1
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Perovic V, Stevanovic K, Bukreyeva N, Paessler S, Maruyama J, López-Serrano S, Darji A, Sencanski M, Radosevic D, Berardozzi S, Botta B, Mori M, Glisic S. Exploring the Antiviral Potential of Natural Compounds against Influenza: A Combined Computational and Experimental Approach. Int J Mol Sci 2024; 25:4911. [PMID: 38732151 PMCID: PMC11084791 DOI: 10.3390/ijms25094911] [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: 03/19/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
The influenza A virus nonstructural protein 1 (NS1), which is crucial for viral replication and immune evasion, has been identified as a significant drug target with substantial potential to contribute to the fight against influenza. The emergence of drug-resistant influenza A virus strains highlights the urgent need for novel therapeutics. This study proposes a combined theoretical criterion for the virtual screening of molecular libraries to identify candidate NS1 inhibitors. By applying the criterion to the ZINC Natural Product database, followed by ligand-based virtual screening and molecular docking, we proposed the most promising candidate as a potential NS1 inhibitor. Subsequently, the selected natural compound was experimentally evaluated, revealing measurable virus replication inhibition activity in cell culture. This approach offers a promising avenue for developing novel anti-influenza agents targeting the NS1 protein.
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Affiliation(s)
- Vladimir Perovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
| | - Kristina Stevanovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
| | - Natalya Bukreyeva
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Junki Maruyama
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Sergi López-Serrano
- Infection Biology Laboratory, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
- Institut de Recerca en Tecnologies Agroalimentaries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ayub Darji
- Institut de Recerca en Tecnologies Agroalimentaries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Milan Sencanski
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
| | - Draginja Radosevic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
| | - Simone Berardozzi
- Department of Chemistry and Technologies of Drugs, Sapienza University of Roma, 00185 Roma, Italy
- CLNS—Center for Life Nano Sciences@Sapienza, Istituto Italiano di Tecnologia, 00161 Roma, Italy
| | - Bruno Botta
- Department of Chemistry and Technologies of Drugs, Sapienza University of Roma, 00185 Roma, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy;
| | - Sanja Glisic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, 11001 Belgrade, Serbia; (K.S.); (M.S.); (D.R.)
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2
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Blake ME, Kleinpeter AB, Jureka AS, Petit CM. Structural Investigations of Interactions between the Influenza a Virus NS1 and Host Cellular Proteins. Viruses 2023; 15:2063. [PMID: 37896840 PMCID: PMC10612106 DOI: 10.3390/v15102063] [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: 08/22/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The Influenza A virus is a continuous threat to public health that causes yearly epidemics with the ever-present threat of the virus becoming the next pandemic. Due to increasing levels of resistance, several of our previously used antivirals have been rendered useless. There is a strong need for new antivirals that are less likely to be susceptible to mutations. One strategy to achieve this goal is structure-based drug development. By understanding the minute details of protein structure, we can develop antivirals that target the most conserved, crucial regions to yield the highest chances of long-lasting success. One promising IAV target is the virulence protein non-structural protein 1 (NS1). NS1 contributes to pathogenicity through interactions with numerous host proteins, and many of the resulting complexes have been shown to be crucial for virulence. In this review, we cover the NS1-host protein complexes that have been structurally characterized to date. By bringing these structures together in one place, we aim to highlight the strength of this field for drug discovery along with the gaps that remain to be filled.
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Affiliation(s)
| | | | | | - Chad M. Petit
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.E.B.)
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3
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Marsili G, Acchioni C, Remoli AL, Amatore D, Sgarbanti R, De Angelis M, Orsatti R, Acchioni M, Astolfi A, Iraci N, Puzelli S, Facchini M, Perrotti E, Cecchetti V, Sabatini S, Superti F, Agamennone M, Barreca ML, Hiscott J, Nencioni L, Sgarbanti M. Identification of Anti-Influenza A Compounds Inhibiting the Viral Non-Structural Protein 1 (NS1) Using a Type I Interferon-Driven Screening Strategy. Int J Mol Sci 2023; 24:10495. [PMID: 37445672 DOI: 10.3390/ijms241310495] [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: 05/15/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
There is an urgent need to identify efficient antiviral compounds to combat existing and emerging RNA virus infections, particularly those related to seasonal and pandemic influenza outbreaks. While inhibitors of the influenza viral integral membrane proton channel protein (M2), neuraminidase (NA), and cap-dependent endonuclease are available, circulating influenza viruses acquire resistance over time. Thus, the need for the development of additional anti-influenza drugs with novel mechanisms of action exists. In the present study, a cell-based screening assay and a small molecule library were used to screen for activities that antagonized influenza A non-structural protein 1 (NS1), a highly conserved, multifunctional accessory protein that inhibits the type I interferon response against influenza. Two potential anti-influenza agents, compounds 157 and 164, were identified with anti-NS1 activity, resulting in the reduction of A/PR/8/34(H1N1) influenza A virus replication and the restoration of IFN-β expression in human lung epithelial A549 cells. A 3D pharmacophore modeling study of the active compounds provided a glimpse of the structural motifs that may contribute to anti-influenza virus activity. This screening approach is amenable to a broader analysis of small molecule compounds to inhibit other viral targets.
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Affiliation(s)
- Giulia Marsili
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Chiara Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Anna Lisa Remoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Donatella Amatore
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
| | - Rossella Sgarbanti
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
| | - Marta De Angelis
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Roberto Orsatti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marta Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Nunzio Iraci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Simona Puzelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marzia Facchini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Edvige Perrotti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Fabiana Superti
- National Centre for Innovative Technologies in Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Mariangela Agamennone
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - John Hiscott
- Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
| | - Lucia Nencioni
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
| | - Marco Sgarbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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4
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Mertowska P, Smolak K, Mertowski S, Grywalska E. Immunomodulatory Role of Interferons in Viral and Bacterial Infections. Int J Mol Sci 2023; 24:10115. [PMID: 37373262 DOI: 10.3390/ijms241210115] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Interferons are a group of immunomodulatory substances produced by the human immune system in response to the presence of pathogens, especially during viral and bacterial infections. Their remarkably diverse mechanisms of action help the immune system fight infections by activating hundreds of genes involved in signal transduction pathways. In this review, we focus on discussing the interplay between the IFN system and seven medically important and challenging viruses (herpes simplex virus (HSV), influenza, hepatitis C virus (HCV), lymphocytic choriomeningitis virus (LCMV), human immunodeficiency virus (HIV), Epstein-Barr virus (EBV), and SARS-CoV coronavirus) to highlight the diversity of viral strategies. In addition, the available data also suggest that IFNs play an important role in the course of bacterial infections. Research is currently underway to identify and elucidate the exact role of specific genes and effector pathways in generating the antimicrobial response mediated by IFNs. Despite the numerous studies on the role of interferons in antimicrobial responses, many interdisciplinary studies are still needed to understand and optimize their use in personalized therapeutics.
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Affiliation(s)
- Paulina Mertowska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Konrad Smolak
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Sebastian Mertowski
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Ewelina Grywalska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland
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5
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Jiang L, Chen H, Li C. Advances in deciphering the interactions between viral proteins of influenza A virus and host cellular proteins. CELL INSIGHT 2023; 2:100079. [PMID: 37193064 PMCID: PMC10134199 DOI: 10.1016/j.cellin.2023.100079] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/28/2023] [Accepted: 01/28/2023] [Indexed: 05/18/2023]
Abstract
Influenza A virus (IAV) poses a severe threat to the health of animals and humans. The genome of IAV consists of eight single-stranded negative-sense RNA segments, encoding ten essential proteins as well as certain accessory proteins. In the process of virus replication, amino acid substitutions continuously accumulate, and genetic reassortment between virus strains readily occurs. Due to this high genetic variability, new viruses that threaten animal and human health can emerge at any time. Therefore, the study on IAV has always been a focus of veterinary medicine and public health. The replication, pathogenesis, and transmission of IAV involve intricate interplay between the virus and host. On one hand, the entire replication cycle of IAV relies on numerous proviral host proteins that effectively allow the virus to adapt to its host and support its replication. On the other hand, some host proteins play restricting roles at different stages of the viral replication cycle. The mechanisms of interaction between viral proteins and host cellular proteins are currently receiving particular interest in IAV research. In this review, we briefly summarize the current advances in our understanding of the mechanisms by which host proteins affect virus replication, pathogenesis, or transmission by interacting with viral proteins. Such information about the interplay between IAV and host proteins could provide insights into how IAV causes disease and spreads, and might help support the development of antiviral drugs or therapeutic approaches.
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Affiliation(s)
- Li Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chengjun Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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6
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Cunha AES, Loureiro RJS, Simões CJV, Brito RMM. Unveiling New Druggable Pockets in Influenza Non-Structural Protein 1: NS1-Host Interactions as Antiviral Targets for Flu. Int J Mol Sci 2023; 24:ijms24032977. [PMID: 36769298 PMCID: PMC9918223 DOI: 10.3390/ijms24032977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Influenza viruses are responsible for significant morbidity and mortality worldwide in winter seasonal outbreaks and in flu pandemics. Influenza viruses have a high rate of evolution, requiring annual vaccine updates and severely diminishing the effectiveness of the available antivirals. Identifying novel viral targets and developing new effective antivirals is an urgent need. One of the most promising new targets for influenza antiviral therapy is non-structural protein 1 (NS1), a highly conserved protein exclusively expressed in virus-infected cells that mediates essential functions in virus replication and pathogenesis. Interaction of NS1 with the host proteins PI3K and TRIM25 is paramount for NS1's role in infection and pathogenesis by promoting viral replication through the inhibition of apoptosis and suppressing interferon production, respectively. We, therefore, conducted an analysis of the druggability of this viral protein by performing molecular dynamics simulations on full-length NS1 coupled with ligand pocket detection. We identified several druggable pockets that are partially conserved throughout most of the simulation time. Moreover, we found out that some of these druggable pockets co-localize with the most stable binding regions of the protein-protein interaction (PPI) sites of NS1 with PI3K and TRIM25, which suggests that these NS1 druggable pockets are promising new targets for antiviral development.
