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Hou YN, Zhang LJ, Du L, Fu DD, Li J, Liu L, Xu PF, Zheng YW, Pang DW, Tang HW. Analyzing the factors affecting virus invasion by quantitative single-particle analysis. Virulence 2024; 15:2367671. [PMID: 38910312 PMCID: PMC11197921 DOI: 10.1080/21505594.2024.2367671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/09/2024] [Indexed: 06/25/2024] Open
Abstract
Viral diseases are among the main threats to public health. Understanding the factors affecting viral invasion is important for antiviral research. Until now, it was known that most viruses have very low plaque-forming unit (PFU)-to-particle ratios. However, further investigation is required to determine the underlying factors. Here, using quantitative single-particle analysis methods, the invasion of Semliki Forest virus (SFV), Japanese encephalitis virus (JEV), and influenza A virus (IAV) containing attachment to the cell surface, entry into the cell, transport towards the cell interior, and fusion with endosomes to release nucleocapsids were quantitatively analysed in parallel. It was found that for SFV with an PFU-to-particle ratio of approximately 1:2, an entry efficiency of approximately 31% limited infection. For JEV, whose PFU-to-particle ratio was approximately 1:310, an attachment efficiency of approximately 27% and an entry efficiency of 10% were the main factors limiting its infection. Meanwhile, for IAV with PFU-to-particle ratios of 1:8100, 5% attachment efficiency, 9% entry efficiency, and 53% fusion efficiency significantly limited its infection. These results suggest that viruses with different infectivities have different limited steps in the invasion process. Moreover, there are significant differences in attachment efficiencies among viruses, emphasizing the pivotal role of attachment in viral invasion. The influence of the virus purification method on virus invasion was also investigated. This study, for the first time, reports the efficiencies of different stages of virus invasion, leading to a better understanding of virus invasion and providing a protocol to quantitatively analyse the virus invasion efficiency.
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Affiliation(s)
- Yi-Ning Hou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Li-Juan Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Lei Du
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Dan-Dan Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Jing Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Liu Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Peng-Fei Xu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Ya-Wen Zheng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Dai-Wen Pang
- College of Chemistry, Nankai University, Tianjin, China
| | - Hong-Wu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
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Griffon AF, Rault L, Simon-Lorière E, Dupont-Rouzeyrol M, Inizan C. Development of a competition assay to assess the in vitro fitness of dengue virus serotypes using an optimized serotype-specific qRT-PCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.611934. [PMID: 39314409 PMCID: PMC11419098 DOI: 10.1101/2024.09.10.611934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Background Comparing the in vitro fitness of dengue virus (DENV) isolates is a pivotal approach to assess the contribution of DENV strains' replicative fitness to epidemiological contexts, including serotype replacements. Competition assays are the gold standard to compare the in vitro replicative fitness of viral strains. Implementing competition assays between DENV serotypes requires an experimental setup and an appropriate read-out to quantify the viral progeny of strains belonging to different serotypes. Results In the current study, we optimized an existing serotyping qRT-PCR by adapting primer/probe design and multiplexing the serotype-specific qRT-PCR reactions, allowing to accurately detect and quantify all four DENV serotypes. The qRT-PCR was specific, had a limit of detection of at least 5.08×101, 5.16×101, 7.14×101 and 1.36 ×101 genome copies/μL, an efficiency of 1.993, 1.975, 1.902, 1.898 and a linearity (R2) of 0.99975, 0.99975, 0.9985, 0.99965 for DENV-1, -2, -3 and -4 respectively. Challenge of this multiplex serotype-specific qRT-PCR on mixes of viral supernatants containing known concentrations of strains from two serotypes evidenced an accurate quantification of the amount of genome copies of each serotype. We next developed an in vitro assay to compare the replicative fitness of two DENV serotypes in the human hepatic cell line HuH7: quantification of the viral progeny of each serotype in the inoculum and the supernatant using the serotype-specific multiplex qRT-PCR unveiled an enrichment of the supernatant in DENV-1 genome copies, uncovering the enhanced replicative fitness of this DENV-1 isolate. Conclusions This optimized qRT-PCR combined to a relevant cellular model allowed to accurately quantify the viral progeny of two DENV strains belonging to two different serotypes in a competition assay, allowing to determine which strain had a replicative advantage. This reliable experimental setup is adaptable to the comparative study of the replicative fitness of any DENV serotypes.
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Affiliation(s)
- Anne-Fleur Griffon
- Dengue and Arboviroses - Research and Expertise Unit - Institut Pasteur in New Caledonia - Pasteur Network, Dumbéa-sur-Mer, New Caledonia
| | - Loeïza Rault
- Dengue and Arboviroses - Research and Expertise Unit - Institut Pasteur in New Caledonia - Pasteur Network, Dumbéa-sur-Mer, New Caledonia
| | - Etienne Simon-Lorière
- Evolutionary genomics of RNA viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Myrielle Dupont-Rouzeyrol
- Dengue and Arboviroses - Research and Expertise Unit - Institut Pasteur in New Caledonia - Pasteur Network, Dumbéa-sur-Mer, New Caledonia
| | - Catherine Inizan
- Dengue and Arboviroses - Research and Expertise Unit - Institut Pasteur in New Caledonia - Pasteur Network, Dumbéa-sur-Mer, New Caledonia
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Yu X, Zhu Y, Yin G, Wang Y, Shi X, Cheng G. Exploiting hosts and vectors: viral strategies for facilitating transmission. EMBO Rep 2024; 25:3187-3201. [PMID: 39048750 PMCID: PMC11315993 DOI: 10.1038/s44319-024-00214-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 04/17/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Viruses have developed various strategies to ensure their survival and transmission. One intriguing strategy involves manipulating the behavior of infected arthropod vectors and hosts. Through intricate interactions, viruses can modify vector behavior, aiding in crossing barriers and improving transmission to new hosts. This manipulation may include altering vector feeding preferences, thus promoting virus transmission to susceptible individuals. In addition, viruses employ diverse dissemination methods, including cell-to-cell and intercellular transmission via extracellular vesicles. These strategies allow viruses to establish themselves in favorable environments, optimize replication, and increase the likelihood of spreading to other individuals. Understanding these complex viral strategies offers valuable insights into their biology, transmission dynamics, and potential interventions for controlling infections. Unraveling interactions between viruses, hosts, and vectors enables the development of targeted approaches to effectively mitigate viral diseases and prevent transmission.
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Affiliation(s)
- Xi Yu
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yibin Zhu
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, China
| | - Gang Yin
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Yibaina Wang
- China National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Xiaolu Shi
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, China
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, 100084, China.
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China.
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, China.
- Southwest United Graduate School, Kunming, 650092, China.
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4
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Liu J, Guo Z, Li W, Zhang X, Liang C, Cui Z. Packaging Quantum Dots in Viral Particles via a Strep-tag II/Streptavidin System for Single-Virus Tracking. NANO LETTERS 2024; 24:2821-2830. [PMID: 38407052 DOI: 10.1021/acs.nanolett.3c04570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Single-virus tracking provides a powerful tool for studying virus infection with high spatiotemporal resolution. Quantum dots (QDs) are used to label and track viral particles due to their brightness and photostability. However, labeling viral particles with QDs is not easy. We developed a new method for labeling viral particles with QDs by using the Strep-tag II/streptavidin system. In this method, QDs were site-specifically ligated to viral proteins in live cells and then packaged into viral-like particles (VLPs) of tick-borne encephalitis virus (TBEV) and Ebola virus during viral assembly. With TBEV VLP-QDs, we tracked the clathrin-mediated endocytic entry of TBEV and studied its intracellular dynamics at the single-particle level. Our Strep-tag II/streptavidin labeling procedure eliminates the need for BirA protein expression or biotin addition, providing a simple and general method for site-specifically labeling viral particles with QDs for single-virus tracking.
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Affiliation(s)
- Ji Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhengyuan Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wei Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Cuiqin Liang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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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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Pustijanac E, Buršić M, Talapko J, Škrlec I, Meštrović T, Lišnjić D. Tick-Borne Encephalitis Virus: A Comprehensive Review of Transmission, Pathogenesis, Epidemiology, Clinical Manifestations, Diagnosis, and Prevention. Microorganisms 2023; 11:1634. [PMID: 37512806 PMCID: PMC10383662 DOI: 10.3390/microorganisms11071634] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, can cause serious infection of the central nervous system in humans, resulting in potential neurological complications and fatal outcomes. TBEV is primarily transmitted to humans through infected tick bites, and the viral agent circulates between ticks and animals, such as deer and small mammals. The occurrence of the infection aligns with the seasonal activity of ticks. As no specific antiviral therapy exists for TBEV infection, treatment approaches primarily focus on symptomatic relief and support. Active immunization is highly effective, especially for individuals in endemic areas. The burden of TBEV infections is increasing, posing a growing health concern. Reported incidence rates rose from 0.4 to 0.9 cases per 100,000 people between 2015 and 2020. The Baltic and Central European countries have the highest incidence, but TBE is endemic across a wide geographic area. Various factors, including social and environmental aspects, improved medical awareness, and advanced diagnostics, have contributed to the observed increase. Diagnosing TBEV infection can be challenging due to the non-specific nature of the initial symptoms and potential co-infections. Accurate diagnosis is crucial for appropriate management, prevention of complications, and effective control measures. In this comprehensive review, we summarize the molecular structure of TBEV, its transmission and circulation in natural environments, the pathogenesis of TBEV infection, the epidemiology and global distribution of the virus, associated risk factors, clinical manifestations, and diagnostic approaches. By improving understanding of these aspects, we aim to enhance knowledge and promote strategies for timely and accurate diagnosis, appropriate management, and the implementation of effective control measures against TBEV infections.
