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Liu M, Chen YY, Twu NC, Wu MC, Fang ZS, Dubruel A, Chang SC, Wu CF, Lo DY, Chen HW. A novel goose-origin Tembusu virus exhibits pathogenicity in day-old chicks with evidence of direct contact transmission. Poult Sci 2024; 103:103332. [PMID: 38128459 PMCID: PMC10776645 DOI: 10.1016/j.psj.2023.103332] [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: 09/11/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
In late 2020, an outbreak of Tembusu virus (TMUV)-associated disease occurred in a 45-day-old white Roman geese flock in Taiwan. Here, we present the identification and isolation of a novel goose-origin TMUV strain designated as NTU/C225/2020. The virus was successfully isolated using minimal-pathogen-free duck embryos. Phylogenetic analysis of the polyprotein gene showed that NTU/C225/2020 clustered together with the earliest isolates from Malaysia and was most closely related to the first Taiwanese TMUV strain, TP1906. Genomic analysis revealed significant amino acid variations among TMUV isolates in NS1 and NS2A protein regions. In the present study, we characterized the NTU/C225/2020 culture in duck embryos, chicken embryos, primary duck embryonated fibroblasts, and DF-1 cells. All host systems were susceptible to NTU/C225/2020 infection, with observable lesions. In addition, animal experiments showed that the intramuscular inoculation of NTU/C225/2020 resulted in growth retardation and hyperthermia in day-old chicks. Gross lesions in the infected chicks included hepatomegaly, hyperemic thymus, and splenomegaly. Viral loads and histopathological damage were displayed in various tissues of both inoculated and naïve co-housed chicks, confirming the direct chick-to-chick contact transmission of TMUV. This is the first in vivo study of a local TMUV strain in Taiwan. Our findings provide essential information for TMUV propagation and suggest a potential risk of disease outbreak in chicken populations.
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Affiliation(s)
- Min Liu
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Yao-Yun Chen
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Ning-Chieh Twu
- Department of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Meng-Chi Wu
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Zih-Syun Fang
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Alexandre Dubruel
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Chung Chang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Ching-Fen Wu
- Department of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Dan-Yuan Lo
- Department of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Hui-Wen Chen
- Department of Veterinary Medicine, National Taiwan University, Taipei, Taiwan; Animal Resource Center, National Taiwan University, Taipei, Taiwan.
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Akram M, Hameed S, Hassan A, Khan KM. Development in the Inhibition of Dengue Proteases as Drug Targets. Curr Med Chem 2024; 31:2195-2233. [PMID: 37723635 DOI: 10.2174/0929867331666230918110144] [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: 03/20/2023] [Revised: 06/24/2023] [Accepted: 08/04/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Viral infections continue to increase morbidity and mortality severely. The flavivirus genus has fifty different species, including the dengue, Zika, and West Nile viruses that can infect 40% of individuals globally, who reside in at least a hundred different countries. Dengue, one of the oldest and most dangerous human infections, was initially documented by the Chinese Medical Encyclopedia in the Jin period. It was referred to as "water poison," connected to flying insects, i.e., Aedes aegypti and Aedes albopictus. DENV causes some medical expressions like dengue hemorrhagic fever, acute febrile illness, and dengue shock syndrome. OBJECTIVE According to the World Health Organization report of 2012, 2500 million people are in danger of contracting dengue fever worldwide. According to a recent study, 96 million of the 390 million dengue infections yearly show some clinical or subclinical severity. There is no antiviral drug or vaccine to treat this severe infection. It can be controlled by getting enough rest, drinking plenty of water, and using painkillers. The first dengue vaccine created by Sanofi, called Dengvaxia, was previously approved by the USFDA in 2019. All four serotypes of the DENV1-4 have shown re-infection in vaccine recipients. However, the usage of Dengvaxia has been constrained by its adverse effects. CONCLUSION Different classes of compounds have been reported against DENV, such as nitrogen-containing heterocycles (i.e., imidazole, pyridine, triazoles quinazolines, quinoline, and indole), oxygen-containing heterocycles (i.e., coumarins), and some are mixed heterocyclic compounds of S, N (thiazole, benzothiazine, and thiazolidinediones), and N, O (i.e., oxadiazole). There have been reports of computationally designed compounds to impede the molecular functions of specific structural and non-structural proteins as potential therapeutic targets. This review summarized the current progress in developing dengue protease inhibitors.
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Affiliation(s)
- Muhammad Akram
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Shehryar Hameed
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, 75720, Pakistan
| | - Abbas Hassan
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Khalid Mohammed Khan
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, 75720, Pakistan
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Zaib S, Rana N, Ali HS, Ur Rehman M, Awwad NS, Ibrahium HA, Khan I. Identification of potential inhibitors targeting yellow fever virus helicase through ligand and structure-based computational studies. J Biomol Struct Dyn 2023:1-18. [PMID: 38109183 DOI: 10.1080/07391102.2023.2294839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
Yellow fever is a flavivirus having plus-sensed RNA which encodes a single polyprotein. Host proteases cut this polyprotein into seven nonstructural proteins including a vital NS3 protein. The present study aims to identify the most effective inhibitor against the helicase (NS3) using different advanced ligand and structure-based computational studies. A set of 300 ligands was selected against helicase by chemical structural similarity model, which are similar to S-adenosyl-l-cysteine using infiniSee. This tool screens billions of compounds through a similarity search from in-built chemical spaces (CHEMriya, Galaxi, KnowledgeSpace and REALSpace). The pharmacophore was designed from ligands in the library that showed same features. According to the sequence of ligands, six compounds (29, 87, 99, 116, 148, and 208) were taken for pharmacophore designing against helicase protein. Subsequently, compounds from the library which showed the best pharmacophore shared-features were docked using FlexX functionality of SeeSAR and their optibrium properties were analyzed. Afterward, their ADME was improved by replacing the unfavorable fragments, which resulted in the generation of new compounds. The selected best compounds (301, 302, 303 and 304) were docked using SeeSAR and their pharmacokinetics and toxicological properties were evaluated using SwissADME. The optimal inhibitor for yellow fever helicase was 2-amino-N-(4-(dimethylamino)thiazol-2-yl)-4-methyloxazole-5-carboxamide (302), which exhibits promising potential for drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry and the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Mujeeb Ur Rehman
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Nasser S Awwad
- Department of Chemistry, King Khalid University, Abha, Saudi Arabia
| | - Hala A Ibrahium
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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Caldwell HS, Kuo L, Pata JD, Dupuis AP, Arnold JJ, Yeager C, Stout J, Koetzner CA, Payne AF, Bialosuknia SM, Banker EM, Nolen TA, Cameron CE, Ciota AT. Maintenance of a host-specific minority mutation in the West Nile virus NS3. iScience 2023; 26:107468. [PMID: 37593454 PMCID: PMC10428113 DOI: 10.1016/j.isci.2023.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
West Nile virus (WNV), the most prevalent arthropod-borne virus (arbovirus) in the United States, is maintained in a cycle between Culex spp. mosquitoes and birds. Arboviruses exist within hosts and vectors as a diverse set of closely related genotypes. In theory, this genetic diversity can facilitate adaptation to distinct environments during host cycling, yet host-specific fitness of minority genotypes has not been assessed. Utilizing WNV deep-sequencing data, we previously identified a naturally occurring, mosquito-biased substitution, NS3 P319L. Using both cell culture and experimental infection in natural hosts, we demonstrated that this substitution confers attenuation in vertebrate hosts and increased transmissibility by mosquitoes. Biochemical assays demonstrated temperature-sensitive ATPase activity consistent with host-specific phenotypes. Together these data confirm the maintenance of host-specific minority variants in arbovirus mutant swarms, suggest a unique role for NS3 in viral fitness, and demonstrate that intrahost sequence data can inform mechanisms of host-specific adaptation.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
| | - Lili Kuo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alan P. Dupuis
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Jamie J. Arnold
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Calvin Yeager
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jessica Stout
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Cheri A. Koetzner
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Anne F. Payne
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Sean M. Bialosuknia
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Elyse M. Banker
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Taylor A. Nolen
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Craig E. Cameron
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
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Yang Z, Wang H, Yang S, Wang X, Shen Q, Ji L, Zeng J, Zhang W, Gong H, Shan T. Virome diversity of ticks feeding on domestic mammals in China. Virol Sin 2023; 38:208-221. [PMID: 36781125 PMCID: PMC10176445 DOI: 10.1016/j.virs.2023.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses. From 2017 to 2018, 640 ticks were collected in eight different provinces in central and western China. Six species were detected, including H.longicornis, De.everestianus, Rh.microplus, Rh.turanicus, Rh.sanguineous, and Hy.asiaticum. Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform, resulting in 13.44 G (5.88 × 107) of 250-bp-end reads, in which 2,437,941 are viral reads. We found 27 nearly complete genome sequences, including 16 genome sequences encoding entire protein-coding regions (lack of 3' or 5' end non-coding regions) and complete viral genomes, distributed in the arboviral family (Chuviridae, Rhabdoviridae, Nairoviridae, Phenuiviridae, Flaviviridae, Iflaviridae) as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans. In addition, 13 virus sequences found in Chuviridae, Nairoviridae, Flaviviridae, Iflaviridae, Hepeviridae, Parvoviridae, and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera. Besides, an epidemiological survey shows a high prevalence (9.38% and 15.63%) of two viruses (Ovine Copiparvovirus and Bovine parvovirus 2) in the tick cohort.
