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Hsia JZ, Liu D, Haynes L, Cruz-Cosme R, Tang Q. Lipid Droplets: Formation, Degradation, and Their Role in Cellular Responses to Flavivirus Infections. Microorganisms 2024; 12:647. [PMID: 38674592 PMCID: PMC11051834 DOI: 10.3390/microorganisms12040647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Lipid droplets (LDs) are cellular organelles derived from the endoplasmic reticulum (ER), serving as lipid storage sites crucial for maintaining cellular lipid homeostasis. Recent attention has been drawn to their roles in viral replication and their interactions with viruses. However, the precise biological functions of LDs in viral replication and pathogenesis remain incompletely understood. To elucidate the interaction between LDs and viruses, it is imperative to comprehend the biogenesis of LDs and their dynamic interactions with other organelles. In this review, we explore the intricate pathways involved in LD biogenies within the cytoplasm, encompassing the uptake of fatty acid from nutrients facilitated by CD36-mediated membranous protein (FABP/FATP)-FA complexes, and FA synthesis via glycolysis in the cytoplasm and the TCL cycle in mitochondria. While LD biogenesis primarily occurs in the ER, matured LDs are intricately linked to multiple organelles. Viral infections can lead to diverse consequences in terms of LD status within cells post-infection, potentially involving the breakdown of LDs through the activation of lipophagy. However, the exact mechanisms underlying LD destruction or accumulation by viruses remain elusive. The significance of LDs in viral replication renders them effective targets for developing broad-spectrum antivirals. Moreover, considering that reducing neutral lipids in LDs is a strategy for anti-obesity treatment, LD depletion may not pose harm to cells. This presents LDs as promising antiviral targets for developing therapeutics that are minimally or non-toxic to the host.
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Affiliation(s)
| | | | | | | | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC 20059, USA; (J.Z.H.); (D.L.); (L.H.); (R.C.-C.)
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2
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Jablunovsky A, Jose J. The Dynamic Landscape of Capsid Proteins and Viral RNA Interactions in Flavivirus Genome Packaging and Virus Assembly. Pathogens 2024; 13:120. [PMID: 38392858 PMCID: PMC10893219 DOI: 10.3390/pathogens13020120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The Flavivirus genus of the Flaviviridae family of enveloped single-stranded RNA viruses encompasses more than 70 members, many of which cause significant disease in humans and livestock. Packaging and assembly of the flavivirus RNA genome is essential for the formation of virions, which requires intricate coordination of genomic RNA, viral structural, and nonstructural proteins in association with virus-induced, modified endoplasmic reticulum (ER) membrane structures. The capsid (C) protein, a small but versatile RNA-binding protein, and the positive single-stranded RNA genome are at the heart of the elusive flavivirus assembly process. The nucleocapsid core, consisting of the genomic RNA encapsidated by C proteins, buds through the ER membrane, which contains viral glycoproteins prM and E organized as trimeric spikes into the lumen, forming an immature virus. During the maturation process, which involves the low pH-mediated structural rearrangement of prM and E and furin cleavage of prM in the secretory pathway, the spiky immature virus with a partially ordered nucleocapsid core becomes a smooth, mature virus with no discernible nucleocapsid. This review focuses on the mechanisms of genome packaging and assembly by examining the structural and functional aspects of C protein and viral RNA. We review the current lexicon of critical C protein features and evaluate interactions between C and genomic RNA in the context of assembly and throughout the life cycle.
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Affiliation(s)
- Anastazia Jablunovsky
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA;
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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3
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Henriques P, Rosa A, Caldeira-Araújo H, Soares P, Vigário AM. Flying under the radar - impact and factors influencing asymptomatic DENV infections. Front Cell Infect Microbiol 2023; 13:1284651. [PMID: 38076464 PMCID: PMC10704250 DOI: 10.3389/fcimb.2023.1284651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
The clinical outcome of DENV and other Flaviviruses infections represents a spectrum of severity that ranges from mild manifestations to severe disease, which can ultimately lead to death. Nonetheless, most of these infections result in an asymptomatic outcome that may play an important role in the persistent circulation of these viruses. Also, although little is known about the mechanisms that lead to these asymptomatic infections, they are likely the result of a complex interplay between viral and host factors. Specific characteristics of the infecting viral strain, such as its replicating efficiency, coupled with host factors, like gene expression of key molecules involved in the immune response or in the protection against disease, are among crucial factors to study. This review revisits recent data on factors that may contribute to the asymptomatic outcome of the world's widespread DENV, highlighting the importance of silent infections in the transmission of this pathogen and the immune status of the host.
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Affiliation(s)
- Paulo Henriques
- Projecto Medicina, Faculdade de Ciências da Vida, Universidade da Madeira, Funchal, Portugal
| | - Alexandra Rosa
- Projecto Medicina, Faculdade de Ciências da Vida, Universidade da Madeira, Funchal, Portugal
| | - Helena Caldeira-Araújo
- Projecto Medicina, Faculdade de Ciências da Vida, Universidade da Madeira, Funchal, Portugal
- CQM-Centro de Química da Madeira, Universidade da Madeira, Funchal, Portugal
| | - Pedro Soares
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), Braga, Portugal
- Department of Biology, Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Ana Margarida Vigário
- Projecto Medicina, Faculdade de Ciências da Vida, Universidade da Madeira, Funchal, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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4
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Safi R, Sánchez-Álvarez M, Bosch M, Demangel C, Parton RG, Pol A. Defensive-lipid droplets: Cellular organelles designed for antimicrobial immunity. Immunol Rev 2023; 317:113-136. [PMID: 36960679 DOI: 10.1111/imr.13199] [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: 03/25/2023]
Abstract
Microbes have developed many strategies to subvert host organisms, which, in turn, evolved several innate immune responses. As major lipid storage organelles of eukaryotes, lipid droplets (LDs) are an attractive source of nutrients for invaders. Intracellular viruses, bacteria, and protozoan parasites induce and physically interact with LDs, and the current view is that they "hijack" LDs to draw on substrates for host colonization. This dogma has been challenged by the recent demonstration that LDs are endowed with a protein-mediated antibiotic activity, which is upregulated in response to danger signals and sepsis. Dependence on host nutrients could be a generic "Achilles' heel" of intracellular pathogens and LDs a suitable chokepoint harnessed by innate immunity to organize a front-line defense. Here, we will provide a brief overview of the state of the conflict and discuss potential mechanisms driving the formation of the 'defensive-LDs' functioning as hubs of innate immunity.
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Affiliation(s)
- Rémi Safi
- Lipid Trafficking and Disease Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Miguel Sánchez-Álvarez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Instituto de Investigaciones Biomédicas Alberto Sols (IIB), Madrid, Spain
| | - Marta Bosch
- Lipid Trafficking and Disease Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Department of Biomedical Sciences, Faculty of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Caroline Demangel
- Immunobiology and Therapy Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, Paris, France
| | - Robert G Parton
- Institute for Molecular Bioscience (IMB), Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis (CMM), University of Queensland, Brisbane, Queensland, Australia
| | - Albert Pol
- Lipid Trafficking and Disease Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Department of Biomedical Sciences, Faculty of Medicine, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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5
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Dyson HJ. Vital for Viruses: Intrinsically Disordered Proteins. J Mol Biol 2023; 435:167860. [PMID: 37330280 PMCID: PMC10656058 DOI: 10.1016/j.jmb.2022.167860] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/19/2023]
Abstract
Viruses infect all kingdoms of life; their genomes vary from DNA to RNA and in size from 2kB to 1 MB or more. Viruses frequently employ disordered proteins, that is, protein products of virus genes that do not themselves fold into independent three-dimensional structures, but rather, constitute a versatile molecular toolkit to accomplish a range of functions necessary for viral infection, assembly, and proliferation. Interestingly, disordered proteins have been discovered in almost all viruses so far studied, whether the viral genome consists of DNA or RNA, and whatever the configuration of the viral capsid or other outer covering. In this review, I present a wide-ranging set of stories illustrating the range of functions of IDPs in viruses. The field is rapidly expanding, and I have not tried to include everything. What is included is meant to be a survey of the variety of tasks that viruses accomplish using disordered proteins.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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6
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Barbosa GM, Morando MA, Da Poian AT, Almeida FCL. The 1H, 15N and 13C resonance assignments of dengue virus capsid protein with the deletion of the intrinsically disordered N-terminal region. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:23-26. [PMID: 36723824 DOI: 10.1007/s12104-022-10115-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/29/2022] [Indexed: 06/02/2023]
Abstract
Dengue virus belongs to the Flaviviridae family, being responsible for an endemic arboviral disease in humans. It is an enveloped virus, whose genome is a positive-stranded RNA packaged by the capsid protein. Dengue virus capsid protein (DENVC) forms homodimers in solution organized in 4 α-helices and an intrinsically disordered N-terminal region. The N-terminal region is involved in the binding of membranous structures in host cells and in the recognition of nucleotides. Here we report the 1H, 15N and 13C resonance assignments of the DENVC with the deletion of the first 19 intrinsically disordered residues. The backbone chemical shift perturbations suggest changes in the α1 and α2 helices between full length and the truncated proteins.