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Affiliation(s)
- Andreia E. S. Cunha
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui J. S. Loureiro
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Correspondence: (R.J.S.L.); (R.M.M.B.)
| | - Carlos J. V. Simões
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- BSIM Therapeutics, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Rui M. M. Brito
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- BSIM Therapeutics, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
- Correspondence: (R.J.S.L.); (R.M.M.B.)
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7
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Naceri S, Marc D, Blot R, Flatters D, Camproux AC. Druggable Pockets at the RNA Interface Region of Influenza A Virus NS1 Protein Are Conserved across Sequence Variants from Distinct Subtypes. Biomolecules 2022; 13:biom13010064. [PMID: 36671449 PMCID: PMC9855689 DOI: 10.3390/biom13010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/24/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
Influenza A viruses still represent a major health issue, for both humans and animals. One of the main viral proteins of interest to target is the NS1 protein, which counters the host immune response and promotes viral replication. NS1 is a homodimer composed of a dimeric RNA-binding domain (RBD), which is structurally stable and conserved in sequence, and two effector domains that are tethered to the RBD by linker regions. This linker flexibility leads to NS1 polymorphism and can therefore exhibit different forms. Previously, we identified a putative drug-binding site, located in the RBD interface in a crystal structure of NS1. This pocket could be targeted to block RNA binding and inhibit NS1 activities. The objective of the present study is to confirm the presence of this druggable site, whatever the sequence variants, in order to develop a universal therapeutic compound that is insensitive to sequence variations and structural flexibility. Using a set of four NS1 full-length structures, we combined different bioinformatics approaches such as pocket tracking along molecular dynamics simulations, druggability prediction and classification. This protocol successfully confirmed a frequent large binding-site that is highly druggable and shared by different NS1 forms, which is promising for developing a robust NS1-targeted therapy.
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Affiliation(s)
- Sarah Naceri
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, INSERM, Université Paris Cité, F-75013 Paris, France
| | - Daniel Marc
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Rachel Blot
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, INSERM, Université Paris Cité, F-75013 Paris, France
| | - Delphine Flatters
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, INSERM, Université Paris Cité, F-75013 Paris, France
- Correspondence: (D.F.); (A.-C.C.)
| | - Anne-Claude Camproux
- Unité de Biologie Fonctionnelle et Adaptative, CNRS, INSERM, Université Paris Cité, F-75013 Paris, France
- Correspondence: (D.F.); (A.-C.C.)
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8
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Chen N, Zhang B, Deng L, Liang B, Ping J. Virus-host interaction networks as new antiviral drug targets for IAV and SARS-CoV-2. Emerg Microbes Infect 2022; 11:1371-1389. [PMID: 35476817 PMCID: PMC9132403 DOI: 10.1080/22221751.2022.2071175] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, SARS-CoV-2, especially the Omicron strain, is ravaging the world and even co-infecting human beings with IAV, which is a serious threat to human public health. As of yet, no specific antiviral drug has been discovered for SARS-CoV-2. This requires deeper understandings of the molecular mechanisms of SARS-CoV-2-host interaction, to explore antiviral drug targets and provide theoretical basis for developing anti-SARS-CoV-2 drugs. This article discussed IAV, which has been comprehensively studied and is expected to provide the most important reference value for the SARS-CoV-2 study apart from members of the Coronaviridae family. We wish to establish a theoretical system for the studies on virus-host interaction. Previous studies have shown that host PRRs recognize RNAs of IAV or SARS-CoV-2 and then activate innate immune signaling pathways to induce the expression of host restriction factors, such as ISGs, to ultimately inhibit viral replication. Meanwhile, viruses have also evolved various regulatory mechanisms to antagonize host innate immunity at transcriptional, translational, post-translational modification, and epigenetic levels. Besides, viruses can hijack supportive host factors for their replication. Notably, the race between host antiviral innate immunity and viral antagonism of host innate immunity forms virus-host interaction networks. Additionally, the viral replication cycle is co-regulated by proteins, ncRNAs, sugars, lipids, hormones, and inorganic salts. Given this, we updated the mappings of antiviral drug targets based on virus-host interaction networks and proposed an innovative idea that virus-host interaction networks as new antiviral drug targets for IAV and SARS-CoV-2 from the perspectives of viral immunology and systems biology.
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Affiliation(s)
- Na Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Baoge Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Lulu Deng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bing Liang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Jihui Ping
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People's Republic of China
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9
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The Contribution of Viral Proteins to the Synergy of Influenza and Bacterial Co-Infection. Viruses 2022; 14:v14051064. [PMID: 35632805 PMCID: PMC9143653 DOI: 10.3390/v14051064] [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: 04/06/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
A severe course of acute respiratory disease caused by influenza A virus (IAV) infection is often linked with subsequent bacterial superinfection, which is difficult to cure. Thus, synergistic influenza-bacterial co-infection represents a serious medical problem. The pathogenic changes in the infected host are accelerated as a consequence of IAV infection, reflecting its impact on the host immune response. IAV infection triggers a complex process linked with the blocking of innate and adaptive immune mechanisms required for effective antiviral defense. Such disbalance of the immune system allows for easier initiation of bacterial superinfection. Therefore, many new studies have emerged that aim to explain why viral-bacterial co-infection can lead to severe respiratory disease with possible fatal outcomes. In this review, we discuss the key role of several IAV proteins-namely, PB1-F2, hemagglutinin (HA), neuraminidase (NA), and NS1-known to play a role in modulating the immune defense of the host, which consequently escalates the development of secondary bacterial infection, most often caused by Streptococcus pneumoniae. Understanding the mechanisms leading to pathological disorders caused by bacterial superinfection after the previous viral infection is important for the development of more effective means of prevention; for example, by vaccination or through therapy using antiviral drugs targeted at critical viral proteins.
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10
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Lubna S, Chinta S, Burra P, Vedantham K, Ray S, Bandyopadhyay D. New substitutions on NS1 protein from influenza A (H1N1) virus: Bioinformatics analyses of Indian strains isolated from 2009 to 2020. Health Sci Rep 2022; 5:e626. [PMID: 35509388 PMCID: PMC9059196 DOI: 10.1002/hsr2.626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Syeda Lubna
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
| | - Suma Chinta
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
| | - Prakruthi Burra
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
| | - Kiranmayi Vedantham
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
| | | | - Debashree Bandyopadhyay
- Birla Institute of Technology and Science, Pilani, Hyderabad Campus Hyderabad Telangana India
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11
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Chua SCJH, Cui J, Engelberg D, Lim LHK. A Review and Meta-Analysis of Influenza Interactome Studies. Front Microbiol 2022; 13:869406. [PMID: 35531276 PMCID: PMC9069142 DOI: 10.3389/fmicb.2022.869406] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/23/2022] [Indexed: 11/29/2022] Open
Abstract
Annually, the influenza virus causes 500,000 deaths worldwide. Influenza-associated mortality and morbidity is especially high among the elderly, children, and patients with chronic diseases. While there are antivirals available against influenza, such as neuraminidase inhibitors and adamantanes, there is growing resistance against these drugs. Thus, there is a need for novel antivirals for resistant influenza strains. Host-directed therapies are a potential strategy for influenza as host processes are conserved and are less prone mutations as compared to virus-directed therapies. A literature search was performed for papers that performed viral–host interaction screens and the Reactome pathway database was used for the bioinformatics analysis. A total of 15 studies were curated and 1717 common interactors were uncovered among all these studies. KEGG analysis, Enrichr analysis, STRING interaction analysis was performed on these interactors. Therefore, we have identified novel host pathways that can be targeted for host-directed therapy against influenza in our review.
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Affiliation(s)
- Sonja Courtney Jun Hui Chua
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- CREATE-NUS-HUJ Cellular & Molecular Mechanisms of Inflammation Programme, National University of Singapore, Singapore, Singapore
| | - Jianzhou Cui
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - David Engelberg
- CREATE-NUS-HUJ Cellular & Molecular Mechanisms of Inflammation Programme, National University of Singapore, Singapore, Singapore
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biological Chemistry, The Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lina Hsiu Kim Lim
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- *Correspondence: Lina Hsiu Kim Lim,
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12
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Naceri S, Marc D, Camproux AC, Flatters D. Influenza A Virus NS1 Protein Structural Flexibility Analysis According to Its Structural Polymorphism Using Computational Approaches. Int J Mol Sci 2022; 23:ijms23031805. [PMID: 35163728 PMCID: PMC8836794 DOI: 10.3390/ijms23031805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 01/27/2023] Open
Abstract
Influenza A viruses are highly contagious RNA viruses that cause respiratory tract infections in humans and animals. Their non-structural protein NS1, a homodimer of two 230-residue chains, is the main viral factor in counteracting the antiviral defenses of the host cell. Its RNA-binding domain is an obligate dimer that is connected to each of the two effector domains by a highly flexible unstructured linker region of ten amino acids. The flexibility of NS1 is a key property that allows its effector domains and its RNA binding domain to interact with several protein partners or RNAs. The three-dimensional structures of full-length NS1 dimers revealed that the effector domains could adopt three distinct conformations as regards their mutual interactions and their orientation relative to the RNA binding domain (closed, semi-open and open). The origin of this structural polymorphism is currently being investigated and several hypotheses are proposed, among which one posits that it is a strain-specific property. In the present study, we explored through computational molecular modeling the dynamic and flexibility properties of NS1 from three important influenza virus A strains belonging to three distinct subtypes (H1N1, H6N6, H5N1), for which at least one conformation is available in the Protein Data Bank. In order to verify whether NS1 is stable in three forms for the three strains, we constructed homology models if the corresponding forms were not available in the Protein Data Bank. Molecular dynamics simulations were performed in order to predict the stability over time of the three distinct sequence variants of NS1, in each of their three distinct conformations. Our results favor the co-existence of three stable structural forms, regardless of the strain, but also suggest that the length of the linker, along with the presence of specific amino acids, modulate the dynamic properties and the flexibility of NS1.
