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Wu S, Gabelli SB, Sohn J. The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS. Nat Commun 2024; 15:4012. [PMID: 38740774 PMCID: PMC11091121 DOI: 10.1038/s41467-024-48365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2'-5'/3'-5'-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.
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Affiliation(s)
- Shuai Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Discovery Chemistry, Merck Laboratories, West Point, PA, USA
| | - Jungsan Sohn
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Li J, Xiong M, Liu J, Zhang F, Li M, Zhao W, Xu Y. Discovery of novel cGAS inhibitors based on natural flavonoids. Bioorg Chem 2023; 140:106802. [PMID: 37666112 DOI: 10.1016/j.bioorg.2023.106802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) plays an important role in the inflammatory response. It has been reported that aberrant activation of cGAS is associated with a variety of immune-mediated inflammatory disorders. The development of small molecule inhibitors of cGAS has been considered as a promising therapeutic strategy for the diseases. Flavonoids, a typical class of natural products, are known for their anti-inflammatory activities. Although cGAS is closely associated with inflammation, the potential effects of natural flavonoid compounds on cGAS have been rarely studied. Therefore, we screened an in-house natural flavonoid library by pyrophosphatase (PPiase) coupling assay and identified novel cGAS inhibitors baicalein and baicalin. Subsequently, crystal structures of the two natural flavonoids in complex with human cGAS were determined, which provide mechanistic insight into the anti-inflammatory activities of baicalein and baicalin at the molecular level. After that, a virtual screening based on the crystal structures of baicalein and baicalin in complex with human cGAS was performed. As a result, compound C20 was identified to inhibit both human and mouse cGAS with IC50 values of 2.28 and 1.44 μM, respectively, and its detailed interactions with human cGAS were further revealed by the X-ray crystal structure determination. These results demonstrate the potential of natural products used as hits in drug discovery and provide valuable hints for further development of cGAS inhibitors.
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Affiliation(s)
- Jiameng Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayuan Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fengping Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Wenfeng Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Yechun Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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3
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Zhang J, Zhou EC, He Y, Chai ZL, Ji BZ, Tu Y, Wang HL, Wu WQ, Liu Y, Zhang XH, Liu Y. ZYG11B potentiates the antiviral innate immune response by enhancing cGAS-DNA binding and condensation. Cell Rep 2023; 42:112278. [PMID: 36933219 DOI: 10.1016/j.celrep.2023.112278] [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: 08/22/2022] [Revised: 01/17/2023] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
As a key dsDNA recognition receptor, cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS) plays a vital role in innate immune responses. Activated cGAS, by sensing DNA, catalyzes the synthesis of the secondary messenger cyclic GMP-AMP (cGAMP), which subsequently activates downstream signaling to induce production of interferons and inflammatory cytokines. Here, we report Zyg-11 family member B (ZYG11B) as a potent amplifier in cGAS-mediated immune responses. Knockdown of ZYG11B impairs production of cGAMP and subsequent transcription of interferon and inflammatory cytokines. Mechanistically, ZYG11B enhances cGAS-DNA binding affinity, potentiates cGAS-DNA condensation, and stabilizes the cGAS-DNA condensed complex. Moreover, herpes simplex virus 1 (HSV-1) infection induces ZYG11B degradation in a cGAS-unrelated manner. Our findings not only reveal an important role of ZYG11B in the early stage of DNA-induced cGAS activation but also indicate a viral strategy to dampen the innate immune response.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China; College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Er-Chi Zhou
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yan He
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China; College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ze-Lin Chai
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China; College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ben-Zhe Ji
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China; College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yi Tu
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China; College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Han-Ling Wang
- Xi'an Jiaotong-Livepool University, Suzhou 215123, China
| | - Wen-Qiang Wu
- College of Life Science, Henan University, Kaifeng 475001, China
| | - Yong Liu
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China; College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Liu
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China; College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Akkuş-Dağdeviren ZB, Fürst A, David Friedl J, Tribus M, Bernkop-Schnürch A. Nanoarchitectonics of Layer-by-Layer (LbL) coated nanostructured lipid carriers (NLCs) for Enzyme-Triggered charge reversal. J Colloid Interface Sci 2023; 629:541-553. [PMID: 36088699 DOI: 10.1016/j.jcis.2022.08.190] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/19/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022]
Abstract