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Affiliation(s)
- Glauce M Barbosa
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Maria A Morando
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Centro de Desenvolvimento de Tecnologia em Saúde, Fiocruz, Rio de Janeiro, 21040-361, Brazil
| | - Andrea T Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
- National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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7
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Boon PLS, Martins AS, Lim XN, Enguita FJ, Santos NC, Bond PJ, Wan Y, Martins IC, Huber RG. Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging. Int J Mol Sci 2023; 24:ijms24098158. [PMID: 37175867 PMCID: PMC10179140 DOI: 10.3390/ijms24098158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. Whereas the structure of the envelope is clearly defined, the structure of the packaged genome in complex with C proteins remains elusive. Here, we investigated the interactions of C proteins with viral RNA, in solution and inside mature virions, via footprinting and cross-linking experiments. We demonstrated that C protein interaction with DENV genomes saturates at an RNA:C protein ratio below 1:250. Moreover, we also showed that the length of the RNA genome interaction sites varies, in a multimodal distribution, consistent with the C protein binding to each RNA site mostly in singlets or pairs (and, in some instances, higher numbers). We showed that interaction sites are preferentially sites with low base pairing, as previously measured by 2'-acetylation analyzed by primer extension (SHAPE) reactivity indicating structuredness. We found a clear association pattern emerged: RNA-C protein binding sites are strongly associated with long-range RNA-RNA interaction sites, particularly inside virions. This, in turn, explains the need for C protein in viral genome packaging: the protein has a chief role in coordinating these key interactions, promoting proper packaging of viral RNA. Such sites are, thus, highly consequential for viral assembly, and, as such, may be targeted in future drug development strategies against these and related viruses.
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Affiliation(s)
- Priscilla L S Boon
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Xin Ni Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Yue Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
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8
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Self-assembly of dengue virus empty capsid-like particles in solution. iScience 2023; 26:106197. [PMID: 36890794 PMCID: PMC9986514 DOI: 10.1016/j.isci.2023.106197] [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: 04/26/2022] [Revised: 09/11/2022] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Nucleocapsid (NC) assembly is an essential step of the virus replication cycle. It ensures genome protection and transmission among hosts. Flaviviruses are human viruses for which envelope structure is well known, whereas no information on NC organization is available. Here we designed a dengue virus capsid protein (DENVC) mutant in which a highly positive spot conferred by arginine 85 in α4-helix was replaced by a cysteine residue, simultaneously removing the positive charge and restricting the intermolecular motion through the formation of a disulfide cross-link. We showed that the mutant self-assembles into capsid-like particles (CLP) in solution without nucleic acids. Using biophysical techniques, we investigated capsid assembly thermodynamics, showing that an efficient assembly is related to an increased DENVC stability due to α4/α4' motion restriction. To our knowledge, this is the first time that flaviviruses' empty capsid assembly is obtained in solution, revealing the R85C mutant as a powerful tool to understand the NC assembly mechanism.
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9
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Dengue virus infection - a review of pathogenesis, vaccines, diagnosis and therapy. Virus Res 2023; 324:199018. [PMID: 36493993 DOI: 10.1016/j.virusres.2022.199018] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/19/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
The transmission of dengue virus (DENV) from an infected Aedes mosquito to a human, causes illness ranging from mild dengue fever to fatal dengue shock syndrome. The similar conserved structure and sequence among distinct DENV serotypes or different flaviviruses has resulted in the occurrence of cross reaction followed by antibody-dependent enhancement (ADE). Thus far, the vaccine which can provide effective protection against infection by different DENV serotypes remains the biggest hurdle to overcome. Therefore, deep investigation is crucial for the potent and effective therapeutic drugs development. In addition, the cross-reactivity of flaviviruses that leads to false diagnosis in clinical settings could result to delay proper intervention management. Thus, the accurate diagnostic with high specificity and sensitivity is highly required to provide prompt diagnosis in respect to render early treatment for DENV infected individuals. In this review, the recent development of neutralizing antibodies, antiviral agents, and vaccine candidates in therapeutic platform for DENV infection will be discussed. Moreover, the discovery of antigenic cryptic epitopes, principle of molecular mimicry, and application of single-chain or single-domain antibodies towards DENV will also be presented.
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10
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Rajapaksha SP, Nawagamuwage SU. Anticorrelated position fluctuation of lipids in forming membrane water pores: molecular dynamics simulations study with dengue virus capsid protein. J Biomol Struct Dyn 2022; 40:11395-11404. [PMID: 34343444 DOI: 10.1080/07391102.2021.1958698] [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: 10/20/2022]
Abstract
The traffic of molecules into or out of cells is regulated by many membrane-associated mechanisms. Membrane pores are considered as one of the major passage mechanisms, although molecular-level understanding of pore formation is still vague. The opening of a membrane pore depends on many factors, including the influence of some proteins. The ability of the cell-penetrating peptides and supercharged proteins to form membrane pores has been reported. We studied pore formation through dipalmitoylphosphatidylcholine (DPPC) lipid bilayers by supercharged dengue virus capsid (C) protein. Atomistic molecular dynamics simulations confirmed the formation of membrane pores by a combined effect of the C protein and the membrane electric field. Analyses of simulated trajectories showed highly correlated vertical position fluctuations between the Cα atom of the membrane-anchored arginine residues and the phosphorus atoms of the surrounding DPPC lipids. Certain regions of the bilayer were negatively correlated while the others were positively correlated with respect to the fluctuations of the Cα atom of the anchored arginine residues. When positively correlated lipids in one leaflet vertically aligned with the negatively correlated lipids in the other leaflet, a local anticorrelated region was generated by weakening the bilayer. The membrane pore was always formed close to this anticorrelated region. Once formed, the C protein followed the hydrated pathway provided by the water-filled pores to cross the membrane.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suneth P Rajapaksha
- Department of Chemistry, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Sithara U Nawagamuwage
- Department of Chemistry, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
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11
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Dengue, West Nile, and Zika Viruses: Potential Novel Antiviral Biologics Drugs Currently at Discovery and Preclinical Development Stages. Pharmaceutics 2022; 14:pharmaceutics14112535. [PMID: 36432726 PMCID: PMC9697021 DOI: 10.3390/pharmaceutics14112535] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Dengue, West Nile and Zika viruses are vector-borne flaviviruses responsible for numerous disease outbreaks in both Hemispheres. Despite relatively low mortality, infection may lead to potentially severe situations such as (depending on the virus): hypovolemic shock, encephalitis, acute flaccid paralysis, Guillain-Barré syndrome, congenital malformations (e.g., microcephaly) and, in some situations, death. Moreover, outbreaks also have major socioeconomic repercussions, especially in already vulnerable societies. Thus far, only generic symptoms relief is possible, as there are no specific treatments available yet. Dengvaxia was the world's first dengue vaccine. However, it is not fully effective. Prophylactic approaches against West Nile and Zika viruses are even more limited. Therefore, therapeutic strategies are required and will be discussed hereafter. We will first briefly present these viruses' epidemiology, life cycle and structure. Then, we introduce the clinical presentation, diagnosis approaches and available vaccines. Finally, we list and discuss promising compounds at discovery and preclinical development stages already deposited at the GlobalData database and divided into three main types, according to therapeutic molecule: antibody-based, peptide-based molecules and, other compounds. To conclude, we discuss and compare promising developments, useful for future therapies against these three flaviviruses of major concern to human health.
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12
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Qin ZL, Yao QF, Ren H, Zhao P, Qi ZT. Lipid Droplets and Their Participation in Zika Virus Infection. Int J Mol Sci 2022; 23:ijms232012584. [PMID: 36293437 PMCID: PMC9604050 DOI: 10.3390/ijms232012584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
Lipid droplets (LDs) are highly conserved and dynamic intracellular organelles. Their functions are not limited to serving as neutral lipid reservoirs; they also participate in non-energy storage functions, such as cell lipid metabolism, protection from cell stresses, maintaining protein homeostasis, and regulating nuclear function. During a Zika virus (ZIKV) infection, the viruses hijack the LDs to provide energy and lipid sources for viral replication. The co-localization of ZIKV capsid (C) protein with LDs supports its role as a virus replication platform and a key compartment for promoting the generation of progeny virus particles. However, in view of the multiple functions of LDs, their role in ZIKV infection needs further elucidation. Here, we review the basic mechanism of LD biogenesis and biological functions and discuss how ZIKV infection utilizes these effects of LDs to facilitate virus replication, along with the future application strategy of developing new antiviral drugs based on the interaction of ZIKV with LDs.
