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Alotaibi F, Aba Alkhayl FF, Foudah AI, Azhar Kamal M, Moglad EH, Khan S, Rehman ZU, Warsi MK, Jawaid T, Alam A. Investigating the effects of four medicinal plants against dengue virus through QSAR modeling and molecular dynamics studies. J Biomol Struct Dyn 2024:1-18. [PMID: 38197579 DOI: 10.1080/07391102.2024.2301744] [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: 09/21/2023] [Accepted: 12/28/2023] [Indexed: 01/11/2024]
Abstract
The Dengue virus (DENV) has been increasingly recognized as a prevalent viral pathogen responsible for global transmission of infection. It has been established that DENV's NS5 methyltransferase (MTase) controls viral replication. As a result, NS5 MTase is considered a potentially useful drug target for DENV. In this study, the two phases of virtual screening were conducted using the ML-based QSAR model and molecular docking to identify potential compounds against NS5 of DENV. Four medicinal plants [Aloe vera, Cannabis sativa (Hemp), Ocimum sanctum (Holy Basil; Tulsi), and Zingiber officinale (Ginger)] that showed anti-viral properties were selected for sourcing the phytochemicals and screening them against NS5. Additionally, re-docking at higher exhaustiveness and interaction analysis were performed which resulted in the identification of the top four hits (135398658, 5281675, 119394, and 969516) which showed comparable results with the control Sinefungin (SFG). Post molecular dynamics simulation, 135398658 showed the lowest RMSD (0.4-0.5 nm) and the maximum number of hydrogen bonds (eight hydrogen bonds) after the control while 5281675 and 969516 showed comparable hydrogen bonds to the control. These compounds showed direct interactions with the catalytic site residues GLU111 and ASP131, in addition to this these compounds showed stable complex formation as depicted by principal component analysis and free energy landscape. 135398658 showed lower total binding free energy (ΔGTotal = -36.56 kcal/mol) than the control, while 5281675 had comparable values to the control (ΔGTotal = -34.1 kcal/mol). Overall, the purpose of this study was to identify phytochemicals that inhibit NS5 function, that could be further tested experimentally to treat dengue virus (DENV).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faisal Alotaibi
- Department of Pharmacy Practice, College of Pharmacy, Shaqra University, Al-Dawadmi, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ahmed I Foudah
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Ehssan H Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- Department of Microbiology and Parasitology, Medicinal and Aromatic Plants Research Institute, National Center for Research, Khartoum, Sudan
| | - Shamshir Khan
- Department of Pharmacognosy & Pharmaceutical Chemistry, College of Dentistry and Pharmacy, Buraydah Private Colleges, Buraydah, Saudi Arabia
| | - Zia Ur Rehman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohiuddin Khan Warsi
- Department of Biological Sciences, Faculty of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Talha Jawaid
- Department of Pharmacology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Aftab Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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2
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Samrat SK, Bashir Q, Zhang R, Huang Y, Liu Y, Wu X, Brown T, Wang W, Zheng YG, Zhang QY, Chen Y, Li Z, Li H. A universal fluorescence polarization high throughput screening assay to target the SAM-binding sites of SARS-CoV-2 and other viral methyltransferases. Emerg Microbes Infect 2023; 12:2204164. [PMID: 37060263 PMCID: PMC10165934 DOI: 10.1080/22221751.2023.2204164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/16/2023]
Abstract
SARS-CoV-2 has caused a global pandemic with significant humanity and economic loss since 2020. Currently, only limited options are available to treat SARS-CoV-2 infections for vulnerable populations. In this study, we report a universal fluorescence polarization (FP)-based high throughput screening (HTS) assay for SAM-dependent viral methyltransferases (MTases), using a fluorescent SAM-analogue, FL-NAH. We performed the assay against a reference MTase, NSP14, an essential enzyme for SARS-CoV-2 to methylate the N7 position of viral 5'-RNA guanine cap. The assay is universal and suitable for any SAM-dependent viral MTases such as the SARS-CoV-2 NSP16/NSP10 MTase complex and the NS5 MTase of Zika virus (ZIKV). Pilot screening demonstrated that the HTS assay was very robust and identified two candidate inhibitors, NSC 111552 and 288387. The two compounds inhibited the FL-NAH binding to the NSP14 MTase with low micromolar IC50. We used three functional MTase assays to unambiguously verified the inhibitory potency of these molecules for the NSP14 N7-MTase function. Binding studies indicated that these molecules are bound directly to the NSP14 MTase with similar low micromolar affinity. Moreover, we further demonstrated that these molecules significantly inhibited the SARS-CoV-2 replication in cell-based assays at concentrations not causing cytotoxicity. Furthermore, NSC111552 significantly synergized with known SARS-CoV-2 drugs including nirmatrelvir and remdesivir. Finally, docking suggested that these molecules bind specifically to the SAM-binding site on the NSP14 MTase. Overall, these molecules represent novel and promising candidates to further develop broad-spectrum inhibitors for the management of viral infections.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Qamar Bashir
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Ran Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yiding Huang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yuchen Liu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Xiangmeng Wu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Wei Wang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yin Chen
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson, AZ, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ, USA
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3
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Chen H, Lin S, Yang F, Chen Z, Guo L, Yang J, Lin X, Wang L, Duan Y, Wen A, Zhang X, Dai Y, Yin K, Yuan X, Yu C, He Y, He B, Cao Y, Dong H, Li J, Zhao Q, Liu Q, Lu G. Structural and functional basis of low-affinity SAM/SAH-binding in the conserved MTase of the multi-segmented Alongshan virus distantly related to canonical unsegmented flaviviruses. PLoS Pathog 2023; 19:e1011694. [PMID: 37831643 PMCID: PMC10575543 DOI: 10.1371/journal.ppat.1011694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Alongshan virus (ALSV), a newly discovered member of unclassified Flaviviridae family, is able to infect humans. ALSV has a multi-segmented genome organization and is evolutionarily distant from canonical mono-segmented flaviviruses. The virus-encoded methyltransferase (MTase) plays an important role in viral replication. Here we show that ALSV MTase readily binds S-adenosyl-L-methionine (SAM) and S-adenosyl-L-homocysteine (SAH) but exhibits significantly lower affinities than canonical flaviviral MTases. Structures of ALSV MTase in the free and SAM/SAH-bound forms reveal that the viral enzyme possesses a unique loop-element lining side-wall of the SAM/SAH-binding pocket. While the equivalent loop in flaviviral MTases half-covers SAM/SAH, contributing multiple hydrogen-bond interactions; the pocket-lining loop of ALSV MTase is of short-length and high-flexibility, devoid of any physical contacts with SAM/SAH. Subsequent mutagenesis data further corroborate such structural difference affecting SAM/SAH-binding. Finally, we also report the structure of ALSV MTase bound with sinefungin, an SAM-analogue MTase inhibitor. These data have delineated the basis for the low-affinity interaction between ALSV MTase and SAM/SAH and should inform on antiviral drug design.
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Affiliation(s)
- Hua Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fanli Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xi Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Wang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Duan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ao Wen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xindan Zhang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yushan Dai
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Keqing Yin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xin Yuan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chongzhang Yu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yarong He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian Li
- School of Basic Medical Sciences, Chengdu University, Chengdu, Sichuan, China
| | - Qi Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Quan Liu
- Center of Infectious diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, State Key Laboratory of Zoonotic Diseases, Changchun, Jilin, China
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Samrat SK, Bashir Q, Huang Y, Trieshmann CW, Tharappel AM, Zhang R, Chen K, Geoge Zheng Y, Li Z, Li H. Broad-Spectrum Small-Molecule Inhibitors Targeting the SAM-Binding Site of Flavivirus NS5 Methyltransferase. ACS Infect Dis 2023; 9:1319-1333. [PMID: 37348028 PMCID: PMC10436986 DOI: 10.1021/acsinfecdis.2c00571] [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] [Indexed: 06/24/2023]
Abstract
Flavivirus infections, such as those caused by dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV), pose a rising threat to global health. There are no FDA-approved drugs for flaviviruses, although a small number of flaviviruses have vaccines. For flaviviruses or unknown viruses that may appear in the future, it is particularly desirable to identify broad-spectrum inhibitors. The NS5 protein is regarded as one of the most promising flavivirus drug targets because it is conserved across flaviviruses. In this study, we used FL-NAH, a fluorescent analog of the methyl donor S-adenosyl methionine (SAM), to develop a fluorescence polarization (FP)-based high throughput screening (HTS) assay to specifically target methyltransferase (MTase), a vital enzyme for flaviviruses that methylates the N7 and 2'-O positions of the viral 5'-RNA cap. Pilot screening identified two candidate MTase inhibitors, NSC 111552 and 288387. The two compounds inhibited the FL-NAH binding to the DENV3 MTase with low micromolar IC50. Functional assays verified the inhibitory potency of these molecules for the flavivirus MTase activity. Binding studies indicated that these molecules are bound directly to the DENV3 MTase with similar low micromolar affinity. Furthermore, we showed that these compounds greatly reduced ZIKV replication in cell-based experiments at dosages that did not cause cytotoxicity. Finally, docking studies revealed that these molecules bind to the SAM-binding region on the DENV3 MTase, and further mutagenesis studies verified residues important for the binding of these compounds. Overall, these compounds are innovative and attractive candidates for the development of broad-spectrum inhibitors for the treatment of flavivirus infections.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Qamar Bashir
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Yiding Huang
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Carl William Trieshmann
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, 30602, USA
| | - Anil Mathew Tharappel
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Ran Zhang
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Ke Chen
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Y. Geoge Zheng
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, 30602, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson AZ, 85721, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
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5
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Shukla R, Chandra A, Kumar A, Kandpal P, Avashthi H, Goel VK, Qamar I, Singh N, Kelvin DJ, Singh TR. Repurposing of drugs against methyltransferase as potential Zika virus therapies. Sci Rep 2023; 13:7870. [PMID: 37188743 PMCID: PMC10184974 DOI: 10.1038/s41598-023-33341-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
In recent years, the outbreak of infectious disease caused by Zika Virus (ZIKV) has posed a major threat to global public health, calling for the development of therapeutics to treat ZIKV disease. Several possible druggable targets involved in virus replication have been identified. In search of additional potential inhibitors, we screened 2895 FDA-approved compounds using Non-Structural Protein 5 (NS5) as a target utilizing virtual screening of in-silco methods. The top 28 compounds with the threshold of binding energy -7.2 kcal/mol value were selected and were cross-docked on the three-dimensional structure of NS5 using AutoDock Tools. Of the 2895 compounds screened, five compounds (Ceforanide, Squanavir, Amcinonide, Cefpiramide, and Olmesartan_Medoxomil) ranked highest based on filtering of having the least negative interactions with the NS5 and were selected for Molecular Dynamic Simulations (MDS) studies. Various parameters such as RMSD, RMSF, Rg, SASA, PCA and binding free energy were calculated to validate the binding of compounds to the target, ZIKV-NS5. The binding free energy was found to be -114.53, -182.01, -168.19, -91.16, -122.56, and -150.65 kJ mol-1 for NS5-SFG, NS5-Ceforanide, NS5-Squanavir, NS5-Amcinonide, NS5-Cefpiramide, and NS5-Ol_Me complexes respectively. The binding energy calculations suggested Cefpiramide and Olmesartan_Medoxomil (Ol_Me) as the most stable compounds for binding to NS5, indicating a strong rationale for their use as lead compounds for development of ZIKV inhibitors. As these drugs have been evaluated on pharmacokinetics and pharmacodynamics parameters only, in vitro and in vivo testing and their impact on Zika viral cell culture may suggest their clinical trials on ZIKV patients.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India
- School of Physical Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
- European Virus Bioinformatics Center, Leutragraben 1, Jena, Germany
| | | | - Himanshu Avashthi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, India
| | - Vijay Kumar Goel
- School of Physical Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India.
| | - David J Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China.
