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Metibemu DS, Adeyinka OS, Falode J, Crown O, Ogungbe IV. Inhibitors of the Structural and Nonstructural Proteins of Alphaviruses. ACS Infect Dis 2024; 10:2507-2524. [PMID: 38992989 DOI: 10.1021/acsinfecdis.4c00254] [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] [Indexed: 07/13/2024]
Abstract
The Alphavirus genus includes viruses that cause encephalitis due to neuroinvasion and viruses that cause arthritis due to acute and chronic inflammation. There is no approved therapeutic for alphavirus infections, but significant efforts are ongoing, more so in recent years, to develop vaccines and therapeutics for alphavirus infections. This review article highlights some of the major advances made so far to identify small molecules that can selectively target the structural and the nonstructural proteins in alphaviruses with the expectation that persistent investigation of an increasingly expanding chemical space through a variety of structure-based design and high-throughput screening strategies will yield candidate drugs for clinical studies. While most of the works discussed are still in the early discovery to lead optimization stages, promising avenues remain for drug development against this family of viruses.
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Affiliation(s)
- Damilohun Samuel Metibemu
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
| | - Olawale Samuel Adeyinka
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
| | - John Falode
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
| | - Olamide Crown
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
| | - Ifedayo Victor Ogungbe
- Chemistry and Biotechnology Science and Engineering Programs, The University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, Alabama 35899, United States
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2
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Davuluri KS, Shukla S, Kakade M, Cherian S, Alagarasu K, Parashar D. Explorations on the antiviral potential of zinc and magnesium salts against chikungunya virus: implications for therapeutics. Front Cell Infect Microbiol 2024; 14:1335189. [PMID: 38895735 PMCID: PMC11183322 DOI: 10.3389/fcimb.2024.1335189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/09/2024] [Indexed: 06/21/2024] Open
Abstract
Background Chikungunya virus (CHIKV), which causes chikungunya fever, is an arbovirus of public health concern with no approved antiviral therapies. A significant proportion of patients develop chronic arthritis after an infection. Zinc and magnesium salts help the immune system respond effectively against viral infections. This study explored the antiviral potential of zinc sulphate, zinc acetate, and magnesium sulphate against CHIKV infection. Methods The highest non-toxic concentration of the salts (100 µM) was used to assess the prophylactic, virucidal, and therapeutic anti-CHIKV activities. Dose-dependent antiviral effects were investigated to find out the 50% inhibitory concentration of the salts. Entry bypass assay was conducted to find out whether the salts affect virus entry or post entry stages. Virus output in all these experiments was estimated using a focus-forming unit assay, real-time RT-PCR, and immunofluorescence assay. Results Different time- and temperature-dependent assays revealed the therapeutic antiviral activity of zinc and magnesium salts against CHIKV. A minimum exposure of 4 hours and treatment initiation within 1 to 2 hours of infection are required for inhibition of CHIKV. Entry assays revealed that zinc salt affected virus-entry. Entry bypass assays suggested that both salts affected post-entry stages of CHIKV. In infected C57BL6 mice orally fed with zinc and magnesium salts, a reduction in viral RNA copy number was observed. Conclusion The study results suggest zinc salts exert anti-CHIKV activity at entry and post entry stages of the virus life cycle, while magnesium salt affect CHIKV at post entry stages. Overall, the study highlights the significant antiviral potential of zinc sulphate, zinc acetate, and magnesium sulphate against CHIKV, which can be exploited in designing potential therapeutic strategies for early treatment of chikungunya patients, thereby reducing the virus-associated persistent arthritis.