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13
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Identification of putative binding interface of PI(3,5)P2 lipid on rice black-streaked dwarf virus (RBSDV) P10 protein. Virology 2022; 570:81-95. [DOI: 10.1016/j.virol.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/27/2022] [Indexed: 11/18/2022]
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14
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Kapuganti SK, Bhardwaj A, Kumar P, Bhardwaj T, Nayak N, Uversky VN, Giri R. Role of structural disorder in the multi-functionality of flavivirus proteins. Expert Rev Proteomics 2022; 19:183-196. [PMID: 35655146 DOI: 10.1080/14789450.2022.2085563] [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: 01/07/2023]
Abstract
INTRODUCTION The life cycle of a virus involves interacting with the host cell, entry, hijacking host machinery for viral replication, evading the host's immune system, and releasing mature virions. However, viruses, being small in size, can only harbor a genome large enough to code for the minimal number of proteins required for the replication and maturation of the virions. As a result, many viral proteins are multifunctional machines that do not directly obey the classic structure-function paradigm. Often, such multifunctionality is rooted in intrinsic disorder that allows viral proteins to interact with various cellular factors and remain functional in the hostile environment of different cellular compartments. AREAS COVERED This report covers the classification of flaviviruses, their proteome organization, and the prevalence of intrinsic disorder in the proteomes of different flaviviruses. Further, we have summarized the speculations made about the apparent roles of intrinsic disorder in the observed multifunctionality of flaviviral proteins. EXPERT OPINION Small sizes of viral genomes impose multifunctionality on their proteins, which is dependent on the excessive usage of intrinsic disorder. In fact, intrinsic disorder serves as a universal functional tool, weapon, and armor of viruses and clearly plays an important role in their functionality and evolution.
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Affiliation(s)
| | - Aparna Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Namyashree Nayak
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
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15
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Mebus-Antunes NC, Ferreira WS, Barbosa GM, Neves-Martins TC, Weissmuller G, Almeida FCL, Da Poian AT. The interaction of dengue virus capsid protein with negatively charged interfaces drives the in vitro assembly of nucleocapsid-like particles. PLoS One 2022; 17:e0264643. [PMID: 35231063 PMCID: PMC8887749 DOI: 10.1371/journal.pone.0264643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/15/2022] [Indexed: 01/06/2023] Open
Abstract
Dengue virus (DENV) causes a major arthropod-borne viral disease, with 2.5 billion people living in risk areas. DENV consists in a 50 nm-diameter enveloped particle in which the surface proteins are arranged with icosahedral symmetry, while information about nucleocapsid (NC) structural organization is lacking. DENV NC is composed of the viral genome, a positive-sense single-stranded RNA, packaged by the capsid (C) protein. Here, we established the conditions for a reproducible in vitro assembly of DENV nucleocapsid-like particles (NCLPs) using recombinant DENVC. We analyzed NCLP formation in the absence or presence of oligonucleotides in solution using small angle X-ray scattering, Rayleigh light scattering as well as fluorescence anisotropy, and characterized particle structural properties using atomic force and transmission electron microscopy imaging. The experiments in solution comparing 2-, 5- and 25-mer oligonucleotides established that 2-mer is too small and 5-mer is sufficient for the formation of NCLPs. The assembly process was concentration-dependent and showed a saturation profile, with a stoichiometry of 1:1 (DENVC:oligonucleotide) molar ratio, suggesting an equilibrium involving DENVC dimer and an organized structure compatible with NCLPs. Imaging methods proved that the decrease in concentration to sub-nanomolar concentrations of DENVC allows the formation of regular spherical NCLPs after protein deposition on mica or carbon surfaces, in the presence as well as in the absence of oligonucleotides, in this latter case being surface driven. Altogether, the results suggest that in vitro assembly of DENV NCLPs depends on DENVC charge neutralization, which must be a very coordinated process to avoid unspecific aggregation. Our hypothesis is that a specific highly positive spot in DENVC α4-α4' is the main DENVC-RNA binding site, which is required to be firstly neutralized to allow NC formation.
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Affiliation(s)
- Nathane C. Mebus-Antunes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wellington S. Ferreira
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Glauce M. Barbosa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thais C. Neves-Martins
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto Weissmuller
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C. L. Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrea T. Da Poian
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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16
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Farelo MA, Korrou-Karava D, Brooks KF, Russell TA, Maringer K, Mayerhofer PU. Dengue and Zika Virus Capsid Proteins Contain a Common PEX19-Binding Motif. Viruses 2022; 14:v14020253. [PMID: 35215846 PMCID: PMC8874546 DOI: 10.3390/v14020253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses such as dengue virus (DENV) and Zika virus (ZIKV) have evolved sophisticated mechanisms to suppress the host immune system. For instance, flavivirus infections were found to sabotage peroxisomes, organelles with an important role in innate immunity. The current model suggests that the capsid (C) proteins of DENV and ZIKV downregulate peroxisomes, ultimately resulting in reduced production of interferons by interacting with the host protein PEX19, a crucial chaperone in peroxisomal biogenesis. Here, we aimed to explore the importance of peroxisomes and the role of C interaction with PEX19 in the flavivirus life cycle. By infecting cells lacking peroxisomes we show that this organelle is required for optimal DENV replication. Moreover, we demonstrate that DENV and ZIKV C bind PEX19 through a conserved PEX19-binding motif, which is also commonly found in cellular peroxisomal membrane proteins (PMPs). However, in contrast to PMPs, this interaction does not result in the targeting of C to peroxisomes. Furthermore, we show that the presence of C results in peroxisome loss due to impaired peroxisomal biogenesis, which appears to occur by a PEX19-independent mechanism. Hence, these findings challenge the current model of how flavivirus C might downregulate peroxisomal abundance and suggest a yet unknown role of peroxisomes in flavivirus biology.
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Affiliation(s)
- Mafalda A. Farelo
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Despoina Korrou-Karava
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Katrina F. Brooks
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Tiffany A. Russell
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Kevin Maringer
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Correspondence: (K.M.); (P.U.M.)
| | - Peter U. Mayerhofer
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
- Correspondence: (K.M.); (P.U.M.)
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17
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Ortlieb LO, Caruso ÍP, Mebus-Antunes NC, Da Poian AT, Petronilho EDC, Figueroa-Villar JD, Nascimento CJ, Almeida FCL. Searching for drug leads targeted to the hydrophobic cleft of dengue virus capsid protein. J Enzyme Inhib Med Chem 2021; 37:287-298. [PMID: 34894959 PMCID: PMC8667904 DOI: 10.1080/14756366.2021.2004591] [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: 11/24/2022] Open
Abstract
We synthesised and screened 18 aromatic derivatives of guanylhydrazones and oximes aromatic for their capacity to bind to dengue virus capsid protein (DENVC). The intended therapeutic target was the hydrophobic cleft of DENVC, which is a region responsible for its anchoring in lipid droplets in the infected cells. The inhibition of this process completely suppresses virus infectivity. Using NMR, we describe five compounds able to bind to the α1-α2 interface in the hydrophobic cleft. Saturation transfer difference experiments showed that the aromatic protons of the ligands are important for the interaction with DENVC. Fluorescence binding isotherms indicated that the selected compounds bind at micromolar affinities, possibly leading to binding-induced conformational changes. NMR-derived docking calculations of ligands showed that they position similarly in the hydrophobic cleft. Cytotoxicity experiments and calculations of in silico drug properties suggest that these compounds may be promising candidates in the search for antivirals targeting DENVC.
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Affiliation(s)
- Liliane O Ortlieb
- Department of Chemistry, Military Institute of Engineering (IME), Rio de Janeiro, Brazil.,Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ícaro P Caruso
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Multiuser Center for Biomolecular Innovation (CMIB) and Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Nathane C Mebus-Antunes
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Andrea T Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Elaine da C Petronilho
- Department of Chemistry, Military Institute of Engineering (IME), Rio de Janeiro, Brazil
| | | | - Claudia J Nascimento
- Department of Natural Sciences, Institute of Biosciences, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM) and National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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18
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Farfan-Morales CN, Cordero-Rivera CD, Reyes-Ruiz JM, Hurtado-Monzón AM, Osuna-Ramos JF, González-González AM, De Jesús-González LA, Palacios-Rápalo SN, Del Ángel RM. Anti-flavivirus Properties of Lipid-Lowering Drugs. Front Physiol 2021; 12:749770. [PMID: 34690817 PMCID: PMC8529048 DOI: 10.3389/fphys.2021.749770] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Although Flaviviruses such as dengue (DENV) and zika (ZIKV) virus are important human pathogens, an effective vaccine or antiviral treatment against them is not available. Hence, the search for new strategies to control flavivirus infections is essential. Several studies have shown that the host lipid metabolism could be an antiviral target because cholesterol and other lipids are required during the replicative cycle of different Flaviviridae family members. FDA-approved drugs with hypolipidemic effects could be an alternative for treating flavivirus infections. However, a better understanding of the regulation between host lipid metabolism and signaling pathways triggered during these infections is required. The metabolic pathways related to lipid metabolism modified during DENV and ZIKV infection are analyzed in this review. Additionally, the role of lipid-lowering drugs as safe host-targeted antivirals is discussed.