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Affiliation(s)
- Sarah Naceri
- Université de Paris, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France; (S.N.); (A.-C.C.)
| | - Daniel Marc
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, 37380 Nouzilly, France;
- UMR1282, Infectiologie et Santé Publique, Université de Tours, 37000 Tours, France
| | - Anne-Claude Camproux
- Université de Paris, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France; (S.N.); (A.-C.C.)
| | - Delphine Flatters
- Université de Paris, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France; (S.N.); (A.-C.C.)
- Correspondence:
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13
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Silva LR, da Silva-Júnior EF. Multi-Target Approaches of Epigallocatechin-3-O-gallate (EGCG) and its Derivatives Against Influenza Viruses. Curr Top Med Chem 2022; 22:1485-1500. [PMID: 35086449 DOI: 10.2174/1568026622666220127112056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/13/2021] [Accepted: 12/30/2021] [Indexed: 11/22/2022]
Abstract
Influenza viruses (INFV), Orthomyxoviridae family, are mainly transmitted among humans, via aerosols or droplets from the respiratory secretions. However, fomites could be a potential transmission pathway. Annually, seasonal INFV infections account for 290-650 thousand deaths worldwide. Currently, there are two classes of approved drugs to treat INFV infections, being neuraminidase (NA) inhibitors and blockers of matrix-2 (M2) ion channel. However, cases of resistance have been observed for both chemical classes, reducing the efficacy of treatment. The emergence of influenza outbreaks and pandemics calls for new antiviral molecules more effective and that could overcome the current resistance to anti-influenza drugs. In this context, polyphenolic compounds are found in various plants and these have displayed different multi-target approaches against diverse pathogens. Among these, green tea (Camellia sinensis) catechins, in special epigallocatechin-3-O-gallate (EGCG), have demonstrated significant activities against the two most relevant human INFV, subtypes A and lineages B. In this sense, EGCG has been found a promising multi-target agent against INFV since can act inhibiting NA, hemagglutination (HA), RNA-dependent RNA polymerase (RdRp), and viral entry/adsorption. In general, the lack of knowledge about potential multi-target natural products prevents an adequate exploration of them, increasing the time for developing multi-target drugs. Then, this review aimed to compile to most relevant studies showing the anti-INFV effects of EGCG and its derivatives, which could become antiviral drug prototypes in the future.
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Affiliation(s)
- Leandro Rocha Silva
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Melo Mota Avenue, 57072-970, AC Simões campus, Maceió, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Melo Mota Avenue, 57072-970, AC Simões campus, Maceió, Brazil
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14
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Trigueiro-Louro J, Santos LA, Almeida F, Correia V, Brito RMM, Rebelo-de-Andrade H. NS1 protein as a novel anti-influenza target: Map-and-mutate antiviral rationale reveals new putative druggable hot spots with an important role on viral replication. Virology 2022; 565:106-116. [PMID: 34773868 DOI: 10.1016/j.virol.2021.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 01/28/2023]
Abstract
Influenza NS1 is a promising anti-influenza target, considering its conserved and druggable structure, and key function in influenza replication and pathogenesis. Notwithstanding, target identification and validation, strengthened by experimental data, are lacking. Here, we further explored our previously designed structure-based antiviral rationale directed to highly conserved druggable NS1 regions across a broad spectrum of influenza A viruses. We aimed to identify NS1-mutated viruses exhibiting a reduced growth phenotype and/or an altered cell apoptosis profile. We found that NS1 mutations Y171A, K175A (consensus druggable pocket 1), W102A (consensus druggable pocket 3), Q121A and G184P (multiple consensus druggable pockets) - located at hot spots amenable for pharmacological modulation - significantly impaired A(H1N1)pdm09 virus replication, in vitro. This is the first time that NS1-K175A, -W102A, and -Q121A mutations are characterized. Our map-and-mutate strategy provides the basis to establish the NS1 as a promising target using a rationale with a higher resilience to resistance development.
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Affiliation(s)
- João Trigueiro-Louro
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Luís A Santos
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Filipe Almeida
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Vanessa Correia
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rui M M Brito
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Helena Rebelo-de-Andrade
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
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15
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Integrating molecular modelling methods to advance influenza A virus drug discovery. Drug Discov Today 2020; 26:503-510. [PMID: 33220433 DOI: 10.1016/j.drudis.2020.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/20/2020] [Accepted: 11/11/2020] [Indexed: 11/20/2022]
Abstract
Since the discovery of the anti-influenza drugs oseltamivir and zanamivir using computer-aided drug design methods, there have been significant applications of molecular modelling methodologies applied to influenza A virus drug discovery, such as molecular dynamics (MD) simulation, molecular docking, and virtual screening (VS). In this review, we provide a brief general introduction to molecular modelling in the context of drug discovery and then focus on the advances and impact of integrating these methods with specific reference to potential influenza A antiviral drug targets.
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16
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Raza S, Abbas G, Azam SS. Screening Pipeline for Flavivirus Based Inhibitors for Zika Virus NS1. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1751-1761. [PMID: 30990437 DOI: 10.1109/tcbb.2019.2911081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In-silico pipeline is applied for identifying and designing novel inhibitors against ZIKV NS1 protein. Comparative molecular docking studies are performed to explore the binding of structurally diverse compounds to ZIKV NS1 by AutoDock/Vina and GOLD. The Zika virus (ZIKV) is a flavivirus, responsible for life-threatening infections and transmitted by Aedes mosquitoes in other organisms. It is associated with Guillain Barre Syndrome (GBS) and microcephaly. This epidemic increase in GBS and microcephaly convoyed the World Health Organization to affirm ZIKV a public health crisis. To combat the ZIKV infections, non-structural protein 1 (NS1), a major host-interaction molecule contributing towards replication, pathogenesis and immune evasion is targeted in the current study. For this purpose, a comprehensive study is required to develop potential novel antiviral inhibitors. Three compounds were identified through docking programs exhibiting properties which are non-toxic to human host and could inhibit the elusive ZIKV. Significant interaction with active site residues and H-bond interactions with the key residues were analyzed for these compounds using molecular dynamics simulation. Free energy calculation predicted higher affinity of Deoxycalyxin-A for ZIKV NS1. This study contributes towards fighting ZIKV infections and can help researchers in designing drug for the treatment of ZIKV.
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17
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Wacquiez A, Coste F, Kut E, Gaudon V, Trapp S, Castaing B, Marc D. Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1. Viruses 2020; 12:E947. [PMID: 32867106 PMCID: PMC7552008 DOI: 10.3390/v12090947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 11/16/2022] Open
Abstract
The non-structural protein NS1 of influenza A viruses is an RNA-binding protein of which its activities in the infected cell contribute to the success of the viral cycle, notably through interferon antagonism. We have previously shown that NS1 strongly binds RNA aptamers harbouring virus-specific sequence motifs (Marc et al., Nucleic Acids Res. 41, 434-449). Here, we started out investigating the putative role of one particular virus-specific motif through the phenotypic characterization of mutant viruses that were genetically engineered from the parental strain WSN. Unexpectedly, our data did not evidence biological importance of the putative binding of NS1 to this specific motif (UGAUUGAAG) in the 3'-untranslated region of its own mRNA. Next, we sought to identify specificity determinants in the NS1-RNA interaction through interaction assays in vitro with several RNA ligands and through solving by X-ray diffraction the 3D structure of several complexes associating NS1's RBD with RNAs of various affinities. Our data show that the RBD binds the GUAAC motif within double-stranded RNA helices with an apparent specificity that may rely on the sequence-encoded ability of the RNA to bend its axis. On the other hand, we showed that the RBD binds to the virus-specific AGCAAAAG motif when it is exposed in the apical loop of a high-affinity RNA aptamer, probably through a distinct mode of interaction that still requires structural characterization. Our data are consistent with more than one mode of interaction of NS1's RBD with RNAs, recognizing both structure and sequence determinants.
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MESH Headings
- 3' Untranslated Regions
- Animals
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Cell Line
- Humans
- Influenza A Virus, H1N1 Subtype/chemistry
- Influenza A Virus, H7N1 Subtype/chemistry
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Domains
- RNA/chemistry
- RNA/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- SELEX Aptamer Technique
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Alan Wacquiez
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Franck Coste
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Emmanuel Kut
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Sascha Trapp
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Daniel Marc
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
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18
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Farooq QUA, Shaukat Z, Aiman S, Zhou T, Li C. A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host. BMC Infect Dis 2020; 20:480. [PMID: 32631335 PMCID: PMC7339526 DOI: 10.1186/s12879-020-05214-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 06/30/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Influenza A virus (IAV) infection is a serious public health problem not only in South East Asia but also in European and African countries. Scientists are using network biology to dig deep into the essential host factors responsible for regulation of virus infections. Researchers can explore the virus invasion into the host cells by studying the virus-host relationship based on their protein-protein interaction network. METHODS In this study, we present a comprehensive IAV-host protein-protein interaction network that is obtained based on the literature-curated protein interaction datasets and some important interaction databases. The network is constructed in Cytoscape and analyzed with its plugins including CytoHubba, CytoCluster, MCODE, ClusterViz and ClusterOne. In addition, Gene Ontology and KEGG enrichment analyses are performed on the highly IAV-associated human proteins. We also compare the current results with those from our previous study on Hepatitis C Virus (HCV)-host protein-protein interaction network in order to find out valuable information. RESULTS We found out 1027 interactions among 829 proteins of which 14 are viral proteins and 815 belong to human proteins. The viral protein NS1 has the highest number of associations with human proteins followed by NP, PB2 and so on. Among human proteins, LNX2, MEOX2, TFCP2, PRKRA and DVL2 have the most interactions with viral proteins. Based on KEGG pathway enrichment analysis of the highly IAV-associated human proteins, we found out that they are enriched in the KEGG pathway of basal cell carcinoma. Similarly, the result of KEGG analysis of the common host factors involved in IAV and HCV infections shows that these factors are enriched in the infection pathways of Hepatitis B Virus (HBV), Viral Carcinoma, measles and certain other viruses. CONCLUSION It is concluded that the list of proteins we identified might be used as potential drug targets for the drug design against the infectious diseases caused by Influenza A Virus and other viruses.