- Department of Microbiology and Immunology, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada.
- Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada.
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India.
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India.
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Furtado ND, de Mello IS, de Godoy AS, Noske GD, Oliva G, Canard B, Decroly E, Bonaldo MC. Amino Acid Polymorphisms on the Brazilian Strain of Yellow Fever Virus Methyltransferase Are Related to the Host's Immune Evasion Mediated by Type I Interferon. Viruses 2023; 15:191. [PMID: 36680231 PMCID: PMC9863089 DOI: 10.3390/v15010191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Since late 2016, a yellow fever virus (YFV) variant carrying a set of nine amino acid variations has circulated in South America. Three of them were mapped on the methyltransferase (MTase) domain of viral NS5 protein. To assess whether these changes affected viral infectivity, we synthesized YFV carrying the MTase of circulating lineage as well as its isoform with the residues of the previous strains (NS5 K101R, NS5 V138I, and NS5 G173S). We observed a slight difference in viral growth properties and plaque phenotype between the two synthetic YFVs. However, the MTase polymorphisms associated with the Brazilian strain of YFV (2016-2019) confer more susceptibility to the IFN-I. In addition, in vitro MTase assay revealed that the interaction between the YFV MTase and the methyl donor molecule (SAM) is altered in the Brazilian MTase variant. Altogether, the results reported here describe that the MTase carrying the molecular signature of the Brazilian YFV circulating since 2016 might display a slight decrease in its catalytic activity but virtually no effect on viral fitness in the parameters comprised in this study. The most marked influence of these residues stands in the immune escape against the antiviral response mediated by IFN-I.
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Affiliation(s)
- Nathália Dias Furtado
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Iasmim Silva de Mello
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Andre Schutzer de Godoy
- Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos-USP, São Paulo 13563-120, Brazil
| | - Gabriela Dias Noske
- Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos-USP, São Paulo 13563-120, Brazil
| | - Glaucius Oliva
- Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos-USP, São Paulo 13563-120, Brazil
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS, UMR7257, 13009 Marseille, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS, UMR7257, 13009 Marseille, France
| | - Myrna C. Bonaldo
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro 21040-900, Brazil
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7
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Ferrero DS, Albentosa-González L, Mas A, Verdaguer N. Structure and function of the NS5 methyltransferase domain from Usutu virus. Antiviral Res 2022; 208:105460. [DOI: 10.1016/j.antiviral.2022.105460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/24/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
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8
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Ding P, Summers MF. Sequestering the 5′‐cap for viral RNA packaging. Bioessays 2022; 44:e2200104. [PMID: 36101513 DOI: 10.1002/bies.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/11/2022]
Abstract
Many viruses evolved mechanisms for capping the 5'-ends of their plus-strand RNAs as a means of hijacking the eukaryotic messenger RNA (mRNA) splicing/translation machinery. Although capping is critical for replication, the RNAs of these viruses have other essential functions including their requirement to be packaged as either genomes or pre-genomes into progeny viruses. Recent studies indicate that human immunodeficiency virus type-1 (HIV-1) RNAs are segregated between splicing/translation and packaging functions by a mechanism that involves structural sequestration of the 5'-cap. Here, we examined studies reported for other viruses and retrotransposons that require both selective packaging of their RNAs and 5'-RNA capping for host-mediated translation. Our findings suggest that viruses and retrotransposons have evolved multiple mechanisms to control 5'-cap accessibility, consistent with the hypothesis that removal or sequestration of the 5' cap enables packageable RNAs to avoid capture by the cellular RNA processing and translation machinery.
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Affiliation(s)
- Pengfei Ding
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
| | - Michael F. Summers
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
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9
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Desantis J, Felicetti T, Cannalire R. An overview on small molecules acting as broad spectrum-agents for yellow fever infection. Expert Opin Drug Discov 2022; 17:755-773. [PMID: 35638299 DOI: 10.1080/17460441.2022.2084529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Yellow Fever virus (YFV) is a mosquito-borne flavivirus, endemic in 47 countries in Africa and South America, which causes febrile symptoms that can evolve in 15% of the patients to serious haemorrhagic conditions, liver injury, and multiorgan failure. Although a highly effective vaccine (YF-17D vaccine) is available, to date, no antiviral drugs have been approved for the prevention and treatment of YFV infections. AREAS COVERED This review article focuses on the description of viral targets that have been considered within YFV and flavivirus drug discovery studies and on the most relevant candidates reported so far that elicit broad-spectrum inhibition against relevant strains and mutants of YFV. EXPERT OPINION Considering the growing interest on (re)emerging vector-borne viral infections, it is expected that flavivirus drug discovery will quickly deliver potential candidates for clinical evaluation. Due to similarity among flaviviral targets, several candidates identified against different flaviviruses have shown broad-spectrum activity, thus exhibiting anti-YFV activity, as well. In this regard, it would be desirable to routinely include the assessment of antiviral activity against different YFV strains. On the other hand, the development of host targeting agents are still at an initial stage and deserve further focused efforts.
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Affiliation(s)
- Jenny Desantis
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Napoli "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
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10
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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11
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Deymier S, Louvat C, Fiorini F, Cimarelli A. ISG20: an enigmatic antiviral RNase targeting multiple viruses. FEBS Open Bio 2022; 12:1096-1111. [PMID: 35174977 PMCID: PMC9157404 DOI: 10.1002/2211-5463.13382] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/31/2022] [Accepted: 02/15/2022] [Indexed: 11/25/2022] Open
Abstract
Interferon‐stimulated gene 20 kDa protein (ISG20) is a relatively understudied antiviral protein capable of inhibiting a broad spectrum of viruses. ISG20 exhibits strong RNase properties, and it belongs to the large family of DEDD exonucleases, present in both prokaryotes and eukaryotes. ISG20 was initially characterized as having strong RNase activity in vitro, suggesting that its inhibitory effects are mediated via direct degradation of viral RNAs. This mechanism of action has since been further elucidated and additional antiviral activities of ISG20 highlighted, including direct degradation of deaminated viral DNA and translational inhibition of viral RNA and nonself RNAs. This review focuses on the current understanding of the main molecular mechanisms of viral inhibition by ISG20 and discusses the latest developments on the features that govern specificity or resistance to its action.
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Affiliation(s)
- Séverine Deymier
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon Inserm, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieur de Lyon, U1111, Lyon, France
| | | | | | - Andrea Cimarelli
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon Inserm, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieur de Lyon, U1111, Lyon, France
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12
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Li Y. Molecular epidemiology of yellow fever virus in Africa: A perspective of the phylogeographic split between East/Central African and West African lineages. Acta Trop 2022; 225:106199. [PMID: 34740635 DOI: 10.1016/j.actatropica.2021.106199] [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: 04/16/2021] [Revised: 07/14/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022]
Abstract
Yellow fever (YF) is a major public-health problem in Africa. Yellow fever virus (YFV), the etiological agent responsible for the disease, exhibits clear delineation of phylogeography between East/Central Africa and West Africa. In order to decipher the genetic nature of the YFV epidemic between these areas, we performed a genome-wide study on its African isolates using the McDonald-Kreitman (MK) test in combination with the type II functional divergence analysis. The results showed that adaptive genetic diversifications have occurred on viral nonstructural protein 1 (NS1) and NS5, which are essential for viral genome replication and immune antagonism, with the East/Central African-West African epidemic split. On both proteins, a number of amino acid replacements have been favored by functional divergence. These findings could help to bridge the gap between the phylogeographic delineation and niche adaptation underlying the YFV-epidemic across Africa and shed light on viral determinants of this process.
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Affiliation(s)
- Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China.
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13
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Abstract
Flaviviruses such as dengue, Japanese encephalitis, West Nile, Yellow Fever and Zika virus, cause viral hemorrhagic fever and encephalitis in humans. However, antiviral therapeutics to treat or prevent flavivirus infections are not yet available. Thus, there is pressing need to develop therapeutics and vaccines that target flavivirus infections. All flaviviruses carry a positive-sense single-stranded RNA genome, which encodes ten proteins; three structural proteins form the virus shell, and seven nonstructural (NS) proteins are involved in replication of the viral genome. While all NS proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) are part of a functional membrane-bound replication complex, enzymatic activities required for flaviviral replication reside in only two NS proteins, NS3 and NS5. NS3 functions as a protease, helicase, and triphosphatase, and NS5 as a capping enzyme, methyltransferase, and RNA-dependent RNA polymerase. In this chapter, we provide an overview of viral replication focusing on the structure and function of NS3 and NS5 replicases. We further describe strategies and examples of current efforts to identify potential flavivirus inhibitors against NS3 and NS5 enzymatic activities that can be developed as therapeutic agents to combat flavivirus infections.
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Affiliation(s)
- Ekaterina Knyazhanskaya
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States.