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Affiliation(s)
- Carlos Noe Farfan-Morales
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Carlos Daniel Cordero-Rivera
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - José Manuel Reyes-Ruiz
- Unidad Médica de Alta Especialidad, Hospital de Especialidades No. 14, Centro Médico Nacional "Adolfo Ruiz Cortines," Instituto Mexicano del Seguro Social, Heroica Veracruz, Mexico
| | - Arianna M Hurtado-Monzón
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Juan Fidel Osuna-Ramos
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Arely M González-González
- Laboratorio de Ingeniería Tisular y Medicina Traslacional, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis Adrián De Jesús-González
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Selvin Noé Palacios-Rápalo
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
| | - Rosa María Del Ángel
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (CINVESTAV-IPN), Mexico City, Mexico
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19
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Dixit NK. Design of Monovalent and Chimeric Tetravalent Dengue Vaccine Using an Immunoinformatics Approach. Int J Pept Res Ther 2021; 27:2607-2624. [PMID: 34602919 PMCID: PMC8475484 DOI: 10.1007/s10989-021-10277-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/15/2022]
Abstract
An immunoinformatics technique was used to predict a monovalent amide immunogen candidate capable of producing therapeutic antibodies as well as a potent immunogen candidate capable of acting as a universal vaccination against all dengue fever virus serotypes. The capsid protein is an attractive goal for anti-DENV due to its position in the dengue existence cycle. The widely accessible immunological data, advances in antigenic peptide prediction using reverse vaccinology, and the introduction of molecular docking in immunoinformatics have directed vaccine manufacturing. The C-proteins of DENV-1-4 serotypes were known as antigens to assist with logical design. Binding epitopes for TC cells, TH cells, and B cells is predicted from structural dengue virus capsid proteins. Each T cell epitope of C-protein integrated with a B cell as a templet was used as a vaccine and produce antibodies in contrast to serotype of the dengue virus. A chimeric tetravalent vaccine was created by combining four vaccines, each representing four dengue serotypes, to serve as a standard vaccine candidate for all four Sero groups. The LKRARNRVS, RGFRKEIGR, KNGAIKVLR, and KAINVLRGF from dengue 1, dengue 2, dengue 3, and dengue 4 epitopes may be essential immunotherapeutic representatives for controlling outbreaks.
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Affiliation(s)
- Neeraj Kumar Dixit
- Department of Biotechnology, Saroj Institute of Technology & Management, Lucknow, Utter Pradesh India
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20
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Monson EA, Trenerry AM, Laws JL, Mackenzie JM, Helbig KJ. Lipid droplets and lipid mediators in viral infection and immunity. FEMS Microbiol Rev 2021; 45:fuaa066. [PMID: 33512504 PMCID: PMC8371277 DOI: 10.1093/femsre/fuaa066] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Lipid droplets (LDs) contribute to key pathways important for the physiology and pathophysiology of cells. In a homeostatic view, LDs regulate the storage of neutral lipids, protein sequestration, removal of toxic lipids and cellular communication; however, recent advancements in the field show these organelles as essential for various cellular stress response mechanisms, including inflammation and immunity, with LDs acting as hubs that integrate metabolic and inflammatory processes. The accumulation of LDs has become a hallmark of infection, and is often thought to be virally driven; however, recent evidence is pointing to a role for the upregulation of LDs in the production of a successful immune response to viral infection. The fatty acids housed in LDs are also gaining interest due to the role that these lipid species play during viral infection, and their link to the synthesis of bioactive lipid mediators that have been found to have a very complex role in viral infection. This review explores the role of LDs and their subsequent lipid mediators during viral infections and poses a paradigm shift in thinking in the field, whereby LDs may play pivotal roles in protecting the host against viral infection.
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Affiliation(s)
- Ebony A Monson
- School of Life Sciences, La Trobe University, Melbourne, Australia, 3083
| | - Alice M Trenerry
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia, 3000
| | - Jay L Laws
- School of Life Sciences, La Trobe University, Melbourne, Australia, 3083
| | - Jason M Mackenzie
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia, 3000
| | - Karla J Helbig
- School of Life Sciences, La Trobe University, Melbourne, Australia, 3083
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21
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Neves-Martins TC, Mebus-Antunes NC, Caruso IP, Almeida FCL, Da Poian AT. Unique structural features of flaviviruses' capsid proteins: new insights on structure-function relationship. Curr Opin Virol 2021; 47:106-112. [PMID: 33721656 DOI: 10.1016/j.coviro.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 10/21/2022]
Abstract
The Flaviviridae family comprises important human pathogens, including Dengue, Zika, West Nile, Yellow Fever and Japanese Encephalitis viruses. The viral genome, a positive-sense single-stranded RNA, is packaged by a single protein, the capsid protein, which is a small and highly basic protein that form intertwined homodimers in solution. Atomic-resolution structures of four flaviviruses capsid proteins were solved either in solution by nuclear magnetic resonance spectroscopy, or after protein crystallization by X-ray diffraction. Analyses of these structures revealed very particular properties, namely (i) the predominance of quaternary contacts maintaining the structure; (ii) a highly electropositive surface throughout the protein; and (iii) a flexible helix (α1). The goal of this review is to discuss the role of these features in protein structure-function relationship.
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Affiliation(s)
- Thais C Neves-Martins
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil
| | - Nathane C Mebus-Antunes
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil
| | - Icaro P Caruso
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil; Multiuser Center for Biomolecular Innovation (CMIB) and Department of Physics, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000, São José do Rio Preto, SP, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil; National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil.
| | - Andrea T Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis (IBqM), Federal University of Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil.
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22
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Maddipati VC, Mittal L, Mantipally M, Asthana S, Bhattacharyya S, Gundla R. A Review on the Progress and Prospects of Dengue Drug Discovery Targeting NS5 RNA- Dependent RNA Polymerase. Curr Pharm Des 2021; 26:4386-4409. [PMID: 32445444 DOI: 10.2174/1381612826666200523174753] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/15/2020] [Indexed: 02/08/2023]
Abstract
Dengue virus (DENV) infection threatens the health and wellbeing of almost 100 million people in the world. Vectored by mosquitoes, DENV may cause a severe disease in human hosts called Dengue hemorrhagic fever (DHF)/Dengue shock syndrome (DSS), which is not preventable by any known drug. In the absence of a universally-accepted vaccine, a drug capable of inhibiting DENV multiplication is an urgent and unmet clinical need. Here we summarize inhibitory strategies by targeting either host biochemical pathways or virus-encoded proteins. A variety of approaches have been generated to design Directly-acting anti-virals or DAAs targeting different DENV proteins, with diverse success. Among them, DAAs targeting genome replicating viral enzymes have proven effective against many viruses including, Human Immuno-deficiency Virus and Hepatitis C Virus. DAAs may be derived either from existing compound libraries of novel molecules and plant secondary metabolites or devised through Computer-aided Drug design (CADD) methods. Here, we focus on compounds with reported DAA-activity against the DENV RNA-dependent RNA polymerase (RdRp), which replicate the viral RNA genome. The structure-activity relationship (SAR) and toxicity of the natural compounds, including secondary plant metabolites, have been discussed in detail. We have also tabulated novel compounds with known anti-RdRp activity. We concluded with a list of DAAs for which a co-crystal structure with RdRp is reported. Promising hit compounds are often discarded due to poor selectivity or unsuitable pharmacokinetics. We hope this review will provide a useful reference for further studies on the development of an anti-DENV drug.
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Affiliation(s)
- Venkatanarayana C Maddipati
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Manohar Mantipally
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rdMilestone, Faridabad-Gurugram Expressway, Faridabad - 121001, Haryana, India
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad 502329, Telangana, India
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23
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Yong XE, Raghuvamsi PV, Anand GS, Wohland T, Sharma KK. Dengue virus strain 2 capsid protein switches the annealing pathway and reduces intrinsic dynamics of the conserved 5' untranslated region. RNA Biol 2021; 18:718-731. [PMID: 33406991 PMCID: PMC8078513 DOI: 10.1080/15476286.2020.1860581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The capsid protein of dengue virus strain 2 (DENV2C) promotes nucleic acid structural rearrangements using chaperone activity. However, the role of DENV2C during the interaction of RNA elements in the conserved 5' untranslated region (5'UTR) to the 3' untranslated region (3'UTR) is still unclear. Thus, we investigated the effect of DENV2C on the annealing mechanism of two RNA hairpin elements from the 5'UTR to their complementary sequences during (+)/(-) ds-RNAformation and (+) RNA circularization. DENV2C was found to switch the annealing pathway for RNA elements involved in (+)/(-) ds-RNA formation, but not for RNA elements related to (+) RNA circularization. In addition, we also determined that DENV2C modulates intrinsic dynamics and reduces kinetically trapped unfavourable conformations of the 5'UTR sequence. Thus, our results provide mechanistic insights by which DENV2C chaperones the interactions between RNA elements at the 5' and 3' ends during genome recombination, a prerequisite for DENV replication.