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Affiliation(s)
- Zijun Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China; Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jian Zeng
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
| | - Haiyan Gong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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6
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Teramoto T, Choi KH, Padmanabhan R. Flavivirus proteases: The viral Achilles heel to prevent future pandemics. Antiviral Res 2023; 210:105516. [PMID: 36586467 PMCID: PMC10062209 DOI: 10.1016/j.antiviral.2022.105516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022]
Abstract
Flaviviruses are important human pathogens and include dengue (DENV), West Nile (WNV), Yellow fever virus (YFV), Japanese encephalitis (JEV) and Zika virus (ZIKV). DENV, transmitted by mosquitoes, causes diseases ranging in severity from mild dengue fever with non-specific flu-like symptoms to fatal dengue hemorrhagic fever and dengue shock syndrome. DENV infections are caused by four serotypes, DENV1-4, which interact differently with antibodies in blood serum. The incidence of DENV infection has increased dramatically in recent decades and the CDC estimates 400 million dengue infections occur each year, resulting in ∼25,000 deaths mostly among children and elderly people. Similarly, ZIKV infections are caused by infected mosquito bites to humans, can be transmitted sexually and through blood transfusions. If a pregnant woman is infected, the virus can cross the placental barrier and can spread to her fetus, causing severe brain malformations in the child including microcephaly and other birth defects. It is noteworthy that the neurological manifestations of ZIKV were also observed in DENV endemic regions, suggesting that pre-existing antibody response to DENV could augment ZIKV infection. WNV, previously unknown in the US (and known to cause only mild disease in Middle East), first arrived in New York city in 1999 (NY99) and spread throughout the US and Canada by Culex mosquitoes and birds. WNV is now endemic in North America. Thus, emerging and re-emerging flaviviruses are significant threat to human health. However, vaccines are available for only a limited number of flaviviruses, and antiviral therapies are not available for any flavivirus. Hence, there is an urgent need to develop therapeutics that interfere with essential enzymatic steps, such as protease in the flavivirus lifecycle as these viruses possess significant threat to future pandemics. In this review, we focus on our E. coli expression of NS2B hydrophilic domain (NS2BH) covalently linked to NS3 protease domain (NS3Pro) in their natural context which is processed by the combined action of both subunits of the NS2B-NS3Pro precursor. Biochemical activities of the viral protease such as solubility and autoproteolysis of NS2BH-NS3Pro linkage depended on the C-terminal portion of NS2BH linked to the NS3Pro domain. Since 2008, we also focus on the use of the recombinant protease in high throughput screens and characterization of small molecular compounds identified in these screens.
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Affiliation(s)
- Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA.
| | - Kyung H Choi
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47406, USA.
| | - Radhakrishnan Padmanabhan
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA.
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Salgado Á, de Melo-Minardi RC, Giovanetti M, Veloso A, Morais-Rodrigues F, Adelino T, de Jesus R, Tosta S, Azevedo V, Lourenco J, Alcantara LCJ. Machine learning models exploring characteristic single-nucleotide signatures in yellow fever virus. PLoS One 2022; 17:e0278982. [PMID: 36508435 PMCID: PMC9744328 DOI: 10.1371/journal.pone.0278982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Yellow fever virus (YFV) is the agent of the most severe mosquito-borne disease in the tropics. Recently, Brazil suffered major YFV outbreaks with a high fatality rate affecting areas where the virus has not been reported for decades, consisting of urban areas where a large number of unvaccinated people live. We developed a machine learning framework combining three different algorithms (XGBoost, random forest and regularized logistic regression) to analyze YFV genomic sequences. This method was applied to 56 YFV sequences from human infections and 27 from non-human primate (NHPs) infections to investigate the presence of genetic signatures possibly related to disease severity (in human related sequences) and differences in PCR cycle threshold (Ct) values (in NHP related sequences). Our analyses reveal four non-synonymous single nucleotide variations (SNVs) on sequences from human infections, in proteins NS3 (E614D), NS4a (I69V), NS5 (R727G, V643A) and six non-synonymous SNVs on NHP sequences, in proteins E (L385F), NS1 (A171V), NS3 (I184V) and NS5 (N11S, I374V, E641D). We performed comparative protein structural analysis on these SNVs, describing possible impacts on protein function. Despite the fact that the dataset is limited in size and that this study does not consider virus-host interactions, our work highlights the use of machine learning as a versatile and fast initial approach to genomic data exploration.
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Affiliation(s)
- Álvaro Salgado
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail: (AS); (LCJA); (JL)
| | - Raquel C. de Melo-Minardi
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Adriano Veloso
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francielly Morais-Rodrigues
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Talita Adelino
- Laboratório Central de Saúde Pública, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - José Lourenco
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (AS); (LCJA); (JL)
| | - Luiz Carlos J. Alcantara
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- * E-mail: (AS); (LCJA); (JL)
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Anindita PD, Halbeisen M, Řeha D, Tuma R, Franta Z. Mechanistic insight into the RNA stimulated-ATPase activity of tick-borne encephalitis virus helicase. J Biol Chem 2022; 298:102383. [PMID: 35987382 PMCID: PMC9490040 DOI: 10.1016/j.jbc.2022.102383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/05/2022] Open
Abstract
The helicase domain of nonstructural protein 3 (NS3H) unwinds the double-stranded RNA replication intermediate in an ATP-dependent manner during the flavivirus life cycle. While the ATP hydrolysis mechanism of Dengue and Zika viruses NS3H has been extensively studied, little is known in the case of the tick-borne encephalitis virus NS3H. We demonstrate that ssRNA binds with nanomolar affinity to NS3H and strongly stimulates the ATP hydrolysis cycle, whereas ssDNA binds only weakly and inhibits ATPase activity in a noncompetitive manner. Thus, NS3H is an RNA-specific helicase, whereas DNA might act as an allosteric inhibitor. Using modeling, we explored plausible allosteric mechanisms by which ssDNA inhibits the ATPase via nonspecific binding in the vicinity of the active site and ATP repositioning. We captured several structural snapshots of key ATP hydrolysis stages using X-ray crystallography. One intermediate, in which the inorganic phosphate and ADP remained trapped inside the ATPase site after hydrolysis, suggests that inorganic phosphate release is the rate-limiting step. Using structure-guided modeling and molecular dynamics simulation, we identified putative RNA-binding residues and observed that the opening and closing of the ATP-binding site modulates RNA affinity. Site-directed mutagenesis of the conserved RNA-binding residues revealed that the allosteric activation of ATPase activity is primarily communicated via an arginine residue in domain 1. In summary, we characterized conformational changes associated with modulating RNA affinity and mapped allosteric communication between RNA-binding groove and ATPase site of tick-borne encephalitis virus helicase.
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Affiliation(s)
| | - Marco Halbeisen
- Department of Chemistry, Faculty of Science, University of South Bohemia, Czech Republic
| | - David Řeha
- Department of Chemistry, Faculty of Science, University of South Bohemia, Czech Republic
| | - Roman Tuma
- Department of Chemistry, Faculty of Science, University of South Bohemia, Czech Republic
| | - Zdenek Franta
- Department of Chemistry, Faculty of Science, University of South Bohemia, Czech Republic.
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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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Caldwell HS, Pata JD, Ciota AT. The Role of the Flavivirus Replicase in Viral Diversity and Adaptation. Viruses 2022; 14:1076. [PMID: 35632818 PMCID: PMC9143365 DOI: 10.3390/v14051076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses include several emerging and re-emerging arboviruses which cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses readily alternate and adapt to different hosts and environments. Here, we review a subset of the different aspects of flaviviral biology which impact host switching and viral fitness. These include the mechanism of replication and structural biology of the NS3 and NS5 proteins, which reproduce the viral genome; rates of mutation resulting from this replication and the role of mutational frequency in viral fitness; and the theory of quasispecies evolution and how it contributes to our understanding of genetic and phenotypic plasticity.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
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11
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Du Pont KE, McCullagh M, Geiss BJ. Conserved motifs in the flavivirus NS3 RNA helicase enzyme. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1688. [PMID: 34472205 PMCID: PMC8888775 DOI: 10.1002/wrna.1688] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Flaviviruses are a major health concern because over half of the world population is at risk of infection and there are very few antiviral therapeutics to treat diseases resulting from infection. Replication is an essential part of the flavivirus survival. One of the viral proteins, NS3 helicase, is critical for unwinding the double stranded RNA intermediate during flaviviral replication. The helicase performs the unwinding of the viral RNA intermediate structure in an ATP-dependent manner. NS3 helicase is a member of the Viral/DEAH-like subfamily of the superfamily 2 helicase containing eight highly conserved structural motifs (I, Ia, II, III, IV, IVa, V, and VI) localized between the ATP-binding and RNA-binding pockets. Of these structural motifs only three are well characterized for function in flaviviruses (I, II, and VI). The roles of the other structural motifs are not well understood for NS3 helicase function, but comparison of NS3 with other superfamily 2 helicases within the viral/DEAH-like, DEAH/RHA, and DEAD-box subfamilies can be used to elucidate the roles of these structural motifs in the flavivirus NS3 helicase. This review aims to summarize the role of each conserved structural motif within flavivirus NS3 in RNA helicase function. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Kelly E. Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
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12
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Lin M, Cui W, Tian H, Zhang Y, Chen C, Yang X, Chi H, Mu Z, Chen C, Wang Z, Ji X, Yang H, Lin Z. Structural Basis of Zika Virus Helicase in RNA Unwinding and ATP Hydrolysis. ACS Infect Dis 2022; 8:150-158. [PMID: 34904824 DOI: 10.1021/acsinfecdis.1c00455] [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: 11/29/2022]
Abstract
The flavivirus nonstructural protein 3 helicase (NS3hel) is a multifunctional domain protein that is associated with DNA/RNA helicase, nucleoside triphosphatase (NTPase), and RNA 5'-triphosphatase (RTPase) activities. As an NTPase-dependent superfamily 2 (SF2) member, NS3hel employs an NTP-driven motor force to unwind double-stranded RNA while translocating along single-stranded RNA and is extensively involved in the viral replication process. Although the structures of SF2 helicases are widely investigated as promising drug targets, the mechanism of energy transduction between NTP hydrolysis and the RNA binding sites in ZIKV NS3hel remains elusive. Here, we report the crystal structure of ZIKV NS3hel in complex with its natural substrates ATP-Mn2+ and ssRNA. Distinct from other members of the Flavivirus genus, ssRNA binding to ZIKV NS3hel induces relocation of the active water molecules and ATP-associated metal ions in the NTP hydrolysis active site, which promotes the hydrolysis of ATP and the production of AMP. Our findings highlight the importance of the allosteric role of ssRNA on the modulation of ATP hydrolysis and energy utilization.
