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Din GU, Hasham K, Amjad MN, Hu Y. Natural History of Influenza B Virus-Current Knowledge on Treatment, Resistance and Therapeutic Options. Curr Issues Mol Biol 2023; 46:183-199. [PMID: 38248316 PMCID: PMC10814056 DOI: 10.3390/cimb46010014] [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: 10/23/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Influenza B virus (IBV) significantly impacts the health and the economy of the global population. WHO global health estimates project 1 billion flu cases annually, with 3 to 5 million resulting in severe disease and 0.3 to 0.5 million influenza-related deaths worldwide. Influenza B virus epidemics result in significant economic losses due to healthcare expenses, reduced workforce productivity, and strain on healthcare systems. Influenza B virus epidemics, such as the 1987-1988 Yamagata lineage outbreak and the 2001-2002 Victoria lineage outbreak, had a significant global impact. IBV's fast mutation and replication rates facilitate rapid adaptation to the environment, enabling the evasion of existing immunity and the development of resistance to virus-targeting treatments. This leads to annual outbreaks and necessitates the development of new vaccination formulations. This review aims to elucidate IBV's evolutionary genomic organization and life cycle and provide an overview of anti-IBV drugs, resistance, treatment options, and prospects for IBV biology, emphasizing challenges in preventing and treating IBV infection.
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Affiliation(s)
- Ghayyas Ud Din
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, No. 320 Yueyang Road, Shanghai 200031, China; (G.U.D.)
- University of Chinese Academy of Sciences, Beijing 100040, China
| | - Kinza Hasham
- Sundas Molecular Analysis Center, Sundas Foundation Gujranwala Punjab Pakistan, Gujranwala 50250, Pakistan
| | - Muhammad Nabeel Amjad
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, No. 320 Yueyang Road, Shanghai 200031, China; (G.U.D.)
- University of Chinese Academy of Sciences, Beijing 100040, China
| | - Yihong Hu
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, No. 320 Yueyang Road, Shanghai 200031, China; (G.U.D.)
- University of Chinese Academy of Sciences, Beijing 100040, China
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2
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Kedia N, Banerjee S, Mondal A. A Comprehensive Roadmap Towards the Generation of an Influenza B Reporter Assay Using a Single DNA Polymerase-Based Cloning of the Reporter RNA Construct. Front Microbiol 2022; 13:868367. [PMID: 35694292 PMCID: PMC9174941 DOI: 10.3389/fmicb.2022.868367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
The mini-genome reporter assay is a key tool for conducting RNA virus research. However, procedural complications and the lack of adequate literature pose a major challenge in developing these assay systems. Here, we present a novel, yet generic and simple, cloning strategy for the construction of an influenza B virus reporter RNA template and describe an extensive standardization of the reporter RNP/polymerase activity assay for monitoring viral RNA synthesis in an infection-free setting. Using this assay system, we showed for the first time the effect of viral protein NS1 and host protein kinase C delta (PKCD) on influenza B virus RNA synthesis. In addition, the assay system showed promising results in evaluating the efficacy of antiviral drugs targeting viral RNA synthesis and virus propagation. Together, this work offers a detailed protocol for the standardization of the influenza virus minigenome assay and an excellent tool for screening of host factors and antivirals in a fast, user-friendly, and high-throughput manner.
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3
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Chen W, Shao J, Ying Z, Du Y, Yu Y. Approaches for discovery of small-molecular antivirals targeting to influenza A virus PB2 subunit. Drug Discov Today 2022; 27:1545-1553. [PMID: 35247593 DOI: 10.1016/j.drudis.2022.02.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 11/03/2022]
Abstract
Influenza is an acute respiratory infectious disease caused by influenza virus, leading to huge morbidity and mortality in humans worldwide. Despite the availability of antivirals in the clinic, the emergence of resistant strains calls for antivirals with novel mechanisms of action. The PB2 subunit of the influenza A virus polymerase is a promising target because of its vital role in the 'cap-snatching' mechanism. In this review, we summarize the technologies and medicinal chemistry strategies for hit identification, hit-to-lead and lead-to-candidate optimization, and current challenges in PB2 inhibitor development, as well as offering insights for the fight against drug resistance.