HYPOTHESIS Combined usage of Layer-by-Layer (LbL) coating and alkaline phosphatase (ALP) - responsive charge reversal strategies can improve the cellular internalisation of the colloidal drug delivery systems by also decreasing their cytotoxic effects. EXPERIMENTS Anionic core NLCs were formed by combining the melt emulsification method and ultrasonication. The resulting core NLCs were coated sequentially first with protamine (Prot NLCs) and then with sodium tripolyphosphate (TPP) or sodium polyphosphate (Graham's salt, PP) generating TPP or PP NLCs, respectively. The developed NLCs were characterised regarding their size and zeta potential. Enzyme-induced charge reversal of the TPP and PP NLCs was evaluated by zeta potential measurements upon their incubation with alkaline phosphatase (ALP). In parallel, time-dependent phosphate release was monitored in the presence of isolated as well as cell-associated ALP. Morphological evaluations were performed by scanning electron microscopy (SEM) studies. Moreover, cell viability and cellular uptake studies were carried out in vitro on Caco-2 cells. FINDINGS The core NLCs were obtained with a mean size of 272.27 ± 5.23 nm and a zeta potential of -25.70 ± 0.26 mV. Upon coating with protamine, the zeta potential raised to positive values with a total change up to Δ29.3 mV also displaying an increase in particle size. The second layer coating with TPP and PP provided a negative surface charge. Subsequent to ALP treatment, the zeta potential of the TPP and PP NLCs reversed from negative to positive values with total changes of Δ8.56 and Δ7.47 mV, respectively. Conformably, significant amounts of phosphate were released from both formulations. Compared with core NLCs, improved cellular viability as well as increased cellular uptake were observed in case of Prot, TPP and PP NLCs.
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Affiliation(s)
- Zeynep Burcu Akkuş-Dağdeviren
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Andrea Fürst
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Julian David Friedl
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Martina Tribus
- Institute of Mineralogy and Petrography, University of Innsbruck, Innrain 52, 6020 Innsbruck, Austria
| | - Andreas Bernkop-Schnürch
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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Karanja CW, Yeboah KS, Ong WWS, Sintim HO. A STING-based fluorescent polarization assay for monitoring activities of cyclic dinucleotide metabolizing enzymes. RSC Chem Biol 2020; 2:206-214. [PMID: 34458783 PMCID: PMC8341399 DOI: 10.1039/d0cb00187b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/29/2020] [Indexed: 12/17/2022] Open
Abstract
Cyclic dinucleoties, such as cGAMP, c-di-GMP and c-di-AMP, are fascinating second messengers with diverse roles in both prokaryotes and eukaryotes. Consequently there is a need for simple and inexpensive methods for profiling these compounds in biological media, monitoring their synthesis or degradation by enzymes and for identifying inhibitors of proteins that metabolize or bind to these dinucleotides. Since 2011, when we reported the first simple method to detect c-di-GMP (S. Nakayama, I. Kelsey, J. Wang, K. Roelofs, B. Stefane, Y. Luo, V. T. Lee and H. O. Sintim, J. Am. Chem. Soc., 2011, 133, 4856) or in 2014 when we revealed another surprisingly simple assay to detect c-di-AMP (J. Zhou, D. A. Sayre, Y. Zheng, H. Szmacinski and H. O. Sintim, Anal. Chem., 2014, 86, 2412), there have been efforts to develop assays to detect cyclic dinucleotides by others. However a unified and simple assay, which can be used for all cyclic dinucleotides is lacking. Here, we investigate STING binding by various fluorescein-labeled c-di-GMP, c-di-AMP and cGAMP, using fluorescent polarization (FP). Fluorescein-labeled c-di-GMP (F-c-di-GMP) was found to be the best binder of STING. This probe could be displaced by unlabeled cGAMP, c-di-AMP or c-di-GMP and hence it is a universal probe, which can be used to monitor all three dinucleotides. HPLC analysis was used to validate the new F-c-di-GMP-based FP assay. Cyclic dinucleoties, such as cGAMP, c-di-GMP and c-di-AMP, are fascinating second messengers with diverse roles in both prokaryotes and eukaryotes.![]()
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Affiliation(s)
- Caroline W Karanja
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA
| | - Kofi S Yeboah
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA
| | - Wilson W S Ong
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA
| | - Herman O Sintim
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA.,Institute for Drug Discovery, Purdue University 720 Clinic Drive West Lafayette IN 47907 USA .,Purdue Institute of Inflammation, Immunology, and Infectious Disease West Lafayette IN 47907 USA
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Hertzog J, Rehwinkel J. Regulation and inhibition of the DNA sensor cGAS. EMBO Rep 2020; 21:e51345. [PMID: 33155371 PMCID: PMC7726805 DOI: 10.15252/embr.202051345] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Cell-autonomous sensing of nucleic acids is essential for host defence against invading pathogens by inducing antiviral and inflammatory cytokines. cGAS has emerged in recent years as a non-redundant DNA sensor important for detection of many viruses and bacteria. Upon binding to DNA, cGAS synthesises the cyclic dinucleotide 2'3'-cGAMP that binds to the adaptor protein STING and thereby triggers IRF3- and NFκB-dependent transcription. In addition to infection, the pathophysiology of an ever-increasing number of sterile inflammatory conditions in humans involves the recognition of DNA through cGAS. Consequently, the cGAS/STING signalling axis has emerged as an attractive target for pharmacological modulation. However, the development of cGAS and STING inhibitors has just begun and a need for specific and effective compounds persists. In this review, we focus on cGAS and explore how its activation by immunostimulatory DNA is regulated by cellular mechanisms, viral immune modulators and small molecules. We further use our knowledge of cGAS modulation by cells and viruses to conceptualise potential new ways of pharmacological cGAS targeting.