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Affiliation(s)
- Xin Ee Yong
- NUS Graduate School for integrative Sciences and Engineering Programme, National University of Singapore, Singapore.,Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | | | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kamal K Sharma
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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24
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Harsh S, Eleftherianos I. Flavivirus Infection and Regulation of Host Immune and Tissue Homeostasis in Insects. Front Immunol 2020; 11:618801. [PMID: 33329613 PMCID: PMC7733989 DOI: 10.3389/fimmu.2020.618801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 11/16/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sneh Harsh
- Infection and Innate Immunity Lab, Department of Biological Sciences, Institute for Biomedical Sciences, The George Washington University, Washington, DC, United States.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Ioannis Eleftherianos
- Infection and Innate Immunity Lab, Department of Biological Sciences, Institute for Biomedical Sciences, The George Washington University, Washington, DC, United States
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25
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Saumya KU, Kumar D, Kumar P, Giri R. Unlike dengue virus, the conserved 14–23 residues in N-terminal region of Zika virus capsid is not involved in lipid interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183440. [DOI: 10.1016/j.bbamem.2020.183440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 12/19/2022]
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26
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Liu B, Gao TT, Fu XY, Xu ZH, Ren H, Zhao P, Qi ZT, Qin ZL. PTEN Lipid Phosphatase Activity Enhances Dengue Virus Production through Akt/FoxO1/Maf1 Signaling. Virol Sin 2020; 36:412-423. [PMID: 33044659 DOI: 10.1007/s12250-020-00291-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/31/2020] [Indexed: 01/19/2023] Open
Abstract
Dengue virus (DENV) is an arthropod-borne viral pathogen and a global health burden. Knowledge of the DENV-host interactions that mediate virus pathogenicity remains limited. Host lipid metabolism is hijacked by DENV for virus replication in which lipid droplets (LDs) play a key role during the virus lifecycle. In this study, we reveal a novel role for phosphatase and tensin homolog deleted on chromosome 10 (PTEN) in LDs-mediated DENV infection. We demonstrate that PTEN expression is downregulated upon DENV infection through post-transcriptional regulation and, in turn, PTEN overexpression enhances DENV replication. PTEN lipid phosphatase activity was found to decrease cellular LDs area and number through Akt/FoxO1/Maf1 signaling, which, together with autophagy, enhanced DENV replication and virus production. We therefore provide mechanistic insight into the interaction between lipid metabolism and the DENV replication cycle.
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Affiliation(s)
- Bin Liu
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, 200433, China
| | - Ting-Ting Gao
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, 200433, China.,Department of Nephrology, The Air Force Hospital from Northern Theater of PLA, Shenyang 110042, China
| | - Xiao-Yu Fu
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, 200433, China
| | - Zhen-Hao Xu
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, 200433, China
| | - Hao Ren
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, 200433, China
| | - Ping Zhao
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, 200433, China
| | - Zhong-Tian Qi
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, 200433, China.
| | - Zhao-Ling Qin
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, Shanghai, 200433, China.
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Silva NM, Santos NC, Martins IC. Dengue and Zika Viruses: Epidemiological History, Potential Therapies, and Promising Vaccines. Trop Med Infect Dis 2020; 5:E150. [PMID: 32977703 PMCID: PMC7709709 DOI: 10.3390/tropicalmed5040150] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/05/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022] Open
Abstract
Dengue virus (DENV), which can lead to fatal hemorrhagic fever, affects 390 million people worldwide. The closely related Zika virus (ZIKV) causes microcephaly in newborns and Guillain-Barré syndrome in adults. Both viruses are mostly transmitted by Aedes albopictus and Aedes aegypti mosquitoes, which, due to globalization of trade and travel alongside climate change, are spreading worldwide, paving the way to DENV and ZIKV transmission and the occurrence of new epidemics. Local outbreaks have already occurred in temperate climates, even in Europe. As there are no specific treatments, these viruses are an international public health concern. Here, we analyze and discuss DENV and ZIKV outbreaks history, clinical and pathogenesis features, and modes of transmission, supplementing with information on advances on potential therapies and restraining measures. Taking advantage of the knowledge of the structure and biological function of the capsid (C) protein, a relatively conserved protein among flaviviruses, within a genus that includes DENV and ZIKV, we designed and patented a new drug lead, pep14-23 (WO2008/028939A1). It was demonstrated that it inhibits the interaction of DENV C protein with the host lipid system, a process essential for viral replication. Such an approach can be used to develop new therapies for related viruses, such as ZIKV.
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Affiliation(s)
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal;
| | - Ivo C. Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal;
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He Y, Wang M, Chen S, Cheng A. The role of capsid in the flaviviral life cycle and perspectives for vaccine development. Vaccine 2020; 38:6872-6881. [PMID: 32950301 PMCID: PMC7495249 DOI: 10.1016/j.vaccine.2020.08.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 02/09/2023]
Abstract
The structure and function of flaviviral capsid are very flexible. The capsid gene contains conserved RNA secondary structures. Both steps of assembly and dissociation of nucleocapsid complexes are obscure. Capsid mutant viruses are highly attenuated and immunogenic. ΔC-replicon and single-round infectious particles are promising vaccine approaches.
The arthropod-borne flaviviruses cause a series of diseases in humans and pose a significant threat to global public health. In this review, we aimed to summarize the structure of the capsid protein (CP), its relevant multiple functions in the viral life cycle and innovative vaccines targeting CP. The flaviviral CP is the smallest structural protein and forms a homodimer by antiparallel α-helixes. Its primary function is to package the genomic RNA; however, both steps of assembly and dissociation of nucleocapsid complexes (NCs) have been obscure until now; in fact, flaviviral budding is NC-free, demonstrated by the subviral particles that generally exist in flavivirus infection. In infected cells, CPs associate with lipid droplets, which possibly store CPs prior to packaging. However, the function of nuclear localization of CPs remains unknown. Moreover, introducing deletions into CPs can be used to rationally design safe and effective live-attenuated vaccines or noninfectious replicon vaccines and single-round infectious particles, the latter two representing promising approaches for innovative flaviviral vaccine development.
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Affiliation(s)
- Yu He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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29
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Peptides targeting dengue viral nonstructural protein 1 inhibit dengue virus production. Sci Rep 2020; 10:12933. [PMID: 32737386 PMCID: PMC7395749 DOI: 10.1038/s41598-020-69515-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Viruses manipulate the life cycle in host cells via the use of viral properties and host machineries. Development of antiviral peptides against dengue virus (DENV) infection has previously been concentrated on blocking the actions of viral structural proteins and enzymes in virus entry and viral RNA processing in host cells. In this study, we proposed DENV NS1, which is a multifunctional non-structural protein indispensable for virus production, as a new target for inhibition of DENV infection by specific peptides. We performed biopanning assays using a phage-displayed peptide library and identified 11 different sequences of 12-mer peptides binding to DENV NS1. In silico analyses of peptide-protein interactions revealed 4 peptides most likely to bind to DENV NS1 at specific positions and their association was analysed by surface plasmon resonance. Treatment of Huh7 cells with these 4 peptides conjugated with N-terminal fluorescent tag and C-terminal cell penetrating tag at varying time-of-addition post-DENV infection could inhibit the production of DENV-2 in a time- and dose-dependent manner. The inhibitory effects of the peptides were also observed in other virus serotypes (DENV-1 and DENV-4), but not in DENV-3. These findings indicate the potential application of peptides targeting DENV NS1 as antiviral agents against DENV infection.
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30
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West Nile Virus: An Update on Pathobiology, Epidemiology, Diagnostics, Control and "One Health" Implications. Pathogens 2020; 9:pathogens9070589. [PMID: 32707644 PMCID: PMC7400489 DOI: 10.3390/pathogens9070589] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
West Nile virus (WNV) is an important zoonotic flavivirus responsible for mild fever to severe, lethal neuroinvasive disease in humans, horses, birds, and other wildlife species. Since its discovery, WNV has caused multiple human and animal disease outbreaks in all continents, except Antarctica. Infections are associated with economic losses, mainly due to the cost of treatment of infected patients, control programmes, and loss of animals and animal products. The pathogenesis of WNV has been extensively investigated in natural hosts as well as in several animal models, including rodents, lagomorphs, birds, and reptiles. However, most of the proposed pathogenesis hypotheses remain contentious, and much remains to be elucidated. At the same time, the unavailability of specific antiviral treatment or effective and safe vaccines contribute to the perpetuation of the disease and regular occurrence of outbreaks in both endemic and non-endemic areas. Moreover, globalisation and climate change are also important drivers of the emergence and re-emergence of the virus and disease. Here, we give an update of the pathobiology, epidemiology, diagnostics, control, and “One Health” implications of WNV infection and disease.