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14
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Kasprzyk R, Jemielity J. Enzymatic Assays to Explore Viral mRNA Capping Machinery. Chembiochem 2021; 22:3236-3253. [PMID: 34291555 PMCID: PMC8426721 DOI: 10.1002/cbic.202100291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/21/2021] [Indexed: 12/25/2022]
Abstract
In eukaryotes, mRNA is modified by the addition of the 7-methylguanosine (m7 G) 5' cap to protect mRNA from premature degradation, thereby enhancing translation and enabling differentiation between self (endogenous) and non-self RNAs (e. g., viral ones). Viruses often develop their own mRNA capping pathways to augment the expression of their proteins and escape host innate immune response. Insights into this capping system may provide new ideas for therapeutic interventions and facilitate drug discovery, e. g., against viruses that cause pandemic outbreaks, such as beta-coronaviruses SARS-CoV (2002), MARS-CoV (2012), and the most recent SARS-CoV-2. Thus, proper methods for the screening of large compound libraries are required to identify lead structures that could serve as a basis for rational antiviral drug design. This review summarizes the methods that allow the monitoring of the activity and inhibition of enzymes involved in mRNA capping.
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Affiliation(s)
- Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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15
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Molecular Insights into the Flavivirus Replication Complex. Viruses 2021; 13:v13060956. [PMID: 34064113 PMCID: PMC8224304 DOI: 10.3390/v13060956] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/17/2021] [Accepted: 05/17/2021] [Indexed: 12/11/2022] Open
Abstract
Flaviviruses are vector-borne RNA viruses, many of which are clinically relevant human viral pathogens, such as dengue, Zika, Japanese encephalitis, West Nile and yellow fever viruses. Millions of people are infected with these viruses around the world each year. Vaccines are only available for some members of this large virus family, and there are no effective antiviral drugs to treat flavivirus infections. The unmet need for vaccines and therapies against these flaviviral infections drives research towards a better understanding of the epidemiology, biology and immunology of flaviviruses. In this review, we discuss the basic biology of the flavivirus replication process and focus on the molecular aspects of viral genome replication. Within the virus-induced intracellular membranous compartments, flaviviral RNA genome replication takes place, starting from viral poly protein expression and processing to the assembly of the virus RNA replication complex, followed by the delivery of the progeny viral RNA to the viral particle assembly sites. We attempt to update the latest understanding of the key molecular events during this process and highlight knowledge gaps for future studies.
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16
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Sutto-Ortiz P, Tcherniuk S, Ysebaert N, Abeywickrema P, Noël M, Decombe A, Debart F, Vasseur JJ, Canard B, Roymans D, Rigaux P, Eléouët JF, Decroly E. The methyltransferase domain of the Respiratory Syncytial Virus L protein catalyzes cap N7 and 2'-O-methylation. PLoS Pathog 2021; 17:e1009562. [PMID: 33956914 PMCID: PMC8130918 DOI: 10.1371/journal.ppat.1009562] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a negative sense single-stranded RNA virus and one of the main causes of severe lower respiratory tract infections in infants and young children. RSV RNA replication/transcription and capping are ensured by the viral Large (L) protein. The L protein contains a polymerase domain associated with a polyribonucleotidyl transferase domain in its N-terminus, and a methyltransferase (MTase) domain followed by the C-terminal domain (CTD) enriched in basic amino acids at its C-terminus. The MTase-CTD of Mononegavirales forms a clamp to accommodate RNA that is subsequently methylated on the cap structure and depending on the virus, on internal positions. These enzymatic activities are essential for efficient viral mRNA translation into proteins, and to prevent the recognition of uncapped viral RNA by innate immunity sensors. In this work, we demonstrated that the MTase-CTD of RSV, as well as the full-length L protein in complex with phosphoprotein (P), catalyzes the N7- and 2’-O-methylation of the cap structure of a short RNA sequence that corresponds to the 5’ end of viral mRNA. Using different experimental systems, we showed that the RSV MTase-CTD methylates the cap structure with a preference for N7-methylation as first reaction. However, we did not observe cap-independent internal methylation, as recently evidenced for the Ebola virus MTase. We also found that at μM concentrations, sinefungin, a S-adenosylmethionine analogue, inhibits the MTase activity of the RSV L protein and of the MTase-CTD domain. Altogether, these results suggest that the RSV MTase domain specifically recognizes viral RNA decorated by a cap structure and catalyzes its methylation, which is required for translation and innate immune system subversion. Respiratory syncytial virus (RSV) is responsible of infant bronchiolitis and severe lower respiratory tract infections in infants and young children, and the leading cause of hospitalization in children under one year of age. However, we still lack a vaccine and therapeutics against this important pathogen. The main enzymatic activities involved in RSV propagation are embedded in the Large (L) protein that contains the polymerase domain and also all the activities required for RNA cap structure synthesis and methylation. These post-transcriptional RNA modifications play a key role in virus replication because cap N7-methylation is required for viral RNA translation into proteins, and 2’-O-methylation hides viral RNA from innate immunity detection. Viral methyltransferase (MTase) activities are now considered potential antiviral targets because their inhibition might limit the virus production and strengthen early virus detection by innate immunity sensors. In this work, we compared the enzymatic activities of the MTase expressed as a single domain or in the context of the full-length L protein. We demonstrated that the MTase protein catalyzes the specific methylation of the cap structure at both N7- and 2’-O-positions, and we obtained the proof of concept that a S-adenosylmethionine analogue can inhibit the MTase activity of the L protein.
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Affiliation(s)
| | - Sergey Tcherniuk
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, Jouy en Josas, France
| | - Nina Ysebaert
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | | | - Mathieu Noël
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | - Alice Decombe
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Françoise Debart
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Bruno Canard
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Dirk Roymans
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, Jouy en Josas, France
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
- * E-mail:
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17
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Song W, Zhang H, Zhang Y, Chen Y, Lin Y, Han Y, Jiang J. Identification and Characterization of Zika Virus NS5 Methyltransferase Inhibitors. Front Cell Infect Microbiol 2021; 11:665379. [PMID: 33898335 PMCID: PMC8058401 DOI: 10.3389/fcimb.2021.665379] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/19/2021] [Indexed: 01/19/2023] Open
Abstract
The recurring outbreak of Zika virus (ZIKV) worldwide makes an emergent demand for novel, safe and efficacious anti-ZIKV agents. ZIKV non-structural protein 5 (NS5) methyltransferase (MTase), which is essential for viral replication, is regarded as a potential drug target. In our study, a luminescence-based methyltransferase assay was used to establish the ZIKV NS5 MTase inhibitor screening model. Through screening a natural product library, we found theaflavin, a polyphenol derived from tea, could inhibit ZIKV NS5 MTase activity with a 50% inhibitory concentration (IC50) of 10.10 μM. Molecular docking and site-directed mutagenesis analyses identified D146 as the key amino acid in the interaction between ZIKV NS5 MTase and theaflavin. The SPR assay indicated that theaflavin had a stronger binding activity with ZIKV NS5 wild-type (WT)-MTase than it with D146A-MTase. Moreover, theaflavin exhibited a dose dependent inhibitory effect on ZIKV replication with a 50% effective concentration (EC50) of 8.19 μM. All these results indicate that theaflavin is likely to be a promising lead compound against ZIKV.
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Affiliation(s)
- Weibao Song
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongjuan Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Chen
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanxing Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiandong Jiang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Maddipati VC, Mittal L, Mantipally M, Asthana S, Bhattacharyya S, Gundla R. A Review on the Progress and Prospects of Dengue Drug Discovery Targeting NS5 RNA- Dependent RNA Polymerase. Curr Pharm Des 2021; 26:4386-4409. [PMID: 32445444 DOI: 10.2174/1381612826666200523174753] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/15/2020] [Indexed: 02/08/2023]
Abstract
Dengue virus (DENV) infection threatens the health and wellbeing of almost 100 million people in the world. Vectored by mosquitoes, DENV may cause a severe disease in human hosts called Dengue hemorrhagic fever (DHF)/Dengue shock syndrome (DSS), which is not preventable by any known drug. In the absence of a universally-accepted vaccine, a drug capable of inhibiting DENV multiplication is an urgent and unmet clinical need. Here we summarize inhibitory strategies by targeting either host biochemical pathways or virus-encoded proteins. A variety of approaches have been generated to design Directly-acting anti-virals or DAAs targeting different DENV proteins, with diverse success. Among them, DAAs targeting genome replicating viral enzymes have proven effective against many viruses including, Human Immuno-deficiency Virus and Hepatitis C Virus. DAAs may be derived either from existing compound libraries of novel molecules and plant secondary metabolites or devised through Computer-aided Drug design (CADD) methods. Here, we focus on compounds with reported DAA-activity against the DENV RNA-dependent RNA polymerase (RdRp), which replicate the viral RNA genome. The structure-activity relationship (SAR) and toxicity of the natural compounds, including secondary plant metabolites, have been discussed in detail. We have also tabulated novel compounds with known anti-RdRp activity. We concluded with a list of DAAs for which a co-crystal structure with RdRp is reported. Promising hit compounds are often discarded due to poor selectivity or unsuitable pharmacokinetics. We hope this review will provide a useful reference for further studies on the development of an anti-DENV drug.
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Affiliation(s)
- Venkatanarayana C Maddipati
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Manohar Mantipally
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
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Ruggieri A, Helm M, Chatel-Chaix L. An epigenetic 'extreme makeover': the methylation of flaviviral RNA (and beyond). RNA Biol 2021; 18:696-708. [PMID: 33356825 DOI: 10.1080/15476286.2020.1868150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Beyond their high clinical relevance worldwide, flaviviruses (comprising dengue and Zika viruses) are of particular interest to understand the spatiotemporal control of RNA metabolism. Indeed, their positive single-stranded viral RNA genome (vRNA) undergoes in the cytoplasm replication, translation and encapsidation, three steps of the flavivirus life cycle that are coordinated through a fine-tuned equilibrium. Over the last years, RNA methylation has emerged as a powerful mechanism to regulate messenger RNA metabolism at the posttranscriptional level. Not surprisingly, flaviviruses exploit RNA epigenetic strategies to control crucial steps of their replication cycle as well as to evade sensing by the innate immune system. This review summarizes the current knowledge about vRNA methylation events and their impacts on flavivirus replication and pathogenesis. We also address the important challenges that the field of epitranscriptomics faces in reliably and accurately identifying RNA methylation sites, which should be considered in future studies on viral RNA modifications.