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Affiliation(s)
- Qurat Ul Ain Farooq
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
| | - Zeeshan Shaukat
- Faculty of Information Technology, Beijing University of Technology, Beijing, 100124, China
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
| | - Tong Zhou
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China.
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19
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Molecular Dynamics Simulations of Influenza A Virus NS1 Reveal a Remarkably Stable RNA-Binding Domain Harboring Promising Druggable Pockets. Viruses 2020; 12:v12050537. [PMID: 32422922 PMCID: PMC7290946 DOI: 10.3390/v12050537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
The non-structural protein NS1 of influenza A viruses is considered to be the major antagonist of the interferon system and antiviral defenses of the cell. It could therefore represent a suitable target for novel antiviral strategies. As a first step towards the identification of small compounds targeting NS1, we here investigated the druggable potential of its RNA-binding domain since this domain is essential to the biological activities of NS1. We explored the flexibility of the full-length protein by running molecular dynamics simulations on one of its published crystal structures. While the RNA-binding domain structure was remarkably stable along the simulations, we identified a flexible site at the two extremities of the “groove” that is delimited by the antiparallel α-helices that make up its RNA-binding interface. This groove region is able to form potential binding pockets, which, in 60% of the conformations, meet the druggability criteria. We characterized these pockets and identified the residues that contribute to their druggability. All the residues involved in the druggable pockets are essential at the same time to the stability of the RNA-binding domain and to the biological activities of NS1. They are also strictly conserved across the large sequence diversity of NS1, emphasizing the robustness of this search towards the identification of broadly active NS1-targeting compounds.
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20
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Molecular Basis of the Ternary Interaction between NS1 of the 1918 Influenza A Virus, PI3K, and CRK. Viruses 2020; 12:v12030338. [PMID: 32244879 PMCID: PMC7150778 DOI: 10.3390/v12030338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 01/10/2023] Open
Abstract
The 1918 influenza A virus (IAV) caused the worst flu pandemic in human history. Non-structural protein 1 (NS1) is an important virulence factor of the 1918 IAV and antagonizes host antiviral immune responses. NS1 increases virulence by activating phosphoinositide 3-kinase (PI3K) via binding to the p85β subunit of PI3K. Intriguingly, unlike the NS1 of other human IAV strains, 1918 NS1 hijacks another host protein, CRK, to form a ternary complex with p85β, resulting in hyperactivation of PI3K. However, the molecular basis of the ternary interaction between 1918 NS1, CRK, and PI3K remains elusive. Here, we report the structural and thermodynamic bases of the ternary interaction. We find that the C-terminal tail (CTT) of 1918 NS1 remains highly flexible in the complex with p85β. Thus, the CTT of 1918 NS1 in the complex with PI3K can efficiently hijack CRK. Notably, our study indicates that 1918 NS1 enhances its affinity to p85β in the presence of CRK, which might result in enhanced activation of PI3K. Our results provide structural insight into how 1918 NS1 hijacks two host proteins simultaneously.
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21
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Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses. Proc Natl Acad Sci U S A 2020; 117:6550-6558. [PMID: 32152123 DOI: 10.1073/pnas.1920582117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The 1918 influenza A virus (IAV) caused the most severe flu pandemic in recorded human history. Nonstructural protein 1 (NS1) is an important virulence factor of the 1918 IAV. NS1 antagonizes host defense mechanisms through interactions with multiple host factors. One pathway by which NS1 increases virulence is through the activation of phosphoinositide 3-kinase (PI3K) by binding to its p85β subunit. Here we present the mechanism underlying the molecular recognition of the p85β subunit by 1918 NS1. Using X-ray crystallography, we determine the structure of 1918 NS1 complexed with p85β of human PI3K. We find that the 1918 NS1 effector domain (1918 NS1ED) undergoes a conformational change to bind p85β. Using NMR relaxation dispersion and molecular dynamics simulation, we identify that free 1918 NS1ED exists in a dynamic equilibrium between p85β-binding-competent and -incompetent conformations in the submillisecond timescale. Moreover, we discover that NS1ED proteins of 1918 (H1N1) and Udorn (H3N2) strains exhibit drastically different conformational dynamics and binding kinetics to p85β. These results provide evidence of strain-dependent conformational dynamics of NS1. Using kinetic modeling based on the experimental data, we demonstrate that 1918 NS1ED can result in the faster hijacking of p85β compared to Ud NS1ED, although the former has a lower affinity to p85β than the latter. Our results suggest that the difference in binding kinetics may impact the competition with cellular antiviral responses for the activation of PI3K. We anticipate that our findings will increase the understanding of the strain-dependent behaviors of influenza NS1 proteins.
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22
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Rosário-Ferreira N, Preto AJ, Melo R, Moreira IS, Brito RMM. The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection. Int J Mol Sci 2020; 21:E1511. [PMID: 32098424 PMCID: PMC7073157 DOI: 10.3390/ijms21041511] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 01/07/2023] Open
Abstract
Influenza (flu) is a contagious viral disease, which targets the human respiratory tract and spreads throughout the world each year. Every year, influenza infects around 10% of the world population and between 290,000 and 650,000 people die from it according to the World Health Organization (WHO). Influenza viruses belong to the Orthomyxoviridae family and have a negative sense eight-segment single-stranded RNA genome that encodes 11 different proteins. The only control over influenza seasonal epidemic outbreaks around the world are vaccines, annually updated according to viral strains in circulation, but, because of high rates of mutation and recurrent genetic assortment, new viral strains of influenza are constantly emerging, increasing the likelihood of pandemics. Vaccination effectiveness is limited, calling for new preventive and therapeutic approaches and a better understanding of the virus-host interactions. In particular, grasping the role of influenza non-structural protein 1 (NS1) and related known interactions in the host cell is pivotal to better understand the mechanisms of virus infection and replication, and thus propose more effective antiviral approaches. In this review, we assess the structure of NS1, its dynamics, and multiple functions and interactions, to highlight the central role of this protein in viral biology and its potential use as an effective therapeutic target to tackle seasonal and pandemic influenza.
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Affiliation(s)
- Nícia Rosário-Ferreira
- Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, 3060-197 Cantanhede, Portugal
| | - António J. Preto
- CNC—Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, 3060-197 Cantanhede, Portugal
| | - Rita Melo
- CNC—Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, 3060-197 Cantanhede, Portugal
- Centro de Ciências e Tecnologias Nucleares and Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, 2695-066 Bobadela LRS, Portugal
| | - Irina S. Moreira
- CNC—Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, 3060-197 Cantanhede, Portugal
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Rui M. M. Brito
- Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
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23
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Woo HM, Lee JM, Kim CJ, Lee JS, Jeong YJ. Recovery of TRIM25-Mediated RIG-I Ubiquitination through Suppression of NS1 by RNA Aptamers. Mol Cells 2019; 42:721-728. [PMID: 31600868 PMCID: PMC6821451 DOI: 10.14348/molcells.2019.0157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/28/2019] [Accepted: 09/01/2019] [Indexed: 11/27/2022] Open
Abstract
Non-structural protein 1 (NS1) of influenza virus has been shown to inhibit the innate immune response by blocking the induction of interferon (IFN). In this study, we isolated two single-stranded RNA aptamers specific to NS1 with K d values of 1.62 ± 0.30 nM and 1.97 ± 0.27 nM, respectively, using a systematic evolution of ligand by exponential enrichment (SELEX) procedure. The selected aptamers were able to inhibit the interaction of NS1 with tripartite motif-containing protein 25 (TRIM25), and suppression of NS1 enabled retinoic acid inducible gene I (RIG-I) to be ubiquitinated regularly by TRIM25. Additional luciferase reporter assay and quantitative real-time PCR (RT-PCR) experiments demonstrated that suppression of NS1 by the selected aptamers induced IFN production. It is noted that viral replication was also inhibited through IFN induction in the presence of the selected aptamers. These results suggest that the isolated aptamers are strongly expected to be new therapeutic agents against influenza infection.
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Affiliation(s)
- Hye-Min Woo
- School of Applied Chemistry, Kookmin University, Seoul 02707,
Korea
- Division of Emerging Infectious Disease and Vector Research, Korea National Institute of Health, Cheongju 28159,
Korea
| | - Jin-Moo Lee
- School of Applied Chemistry, Kookmin University, Seoul 02707,
Korea
- Pharmacological Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju 28159,
Korea
| | - Chul-Joong Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134,
Korea
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134,
Korea
| | - Yong-Joo Jeong
- School of Applied Chemistry, Kookmin University, Seoul 02707,
Korea
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24
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New therapeutic targets for the prevention of infectious acute exacerbations of COPD: role of epithelial adhesion molecules and inflammatory pathways. Clin Sci (Lond) 2019; 133:1663-1703. [PMID: 31346069 DOI: 10.1042/cs20181009] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/15/2022]
Abstract
Chronic respiratory diseases are among the leading causes of mortality worldwide, with the major contributor, chronic obstructive pulmonary disease (COPD) accounting for approximately 3 million deaths annually. Frequent acute exacerbations (AEs) of COPD (AECOPD) drive clinical and functional decline in COPD and are associated with accelerated loss of lung function, increased mortality, decreased health-related quality of life and significant economic costs. Infections with a small subgroup of pathogens precipitate the majority of AEs and consequently constitute a significant comorbidity in COPD. However, current pharmacological interventions are ineffective in preventing infectious exacerbations and their treatment is compromised by the rapid development of antibiotic resistance. Thus, alternative preventative therapies need to be considered. Pathogen adherence to the pulmonary epithelium through host receptors is the prerequisite step for invasion and subsequent infection of surrounding structures. Thus, disruption of bacterial-host cell interactions with receptor antagonists or modulation of the ensuing inflammatory profile present attractive avenues for therapeutic development. This review explores key mediators of pathogen-host interactions that may offer new therapeutic targets with the potential to prevent viral/bacterial-mediated AECOPD. There are several conceptual and methodological hurdles hampering the development of new therapies that require further research and resolution.
