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Manjula S, Kalaiarasi C, Jaganathan R, Kumaradhas P. The effect of genotype variation and M423 resistance mutations to the binding of phosphonomidate-based inhibitor IDX17119 with the thumb-II domain of Hepatitis C virus RdRp: an integrated molecular dynamics and binding free energy study. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2136371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Saravanan Manjula
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Chinnasamy Kalaiarasi
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Ramakrishnan Jaganathan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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2
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Liu Q, Kwan KY, Cao T, Yan B, Ganesan K, Jia L, Zhang F, Lim C, Wu Y, Feng Y, Chen Z, Liu L, Chen J. Broad-spectrum antiviral activity of Spatholobus suberectus Dunn against SARS-CoV-2, SARS-CoV-1, H5N1, and other enveloped viruses. Phytother Res 2022; 36:3232-3247. [PMID: 35943221 PMCID: PMC9537938 DOI: 10.1002/ptr.7452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/05/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023]
Abstract
The current COVID-19 pandemic caused by SARS-Cov-2 is responsible for more than 6 million deaths globally. The development of broad-spectrum and cost-effective antivirals is urgently needed. Medicinal plants are renowned as a complementary approach in which antiviral natural products have been established as safe and effective drugs. Here, we report that the percolation extract of Spatholobus suberectus Dunn (SSP) is a broad-spectrum viral entry inhibitor against SARS-CoV-1/2 and other enveloped viruses. The viral inhibitory activities of the SSP were evaluated by using pseudotyped SARS-CoV-1 and 2, HIV-1ADA and HXB2 , and H5N1. SSP effectively inhibited viral entry and with EC50 values ranging from 3.6 to 5.1 μg/ml. Pre-treatment of pseudovirus or target cells with SSP showed consistent inhibitory activities with the respective EC50 value of 2.3 or 2.1 μg/ml. SSP blocked both SARS-CoV-2 spike glycoprotein and the host ACE2 receptor. In vivo studies indicated that there was no abnormal toxicity and behavior in long-term SSP treatment. Based on these findings, we concluded that SSP has the potential to be developed as a drug candidate for preventing and treating COVID-19 and other emerging enveloped viruses.
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Affiliation(s)
- Qingqing Liu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Shenzhen Institute of Research and Innovation, University of Hong Kong, Shenzhen, China
| | - Ka-Yi Kwan
- AIDS Institute, State Key Laboratory of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tianyu Cao
- AIDS Institute, State Key Laboratory of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Immunology and Department of Dermatology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Bingpeng Yan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kumar Ganesan
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lei Jia
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Shenzhen Institute of Research and Innovation, University of Hong Kong, Shenzhen, China
| | - Feng Zhang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Shenzhen Institute of Research and Innovation, University of Hong Kong, Shenzhen, China
| | - Chunyu Lim
- AIDS Institute, State Key Laboratory of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yaobin Wu
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Medical Biomechanics, Department of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhiwei Chen
- AIDS Institute, State Key Laboratory of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Li Liu
- AIDS Institute, State Key Laboratory of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jianping Chen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Shenzhen Institute of Research and Innovation, University of Hong Kong, Shenzhen, China
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Alam MS, Uddin MS, Shamsuddin T, Rubayed M, Sharmin T, Akter R, Hosen SMZ. Repurposing of existing antibiotics for the treatment of diabetes mellitus. In Silico Pharmacol 2022; 10:4. [PMID: 35273901 PMCID: PMC8898203 DOI: 10.1007/s40203-021-00118-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 11/22/2021] [Indexed: 02/02/2023] Open
Abstract
Proline specific serine protease enzyme, dipeptidyl peptidase IV (DPP-4) has become a promising target for diabetes, as it stops glucagon-like peptide 1 (GLP-1) from becoming inactive, resulting in higher levels of active GLP-1. This lowers glucose levels by increasing insulin secretion and decreasing glucagon secretion. DPP-4 is also linked to a higher BMI and a 0.7 to 1% reduction in HbA1c. Currently available DPP-4 inhibitor drugs showed less promising anti-diabetic activity as this class associated with many side effects due to non-selectivity and therefore searching on more potent DPP-4 inhibitors are still ongoing. In our present study, we investigate the inhibition of DPP-4 through a series of antibiotic compounds which were previously reported to be used in diabetic foot infections and compared with existing DPP-4 inhibitors. To obtain this objective, three-dimensional crystal structure of DPP-4 was retrieved from the protein data bank (PDB id: 1 × 70). A systematic computational method combining molecular docking, MM-GBSA binding energy calculation, MD simulations, MM-PBSA binding free energy calculations and ADME were used to find best DPP-4 inhibitor. Molecular docking results revealed that clindamycin has a higher affinity towards the catalytic sides of DPP-4 and built solid hydrophobic and polar interactions with the amino acids involved in the binding region of DPP-4, such as S1 subsite, S2 subsite and S2 extensive subsite. MD simulations results showed clindamycin as potent virtual hit and suggested that it binds with DPP-4 in competitive manner, which virtually indicate that besides antibiotic activity clindamycin has anti-diabetic activity. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00118-6.