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Affiliation(s)
- Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Centre for Integrative Infectious Disease Research University of Heidelberg, Heidelberg, Germany
| | - Mark Helm
- Johannes Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Mainz, Germany
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
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20
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Two RNA Tunnel Inhibitors Bind in Highly Conserved Sites in Dengue Virus NS5 Polymerase: Structural and Functional Studies. J Virol 2020; 94:JVI.01130-20. [PMID: 32907977 DOI: 10.1128/jvi.01130-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/29/2020] [Indexed: 11/20/2022] Open
Abstract
Dengue virus (DENV) NS5 RNA-dependent RNA polymerase (RdRp), an important drug target, synthesizes viral RNA and is essential for viral replication. While a number of allosteric inhibitors have been reported for hepatitis C virus RdRp, few have been described for DENV RdRp. Following a diverse compound screening campaign and a rigorous hit-to-lead flowchart combining biochemical and biophysical approaches, two DENV RdRp nonnucleoside inhibitors were identified and characterized. These inhibitors show low- to high-micromolar inhibition in DENV RNA polymerization and cell-based assays. X-ray crystallography reveals that they bind in the enzyme RNA template tunnel. One compound (NITD-434) induced an allosteric pocket at the junction of the fingers and palm subdomains by displacing residue V603 in motif B. Binding of another compound (NITD-640) ordered the fingers loop preceding the F motif, close to the RNA template entrance. Most of the amino acid residues that interacted with these compounds are highly conserved in flaviviruses. Both sites are important for polymerase de novo initiation and elongation activities and essential for viral replication. This work provides evidence that the RNA tunnel in DENV RdRp offers interesting target sites for inhibition.IMPORTANCE Dengue virus (DENV), an important arthropod-transmitted human pathogen that causes a spectrum of diseases, has spread dramatically worldwide in recent years. Despite extensive efforts, the only commercial vaccine does not provide adequate protection to naive individuals. DENV NS5 polymerase is a promising drug target, as exemplified by the development of successful commercial drugs against hepatitis C virus (HCV) polymerase and HIV-1 reverse transcriptase. High-throughput screening of compound libraries against this enzyme enabled the discovery of inhibitors that induced binding sites in the RNA template channel. Characterizations by biochemical, biophysical, and reverse genetics approaches provide a better understanding of the biological relevance of these allosteric sites and the way forward to design more-potent inhibitors.
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21
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Felicetti T, Manfroni G, Cecchetti V, Cannalire R. Broad-Spectrum Flavivirus Inhibitors: a Medicinal Chemistry Point of View. ChemMedChem 2020; 15:2391-2419. [PMID: 32961008 DOI: 10.1002/cmdc.202000464] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/16/2020] [Indexed: 12/16/2022]
Abstract
Infections by flaviviruses, such as Dengue, West Nile, Yellow Fever and Zika viruses, represent a growing risk for global health. There are vaccines only for few flaviviruses while no effective treatments are available. Flaviviruses share epidemiological, structural, and ecologic features and often different viruses can co-infect the same host. Therefore, the identification of broad-spectrum inhibitors is highly desirable either for known flaviviruses or for viruses that likely will emerge in the future. Strategies targeting both virus and host factors have been pursued to identify broad-spectrum antiflaviviral agents. In this review, we describe the most promising and best characterized targets and their relative broad-spectrum inhibitors, identified by drug repurposing/libraries screenings and by focused medicinal chemistry campaigns. Finally, we discuss about future strategies to identify new broad-spectrum antiflavivirus agents.
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Affiliation(s)
- Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123, Perugia, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Napoli "Federico II", via D. Montesano 49, 80131, Napoli, Italy
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22
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Kasprzyk R, Fido M, Mamot A, Wanat P, Smietanski M, Kopcial M, Cowling VH, Kowalska J, Jemielity J. Direct High-Throughput Screening Assay for mRNA Cap Guanine-N7 Methyltransferase Activity. Chemistry 2020; 26:11266-11275. [PMID: 32259329 PMCID: PMC7262028 DOI: 10.1002/chem.202001036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Indexed: 12/16/2022]
Abstract
In eukaryotes, mature mRNA is formed through modifications of precursor mRNA, one of which is 5' cap biosynthesis, involving RNA cap guanine-N7 methyltransferase (N7-MTase). N7-MTases are also encoded by some eukaryotic viruses and facilitate their replication. N7-MTase inhibitors have therapeutic potential, but their discovery is difficult because long RNA substrates are usually required for activity. Herein, we report a universal N7-MTase activity assay based on small-molecule fluorescent probes. We synthesized 12 fluorescent substrate analogues (GpppA and GpppG derivatives) varying in the dye type, dye attachment site, and linker length. GpppA labeled with pyrene at the 3'-O position of adenosine acted as an artificial substrate with the properties of a turn-off probe for all three tested N7-MTases (human, parasite, and viral). Using this compound, a N7-MTase inhibitor assay adaptable to high-throughput screening was developed and used to screen synthetic substrate analogues and a commercial library. Several inhibitors with nanomolar activities were identified.
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Affiliation(s)
- Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
| | - Mateusz Fido
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02093, Warsaw, Poland
| | - Adam Mamot
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02093, Warsaw, Poland
| | - Przemyslaw Wanat
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02093, Warsaw, Poland
| | - Miroslaw Smietanski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
| | - Michal Kopcial
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
| | - Victoria H Cowling
- Centre of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH, Dundee, UK
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
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23
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Porcine Epidemic Diarrhea Virus Deficient in RNA Cap Guanine-N-7 Methylation Is Attenuated and Induces Higher Type I and III Interferon Responses. J Virol 2020; 94:JVI.00447-20. [PMID: 32461321 DOI: 10.1128/jvi.00447-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/16/2020] [Indexed: 12/23/2022] Open
Abstract
The 5' cap methylation of viral RNA plays important roles in RNA stability, efficient translation, and immune evasion. Thus, RNA cap methylation is an attractive target for antiviral discovery and development of new live attenuated vaccines. For coronaviruses, RNA cap structure is first methylated at the guanine-N-7 (G-N-7) position by nonstructural protein 14 (nsp14), which facilitates and precedes the subsequent ribose 2'-O methylation by the nsp16-nsp10 complex. Using porcine epidemic diarrhea virus (PEDV), an Alphacoronavirus, as a model, we showed that G-N-7 methyltransferase (G-N-7 MTase) of PEDV nsp14 methylated RNA substrates in a sequence-unspecific manner. PEDV nsp14 can efficiently methylate RNA substrates with various lengths in both neutral and alkaline pH environments and can methylate cap analogs (GpppA and GpppG) and single-nucleotide GTP but not ATP, CTP, or UTP. Mutations to the S-adenosyl-l-methionine (SAM) binding motif in the nsp14 abolished the G-N-7 MTase activity and were lethal to PEDV. However, recombinant rPEDV-D350A with a single mutation (D350A) in nsp14, which retained 29.0% of G-N-7 MTase activity, was viable. Recombinant rPEDV-D350A formed a significantly smaller plaque and had significant defects in viral protein synthesis and viral replication in Vero CCL-81 cells and intestinal porcine epithelial cells (IPEC-DQ). Notably, rPEDV-D350A induced significantly higher expression of both type I and III interferons in IPEC-DQ cells than the parental rPEDV. Collectively, our results demonstrate that G-N-7 MTase activity of PEDV modulates viral replication, gene expression, and innate immune responses.IMPORTANCE Coronaviruses (CoVs) include a wide range of important human and animal pathogens. Examples of human CoVs include severe acute respiratory syndrome coronavirus (SARS-CoV-1), Middle East respiratory syndrome coronavirus (MERS-CoV), and the most recently emerged SARS-CoV-2. Examples of pig CoVs include porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and swine enteric alphacoronavirus (SeACoV). There are no vaccines or antiviral drugs for most of these viruses. All known CoVs encode a bifunctional nsp14 protein which possesses ExoN and guanine-N-7 methyltransferase (G-N-7 MTase) activities, responsible for replication fidelity and RNA cap G-N-7 methylation, respectively. Here, we biochemically characterized G-N-7 MTase of PEDV nsp14 and found that G-N-7 MTase-deficient PEDV was defective in replication and induced greater responses of type I and III interferons. These findings highlight that CoV G-N-7 MTase may be a novel target for rational design of live attenuated vaccines and antiviral drugs.
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24
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Wu J, Chi H, Fu Y, Cao A, Shi J, Zhu M, Zhang L, Hua D, Huang J. The antiviral protein viperin interacts with the viral N protein to inhibit proliferation of porcine epidemic diarrhea virus. Arch Virol 2020; 165:2279-2289. [PMID: 32719955 PMCID: PMC7382991 DOI: 10.1007/s00705-020-04747-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/22/2020] [Indexed: 12/15/2022]
Abstract
In the early stage of virus infection, the pattern recognition receptor (PRR) signaling pathway of the host cell is activated to induce interferon production, activating interferon-stimulated genes (ISGs) that encode antiviral proteins that exert antiviral effects. Viperin is one of the innate antiviral proteins that exert broad-spectrum antiviral effects by various mechanisms. Porcine epidemic diarrhea virus (PEDV) is a coronavirus that causes huge losses to the pig industry. Research on early antiviral responses in the gastrointestinal tract is essential for developing strategies to prevent the spread of PEDV. In this study, we investigated the mechanisms of viperin in PEDV-infected IPEJ-C2 cells. Increased expression of interferon and viperin and decreased replication of PEDV with a clear reduction in the viral load were observed in PEDV-infected IPEC-J2 cells. Amino acids 1-50 of porcine viperin contain an endoplasmic reticulum signal sequence that allows viperin to be anchored to the endoplasmic reticulum and are necessary for its function in inhibiting PEDV proliferation. The interaction of the viperin S-adenosylmethionine domain with the N protein of PEDV was confirmed via confocal laser scanning microscopy and co-immunoprecipitation. This interaction might interfere with viral replication or assembly to reduce virus proliferation. Our results highlight a potential mechanism whereby viperin is able to inhibit PEDV replication and play an antiviral role in innate immunity.
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Affiliation(s)
- Jiaqi Wu
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Heng Chi
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Yali Fu
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Aiping Cao
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Jingxuan Shi
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Min Zhu
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Deping Hua
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, China.