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Affiliation(s)
- Emina Pustijanac
- Faculty of Natural Sciences, Juraj Dobrila University of Pula, 52100 Pula, Croatia
| | - Moira Buršić
- Faculty of Natural Sciences, Juraj Dobrila University of Pula, 52100 Pula, Croatia
| | - Jasminka Talapko
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Ivana Škrlec
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Tomislav Meštrović
- University Centre Varaždin, University North, 42000 Varaždin, Croatia
- Institute for Health Metrics and Evaluation and the Department of Health Metrics Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dubravka Lišnjić
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
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7
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Liu D, Pan L, Zhai H, Qiu HJ, Sun Y. Virus tracking technologies and their applications in viral life cycle: research advances and future perspectives. Front Immunol 2023; 14:1204730. [PMID: 37334362 PMCID: PMC10272434 DOI: 10.3389/fimmu.2023.1204730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Viruses are simple yet highly pathogenic microorganisms that parasitize within cells and pose serious threats to the health, economic development, and social stability of both humans and animals. Therefore, it is crucial to understand the dynamic mechanism of virus infection in hosts. One effective way to achieve this is through virus tracking technology, which utilizes fluorescence imaging to track the life processes of virus particles in living cells in real-time, providing a comprehensively and detailed spatiotemporal dynamic process and mechanism of virus infection. This paper provides a broad overview of virus tracking technology, including the selection of fluorescent labels and virus labeling components, the development of imaging microscopes, and its applications in various virus studies. Additionally, we discuss the possibilities and challenges of its future development, offering theoretical guidance and technical support for effective prevention and control of the viral disease outbreaks and epidemics.
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Affiliation(s)
| | | | | | - Hua-Ji Qiu
- *Correspondence: Hua-Ji Qiu, ; Yuan Sun,
| | - Yuan Sun
- *Correspondence: Hua-Ji Qiu, ; Yuan Sun,
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8
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Upasani V, ter Ellen BM, Sann S, Lay S, Heng S, Laurent D, Ly S, Duong V, Dussart P, Smit JM, Cantaert T, Rodenhuis-Zybert IA. Characterization of soluble TLR2 and CD14 levels during acute dengue virus infection. Heliyon 2023; 9:e17265. [PMID: 37416678 PMCID: PMC10320027 DOI: 10.1016/j.heliyon.2023.e17265] [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] [Received: 09/09/2022] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
Dengue virus infection results in a broad spectrum of diseases ranging from mild dengue fever (DF) to severe dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Hitherto, there is no consensus biomarker for the prediction of severe dengue disease in patients. Yet, early identification of patients who progress to severe dengue is pivotal for better clinical management. We have recently reported that an increased frequency of classical (CD14 ++CD16-) monocytes with sustained high TLR2 expression in acutely infected dengue patients correlates with severe dengue development. Here, we hypothesized that the relatively lower TLR2 and CD14 expression in mild dengue patients is due to the shedding of their soluble forms (sTLR2 and sCD14) and that these could be used as indicators of disease progression. Therefore, using commercial sandwich ELISAs, we evaluated the release of sTLR2 and sCD14 by peripheral blood mononuclear cells (PBMCs) in response to in vitro dengue virus (DENV) infection and assessed their levels in acute-phase plasma of 109 dengue patients. We show that while both sTLR2 and sCD14 are released by PBMCs in response to DENV infection in vitro, their co-circulation in an acute phase of the disease is not always apparent. In fact, sTLR2 was found only in 20% of patients irrespective of disease status. In contrast, sCD14 levels were detected in all patients and were significantly elevated in DF patients when compared to DHF patients and age-matched healthy donors. Altogether, our results suggest that sCD14 may help in identifying patients at risk of severe dengue at hospital admittance.
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Affiliation(s)
- Vinit Upasani
- Immunology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Bram M. ter Ellen
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Sotheary Sann
- Immunology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Sokchea Lay
- Immunology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Sothy Heng
- Kantha Bopha Children Hospital, Phnom Penh, Cambodia
| | - Denis Laurent
- Kantha Bopha Children Hospital, Phnom Penh, Cambodia
| | - Sowath Ly
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Jolanda M. Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Tineke Cantaert
- Immunology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh, Cambodia
| | - Izabela A. Rodenhuis-Zybert
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
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9
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Single-virus tracking with quantum dots in live cells. Nat Protoc 2023; 18:458-489. [PMID: 36451053 DOI: 10.1038/s41596-022-00775-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/16/2022] [Indexed: 12/05/2022]
Abstract
Single-virus tracking (SVT) offers the opportunity to monitor the journey of individual viruses in real time and to explore the interactions between viral and cellular structures in live cells, which can assist in characterizing the complex infection process and revealing the associated dynamic mechanisms. However, the low brightness and poor photostability of conventional fluorescent tags (e.g., organic dyes and fluorescent proteins) greatly limit the development of the SVT technique, and challenges remain in performing multicolor SVT over long periods of time. Owing to the outstanding photostability, high brightness and narrow emission with tunable color range of quantum dots (QDs), QD-based SVT (QSVT) enables us to follow the fate of individual viruses interacting with different cellular structures at the single-virus level for milliseconds to hours, providing more accurate and detailed information regarding viral infection in live cells. So far, the QSVT technique has yielded spectacular achievements in uncovering the mechanisms associated with virus entry, trafficking and egress. Here, we provide a detailed protocol for QSVT implementation using the viruses that we have previously studied systematically as an example. The specific procedures for performing QSVT experiments in live cells are described, including virus preparation, the QD labeling strategies, imaging approaches, image processing and data analysis. The protocol takes 1-2 weeks from the preparation of viruses and cellular specimens to image acquisition, and 1 d for image processing and data analysis.
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Johnson C, Exell J, Lin Y, Aguilar J, Welsher KD. Capturing the start point of the virus-cell interaction with high-speed 3D single-virus tracking. Nat Methods 2022; 19:1642-1652. [PMID: 36357694 PMCID: PMC10154077 DOI: 10.1038/s41592-022-01672-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 09/30/2022] [Indexed: 11/12/2022]
Abstract
The early stages of the virus-cell interaction have long evaded observation by existing microscopy methods due to the rapid diffusion of virions in the extracellular space and the large three-dimensional cellular structures involved. Here we present an active-feedback single-particle tracking method with simultaneous volumetric imaging of the live cell environment called 3D-TrIm to address this knowledge gap. 3D-TrIm captures the extracellular phase of the infectious cycle in what we believe is unprecedented detail. We report what are, to our knowledge, previously unobserved phenomena in the early stages of the virus-cell interaction, including skimming contact events at the millisecond timescale, orders of magnitude change in diffusion coefficient upon binding and cylindrical and linear diffusion modes along cellular protrusions. Finally, we demonstrate how this method can move single-particle tracking from simple monolayer culture toward more tissue-like conditions by tracking single virions in tightly packed epithelial cells. This multiresolution method presents opportunities for capturing fast, three-dimensional processes in biological systems.
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Affiliation(s)
| | - Jack Exell
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Yuxin Lin
- Department of Chemistry, Duke University, Durham, NC, USA
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Aguilar Briseño JA, Ramos Pereira L, van der Laan M, Pauzuolis M, ter Ellen BM, Upasani V, Moser J, de Souza Ferreira LC, Smit JM, Rodenhuis-Zybert IA. TLR2 axis on peripheral blood mononuclear cells regulates inflammatory responses to non-infectious immature dengue virus particles. PLoS Pathog 2022; 18:e1010499. [PMID: 36240261 PMCID: PMC9605289 DOI: 10.1371/journal.ppat.1010499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/26/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Severe dengue virus (DENV) infection is characterized by exacerbated inflammatory responses that lead to endothelial dysfunction and plasma leakage. We have recently demonstrated that Toll-like receptor 2 (TLR2) on blood monocytes senses DENV infection leading to endothelial activation. Here, we report that non-infectious immature DENV particles, which are released in large numbers by DENV-infected cells, drive endothelial activation via the TLR2 axis. We show that fully immature DENV particles induce a rapid, within 6 hours post-infection, inflammatory response in PBMCs. Furthermore, pharmacological blocking of TLR2/TLR6/CD14 and/or NF-kB prior to exposure of PBMCs to immature DENV reduces the initial production of inter alia TNF-α and IL-1β by monocytes and prevents endothelial activation. However, prolonged TLR2 block induces TNF-α production and leads to exacerbated endothelial activation, indicating that TLR2-mediated responses play an important role not only in the initiation but also the resolution of inflammation. Altogether, these data indicate that the maturation status of the virus has the potential to influence the kinetics and extent of inflammatory responses during DENV infection.
