School of Life Science, Hokkaido University, Sapporo Hokkaido, Japan
| | - Akinori Endo
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chikashi Obuse
- Graduate School of Life Science, Hokkaido University, Sapporo Hokkaido, Japan
| | - Simon J Boulton
- The Francis Crick Institute, Clare Hall Laboratories, South Mimms, UK
| | - Angus I Lamond
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Anne D Donaldson
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK
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9
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Puigvert JC, Sanjiv K, Helleday T. Targeting DNA repair, DNA metabolism and replication stress as anti-cancer strategies. FEBS J 2015; 283:232-45. [DOI: 10.1111/febs.13574] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/04/2015] [Accepted: 10/21/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Jordi Carreras Puigvert
- Science for Life Laboratory; Division of Translational Medicine and Chemical Biology; Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm Sweden
| | - Kumar Sanjiv
- Science for Life Laboratory; Division of Translational Medicine and Chemical Biology; Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm Sweden
| | - Thomas Helleday
- Science for Life Laboratory; Division of Translational Medicine and Chemical Biology; Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm Sweden
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Huang K, Shi B, Xu W, Ding J, Yang Y, Liu H, Zhuang X, Chen X. Reduction-responsive polypeptide nanogel delivers antitumor drug for improved efficacy and safety. Acta Biomater 2015; 27:179-193. [PMID: 26320542 DOI: 10.1016/j.actbio.2015.08.049] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/26/2015] [Accepted: 08/26/2015] [Indexed: 12/11/2022]
Abstract
Chemotherapy plays an irreplaceable role in the treatment of various malignant tumors today. The traditional drug formulations lack of selectivity, cause serious damage to normal tissues, and can't achieve a desired therapeutic efficacy. For this situation, a facilely prepared reduction-responsive polypeptide nanogel was employed for targeting intracellular delivery of antitumor drug in this study. Doxorubicin (DOX) as a model drug was loaded into nanogel through a sequential dispersion and dialysis approach with a drug loading efficiency (DLE) of 56.8wt.%. The loading nanogel, i.e., NG/DOX, exhibited a medium hydrodynamic radius of 56.1±3.5nm, glutathione-accelerated DOX release, and efficient cellular uptake and proliferation inhibition. Moreover, NG/DOX exhibited upregulated intratumoral accumulation and improved antitumor efficacy toward HepG2 hepatoma-xenografted BALB/c nude mouse model compared with free drug. The enhanced tumor suppression of NG/DOX was further confirmed by the histopathological and immunohistochemical analyses. Furthermore, the excellent in vivo security of NG/DOX was systematically demonstrated by the variation detection of body weight, histopathological assay, levels of bone marrow cell micronucleus rate (BMMR) and white blood cells (WBCs), and detection of clinical parameters in corresponding organs and serum. With controllable large-scale preparation and fascinating properties in vitro and in vivo, the reduction-responsive polypeptide nanogel is revealed to exhibit great potential for on-demand intracellular delivery of antitumor drugs, and shows a good prospect for clinical chemotherapy. STATEMENT OF SIGNIFICANCE The traditional drug formulations lack of selectivity, cause serious damage to normal tissues, and can't achieve a desired therapeutic effect. For this situation, a facilely prepared reduction-responsive polypeptide nanogel is employed for targeting intracellular delivery of antitumor drug in this study. The laden nanogel keeps structural integrity and less drug release in the circulatory system after intravenous injection, releases the payload triggered by the intracellular high concentration of GSH, and exhibits the excellent tumor inhibition and security in vivo. Furthermore, the other hydrophobic antitumor drugs can also be on-demand delivered by the smart nanogel. All of the above advantages confirm the bright prospect of reduction-responsive nanogel on the road of malignancy chemotherapy.
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Affiliation(s)
- Kexin Huang
- Center for Biological Experiment, College of Basic Medicine, Jilin University, Changchun 130021, People's Republic of China
| | - Bo Shi
- Center for Biological Experiment, College of Basic Medicine, Jilin University, Changchun 130021, People's Republic of China
| | - Weiguo Xu
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China.
| | - Yu Yang
- Center for Biological Experiment, College of Basic Medicine, Jilin University, Changchun 130021, People's Republic of China
| | - Haiyan Liu
- Center for Biological Experiment, College of Basic Medicine, Jilin University, Changchun 130021, People's Republic of China.
| | - Xiuli Zhuang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
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