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Affiliation(s)
- Ter Yong Tan
- Programme in Emerging Infectious Diseases, Duke–National University of Singapore Medical School, Singapore, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Guntur Fibriansah
- Programme in Emerging Infectious Diseases, Duke–National University of Singapore Medical School, Singapore, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Shee-Mei Lok
- Programme in Emerging Infectious Diseases, Duke–National University of Singapore Medical School, Singapore, Singapore
- Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
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32
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Martins IC, Santos NC. Intrinsically disordered protein domains in flavivirus infection. Arch Biochem Biophys 2020; 683:108298. [PMID: 32045581 DOI: 10.1016/j.abb.2020.108298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered protein regions are at the core of biological processes and involved in key protein-ligand interactions. The Flavivirus proteins, of viruses of great biomedical importance such as Zika and dengue viruses, exemplify this. Several proteins of these viruses have disordered regions that are of the utmost importance for biological activity. Disordered proteins can adopt several conformations, each able to interact with and/or bind to different ligands. In fact, such interactions can help stabilize a particular fold. Moreover, by being promiscuous in the number of target molecules they can bind to, these protein regions increase the number of functions that their small proteome (10 proteins) can achieve. A folding energy waterfall better describes the protein folding landscape of these proteins. A disordered protein can be thought as rolling down the folding energy cascade, in order "to fall, fold and function". This is the case of many viral protein regions, as seen in the flaviviruses proteome. Given their small size, flaviviruses are a good model system for understanding the role of intrinsically disordered protein regions in viral function. Finally, studying these viruses disordered protein regions will certainly contribute to the development of therapeutic approaches against such promising (yet challenging) targets.
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Affiliation(s)
- Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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Sinigaglia A, Peta E, Riccetti S, Barzon L. New avenues for therapeutic discovery against West Nile virus. Expert Opin Drug Discov 2020; 15:333-348. [DOI: 10.1080/17460441.2020.1714586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Elektra Peta
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Silvia Riccetti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
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Understanding Flavivirus Capsid Protein Functions: The Tip of the Iceberg. Pathogens 2020; 9:pathogens9010042. [PMID: 31948047 PMCID: PMC7168633 DOI: 10.3390/pathogens9010042] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/18/2022] Open
Abstract
Flaviviruses are enveloped positive-sense single-stranded RNA arboviruses, infectious to humans and many other animals and are transmitted primarily via tick or mosquito vectors. Capsid is the primary structural protein to interact with viral genome within virus particles and is therefore necessary for efficient packaging. However, in cells, capsid interacts with many proteins and nucleic acids and we are only beginning to understand the broad range of functions of flaviviral capsids. It is known that capsid dimers interact with the membrane of lipid droplets, aiding in both viral packaging and storage of capsid prior to packaging. However, capsid dimers can bind a range of nucleic acid templates in vitro, and likely interact with a range of targets during the flavivirus lifecycle. Capsid may interact with host RNAs, resulting in altered RNA splicing and RNA transcription. Capsid may also bind short interfering-RNAs and has been proposed to sequester these species to protect flaviviruses from the invertebrate siRNA pathways. Capsid can also be found in the nucleolus, where it wreaks havoc on ribosome biogenesis. Here we review flavivirus capsid structure, nucleic acid interactions and how these give rise to multiple functions. We also discuss how these features might be exploited either in the design of effective antivirals or novel vaccine strategies.
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35
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Abdullah AA, Lee YK, Chin SP, Lim SK, Lee VS, Othman R, Othman S, Rahman NA, Yusof R, Heh CH. Discovery of Dengue Virus Inhibitors. Curr Med Chem 2020; 27:4945-5036. [PMID: 30514185 DOI: 10.2174/0929867326666181204155336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/11/2018] [Accepted: 11/22/2018] [Indexed: 11/22/2022]
Abstract
To date, there is still no approved anti-dengue agent to treat dengue infection in the market. Although the only licensed dengue vaccine, Dengvaxia is available, its protective efficacy against serotypes 1 and 2 of dengue virus was reported to be lower than serotypes 3 and 4. Moreover, according to WHO, the risk of being hospitalized and having severe dengue increased in seronegative individuals after they received Dengvaxia vaccination. Nevertheless, various studies had been carried out in search of dengue virus inhibitors. These studies focused on the structural (C, prM, E) and non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) of dengue virus as well as host factors as drug targets. Hence, this article provides an overall up-to-date review of the discovery of dengue virus inhibitors that are only targeting the structural and non-structural viral proteins as drug targets.
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Affiliation(s)
- Adib Afandi Abdullah
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Yean Kee Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Sek Peng Chin
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - See Khai Lim
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Rozana Othman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Shatrah Othman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abdul Rahman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Rohana Yusof
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Choon Han Heh
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
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36
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Functional Correlation between Subcellular Localizations of Japanese Encephalitis Virus Capsid Protein and Virus Production. J Virol 2019; 93:JVI.00612-19. [PMID: 31315991 DOI: 10.1128/jvi.00612-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/07/2019] [Indexed: 01/16/2023] Open
Abstract
The flavivirus capsid protein is considered to be essential for the formation of nucleocapsid complexes with viral genomic RNA at the viral replication organelle that appears on the endoplasmic reticulum (ER), as well as for incorporation into virus particles. However, this protein is also detected at the lipid droplet (LD) and nucleolus, and physiological roles of these off-site localizations are still unclear. In this study, we made a series of alanine substitution mutants of Japanese encephalitis virus (JEV) capsid protein that cover all polar and hydrophobic amino acid residues to identify the molecular surfaces required for virus particle formation and for localization at the LD and nucleolus. Five mutants exhibited a defect in the formation of infectious particles, and two of these mutants failed to be incorporated into the subviral particles (SVP). Three mutants lost the ability to localize to the nucleolus, and only a single mutant, with mutations at α2, was unable to localize to the LD. Unlike the cytoplasmic capsid protein, the nucleolar capsid protein was resistant to detergent treatment, and the α2 mutant was hypersensitive to detergent treatment. To scrutinize the relationship between these localizations and viral particle formation, we made eight additional alanine substitution mutants and found that all the mutants that did not localize at the LD or nucleolus failed to form normal viral particles. These results support the functional correlation between LD or nucleolus localization of the flaviviral capsid protein and the formation of infectious viral particles.IMPORTANCE This study is the first to report the comprehensive mutagenesis of a flavivirus capsid protein. We assessed the requirement of each molecular surface for infectious viral particle formation as well as for LD and nucleolar localization and found functional relationships between the subcellular localization of the virus capsid protein and infectious virus particle formation. We developed a system to independently assess the packaging of viral RNA and that of the capsid protein and found a molecular surface of the capsid protein that is crucial for packaging of viral RNA but not for packaging of the capsid protein itself. We also characterized the biochemical properties of capsid protein mutants and found that the capsid protein localizes at the nucleolus in a different manner than for its localization to the LD. Our comprehensive alanine-scanning mutagenesis study will aid in the development of antiflavivirus small molecules that can target the flavivirus capsid protein.
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37
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Faustino AF, Martins AS, Karguth N, Artilheiro V, Enguita FJ, Ricardo JC, Santos NC, Martins IC. Structural and Functional Properties of the Capsid Protein of Dengue and Related Flavivirus. Int J Mol Sci 2019; 20:E3870. [PMID: 31398956 PMCID: PMC6720645 DOI: 10.3390/ijms20163870] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Dengue, West Nile and Zika, closely related viruses of the Flaviviridae family, are an increasing global threat, due to the expansion of their mosquito vectors. They present a very similar viral particle with an outer lipid bilayer containing two viral proteins and, within it, the nucleocapsid core. This core is composed by the viral RNA complexed with multiple copies of the capsid protein, a crucial structural protein that mediates not only viral assembly, but also encapsidation, by interacting with host lipid systems. The capsid is a homodimeric protein that contains a disordered N-terminal region, an intermediate flexible fold section and a very stable conserved fold region. Since a better understanding of its structure can give light into its biological activity, here, first, we compared and analyzed relevant mosquito-borne Flavivirus capsid protein sequences and their predicted structures. Then, we studied the alternative conformations enabled by the N-terminal region. Finally, using dengue virus capsid protein as main model, we correlated the protein size, thermal stability and function with its structure/dynamics features. The findings suggest that the capsid protein interaction with host lipid systems leads to minor allosteric changes that may modulate the specific binding of the protein to the viral RNA. Such mechanism can be targeted in future drug development strategies, namely by using improved versions of pep14-23, a dengue virus capsid protein peptide inhibitor, previously developed by us. Such knowledge can yield promising advances against Zika, dengue and closely related Flavivirus.