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Affiliation(s)
- Wenteng Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Jiaan Shao
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, China
| | - Zhimin Ying
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yushen Du
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China(1)
| | - Yongping Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
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4
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Staller E, Barclay WS. Host Cell Factors That Interact with Influenza Virus Ribonucleoproteins. Cold Spring Harb Perspect Med 2021; 11:a038307. [PMID: 32988980 PMCID: PMC8559542 DOI: 10.1101/cshperspect.a038307] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Influenza viruses hijack host cell factors at each stage of the viral life cycle. After host cell entry and endosomal escape, the influenza viral ribonucleoproteins (vRNPs) are released into the cytoplasm where the classical cellular nuclear import pathway is usurped for nuclear translocation of the vRNPs. Transcription takes place inside the nucleus at active host transcription sites, and cellular mRNA export pathways are subverted for export of viral mRNAs. Newly synthesized RNP components cycle back into the nucleus using various cellular nuclear import pathways and host-encoded chaperones. Replication of the negative-sense viral RNA (vRNA) into complementary RNA (cRNA) and back into vRNA requires complex interplay between viral and host factors. Progeny vRNPs assemble at the host chromatin and subsequently exit from the nucleus-processes orchestrated by sets of host and viral proteins. Finally, several host pathways appear to play a role in vRNP trafficking from the nuclear envelope to the plasma membrane for egress.
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Affiliation(s)
- Ecco Staller
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
| | - Wendy S Barclay
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
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5
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Kasprzyk R, Jemielity J. Enzymatic Assays to Explore Viral mRNA Capping Machinery. Chembiochem 2021; 22:3236-3253. [PMID: 34291555 PMCID: PMC8426721 DOI: 10.1002/cbic.202100291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/21/2021] [Indexed: 12/25/2022]
Abstract
In eukaryotes, mRNA is modified by the addition of the 7-methylguanosine (m7 G) 5' cap to protect mRNA from premature degradation, thereby enhancing translation and enabling differentiation between self (endogenous) and non-self RNAs (e. g., viral ones). Viruses often develop their own mRNA capping pathways to augment the expression of their proteins and escape host innate immune response. Insights into this capping system may provide new ideas for therapeutic interventions and facilitate drug discovery, e. g., against viruses that cause pandemic outbreaks, such as beta-coronaviruses SARS-CoV (2002), MARS-CoV (2012), and the most recent SARS-CoV-2. Thus, proper methods for the screening of large compound libraries are required to identify lead structures that could serve as a basis for rational antiviral drug design. This review summarizes the methods that allow the monitoring of the activity and inhibition of enzymes involved in mRNA capping.
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Affiliation(s)
- Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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6
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Takashita E. Influenza Polymerase Inhibitors: Mechanisms of Action and Resistance. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038687. [PMID: 32122918 PMCID: PMC8091960 DOI: 10.1101/cshperspect.a038687] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The influenza virus RNA-dependent RNA polymerase is highly conserved among influenza A, B, C, and D viruses. It comprises three subunits: polymerase basic protein 1 (PB1), polymerase basic protein 2 (PB2), and polymerase acidic protein (PA) in influenza A and B viruses or polymerase 3 protein (P3) in influenza C and D viruses. Because this polymerase is essential for influenza virus replication, it has been considered as a target for antiviral agents. Recently, several polymerase inhibitors that target each subunit have been developed. This review discusses the mechanism of action, antiviral activity, and emergence of resistance to three inhibitors approved for the treatment of influenza or in late-phase clinical trials: the PB1 inhibitor favipiravir, the PB2 inhibitor pimodivir, and the PA inhibitor baloxavir marboxil.
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Affiliation(s)
- Emi Takashita
- Influenza Virus Research Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan
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7
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Krischuns T, Lukarska M, Naffakh N, Cusack S. Influenza Virus RNA-Dependent RNA Polymerase and the Host Transcriptional Apparatus. Annu Rev Biochem 2021; 90:321-348. [PMID: 33770447 DOI: 10.1146/annurev-biochem-072820-100645] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Influenza virus RNA-dependent RNA polymerase (FluPol) transcribes the viral RNA genome in the infected cell nucleus. In the 1970s, researchers showed that viral transcription depends on host RNA polymerase II (RNAP II) activity and subsequently that FluPol snatches capped oligomers from nascent RNAP II transcripts to prime its own transcription. Exactly how this occurs remains elusive. Here, we review recent advances in the mechanistic understanding of FluPol transcription and early events in RNAP II transcription that are relevant to cap-snatching. We describe the known direct interactions between FluPol and the RNAP II C-terminal domain and summarize the transcription-related host factors that have been found to interact with FluPol. We also discuss open questions regarding how FluPol may be targeted to actively transcribing RNAP II and the exact context and timing of cap-snatching, which is presumed to occur after cap completion but before the cap is sequestered by the nuclear cap-binding complex.