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Affiliation(s)
- Mengmeng Lin
- School of Life Sciences, Tianjin University, Tianjin 300072, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Wen Cui
- School of Life Sciences, Tianjin University, Tianjin 300072, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Hongliang Tian
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yan Zhang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Chen Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xiaoyun Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Heng Chi
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Zhongyu Mu
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Haitao Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Zhi Lin
- School of Life Sciences, Tianjin University, Tianjin 300072, China
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13
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Vicenti I, Martina MG, Boccuto A, De Angelis M, Giavarini G, Dragoni F, Marchi S, Trombetta CM, Crespan E, Maga G, Eydoux C, Decroly E, Montomoli E, Nencioni L, Zazzi M, Radi M. System-oriented optimization of multi-target 2,6-diaminopurine derivatives: Easily accessible broad-spectrum antivirals active against flaviviruses, influenza virus and SARS-CoV-2. Eur J Med Chem 2021; 224:113683. [PMID: 34273661 PMCID: PMC8255191 DOI: 10.1016/j.ejmech.2021.113683] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022]
Abstract
The worldwide circulation of different viruses coupled with the increased frequency and diversity of new outbreaks, strongly highlight the need for new antiviral drugs to quickly react against potential pandemic pathogens. Broad-spectrum antiviral agents (BSAAs) represent the ideal option for a prompt response against multiple viruses, new and re-emerging. Starting from previously identified anti-flavivirus hits, we report herein the identification of promising BSAAs by submitting the multi-target 2,6-diaminopurine chemotype to a system-oriented optimization based on phenotypic screening on cell cultures infected with different viruses. Among the synthesized compounds, 6i showed low micromolar potency against Dengue, Zika, West Nile and Influenza A viruses (IC50 = 0.5-5.3 μM) with high selectivity index. Interestingly, 6i also inhibited SARS-CoV-2 replication in different cell lines, with higher potency on Calu-3 cells that better mimic the SARS-CoV-2 infection in vivo (IC50 = 0.5 μM, SI = 240). The multi-target effect of 6i on flavivirus replication was also analyzed in whole cell studies (in vitro selection and immunofluorescence) and against isolated host/viral targets.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marta De Angelis
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia Giavarini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | | | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Cecilia Eydoux
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Marseille, France
| | - Etienne Decroly
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Marseille, France
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy; VisMederi s.r.l, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Lucia Nencioni
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy.
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14
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In Silico Prediction of the Phosphorylation of NS3 as an Essential Mechanism for Dengue Virus Replication and the Antiviral Activity of Quercetin. BIOLOGY 2021; 10:biology10101067. [PMID: 34681164 PMCID: PMC8570334 DOI: 10.3390/biology10101067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022]
Abstract
Simple Summary Dengue is a mosquito-borne virus that infects up to 400 million people worldwide annually. Dengue infection triggers high fever, severe body aches, rash, low platelet count, and could lead to Dengue hemorrhagic fever (DHF) in some cases. There is currently no cure, nor a broadly effective vaccine. The interaction of two viral proteins, nonstructural Proteins 3 and 5 (NS3 and NS5), is required for viral replication in the infected host’s cells. Our computational modeling of NS3 suggested that phosphorylation of a serine residue at position 137 of NS3 by a specific c-Jun N-terminal kinase (JNK) enhances viral replication by increasing the interaction of NS3 and NS5 through structural changes in amino acid residues 49–95. Experimental studies have shown that inhibition of JNK prevents viral replication and have suggested that the plants’ flavonoid Quercetin, Agathis flavone, and Myricetin inhibit Dengue infection. Our molecular simulations revealed that Quercetin binds NS3 and obstructs serine 137 phosphorylation, which may decrease viral replication. This work offers a molecular mechanism that can be used for anti-Dengue drug development. Abstract Dengue virus infection is a global health problem for which there have been challenges to obtaining a cure. Current vaccines and anti-viral drugs can only be narrowly applied in ongoing clinical trials. We employed computational methods based on structure-function relationships between human host kinases and viral nonstructural protein 3 (NS3) to understand viral replication inhibitors’ therapeutic effect. Phosphorylation at each of the two most evolutionarily conserved sites of NS3, serine 137 and threonine 189, compared to the unphosphorylated state were studied with molecular dynamics and docking simulations. The simulations suggested that phosphorylation at serine 137 caused a more remarkable structural change than phosphorylation at threonine 189, specifically located at amino acid residues 49–95. Docking studies supported the idea that phosphorylation at serine 137 increased the binding affinity between NS3 and nonstructural Protein 5 (NS5), whereas phosphorylation at threonine 189 decreased it. The interaction between NS3 and NS5 is essential for viral replication. Docking studies with the antiviral plant flavonoid Quercetin with NS3 indicated that Quercetin physically occluded the serine 137 phosphorylation site. Taken together, these findings suggested a specific site and mechanism by which Quercetin inhibits dengue and possible other flaviviruses.
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15
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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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16
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Zhao R, Wang M, Cao J, Shen J, Zhou X, Wang D, Cao J. Flavivirus: From Structure to Therapeutics Development. Life (Basel) 2021; 11:life11070615. [PMID: 34202239 PMCID: PMC8303334 DOI: 10.3390/life11070615] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/25/2022] Open
Abstract
Flaviviruses are still a hidden threat to global human safety, as we are reminded by recent reports of dengue virus infections in Singapore and African-lineage-like Zika virus infections in Brazil. Therapeutic drugs or vaccines for flavivirus infections are in urgent need but are not well developed. The Flaviviridae family comprises a large group of enveloped viruses with a single-strand RNA genome of positive polarity. The genome of flavivirus encodes ten proteins, and each of them plays a different and important role in viral infection. In this review, we briefly summarized the major information of flavivirus and further introduced some strategies for the design and development of vaccines and anti-flavivirus compound drugs based on the structure of the viral proteins. There is no doubt that in the past few years, studies of antiviral drugs have achieved solid progress based on better understanding of the flavivirus biology. However, currently, there are no fully effective antiviral drugs or vaccines for most flaviviruses. We hope that this review may provide useful information for future development of anti-flavivirus drugs and vaccines.
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Affiliation(s)
- Rong Zhao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Meiyue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Jing Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Jing Shen
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Xin Zhou
- Department of Medical Imaging, Shanxi Medical University, Taiyuan 030001, China;
| | - Deping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
- Correspondence: (D.W.); (J.C.)
| | - Jimin Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
- Correspondence: (D.W.); (J.C.)
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Kim J, Park SJ, Park J, Shin H, Jang YS, Woo JS, Min DH. Identification of a Direct-Acting Antiviral Agent Targeting RNA Helicase via a Graphene Oxide Nanobiosensor. ACS APPLIED MATERIALS & INTERFACES 2021; 13:25715-25726. [PMID: 34036784 DOI: 10.1021/acsami.1c04641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dengue virus (DENV), an arbovirus transmitted by mosquitoes, causes infectious diseases such as dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. Despite the dangers posed by DENV, there are no approved antiviral drugs for treatment of DENV infection. Considering the potential for a global dengue outbreak, rapid development of antiviral agents against DENV infections is crucial as a preemptive measure; thus, the selection of apparent drug targets, such as the viral enzymes involved in the viral life cycle, is recommended. Helicase, a potential drug target in DENV, is a crucial viral enzyme that unwinds double-stranded viral RNA, releasing single-stranded RNA genomes during viral replication. Therefore, an inhibitor of helicase activity could serve as a direct-acting antiviral agent. Here, we introduce an RNA helicase assay based on graphene oxide, which enables fluorescence-based analysis of RNA substrate-specific helicase enzyme activity. This assay demonstrated high reliability and ability for high-throughput screening, identifying a new helicase inhibitor candidate, micafungin (MCFG), from an FDA-approved drug library. As a direct-acting antiviral agent targeting RNA helicase, MCFG inhibits DENV proliferation in cells and an animal model. Notably, in vivo, MCFG treatment reduced viremia, inflammatory cytokine levels, and viral loads in several tissues and improved survival rates by up to 40% in a lethal mouse model. Therefore, we suggest MCFG as a potential direct-acting antiviral drug candidate.
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Affiliation(s)
- Jungho Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Se-Jin Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jisang Park
- Department of Bioactive Material Sciences and Institute of Bioactive Materials, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Molecular Biology and the Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Hojeong Shin
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Suk Jang
- Department of Bioactive Material Sciences and Institute of Bioactive Materials, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Molecular Biology and the Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Jae-Sung Woo
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul 08826, Republic of Korea
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul 06683, Republic of Korea
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18
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Loaiza-Cano V, Monsalve-Escudero LM, Restrepo MP, Quintero-Gil DC, Pulido Muñoz SA, Galeano E, Zapata W, Martinez-Gutierrez M. In Vitro and In Silico Anti-Arboviral Activities of Dihalogenated Phenolic Derivates of L-Tyrosine. Molecules 2021; 26:3430. [PMID: 34198817 PMCID: PMC8201234 DOI: 10.3390/molecules26113430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022] Open
Abstract
Despite the serious public health problem represented by the diseases caused by dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV) viruses, there are still no specific licensed antivirals available for their treatment. Here, we examined the potential anti-arbovirus activity of ten di-halogenated compounds derived from L-tyrosine with modifications in amine and carboxyl groups. The activity of compounds on VERO cell line infection and the possible mechanism of action of the most promising compounds were evaluated. Finally, molecular docking between the compounds and viral and cellular proteins was evaluated in silico with Autodock Vina®, and the molecular dynamic with Gromacs®. Only two compounds (TDC-2M-ME and TDB-2M-ME) inhibited both ZIKV and CHIKV. Within the possible mechanism, in CHIKV, the two compounds decreased the number of genome copies and in the pre-treatment strategy the infectious viral particles. In the ZIKV model, only TDB-2M-ME inhibited the viral protein and demonstrate a virucidal effect. Moreover, in the U937 cell line infected with CHIKV, both compounds inhibited the viral protein and TDB-2M-ME inhibited the viral genome too. Finally, the in silico results showed a favorable binding energy between the compounds and the helicases of both viral models, the NSP3 of CHIKV and cellular proteins DDC and β2 adrenoreceptor.