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Affiliation(s)
- Jonny Hertzog
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Jan Rehwinkel
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
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Li M, Shu HB. Dephosphorylation of cGAS by PPP6C impairs its substrate binding activity and innate antiviral response. Protein Cell 2020; 11:584-599. [PMID: 32474700 PMCID: PMC7381519 DOI: 10.1007/s13238-020-00729-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022] Open
Abstract
The cyclic GMP-AMP (cGAMP) synthase (cGAS) plays a critical role in host defense by sensing cytosolic DNA derived from microbial pathogens or mis-located cellular DNA. Upon DNA binding, cGAS utilizes GTP and ATP as substrates to synthesize cGAMP, leading to MITA-mediated innate immune response. In this study, we identified the phosphatase PPP6C as a negative regulator of cGAS-mediated innate immune response. PPP6C is constitutively associated with cGAS in un-stimulated cells. DNA virus infection causes rapid disassociation of PPP6C from cGAS, resulting in phosphorylation of human cGAS S435 or mouse cGAS S420 in its catalytic pocket. Mutation of this serine residue of cGAS impairs its ability to synthesize cGAMP upon DNA virus infection. In vitro experiments indicate that S420-phosphorylated mcGAS has higher affinity to GTP and enzymatic activity. PPP6C-deficiency promotes innate immune response to DNA virus in various cells. Our findings suggest that PPP6C-mediated dephosphorylation of a catalytic pocket serine residue of cGAS impairs its substrate binding activity and innate immune response, which provides a mechanism for keeping the DNA sensor cGAS inactive in the absence of infection to avoid autoimmune response.
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Affiliation(s)
- Mi Li
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, 430071, China
| | - Hong-Bing Shu
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan, 430071, China.
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Hooy RM, Massaccesi G, Rousseau KE, Chattergoon MA, Sohn J. Allosteric coupling between Mn2+ and dsDNA controls the catalytic efficiency and fidelity of cGAS. Nucleic Acids Res 2020; 48:4435-4447. [PMID: 32170294 PMCID: PMC7192592 DOI: 10.1093/nar/gkaa084] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/24/2020] [Accepted: 03/11/2020] [Indexed: 12/21/2022] Open
Abstract
Cyclic-G/AMP (cGAMP) synthase (cGAS) triggers host innate immune responses against cytosolic double-stranded (ds)DNA arising from genotoxic stress and pathogen invasion. The canonical activation mechanism of cGAS entails dsDNA-binding and dimerization. Here, we report an unexpected activation mechanism of cGAS in which Mn2+ activates monomeric cGAS without dsDNA. Importantly, the Mn2+-mediated activation positively couples with dsDNA-dependent activation in a concerted manner. Moreover, the positive coupling between Mn2+ and dsDNA length-dependent activation requires the cognate ATP/GTP substrate pair, while negative-cooperativity suppresses Mn2+ utilization by either ATP or GTP alone. Additionally, while Mn2+ accelerates the overall catalytic activity, dsDNA length-dependent dimerization specifically accelerates the cyclization of cGAMP. Together, we demonstrate how the intrinsic allostery of cGAS efficiently yet precisely tunes its activity.
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Affiliation(s)
- Richard M Hooy
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Guido Massaccesi
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kimberly E Rousseau
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael A Chattergoon
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jungsan Sohn
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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