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Affiliation(s)
- Tim Krischuns
- Unité Biologie des ARN et Virus Influenza, Département de Virologie, Institut Pasteur, CNRS UMR 3569, F-75015 Paris, France; ,
| | - Maria Lukarska
- European Molecular Biology Laboratory, 38042 Grenoble CEDEX 9, France; .,Current affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA;
| | - Nadia Naffakh
- Unité Biologie des ARN et Virus Influenza, Département de Virologie, Institut Pasteur, CNRS UMR 3569, F-75015 Paris, France; ,
| | - Stephen Cusack
- European Molecular Biology Laboratory, 38042 Grenoble CEDEX 9, France;
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8
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CMTR1-Catalyzed 2'-O-Ribose Methylation Controls Neuronal Development by Regulating Camk2α Expression Independent of RIG-I Signaling. Cell Rep 2020; 33:108269. [PMID: 33086056 PMCID: PMC7574844 DOI: 10.1016/j.celrep.2020.108269] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/10/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic mRNAs are 5′ end capped with a 7-methylguanosine, which is important for processing and translation of mRNAs. Cap methyltransferase 1 (CMTR1) catalyzes 2′-O-ribose methylation of the first transcribed nucleotide (N1 2′-O-Me) to mask mRNAs from innate immune surveillance by retinoic-acid-inducible gene-I (RIG-I). Nevertheless, whether this modification regulates gene expression for neuronal functions remains unexplored. Here, we find that knockdown of CMTR1 impairs dendrite development independent of secretory cytokines and RIG-I signaling. Using transcriptomic analyses, we identify altered gene expression related to dendrite morphogenesis instead of RIG-I-activated interferon signaling, such as decreased calcium/calmodulin-dependent protein kinase 2α (Camk2α). In line with these molecular changes, dendritic complexity in CMTR1-insufficient neurons is rescued by ectopic expression of CaMK2α but not by inactivation of RIG-I signaling. We further generate brain-specific CMTR1-knockout mice to validate these findings in vivo. Our study reveals the indispensable role of CMTR1-catalyzed N1 2′-O-Me in gene regulation for brain development. Every mRNA molecule in neurons is N1 2′-O methylated by CMTR1 CMTR1 is essential for neuromorphogenesis and brain development CMTR1 deficiency does not activate RIG-I and interferon signaling CMTR1 promotes Camk2α expression to support dendrite development
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9
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Li B, Clohisey SM, Chia BS, Wang B, Cui A, Eisenhaure T, Schweitzer LD, Hoover P, Parkinson NJ, Nachshon A, Smith N, Regan T, Farr D, Gutmann MU, Bukhari SI, Law A, Sangesland M, Gat-Viks I, Digard P, Vasudevan S, Lingwood D, Dockrell DH, Doench JG, Baillie JK, Hacohen N. Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection. Nat Commun 2020; 11:164. [PMID: 31919360 PMCID: PMC6952391 DOI: 10.1038/s41467-019-13965-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
Host dependency factors that are required for influenza A virus infection may serve as therapeutic targets as the virus is less likely to bypass them under drug-mediated selection pressure. Previous attempts to identify host factors have produced largely divergent results, with few overlapping hits across different studies. Here, we perform a genome-wide CRISPR/Cas9 screen and devise a new approach, meta-analysis by information content (MAIC) to systematically combine our results with prior evidence for influenza host factors. MAIC out-performs other meta-analysis methods when using our CRISPR screen as validation data. We validate the host factors, WDR7, CCDC115 and TMEM199, demonstrating that these genes are essential for viral entry and regulation of V-type ATPase assembly. We also find that CMTR1, a human mRNA cap methyltransferase, is required for efficient viral cap snatching and regulation of a cell autonomous immune response, and provides synergistic protection with the influenza endonuclease inhibitor Xofluza. Here, Li et al. perform a genome-wide CRISPR screen to identify host dependency factors for influenza A virus infection and show that the host mRNA cap methyltransferase CMTR1 is important for viral cap snatching and that it affects expression of antiviral genes.