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Affiliation(s)
- Vanessa Loaiza-Cano
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (L.M.M.-E.); (D.C.Q.-G.)
| | - Laura Milena Monsalve-Escudero
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (L.M.M.-E.); (D.C.Q.-G.)
| | - Manuel Pastrana Restrepo
- Grupo de Investigación en Productos Naturales Marinos, Universidad de Antioquia, Medellín 050001, Colombia; (M.P.R.); (E.G.)
| | - Diana Carolina Quintero-Gil
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (L.M.M.-E.); (D.C.Q.-G.)
| | | | - Elkin Galeano
- Grupo de Investigación en Productos Naturales Marinos, Universidad de Antioquia, Medellín 050001, Colombia; (M.P.R.); (E.G.)
| | - Wildeman Zapata
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín 050001, Colombia;
| | - Marlen Martinez-Gutierrez
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (L.M.M.-E.); (D.C.Q.-G.)
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19
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Zheng F, Yi W, Liu W, Zhu H, Gong P, Pan Z. A positively charged surface patch on the pestivirus NS3 protease module plays an important role in modulating NS3 helicase activity and virus production. Arch Virol 2021; 166:1633-1642. [PMID: 33787991 DOI: 10.1007/s00705-021-05055-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/08/2021] [Indexed: 10/21/2022]
Abstract
Pestivirus nonstructural protein 3 (NS3) is a multifunctional protein with protease and helicase activities that are essential for virus replication. In this study, we used a combination of biochemical and genetic approaches to investigate the relationship between a positively charged patch on the protease module and NS3 function. The surface patch is composed of four basic residues, R50, K74 and K94 in the NS3 protease domain and H24 in the structurally integrated cofactor NS4APCS. Single-residue or simultaneous four-residue substitutions in the patch to alanine or aspartic acid had little effect on ATPase activity. However, single substitutions of R50, K94 or H24 or a simultaneous four-residue substitution resulted in apparent changes in the helicase activity and RNA-binding ability of NS3. When these mutations were introduced into a classical swine fever virus (CSFV) cDNA clone, a single substitution at K94 or a simultaneous four-residue substitution (Qua_A or Qua_D) impaired the production of infectious virus. Furthermore, the replication efficiency of the CSFV variants was partially correlated with the helicase activity of NS3 in vitro. Our results suggest that the conserved positively charged patch on NS3 plays an important role in modulating the NS3 helicase activity in vitro and CSFV production.
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Affiliation(s)
- Fengwei Zheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weicheng Yi
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weichi Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongchang Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Zishu Pan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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20
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Harima H, Orba Y, Torii S, Qiu Y, Kajihara M, Eto Y, Matsuta N, Hang'ombe BM, Eshita Y, Uemura K, Matsuno K, Sasaki M, Yoshii K, Nakao R, Hall WW, Takada A, Abe T, Wolfinger MT, Simuunza M, Sawa H. An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. Sci Rep 2021; 11:4883. [PMID: 33649491 PMCID: PMC7921595 DOI: 10.1038/s41598-021-84365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.
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Affiliation(s)
- Hayato Harima
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shiho Torii
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshiki Eto
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoya Matsuta
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Bernard M Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia
| | - Yuki Eshita
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Keita Matsuno
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Research in Infectious Diseases, School of Medicine, University College Dublin, Dublin, Ireland.,Global Virus Network, Baltimore, MD, USA
| | - Ayato Takada
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Takashi Abe
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Martin Simuunza
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia. .,Global Virus Network, Baltimore, MD, USA. .,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.
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21
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Fiacre L, Pagès N, Albina E, Richardson J, Lecollinet S, Gonzalez G. Molecular Determinants of West Nile Virus Virulence and Pathogenesis in Vertebrate and Invertebrate Hosts. Int J Mol Sci 2020; 21:ijms21239117. [PMID: 33266206 PMCID: PMC7731113 DOI: 10.3390/ijms21239117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
West Nile virus (WNV), like the dengue virus (DENV) and yellow fever virus (YFV), are major arboviruses belonging to the Flavivirus genus. WNV is emerging or endemic in many countries around the world, affecting humans and other vertebrates. Since 1999, it has been considered to be a major public and veterinary health problem, causing diverse pathologies, ranging from a mild febrile state to severe neurological damage and death. WNV is transmitted in a bird–mosquito–bird cycle, and can occasionally infect humans and horses, both highly susceptible to the virus but considered dead-end hosts. Many studies have investigated the molecular determinants of WNV virulence, mainly with the ultimate objective of guiding vaccine development. Several vaccines are used in horses in different parts of the world, but there are no licensed WNV vaccines for humans, suggesting the need for greater understanding of the molecular determinants of virulence and antigenicity in different hosts. Owing to technical and economic considerations, WNV virulence factors have essentially been studied in rodent models, and the results cannot always be transported to mosquito vectors or to avian hosts. In this review, the known molecular determinants of WNV virulence, according to invertebrate (mosquitoes) or vertebrate hosts (mammalian and avian), are presented and discussed. This overview will highlight the differences and similarities found between WNV hosts and models, to provide a foundation for the prediction and anticipation of WNV re-emergence and its risk of global spread.
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Affiliation(s)
- Lise Fiacre
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Nonito Pagès
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Emmanuel Albina
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Jennifer Richardson
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
| | - Sylvie Lecollinet
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
- Correspondence: ; Tel.: +33-1-43967376
| | - Gaëlle Gonzalez
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
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22
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Kumar D, Sharma N, Aarthy M, Singh SK, Giri R. Mechanistic Insights into Zika Virus NS3 Helicase Inhibition by Epigallocatechin-3-Gallate. ACS OMEGA 2020; 5:11217-11226. [PMID: 32455246 PMCID: PMC7241040 DOI: 10.1021/acsomega.0c01353] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Since 2007, repeated outbreaks of Zika virus (ZIKV) have affected millions of people worldwide and created a global health concern with major complications like microcephaly and Guillain Barre's syndrome. To date, there is not a single Zika-specific licensed drug present in the market. However, in recent months, several antiviral molecules have been screened against ZIKV. Among those, (-)-epigallocatechin-3-gallate (EGCG), a green tea polyphenol, has shown great virucidal potential against flaviviruses including ZIKV. The mechanistic understanding of EGCG-targeting viral proteins is not yet entirely deciphered except that little is known about its interaction with viral envelope protein and viral protease. We designed our current study to find inhibitory actions of EGCG against ZIKV NS3 helicase. NS3 helicase performs a significant role in viral replication by unwinding RNA after hydrolyzing NTP. We employed molecular docking and simulation approach and found significant interactions at the ATPase site and also at the RNA binding site. Further, the enzymatic assay has shown significant inhibition of NTPase activity with an IC50 value of 295.7 nM and Ki of 0.387 ± 0.034 μM. Our study suggests the possibility that EGCG could be considered as a prime backbone molecule for further broad-spectrum inhibitor development against ZIKV and other flaviviruses.
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Affiliation(s)
- Deepak Kumar
- School
of Basic Sciences, Indian Institute of Technology
Mandi, VPO Kamand, Mandi, Himachal Pradesh 175005, India
| | - Nitin Sharma
- School
of Basic Sciences, Indian Institute of Technology
Mandi, VPO Kamand, Mandi, Himachal Pradesh 175005, India
| | - Murali Aarthy
- Department
of Bioinformatics, Computer Aided Drug Design and Molecular Modeling
Lab, Alagappa University, Science Block, Karaikudi 630003, Tamilnadu, India
| | - Sanjeev Kumar Singh
- Department
of Bioinformatics, Computer Aided Drug Design and Molecular Modeling
Lab, Alagappa University, Science Block, Karaikudi 630003, Tamilnadu, India
| | - Rajanish Giri
- School
of Basic Sciences, Indian Institute of Technology
Mandi, VPO Kamand, Mandi, Himachal Pradesh 175005, India
- BioX
Centre, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175005, India
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23
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Pierson TC, Diamond MS. The continued threat of emerging flaviviruses. Nat Microbiol 2020; 5:796-812. [PMID: 32367055 DOI: 10.1038/s41564-020-0714-0] [Citation(s) in RCA: 468] [Impact Index Per Article: 117.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/27/2020] [Indexed: 12/18/2022]
Abstract
Flaviviruses are vector-borne RNA viruses that can emerge unexpectedly in human populations and cause a spectrum of potentially severe diseases including hepatitis, vascular shock syndrome, encephalitis, acute flaccid paralysis, congenital abnormalities and fetal death. This epidemiological pattern has occurred numerous times during the last 70 years, including epidemics of dengue virus and West Nile virus, and the most recent explosive epidemic of Zika virus in the Americas. Flaviviruses are now globally distributed and infect up to 400 million people annually. Of significant concern, outbreaks of other less well-characterized flaviviruses have been reported in humans and animals in different regions of the world. The potential for these viruses to sustain epidemic transmission among humans is poorly understood. In this Review, we discuss the basic biology of flaviviruses, their infectious cycles, the diseases they cause and underlying host immune responses to infection. We describe flaviviruses that represent an established ongoing threat to global health and those that have recently emerged in new populations to cause significant disease. We also provide examples of lesser-known flaviviruses that circulate in restricted areas of the world but have the potential to emerge more broadly in human populations. Finally, we discuss how an understanding of the epidemiology, biology, structure and immunity of flaviviruses can inform the rapid development of countermeasures to treat or prevent human infections as they emerge.
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Affiliation(s)
- Theodore C Pierson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, the National Institutes of Health, Bethesda, MD, USA.