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Affiliation(s)
- Kusuma Sai Davuluri
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
| | - Shridhar Shukla
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
| | - Mahadeo Kakade
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
| | - Sarah Cherian
- Bioinformatics Group, ICMR-National Institute of Virology, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kalichamy Alagarasu
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Deepti Parashar
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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3
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Muslihati A, Septiani NLW, Gumilar G, Nugraha N, Wasisto HS, Yuliarto B. Peptide-Based Flavivirus Biosensors: From Cell Structure to Virological and Serological Detection Methods. ACS Biomater Sci Eng 2024; 10:2041-2061. [PMID: 38526408 DOI: 10.1021/acsbiomaterials.3c01965] [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] [Indexed: 03/26/2024]
Abstract
In tropical and developing countries, mosquito-borne diseases by flaviviruses pose a serious threat to public health. Early detection is critical for preventing their spread, but conventional methods are time-consuming and require skilled technicians. Biosensors have been developed to address this issue, but cross-reactivity with other flaviviruses remains a challenge. Peptides are essentially biomaterials used in diagnostics that allow virological and serological techniques to identify flavivirus selectively. This biomaterial originated as a small protein consisting of two to 50 amino acid chains. They offer flexibility in chemical modification and can be easily synthesized and applied to living cells in the engineering process. Peptides could potentially be developed as robust, low-cost, sensitive, and selective receptors for detecting flaviviruses. However, modification and selection of the receptor agents are crucial to determine the effectiveness of binding between the targets and the receptors. This paper addresses two potential peptide nucleic acids (PNAs) and affinity peptides that can detect flavivirus from another target-based biosensor as well as the potential peptide behaviors of flaviviruses. The PNAs detect flaviviruses based on the nucleotide base sequence of the target's virological profile via Watson-Crick base pairing, while the affinity peptides sense the epitope or immunological profile of the targets. Recent developments in the functionalization of peptides for flavivirus biosensors are explored in this Review by division into electrochemical, optical, and other detection methods.
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Affiliation(s)
- Atqiya Muslihati
- Doctoral Program of Engineering Physics, Faculty of Industrial Technology, Institut Teknologi Bandung, Ganesha 10, Bandung 40132, Indonesia
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- PT Biostark Analitika Inovasi, Bandung 40375, Indonesia
| | - Ni Luh Wulan Septiani
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanotechnology Systems, National Research and Innovation Agency (BRIN), Kawasan Puspiptek, South Tangerang 15134, Indonesia
| | - Gilang Gumilar
- Research Center for Electronics, National Research and Innovation Agency (BRIN), Bandung 40135, Indonesia
| | - Nugraha Nugraha
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanosciences and Nanotechnology (RCNN), Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
| | | | - Brian Yuliarto
- Advanced Functional Material Laboratory, Faculty of Industrial Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
- Research Center for Nanosciences and Nanotechnology (RCNN), Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung 41032, Indonesia
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4
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Wang M, Wang L, Leng P, Guo J, Zhou H. Drugs targeting structural and nonstructural proteins of the chikungunya virus: A review. Int J Biol Macromol 2024; 262:129949. [PMID: 38311132 DOI: 10.1016/j.ijbiomac.2024.129949] [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: 08/26/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 02/06/2024]
Abstract
Chikungunya virus (CHIKV) is a single positive-stranded RNA virus of the Togaviridae family and Alphavirus genus, with a typical lipid bilayer envelope structure, and is the causative agent of human chikungunya fever (CHIKF). The U.S. Food and Drug Administration has recently approved the first chikungunya vaccine, Ixchiq; however, vaccination rates are low, and CHIKF is prevalent owing to its periodic outbreaks. Thus, developing effective anti-CHIKV drugs in clinical settings is imperative. Viral proteins encoded by the CHIKV genome play vital roles in all stages of infection, and developing therapeutic agents that target these CHIKV proteins is an effective strategy to improve CHIKF treatment efficacy and reduce mortality rates. Therefore, in the present review article, we aimed to investigate the basic structure, function, and replication cycle of CHIKV and comprehensively outline the current status and future advancements in anti-CHIKV drug development, specifically targeting nonstructural (ns) proteins, including nsP1, nsP2, nsP3, and nsP4 and structural proteins such as capsid (C), E3, E2, 6K, and E1.
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Affiliation(s)
- Mengke Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lidong Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ping Leng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jinlin Guo
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Traditional Chinese Medicine Hospital, Chongqing 400016, China.