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25
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NS5 from Dengue Virus Serotype 2 Can Adopt a Conformation Analogous to That of Its Zika Virus and Japanese Encephalitis Virus Homologues. J Virol 2019; 94:JVI.01294-19. [PMID: 31597763 DOI: 10.1128/jvi.01294-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/30/2019] [Indexed: 01/07/2023] Open
Abstract
Flavivirus nonstructural protein 5 (NS5) contains an N-terminal methyltransferase (MTase) domain and a C-terminal polymerase (RNA-dependent RNA polymerase [RdRp]) domain fused through a 9-amino-acid linker. While the individual NS5 domains are structurally conserved, in the full-length protein, their relative orientations fall into two classes: the NS5 proteins from Japanese encephalitis virus (JEV) and Zika virus (ZIKV) adopt one conformation, while the NS5 protein from dengue virus serotype 3 (DENV3) adopts another. Here, we report a crystallographic structure of NS5 from DENV2 in a conformation similar to the extended one seen in JEV and ZIKV NS5 crystal structures. Replacement of the DENV2 NS5 linker with DENV1, DENV3, DENV4, JEV, and ZIKV NS5 linkers had modest or minimal effects on in vitro DENV2 MTase and RdRp activities. Heterotypic DENV NS5 linkers attenuated DENV2 replicon growth in cells, while the JEV and ZIKV NS5 linkers abolished replication. Thus, the JEV and ZIKV linkers likely hindered essential DENV2 NS5 interactions with other viral or host proteins within the virus replicative complex. Overall, this work sheds light on the dynamics of the multifunctional flavivirus NS5 protein and its interdomain linker. Targeting the NS5 linker is a possible strategy for producing attenuated flavivirus strains for vaccine design.IMPORTANCE Flaviviruses include important human pathogens, such as dengue virus and Zika virus. NS5 is a nonstructural protein essential for flavivirus RNA replication with dual MTase and RdRp enzyme activities and thus constitutes a major drug target. Insights into NS5 structure, dynamics, and evolution should inform the development of antiviral inhibitors and vaccine design. We found that NS5 from DENV2 can adopt a conformation resembling that of NS5 from JEV and ZIKV. Replacement of the DENV2 NS5 linker with the JEV and ZIKV NS5 linkers abolished DENV2 replication in cells, without significantly impacting in vitro DENV2 NS5 enzymatic activities. We propose that heterotypic flavivirus NS5 linkers impede DENV2 NS5 protein-protein interactions that are essential for virus replication.
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26
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Saw WG, Chan KWK, Vasudevan SG, Grüber G. Zika virus nonstructural protein 5 residue R681 is critical for dimer formation and enzymatic activity. FEBS Lett 2019; 593:1272-1291. [PMID: 31090058 DOI: 10.1002/1873-3468.13437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 11/07/2022]
Abstract
Zika virus (ZIKV) relies on its nonstructural protein 5 (NS5) for capping and synthesis of the viral RNA. Recent small-angle X-ray scattering (SAXS) data of recombinant ZIKV NS5 protein showed that it is dimeric in solution. Here, we present insights into the critical residues responsible for its dimer formation. SAXS studies of the engineered ZIKV NS5 mutants revealed that R681A mutation on NS5 (NS5R681A ) disrupts the dimer formation and affects its RNA-dependent RNA polymerase activity as well as the subcellular localization of NS5R681A in mammalian cells. The critical residues involved in the dimer arrangement of ZIKV NS5 are discussed, and the data provide further insights into the diversity of flaviviral NS5 proteins in terms of their propensity for oligomerization.
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Affiliation(s)
- Wuan-Geok Saw
- Nanyang Technological University, School of Biological Sciences, Singapore
| | - Kitti Wing-Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, Singapore
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27
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Brisse ME, Ly H. Hemorrhagic Fever-Causing Arenaviruses: Lethal Pathogens and Potent Immune Suppressors. Front Immunol 2019; 10:372. [PMID: 30918506 PMCID: PMC6424867 DOI: 10.3389/fimmu.2019.00372] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/14/2019] [Indexed: 12/22/2022] Open
Abstract
Hemorrhagic fevers (HF) resulting from pathogenic arenaviral infections have traditionally been neglected as tropical diseases primarily affecting African and South American regions. There are currently no FDA-approved vaccines for arenaviruses, and treatments have been limited to supportive therapy and use of non-specific nucleoside analogs, such as Ribavirin. Outbreaks of arenaviral infections have been limited to certain geographic areas that are endemic but known cases of exportation of arenaviruses from endemic regions and socioeconomic challenges for local control of rodent reservoirs raise serious concerns about the potential for larger outbreaks in the future. This review synthesizes current knowledge about arenaviral evolution, ecology, transmission patterns, life cycle, modulation of host immunity, disease pathogenesis, as well as discusses recent development of preventative and therapeutic pursuits against this group of deadly viral pathogens.
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Affiliation(s)
- Morgan E Brisse
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, St. Paul, MN, United States.,Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, United States
| | - Hinh Ly
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, United States
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28
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Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories. Proc Natl Acad Sci U S A 2018; 115:E12015-E12023. [PMID: 30509975 DOI: 10.1073/pnas.1717944115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The rotavirus (RV) genome is replicated and packaged into virus progeny in cytoplasmic inclusions called viroplasms, which require interactions between RV nonstructural proteins NSP2 and NSP5. How viroplasms form remains unknown. We previously found two forms of NSP2 in RV-infected cells: a cytoplasmically dispersed dNSP2, which interacts with hypophosphorylated NSP5; and a viroplasm-specific vNSP2, which interacts with hyperphosphorylated NSP5. Other studies report that CK1α, a ubiquitous cellular kinase, hyperphosphorylates NSP5, but requires NSP2 for reasons that are unclear. Here we show that silencing CK1α in cells before RV infection resulted in (i) >90% decrease in RV replication, (ii) disrupted vNSP2 and NSP5 interaction, (iii) dispersion of vNSP2 throughout the cytoplasm, and (iv) reduced vNSP2 protein levels. Together, these data indicate that CK1α directly affects NSP2. Accordingly, an in vitro kinase assay showed that CK1α phosphorylates serine 313 of NSP2 and triggers NSP2 octamers to form a lattice structure as demonstrated by crystallographic analysis. Additionally, a dual-specificity autokinase activity for NSP2 was identified and confirmed by mass spectrometry. Together, our studies show that phosphorylation of NSP2 involving CK1α controls viroplasm assembly. Considering that CK1α plays a role in the replication of other RNA viruses, similar phosphorylation-dependent mechanisms may exist for other virus pathogens that require cytoplasmic virus factories for replication.
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29
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Abstract
West Nile virus (WNV) is an arbovirus with increased global incidence in the last decade. It is also a major cause of human encephalitis in the USA. WNV is an arthropod-transmitted virus that mainly affects birds but humans become infected as incidental dead-end hosts which can cause outbreaks in naïve populations. The main vectors of WNV are mosquitoes of the genus Culex, which preferentially feed on birds. As in many other arboviruses, the characteristics that allow Flaviviruses like WNV to replicate and transmit to different hosts are encrypted in their genome, which also contains information for the production of structural and nonstructural proteins needed for host cell infection. WNV and other Flaviviruses have developed different strategies to establish infection, replication, and successful transmission. Most of these strategies include the diversion of the host's immune responses away from the virus. In this review, we describe the molecular structure and protein function of WNV with emphasis on protein involvement in the modulation of antiviral immune responses.
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30
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Chatrin C, Talapatra SK, Canard B, Kozielski F. The structure of the binary methyltransferase-SAH complex from Zika virus reveals a novel conformation for the mechanism of mRNA capping. Oncotarget 2017; 9:3160-3171. [PMID: 29423037 PMCID: PMC5790454 DOI: 10.18632/oncotarget.23223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/15/2017] [Indexed: 11/25/2022] Open
Abstract
Zika virus, a flavivirus like Dengue and West Nile viruses, poses a significant risk as a pathogen in the category of emerging infectious diseases. Zika infections typically cause nonspecific, mild symptoms, but can also manifest as a neurological disorder like Guillain-Barré syndrome. Infection in pregnant women is linked to microcephaly in newborn infants. The methyltransferase domain of the non-structural protein 5 is responsible for two sequential methylations of the 5′-RNA cap. This is crucial for genome stability, efficient translation, and escape from the host immune response. Here we present the crystal structures of the Zika methyltransferase domain in complex with the methyl-donor SAM and its by-product SAH. The methyltransferase-SAH binary complex presents a new conformation of a “closed” or “obstructed” state that would restrict the binding of new RNA for capping. The combination and comparison of our new structures with recently published Zika methyltransferase structures provide a first glimpse into the structural mechanism of Zika virus mRNA capping.
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Affiliation(s)
- Chatrin Chatrin
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, WC1N 1AX, London, United Kingdom
| | - Sandeep K Talapatra
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, WC1N 1AX, London, United Kingdom
| | - Bruno Canard
- CNRS, Aix Marseille University, AFMB UMR7257, Marseille, France
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, WC1N 1AX, London, United Kingdom
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31
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Boldescu V, Behnam MAM, Vasilakis N, Klein CD. Broad-spectrum agents for flaviviral infections: dengue, Zika and beyond. Nat Rev Drug Discov 2017; 16:565-586. [PMID: 28473729 PMCID: PMC5925760 DOI: 10.1038/nrd.2017.33] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Infections with flaviviruses, such as dengue, West Nile virus and the recently re-emerging Zika virus, are an increasing and probably lasting global risk. This Review summarizes and comments on the opportunities for broad-spectrum agents that are active against multiple flaviviruses. Broad-spectrum activity is particularly desirable to prepare for the next flaviviral epidemic, which could emerge from as-yet unknown or neglected viruses. Potential molecular targets for broad-spectrum antiflaviviral compounds include viral proteins, such as the viral protease or polymerase, and host targets that are exploited by these viruses during entry and replication, including α-glucosidase and proteins involved in nucleoside biosynthesis. Numerous compounds with broad-spectrum antiviral activity have already been identified by target-specific or phenotypic assays. For other compounds, broad-spectrum activity can be anticipated because of their mode of action and molecular targets.