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25
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Trigueiro-Louro JM, Correia V, Santos LA, Guedes RC, Brito RMM, Rebelo-de-Andrade H. To hit or not to hit: Large-scale sequence analysis and structure characterization of influenza A NS1 unlocks new antiviral target potential. Virology 2019; 535:297-307. [PMID: 31104825 DOI: 10.1016/j.virol.2019.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/13/2022]
Abstract
Influenza NS1 protein is among the most promising novel druggable anti-influenza target, based on its structure; multiple interactions; and global function in influenza replication and pathogenesis. Notwithstanding, drug development guidance based on NS1 structural biology is lacking. Here, we design a promising strategy directed to highly conserved druggable regions as a result of an exhaustive large-scale sequence analysis and structure characterization of NS1 protein across human-infecting influenza A subtypes, over the past 100 years. We have identified 3 druggable pockets and 8 new potential hot spot residues in the NS1 protein, not described before, additionally to other 16 sites previously identified, which represent attractive targets for pharmacological modulation. This study provides a rationale towards structure-function studies of NS1 druggable sites, which have the potential to accelerate the NS1 target validation. This research also contributes to a deeper comprehension and insight into the evolutionary dynamics of influenza A NS1 protein.
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Affiliation(s)
- João M Trigueiro-Louro
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Vanessa Correia
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Luís A Santos
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rita C Guedes
- Medicinal Chemistry Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal
| | - Rui M M Brito
- Chemistry Department and Coimbra Chemistry Centre, Faculty of Science and Technology, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Helena Rebelo-de-Andrade
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal; Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
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26
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Patnaik S, Basu D, Southall N, Dehdashti S, Wan KK, Zheng W, Ferrer M, Taylor M, Engel DA, Marugan JJ. Identification, design and synthesis of novel pyrazolopyridine influenza virus nonstructural protein 1 antagonists. Bioorg Med Chem Lett 2019; 29:1113-1119. [PMID: 30852083 DOI: 10.1016/j.bmcl.2019.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/21/2019] [Accepted: 02/26/2019] [Indexed: 11/27/2022]
Abstract
Nonstructural protein 1 (NS1) plays a crucial function in the replication, spread, and pathogenesis of influenza virus by inhibiting the host innate immune response. Here we report the discovery and optimization of novel pyrazolopyridine NS1 antagonists that can potently inhibit influenza A/PR/8/34 replication in MDCK cells, rescue MDCK cells from cytopathic effects of seasonal influenza A strains, reverse NS1-dependent inhibition of IFN-β gene expression, and suppress the slow growth phenotype in NS1-expressing yeast. These pyrazolopyridines will enable researchers to investigate NS1 function during infection and how antagonists can be utilized in the next generation of treatments for influenza infection.
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Affiliation(s)
- Samarjit Patnaik
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
| | - Dipanwita Basu
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, 1300 Jefferson Park Ave., Charlottesville, VA 22908, United States
| | - Noel Southall
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Seameen Dehdashti
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Kanny K Wan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Wei Zheng
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Marc Ferrer
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Mercedes Taylor
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Daniel A Engel
- Alexander BioDiscoveries, LLC, 530 Forrest Rd., Charlottesville, VA 22902, United States.
| | - Juan Jose Marugan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
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27
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Kleinpeter AB, Jureka AS, Falahat SM, Green TJ, Petit CM. Structural analyses reveal the mechanism of inhibition of influenza virus NS1 by two antiviral compounds. J Biol Chem 2018; 293:14659-14668. [PMID: 30076219 DOI: 10.1074/jbc.ra118.004012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/03/2018] [Indexed: 11/06/2022] Open
Abstract
The influenza virus is a significant public health concern causing 250,000-500,000 deaths worldwide each year. Its ability to change quickly results in the potential for rapid generation of pandemic strains for which most individuals would have no antibody protection. This pandemic potential highlights the need for the continuous development of new drugs against influenza virus. As an essential component and well established virulence determinant, NS1 (nonstructural protein 1) of influenza virus is a highly prioritized target for the development of anti-influenza compounds. Here, we used NMR to determine that the NS1 effector domain (NS1ED) derived from the A/Brevig Mission/1/1918 (H1N1) strain of influenza (1918H1N1) binds to two previously described anti-influenza compounds A9 (JJ3297) and A22. We then used X-ray crystallography to determine the three-dimensional structure of the 1918H1N1 NS1ED Furthermore, we mapped the A9/A22-binding site onto our 1918H1N1 NS1ED structure and determined that A9 and A22 interact with the NS1ED in the hydrophobic pocket known to facilitate binding to the 30-kDa subunit of the cleavage and polyadenylation specificity factor (CPSF30), suggesting that the two compounds likely attenuate influenza replication by inhibiting the NS1ED-CPSF30 interaction. Finally, our structure revealed that NS1ED could dimerize via an interface that we termed the α3-α3 dimer. Taken together, the findings presented here provide strong evidence for the mechanism of action of two anti-influenza compounds that target NS1 and contribute significant structural insights into NS1 that we hope will promote and inform the development and optimization of influenza therapies based on A9/A22.
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Affiliation(s)
| | | | - Sally M Falahat
- From the Departments of Biochemistry and Molecular Genetics and
| | - Todd J Green
- Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Chad M Petit
- From the Departments of Biochemistry and Molecular Genetics and
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28
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Dilly S, Fotso Fotso A, Lejal N, Zedda G, Chebbo M, Rahman F, Companys S, Bertrand HC, Vidic J, Noiray M, Alessi MC, Tarus B, Quideau S, Riteau B, Slama-Schwok A. From Naproxen Repurposing to Naproxen Analogues and Their Antiviral Activity against Influenza A Virus. J Med Chem 2018; 61:7202-7217. [DOI: 10.1021/acs.jmedchem.8b00557] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sébastien Dilly
- Gustave Roussy Institute, Paris Saclay University, UMR8200 CNRS, 94805 Villejuif, France
| | - Aurélien Fotso Fotso
- Aix Marseille University, INSERM, INRA, NORT, UMR 1260/1062, 13007 Marseille, France
| | - Nathalie Lejal
- Paris Saclay University, UR 892, INRA, 78352 Jouy en Josas, France
| | - Gloria Zedda
- Bordeaux University, ISM (CNRS-UMR 5255), 33405 Talence, France
| | - Mohamad Chebbo
- Aix Marseille University, INSERM, INRA, NORT, UMR 1260/1062, 13007 Marseille, France
| | - Fryad Rahman
- Aix Marseille University, INSERM, INRA, NORT, UMR 1260/1062, 13007 Marseille, France
| | - Simon Companys
- Bordeaux University, ISM (CNRS-UMR 5255), 33405 Talence, France
| | | | - Jasmina Vidic
- Paris Saclay University, UR 892, INRA, 78352 Jouy en Josas, France
| | - Magali Noiray
- Paris Sud University, Paris Saclay University, UMS IPSIT, Intermol, 92290 Châtenay-Malabry, France
| | | | - Bogdan Tarus
- Paris Saclay University, UR 892, INRA, 78352 Jouy en Josas, France
| | | | - Béatrice Riteau
- Aix Marseille University, INSERM, INRA, NORT, UMR 1260/1062, 13007 Marseille, France
| | - Anny Slama-Schwok
- Gustave Roussy Institute, Paris Saclay University, UMR8200 CNRS, 94805 Villejuif, France
- Paris Saclay University, UR 892, INRA, 78352 Jouy en Josas, France
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29
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Klemm C, Boergeling Y, Ludwig S, Ehrhardt C. Immunomodulatory Nonstructural Proteins of Influenza A Viruses. Trends Microbiol 2018; 26:624-636. [PMID: 29373257 DOI: 10.1016/j.tim.2017.12.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/07/2017] [Accepted: 12/15/2017] [Indexed: 12/23/2022]
Abstract
Influenza epidemics and pandemics still represent a severe public health threat and cause significant morbidity and mortality worldwide. As intracellular parasites, influenza viruses are strongly dependent on the host cell machinery. To ensure efficient production of progeny viruses, viral proteins extensively interfere with cellular signalling pathways to inhibit antiviral responses or to activate virus-supportive functions. Here, we review various functions of the influenza virus nonstructural proteins NS1, PB1-F2, and PA-X in infected cells and how post-transcriptional modifications of these proteins affect the viral life cycle. Furthermore, we discuss newly discovered interactions between these proteins and the antiviral interferon response.
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Affiliation(s)
- Carolin Klemm
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany
| | - Yvonne Boergeling
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany
| | - Stephan Ludwig
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany
| | - Christina Ehrhardt
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany.