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Martin MF, Bonaventure B, McCray NE, Peersen OB, Rozen-Gagnon K, Stapleford KA. Distinct chikungunya virus polymerase palm subdomains contribute to virus replication and virion assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575630. [PMID: 38293111 PMCID: PMC10827052 DOI: 10.1101/2024.01.15.575630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Alphaviruses encode an error-prone RNA-dependent RNA polymerase (RdRp), nsP4, required for genome synthesis, yet how the RdRp functions in the complete alphavirus life cycle is not well-defined. Previous work using chikungunya virus (CHIKV) has established the importance of the nsP4 residue cysteine 483 in maintaining viral genetic fidelity. Given the location of residue C483 in the nsP4 palm domain, we hypothesized that other residues within this domain and surrounding subdomains would also contribute to polymerase function. To test this hypothesis, we designed a panel of nsP4 variants via homology modeling based on the Coxsackievirus B3 3 polymerase. We rescued each variant in both mammalian and mosquito cells and discovered that the palm domain and ring finger subdomain contribute to polymerase host-specific replication and genetic stability. Surprisingly, in mosquito cells, these variants in the ring finger and palm domain were replication competent and produced viral structural proteins, but they were unable to produce infectious progeny, indicating a yet uncharacterized role for the polymerase in viral assembly. Finally, we have identified additional residues in the nsP4 palm domain that influence the genetic diversity of the viral progeny, potentially via an alteration in NTP binding and/or discrimination by the polymerase. Taken together, these studies highlight that distinct nsP4 subdomains regulate multiple processes of the alphavirus life cycle, placing nsP4 in a central role during the switch from RNA synthesis to packaging and assembly.
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Affiliation(s)
- Marie-France Martin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nia E. McCray
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Olve B. Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Kenneth A. Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
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Cao V, Loeanurit N, Hengphasatporn K, Hairani R, Wacharachaisurapol N, Prompila N, Wittayalertpanya S, Shigeta Y, Khotavivattana T, Chavasiri W, Boonyasuppayakorn S. The 8-bromobaicalein alleviated chikungunya-induced musculoskeletal inflammation and reduced the viral load in healthy adult mice. Emerg Microbes Infect 2023; 12:2270074. [PMID: 37842770 PMCID: PMC10653753 DOI: 10.1080/22221751.2023.2270074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023]
Abstract
Chikungunya virus is a re-emerging arbovirus that has caused epidemic outbreaks in recent decades. Patients in older age groups with high viral load and severe immunologic response during acute infection are likely to develop chronic arthritis and severe joint pain. Currently, no antiviral drug is available. Previous studies suggested that a flavone derivative, 8-bromobaicalein, was a potential dengue and Zika replication inhibitor in a cell-based system targeting flaviviral polymerase. Here we characterized that 8-bromobaicalein inhibited chikungunya virus replication with EC50 of 0.49 ± 0.11 µM in Vero cells. The molecular target predicted at viral nsP1 methyltransferase using molecular binding and fragment molecular orbital calculation. Additionally, oral administration of 250 mg/kg twice daily treatment alleviated chikungunya-induced musculoskeletal inflammation and reduced viral load in healthy adult mice. Pharmacokinetic analysis indicated that the 250 mg/kg administration maintained the compound level above EC99.9 for 12 h. Therefore, 8-bromobaicalein should be a potential candidate for further development as a pan-arboviral drug.