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Affiliation(s)
- André F Faustino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nina Karguth
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Vanessa Artilheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Joana C Ricardo
- Centro de Química-Física Molecular, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
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38
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Poonsiri T, Wright GSA, Solomon T, Antonyuk SV. Crystal Structure of the Japanese Encephalitis Virus Capsid Protein. Viruses 2019; 11:E623. [PMID: 31284608 PMCID: PMC6669762 DOI: 10.3390/v11070623] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/29/2022] Open
Abstract
Japanese encephalitis (JE) is inflammation and swelling of the brain caused by the JE virus (JEV), a mosquito-borne member of the Flavivirus family. There are around 68,000 JE cases worldwide each year, many of which result in permanent brain damage and death. There is no specific treatment for JE. Here we present the crystal structure of the JEV capsid protein, a potential drug target, at 1.98 Å, and compare it to other flavivirus capsid proteins. The JEV capsid has a helical secondary structure (α helixes 1-4) and a similar protein fold to the dengue virus (DENV), the West Nile virus (WNV), and the Zika virus (ZIKV) capsid proteins. It forms a homodimer by antiparallel pairing with another subunit (') through α-helix 1-1', 2-2', and 4-4' interactions. This dimeric form is believed to be the building block of the nucleocapsid. The flexibility of the N-terminal α helix-1 allows the formation of closed and open conformations with possible functional importance. The basic C-terminal pairing of α4-4' forms a coiled-coil-like structure, indicating possible nucleic acid binding functionality. However, a comparison with other nucleic acid interacting domains indicates that homodimerization would preclude binding. This is the first JEV capsid protein to be described and is an addition to the structural biology of the Flavivirus.
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Affiliation(s)
- Thanalai Poonsiri
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZB Liverpool, UK
- Health Protection Research Unit on Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
| | - Gareth S A Wright
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZB Liverpool, UK
| | - Tom Solomon
- Health Protection Research Unit on Emerging and Zoonotic Infections, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
- Walton Centre NHS Foundation Trust, L9 7LJ Liverpool, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZB Liverpool, UK.
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39
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Morando MA, Barbosa GM, Cruz-Oliveira C, Da Poian AT, Almeida FCL. Dynamics of Zika Virus Capsid Protein in Solution: The Properties and Exposure of the Hydrophobic Cleft Are Controlled by the α-Helix 1 Sequence. Biochemistry 2019; 58:2488-2498. [PMID: 31034208 DOI: 10.1021/acs.biochem.9b00194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zika virus (ZIKV) became an important public health concern because infection was correlated to the development of microcephaly and other neurological disorders. Although the structure of the virion has been determined by cryo-electron microscopy, information about the nucleocapsid is lacking. We used nuclear magnetic resonance to determine the solution structure and dynamics of full length ZIKV capsid protein (ZIKVC). Although most of the protein is structured as described for the capsid proteins of Dengue and West Nile viruses and for truncated ZIKVC (residues 23-98), here we show important differences in the α-helix 1 and N-terminal intrinsically disordered region (IDR). We distinguished two dynamical regions in the ZIKVC IDR, a highly flexible N-terminal end and a transitional disordered region, indicating that it contains ordered segments rather than being completely flexible. The unique size and orientation of α-helix 1 partially occlude the protein hydrophobic cleft. Measurements of the dynamics of α-helix 1, surface exposure, and thermal susceptibility of each backbone amide 1H in protein structure revealed the occlusion of the hydrophobic cleft by α1/α1' and supported α-helix 1 positional uncertainty. On the basis of the findings described here, we propose that the dynamics of ZIKVC structural elements responds to a structure-driven regulation of interaction of the protein with intracellular hydrophobic interfaces, which would have an impact on the switches that are necessary for nucleocapsid assembly. Subtle differences in the sequence of α-helix 1 have an impact on its size and orientation and on the degree of exposure of the hydrophobic cleft, suggesting that α-helix 1 is a hot spot for evolutionary adaptation of the capsid proteins of flaviviruses.
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Affiliation(s)
- Maria A Morando
- Institute of Medical Biochemistry Leopoldo De Meis, Program of Structural Biology , Federal University of Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN) , Federal University of Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil.,Centro de Desenvolvimento de Tecnologia em Saúde, Fiocruz , Rio de Janeiro 21040-361 , Brazil
| | - Glauce M Barbosa
- Institute of Medical Biochemistry Leopoldo De Meis, Program of Structural Biology , Federal University of Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil
| | - Christine Cruz-Oliveira
- Institute of Medical Biochemistry Leopoldo De Meis, Program of Structural Biology , Federal University of Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN) , Federal University of Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil
| | - Andrea T Da Poian
- Institute of Medical Biochemistry Leopoldo De Meis, Program of Structural Biology , Federal University of Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry Leopoldo De Meis, Program of Structural Biology , Federal University of Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil.,National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN) , Federal University of Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil
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40
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Figueira-Mansur J, Aguilera EA, Stoque RM, Ventura GT, Mohana-Borges R. Mutations in the dimer interfaces of the dengue virus capsid protein affect structural stability and impair RNA-capsid interaction. Sci Rep 2019; 9:2829. [PMID: 30808916 PMCID: PMC6391532 DOI: 10.1038/s41598-019-39185-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/08/2019] [Indexed: 11/09/2022] Open
Abstract
The dengue virus 2 capsid protein (DENV2C) plays a primary structural role in the protection of the viral genome and is crucial for nucleocapsid assembly. In this study, we generated single mutants of DENV2C at L50 and L54 residues of the α2 helix, which was shown to interfere with the integration of the capsid into lipid droplets, and at residues L81 and I88 located in the α4 helix, which was shown to affect viral assembly. We demonstrated that the oligomeric states of DENV2C and its mutants exist primarily in the dimeric state in solution. All single-point mutations introduced in DENV2C promoted reduction in protein stability, an effect that was more pronounced for the L81N and I88N mutants, but not protein unfolding. All the single-point mutations affected the ability of DEN2C to interact with RNA. We concluded that mutations in the α2-α2' and α4-α4' dimer interfaces of DENV2C affect the structural stability of the protein and impair RNA-capsid interaction. These effects were more pronounced for mutations at the L81 and I88 residues in the α4 helix. These results indicate the importance of the α4-α4' dimer interface, which could be studied as a potential target for drug design in the future.
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Affiliation(s)
- Janaina Figueira-Mansur
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Estefania A Aguilera
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael M Stoque
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo T Ventura
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ronaldo Mohana-Borges
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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41
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Fast NMR method to probe solvent accessibility and disordered regions in proteins. Sci Rep 2019; 9:1647. [PMID: 30733478 PMCID: PMC6367444 DOI: 10.1038/s41598-018-37599-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 12/10/2018] [Indexed: 01/12/2023] Open
Abstract
Understanding protein structure and dynamics, which govern key cellular processes, is crucial for basic and applied research. Intrinsically disordered protein (IDP) regions display multifunctionality via alternative transient conformations, being key players in disease mechanisms. IDP regions are abundant, namely in small viruses, allowing a large number of functions out of a small proteome. The relation between protein function and structure is thus now seen from a different perspective: as IDP regions enable transient structural arrangements, each conformer can play different roles within the cell. However, as IDP regions are hard and time-consuming to study via classical techniques (optimized for globular proteins with unique conformations), new methods are required. Here, employing the dengue virus (DENV) capsid (C) protein and the immunoglobulin-binding domain of streptococcal protein G, we describe a straightforward NMR method to differentiate the solvent accessibility of single amino acid N-H groups in structured and IDP regions. We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established 1H-15N HSQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method.
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42
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Martins AS, Carvalho FA, Faustino AF, Martins IC, Santos NC. West Nile Virus Capsid Protein Interacts With Biologically Relevant Host Lipid Systems. Front Cell Infect Microbiol 2019; 9:8. [PMID: 30788291 PMCID: PMC6372508 DOI: 10.3389/fcimb.2019.00008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/11/2019] [Indexed: 01/27/2023] Open
Abstract
West Nile and dengue viruses are closely related flaviviruses, originating mosquito-borne viral infections for which there are no effective and specific treatments. Their capsid proteins sequence and structure are particularly similar, forming highly superimposable α-helical homodimers. Measuring protein-ligand interactions at the single-molecule level yields detailed information of biological and biomedical relevance. In this work, such an approach was successfully applied on the characterization of the West Nile virus capsid protein interaction with host lipid systems, namely intracellular lipid droplets (an essential step for dengue virus replication) and blood plasma lipoproteins. Dynamic light scattering measurements show that West Nile virus capsid protein binds very low-density lipoproteins, but not low-density lipoproteins, and this interaction is dependent of potassium ions. Zeta potential experiments show that the interaction with lipid droplets is also dependent of potassium ions as well as surface proteins. The forces involved on the binding of the capsid protein with lipid droplets and lipoproteins were determined using atomic force microscopy-based force spectroscopy, proving that these interactions are K+-dependent rather than a general dependence of ionic strength. The capsid protein interaction with host lipid systems may be targeted in future therapeutic strategies against different flaviviruses. The biophysical and nanotechnology approaches employed in this study may be applied to characterize the interactions of other important proteins from different viruses, in order to understand their life cycles, as well as to find new strategies to inhibit them.