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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24
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Gao X, Zhu K, Wojdyla JA, Chen P, Qin B, Li Z, Wang M, Cui S. Crystal structure of the NS3-like helicase from Alongshan virus. IUCRJ 2020; 7:375-382. [PMID: 32431821 PMCID: PMC7201283 DOI: 10.1107/s2052252520003632] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/11/2020] [Indexed: 05/05/2023]
Abstract
Alongshan virus (ALSV) is an emerging human pathogen that was identified in China and rapidly spread to the European continent in 2019, raising concerns about public health. ALSV belongs to the distinct Jingmenvirus group within the Flaviviridae family with segmented RNA genomes. While segments 2 and 4 of the ALSV genome encode the VP1-VP3 proteins of unknown origin, segments 1 and 3 encode the NS2b-NS3 and NS5 proteins, which are related to Flavivirus nonstructural proteins, suggesting an evolutionary link between segmented and unsegmented viruses within the Flaviviridae family. Here, the enzymatic activity of the ALSV NS3-like helicase (NS3-Hel) was characterized and its crystal structure was determined to 2.9 Å resolution. ALSV NS3-Hel exhibits an ATPase activity that is comparable to those measured for Flavivirus NS3 helicases. The structure of ALSV NS3-Hel exhibits an overall fold similar to those of Flavivirus NS3 helicases. Despite the limited amino-acid sequence identity between ALSV NS3-Hel and Flavivirus NS3 helicases, structural features at the ATPase active site and the RNA-binding groove remain conserved in ALSV NS3-Hel. These findings provide a structural framework for drug design and suggest the possibility of developing a broad-spectrum antiviral drug against both Flavivirus and Jingmenvirus.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | | | - Pu Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | - Ziheng Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | - Meitian Wang
- Swiss Light Source at the Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
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25
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Chong LC, Khan AM. Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design. BMC Genomics 2019; 20:921. [PMID: 31874646 PMCID: PMC6929274 DOI: 10.1186/s12864-019-6311-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 11/24/2022] Open
Abstract
Background The sequence diversity of dengue virus (DENV) is one of the challenges in developing an effective vaccine against the virus. Highly conserved, serotype-specific (HCSS), immune-relevant DENV sequences are attractive candidates for vaccine design, and represent an alternative to the approach of selecting pan-DENV conserved sequences. The former aims to limit the number of possible cross-reactive epitope variants in the population, while the latter aims to limit the cross-reactivity between the serotypes to favour a serotype-specific response. Herein, we performed a large-scale systematic study to map and characterise HCSS sequences in the DENV proteome. Methods All reported DENV protein sequence data for each serotype was retrieved from the NCBI Entrez Protein (nr) Database (txid: 12637). The downloaded sequences were then separated according to the individual serotype proteins by use of BLASTp search, and subsequently removed for duplicates and co-aligned across the serotypes. Shannon’s entropy and mutual information (MI) analyses, by use of AVANA, were performed to measure the diversity within and between the serotype proteins to identify HCSS nonamers. The sequences were evaluated for the presence of promiscuous T-cell epitopes by use of NetCTLpan 1.1 and NetMHCIIpan 3.2 server for human leukocyte antigen (HLA) class I and class II supertypes, respectively. The predicted epitopes were matched to reported epitopes in the Immune Epitope Database. Results A total of 2321 nonamers met the HCSS selection criteria of entropy < 0.25 and MI > 0.8. Concatenating these resulted in a total of 337 HCSS sequences. DENV4 had the most number of HCSS nonamers; NS5, NS3 and E proteins had among the highest, with none in the C and only one in prM. The HCSS sequences were immune-relevant; 87 HCSS sequences were both reported T-cell epitopes/ligands in human and predicted epitopes, supporting the accuracy of the predictions. A number of the HCSS clustered as immunological hotspots and exhibited putative promiscuity beyond a single HLA supertype. The HCSS sequences represented, on average, ~ 40% of the proteome length for each serotype; more than double of pan-DENV sequences (conserved across the four serotypes), and thus offer a larger choice of sequences for vaccine target selection. HCSS sequences of a given serotype showed significant amino acid difference to all the variants of the other serotypes, supporting the notion of serotype-specificity. Conclusion This work provides a catalogue of HCSS sequences in the DENV proteome, as candidates for vaccine target selection. The methodology described herein provides a framework for similar application to other pathogens.
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Affiliation(s)
- Li Chuin Chong
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Jalan MAEPS Perdana, 43400, Serdang, Selangor Darul Ehsan, Malaysia
| | - Asif M Khan
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Jalan MAEPS Perdana, 43400, Serdang, Selangor Darul Ehsan, Malaysia.
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26
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Gaunt MW, Gubler DJ, Pettersson JHO, Kuno G, Wilder-Smith A, de Lamballerie X, Gould EA, Falconar AK. Recombination of B- and T-cell epitope-rich loci from Aedes- and Culex-borne flaviviruses shapes Zika virus epidemiology. Antiviral Res 2019; 174:104676. [PMID: 31837392 DOI: 10.1016/j.antiviral.2019.104676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 02/07/2023]
Abstract
Sporadic human Zika virus (ZIKV) infections have been recorded in Africa and Asia since the 1950s. Major epidemics occurred only after ZIKV emerged in the Pacific islands and spread to the Americas. Specific biological determinants of the explosive epidemic nature of ZIKV have not been identified. Phylogenetic studies revealed incongruence in ZIKV placement in relation to Aedes-borne dengue viruses (DENV) and Culex-borne flaviviruses. We hypothesized that this incongruence reflects interspecies recombination resulting in ZIKV evasion of cross-protective T-cell immunity. We investigated ZIKV phylogenetic incongruence in relation to: DENV T-cell epitope maps experimentally identified ex vivo, published B-cell epitope loci, and CD8+ T-cell epitopes predicted in silico for mosquito-borne flaviviruses. Our findings demonstrate that the ZIKV proteome is a hybrid of Aedes-borne DENV proteins interspersed amongst Culex-borne flavivirus proteins derived through independent interspecies recombination events. These analyses infer that DENV-associated proteins in the ZIKV hybrid proteome generated immunodominant human B-cell responses, whereas ZIKV recombinant derived Culex-borne flavivirus-associated proteins generated immunodominant CD8+ and/or CD4+ T-cell responses. In silico CD8+ T-cell epitope ZIKV cross-reactive prediction analyses verified this observation. We propose that by acquiring cytotoxic T-cell epitope-rich regions from Culex-borne flaviviruses, ZIKV evaded DENV-generated T-cell immune cross-protection. Thus, Culex-borne flaviviruses, including West Nile virus and Japanese encephalitis virus, might induce cross-protective T-cell responses against ZIKV. This would explain why explosive ZIKV epidemics occurred in DENV-endemic regions of Micronesia, Polynesia and the Americas where Culex-borne flavivirus outbreaks are infrequent and why ZIKV did not cause major epidemics in Asia where Culex-borne flaviviruses are widespread.
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Affiliation(s)
- Michael W Gaunt
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Duane J Gubler
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, 169857, Singapore
| | - John H-O Pettersson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Goro Kuno
- 1648 Collindale Dr, Fort Collins, CO, 80525, USA
| | - Annelies Wilder-Smith
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Department of Public Health and Clinical Medicine, Epidemiology and Public Health, Umeå University, Umeå, Sweden; Heidelberg Institute of Global Health, University of Heidelberg, Germany
| | - Xavier de Lamballerie
- UMR "Unité des Virus Emergents", Aix-Marseille Université-IRD 190, Inserm, 1207-IHU Méditerranée Infection, Marseille, France
| | - Ernest A Gould
- UMR "Unité des Virus Emergents", Aix-Marseille Université-IRD 190, Inserm, 1207-IHU Méditerranée Infection, Marseille, France
| | - Andrew K Falconar
- Departmento de Medicina, Universidad del Norte, Barranquilla, Colombia
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27
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Kumar D, Aarthy M, Kumar P, Singh SK, Uversky VN, Giri R. Targeting the NTPase site of Zika virus NS3 helicase for inhibitor discovery. J Biomol Struct Dyn 2019; 38:4827-4837. [DOI: 10.1080/07391102.2019.1689851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Deepak Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Murali Aarthy
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University, Karaikudi, Tamilnadu
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University, Karaikudi, Tamilnadu
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Moscow, Russia
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
- BioX Centre, Indian Institute of Technology Mandi, Mandi, India
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28
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Yellow Fever: Integrating Current Knowledge with Technological Innovations to Identify Strategies for Controlling a Re-Emerging Virus. Viruses 2019; 11:v11100960. [PMID: 31627415 PMCID: PMC6832525 DOI: 10.3390/v11100960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/11/2019] [Indexed: 01/17/2023] Open
Abstract
Yellow fever virus (YFV) represents a re-emerging zoonotic pathogen, transmitted by mosquito vectors to humans from primate reservoirs. Sporadic outbreaks of YFV occur in endemic tropical regions, causing a viral hemorrhagic fever (VHF) associated with high mortality rates. Despite a highly effective vaccine, no antiviral treatments currently exist. Therefore, YFV represents a neglected tropical disease and is chronically understudied, with many aspects of YFV biology incompletely defined including host range, host–virus interactions and correlates of host immunity and pathogenicity. In this article, we review the current state of YFV research, focusing on the viral lifecycle, host responses to infection, species tropism and the success and associated limitations of the YFV-17D vaccine. In addition, we highlight the current lack of available treatments and use publicly available sequence and structural data to assess global patterns of YFV sequence diversity and identify potential drug targets. Finally, we discuss how technological advances, including real-time epidemiological monitoring of outbreaks using next-generation sequencing and CRISPR/Cas9 modification of vector species, could be utilized in future battles against this re-emerging pathogen which continues to cause devastating disease.