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Affiliation(s)
- Van Cao
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Interdisciplinary Program in Microbiology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- DaNang University of Medical Technology and Pharmacy, DaNang, Vietnam
| | - Naphat Loeanurit
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Rita Hairani
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Noppadol Wacharachaisurapol
- Clinical Pharmakokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nantaporn Prompila
- Chula Pharmacokinetic Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Supeecha Wittayalertpanya
- Clinical Pharmakokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Chula Pharmacokinetic Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Siwaporn Boonyasuppayakorn
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Vaccine Research and Development, Chulalongkorn University (Chula-VRC), Bangkok, Thailand
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7
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de Jesús López Medina Y, Tamayo-Molina YS, Valdés-López JF, Urcuqui-Inchima S. Protective Effects of Caffeine on Chikungunya and Zika Virus Infections: An in Vitro and in Silico Study. Chem Biodivers 2023; 20:e202300192. [PMID: 37489706 DOI: 10.1002/cbdv.202300192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 07/26/2023]
Abstract
Infection by viruses Chikungunya (CHIKV) and Zika (ZIKV) continue to be serious problems in tropical and subtropical areas of the world. Here, we evaluated the antiviral and virucidal activity of caffeine against CHIKV and ZIKV in Vero, A549, and Huh-7 cell lines. Results showed that caffeine displays antiviral properties against both viruses. By pre-and post-infection treatment, caffeine significantly inhibited CHIKV and ZIKV replication in a dose-dependent manner. Furthermore, caffeine showed a virucidal effect against ZIKV. Molecular docking suggests the possible binding of caffeine with envelope protein and RNA-dependent RNA polymerase of CHIKV and ZIKV. This is the first study that showed an antiviral effect of caffeine against CHIKV and ZIKV. Although further studies are needed to better understand the mechanism of caffeine-mediated repression of viral replication, caffeine appears to be a promising compound that could be used for in vivo studies, perhaps in synergy with other compounds present in daily beverages.
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Affiliation(s)
| | | | - Juan Felipe Valdés-López
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Silvio Urcuqui-Inchima
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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8
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Paschoalino M, Marinho MDS, Santos IA, Grosche VR, Martins DOS, Rosa RB, Jardim ACG. An update on the development of antiviral against Mayaro virus: from molecules to potential viral targets. Arch Microbiol 2023; 205:106. [PMID: 36881172 PMCID: PMC9990066 DOI: 10.1007/s00203-023-03441-y] [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: 11/19/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Mayaro virus (MAYV), first isolated in 1954 in Trinidad and Tobago islands, is the causative agent of Mayaro fever, a disease characterized by fever, rashes, headaches, myalgia, and arthralgia. The infection can progress to a chronic condition in over 50% of cases, with persistent arthralgia, which can lead to the disability of the infected individuals. MAYV is mainly transmitted through the bite of the female Haemagogus spp. mosquito genus. However, studies demonstrate that Aedes aegypti is also a vector, contributing to the spread of MAYV beyond endemic areas, given the vast geographical distribution of the mosquito. Besides, the similarity of antigenic sites with other Alphavirus complicates the diagnoses of MAYV, contributing to underreporting of the disease. Nowadays, there are no antiviral drugs available to treat infected patients, being the clinical management based on analgesics and non-steroidal anti-inflammatory drugs. In this context, this review aims to summarize compounds that have demonstrated antiviral activity against MAYV in vitro, as well as discuss the potentiality of viral proteins as targets for the development of antiviral drugs against MAYV. Finally, through rationalization of the data presented herein, we wish to encourage further research encompassing these compounds as potential anti-MAYV drug candidates.
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Affiliation(s)
- Marina Paschoalino
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | | | - Igor Andrade Santos
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Victória Riquena Grosche
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.,Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Daniel Oliveira Silva Martins
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.,Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Rafael Borges Rosa
- Institute Aggeu Magalhães, Fiocruz Pernambuco, Recife, Pernambuco, Brazil.,Rodents Animal Facilities Complex, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil. .,Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil.