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30
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Dzananovic E, McKenna SA, Patel TR. Viral proteins targeting host protein kinase R to evade an innate immune response: a mini review. Biotechnol Genet Eng Rev 2018; 34:33-59. [PMID: 29716441 DOI: 10.1080/02648725.2018.1467151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The innate immune system offers a first line of defense by neutralizing foreign pathogens such as bacteria, fungi, and viruses. These pathogens express molecules (RNA and proteins) that have discrete structures, known as the pathogen-associated molecular patterns that are recognized by a highly specialized class of host proteins called pattern recognition receptors to facilitate the host's immune response against infection. The RNA-dependent Protein Kinase R (PKR) is one of the host's pattern recognition receptors that is a key component of an innate immune system. PKR recognizes imperfectly double-stranded non-coding viral RNA molecules via its N-terminal double-stranded RNA binding motifs, undergoes phosphorylation of the C-terminal kinase domain, ultimately resulting in inhibition of viral protein translation by inhibiting the guanine nucleotide exchange activity of eukaryotic initiation factor 2α. Not surprisingly, viruses have evolved mechanisms by which viral non-coding RNA or protein molecules inhibit PKR's activation and/or its downstream activity to allow viral replication. In this review, we will highlight the role of viral proteins in inhibiting PKR's activity and summarize currently known mechanisms by which viral proteins execute such inhibitory activity.
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Affiliation(s)
- Edis Dzananovic
- a Plant Pathology, Plant Protection and Molecular Biology , Agriculture and Agri-Food Canada , Saskatoon , Canada
| | - Sean A McKenna
- b Department of Chemistry, Manitoba Institute for Materials, Department of Biochemistry and Medical Genetics , University of Manitoba , Winnipeg , Canada
| | - Trushar R Patel
- c Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada.,d DiscoveryLab, Faculty of Medicine & Dentistry , University of Alberta , Edmonton , Canada.,e Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine , University of Calgary , Calgary , Canada
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31
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Leiva R, Barniol-Xicota M, Codony S, Ginex T, Vanderlinden E, Montes M, Caffrey M, Luque FJ, Naesens L, Vázquez S. Aniline-Based Inhibitors of Influenza H1N1 Virus Acting on Hemagglutinin-Mediated Fusion. J Med Chem 2017; 61:98-118. [PMID: 29220568 DOI: 10.1021/acs.jmedchem.7b00908] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Two series of easily accessible anilines were identified as inhibitors of influenza A virus subtype H1N1, and extensive chemical synthesis and analysis of the structure-activity relationship were performed. The compounds were shown to interfere with low pH-induced membrane fusion mediated by the H1 and H5 (group 1) hemagglutinin (HA) subtypes. A combination of virus resistance, HA interaction, and molecular dynamics simulation studies elucidated the binding site of these aniline-based influenza fusion inhibitors, which significantly overlaps with the pocket occupied by some H3 HA-specific inhibitors, indicating the high relevance of this cavity for drug design.
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Affiliation(s)
- Rosana Leiva
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Marta Barniol-Xicota
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Sandra Codony
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Tiziana Ginex
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Prat de la Riba 171, Santa Coloma de Gramanet E-08921, Spain
| | | | - Marta Montes
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago , 900 South Ashland Avenue, Chicago, Illinois 60607, United States
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Prat de la Riba 171, Santa Coloma de Gramanet E-08921, Spain
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven , B-3000 Leuven, Belgium
| | - Santiago Vázquez
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
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32
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Vasin AV, Petrova-Brodskaya AV, Plotnikova MA, Tsvetkov VB, Klotchenko SA. EVOLUTIONARY DYNAMICS OF STRUCTURAL AND FUNCTIONAL DOMAINS OF INFLUENZA A VIRUS NS1 PROTEIN. Vopr Virusol 2017; 62:246-258. [PMID: 36494956 DOI: 10.18821/0507-4088-2017-62-6-246-258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Indexed: 12/13/2022]
Abstract
Influenza A virus (IAV) NS1 protein is one of the key viral factors responsible for virus-host interactions. NS1 counteracts host antiviral defense, participates in the processing and export of cellular mRNAs, regulates the activity of viral RNA polymerase and the expression of viral genes, and influences the cellular signaling systems. Multiple NS1 functions are carried out due to the interactions with cellular factors, the number of which exceeds one hundred. It is noteworthy that only two segments of IAV genome - NS and NP - did not undergo reassortment and evolved in the course of genetic drift, beginning with the pandemic of 1918 to the present. This fact may indicate the importance of NS1 and its numerous interactions with cellular factors in the interspecific adaptation of the virus. The review presents data on the evolution of the human IAV NS1 protein and analysis of the amino acid substitutions in the main structural and functional domains of NS1 protein during evolution.
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Affiliation(s)
- A V Vasin
- Research Institute of Influenza.,Peter the Great St. Petersburg Polytechnic University
| | - A V Petrova-Brodskaya
- Research Institute of Influenza.,Peter the Great St. Petersburg Polytechnic University
| | | | - V B Tsvetkov
- Research Institute of Influenza.,A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences.,Federal Research and Clinical Center of Physical-Chemical Medicine
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33
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Shin WJ, Seong BL. Type II transmembrane serine proteases as potential target for anti-influenza drug discovery. Expert Opin Drug Discov 2017; 12:1139-1152. [DOI: 10.1080/17460441.2017.1372417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Woo-Jin Shin
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
- Vaccine Translational Research Center, Yonsei University, Seoul, South Korea
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34
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Coch C, Stümpel JP, Lilien-Waldau V, Wohlleber D, Kümmerer BM, Bekeredjian-Ding I, Kochs G, Garbi N, Herberhold S, Schuberth-Wagner C, Ludwig J, Barchet W, Schlee M, Hoerauf A, Bootz F, Staeheli P, Hartmann G, Hartmann E. RIG-I Activation Protects and Rescues from Lethal Influenza Virus Infection and Bacterial Superinfection. Mol Ther 2017; 25:2093-2103. [PMID: 28760668 DOI: 10.1016/j.ymthe.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 07/02/2017] [Accepted: 07/05/2017] [Indexed: 12/25/2022] Open
Abstract
Influenza A virus infection causes substantial morbidity and mortality in seasonal epidemic outbreaks, and more efficient treatments are urgently needed. Innate immune sensing of viral nucleic acids stimulates antiviral immunity, including cell-autonomous antiviral defense mechanisms that restrict viral replication. RNA oligonucleotide ligands that potently activate the cytoplasmic helicase retinoic-acid-inducible gene I (RIG-I) are promising candidates for the development of new antiviral therapies. Here, we demonstrate in an Mx1-expressing mouse model of influenza A virus infection that a single intravenous injection of low-dose RIG-I ligand 5'-triphosphate RNA (3pRNA) completely protected mice from a lethal challenge with influenza A virus for at least 7 days. Furthermore, systemic administration of 3pRNA rescued mice with pre-established fulminant influenza infection and prevented the fatal effects of a streptococcal superinfection. Type I interferon, but not interferon-λ, was required for the therapeutic effect. Our results suggest that the use of RIG-I activating oligonucleotide ligands has the clinical potential to confine influenza epidemics when a strain-specific vaccine is not yet available and to reduce lethality of influenza in severely infected patients.
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Affiliation(s)
- Christoph Coch
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany.
| | - Jan Phillip Stümpel
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Vanessa Lilien-Waldau
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology and Experimental Oncology, TU Munich, 81675 Munich, Germany
| | - Beate M Kümmerer
- Institute of Virology, University Hospital Bonn, 53105 Bonn, Germany
| | - Isabelle Bekeredjian-Ding
- Division of Microbiology, Paul-Ehrlich Institute, 63225 Langen, Germany; Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, 53127 Bonn, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center Freiburg, 79104 Freiburg, Germany
| | - Natalio Garbi
- Institute of Experimental Immunology, University Hospital Bonn, 53127 Bonn, Germany
| | - Stephan Herberhold
- Department of Otolaryngology, University Hospital Bonn, 53127 Bonn, Germany
| | - Christine Schuberth-Wagner
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Janos Ludwig
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Winfried Barchet
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, 53127 Bonn, Germany
| | - Friedrich Bootz
- Department of Otolaryngology, University Hospital Bonn, 53127 Bonn, Germany
| | - Peter Staeheli
- Institute of Virology, Medical Center Freiburg, 79104 Freiburg, Germany
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Evelyn Hartmann
- Department of Otolaryngology, University Hospital Bonn, 53127 Bonn, Germany
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35
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Barba M, Daly JM. The Influenza NS1 Protein: What Do We Know in Equine Influenza Virus Pathogenesis? Pathogens 2016; 5:pathogens5030057. [PMID: 27589809 PMCID: PMC5039437 DOI: 10.3390/pathogens5030057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/22/2022] Open
Abstract
Equine influenza virus remains a serious health and potential economic problem throughout most parts of the world, despite intensive vaccination programs in some horse populations. The influenza non-structural protein 1 (NS1) has multiple functions involved in the regulation of several cellular and viral processes during influenza infection. We review the strategies that NS1 uses to facilitate virus replication and inhibit antiviral responses in the host, including sequestering of double-stranded RNA, direct modulation of protein kinase R activity and inhibition of transcription and translation of host antiviral response genes such as type I interferon. Details are provided regarding what it is known about NS1 in equine influenza, especially concerning C-terminal truncation. Further research is needed to determine the role of NS1 in equine influenza infection, which will help to understand the pathophysiology of complicated cases related to cytokine imbalance and secondary bacterial infection, and to investigate new therapeutic and vaccination strategies.
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Affiliation(s)
- Marta Barba
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.
| | - Janet M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington LE12 5RD, UK.