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29
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Valente AP, Moraes AH. Zika virus proteins at an atomic scale: how does structural biology help us to understand and develop vaccines and drugs against Zika virus infection? J Venom Anim Toxins Incl Trop Dis 2019; 25:e20190013. [PMID: 31523227 PMCID: PMC6727858 DOI: 10.1590/1678-9199-jvatitd-2019-0013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In Brazil and in other tropical areas Zika virus infection was directly associated with clinical complications as microcephaly in newborn children whose mothers were infected during pregnancy and the Guillain-Barré syndrome in adults. Recently, research has been focused on developing new vaccines and drug candidates against Zika virus infection since none of those are available. In order to contribute to vaccine and drug development efforts, it becomes important the understanding of the molecular basis of the Zika virus recognition, infection and blockade. To this purpose, it is essential the structural determination of the Zika virus proteins. The genome sequencing of the Zika virus identified ten proteins, being three structural (protein E, protein C and protein prM) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). Together, these proteins are the main targets for drugs and antibody recognition. Here we examine new discoveries on high-resolution structural biology of Zika virus, observing the interactions and functions of its proteins identified via state-of-art structural methodologies as X-ray crystallography, nuclear magnetic resonance spectroscopy and cryogenic electronic microscopy. The aim of the present study is to contribute to the understanding of the structural basis of Zika virus infection at an atomic level and to point out similarities and differences to others flaviviruses.
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Affiliation(s)
- Ana Paula Valente
- National Center of Magnetic Resonance, Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Adolfo Henrique Moraes
- Department of Chemistry, Institute of Exact Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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Wang Y, Zhang S, Tang Y, Diao Y. Screening of Duck Tembusu Virus NS3 Interacting Host Proteins and Identification of Its Specific Interplay Domains. Viruses 2019; 11:E740. [PMID: 31408972 PMCID: PMC6722602 DOI: 10.3390/v11080740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 07/19/2019] [Accepted: 08/02/2019] [Indexed: 01/01/2023] Open
Abstract
NS3 protein is a member of the non-structural protein of duck Tembusu virus (DTMUV), which contains three domains, each of which has serine protease, nucleotide triphosphatase, and RNA helicase activities, respectively. It performs a variety of biological functions that are involved in the regulation of the viral life cycle and host immune response. Based on the yeast two-hybrid system, we successfully transformed pGBKT7-NS3 bait plasmid into Y2H Gold, tested it to prove that it has no self-activation and toxicity, and then hybridized it with the prey yeast strain of the duck embryo fibroblast cDNA library for screening. After high-stringency selection, positive alignment with the National Center for Biotechnology Information database revealed nine potential interactive proteins: MGST1, ERCC4, WIF1, WDR75, ACBD3, PRDX1, RPS7, ND5, and LDHA. The most interesting one (PRDX1) was selected to be verified with full-length NS3 protein and its three domains S7/DEXDc/HELICc using yeast regressive verification and GST Pull-Down assay. It denoted that PRDX1 does indeed interact with HELICc domains of NS3. NS3 is involved in the RNA uncoiling process of viral replication, which may cause mitochondrial overload to create oxidative stress (OS) during DTMUV attack. We deduced that the HELICc domain binding partner PRDX1, which regulates the p38/mitogen-activated protein kinase pathway (p38/MAPK) to avert OS, causing apoptosis, making it possible for viruses to escape host immune responses.
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Affiliation(s)
- Yawen Wang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
| | - Shuai Zhang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China.
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China.
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China.
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China.
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China.
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Road, Tai'an 271018, China.
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Dubankova A, Boura E. Structure of the yellow fever NS5 protein reveals conserved drug targets shared among flaviviruses. Antiviral Res 2019; 169:104536. [PMID: 31202975 DOI: 10.1016/j.antiviral.2019.104536] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/23/2022]
Abstract
Yellow fever virus (YFV) is responsible for devastating outbreaks of Yellow fever (YF) in humans and is associated with high mortality rates. Recent large epidemics and epizootics and exponential increases in the numbers of YF cases in humans and non-human primates highlight the increasing threat YFV poses, despite the availability of an effective YFV vaccine. YFV is the first human virus discovered, but the structures of several of the viral proteins remain poorly understood. Here we report the structure of the full-length NS5 protein, a key enzyme for the replication of flaviviruses that contains both a methyltransferase domain and an RNA dependent RNA polymerase domain, at 3.1 Å resolution. The viral polymerase adopts right-hand fold, demonstrating the similarities of the Yellow fever, Dengue and Zika polymerases. Together this data suggests NS5 as a prime and ideal target for the design of pan-flavivirus inhibitors.
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Affiliation(s)
- Anna Dubankova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic.
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32
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Dighe SN, Ekwudu O, Dua K, Chellappan DK, Katavic PL, Collet TA. Recent update on anti-dengue drug discovery. Eur J Med Chem 2019; 176:431-455. [PMID: 31128447 DOI: 10.1016/j.ejmech.2019.05.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/12/2019] [Accepted: 05/06/2019] [Indexed: 01/27/2023]
Abstract
Dengue is the most important arthropod-borne viral disease of humans, with more than half of the global population living in at-risk areas. Despite the negative impact on public health, there are no antiviral therapies available, and the only licensed vaccine, Dengvaxia®, has been contraindicated in children below nine years of age. In an effort to combat dengue, several small molecules have entered into human clinical trials. Here, we review anti-DENV molecules and their drug targets that have been published within the past five years (2014-2018). Further, we discuss their probable mechanisms of action and describe a role for classes of clinically approved drugs and also an unclassified class of anti-DENV agents. This review aims to enhance our understanding of novel agents and their cognate targets in furthering innovations in the use of small molecules for dengue drug therapies.
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Affiliation(s)
- Satish N Dighe
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia.
| | - O'mezie Ekwudu
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University (IMU), Bukit Jalil, Kuala Lumpur, 57000, Malaysia
| | - Peter L Katavic
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Trudi A Collet
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
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de Godoy AS, Sachetto Fernandes R, Campos Aguiar AC, Vieira Bueno R, de Moraes Roso Mesquita NC, Carvalho Guido RV, Oliva G. Structural and mechanistic insight from antiviral and antiparasitic enzyme drug targets for tropical infectious diseases. Curr Opin Struct Biol 2019; 59:65-72. [PMID: 30954758 DOI: 10.1016/j.sbi.2019.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 02/23/2019] [Accepted: 02/28/2019] [Indexed: 12/28/2022]
Abstract
With almost half of the world population living at risk, tropical infectious diseases cause millions of deaths every year in developing countries. Considering the lack of economic prospects for investment in this field, approaches aiming the rational design of compounds, such as structure-based drug discovery (SBDD), fragment screening, target-based drug discovery, and drug repurposing are of special interest. Herein, we focused in the advances on the field of SBDD targeting arboviruses such as dengue, yellow fever, zika and chikungunya enzymes of the RNA replication complex (RC) and enzymes involved in a variety of pathways essential to ensure parasitic survival in the host, for malaria, Chagas e leishmaniasis diseases. We also highlighted successful examples such as promising new inhibitors and molecules already in preclinical/clinical phase tests, major gaps in the field and perspectives for the future of drug design for tropical diseases.
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Affiliation(s)
- Andre Schutzer de Godoy
- Institute of Physics of São Carlos, University of São Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, São Carlos 13563-120, Brazil
| | - Rafaela Sachetto Fernandes
- Institute of Physics of São Carlos, University of São Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, São Carlos 13563-120, Brazil
| | - Anna Caroline Campos Aguiar
- Institute of Physics of São Carlos, University of São Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, São Carlos 13563-120, Brazil
| | - Renata Vieira Bueno
- Institute of Physics of São Carlos, University of São Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, São Carlos 13563-120, Brazil
| | | | - Rafael Victorio Carvalho Guido
- Institute of Physics of São Carlos, University of São Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, São Carlos 13563-120, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, São Carlos 13563-120, Brazil.
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Zhu G, Pan A, Grüber G, Lu L. Conformational states of Zika virus non-structural protein 3 determined by molecular dynamics simulations with small-angle X-Ray scattering data. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:13-19. [PMID: 30291845 DOI: 10.1016/j.pbiomolbio.2018.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/17/2018] [Accepted: 09/29/2018] [Indexed: 11/16/2022]
Abstract
Zika virus (ZIKV) has become a great public health emergency. Its non-structural protein 3 (NS3) is a key enzyme in viral replication and has been considered as a potential therapeutic target. A conformational characterization of ZIKV NS3 is critical for a comprehensive understanding of its molecular interactions and functions. However, the high conformational flexibility of solution NS3 obstacles the structural characterization of NS3 solely from the experimental observable that averages over its heterogeneous conformations. Here, we employed replica exchange with solute tempering (REST) method to simulate the di-domain protein ZIKV NS3. Three independent MD simulations identified a conserved conformational ensemble of NS3, consisting of a major conformational state and several minor states from compact to loose conformations. The major state agrees well with the scattering profile from small-angle X-ray scattering (SAXS) experiments. Moreover, the simulated ensemble is supported by a direct data-fitting result that requires both short- and long-range structural contacts to recover the experimental data. We discussed the interplay between simulation and experiment in ensemble construction of flexible biomolecules and shed light on the physically derived conformational ensembles.
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Affiliation(s)
- Guanhua Zhu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Ankita Pan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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Lei Y, Takeda K, Yu L. Impaired heterologous protein-protein interaction is an essential cause for non-viability of WNV/DENV recombinants. Virology 2018; 524:140-150. [PMID: 30195251 DOI: 10.1016/j.virol.2018.08.013] [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: 05/04/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 10/28/2022]
Abstract
Flavivirus RNA replication starts at 3'-end, where it folds into a highly conserved stem-loop structure. We attempted to identify the viral non-structural proteins (NSPs) that might specifically interact with the 3'-stemloop (3'SL) through a genetic approach. WNV/DENV2 chimeric recombinants that contain Dengue2 (DENV2) gene(s) in West Nile virus (WNV) backbone were tested for replication competence. Three of seven recombinant viruses, containing the DENV2 NS1, NS2A, or NS4B gene and terminated with a mutated 3'SL (MutC 3'SL), were viable. Of these three, only those bearing the DENV2 NS1 and NS2A substitutions remained infectious when the MutC 3'SL was replaced by the wildtype WNV 3'SL. However, none of the seven chimeric recombinants bearing the DENV2 3'SL were viable. We then investigated the causes for failed replication of WNV/DENV2 chimeric recombinants. Proteolytic cleavage of NS polyproteins was defective by heterologous protease NS2B/3, but was efficient by homologous DENV2 NS2B/3 protease. Whereas, the heterologous polyproteins that contained DENV2 homologous protease were found to produce abnormal vesicles. WNV/DENV2 recombinants expressing the DENV2 homologous protease did not produce infectious virus either. We examined NS protein-protein interaction (PPI) and found that heterologous PPI (hPPI) between WNV and DENV2 NSPs were impaired to various degrees. Insufficient PPIs occurred mainly between heterologous NS2B and NS3; NS2B and NS4A; NS3 and NS5, correlating to those non-viability of substitution mutants. Our results indicate that impaired PPI may decrease protease activity and affect vesicle formation, and is the essential cause for non-viability of the WNV/DENV2 recombinants.