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Affiliation(s)
- Muhammad Shaiful Alam
- Molecular Modeling Drug-Design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories, Chattogram, 4220 Bangladesh
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, 4202 Bangladesh
| | - Md. Sohorab Uddin
- Department of Pharmacy, University of Chittagong, Chattogram, 4331 Bangladesh
| | - Tahmida Shamsuddin
- Department of Applied Chemistry, University of Chittagong, Chattogram, 4331 Bangladesh
| | - Maruf Rubayed
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, 4202 Bangladesh
| | - Tania Sharmin
- Molecular Modeling Drug-Design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories, Chattogram, 4220 Bangladesh
| | - Rasheda Akter
- Molecular Modeling Drug-Design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories, Chattogram, 4220 Bangladesh
| | - S. M. Zahid Hosen
- Molecular Modeling Drug-Design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories, Chattogram, 4220 Bangladesh
- Pancreatic Research Group, Ingham Institute for Applied Medical Research, Faculty of Medicine, South Western Sydney Clinical School, The University of New South Wales 2170, Sydney, Australia
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Zhang J, Murugan NA, Tian Y, Bertagnin C, Fang Z, Kang D, Kong X, Jia H, Sun Z, Jia R, Gao P, Poongavanam V, Loregian A, Xu W, Ma X, Ding X, Huang B, Zhan P, Liu X. Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant. J Med Chem 2018; 61:9976-9999. [PMID: 30365885 DOI: 10.1021/acs.jmedchem.8b01065] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Natarajan Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Ye Tian
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong P. R. China
| | - Chiara Bertagnin
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Zengjun Fang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
- The Second Hospital of Shandong University, No. 247 Beiyuan Avenue, 250033 Jinan, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Xiujie Kong
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Haiyong Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Zhuosen Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Wenfang Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, 1, Jiaoxiao Road, 250023 Jinan, Shandong, P. R. China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, 1, Jiaoxiao Road, 250023 Jinan, Shandong, P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P. R. China
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Glanz VY, Myasoedova VA, Grechko AV, Orekhov AN. Inhibition of sialidase activity as a therapeutic approach. DRUG DESIGN DEVELOPMENT AND THERAPY 2018; 12:3431-3437. [PMID: 30349196 PMCID: PMC6186905 DOI: 10.2147/dddt.s176220] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The demand for novel anti-influenza drugs persists, which is highlighted by the recent pandemics of influenza affecting thousands of people across the globe. One of the approaches to block the virus spreading is inhibiting viral sialidase (neuraminidase). This enzyme cleaves the sialic acid link between the newly formed virions and the host cell surface liberating the virions from the cell and maintaining the cycle of infection. Viral neuraminidases appear therefore as attractive therapeutic targets for preventing further spread of influenza infection. Compared to ion channel blockers that were the first approved anti-influenza drugs, neuraminidase inhibitors are well tolerated and target both influenza A and B viruses. Moreover, neuraminidase/sialidase inhibitors may be useful for managing some other human pathologies, such as cancer. In this review, we discuss the available knowledge on neuraminidase or sialidase inhibitors, their design, clinical application, and the current challenges.