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Gusho E, Baskar D, Banerjee S. New advances in our understanding of the "unique" RNase L in host pathogen interaction and immune signaling. Cytokine 2016; 133:153847. [PMID: 27595182 PMCID: PMC7128181 DOI: 10.1016/j.cyto.2016.08.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/08/2016] [Accepted: 08/08/2016] [Indexed: 12/22/2022]
Abstract
Ever since the discovery of the existence of an interferon (IFN)-regulated ribonuclease, significant advances have been made in understanding the mechanism and associated regulatory effects of its action. What had been studied initially as a "unique" endoribonuclease is currently known as ribonuclease L (RNase L where "L" stands for latent). Some of the key developments include discovery of the RNase L signaling pathway, its structural characterization, and its molecular cloning. RNase L has been implicated in antiviral and antibacterial defense, as well as in hereditary prostate cancer. RNase L is activated by 2'-5' linked oligoadenylates (2-5A), which are synthesized by the oligoadenylate synthetases (OASs), a family of IFN-regulated pathogen recognition receptors that sense double-stranded RNAs. Activated RNase L cleaves single stranded RNAs, including viral RNAs and cellular RNAs. The catalytic activity of RNase L has been found to lead into the activation of several cellular signaling pathways, including those involved in autophagy, apoptosis, IFN-β production, NLRP3 inflammasome activation leading to IL-1β secretion, inhibition of cell migration, and cell adhesion. In this review, we will highlight the newest advances in our understanding of the catalytic role of RNase L in the context of different cellular pathways and extend the scope of these findings to discussion of potential therapeutic targets for antimicrobial drug development.
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Affiliation(s)
- Elona Gusho
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue Cleveland, OH 44195, USA
| | - Danika Baskar
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue Cleveland, OH 44195, USA; Pediatrics Division Office, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA(1)
| | - Shuvojit Banerjee
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue Cleveland, OH 44195, USA.
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37
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Recent discoveries of influenza A drug target sites to combat virus replication. Biochem Soc Trans 2016; 44:932-6. [DOI: 10.1042/bst20160002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 11/17/2022]
Abstract
Sequence variations in the binding sites of influenza A proteins are known to limit the effectiveness of current antiviral drugs. Clinically, this leads to increased rates of virus transmission and pathogenicity. Potential influenza A inhibitors are continually being discovered as a result of high-throughput cell based screening studies, whereas the application of computational tools to aid drug discovery has further increased the number of predicted inhibitors reported. This review brings together the aspects that relate to the identification of influenza A drug target sites and the findings from recent antiviral drug discovery strategies.
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Yen HL. Current and novel antiviral strategies for influenza infection. Curr Opin Virol 2016; 18:126-34. [DOI: 10.1016/j.coviro.2016.05.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/15/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
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Identification of a Highly Conserved Epitope on Avian Influenza Virus Non-Structural Protein 1 Using a Peptide Microarray. PLoS One 2016; 11:e0149868. [PMID: 26938453 PMCID: PMC4777286 DOI: 10.1371/journal.pone.0149868] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/05/2016] [Indexed: 11/20/2022] Open
Abstract
Avian influenza virus (AIV) non-structural protein 1 (NS1) is a multifunctional protein. It is present at high levels in infected cells and can be used for AIV detection and diagnosis. In this study, we generated monoclonal antibody (MAb) D7 against AIV NS1 protein by immunization of BALB/c mice with purified recombinant NS1 protein expressed in Escherichia coli. Isotype determination revealed that the MAb was IgG1/κ-type subclass. To identify the epitope of the MAb D7, the NS1 protein was truncated into a total of 225 15-mer peptides with 14 amino acid overlaps, which were spotted for a peptide microarray. The results revealed that the MAb D7 recognized the consensus DAPF motif. Furthermore, the AIV NS1 protein with the DAPF motif deletion was transiently expressed in 293T cells and failed to react with MAb D7. Subsequently, the DAPF motif was synthesized with an elongated GSGS linker at both the C- and N-termini. The MAb D7 reacted with the synthesized peptide both in enzyme-linked immunosorbent assay (ELISA) and dot-blot assays. From these results, we concluded that DAPF motif is the epitope of MAb D7. To our knowledge, this is the first report of a 4-mer epitope on the NS1 protein of AIV that can be recognized by MAb using a peptide microarray, which is able to simplify epitope identification, and that could serve as the basis for immune responses against avian influenza.
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Yang Y, Ye F, Zhu N, Wang W, Deng Y, Zhao Z, Tan W. Middle East respiratory syndrome coronavirus ORF4b protein inhibits type I interferon production through both cytoplasmic and nuclear targets. Sci Rep 2015; 5:17554. [PMID: 26631542 PMCID: PMC4668369 DOI: 10.1038/srep17554] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel and highly pathogenic human coronavirus and has quickly spread to other countries in the Middle East, Europe, North Africa and Asia since 2012. Previous studies have shown that MERS-CoV ORF4b antagonizes the early antiviral alpha/beta interferon (IFN-α/β) response, which may significantly contribute to MERS-CoV pathogenesis; however, the underlying mechanism is poorly understood. Here, we found that ORF4b in the cytoplasm could specifically bind to TANK binding kinase 1 (TBK1) and IκB kinase epsilon (IKKε), suppress the molecular interaction between mitochondrial antiviral signaling protein (MAVS) and IKKε, and inhibit IFN regulatory factor 3 (IRF3) phosphorylation and subsequent IFN-β production. Further analysis showed that ORF4b could also inhibit IRF3 and IRF7-induced production of IFN-β, whereas deletion of the nuclear localization signal of ORF4b abrogated its ability to inhibit IRF3 and IRF7-induced production of IFN-β, but not IFN-β production induced by RIG-I, MDA5, MAVS, IKKε, and TBK-1, suggesting that ORF4b could inhibit the induction of IFN-β in both the cytoplasm and nucleus. Collectively, these results indicate that MERS-CoV ORF4b inhibits the induction of type I IFN through a direct interaction with IKKε/TBK1 in the cytoplasm, and also in the nucleus with unknown mechanism. Viruses have evolved multiple strategies to evade or thwart a host's antiviral responses. A novel human coronavirus (HCoV), Middle East respiratory syndrome coronavirus (MERS-CoV), is distinguished from other coronaviruses by its high pathogenicity and mortality. However, virulence determinants that distinguish MERS-CoV from other HCoVs have yet to be identified. MERS-CoV ORF4b antagonizes the early antiviral response, which may contribute to MERS-CoV pathogenesis. Here, we report the identification of the interferon (IFN) antagonism mechanism of MERS-CoV ORF4b. MERS-CoV ORF4b inhibits the production of type I IFN through a direct interaction with IKKε/TBK1 in the cytoplasm, and also in the nucleus with unknown mechanism. These findings provide a rationale for the novel pathogenesis of MERS-CoV as well as a basis for developing a candidate therapeutic against this virus.
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Affiliation(s)
- Yang Yang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Fei Ye
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Na Zhu
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wenling Wang
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yao Deng
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhengdong Zhao
- Key Laboratory of Pathogen System Biology, Ministry of Health; Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, 100176, China
| | - Wenjie Tan
- Key Laboratory of Medical Virology, Ministry of Health; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
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Monod A, Swale C, Tarus B, Tissot A, Delmas B, Ruigrok RW, Crépin T, Slama-Schwok A. Learning from structure-based drug design and new antivirals targeting the ribonucleoprotein complex for the treatment of influenza. Expert Opin Drug Discov 2015; 10:345-71. [PMID: 25792362 DOI: 10.1517/17460441.2015.1019859] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Influenza viruses are a threat to human health. There are presently only two methods for treating influenza: vaccines, which require yearly updates, and two classes of antivirals that suffer with the problem of resistance by current human influenza viruses; this is especially the case with amantadine and rimantadine. Consequently, there is an urgent need for the development of new antivirals with new mechanisms of action. AREAS COVERED In this review, the authors focus on viral protein domains, their associated activity and their inhibition by small molecules defined by a structure-based design with a special emphasis on the ribonucleoprotein complex and its inhibitors. Several new classes of antiviral candidates targeting viral replication through individual domains of the polymerase and the nucleoprotein (NP) have been developed through structure-based design. EXPERT OPINION To date, the antivirals targeting neuraminidase are by far the most developed and potent. Antiviral candidates targeting the NP and polymerase domains are in the pipeline but their pharmacokinetics needs further studies. The recently published structures of the polymerase expand the possibilities for development of new antivirals. Combination therapies targeting conserved viral targets and new cellular proteins or exploiting drug promiscuity hold promises to fight against the emergence of resistance.
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Affiliation(s)
- Alexandre Monod
- University of Grenoble Alpes-EMBL-CNRS, Unit for Virus Host-Cell Interactions , 71 avenue des Martyrs, 38042 Grenoble , France
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Shen Z, Lou K, Wang W. New small-molecule drug design strategies for fighting resistant influenza A. Acta Pharm Sin B 2015; 5:419-30. [PMID: 26579472 PMCID: PMC4629447 DOI: 10.1016/j.apsb.2015.07.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/05/2015] [Indexed: 11/24/2022] Open
Abstract
Influenza A virus is the major cause of seasonal or pandemic flu worldwide. Two main treatment strategies-vaccination and small molecule anti-influenza drugs are currently available. As an effective vaccine usually takes at least 6 months to develop, anti-influenza small molecule drugs are more effective for the first line of protection against the virus during an epidemic outbreak, especially in the early stage. Two major classes of anti-influenza drugs currently available are admantane-based M2 protein blockers (amantadine and rimantadine) and neuraminidase (NA) inhibitors (oseltamivir, zanamivir, and peramivir). However, the continuous evolvement of influenza A virus and the rapid emergence of resistance to current drugs, particularly to amantadine, rimantadine, and oseltamivir, have raised an urgent need for developing new anti-influenza drugs against resistant forms of influenza A virus. In this review, we first give a brief introduction of the molecular mechanisms behind resistance, and then discuss new strategies in small-molecule drug development to overcome influenza A virus resistance targeting mutant M2 proteins and neuraminidases, and other viral proteins not associated with current drugs.