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Affiliation(s)
- Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Filomena A Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - André F Faustino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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43
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Dengue drug discovery: Progress, challenges and outlook. Antiviral Res 2018; 163:156-178. [PMID: 30597183 DOI: 10.1016/j.antiviral.2018.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/14/2022]
Abstract
In the context of the only available vaccine (DENGVAXIA) that was marketed in several countries, but poses higher risks to unexposed individuals, the development of antivirals for dengue virus (DENV), whilst challenging, would bring significant benefits to public health. Here recent progress in the field of DENV drug discovery made in academic laboratories and industry is reviewed. Characteristics of an ideal DENV antiviral molecule, given the specific immunopathology provoked by this acute viral infection, are described. New chemical classes identified from biochemical, biophysical and phenotypic screens that target viral (especially NS4B) and host proteins, offer promising opportunities for further development. In particular, new methodologies ("omics") can accelerate the discovery of much awaited flavivirus specific inhibitors. Challenges and opportunities in lead identification activities as well as the path to clinical development of dengue drugs are discussed. To galvanize DENV drug discovery, collaborative public-public partnerships and open-access resources will greatly benefit both the DENV research community and DENV patients.
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Mazeaud C, Freppel W, Chatel-Chaix L. The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis. Front Genet 2018. [PMID: 30564270 DOI: 10.3389/fgene.2018.00595/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.
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Affiliation(s)
- Clément Mazeaud
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
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45
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Mazeaud C, Freppel W, Chatel-Chaix L. The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis. Front Genet 2018; 9:595. [PMID: 30564270 PMCID: PMC6288177 DOI: 10.3389/fgene.2018.00595] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/15/2018] [Indexed: 12/11/2022] Open
Abstract
The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.
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Affiliation(s)
- Clément Mazeaud
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
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46
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Martins AS, Martins IC, Santos NC. Methods for Lipid Droplet Biophysical Characterization in Flaviviridae Infections. Front Microbiol 2018; 9:1951. [PMID: 30186265 PMCID: PMC6110928 DOI: 10.3389/fmicb.2018.01951] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/02/2018] [Indexed: 01/14/2023] Open
Abstract
Lipid droplets (LDs) are intracellular organelles for neutral lipid storage, originated from the endoplasmic reticulum. They play an essential role in lipid metabolism and cellular homeostasis. In fact, LDs are complex organelles, involved in many more cellular processes than those initially proposed. They have been extensively studied in the context of LD-associated pathologies. In particular, LDs have emerged as critical for virus replication and assembly. Viruses from the Flaviviridae family, namely dengue virus (DENV), hepatitis C virus (HCV), West Nile virus (WNV), and Zika virus (ZIKV), interact with LDs to usurp the host lipid metabolism for their own viral replication and pathogenesis. In general, during Flaviviridae infections it is observed an increasing number of host intracellular LDs. Several viral proteins interact with LDs during different steps of the viral life cycle. The HCV core protein and DENV capsid protein, extensively interact with LDs to regulate their replication and assembly. Detailed studies of LDs in viral infections may contribute for the development of possible inhibitors of key steps of viral replication. Here, we reviewed different techniques that can be used to characterize LDs isolated from infected or non-infected cells. Microscopy studies have been commonly used to observe LDs accumulation and localization in infected cell cultures. Fluorescent dyes, which may affect LDs directly, are widely used to probe LDs but there are also approaches that do not require the use of fluorescence, namely stimulated Raman scattering, electron and atomic force microscopy-based approaches. These three are powerful techniques to characterize LDs morphology. Raman scattering microscopy allows studying LDs in a single cell. Electron and atomic force microscopies enable a better characterization of LDs in terms of structure and interaction with other organelles. Other biophysical techniques, such as dynamic light scattering and zeta potential are also excellent to characterize LDs in terms of size in a simple and fast way and test possible LDs interaction with viral proteins. These methodologies are reviewed in detail, in the context of viral studies.
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Affiliation(s)
- Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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47
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Molecular Recognition Features in Zika Virus Proteome. J Mol Biol 2018; 430:2372-2388. [DOI: 10.1016/j.jmb.2017.10.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 12/23/2022]
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48
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Boon PLS, Saw WG, Lim XX, Raghuvamsi PV, Huber RG, Marzinek JK, Holdbrook DA, Anand GS, Grüber G, Bond PJ. Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble. ACS Chem Biol 2018; 13:1621-1630. [PMID: 29792674 DOI: 10.1021/acschembio.8b00231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 11 kDa, positively charged dengue capsid protein (C protein) exists stably as a homodimer and colocalizes with the viral genome within mature viral particles. Its core is composed of four alpha helices encompassing a small hydrophobic patch that may interact with lipids, but approximately 20% of the protein at the N-terminus is intrinsically disordered, making it challenging to elucidate its conformational landscape. Here, we combine small-angle X-ray scattering (SAXS), amide hydrogen-deuterium exchange mass spectrometry (HDXMS), and atomic-resolution molecular dynamics (MD) simulations to probe the dynamics of dengue C proteins. We show that the use of MD force fields (FFs) optimized for intrinsically disordered proteins (IDPs) is necessary to capture their conformational landscape and validate the computationally generated ensembles with reference to SAXS and HDXMS data. Representative ensembles of the C protein dimer are characterized by alternating, clamp-like exposure and occlusion of the internal hydrophobic patch, as well as by residual helical structure at the disordered N-terminus previously identified as a potential source of autoinhibition. Such dynamics are likely to determine the multifunctionality of the C protein during the flavivirus life cycle and hence impact the design of novel antiviral compounds.
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Affiliation(s)
- Priscilla L. S. Boon
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
- NUS Graduate School for Integrated Sciences and Engineering, National University of Singapore, #05-01, 28 Medical Drive, Singapore 117456
| | - Wuan Geok Saw
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
| | - Xin Xiang Lim
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Palur Venkata Raghuvamsi
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Roland G. Huber
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
| | - Jan K. Marzinek
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Daniel A. Holdbrook
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
| | - Ganesh S. Anand
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
| | - Gerhard Grüber
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
| | - Peter J. Bond
- Bioinformatics institute (BII), Agency for Science, Technology and Research (A*STAR), #07-01 Matrix, 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 14 Science Drive 4, Singapore 117543
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49
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Gomes B, Augusto MT, Felício MR, Hollmann A, Franco OL, Gonçalves S, Santos NC. Designing improved active peptides for therapeutic approaches against infectious diseases. Biotechnol Adv 2018; 36:415-429. [PMID: 29330093 DOI: 10.1016/j.biotechadv.2018.01.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/13/2017] [Accepted: 01/06/2018] [Indexed: 12/25/2022]
Abstract
Infectious diseases are one of the main causes of human morbidity and mortality. In the last few decades, pathogenic microorganisms' resistance to conventional drugs has been increasing, and it is now pinpointed as a major worldwide health concern. The need to search for new therapeutic options, as well as improved treatment outcomes, has therefore increased significantly, with biologically active peptides representing a new alternative. A substantial research effort is being dedicated towards their development, especially due to improved biocompatibility and target selectivity. However, the inherent limitations of peptide drugs are restricting their application. In this review, we summarize the current status of peptide drug development, focusing on antiviral and antimicrobial peptide activities, highlighting the design improvements needed, and those already being used, to overcome the drawbacks of the therapeutic application of biologically active peptides.
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Affiliation(s)
- Bárbara Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marcelo T Augusto
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Mário R Felício
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Axel Hollmann
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal; Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Buenos Aires, Argentina; Laboratory of Biointerfaces and Biomimetic Systems, CITSE, National University of Santiago del Estero-CONICET, Santiago del Estero, Argentina
| | - Octávio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.
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50
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Zhang J, Lan Y, Sanyal S. Modulation of Lipid Droplet Metabolism-A Potential Target for Therapeutic Intervention in Flaviviridae Infections. Front Microbiol 2017; 8:2286. [PMID: 29234310 PMCID: PMC5712332 DOI: 10.3389/fmicb.2017.02286] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
Lipid droplets (LDs) are endoplasmic reticulum (ER)-related dynamic organelles that store and regulate fatty acids and neutral lipids. They play a central role in cellular energy storage, lipid metabolism and cellular homeostasis. It has become evident that viruses have co-evolved in order to exploit host lipid metabolic pathways. This is especially characteristic of the Flaviviridae family, including hepatitis C virus (HCV) and several flaviviruses. Devoid of an appropriate lipid biosynthetic machinery of their own, these single-strand positive-sense RNA viruses can induce dramatic changes in host metabolic pathways to establish a favorable environment for viral multiplication and acquire essential components to facilitate their assembly and traffic. Here we have reviewed the current knowledge on the intracellular life cycle of those from the Flaviviridae family, with particular emphasis on HCV and dengue virus (DENV), and their association with the biosynthesis and metabolism of LDs, with the aim to identify potential antiviral targets for development of novel therapeutic interventions.
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Affiliation(s)
- Jingshu Zhang
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Yun Lan
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
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