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Affiliation(s)
- José Alberto Aguilar Briseño
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Lennon Ramos Pereira
- Vaccine Development Laboratory, Microbiology Department, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marleen van der Laan
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Mindaugas Pauzuolis
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Bram M. ter Ellen
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Vinit Upasani
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Immunology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Jill Moser
- Departments of Critical Care, Pathology & Medical Biology, Medical Biology section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Luís Carlos de Souza Ferreira
- Vaccine Development Laboratory, Microbiology Department, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jolanda M. Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Izabela A. Rodenhuis-Zybert
- Department of Medical Microbiology and Infection Prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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12
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Lee MF, Voon GZ, Lim HX, Chua ML, Poh CL. Innate and adaptive immune evasion by dengue virus. Front Cell Infect Microbiol 2022; 12:1004608. [PMID: 36189361 PMCID: PMC9523788 DOI: 10.3389/fcimb.2022.1004608] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Dengue is a mosquito-borne disease which causes significant public health concerns in tropical and subtropical countries. Dengue virus (DENV) has evolved various strategies to manipulate the innate immune responses of the host such as ‘hiding’ in the ultrastructure of the host, interfering with the signaling pathway through RNA modifications, inhibiting type 1 IFN production, as well as inhibiting STAT1 phosphorylation. DENV is also able to evade the adaptive immune responses of the host through antigenic variation, antigen-dependent enhancement (ADE), partial maturation of prM proteins, and inhibition of antigen presentation. miRNAs are important regulators of both innate and adaptive immunity and they have been shown to play important roles in DENV replication and pathogenesis. This makes them suitable candidates for the development of anti-dengue therapeutics. This review discusses the various strategies employed by DENV to evade innate and adaptive immunity. The role of miRNAs and DENV non-structural proteins (NS) are promising targets for the development of anti-dengue therapeutics.
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13
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Latanova A, Starodubova E, Karpov V. Flaviviridae Nonstructural Proteins: The Role in Molecular Mechanisms of Triggering Inflammation. Viruses 2022; 14:v14081808. [PMID: 36016430 PMCID: PMC9414172 DOI: 10.3390/v14081808] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022] Open
Abstract
Members of the Flaviviridae family are posing a significant threat to human health worldwide. Many flaviviruses are capable of inducing severe inflammation in humans. Flaviviridae nonstructural proteins, apart from their canonical roles in viral replication, have noncanonical functions strongly affecting antiviral innate immunity. Among these functions, antagonism of type I IFN is the most investigated; meanwhile, more data are accumulated on their role in the other pathways of innate response. This review systematizes the last known data on the role of Flaviviridae nonstructural proteins in molecular mechanisms of triggering inflammation, with an emphasis on their interactions with TLRs and RLRs, interference with NF-κB and cGAS-STING signaling, and activation of inflammasomes.
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14
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Virucidal Activity of the Pyridobenzothiazolone Derivative HeE1-17Y against Enveloped RNA Viruses. Viruses 2022; 14:v14061157. [PMID: 35746629 PMCID: PMC9228864 DOI: 10.3390/v14061157] [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] [Received: 04/12/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023] Open
Abstract
Pyridobenzothiazolone derivatives are a promising class of broad-spectrum antivirals. However, the mode of action of these compounds remains poorly understood. The HeE1-17Y derivative has already been shown to be a potent compound against a variety of flaviviruses of global relevance. In this work, the mode of action of HeE1-17Y has been studied for West Nile virus taking advantage of reporter replication particles (RRPs). Viral infectivity was drastically reduced by incubating the compound with the virus before infection, thus suggesting a direct interaction with the viral particles. Indeed, RRPs incubated with the inhibitor appeared to be severely compromised in electron microscopy analysis. HeE1-17Y is active against other enveloped viruses, including SARS-CoV-2, but not against two non-enveloped viruses, suggesting a virucidal mechanism that involves the alteration of the viral membrane.
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15
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Wu K, Vedelaar TA, Damle VG, Morita A, Mougnaud J, San Martin CR, Zhang Y, van der Pol DP, Ende-Metselaar H, Zybert IR, Schirhagl R. Applying NV center-based quantum sensing to study intracellular free radical response upon viral infections. Redox Biol 2022; 52:102279. [PMID: 35349928 PMCID: PMC8965164 DOI: 10.1016/j.redox.2022.102279] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 02/08/2023] Open
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16
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Hou W, Kang W, Li Y, Shan Y, Wang S, Liu F. Dynamic Dissection of Dynein and Kinesin-1 Cooperatively Mediated Intercellular Transport of Porcine Epidemic Diarrhea Coronavirus along Microtubule Using Single Virus Tracking. Virulence 2021; 12:615-629. [PMID: 33538234 PMCID: PMC7872075 DOI: 10.1080/21505594.2021.1878748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It is now clear that the intercellular transport on microtubules by dynein and kinesin-1 motors has an important role in the replication and spread of many viruses. Porcine epidemic diarrhea virus (PEDV) is an enveloped, single-stranded RNA virus of the Coronavirus family, which can infect swine of all ages and cause severe economic losses in the swine industry. Elucidating the molecular mechanisms of the intercellular transport of PEDV through microtubule, dynein and kinesin-1 will be crucial for understanding its pathogenesis. Here, we demonstrate that microtubule, dynein, and kinesin-1 are involved in PEDV infection and can influence PEDV fusion and accumulation in the perinuclear region but cannot affect PEDV attachment or internalization. Furthermore, we adopted a single-virus tracking technique to dynamically observe PEDV intracellular transport with five different types: unidirectional movement toward microtubule plus ends; unidirectional movement toward microtubule minus ends; bidirectional movement along the same microtubule; bidirectional movement along different microtubules and motionless state. Among these types, the functions of dynein and kinesin-1 in PEDV intercellular transport were further analyzed by single-virus tracking and found that dynein and kinesin-1 mainly transport PEDV to the minus and plus ends of the microtubules, respectively; meanwhile, they also can transport PEDV to the opposite ends of the microtubules different from their conventional transport directions and also coordinate the bidirectional movement of PEDV along the same or different microtubules through their cooperation. These results provided deep insights and references to understand the pathogenesis of PEDV as well as to develop vaccines and treatments.
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Affiliation(s)
- Wei Hou
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University , Nanjing, Jiangsu, China
| | - Wenjie Kang
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University , Nanjing, Jiangsu, China
| | - Yangyang Li
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University , Nanjing, Jiangsu, China
| | - Yanke Shan
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University , Nanjing, Jiangsu, China
| | - Shouyu Wang
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University , Nanjing, Jiangsu, China.,Computational Optics Laboratory, Jiangnan University , Wuxi, Jiangsu, China
| | - Fei Liu
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University , Nanjing, Jiangsu, China
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17
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Universal Dengue Vaccine Elicits Neutralizing Antibodies against Strains from All Four Dengue Virus Serotypes. J Virol 2021; 95:JVI.00658-20. [PMID: 33208445 DOI: 10.1128/jvi.00658-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022] Open
Abstract
Any potential dengue virus (DENV) vaccine needs to elicit protective immunity against strains from all four serotypes to avoid potential antibody-dependent enhancement (ADE). In this study, four independent DENV envelope (E) glycoproteins were generated using wild-type E sequences from viruses isolated between 1943 and 2006 using computationally optimized broadly reactive antigen (COBRA) methodology. COBRA and wild-type E antigens were expressed on the surface of subvirion viral particles (SVPs). Four separate wild-type E antigens were used for each serotype. Mice vaccinated with wild-type DENV SVPs had anti-E IgG antibodies that neutralized serotype-specific viruses. COBRA DENV SVPs elicited a broader breadth of antibodies that neutralized strains across all four serotypes. Two COBRA DENV vaccine candidates that elicited the broadest breadth of neutralizing antibodies in mice were used to vaccinate rhesus macaques (Macaca mulatta) that either were immunologically naive to any DENV serotype or had preexisting antibodies to DENV. Antibodies elicited by COBRA DENV E immunogens neutralized all 12 strains of DENV in vitro, which was comparable to antibodies elicited by a tetravalent wild-type E SVP vaccination mixture. Therefore, using a single DENV COBRA E protein can elicit neutralizing antibodies against strains representing all four serotypes of DENV in both naive and dengue virus-preimmune populations.IMPORTANCE Dengue virus infects millions of people living in tropical areas of the world. Dengue virus-induced diseases can range from mild to severe with death. An effective vaccine will need to neutralize viruses from all four serotypes of dengue virus without inducing enhanced disease. A dengue virus E vaccine candidate generated by computationally optimized broadly reactive antigen algorithms elicits broadly neutralizing protection for currently circulating strains from all four serotypes regardless of immune status. Most dengue vaccines in development formulate four separate components based on prM-E from a wild-type strain representing each serotype. Designing a monovalent vaccine that elicits protective immunity against all four serotypes is an effective and economical strategy.
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18
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Park A, Graceffa O, Rawle RJ. Kinetic Modeling of West Nile Virus Fusion Indicates an Off-Pathway State. ACS Infect Dis 2020; 6:3260-3268. [PMID: 33201665 DOI: 10.1021/acsinfecdis.0c00637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
West Nile virus (WNV) is a prominent mosquito-borne flavivirus that causes febrile illness in humans. To infect host cells, WNV virions first bind to plasma membrane receptors, then initiate membrane fusion following endocytosis. The viral transmembrane E protein, triggered by endosomal pH, catalyzes fusion while undergoing a dimer-to-trimer transition. Previously, single-particle WNV fusion data was interrogated with a stochastic cellular automaton simulation, which modeled the E proteins during the fusion process. The results supported a linear fusion mechanism, with E protein trimerization being rate-limiting. Here, we present corrections to the previous simulation, and apply them to the WNV fusion data. We observe that a linear mechanism is no longer sufficient to fit the data. Instead, an off-pathway state is necessary; these results are corroborated by per virus chemical kinetics modeling. When compared with a similar Zika virus fusion model, this suggests that off-pathway fusion mechanisms may characterize flaviviruses more broadly.