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Affiliation(s)
- Zuyuan Shen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, and State Key Laboratory of Bioengineering Reactor, East China University of Science and Technology, Shanghai 200237, China
| | - Kaiyan Lou
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, and State Key Laboratory of Bioengineering Reactor, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, and State Key Laboratory of Bioengineering Reactor, East China University of Science and Technology, Shanghai 200237, China
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
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Killip MJ, Fodor E, Randall RE. Influenza virus activation of the interferon system. Virus Res 2015; 209:11-22. [PMID: 25678267 PMCID: PMC4638190 DOI: 10.1016/j.virusres.2015.02.003] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 12/24/2022]
Abstract
We summarise the literature regarding activation of the IFN response by influenza viruses. We consider evidence concerning the identity of the viral RNA responsible for IFN induction. The link between IFN induction and defective virus genomes is discussed.
The host interferon (IFN) response represents one of the first barriers that influenza viruses must surmount in order to establish an infection. Many advances have been made in recent years in understanding the interactions between influenza viruses and the interferon system. In this review, we summarise recent work regarding activation of the type I IFN response by influenza viruses, including attempts to identify the viral RNA responsible for IFN induction, the stage of the virus life cycle at which it is generated and the role of defective viruses in this process.
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Affiliation(s)
- Marian J Killip
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK; Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Richard E Randall
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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Barnwal B, Mok CK, Wu J, Diwakar MK, Gupta G, Zeng Q, Chow VTK, Song J, Yuan YA, Tan YJ. A monoclonal antibody binds to threonine 49 in the non-structural 1 protein of influenza A virus and interferes with its ability to modulate viral replication. Antiviral Res 2015; 116:55-61. [PMID: 25666762 PMCID: PMC7113856 DOI: 10.1016/j.antiviral.2015.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 12/10/2014] [Accepted: 01/30/2015] [Indexed: 01/01/2023]
Abstract
The emergence of resistant influenza A viruses highlights the continuous requirement of new antiviral drugs that can treat the viral infection. Non-structural 1 (NS1) protein, an indispensable component for efficient virus replication, can be used as a potential target for generating new antiviral agents. Here, we study the interaction of 2H6 monoclonal antibody with NS1 protein and also determine whether influenza virus replication can be inhibited by blocking NS1. The 2H6-antigen binding fragment (Fab) forms a multimeric complex with the NS1 RNA-binding domain (RBD). T49, a residue which forms a direct hydrogen bond with double stranded RNA, in NS1 protein was found to be critical for its interaction with 2H6 antibody. NS1(RBD) has high affinity to 2H6 with KD of 43.5±4.24nM whereas NS1(RBD)-T49A has more than 250 times lower affinity towards 2H6. Interestingly, the intracellular expression of 2H6-single-chain variable fragment (scFv) in mammalian cells caused a reduction in viral growth and the M1 viral protein level was significantly reduced in 2H6-scFv transfected cells in comparison to vector transfected cells at 12h post infection. These results indicate that the tight binding of 2H6 to NS1 could lead to reduction in viral replication and release of progeny virus. In future, 2H6 antibody in combination with other neutralizing antibodies can be used to increase the potency of viral inhibition.
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Affiliation(s)
- Bhaskar Barnwal
- Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Chee-Keng Mok
- Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Jianping Wu
- Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Mandakhalikar Kedar Diwakar
- Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Qi Zeng
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore
| | - Vincent Tak Kwong Chow
- Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Y Adam Yuan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore; National University of Singapore (Suzhou) Research Institute, Suzhou Industrial Park, Jiangsu 215123, China
| | - Yee-Joo Tan
- Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore; Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore.
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Abstract
The non-structural protein 1 of influenza virus (NS1) is a relatively small polypeptide with an outstanding number of ascribed functions. NS1 is the main viral antagonist of the innate immune response during influenza virus infection, chiefly by inhibiting the type I interferon system at multiple steps. As such, its role is critical to overcome the first barrier the host presents to halt the viral infection. However, the pro-viral activities of this well-studied protein go far beyond and include regulation of viral RNA and protein synthesis, and disruption of the host cell homeostasis by dramatically affecting general gene expression while tweaking the PI3K signaling network. Because of all of this, NS1 is a key virulence factor that impacts influenza pathogenesis, and adaptation to new hosts, making it an attractive target for control strategies. Here, we will overview the many roles that have been ascribed to the NS1 protein, and give insights into the sequence features and structural properties that make them possible, highlighting the need to understand how NS1 can actually perform all of these functions during viral infection.
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Affiliation(s)
- Juan Ayllon
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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46
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Abstract
UNLABELLED Influenza A virus (IAV) infections are influenced by type 1 interferon-mediated antiviral defenses and by viral countermeasures to these defenses. When IAV NS1 protein is disabled, RNase L restricts virus replication; however, the RNAs targeted for cleavage by RNase L under these conditions have not been defined. In this study, we used deep-sequencing methods to identify RNase L cleavage sites within host and viral RNAs from IAV PR8ΔNS1-infected A549 cells. Short hairpin RNA knockdown of RNase L allowed us to distinguish between RNase L-dependent and RNase L-independent cleavage sites. RNase L-dependent cleavage sites were evident at discrete locations in IAV RNA segments (both positive and negative strands). Cleavage in PB2, PB1, and PA genomic RNAs suggests that viral RNPs are susceptible to cleavage by RNase L. Prominent amounts of cleavage mapped to specific regions within IAV RNAs, including some areas of increased synonymous-site conservation. Among cellular RNAs, RNase L-dependent cleavage was most frequent at precise locations in rRNAs. Our data show that RNase L targets specific sites in both host and viral RNAs to restrict influenza virus replication when NS1 protein is disabled. IMPORTANCE RNase L is a critical component of interferon-regulated and double-stranded-RNA-activated antiviral host responses. We sought to determine how RNase L exerts its antiviral activity during influenza virus infection. We enhanced the antiviral activity of RNase L by disabling a viral protein, NS1, that inhibits the activation of RNase L. Then, using deep-sequencing methods, we identified the host and viral RNAs targeted by RNase L. We found that RNase L cleaved viral RNAs and rRNAs at very precise locations. The direct cleavage of IAV RNAs by RNase L highlights an intimate battle between viral RNAs and an antiviral endonuclease.
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47
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Marc D. Influenza virus non-structural protein NS1: interferon antagonism and beyond. J Gen Virol 2014; 95:2594-2611. [PMID: 25182164 DOI: 10.1099/vir.0.069542-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Most viruses express one or several proteins that counter the antiviral defences of the host cell. This is the task of non-structural protein NS1 in influenza viruses. Absent in the viral particle, but highly expressed in the infected cell, NS1 dramatically inhibits cellular gene expression and prevents the activation of key players in the IFN system. In addition, NS1 selectively enhances the translation of viral mRNAs and may regulate the synthesis of viral RNAs. Our knowledge of the virus and of NS1 has increased dramatically during the last 15 years. The atomic structure of NS1 has been determined, many cellular partners have been identified and its multiple activities have been studied in depth. This review presents our current knowledge, and attempts to establish relationships between the RNA sequence, the structure of the protein, its ligands, its activities and the pathogenicity of the virus. A better understanding of NS1 could help in elaborating novel antiviral strategies, based on either live vaccines with altered NS1 or on small-compound inhibitors of NS1.
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Affiliation(s)
- Daniel Marc
- Université François Rabelais, UMR1282 Infectiologie et Santé Publique, 37000 Tours, France.,Pathologie et Immunologie Aviaire, INRA, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
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48
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Abstract
During infection, the influenza A virus non-structural protein 1 (NS1) interacts with a diverse range of viral and cellular factors to antagonize host antiviral defences and promote viral replication. Here, I review the structural basis for some of these functions and discuss the emerging view that NS1 cannot simply be regarded as a 'static' protein with a single structure. Rather, the dynamic property of NS1 to adopt various quaternary conformations is critical for its multiple activities. Understanding NS1 plasticity, and the mechanisms governing this plasticity, will be essential for assessing both fundamental protein function and the consequences of strain-dependent polymorphisms in this important virulence factor.
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Affiliation(s)
- Benjamin G Hale
- MRC - University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow, G11 5JR, UK
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49
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Rand U, Hillebrand U, Sievers S, Willenberg S, Köster M, Hauser H, Wirth D. Uncoupling of the dynamics of host-pathogen interaction uncovers new mechanisms of viral interferon antagonism at the single-cell level. Nucleic Acids Res 2014; 42:e109. [PMID: 24895433 PMCID: PMC4117750 DOI: 10.1093/nar/gku492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Antiviral defence in mammals is mediated through type-I interferons (IFNs). Viruses antagonise this process through expression of IFN antagonist proteins (IAPs). Understanding and modelling of viral escape mechanisms and the dynamics of IAP action has the potential to facilitate the development of specific and safe drugs. Here, we describe the dynamics of interference by selected viral IAPs, NS1 from Influenza A virus and NS3/4A from Hepatitis C virus. We used Tet-inducible IAP gene expression to uncouple this process from virus-driven dynamics. Stochastic activation of the IFN-β gene required the use of single-cell live imaging to define the efficacy of the inhibitors during the virus-induced signalling processes. We found significant correlation between the onset of IAP expression and halted IFN-β expression in cells where IFN-β induction had already occurred. These data indicate that IAPs not only prevent antiviral signalling prior to IFN-β induction, but can also stop the antiviral response even after it has been activated. We found reduced NF-κB activation to be the underlying mechanism by which activated IFN expression can be blocked. This work demonstrates a new mechanism by which viruses can antagonise the IFN response.
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Affiliation(s)
- Ulfert Rand
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Upneet Hillebrand
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Stephanie Sievers
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Steffi Willenberg
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Mario Köster
- Gene Regulation and Differentiation, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Hansjörg Hauser
- Gene Regulation and Differentiation, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Dagmar Wirth
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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50
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The PDZ-binding motif of the avian NS1 protein affects transmission of the 2009 influenza A(H1N1) virus. Biochem Biophys Res Commun 2014; 449:19-25. [DOI: 10.1016/j.bbrc.2014.04.132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 04/25/2014] [Indexed: 11/19/2022]
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