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Affiliation(s)
- Veaceslav Boldescu
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry of the Academy of Sciences of Moldova, Academiei 3, 2028 Chisinau, Moldova
| | - Mira A. M. Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nikos Vasilakis
- Dept. of Pathology and Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases and Institute for Human Infections and Immunity, 2.138D Keiller Bldg, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555–0609, USA
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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32
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El Sahili A, Lescar J. Dengue Virus Non-Structural Protein 5. Viruses 2017; 9:E91. [PMID: 28441781 PMCID: PMC5408697 DOI: 10.3390/v9040091] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/15/2017] [Accepted: 04/20/2017] [Indexed: 12/17/2022] Open
Abstract
The World Health Organization estimates that the yearly number of dengue cases averages 390 million. This mosquito-borne virus disease is endemic in over 100 countries and will probably continue spreading, given the observed trend in global warming. So far, there is no antiviral drug available against dengue, but a vaccine has been recently marketed. Dengue virus also serves as a prototype for the study of other pathogenic flaviviruses that are emerging, like West Nile virus and Zika virus. Upon viral entry into the host cell and fusion of the viral lipid membrane with the endosomal membrane, the viral RNA is released and expressed as a polyprotein, that is then matured into three structural and seven non-structural (NS) proteins. The envelope, membrane and capsid proteins form the viral particle while NS1-NS2A-NS2B-NS3-NS4A-NS4B and NS5 assemble inside a cellular replication complex, which is embedded in endoplasmic reticulum (ER)-derived vesicles. In addition to their roles in RNA replication within the infected cell, NS proteins help the virus escape the host innate immunity and reshape the host-cell inner structure. This review focuses on recent progress in characterizing the structure and functions of NS5, a protein responsible for the replication and capping of viral RNA that represents a promising drug target.
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Affiliation(s)
- Abbas El Sahili
- School of Biological Sciences, Nanyang Technological University, Nanyang Institute for Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore.
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Nanyang Institute for Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921, Singapore.
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33
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da Fonseca NJ, Lima Afonso MQ, Pedersolli NG, de Oliveira LC, Andrade DS, Bleicher L. Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains. Biochem Biophys Res Commun 2017; 492:565-571. [PMID: 28087275 DOI: 10.1016/j.bbrc.2017.01.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
Abstract
Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets. This study provides a complete conservation and coevolution analysis on all flaviviruses non-structural proteins, with results mapped on all well-annotated available sequences. A literature review on the residues found in the analysis enabled us to compile available information on their roles and distribution among different flaviviruses. Also, we provide the mapping of conserved and coevolved residues for all sequences currently in SwissProt as a supplementary material, so that particularities in different viruses can be easily analyzed.
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Affiliation(s)
- Néli José da Fonseca
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Marcelo Querino Lima Afonso
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Natan Gonçalves Pedersolli
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Lucas Carrijo de Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Dhiego Souto Andrade
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
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34
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Urbonavičius J, Rutkienė R, Lopato A, Tauraitė D, Stankevičiūtė J, Aučynaitė A, Kaliniene L, van Tilbeurgh H, Meškys R. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. RNA (NEW YORK, N.Y.) 2016; 22:1871-1883. [PMID: 27852927 PMCID: PMC5113207 DOI: 10.1261/rna.057059.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G; and C7-methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity. We also show that substitutions of individual conservative amino acids of P. abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37. We further demonstrate that aTrm5a-type enzyme SSO2439 from Sulfolobus solfataricus, which has no N1-methyltransferase activity, exhibits C7-methyltransferase activity, thereby producing imG2 from imG-14. We thus suggest renaming such aTrm5a methyltransferases as Taw21 to distinguish between monofunctional and bifunctional aTrm5a enzymes.
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Affiliation(s)
- Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius 10223, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Anželika Lopato
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius 10223, Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Jonita Stankevičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Herman van Tilbeurgh
- Institut de Biologie Intégrative de la Cellule, I2BC, CNRS Université Paris-Sud UMR9198, Orsay, France
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
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Lim SP, Noble CG, Seh CC, Soh TS, El Sahili A, Chan GKY, Lescar J, Arora R, Benson T, Nilar S, Manjunatha U, Wan KF, Dong H, Xie X, Shi PY, Yokokawa F. Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling. PLoS Pathog 2016; 12:e1005737. [PMID: 27500641 PMCID: PMC4976923 DOI: 10.1371/journal.ppat.1005737] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/09/2016] [Indexed: 11/24/2022] Open
Abstract
Flaviviruses comprise major emerging pathogens such as dengue virus (DENV) or Zika virus (ZIKV). The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase (RdRp) domain of non-structural protein 5 (NS5). This essential enzymatic activity renders the RdRp attractive for antiviral therapy. NS5 synthesizes viral RNA via a “de novo” initiation mechanism. Crystal structures of the flavivirus RdRp revealed a “closed” conformation reminiscent of a pre-initiation state, with a well ordered priming loop that extrudes from the thumb subdomain into the dsRNA exit tunnel, close to the “GDD” active site. To-date, no allosteric pockets have been identified for the RdRp, and compound screening campaigns did not yield suitable drug candidates. Using fragment-based screening via X-ray crystallography, we found a fragment that bound to a pocket of the apo-DENV RdRp close to its active site (termed “N pocket”). Structure-guided improvements yielded DENV pan-serotype inhibitors of the RdRp de novo initiation activity with nano-molar potency that also impeded elongation activity at micro-molar concentrations. Inhibitors exhibited mixed inhibition kinetics with respect to competition with the RNA or GTP substrate. The best compounds have EC50 values of 1–2 μM against all four DENV serotypes in cell culture assays. Genome-sequencing of compound-resistant DENV replicons, identified amino acid changes that mapped to the N pocket. Since inhibitors bind at the thumb/palm interface of the RdRp, this class of compounds is proposed to hinder RdRp conformational changes during its transition from initiation to elongation. This is the first report of a class of pan-serotype and cell-active DENV RdRp inhibitors. Given the evolutionary conservation of residues lining the N pocket, these molecules offer insights to treat other serious conditions caused by flaviviruses. Dengue virus (DENV) is the world’s most prevalent mosquito-borne viral disease and nearly 40% of the world’s population is at risk of infection. Currently, no specific drugs are available to treat dengue or other flaviviral diseases. DENV NS5 is a large protein of 900 amino acids composed of two domains with key enzymatic activities for viral RNA replication in the host cell and constitutes a prime target for the design of anti-viral inhibitors. We performed a fragment-based screening by X-ray crystallography targeting the DENV NS5 polymerase and identified an allosteric binding pocket at the base of the thumb subdomain close to the enzyme active site. Potent inhibitors active in both DENV polymerase biochemical and cell-based assays were developed through structure-guided design. Resistant virus replicons grown in the presence of the inhibitor, harbored amino acid changes that mapped to the compound binding site. The proposed mode of action for this class of inhibitors is by impeding RdRp protein conformational changes during the transition from initiation to elongation phase of enzyme activity.
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Affiliation(s)
| | | | | | - Tingjin Sherryl Soh
- Novartis Institute for Tropical Diseases, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore.,UPMC UMRS CR7-CNRS ERL 8255-INSERM U1135 Centre d'Immunologie et des Maladies Infectieuses, Centre Hospitalier Universitaire Pitié-Salpêtrière, Faculté de Médecine Pierre et Marie Curie, Paris, France
| | - Rishi Arora
- Novartis Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Timothy Benson
- Novartis Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Shahul Nilar
- Novartis Institute for Tropical Diseases, Singapore
| | | | - Kah Fei Wan
- Novartis Institute for Tropical Diseases, Singapore
| | | | - Xuping Xie
- Novartis Institute for Tropical Diseases, Singapore
| | - Pei-Yong Shi
- Novartis Institute for Tropical Diseases, Singapore
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Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 456] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
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Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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Molecular basis for specific viral RNA recognition and 2'-O-ribose methylation by the dengue virus nonstructural protein 5 (NS5). Proc Natl Acad Sci U S A 2015; 112:14834-9. [PMID: 26578813 DOI: 10.1073/pnas.1514978112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Dengue virus (DENV) causes several hundred million human infections and more than 20,000 deaths annually. Neither an efficacious vaccine conferring immunity against all four circulating serotypes nor specific drugs are currently available to treat this emerging global disease. Capping of the DENV RNA genome is an essential structural modification that protects the RNA from degradation by 5' exoribonucleases, ensures efficient expression of viral proteins, and allows escape from the host innate immune response. The large flavivirus nonstructural protein 5 (NS5) (105 kDa) has RNA methyltransferase activities at its N-terminal region, which is responsible for capping the virus RNA genome. The methyl transfer reactions are thought to occur sequentially using the strictly conserved flavivirus 5' RNA sequence as substrate (GpppAG-RNA), leading to the formation of the 5' RNA cap: G0pppAG-RNA → (m7)G0pppAG-RNA ("cap-0")→(m7)G0pppAm2'-O-G-RNA ("cap-1"). To elucidate how viral RNA is specifically recognized and methylated, we determined the crystal structure of a ternary complex between the full-length NS5 protein from dengue virus, an octameric cap-0 viral RNA substrate bearing the authentic DENV genomic sequence (5'-(m7)G0pppA1G2U3U4G5U6U7-3'), and S-adenosyl-l-homocysteine (SAH), the by-product of the methylation reaction. The structure provides for the first time, to our knowledge, a molecular basis for specific adenosine 2'-O-methylation, rationalizes mutagenesis studies targeting the K61-D146-K180-E216 enzymatic tetrad as well as residues lining the RNA binding groove, and offers previously unidentified mechanistic and evolutionary insights into cap-1 formation by NS5, which underlies innate immunity evasion by flaviviruses.
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Brecher M, Chen H, Li Z, Banavali NK, Jones SA, Zhang J, Kramer LD, Li H. Identification and Characterization of Novel Broad-Spectrum Inhibitors of the Flavivirus Methyltransferase. ACS Infect Dis 2015; 1:340-9. [PMID: 26726314 DOI: 10.1021/acsinfecdis.5b00070] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Flavivirus methyltransferase (MTase) is essential for viral replication. Here we report the identification of small molecules through virtual screening that putatively bind to the SAM-binding site of flavivirus MTase and inhibit its function. Six of these computationally predicted binders were identified to show significant MTase inhibition with low micromolar inhibitory activity. The most active compounds showed broad-spectrum activity against the MTase proteins of other flaviviruses. Two of these compounds also showed low cytotoxicity and high antiviral efficacy in cell-based assays. Competitive binding analyses indicated that the inhibitors performed their inhibitory function through competitive binding to the SAM cofactor binding site of the MTase. The crystal structure of the MTase-inhibitor complex further supports the mode of action and provides routes for their further optimization as flavivirus MTase inhibitors.