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Affiliation(s)
- Abraham Park
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, United States
| | - Olivia Graceffa
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, United States
| | - Robert J. Rawle
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, United States
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19
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Zuzic L, Marzinek JK, Warwicker J, Bond PJ. A Benzene-Mapping Approach for Uncovering Cryptic Pockets in Membrane-Bound Proteins. J Chem Theory Comput 2020; 16:5948-5959. [PMID: 32786908 DOI: 10.1021/acs.jctc.0c00370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics (MD) simulations in combination with small organic probes present in the solvent have previously been used as a method to reveal cryptic pockets that may not have been identified in experimental structures. We report such a method implemented within the CHARMM force field using the GROMACS simulation package to effectively explore cryptic pockets on the surfaces of membrane-embedded proteins using benzene as a probe molecule. This method, for which we have made implementation files freely available, relies on modified nonbonded parameters in addition to repulsive potentials between membrane lipids and benzene molecules. The method was tested on part of the outer shell of the dengue virus (DENV), for which research into a safe and effective neutralizing antibody or drug molecule is still ongoing. In particular, the envelope (E) protein, associated with the membrane (M) protein, is a lipid membrane-embedded complex which forms a dimer in the mature viral envelope. Solvent mapping was performed for the full, membrane-embedded EM protein complex and compared with similar calculations performed for the isolated, soluble E protein ectodomain dimer in the solvent. Ectodomain-only simulations with benzene exhibited unfolding effects not observed in the more physiologically relevant membrane-associated systems. A cryptic pocket which has been experimentally shown to bind n-octyl-β-d-glucoside detergent was consistently revealed in all benzene-containing simulations. The addition of benzene also enhanced the flexibility and hydrophobic exposure of cryptic pockets at a key, functional interface in the E protein and revealed a novel, potentially druggable pocket that may be targeted to prevent conformational changes associated with viral entry into the cell.
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Affiliation(s)
- Lorena Zuzic
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore.,Department of Chemistry, Faculty of Science and Engineering, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore
| | - Jim Warwicker
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
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20
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Kumar D, Meena MK, Kumari K, Patel R, Jayaraj A, Singh P. In-silico prediction of novel drug-target complex of nsp3 of CHIKV through molecular dynamic simulation. Heliyon 2020; 6:e04720. [PMID: 32904235 PMCID: PMC7452467 DOI: 10.1016/j.heliyon.2020.e04720] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/15/2020] [Accepted: 08/11/2020] [Indexed: 12/22/2022] Open
Abstract
Literature reported that nsp3 of CHIKV is an important target for the designing of drug as it involves in the replication, survival etc. Herein, about eighteen million molecules available in the ZINC database are filtered against nsp3 using RASPD. Top five hit drug molecules were then taken from the total screened molecules (6988) from ZINC database. Then, a one pot-three components reaction is designed to get the pyrazolophthalazine and its formation was studied using DFT method. Authors created a library of 200 compounds using the product obtained in the reaction and filtered against nsp3 of CHIKV based on docking using iGEMDOCK, a computational tool. Authors have studied the best molecules after applying the the Lipinski's rule of five and bioactive score. Further, the authors took the best compound i.e. CMPD178 and performed the MD simulations and tdMD simulations with nsp3 protease using AMBER18. MD trajectories were studied to collect the information about the nsp3 of CHIKV with and without screened compound and then, MM-GBSA calculations were performed to calculate change in binding free energies for the formation of complex. The aim of the work is to find the potential candidate as promising inhibitor against nsp3 of CHIKV.
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Affiliation(s)
- Durgesh Kumar
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.,Department of Chemistry, University of Delhi, Delhi, India
| | - Mahendra Kumar Meena
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.,Department of Chemistry, University of Delhi, Delhi, India
| | - Kamlesh Kumari
- Deparment of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Rajan Patel
- CIRBS, Jamia Millia Islamia, New Delhi, India
| | | | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
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21
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Hoornweg TE, Bouma EM, van de Pol DP, Rodenhuis-Zybert IA, Smit JM. Chikungunya virus requires an intact microtubule network for efficient viral genome delivery. PLoS Negl Trop Dis 2020; 14:e0008469. [PMID: 32764759 PMCID: PMC7413472 DOI: 10.1371/journal.pntd.0008469] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/10/2020] [Indexed: 11/25/2022] Open
Abstract
Chikungunya virus (CHIKV) is a re-emerging mosquito-borne alphavirus, which has rapidly spread around the globe thereby causing millions of infections. CHIKV is an enveloped virus belonging to the Togaviridae family and enters its host cell primarily via clathrin-mediated endocytosis. Upon internalization, the endocytic vesicle containing the virus particle moves through the cell and delivers the virus to early endosomes where membrane fusion is observed. Thereafter, the nucleocapsid dissociates and the viral RNA is translated into proteins. In this study, we examined the importance of the microtubule network during the early steps of infection and dissected the intracellular trafficking behavior of CHIKV particles during cell entry. We observed two distinct CHIKV intracellular trafficking patterns prior to membrane hemifusion. Whereas half of the CHIKV virions remained static during cell entry and fused in the cell periphery, the other half showed fast-directed microtubule-dependent movement prior to delivery to Rab5-positive early endosomes and predominantly fused in the perinuclear region of the cell. Disruption of the microtubule network reduced the number of infected cells. At these conditions, membrane hemifusion activity was not affected yet fusion was restricted to the cell periphery. Furthermore, follow-up experiments revealed that disruption of the microtubule network impairs the delivery of the viral genome to the cell cytosol. We therefore hypothesize that microtubules may direct the particle to a cellular location that is beneficial for establishing infection or aids in nucleocapsid uncoating. Chikungunya virus (CHIKV) is an alphavirus that is transmitted to humans by infected mosquitoes. Disease symptoms can include fever, rash, myalgia, and long-lasting debilitating joint pains. Unfortunately, there is currently no licensed vaccine or antiviral treatment available to combat CHIKV. Understanding the virus:host interactions during the replication cycle of the virus is crucial for the development of effective antiviral therapies. In this study we elucidated the trafficking behavior of CHIKV particles early in infection. During cell entry, CHIKV virions require an intact microtubule network for efficient delivery of the viral genome into the host cell thereby increasing the chance to productively infect a cell.
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Affiliation(s)
- Tabitha E. Hoornweg
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ellen M. Bouma
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Denise P.I. van de Pol
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Izabela A. Rodenhuis-Zybert
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Jolanda M. Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands
- * E-mail:
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22
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TLR2 on blood monocytes senses dengue virus infection and its expression correlates with disease pathogenesis. Nat Commun 2020; 11:3177. [PMID: 32576819 PMCID: PMC7311456 DOI: 10.1038/s41467-020-16849-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Vascular permeability and plasma leakage are immune-pathologies of severe dengue virus (DENV) infection, but the mechanisms underlying the exacerbated inflammation during DENV pathogenesis are unclear. Here, we demonstrate that TLR2, together with its co-receptors CD14 and TLR6, is an innate sensor of DENV particles inducing inflammatory cytokine expression and impairing vascular integrity in vitro. Blocking TLR2 prior to DENV infection in vitro abrogates NF-κB activation while CD14 and TLR6 block has a moderate effect. Moreover, TLR2 block prior to DENV infection of peripheral blood mononuclear cells prevents activation of human vascular endothelium, suggesting a potential role of the TLR2-responses in vascular integrity. TLR2 expression on CD14 + + classical monocytes isolated in an acute phase from DENV-infected pediatric patients correlates with severe disease development. Altogether, these data identify a role for TLR2 in DENV infection and provide insights into the complex interaction between the virus and innate receptors that may underlie disease pathogenesis.
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23
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Abstract
Quantum dots (QDs) possess optical properties of superbright fluorescence, excellent photostability, narrow emission spectra, and optional colors. Labeled with QDs, single molecules/viruses can be rapidly and continuously imaged for a long time, providing more detailed information than when labeled with other fluorophores. While they are widely used to label proteins in single-molecule-tracking studies, QDs have rarely been used to study virus infection, mainly due to a lack of accepted labeling strategies. Here, we report a general method to mildly and readily label enveloped viruses with QDs. Lipid-biotin conjugates were used to recognize and mark viral lipid membranes, and streptavidin-QD conjugates were used to light them up. Such a method allowed enveloped viruses to be labeled in 2 h with specificity and efficiency up to 99% and 98%, respectively. The intact morphology and the native infectivity of viruses were preserved. With the aid of this QD labeling method, we lit wild-type and mutant Japanese encephalitis viruses up, tracked their infection in living Vero cells, and found that H144A and Q258A substitutions in the envelope protein did not affect the virus intracellular trafficking. The lipid-specific QD labeling method described in this study provides a handy and practical tool to readily "see" the viruses and follow their infection, facilitating the widespread use of single-virus tracking and the uncovering of complex infection mechanisms.IMPORTANCE Virus infection in host cells is a complex process comprising a large number of dynamic molecular events. Single-virus tracking is a versatile technique to study these events. To perform this technique, viruses must be fluorescently labeled to be visible to fluorescence microscopes. The quantum dot is a kind of fluorescent tag that has many unique optical properties. It has been widely used to label proteins in single-molecule-tracking studies but rarely used to study virus infection, mainly due to the lack of an accepted labeling method. In this study, we developed a lipid-specific method to readily, mildly, specifically, and efficiently label enveloped viruses with quantum dots by recognizing viral envelope lipids with lipid-biotin conjugates and recognizing these lipid-biotin conjugates with streptavidin-quantum dot conjugates. It is not only applicable to normal viruses, but also competent to label the key protein-mutated viruses and the inactivated highly virulent viruses, providing a powerful tool for single-virus tracking.