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Affiliation(s)
- Yingfen Lei
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852, USA; Department of Microbiology, The Fourth Military Medical University, 17 Changle Xilu, Xi'an, Shaanxi 710032, PR China
| | - Kazuyo Takeda
- Microscopy and Imaging Core Facility, Office of Vaccines Research and Review Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Li Yu
- Division of Viral Products, Office of Vaccines Research and Review Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
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36
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Dwivedi VD, Tripathi IP, Tripathi RC, Bharadwaj S, Mishra SK. Genomics, proteomics and evolution of dengue virus. Brief Funct Genomics 2018; 16:217-227. [PMID: 28073742 DOI: 10.1093/bfgp/elw040] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genome of a pathogenic organism possesses a specific order of nucleotides that contains not only information about the synthesis and expression of proteomes, which are required for its growth and survival, but also about its evolution. Inhibition of any particular protein, which is required for the survival of that pathogenic organism, can be used as a potential therapeutic target for the development of effective drugs to treat its infections. In this review, the genomics, proteomics and evolution of dengue virus have been discussed, which will be helpful in better understanding of its origin, growth, survival and evolution, and may contribute toward development of new efficient anti-dengue drugs.
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37
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Rumlová M, Ruml T. In vitro methods for testing antiviral drugs. Biotechnol Adv 2018; 36:557-576. [PMID: 29292156 PMCID: PMC7127693 DOI: 10.1016/j.biotechadv.2017.12.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/24/2022]
Abstract
Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses.
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Affiliation(s)
- Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
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38
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Li L, Wang J, Jia Z, Shaw N. Structural view of the helicase reveals that Zika virus uses a conserved mechanism for unwinding RNA. Acta Crystallogr F Struct Biol Commun 2018; 74:205-213. [PMID: 29633968 PMCID: PMC5894106 DOI: 10.1107/s2053230x18003813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 03/05/2018] [Indexed: 02/05/2023] Open
Abstract
Recent studies suggest a link between infection by Zika virus (ZIKV) and the development of neurological complications. The lack of ZIKV-specific therapeutics has alarmed healthcare professionals worldwide. Here, crystal structures of apo and AMPPNP- and Mn2+-bound forms of the essential helicase of ZIKV refined to 1.78 and 1.3 Å resolution, respectively, are reported. The structures reveal a conserved trimodular topology of the helicase. ATP and Mn2+ are tethered between two RecA-like domains by conserved hydrogen-bonding interactions. The binding of ligands induces the movement of backbone Cα and side-chain atoms. Numerous solvent molecules are observed in the vicinity of the AMPPNP, suggesting a role in catalysis. These high-resolution structures could be useful for the design of inhibitors targeting the helicase of ZIKV for the treatment of infections caused by ZIKV.
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Affiliation(s)
- Lei Li
- State Key Laboratory of Biotherapy and Cancer Center/National Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Jin Wang
- State Key Laboratory of Biotherapy and Cancer Center/National Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, People’s Republic of China
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Zhihui Jia
- Laboratory of Structural Biology and MOE Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Neil Shaw
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, People’s Republic of China
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Gómez MM, Abreu FVSD, Santos AACD, Mello ISD, Santos MP, Ribeiro IP, Ferreira-de-Brito A, Miranda RMD, Castro MGD, Ribeiro MS, Laterrière Junior RDC, Aguiar SF, Meira GLS, Antunes D, Torres PHM, Mir D, Vicente ACP, Guimarães ACR, Caffarena ER, Bello G, Lourenço-de-Oliveira R, Bonaldo MC. Genomic and structural features of the yellow fever virus from the 2016-2017 Brazilian outbreak. J Gen Virol 2018; 99:536-548. [PMID: 29469689 DOI: 10.1099/jgv.0.001033] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Southeastern Brazil has been suffering a rapid expansion of a severe sylvatic yellow fever virus (YFV) outbreak since late 2016, which has reached one of the most populated zones in Brazil and South America, heretofore a yellow fever-free zone for more than 70 years. In the current study, we describe the complete genome of 12 YFV samples from mosquitoes, humans and non-human primates from the Brazilian 2017 epidemic. All of the YFV sequences belong to the modern lineage (sub-lineage 1E) of South American genotype I, having been circulating for several months prior to the December 2016 detection. Our data confirm that viral strains associated with the most severe YF epidemic in South America in the last 70 years display unique amino acid substitutions that are mainly located in highly conserved positions in non-structural proteins. Our data also corroborate that YFV has spread southward into Rio de Janeiro state following two main sylvatic dispersion routes that converged at the border of the great metropolitan area comprising nearly 12 million unvaccinated inhabitants. Our original results can help public health authorities to guide the surveillance, prophylaxis and control measures required to face such a severe epidemiological problem. Finally, it will also inspire other workers to further investigate the epidemiological and biological significance of the amino acid polymorphisms detected in the Brazilian 2017 YFV strains.
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Affiliation(s)
- Mariela Martínez Gómez
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Filipe Vieira Santos de Abreu
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Instituto Federal do Norte de Minas Gerais, Salinas, MG, Brazil
| | | | - Iasmim Silva de Mello
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marta Pereira Santos
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ieda Pereira Ribeiro
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Anielly Ferreira-de-Brito
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Rafaella Moraes de Miranda
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcia Gonçalves de Castro
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Mario Sergio Ribeiro
- Superintendência de Vigilância Epidemiológica e Ambiental, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil
| | | | | | | | - Deborah Antunes
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Daiana Mir
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Carolina Paulo Vicente
- Laboratório de Genética Molecular de Microorganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Carolina Ramos Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ernesto Raul Caffarena
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ricardo Lourenço-de-Oliveira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Myrna Cristina Bonaldo
- Laboratório de Biologia Molecular de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Kazmirchuk T, Dick K, Burnside DJ, Barnes B, Moteshareie H, Hajikarimlou M, Omidi K, Ahmed D, Low A, Lettl C, Hooshyar M, Schoenrock A, Pitre S, Babu M, Cassol E, Samanfar B, Wong A, Dehne F, Green JR, Golshani A. Designing anti-Zika virus peptides derived from predicted human-Zika virus protein-protein interactions. Comput Biol Chem 2017; 71:180-187. [DOI: 10.1016/j.compbiolchem.2017.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/03/2017] [Accepted: 10/27/2017] [Indexed: 01/22/2023]
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Helicase Domain of West Nile Virus NS3 Protein Plays a Role in Inhibition of Type I Interferon Signalling. Viruses 2017; 9:v9110326. [PMID: 29099073 PMCID: PMC5707533 DOI: 10.3390/v9110326] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 11/17/2022] Open
Abstract
West Nile virus (WNV) is a neurotropic flavivirus that can cause encephalitis in mammalian and avian hosts. In America, the virulent WNV strain (NY99) is causing yearly outbreaks of encephalitis in humans and horses, while in Australia the less virulent Kunjin strain of WNV strain has not been associated with significant disease outbreaks until a recent 2011 large outbreak in horses (but not in humans) caused by NSW2011 strain. Using chimeric viruses between NY99 and NSW2011 strains we previously identified a role for the non-structural proteins of NY99 strain and especially the NS3 protein, in enhanced virus replication in type I interferon response-competent cells and increased virulence in mice. To further define the role of NY99 NS3 protein in inhibition of type I interferon response, we have generated and characterised additional chimeric viruses containing the protease or the helicase domains of NY99 NS3 on the background of the NSW2011 strain. The results identified the role for the helicase but not the protease domain of NS3 protein in the inhibition of type I interferon signalling and showed that helicase domain of the more virulent NY99 strain performs this function more efficiently than helicase domain of the less virulent NSW2011 strain. Further analysis with individual amino acid mutants identified two amino acid residues in the helicase domain primarily responsible for this difference. Using chimeric replicons, we also showed that the inhibition of type I interferon (IFN) signalling was independent of other known functions of NS3 in RNA replication and assembly of virus particles.
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42
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Uncoupling of Protease trans-Cleavage and Helicase Activities in Pestivirus NS3. J Virol 2017; 91:JVI.01094-17. [PMID: 28835495 DOI: 10.1128/jvi.01094-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/07/2017] [Indexed: 01/25/2023] Open
Abstract
The nonstructural protein NS3 from the Flaviviridae family is a multifunctional protein that contains an N-terminal protease and a C-terminal helicase, playing essential roles in viral polyprotein processing and genome replication. Here we report a full-length crystal structure of the classical swine fever virus (CSFV) NS3 in complex with its NS4A protease cofactor segment (PCS) at a 2.35-Å resolution. The structure reveals a previously unidentified ∼2,200-Å2 intramolecular protease-helicase interface comprising three clusters of interactions, representing a "closed" global conformation related to the NS3-NS4A cis-cleavage event. Although this conformation is incompatible with protease trans-cleavage, it appears to be functionally important and beneficial to the helicase activity, as the mutations designed to perturb this conformation impaired both the helicase activities in vitro and virus production in vivo Our work reveals important features of protease-helicase coordination in pestivirus NS3 and provides a key basis for how different conformational states may explicitly contribute to certain functions of this natural protease-helicase fusion protein.IMPORTANCE Many RNA viruses encode helicases to aid their RNA genome replication and transcription by unwinding structured RNA. Being naturally fused to a protease participating in viral polyprotein processing, the NS3 helicases encoded by the Flaviviridae family viruses are unique. Therefore, how these two enzyme modules coordinate in a single polypeptide is of particular interest. Here we report a previously unidentified conformation of pestivirus NS3 in complex with its NS4A protease cofactor segment (PCS). This conformational state is related to the protease cis-cleavage event and is optimal for the function of helicase. This work provides an important basis to understand how different enzymatic activities of NS3 may be achieved by the coordination between the protease and helicase through different conformational states.