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Affiliation(s)
- Matthew Brecher
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Hui Chen
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Nilesh K. Banavali
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
- Department of Biomedical Sciences, School of Public Health, State University of New York, P.O. Box 509, Albany, New York 12201 United States
| | - Susan A. Jones
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Jing Zhang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Laura D. Kramer
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
- Department of Biomedical Sciences, School of Public Health, State University of New York, P.O. Box 509, Albany, New York 12201 United States
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
- Department of Biomedical Sciences, School of Public Health, State University of New York, P.O. Box 509, Albany, New York 12201 United States
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Klema VJ, Padmanabhan R, Choi KH. Flaviviral Replication Complex: Coordination between RNA Synthesis and 5'-RNA Capping. Viruses 2015; 7:4640-56. [PMID: 26287232 PMCID: PMC4576198 DOI: 10.3390/v7082837] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/04/2015] [Indexed: 12/28/2022] Open
Abstract
Genome replication in flavivirus requires (-) strand RNA synthesis, (+) strand RNA synthesis, and 51-RNA capping and methylation. To carry out viral genome replication, flavivirus assembles a replication complex, consisting of both viral and host proteins, on the cytoplasmic side of the endoplasmic reticulum (ER) membrane. Two major components of the replication complex are the viral non-structural (NS) proteins NS3 and NS5. Together they possess all the enzymatic activities required for genome replication, yet how these activities are coordinated during genome replication is not clear. We provide an overview of the flaviviral genome replication process, the membrane-bound replication complex, and recent crystal structures of full-length NS5. We propose a model of how NS3 and NS5 coordinate their activities in the individual steps of (-) RNA synthesis, (+) RNA synthesis, and 51-RNA capping and methylation.
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Affiliation(s)
- Valerie J Klema
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555-0647, USA.
| | - Radhakrishnan Padmanabhan
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, DC 20057, USA.
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX 77555-0647, USA.
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Flexibility of NS5 Methyltransferase-Polymerase Linker Region Is Essential for Dengue Virus Replication. J Virol 2015; 89:10717-21. [PMID: 26269182 DOI: 10.1128/jvi.01239-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/03/2015] [Indexed: 11/20/2022] Open
Abstract
We examined the function of the conserved Val/Ile residue within the dengue virus NS5 interdomain linker (residues 263 to 272) by site-directed mutagenesis. Gly substitution or Gly/Pro insertion after the conserved residue increased the linker flexibility and created slightly attenuated viruses. In contrast, Pro substitution abolished virus replication by imposing rigidity in the linker and restricting NS5's conformational plasticity. Our biochemical and reverse genetics experiments demonstrate that NS5 utilizes conformational regulation to achieve optimum viral replication.
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41
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Lim SP, Noble CG, Shi PY. The dengue virus NS5 protein as a target for drug discovery. Antiviral Res 2015; 119:57-67. [DOI: 10.1016/j.antiviral.2015.04.010] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/19/2015] [Accepted: 04/11/2015] [Indexed: 12/25/2022]
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Brecher M, Chen H, Liu B, Banavali NK, Jones SA, Zhang J, Li Z, Kramer LD, Li H. Novel Broad Spectrum Inhibitors Targeting the Flavivirus Methyltransferase. PLoS One 2015; 10:e0130062. [PMID: 26098995 PMCID: PMC4476580 DOI: 10.1371/journal.pone.0130062] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/15/2015] [Indexed: 01/17/2023] Open
Abstract
The flavivirus methyltransferase (MTase) is an essential enzyme that sequentially methylates the N7 and 2’-O positions of the viral RNA cap, using S-adenosyl-L-methionine (SAM) as a methyl donor. We report here that small molecule compounds, which putatively bind to the SAM-binding site of flavivirus MTase and inhibit its function, were identified by using virtual screening. In vitro methylation experiments demonstrated significant MTase inhibition by 13 of these compounds, with the most potent compound displaying sub-micromolar inhibitory activity. The most active compounds showed broad spectrum activity against the MTase proteins of multiple flaviviruses. Two of these compounds also exhibited low cytotoxicity and effectively inhibited viral replication in cell-based assays, providing further structural insight into flavivirus MTase inhibition.
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Affiliation(s)
- Matthew Brecher
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Hui Chen
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Binbin Liu
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Nilesh K. Banavali
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, PO Box 509, New York, 12201, United States of America
| | - Susan A. Jones
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Jing Zhang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Laura D. Kramer
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, PO Box 509, New York, 12201, United States of America
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, PO Box 509, New York, 12201, United States of America
- * E-mail:
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Bullard KM, Gullberg RC, Soltani E, Steel JJ, Geiss BJ, Keenan SM. Murine Efficacy and Pharmacokinetic Evaluation of the Flaviviral NS5 Capping Enzyme 2-Thioxothiazolidin-4-One Inhibitor BG-323. PLoS One 2015; 10:e0130083. [PMID: 26075394 PMCID: PMC4468182 DOI: 10.1371/journal.pone.0130083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/15/2015] [Indexed: 12/25/2022] Open
Abstract
Arthropod-borne flavivirus infection continues to cause significant morbidity and mortality worldwide. Identification of drug targets and novel antiflaviviral compounds to treat these diseases has become a global health imperative. A previous screen of 235,456 commercially available small molecules identified the 2-thioxothiazolidin-4-one family of compounds as inhibitors of the flaviviral NS5 capping enzyme, a promising target for antiviral drug development. Rational drug design methodologies enabled identification of lead compound BG-323 from this series. We have shown previously that BG-323 potently inhibits NS5 capping enzyme activity, displays antiviral effects in dengue virus replicon assays and inhibits growth of West Nile and yellow fever viruses with low cytotoxicity in vitro. In this study we further characterized BG-323’s antiviral activity in vitro and in vivo. We found that BG-323 was able to reduce replication of WNV (NY99) and Powassan viruses in culture, and we were unable to force resistance into WNV (Kunjin) in long-term culture experiments. We then evaluated the antiviral activity of BG-323 in a murine model. Mice were challenged with WNV NY99 and administered BG-323 or mock by IP inoculation immediately post challenge and twice daily thereafter. Mice were bled and viremia was quantified on day three. No significant differences in viremia were observed between BG-323-treated and control groups and clinical scores indicated both BG-323-treated and control mice developed signs of illness on approximately the same day post challenge. To determine whether differences in in vitro and in vivo efficacy were due to unfavorable pharmacokinetic properties of BG-323, we conducted a pharmacokinetic evaluation of this small molecule. Insights from pharmacokinetic studies indicate that BG-323 is cell permeable, has a low efflux ratio and does not significantly inhibit two common cytochrome P450 (CYP P450) isoforms thus suggesting this molecule may be less likely to cause adverse drug interactions. However, the T1/2 of BG-323 was suboptimal and the percent of drug bound to plasma binding proteins was high. Future studies with BG-323 will be aimed at increasing the T1/2 and determining strategies for mitigating the effects of high plasma protein binding, which likely contribute to low in vivo efficacy.
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Affiliation(s)
- Kristen M. Bullard
- University of Northern Colorado, School of Biological Sciences, Greeley, CO, United States of America
| | - Rebekah C. Gullberg
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Elnaz Soltani
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - J. Jordan Steel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brian J. Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail: (SMK); (BJG)
| | - Susan M. Keenan
- University of Northern Colorado, School of Biological Sciences, Greeley, CO, United States of America
- * E-mail: (SMK); (BJG)
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Zhao Y, Soh TS, Zheng J, Chan KWK, Phoo WW, Lee CC, Tay MYF, Swaminathan K, Cornvik TC, Lim SP, Shi PY, Lescar J, Vasudevan SG, Luo D. A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication. PLoS Pathog 2015; 11:e1004682. [PMID: 25775415 PMCID: PMC4361662 DOI: 10.1371/journal.ppat.1004682] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/12/2015] [Indexed: 01/28/2023] Open
Abstract
Flavivirus RNA replication occurs within a replication complex (RC) that assembles on ER membranes and comprises both non-structural (NS) viral proteins and host cofactors. As the largest protein component within the flavivirus RC, NS5 plays key enzymatic roles through its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent-RNA polymerase (RdRp) domains, and constitutes a major target for antivirals. We determined a crystal structure of the full-length NS5 protein from Dengue virus serotype 3 (DENV3) at a resolution of 2.3 Å in the presence of bound SAH and GTP. Although the overall molecular shape of NS5 from DENV3 resembles that of NS5 from Japanese Encephalitis Virus (JEV), the relative orientation between the MTase and RdRp domains differs between the two structures, providing direct evidence for the existence of a set of discrete stable molecular conformations that may be required for its function. While the inter-domain region is mostly disordered in NS5 from JEV, the NS5 structure from DENV3 reveals a well-ordered linker region comprising a short 310 helix that may act as a swivel. Solution Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) analysis reveals an increased mobility of the thumb subdomain of RdRp in the context of the full length NS5 protein which correlates well with the analysis of the crystallographic temperature factors. Site-directed mutagenesis targeting the mostly polar interface between the MTase and RdRp domains identified several evolutionarily conserved residues that are important for viral replication, suggesting that inter-domain cross-talk in NS5 regulates virus replication. Collectively, a picture for the molecular origin of NS5 flexibility is emerging with profound implications for flavivirus replication and for the development of therapeutics targeting NS5. DENV causes widespread mosquito-borne viral infections worldwide and nearly 40% of the world’s population is at risk of being infected. Currently, no licensed vaccines or specific drugs are available to treat severe infections by DENV. NS5 is a large protein of 900 amino acids composed of two domains with several key enzymatic activities for viral RNA replication in the host cell and constitutes a prime target for the design of antiviral inhibitors. We succeeded in trapping a stable conformation of the full-length NS5 protein and report its crystal structure at a resolution of 2.3 Å. This conformation reveals the entire inter-domain region and clarifies the determinants of NS5 flexibility. The inter-domain interface is stabilized by several polar contacts between residues projecting from the MTase and RdRp domains of NS5. Several evolutionarily conserved residues at the interface play a crucial role for virus replication as shown by reverse genetics, although the analogous mutations mostly do not abolish the in vitro enzymatic activities of the recombinant proteins.