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24
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Diosa-Toro M, Prasanth KR, Bradrick SS, Garcia Blanco MA. Role of RNA-binding proteins during the late stages of Flavivirus replication cycle. Virol J 2020; 17:60. [PMID: 32334603 PMCID: PMC7183730 DOI: 10.1186/s12985-020-01329-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/11/2020] [Indexed: 12/21/2022] Open
Abstract
The genus Flavivirus encompasses several worldwide-distributed arthropod-borne viruses including, dengue virus, Japanese encephalitis virus, West Nile virus, yellow fever virus, Zika virus, and tick-borne encephalitis virus. Infection with these viruses manifest with symptoms ranging from febrile illness to life- threatening hypotensive shock and encephalitis. Therefore, flaviviruses pose a great risk to public health. Currently, preventive measures are falling short to control epidemics and there are no antivirals against any Flavivirus.Flaviviruses carry a single stranded positive-sense RNA genome that plays multiple roles in infected cells: it is translated into viral proteins, used as template for genome replication, it is the precursor of the subgenomic flaviviral RNA and it is assembled into new virions. Furthermore, viral RNA genomes are also packaged into extracellular vesicles, e.g. exosomes, which represent an alternate mode of virus dissemination.Because RNA molecules are at the center of Flavivirus replication cycle, viral and host RNA-binding proteins (RBPs) are critical determinants of infection. Numerous studies have revealed the function of RBPs during Flavivirus infection, particularly at the level of RNA translation and replication. These proteins, however, are also critical participants at the late stages of the replication cycle. Here we revise the function of host RBPs and the viral proteins capsid, NS2A and NS3, during the packaging of viral RNA and the assembly of new virus particles. Furthermore, we go through the evidence pointing towards the importance of host RBPs in mediating cellular RNA export with the idea that the biogenesis of exosomes harboring Flavivirus RNA would follow an analogous pathway.
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Affiliation(s)
- Mayra Diosa-Toro
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - K Reddisiva Prasanth
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Global Health, Surveillance & Diagnostics Group, MRIGlobal, Kansas City, MO, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Mariano A Garcia Blanco
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
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25
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Ramanathan HN, Zhang S, Douam F, Mar KB, Chang J, Yang PL, Schoggins JW, Ploss A, Lindenbach BD. A Sensitive Yellow Fever Virus Entry Reporter Identifies Valosin-Containing Protein (VCP/p97) as an Essential Host Factor for Flavivirus Uncoating. mBio 2020; 11:e00467-20. [PMID: 32291299 PMCID: PMC7157815 DOI: 10.1128/mbio.00467-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/16/2020] [Indexed: 01/17/2023] Open
Abstract
While the basic mechanisms of flavivirus entry and fusion are understood, little is known about the postfusion events that precede RNA replication, such as nucleocapsid disassembly. We describe here a sensitive, conditionally replication-defective yellow fever virus (YFV) entry reporter, YFVΔSK/Nluc, to quantitively monitor the translation of incoming, virus particle-delivered genomes. We validated that YFVΔSK/Nluc gene expression can be neutralized by YFV-specific antisera and requires known flavivirus entry pathways and cellular factors, including clathrin- and dynamin-mediated endocytosis, endosomal acidification, YFV E glycoprotein-mediated fusion, and cellular LY6E and RPLP1 expression. The initial round of YFV translation was shown to require cellular ubiquitylation, consistent with recent findings that dengue virus capsid protein must be ubiquitylated in order for nucleocapsid uncoating to occur. Importantly, translation of incoming YFV genomes also required valosin-containing protein (VCP)/p97, a cellular ATPase that unfolds and extracts ubiquitylated client proteins from large complexes. RNA transfection and washout experiments showed that VCP/p97 functions at a postfusion, pretranslation step in YFV entry. Finally, VCP/p97 activity was required by other flaviviruses in mammalian cells and by YFV in mosquito cells. Together, these data support a critical role for VCP/p97 in the disassembly of incoming flavivirus nucleocapsids during a postfusion step in virus entry.IMPORTANCE Flaviviruses are an important group of RNA viruses that cause significant human disease. The mechanisms by which flavivirus nucleocapsids are disassembled during virus entry remain unclear. Here, we used a yellow fever virus entry reporter, which expresses a sensitive reporter enzyme but does not replicate, to show that nucleocapsid disassembly requires the cellular protein-disaggregating enzyme valosin-containing protein, also known as p97.
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Affiliation(s)
- Harish N Ramanathan
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | - Shuo Zhang
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
| | - Florian Douam
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jinhong Chang
- Department of Experimental Therapeutics, The Baruch S. Blumberg Institute, Doylestown, Pennsylvania, USA
| | - Priscilla L Yang
- Department of Microbiology and the Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
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26
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Freitas MN, Marten AD, Moore GA, Tree MO, McBrayer SP, Conway MJ. Extracellular vesicles restrict dengue virus fusion in Aedes aegypti cells. Virology 2020; 541:141-149. [PMID: 32056712 DOI: 10.1016/j.virol.2019.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 01/24/2023]
Abstract
Aedes aegypti is the primary vector of dengue virus (DENV), and acquires this virus from a vertebrate host during blood feeding. Previous literature has shown that vertebrate blood factors such as complement protein C5a and low-density lipoprotein (LDL) influence DENV acquisition in the mosquito. Here, we show that extracellular vesicles in cell culture medium inhibit DENV infection in mosquito cells. Specifically, extracellular vesicles enter into mosquito cells and inhibit an early stage of infection. Extracellular vesicles had no effect on virus cell attachment or entry. Instead, extracellular vesicles restricted virus membrane fusion. Extracellular vesicles only inhibited DENV infection in mosquito cells and not vertebrate cells. These data highlight a novel virus-vector-host interaction that limits virus infection in mosquito cells by restricting virus membrane fusion.
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Affiliation(s)
- Megan N Freitas
- Central Michigan University College of Medicine, Foundational Sciences, Mount Pleasant, MI, 48859, USA
| | - Andrew D Marten
- Central Michigan University College of Medicine, Foundational Sciences, Mount Pleasant, MI, 48859, USA
| | - Gavin A Moore
- Central Michigan University College of Medicine, Foundational Sciences, Mount Pleasant, MI, 48859, USA
| | - Maya O Tree
- Central Michigan University College of Medicine, Foundational Sciences, Mount Pleasant, MI, 48859, USA
| | - Sean P McBrayer
- Central Michigan University College of Medicine, Foundational Sciences, Mount Pleasant, MI, 48859, USA
| | - Michael J Conway
- Central Michigan University College of Medicine, Foundational Sciences, Mount Pleasant, MI, 48859, USA.
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27
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Wang J, Li Y, Wang S, Liu F. Dynamics of transmissible gastroenteritis virus internalization unraveled by single-virus tracking in live cells. FASEB J 2020; 34:4653-4669. [PMID: 32017270 PMCID: PMC7163995 DOI: 10.1096/fj.201902455r] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/20/2019] [Accepted: 01/20/2020] [Indexed: 12/16/2022]
Abstract
Transmissible gastroenteritis virus (TGEV) is a swine enteropathogenic coronavirus that causes significant economic losses in swine industry. Current studies on TGEV internalization mainly focus on viral receptors, but the internalization mechanism is still unclear. In this study, we used single‐virus tracking to obtain the detailed insights into the dynamic events of the TGEV internalization and depict the whole sequential process. We observed that TGEVs could be internalized through clathrin‐ and caveolae‐mediated endocytosis, and the internalization of TGEVs was almost completed within ~2 minutes after TGEVs attached to the cell membrane. Furthermore, the interactions of TGEVs with actin and dynamin 2 in real time during the TGEV internalization were visualized. To our knowledge, this is the first report that single‐virus tracking technique is used to visualize the entire dynamic process of the TGEV internalization: before the TGEV internalization, with the assistance of actin, clathrin, and caveolin 1 would gather around the virus to form the vesicle containing the TGEV, and after ~60 seconds, dynamin 2 would be recruited to promote membrane fission. These results demonstrate that TGEVs enter ST cells via clathrin‐ and caveolae‐mediated endocytic, actin‐dependent, and dynamin 2‐dependent pathways.
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Affiliation(s)
- Jian Wang
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
| | - Yangyang Li
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
| | - Shouyu Wang
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China.,Computational Optics Laboratory, School of Science, Jiangnan University, Wuxi, China
| | - Fei Liu
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
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28
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Liu SL, Wang ZG, Xie HY, Liu AA, Lamb DC, Pang DW. Single-Virus Tracking: From Imaging Methodologies to Virological Applications. Chem Rev 2020; 120:1936-1979. [PMID: 31951121 PMCID: PMC7075663 DOI: 10.1021/acs.chemrev.9b00692] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Uncovering
the mechanisms of virus infection and assembly is crucial
for preventing the spread of viruses and treating viral disease. The
technique of single-virus tracking (SVT), also known as single-virus
tracing, allows one to follow individual viruses at different parts
of their life cycle and thereby provides dynamic insights into fundamental
processes of viruses occurring in live cells. SVT is typically based
on fluorescence imaging and reveals insights into previously unreported
infection mechanisms. In this review article, we provide the readers
a broad overview of the SVT technique. We first summarize recent advances
in SVT, from the choice of fluorescent labels and labeling strategies
to imaging implementation and analytical methodologies. We then describe
representative applications in detail to elucidate how SVT serves
as a valuable tool in virological research. Finally, we present our
perspectives regarding the future possibilities and challenges of
SVT.