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Affiliation(s)
- Victor Yu Glanz
- Department of Genetics, Cytology and Bioengineering, Faculty of Biology and Medicine, Voronezh State University, Voronezh, Russia
| | - Veronika A Myasoedova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Moscow, Russia,
| | - Andrey V Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Alexander N Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Moscow, Russia, .,Institute for Atherosclerosis Research, Skolkovo Innovative Center, Moscow, Russia,
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Lin SH, Cui W, Wang GL, Meng S, Liu YC, Jin HW, Zhang LR, Xie Y. Combined computational and experimental studies of molecular interactions of albuterol sulfate with bovine serum albumin for pulmonary drug nanoparticles. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:2973-2987. [PMID: 27695294 PMCID: PMC5029849 DOI: 10.2147/dddt.s114663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Albumin-based nanoparticles (NPs) are a promising technology for developing drug-carrier systems, with improved deposition and retention profiles in lungs. Improved understanding of these drug–carrier interactions could lead to better drug-delivery systems. The present study combines computational and experimental methods to gain insights into the mechanism of binding of albuterol sulfate (AS) to bovine serum albumin (BSA) on the molecular level. Molecular dynamics simulation and surface plasmon resonance spectroscopy were used to determine that there are two binding sites on BSA for AS: the first of which is a high-affinity site corresponding to AS1 and the second of which appears to represent the integrated functions of several low-affinity sites corresponding to AS2, AS3, and AS8. AS1 was the strongest binding site, established via electrostatic interaction with Glu243 and Asp255 residues in a hydrophobic pocket. Hydrogen bonds and salt bridges played a main role in the critical binding of AS1 to BSA, and water bridges served a supporting role. Based upon the interaction mechanism, BSA NPs loaded with AS were prepared, and their drug-loading efficiency, morphology, and -release profiles were evaluated. Successful clinical development of AS-BSA-NPs may improve therapy and prevention of bronchospasm in patients with reversible obstructive airway disease, and thus provide a solid basis for expanding the role of NPs in the design of new drug-delivery systems.
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Affiliation(s)
- Shao-Hui Lin
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University
| | - Wei Cui
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing
| | - Gui-Ling Wang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University
| | - Shuai Meng
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University
| | - Ying-Chun Liu
- Soft Matter Research Center, Department of Chemistry, Zhejiang University, Hangzhou
| | - Hong-Wei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, People's Republic of China
| | - Liang-Ren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, People's Republic of China
| | - Ying Xie
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, People's Republic of China
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7
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Schaduangrat N, Phanich J, Rungrotmongkol T, Lerdsamran H, Puthavathana P, Ubol S. The significance of naturally occurring neuraminidase quasispecies of H5N1 avian influenza virus on resistance to oseltamivir: a point of concern. J Gen Virol 2016; 97:1311-1323. [PMID: 26935590 DOI: 10.1099/jgv.0.000444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Viral adaptability and survival arise due to the presence of quasispecies populations that are able to escape the immune response or produce drug-resistant variants. However, the presence of H5N1 virus with natural mutations acquired without any drug selection pressure poses a great threat. Cloacal samples collected from the 2004-2005 epidemics in Thailand from Asian open-billed storks revealed one major and several minor quasispecies populations with mutations on the oseltamivir (OTV)-binding site of the neuraminidase gene (NA) without prior exposure to a drug. Therefore, this study investigated the binding between the NA-containing novel mutations and OTV drug using molecular dynamic simulations and plaque inhibition assay. The results revealed that the mutant populations, S236F mutant, S236F/C278Y mutant, A250V/V266A/P271H/G285S mutant and C278Y mutant, had a lower binding affinity with OTV as compared with the WT virus due to rearrangement of amino acid residues and increased flexibility in the 150-loop. This result was further emphasized through the IC50 values obtained for the major population and WT virus, 104.74 nM and 18.30 nM, respectively. Taken together, these data suggest that H5N1 viruses isolated from wild birds have already acquired OTV-resistant point mutations without any exposure to a drug.
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Affiliation(s)
- Nalini Schaduangrat
- Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchatewi, Bangkok 10400, Thailand
| | - Jiraphorn Phanich
- Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hatairat Lerdsamran
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pilaipan Puthavathana
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sukathida Ubol
- Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchatewi, Bangkok 10400, Thailand
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