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Affiliation(s)
- Yongqian Zhao
- Program in Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Tingjin Sherryl Soh
- School of Biological Sciences, Nanyang Technological University, Singapore
- Novartis Institute for Tropical Diseases, Singapore
| | - Jie Zheng
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, Singapore
| | - Wint Wint Phoo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Chin Chin Lee
- Program in Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, Singapore
| | - Moon Y. F. Tay
- Program in Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, Singapore
| | - Kunchithapadam Swaminathan
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Tobias C. Cornvik
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Pei-Yong Shi
- Novartis Institute for Tropical Diseases, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore
- UPMC UMRS CR7—CNRS ERL 8255-INSERM U1135 Centre d’Immunologie et des Maladies Infectieuses, Centre Hospitalier Universitaire Pitié-Salpêtrière, Faculté de Médecine Pierre et Marie Curie, Paris, France
- * E-mail: (JL); (SGV); (DL)
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- * E-mail: (JL); (SGV); (DL)
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- * E-mail: (JL); (SGV); (DL)
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Brecher MB, Li Z, Zhang J, Chen H, Lin Q, Liu B, Li H. Refolding of a fully functional flavivirus methyltransferase revealed that S-adenosyl methionine but not S-adenosyl homocysteine is copurified with flavivirus methyltransferase. Protein Sci 2014; 24:117-28. [PMID: 25352331 DOI: 10.1002/pro.2594] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/09/2023]
Abstract
Methylation of flavivirus RNA is vital for its stability and translation in the infected host cell. This methylation is mediated by the flavivirus methyltransferase (MTase), which methylates the N7 and 2'-O positions of the viral RNA cap by using S-adenosyl-l-methionine (SAM) as a methyl donor. In this report, we demonstrate that SAM, in contrast to the reaction by-product S-adenosyl-l-homocysteine, which was assumed previously, is copurified with the Dengue (DNV) and West Nile virus MTases produced in Escherichia coli (E. coli). This endogenous SAM can be removed by denaturation and refolding of the MTase protein. The refolded MTase of DNV serotype 3 (DNV3) displays methylation activity comparable to native enzyme, and its crystal structure at 2.1 Å is almost identical to that of native MTase. We characterized the binding of Sinefungin (SIN), a previously described SAM-analog inhibitor of MTase function, to the native and refolded DNV3 MTase by isothermal titration calorimetry, and found that SIN binds to refolded MTase with more than 16 times the affinity of SIN binding to the MTase purified natively. Moreover, we show that SAM is also copurified with other flavivirus MTases, indicating that purification by refolding may be a generally applicable tool for studying flavivirus MTase inhibition.
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Affiliation(s)
- Matthew B Brecher
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208
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46
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Construction of plasmid, bacterial expression, purification, and assay of dengue virus type 2 NS5 methyltransferase. Methods Mol Biol 2014; 1138:361-73. [PMID: 24696348 DOI: 10.1007/978-1-4939-0348-1_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Dengue virus (DENV), a member of mosquito-borne flavivirus, causes self-limiting dengue fever as well as life-threatening dengue hemorrhagic fever and dengue shock syndrome. Its positive sense RNA genome has a cap at the 5'-end and no poly(A) tail at the 3'-end. The viral RNA encodes a single polyprotein, C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5. The polyprotein is processed into 3 structural proteins (C, prM, and E) and 7 nonstructural (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5). NS3 and NS5 are multifunctional enzymes performing various tasks in viral life cycle. The N-terminal domain of NS5 has distinct GTP and S-adenosylmethionine (SAM) binding sites. The role of GTP binding site is implicated in guanylyltransferase (GTase) activity of NS5. The SAM binding site is involved in both N-7 and 2'-O-methyltransferase (MTase) activities involved in formation of type I cap. The C-terminal domain of NS5 catalyzes RNA-dependent RNA polymerase (RdRp) activity involved in RNA synthesis. We describe the construction of the MTase domain of NS5 in an E. coli expression vector, purification of the enzyme, and conditions for enzymatic assays of N7- and 2'O-methyltransferase activities that yield the final type I 5'-capped RNA ((7Me)GpppA2'OMe-RNA).
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47
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Biswas P, Kundu A, Ghosh AK. Genome segment 4 of Antheraea mylitta cytoplasmic polyhedrosis virus encodes RNA triphosphatase and methyltransferases. J Gen Virol 2014; 96:95-105. [PMID: 25228490 DOI: 10.1099/vir.0.069716-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cloning and sequencing of Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) genome segment S4 showed that it consists of 3410 nt with a single ORF of 1110 aa which could encode a protein of ~127 kDa (p127). Bioinformatics analysis showed the presence of a 5' RNA triphosphatase (RTPase) domain (LRDR), a S-adenosyl-l-methionine (SAM)-binding (GxGxG) motif and the KDKE tetrad of 2'-O-methyltransferase (MTase), which suggested that S4 may encode RTPase and MTase. The ORF of S4 was expressed in Escherichia coli as a His-tagged fusion protein and purified by nickel-nitrilotriacetic acid affinity chromatography. Biochemical analysis of recombinant p127 showed its RTPase as well as SAM-dependent guanine N(7)-and ribose 2'-O-MTase activities. A MTase assay using in vitro transcribed AmCPV S2 RNA having a 5' G*pppG end showed that guanine N(7) methylation occurred prior to the ribose 2'-O methylation to yield a m(7)GpppG/m(7)GpppGm RNA cap. Mutagenesis of the SAM-binding (GxGxG) motif (G831A) completely abolished N(7)- and 2'-O-MTase activities, indicating the importance of these residues for capping. From the kinetic analysis, the Km values of N(7)-MTase for SAM and RNA were calculated as 4.41 and 0.39 µM, respectively. These results suggested that AmCPV S4-encoded p127 catalyses RTPase and two cap methylation reactions for capping the 5' end of viral RNA.
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Affiliation(s)
- Poulomi Biswas
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Anirban Kundu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ananta Kumar Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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48
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Rational design of human metapneumovirus live attenuated vaccine candidates by inhibiting viral mRNA cap methyltransferase. J Virol 2014; 88:11411-29. [PMID: 25056882 DOI: 10.1128/jvi.00876-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The paramyxoviruses human respiratory syncytial virus (hRSV), human metapneumovirus (hMPV), and human parainfluenza virus type 3 (hPIV3) are responsible for the majority of pediatric respiratory diseases and inflict significant economic loss, health care costs, and emotional burdens. Despite major efforts, there are no vaccines available for these viruses. The conserved region VI (CR VI) of the large (L) polymerase proteins of paramyxoviruses catalyzes methyltransferase (MTase) activities that typically methylate viral mRNAs at positions guanine N-7 (G-N-7) and ribose 2'-O. In this study, we generated a panel of recombinant hMPVs carrying mutations in the S-adenosylmethionine (SAM) binding site in CR VI of L protein. These recombinant viruses were specifically defective in ribose 2'-O methylation but not G-N-7 methylation and were genetically stable and highly attenuated in cell culture and viral replication in the upper and lower respiratory tracts of cotton rats. Importantly, vaccination of cotton rats with these recombinant hMPVs (rhMPVs) with defective MTases triggered a high level of neutralizing antibody, and the rats were completely protected from challenge with wild-type rhMPV. Collectively, our results indicate that (i) amino acid residues in the SAM binding site in the hMPV L protein are essential for 2'-O methylation and (ii) inhibition of mRNA cap MTase can serve as a novel target to rationally design live attenuated vaccines for hMPV and perhaps other paramyxoviruses, such as hRSV and hPIV3. IMPORTANCE Human paramyxoviruses, including hRSV, hMPV, and hPIV3, cause the majority of acute upper and lower respiratory tract infections in humans, particularly in infants, children, the elderly, and immunocompromised individuals. Currently, there is no licensed vaccine available. A formalin-inactivated vaccine is not suitable for these viruses because it causes enhanced lung damage upon reinfection with the same virus. A live attenuated vaccine is the most promising vaccine strategy for human paramyxoviruses. However, it remains a challenge to identify an attenuated virus strain that has an optimal balance between attenuation and immunogenicity. Using reverse genetics, we generated a panel of recombinant hMPVs that were specifically defective in ribose 2'-O methyltransferase (MTase) but not G-N-7 MTase. These MTase-defective hMPVs were genetically stable and sufficiently attenuated but retained high immunogenicity. This work highlights a critical role of 2'-O MTase in paramyxovirus replication and pathogenesis and a new avenue for the development of safe and efficacious live attenuated vaccines for hMPV and other human paramyxoviruses.
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Urbonavičius J, Meškys R, Grosjean H. Biosynthesis of wyosine derivatives in tRNA(Phe) of Archaea: role of a remarkable bifunctional tRNA(Phe):m1G/imG2 methyltransferase. RNA (NEW YORK, N.Y.) 2014; 20:747-753. [PMID: 24837075 PMCID: PMC4024628 DOI: 10.1261/rna.043315.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The presence of tricyclic wyosine derivatives 3'-adjacent to anticodon is a hallmark of tRNA(Phe) in eukaryotes and archaea. In yeast, formation of wybutosine (yW) results from five enzymes acting in a strict sequential order. In archaea, the intermediate compound imG-14 (4-demethylwyosine) is a target of three different enzymes, leading to the formation of distinct wyosine derivatives (yW-86, imG, and imG2). We focus here on a peculiar methyltransferase (aTrm5a) that catalyzes two distinct reactions: N(1)-methylation of guanosine and C(7)-methylation of imG-14, whose function is to allow the production of isowyosine (imG2), an intermediate of the 7-methylwyosine (mimG) biosynthetic pathway. Based on the formation of mesomeric forms of imG-14, a rationale for such dual enzymatic activities is proposed. This bifunctional tRNA:m(1)G/imG2 methyltransferase, acting on two chemically distinct guanosine derivatives located at the same position of tRNA(Phe), is unique to certain archaea and has no homologs in eukaryotes. This enzyme here referred to as Taw22, probably played an important role in the emergence of the multistep biosynthetic pathway of wyosine derivatives in archaea and eukaryotes.
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Affiliation(s)
- Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, LT-08662 Vilnius, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, LT-08662 Vilnius, Lithuania
| | - Henri Grosjean
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Associée à l'Université Paris-Sud 11, FRC 3115, 91190 Gif-sur-Yvette, France
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Schmidt T, Schwede T, Meuwly M. Computational Analysis of Methyl Transfer Reactions in Dengue Virus Methyltransferase. J Phys Chem B 2014; 118:5882-90. [DOI: 10.1021/jp5028564] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tobias Schmidt
- SIB
Swiss Institute of Bioinformatics, Basel, Switzerland Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Torsten Schwede
- SIB
Swiss Institute of Bioinformatics, Basel, Switzerland Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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