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Affiliation(s)
- Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China.,Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China
| | - Hai-Yan Xie
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , P. R. China
| | - An-An Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), and Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM) , Ludwig-Maximilians-Universität , München , 81377 , Germany
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China.,College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology , Wuhan University , Wuhan 430072 , P. R. China
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29
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The use of green fluorescent protein-tagged virus-like particles as a tracer in the early phase of chikungunya infection. Virus Res 2019; 272:197732. [PMID: 31445103 DOI: 10.1016/j.virusres.2019.197732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [Indexed: 11/22/2022]
Abstract
To visually examine the early phase of chikungunya virus (CHIKV) infection in target cells, we constructed a virus-like particle (VLP) in which the envelope protein E1 is fused with green fluorescent protein (GFP). This chikungunya VLP-GFP (CHIK-VLP-EGFP), purified by density gradient fractionation, was observed as 60-70 nm-dia. particles and was detected as tiny puncta of fluorescence in the cells. CHIK-VLP-EGFP showed binding properties similar to those of the wild-type viruses. Most of the fluorescence signals that had bound on Vero cells disappeared within 30 min at 37 °C, but not in the presence of anti-CHIKV neutralizing serum or an endosomal acidification inhibitor (bafilomycin A1), suggesting that the loss of fluorescence signals is due to the disassembly of the viral envelope following the internalization of CHIK-VLP-EGFP. In addition to these results, the fluorescence signals disappeared in highly susceptible Vero and U251MG cells but not in poorly susceptible A549 cells. Thus, CHIK-VLP-EGFP is a useful tool to examine the effects of the CHIKV neutralizing antibodies and antiviral compounds that are effective in the entry phase of CHIKV.
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30
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Neutralization of Acidic Intracellular Vesicles by Niclosamide Inhibits Multiple Steps of the Dengue Virus Life Cycle In Vitro. Sci Rep 2019; 9:8682. [PMID: 31213630 PMCID: PMC6582152 DOI: 10.1038/s41598-019-45095-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/30/2019] [Indexed: 01/20/2023] Open
Abstract
Dengue fever is one of the most important mosquito-borne viral infections in large parts of tropical and subtropical countries and is a significant public health concern and socioeconomic burden. There is an urgent need to develop antivirals that can effectively reduce dengue virus (DENV) replication and decrease viral load. Niclosamide, an antiparasitic drug approved for human use, has been recently identified as an effective antiviral agent against a number of pH-dependent viruses, including flaviviruses. Here, we reveal that neutralization of low-pH intracellular compartments by niclosamide affects multiple steps of the DENV infectious cycle. Specifically, niclosamide-induced endosomal neutralization not only prevents viral RNA replication but also affects the maturation of DENV particles, rendering them non-infectious. We found that niclosamide-induced endosomal neutralization prevented E glycoprotein conformational changes on the virion surface of flaviviruses, resulting in the release of non-infectious immature virus particles with uncleaved pr peptide from host cells. Collectively, our findings support the potential application of niclosamide as an antiviral agent against flavivirus infection and highlight a previously uncharacterized mechanism of action of the drug.
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31
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Novel pan-serotype control RNA for dengue virus typing through real-time reverse transcription-polymerase chain reaction. J Virol Methods 2019; 271:113677. [PMID: 31195032 DOI: 10.1016/j.jviromet.2019.113677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/05/2019] [Accepted: 06/09/2019] [Indexed: 11/21/2022]
Abstract
Dengue virus (DENV) is the causative agent of one of the most important febrile illnesses worldwide. Four DENV serotypes are responsible for a broad clinical spectrum of the disease. Positive controls are costly and required for the validation of molecular test results of DENV serotyping. In this study, we describe the in silico design of the qDENV-Control plasmid with the target sequences to oligonucleotides and probes widely used for DENV serotyping, and the subsequent production of qDENV Control RNA by T7-driven run-off in vitro transcription. The qDENV Control RNA was successfully used to validate the positive and negative DENV serotyping results, allowing its incorporation in routine in-house protocols for virologic surveillance. This Control RNA allowed the absolute quantification of viral RNA copies from unknown samples as required in several fundamental studies.
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32
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Dowd KA, Pierson TC. The Many Faces of a Dynamic Virion: Implications of Viral Breathing on Flavivirus Biology and Immunogenicity. Annu Rev Virol 2019; 5:185-207. [PMID: 30265634 DOI: 10.1146/annurev-virology-092917-043300] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Flaviviruses are arthropod-borne RNA viruses that are a significant threat to global health due to their widespread distribution, ability to cause severe disease in humans, and capacity for explosive spread following introduction into new regions. Members of this genus include dengue, tick-borne encephalitis, yellow fever, and Zika viruses. Vaccination has been a highly successful means to control flaviviruses, and neutralizing antibodies are an important component of a protective immune response. High-resolution structures of flavivirus structural proteins and virions, alone and in complex with antibodies, provide a detailed understanding of viral fusion mechanisms and virus-antibody interactions. However, mounting evidence suggests these structures provide only a snapshot of an otherwise structurally dynamic virus particle. The contribution of the structural ensemble arising from viral breathing to the biology, antigenicity, and immunity of flaviviruses is discussed, including implications for the development and evaluation of flavivirus vaccines.
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Affiliation(s)
- Kimberly A Dowd
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Theodore C Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
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33
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Dighe SN, Ekwudu O, Dua K, Chellappan DK, Katavic PL, Collet TA. Recent update on anti-dengue drug discovery. Eur J Med Chem 2019; 176:431-455. [PMID: 31128447 DOI: 10.1016/j.ejmech.2019.05.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/12/2019] [Accepted: 05/06/2019] [Indexed: 01/27/2023]
Abstract
Dengue is the most important arthropod-borne viral disease of humans, with more than half of the global population living in at-risk areas. Despite the negative impact on public health, there are no antiviral therapies available, and the only licensed vaccine, Dengvaxia®, has been contraindicated in children below nine years of age. In an effort to combat dengue, several small molecules have entered into human clinical trials. Here, we review anti-DENV molecules and their drug targets that have been published within the past five years (2014-2018). Further, we discuss their probable mechanisms of action and describe a role for classes of clinically approved drugs and also an unclassified class of anti-DENV agents. This review aims to enhance our understanding of novel agents and their cognate targets in furthering innovations in the use of small molecules for dengue drug therapies.
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Affiliation(s)
- Satish N Dighe
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia.
| | - O'mezie Ekwudu
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University (IMU), Bukit Jalil, Kuala Lumpur, 57000, Malaysia
| | - Peter L Katavic
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Trudi A Collet
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
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34
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Rinkenberger N, Schoggins JW. Comparative analysis of viral entry for Asian and African lineages of Zika virus. Virology 2019; 533:59-67. [PMID: 31112915 DOI: 10.1016/j.virol.2019.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 12/16/2022]
Abstract
Zika virus (ZIKV) is an emerging pathogen with global health and economic impacts. ZIKV circulates as two major lineages, Asian or African. The Asian lineage has recently been associated with significant disease in humans. Numerous studies have revealed differences between African and Asian ZIKV strains with respect to cellular infectivity, pathogenesis, and immune activation. Less is known about the mechanism of ZIKV entry and whether viral entry differs between strains. Here, we characterized ZIKV entry with two Asian and two African strains. All viruses exhibited a requirement for clathrin-mediated endocytosis and Rab5a function. Additionally, all ZIKV strains tested were sensitive to pH in the range of 6.5-6.1 and were reliant on endosomal acidification for infection. Finally, we provide direct evidence that ZIKV primarily fuses with late endosomes. These findings contribute new insight into the ZIKV entry process and suggest that divergent ZIKV strains enter cells in a highly conserved manner.