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9
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Targeting the alphavirus virus replication process for antiviral development. Antiviral Res 2023; 210:105494. [PMID: 36574906 DOI: 10.1016/j.antiviral.2022.105494] [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: 11/08/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022]
Abstract
Many alphaviruses, including chikungunya virus (CHIKV) are known human pathogens that lack specific and effective antivirals or vaccines available. The upstream portion of the positive-sense single-stranded RNA genome of alphaviruses encodes four nonstructural proteins: nsP1 to nsP4. They are expressed and autoprocessed to nonstructural proteins which assemble into a replication complex (RC) playing multiple essential roles on viral RNA replication and communication with the host components. The assembly of alphavirus RC and its RNA genome initiates the membrane-derived ultrastructure known as spherule which facilitates viral RNA synthesis protected from host immune responses. Recent advances in the molecular understanding of the high-resolution CHIKV RC heteromeric ultrastructure have provided new insights into the viral replication process. Hence, alphavirus RC presents as an ideal multi-enzyme target for the development of structure-based antiviral drugs. Moreover, the alphavirus RC has therapeutic potential in the form of self-amplifying RNA technology against both infectious and non-infectious diseases.
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Nodavirus RNA replication crown architecture reveals proto-crown precursor and viral protein A conformational switching. Proc Natl Acad Sci U S A 2023; 120:e2217412120. [PMID: 36693094 PMCID: PMC9945985 DOI: 10.1073/pnas.2217412120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Positive-strand RNA viruses replicate their genomes in virus-induced membrane vesicles, and the resulting RNA replication complexes are a major target for virus control. Nodavirus studies first revealed viral RNA replication proteins forming a 12-fold symmetric "crown" at the vesicle opening to the cytosol, an arrangement recently confirmed to extend to distantly related alphaviruses. Using cryoelectron microscopy (cryo-EM), we show that mature nodavirus crowns comprise two stacked 12-mer rings of multidomain viral RNA replication protein A. Each ring contains an ~19 nm circle of C-proximal polymerase domains, differentiated by strikingly diverged positions of N-proximal RNA capping/membrane binding domains. The lower ring is a "proto-crown" precursor that assembles prior to RNA template recruitment, RNA synthesis, and replication vesicle formation. In this proto-crown, the N-proximal segments interact to form a toroidal central floor, whose 3.1 Å resolution structure reveals many mechanistic details of the RNA capping/membrane binding domains. In the upper ring, cryo-EM fitting indicates that the N-proximal domains extend radially outside the polymerases, forming separated, membrane-binding "legs." The polymerase and N-proximal domains are connected by a long linker accommodating the conformational switch between the two rings and possibly also polymerase movements associated with RNA synthesis and nonsymmetric electron density in the lower center of mature crowns. The results reveal remarkable viral protein multifunctionality, conformational flexibility, and evolutionary plasticity and insights into (+)RNA virus replication and control.
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Fieulaine S, Tubiana T, Bressanelli S. De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation. Virology 2023; 578:128-140. [PMID: 36527931 DOI: 10.1016/j.virol.2022.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV), a major cause of acute viral hepatitis, is a single-stranded, positive-sense RNA virus. As such, it encodes a 1700-residue replication polyprotein pORF1 that directs synthesis of new viral RNA in infected cells. Here we report extensive modeling with AlphaFold2 of the full-length pORF1, and its production by in vitro translation. From this, we give a detailed update on the breakdown into domains of HEV pORF1. We also provide evidence that pORF1's N-terminal domain is likely to oligomerize to form a dodecameric pore, homologously to what has been described for Chikungunya virus. Beyond providing accurate folds for its five domains, our work highlights that there is no canonical protease encoded in pORF1 and that flexibility in several functionally important regions rather than proteolytic processing may serve to regulate HEV RNA synthesis.
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Affiliation(s)
- Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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12
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Skidmore AM, Bradfute SB. The life cycle of the alphaviruses: From an antiviral perspective. Antiviral Res 2023; 209:105476. [PMID: 36436722 PMCID: PMC9840710 DOI: 10.1016/j.antiviral.2022.105476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
The alphaviruses are a widely distributed group of positive-sense, single stranded, RNA viruses. These viruses are largely arthropod-borne and can be found on all populated continents. These viruses cause significant human disease, and recently have begun to spread into new populations, such as the expansion of Chikungunya virus into southern Europe and the Caribbean, where it has established itself as endemic. The study of alphaviruses is an active and expanding field, due to their impacts on human health, their effects on agriculture, and the threat that some pose as potential agents of biological warfare and terrorism. In this systematic review we will summarize both historic knowledge in the field as well as recently published data that has potential to shift current theories in how alphaviruses are able to function. This review is comprehensive, covering all parts of the alphaviral life cycle as well as a brief overview of their pathology and the current state of research in regards to vaccines and therapeutics for alphaviral disease.