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43
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Brand C, Bisaillon M, Geiss BJ. Organization of the Flavivirus RNA replicase complex. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28815931 DOI: 10.1002/wrna.1437] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/09/2017] [Accepted: 07/13/2017] [Indexed: 12/20/2022]
Abstract
Flaviviruses, such as dengue, Japanese encephalitis, West Nile, yellow fever, and Zika viruses, are serious human pathogens that cause significant morbidity and mortality globally each year. Flaviviruses are single-stranded, positive-sense RNA viruses, and encode two multidomain proteins, NS3 and NS5, that possess all enzymatic activities required for genome replication and capping. NS3 and NS5 interact within virus-induced replication compartments to form the RNA genome replicase complex. Although the individual enzymatic activities of both proteins have been extensively studied and are well characterized, there are still gaps in our understanding of how they interact to efficiently coordinate their respective activities during positive-strand RNA synthesis and capping. Here, we discuss what is known about the structures and functions of the NS3 and NS5 proteins and propose a preliminary NS3:NS5:RNA interaction model based on a large body of literature about how the viral enzymes function, physical restraints between NS3 and NS5, as well as critical steps in the replication process. WIREs RNA 2017, 8:e1437. doi: 10.1002/wrna.1437 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Carolin Brand
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Martin Bisaillon
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA.,School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
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Papageorgiou L, Loukatou S, Sofia K, Maroulis D, Vlachakis D. An updated evolutionary study of Flaviviridae NS3 helicase and NS5 RNA-dependent RNA polymerase reveals novel invariable motifs as potential pharmacological targets. MOLECULAR BIOSYSTEMS 2017; 12:2080-93. [PMID: 26864387 DOI: 10.1039/c5mb00706b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The rate of Flaviviridae family virus infections worldwide has increased dramatically in the last few years. In addition, infections caused by arthropod vector viruses including Hepatitis C, West Nile, Dengue fever, Yellow fever and Japanese encephalitis are emerging throughout the world. Based on a recent taxon update, the Flaviviridae family comprises four main genera; Flavivirus, Hepacivirus, Pestivirus and a recent genus Pegivirus. Although the new scientific classification plays a key role in providing useful information about the relationships between viruses, many new documented viruses remain unclassified. Furthermore, based on the different results of several studies the classification is unclear. In an effort to provide more insights into the classification of viruses, a holistic evolutionary study of the two viral enzymes NS3 helicase and NS5 RNA-dependent RNA polymerase (RdRp) has been conducted in this study. These two viral enzymes are very crucial for the inhibition of viruses due to the fact that they are involved in the survival, proliferation and transmission of viruses. The main goal of this study is the presentation of two novel updated phylogenetic trees of the enzymes NS3 helicase and NS5 RdRp as a reliable phylogeny "map" to correlate the information of the closely related viruses and identify new possible targets for the Flaviviridae family virus inhibition. Despite the earliest trials for drugs against Flaviviridae related viruses, no antiviral drug vaccine has been available to date. Therefore there is an urgent need for research towards the development of efficient antiviral agents.
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Affiliation(s)
- Louis Papageorgiou
- Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece. and Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, University Campus, Athens, 15784, Greece
| | - Styliani Loukatou
- Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece.
| | - Kossida Sofia
- IMGT®, The International ImMunoGeneTics Information System®, Universite de Montpellier, Laboratoire d'ImmunoGenetique Moleculaire LIGM, UPR CNRS 1142, Institut de Genetique Humaine, 141 rue de la Cardonille, Montpellier, 34396 Cedex 5, France
| | - Dimitrios Maroulis
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, University Campus, Athens, 15784, Greece
| | - Dimitrios Vlachakis
- Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece.
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Vidotto A, Morais ATS, Ribeiro MR, Pacca CC, Terzian ACB, Gil LHVG, Mohana-Borges R, Gallay P, Nogueira ML. Systems Biology Reveals NS4B-Cyclophilin A Interaction: A New Target to Inhibit YFV Replication. J Proteome Res 2017; 16:1542-1555. [PMID: 28317380 DOI: 10.1021/acs.jproteome.6b00933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Yellow fever virus (YFV) replication is highly dependent on host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1-DE and LC-MS/MS. We present a total of 207 proteins confirmed using Scaffold 3 Software. Cyclophilin A (CypA), a protein that has been shown to be necessary for the positive regulation of flavivirus replication, was identified as a possible NS4B partner. 59 proteins were found to be significantly increased when compared with a negative control, and CypA exhibited the greatest difference, with a 22-fold change. Fisher's exact test was significant for 58 proteins, and the p value of CypA was the most significant (0.000000019). The Ingenuity Systems software identified 16 pathways, and this analysis indicated sirolimus, an mTOR pathway inhibitor, as a potential inhibitor of CypA. Immunofluorescence and viral plaque assays showed a significant reduction in YFV replication using sirolimus and cyclosporine A (CsA) as inhibitors. Furthermore, YFV replication was strongly inhibited in cells treated with both inhibitors using reporter BHK-21-rep-YFV17D-LucNeoIres cells. Taken together, these data suggest that CypA-NS4B interaction regulates YFV replication. Finally, we present the first evidence that YFV inhibition may depend on NS4B-CypA interaction.
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Affiliation(s)
- Alessandra Vidotto
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Ana T S Morais
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Milene R Ribeiro
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Carolina C Pacca
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Ana C B Terzian
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
| | - Laura H V G Gil
- Departamento de Virologia, Centro de Pesquisa Aggeu Magalhães , Fundação Oswaldo Cruz (FIOCRUZ) - Recife, Pernambuco 50740-465, Brazil
| | - Ronaldo Mohana-Borges
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro - UFRJ , Rio de Janeiro RJ 21941-902, Brazil
| | - Philippe Gallay
- Department of Immunology & Microbial Science, The Scripps Research Institute - La Jolla , San Diego, California 92037, United States
| | - Mauricio L Nogueira
- Laboratório de Virologia, Faculdade de Medicina de José do Rio Preto , São José do Rio Preto, São Paulo 15090-000, Brazil
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Ekins S, Liebler J, Neves BJ, Lewis WG, Coffee M, Bienstock R, Southan C, Andrade CH. Illustrating and homology modeling the proteins of the Zika virus. F1000Res 2016; 5:275. [PMID: 27746901 DOI: 10.12688/f1000research.8213.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/28/2022] Open
Abstract
The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, USA; Collaborations Pharmaceuticals Inc., Fuquay-Varina, NC, USA; Collaborative Drug Discovery Inc, Burlingame, CA, USA
| | | | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
| | - Warren G Lewis
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Megan Coffee
- The International Rescue Committee, New York, NY, USA
| | | | | | - Carolina H Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
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Structure of the NS3 helicase from Zika virus. Nat Struct Mol Biol 2016; 23:752-4. [PMID: 27399257 PMCID: PMC5085289 DOI: 10.1038/nsmb.3258] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/14/2016] [Indexed: 12/27/2022]
Abstract
Zika virus has emerged as a pathogen of major health concern. Here, we present a high-resolution (1.62-Å) crystal structure of the RNA helicase from the French Polynesia strain. The structure is similar to that of the RNA helicase from Dengue virus, with variability in the conformations of loops typically involved in binding ATP and RNA. We identify druggable 'hotspots' that are well suited for in silico and/or fragment-based high-throughput drug discovery.
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48
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Chiang PY, Wu HN. The role of surface basic amino acids of dengue virus NS3 helicase in viral RNA replication and enzyme activities. FEBS Lett 2016; 590:2307-20. [DOI: 10.1002/1873-3468.12232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Pao-Yin Chiang
- Graduate Institute of Life Sciences; National Defense Medical Centre; Taipei Taiwan
- Institute of Molecular Biology; Academia Sinica; Taipei Taiwan
| | - Huey-Nan Wu
- Institute of Molecular Biology; Academia Sinica; Taipei Taiwan
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49
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Abstract
INTRODUCTION Flaviviruses are major causes of infectious disease. The vast global, social and economic impact due to morbidity and mortality associated with diseases caused by these viruses urgently demands effective therapeutic interventions. There is currently no specific antiviral therapy available for the effective clinical treatment of infections by any of the flaviviridae. Development of more effective vaccines and antiviral agents for the prevention and treatment of most flavivirus infections remains a clear public health priority in the 21st century. AREAS COVERED This review describes some of the recent discoveries in the field of flavivirus inhibitor development, with a particular focus on targeting viral proteins. Emphasis is placed on the advances published during the 2012-2015 period. EXPERT OPINION The field of drug discovery targeting viral proteins has progressed slowly in recent years. New information, particularly on structures, location and mechanisms of action of established protein targets have been reported. There have also been studies on repurposing known drugs as templates for targeting flavivirus proteins and these hits could be promising templates for developing new more potent inhibitors. Further research should be conducted to improve in vitro assays that better reflect the conditions found in cellular environments.
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Affiliation(s)
- W Mei Kok
- a Division of Chemistry and Structural Biology, Institute for Molecular Bioscience , The University of Queensland , Brisbane , Australia
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50
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Ekins S, Liebler J, Neves BJ, Lewis WG, Coffee M, Bienstock R, Southan C, Andrade CH. Illustrating and homology modeling the proteins of the Zika virus. F1000Res 2016; 5:275. [PMID: 27746901 PMCID: PMC5040154 DOI: 10.12688/f1000research.8213.2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/30/2016] [Indexed: 12/20/2022] Open
Abstract
The Zika virus (ZIKV) is a flavivirus of the family
Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either
in vitro or
in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, USA; Collaborations Pharmaceuticals Inc., Fuquay-Varina, NC, USA; Collaborative Drug Discovery Inc, Burlingame, CA, USA
| | | | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
| | - Warren G Lewis
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Megan Coffee
- The International Rescue Committee, New York, NY, USA
| | | | | | - Carolina H Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
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