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Affiliation(s)
- Nicholas Rinkenberger
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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35
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Dissecting the Cell Entry Pathway of Baculovirus by Single-Particle Tracking and Quantitative Electron Microscopic Analysis. J Virol 2019; 93:JVI.00033-19. [PMID: 30760565 DOI: 10.1128/jvi.00033-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/05/2019] [Indexed: 02/07/2023] Open
Abstract
The budded virus of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) infects insect cells through mainly clathrin-mediated endocytosis. However, the cell entry pathway of AcMNPV remains unclear. In this study, by using population-based analysis of single-virus tracking and electron microscopy, we investigated the internalization, fusion behavior, and endocytic trafficking of AcMNPV. AcMNPV internalization into host insect cells was facilitated by actin polymerization and dynamin. After incorporation into early endosomes, the AcMNPV envelope fused with the membranes of early endosome, allowing for nucleocapsid release into the cytoplasm. Microtubules were implicated in the bidirectional and long-range transport of virus-containing endosomes. In addition, microtubule depolymerization reduced the motility of virus-bearing early endosomes, impairing the progression of infection beyond enlarged early endosomes. These findings demonstrated that AcMNPV internalization was facilitated by actin polymerization in a dynamin-dependent manner, and nucleocapsid release occurred in early endosomes in a microtubule-dependent manner. This study provides mechanistic and kinetic insights into AcMNPV infection and enhance our understanding of the infection pathway of baculoviruses.IMPORTANCE Baculoviruses are used widely as environmentally benign pesticides, protein expression systems, and potential mammalian gene delivery vectors. Despite the significant application value, little is known about the cell entry and endocytic trafficking pathways of baculoviruses. In this study, we demonstrated that the alphabaculovirus AcMNPV exhibited actin- and microtubule-dependent transport for nucleocapsid release predominantly from within early endosomes. In contrast to AcMNPV transduction in mammalian cells, its infection in host insect cells is facilitated by actin polymerization for internalization and microtubules for endocytic trafficking within early endosomes, implying that AcMNPV exhibits cell type specificity in the requirement of the cytoskeleton network. In addition, experimental depolymerization of microtubules impaired the progression of infection beyond enlarged early endosomes. This is the first study that dissects the cell entry pathway of baculoviruses in host cells at the single-particle level, which advances our understanding of the early steps of baculovirus entry.
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36
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Paskey AC, Frey KG, Schroth G, Gross S, Hamilton T, Bishop-Lilly KA. Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples. BMC Genomics 2019; 20:155. [PMID: 30808306 PMCID: PMC6390631 DOI: 10.1186/s12864-019-5543-2] [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: 10/30/2018] [Accepted: 02/18/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. RESULTS This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. CONCLUSIONS Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
- Leidos, Reston, VA 20190 USA
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
| | | | | | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
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37
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Real-time analysis of quantum dot labeled single porcine epidemic diarrhea virus moving along the microtubules using single particle tracking. Sci Rep 2019; 9:1307. [PMID: 30718724 PMCID: PMC6362069 DOI: 10.1038/s41598-018-37789-9] [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: 08/13/2018] [Accepted: 12/11/2018] [Indexed: 01/27/2023] Open
Abstract
In order to study the infection mechanism of porcine epidemic diarrhea virus (PEDV), which causes porcine epidemic diarrhea, a highly contagious enteric disease, we combined quantum dot labeled method, which could hold intact infectivity of the labeled viruses to the largest extent, with the single particle tracking technique to dynamically and globally visualize the transport behaviors of PEDVs in live Vero cells. Our results were the first time to uncover the dynamic characteristics of PEDVs moving along the microtubules in the host cells. It is found that PEDVs kept restricted motion mode with a relatively stable speed in the cell membrane region; while performed a slow-fast-slow velocity pattern with different motion modes in the cell cytoplasm region and near the microtubule organizing center region. In addition, the return movements of small amount of PEDVs were also observed in the live cells. Collectively, our work is crucial for understanding the movement mechanisms of PEDV in the live cells, and the proposed work also provided important references for further analysis and study on the infection mechanism of PEDVs.
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38
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Dengue virus requires apoptosis linked gene-2-interacting protein X (ALIX) for viral propagation. Virus Res 2019; 261:65-71. [DOI: 10.1016/j.virusres.2018.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 12/04/2018] [Accepted: 12/28/2018] [Indexed: 01/17/2023]
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39
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Isa DM, Chin SP, Chong WL, Zain SM, Rahman NA, Lee VS. Dynamics and binding interactions of peptide inhibitors of dengue virus entry. J Biol Phys 2019; 45:63-76. [PMID: 30680580 DOI: 10.1007/s10867-018-9515-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/28/2018] [Indexed: 01/01/2023] Open
Abstract
In this study, we investigate the binding interactions of two synthetic antiviral peptides (DET2 and DET4) on type II dengue virus (DENV2) envelope protein domain III. These two antiviral peptides are designed based on the domain III of the DENV2 envelope protein, which has shown significant inhibition activity in previous studies and can be potentially modified further to be active against all dengue strains. Molecular docking was performed using AutoDock Vina and the best-ranked peptide-domain III complex was further explored using molecular dynamics simulations. Molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) was used to calculate the relative binding free energies and to locate the key residues of peptide-protein interactions. The predicted binding affinity correlated well with the previous experimental studies. DET4 outperformed DET2 and is oriented within the binding site through favorable vdW and electrostatic interactions. Pairwise residue decomposition analysis has revealed several key residues that contribute to the binding of these peptides. Residues in DET2 interact relatively lesser with the domain III compared to DET4. Dynamic cross-correlation analysis showed that both the DET2 and DET4 trigger different dynamic patterns on the domain III. Correlated motions were seen between the residue pairs of DET4 and the binding site while binding of DET2 results in anti-correlated motion on the binding site. This work showcases the use of computational study in elucidating and explaining the experiment observation on an atomic level.
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Affiliation(s)
- Diyana Mohd Isa
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sek Peng Chin
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Wei Lim Chong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sharifuddin M Zain
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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40
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Abstract
Standard fixed cell confocal microscopy is inherently limited in visualizing dynamic processes involving two- and three-dimensional movement. To overcome these limitations, live cell imaging approaches have been developed to study hepatitis C virus (HCV) entry, replicase protein trafficking, virion assembly, and egress. These studies have relied on fluorescent labeling of viral proteins by epitope tag insertion, genome labeling via nucleophilic dyes, or using lipophilic dyes to label the virion envelope. In this method review, we describe two approaches to study HCV virion trafficking in live cells. Lipophilic labeling of the envelope allows for study of the early events (through virion uncoating/fusion) in the HCV lifecycle. Tetracysteine (TC) tag insertion into the capsid protein permits study of virion assembly and capsid trafficking via binding of a fluorogenic biarsenical dye.
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41
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Zhang LJ, Xia L, Xie HY, Zhang ZL, Pang DW. Quantum Dot Based Biotracking and Biodetection. Anal Chem 2018; 91:532-547. [DOI: 10.1021/acs.analchem.8b04721] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Li-Juan Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology, Wuhan University, Luojia Hill, Wuhan 430072, P.R. China
| | - Li Xia
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology, Wuhan University, Luojia Hill, Wuhan 430072, P.R. China
| | - Hai-Yan Xie
- School of Life Science, Beijing Institute of Technology, Beijing 100081, P.R. China
| | - Zhi-Ling Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology, Wuhan University, Luojia Hill, Wuhan 430072, P.R. China
| | - Dai-Wen Pang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology, Wuhan University, Luojia Hill, Wuhan 430072, P.R. China
- College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, P.R. China
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42
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Diosa-Toro M, Troost B, van de Pol D, Heberle AM, Urcuqui-Inchima S, Thedieck K, Smit JM. Tomatidine, a novel antiviral compound towards dengue virus. Antiviral Res 2018; 161:90-99. [PMID: 30468746 DOI: 10.1016/j.antiviral.2018.11.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/27/2018] [Accepted: 11/18/2018] [Indexed: 11/15/2022]
Abstract
Dengue is the most common arboviral disease worldwide with 96 million symptomatic cases annually. Despite its major impact on global human health and huge economic burden there is no antiviral drug available to treat the disease. The first tetravalent dengue virus vaccine was licensed in 2015 for individuals aged 9 to 45, however, most cases are reported in infants and young children. This, together with the limited efficacy of the vaccine to dengue virus (DENV) serotype 2, stresses the need to continue the search for compounds with antiviral activity to DENV. In this report, we describe tomatidine as a novel compound with potent antiviral properties towards all DENV serotypes and the related Zika virus. The strongest effect was observed for DENV-2 with an EC50 and EC90 value of 0.82 and 1.61 μM, respectively, following infection of Huh7 cells at multiplicity of infection of 1. The selectivity index is 97.7. Time-of-drug-addition experiments revealed that tomatidine inhibits virus particle production when added pre, during and up to 12 h post-infection. Subsequent experiments show that tomatidine predominantly acts at a step after virus-cell binding and membrane fusion but prior to the secretion of progeny virions. Tomatidine was found to control the expression of the cellular protein activating transcription factor 4 (ATF4), yet, this protein is not solely responsible for the observed antiviral effect. Here, we propose tomatidine as a candidate for the treatment of dengue given its potent antiviral activity.
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Affiliation(s)
- Mayra Diosa-Toro
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands; Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, calle 70 No. 52-21, Medellín, Colombia
| | - Berit Troost
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Denise van de Pol
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Alexander Martin Heberle
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Silvio Urcuqui-Inchima
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, calle 70 No. 52-21, Medellín, Colombia
| | - Kathrin Thedieck
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands; Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany
| | - Jolanda M Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9713AV Groningen, the Netherlands.
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43
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Wirawan M, Fibriansah G, Marzinek JK, Lim XX, Ng TS, Sim AYL, Zhang Q, Kostyuchenko VA, Shi J, Smith SA, Verma CS, Anand G, Crowe JE, Bond PJ, Lok SM. Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody. Structure 2018; 27:253-267.e8. [PMID: 30471923 DOI: 10.1016/j.str.2018.10.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/28/2018] [Accepted: 10/15/2018] [Indexed: 11/19/2022]
Abstract
Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti-precursor membrane (prM) protein antibodies. It is unknown how anti-prM antibody-coated particles can undergo membrane fusion since the prM caps the envelope (E) protein fusion loop. Here, we determined cryoelectron microscopy (cryo-EM) maps of the immDENV:anti-prM complex at different pH values, mimicking the extracellular (pH 8.0) or endosomal (pH 5.0) environments. At pH 5.0, there are two structural classes with fewer antibodies bound than at pH 8.0. These classes may represent different maturation states. Molecular simulations, together with the measured high-affinity pr:antibody interaction (versus the weak pr:E interaction) and also the low pH cryo-EM structures, suggest how antibody:pr complex can dislodge from the E protein at low pH. This exposes the E protein fusion loop enhancing virus interaction with endosomes.