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Affiliation(s)
- Andrew M Skidmore
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, 915 Camino de Salud, IDTC Room 3245, Albuquerque, NM, 87131, USA.
| | - Steven B Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, 915 Camino de Salud, IDTC Room 3330A, Albuquerque, NM, 87131, USA.
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Tan YB, Chmielewski D, Law MCY, Zhang K, He Y, Chen M, Jin J, Luo D. Molecular architecture of the Chikungunya virus replication complex. SCIENCE ADVANCES 2022; 8:eadd2536. [PMID: 36449616 PMCID: PMC9710867 DOI: 10.1126/sciadv.add2536] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
To better understand how positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) to synthesize, process, and transport viral RNA in virus-infected cells, we determined both the high-resolution structure of the core RNA replicase of chikungunya virus and the native RC architecture in its cellular context at subnanometer resolution, using in vitro reconstitution and in situ electron cryotomography, respectively. Within the core RNA replicase, the viral polymerase nsP4, which is in complex with nsP2 helicase-protease, sits in the central pore of the membrane-anchored nsP1 RNA-capping ring. The addition of a large cytoplasmic ring next to the C terminus of nsP1 forms the holo-RNA-RC as observed at the neck of spherules formed in virus-infected cells. These results represent a major conceptual advance in elucidating the molecular mechanisms of RNA virus replication and the principles underlying the molecular architecture of RCs, likely to be shared with many pathogenic (+) RNA viruses.
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Affiliation(s)
- Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - David Chmielewski
- Biophysics Graduate Program, Departments of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Michelle Cheok Yien Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Kuo Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yu He
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Jing Jin
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
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Fundamentals of HDX-MS. Essays Biochem 2022; 67:301-314. [PMID: 36251047 PMCID: PMC10070489 DOI: 10.1042/ebc20220111] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming part of the standard repertoire of techniques used by molecular biologists to investigate protein structure and dynamics. This is partly due to the increased use of automation in all stages of the technique and its versatility of application-many proteins that present challenges with techniques such as X-ray crystallography and cryoelectron microscopy are amenable to investigation with HDX-MS. The present review is aimed at scientists who are curious about the technique, and how it may aid their research. It describes the fundamental basis of solvent exchange, the basics of a standard HDX-MS experiment, as well as highlighting emerging novel experimental advances, which point to where the field is heading.
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Characterization of the RNA-dependent RNA polymerase from Chikungunya virus and discovery of a novel ligand as a potential drug candidate. Sci Rep 2022; 12:10601. [PMID: 35732685 PMCID: PMC9217121 DOI: 10.1038/s41598-022-14790-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of Chikungunya fever, an acute febrile and arthritogenic illness with no effective treatments available. The development of effective therapeutic strategies could be significantly accelerated with detailed knowledge of the molecular components behind CHIKV replication. However, drug discovery is hindered by our incomplete understanding of their main components. The RNA-dependent RNA-polymerase (nsP4-CHIKV) is considered the key enzyme of the CHIKV replication complex and a suitable target for antiviral therapy. Herein, the nsP4-CHIKV was extensively characterized through experimental and computational biophysical methods. In the search for new molecules against CHIKV, a compound designated LabMol-309 was identified as a strong ligand of the nsp4-CHIKV and mapped to bind to its active site. The antiviral activity of LabMol-309 was evaluated in cellular-based assays using a CHIKV replicon system and a reporter virus. In conclusion, this study highlights the biophysical features of nsP4-CHIKV and identifies a new compound as a promising antiviral agent against CHIKV infection.
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