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Affiliation(s)
- Melissa Wirawan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Guntur Fibriansah
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Xin Xiang Lim
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Thiam-Seng Ng
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Adelene Y L Sim
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore
| | - Qian Zhang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Victor A Kostyuchenko
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Jian Shi
- Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Scott A Smith
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, TN 37232, USA; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chandra S Verma
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ganesh Anand
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Departments of Pediatrics and Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Peter J Bond
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Shee-Mei Lok
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.
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44
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Growth and adaptation of Zika virus in mammalian and mosquito cells. PLoS Negl Trop Dis 2018; 12:e0006880. [PMID: 30418969 PMCID: PMC6258428 DOI: 10.1371/journal.pntd.0006880] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/26/2018] [Accepted: 09/28/2018] [Indexed: 01/02/2023] Open
Abstract
The recent emergence of Zika virus (ZIKV) in the Americas coincident with increased caseloads of microcephalic infants and Guillain-Barre syndrome has prompted a flurry of research on ZIKV. Much of the research is difficult to compare or repeat because individual laboratories use different virus isolates, growth conditions, and quantitative assays. Here we obtained three readily available contemporary ZIKV isolates and the prototype Ugandan isolate. We generated stocks of each on Vero mammalian cells (ZIKVmam) and C6/36 mosquito cells (ZIKVmos), determined titers by different assays side-by-side, compared growth characteristics using one-step and multi-step growth curves on Vero and C6/36 cells, and examined plaque phenotype. ZIKV titers consistently peaked earlier on Vero cells than on C6/36 cells. Contemporary ZIKV isolates reached peak titer most quickly in a multi-step growth curve when the amplifying cell line was the same as the titering cell line (e.g., ZIKVmam titered on Vero cells). Growth of ZIKVmam on mosquito cells was particularly delayed. These data suggest that the ability to infect and/or replicate in insect cells is limited after growth in mammalian cells. In addition, ZIKVmos typically had smaller, more homogenous plaques than ZIKVmam in a standard plaque assay. We hypothesized that the plaque size difference represented early adaptation to growth in mammalian cells. We plaque purified representative-sized plaques from ZIKVmos and ZIKVmam. ZIKVmos isolates maintained the initial phenotype while plaques from ZIKVmam isolates became larger with passaging. Our results underscore the importance of the cells used to produce viral stocks and the potential for adaptation with minimal cell passages. In addition, these studies provide a foundation to compare current and emerging ZIKV isolates in vitro and in vivo.
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Sharma KK, Marzinek JK, Tantirimudalige SN, Bond PJ, Wohland T. Single-molecule studies of flavivirus envelope dynamics: Experiment and computation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:38-51. [PMID: 30223001 DOI: 10.1016/j.pbiomolbio.2018.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022]
Abstract
Flaviviruses are simple enveloped viruses exhibiting complex structural and functional heterogeneities. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology approaches. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that are employed to investigate flaviviruses. In particular, we review how (i) time-resolved Förster resonance energy transfer (trFRET) was applied to probe dengue envelope conformations; (ii) FRET-fluorescence correlation spectroscopy to investigate dengue envelope intrinsic dynamics and (iii) single particle tracking to follow the path of dengue viruses in cells. We also discuss how such methods may be supported by molecular dynamics (MD) simulations over a range of spatio-temporal scales, to provide complementary data on the structure and dynamics of flaviviral systems. We describe recent improvements in multiscale MD approaches that allowed the simulation of dengue particle envelopes in near-atomic resolution. We hope this review is an incentive for setting up and applying similar single-molecule studies and combine them with MD simulations to investigate structural dynamics of entire flavivirus particles over the nanosecond-to-millisecond time-scale and follow viruses during infection in cells over milliseconds to minutes.
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Affiliation(s)
- Kamal Kant Sharma
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Jan K Marzinek
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Sarala Neomi Tantirimudalige
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Peter J Bond
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Department of Chemistry, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore.
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46
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Qadir A, Riaz M, Saeed M, Shahzad-Ul-Hussan S. Potential targets for therapeutic intervention and structure based vaccine design against Zika virus. Eur J Med Chem 2018; 156:444-460. [PMID: 30015077 DOI: 10.1016/j.ejmech.2018.07.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/28/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
Continuously increasing number of reports of Zika virus (ZIKV) infections and associated severe clinical manifestations, including autoimmune abnormalities and neurological disorders such as neonatal microcephaly and Guillain-Barré syndrome have created alarming situation in various countries. To date, no specific antiviral therapy or vaccine is available against ZIKV. This review provides a comprehensive insight into the potential therapeutic targets and describes viral epitopes of broadly neutralizing antibodies (bNAbs) in vaccine design perspective. Interactions between ZIKV envelope glycoprotein E and cellular receptors mediate the viral fusion and entry to the target cell. Blocking these interactions by targeting cellular receptors or viral structural proteins mediating these interactions or viral surface glycans can inhibit viral entry to the cell. Similarly, different non-structural proteins of ZIKV and un-translated regions (UTRs) of its RNA play essential roles in viral replication cycle and potentiate for therapeutic interventions. Structure based vaccine design requires identity and structural description of the epitopes of bNAbs. We have described different conserved bNAb epitopes present in the ZIKV envelope as potential targets for structure based vaccine design. This review also highlights successes, unanswered questions and future perspectives in relation to therapeutic and vaccine development against ZIKV.
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Affiliation(s)
- Amina Qadir
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Muhammad Riaz
- Department of Chemistry, University of Azad Jammu & Kashmir, Muzaffarabad, Pakistan
| | - Muhammad Saeed
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
| | - Syed Shahzad-Ul-Hussan
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
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47
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Banerjee S, Maurya S, Roy R. Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018; 43:519-540. [PMID: 30002270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule fluorescence methods remain a challenging yet information-rich set of techniques that allow one to probe the dynamics, stoichiometry and conformation of biomolecules one molecule at a time. Viruses are small (nanometers) in size, can achieve cellular infections with a small number of virions and their lifecycle is inherently heterogeneous with a large number of structural and functional intermediates. Single-molecule measurements that reveal the complete distribution of properties rather than the average can hence reveal new insights into virus infections and biology that are inaccessible otherwise. This article highlights some of the methods and recent applications of single-molecule fluorescence in the field of virology. Here, we have focused on new findings in virus-cell interaction, virus cell entry and transport, viral membrane fusion, genome release, replication, translation, assembly, genome packaging, egress and interaction with host immune proteins that underline the advantage of single-molecule approach to the question at hand. Finally, we discuss the challenges, outlook and potential areas for improvement and future use of single-molecule fluorescence that could further aid our understanding of viruses.
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Affiliation(s)
- Sunaina Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
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48
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Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018. [DOI: 10.1007/s12038-018-9769-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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49
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de Wispelaere M, Lian W, Potisopon S, Li PC, Jang J, Ficarro SB, Clark MJ, Zhu X, Kaplan JB, Pitts JD, Wales TE, Wang J, Engen JR, Marto JA, Gray NS, Yang PL. Inhibition of Flaviviruses by Targeting a Conserved Pocket on the Viral Envelope Protein. Cell Chem Biol 2018; 25:1006-1016.e8. [PMID: 29937406 DOI: 10.1016/j.chembiol.2018.05.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/23/2018] [Accepted: 05/16/2018] [Indexed: 11/28/2022]
Abstract
Viral envelope proteins are required for productive viral entry and initiation of infection. Although the humoral immune system provides ample evidence for targeting envelope proteins as an antiviral strategy, there are few pharmacological interventions that have this mode of action. In contrast to classical antiviral targets such as viral proteases and polymerases, viral envelope proteins as a class do not have a well-conserved active site that can be rationally targeted with small molecules. We previously identified compounds that inhibit dengue virus by binding to its envelope protein, E. Here, we show that these small molecules inhibit dengue virus fusion and map the binding site of these compounds to a specific pocket on E. We further demonstrate inhibition of Zika, West Nile, and Japanese encephalitis viruses by these compounds, providing pharmacological evidence for the pocket as a target for developing broad-spectrum antivirals against multiple, mosquito-borne flavivirus pathogens.
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Affiliation(s)
| | - Wenlong Lian
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Supanee Potisopon
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pi-Chun Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA 02215, USA
| | - Jaebong Jang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA 02215, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Department of Oncologic Pathology, Blais Proteomics Center, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, 45 Francis Street, Boston, MA 02115, USA
| | - Margaret J Clark
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Xuling Zhu
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jenifer B Kaplan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jared D Pitts
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA 02215, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Department of Oncologic Pathology, Blais Proteomics Center, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, 45 Francis Street, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA 02215, USA
| | - Priscilla L Yang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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50
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TIM-1 Ubiquitination Mediates Dengue Virus Entry. Cell Rep 2018; 23:1779-1793. [DOI: 10.1016/j.celrep.2018.04.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/06/2018] [Accepted: 04/02/2018] [Indexed: 01/01/2023] Open
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