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Affiliation(s)
- Bo Li
- Harvard University Virology Program, Harvfvard Medical School, Boston, MA02142, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Sara M Clohisey
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Bing Shao Chia
- Harvard University Virology Program, Harvfvard Medical School, Boston, MA02142, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Ang Cui
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - Thomas Eisenhaure
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | | | - Paul Hoover
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | | | - Aharon Nachshon
- School of Molecular Cell Biology and Biotechnology, Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nikki Smith
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Tim Regan
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - David Farr
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Michael U Gutmann
- School of informatics, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | - Syed Irfan Bukhari
- Center for Cancer Research, Massachusetts General hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew Law
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - Irit Gat-Viks
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,School of Molecular Cell Biology and Biotechnology, Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Paul Digard
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Shobha Vasudevan
- Center for Cancer Research, Massachusetts General hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - David H Dockrell
- MRC Center for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - John G Doench
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK. .,Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, EH16 5SA, UK.
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA. .,Massachusetts General Hospital Cancer Center, Boston, MA, 02129, USA.
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10
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Flupyranochromene, a novel inhibitor of influenza virus cap-dependent endonuclease, from Penicillium sp. f28743. J Antibiot (Tokyo) 2019; 72:125-133. [DOI: 10.1038/s41429-018-0134-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/12/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022]
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11
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Pham PTV, Turan K, Nagata K, Kawaguchi A. Biochemical characterization of avian influenza viral polymerase containing PA or PB2 subunit from human influenza A virus. Microbes Infect 2018; 20:353-359. [PMID: 29729434 DOI: 10.1016/j.micinf.2018.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 01/17/2023]
Abstract
Adaptive mutations in viral polymerase, which is composed of PB1, PB2, and PA, of avian influenza viruses are major genetic determinants of the host range. In this study, to elucidate the molecular mechanism of mammalian adaptation of avian viral polymerase, we performed cell-based vRNP reconstitution assays and biochemical analyses using purified recombinant viral polymerase complexes. We found that avian viral polymerase from A/duck/Pennsylvania/10,218/84 (DkPen) enhances the viral polymerase activity in mammalian cells by replacing the PA or PB2 gene with that from human influenza virus A/WSN/33 (WSN). Chimeric constructs between DkPen PA and WSN PA showed that the N-terminal endonuclease domain of WSN PA was essential for the mammalian adaptation of DkPen viral polymerase. We also found that the cap-snatching activity of purified DkPen viral polymerase was more than 5 times weaker than that of WSN in vitro in a PB2 Glu627-dependent manner. However, the cap-snatching activity of DkPen viral polymerase was hardly increased by replacing DkPen PA to WSN PA. These results suggest that the activity of viral genome replication may be enhanced in the DkPen reassortant containing WSN PA.
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Affiliation(s)
- Phu Tran Vinh Pham
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kadir Turan
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Kawaguchi
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan; Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.
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12
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Abstract
Influenza is a negative-sense single-stranded RNA virus with segmented genome. Each segment is encapsidated by a ribonucleoprotein (RNP) complex composed of RNA-dependent RNA polymerase (RdRP) and multiple copies of nucleoprotein (NP). The RNP complex plays a crucial role in viral life cycle, supporting and regulating transcription and replication of viral genome in infected cells. The structural characterization of RdRP and RNP in recent years has shed light on its functions and mechanism of action. In this review, we summarize current understanding on the structure of RNP complex, as well as the structure of each subunit. Crucial functions of RNP are also discussed.
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Affiliation(s)
- Chun-Yeung Lo
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China
| | - Yun-Sang Tang
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China
| | - Pang-Chui Shaw
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China.
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13
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Development of an Alternative Modified Live Influenza B Virus Vaccine. J Virol 2017; 91:JVI.00056-17. [PMID: 28381580 PMCID: PMC5446642 DOI: 10.1128/jvi.00056-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/31/2017] [Indexed: 12/27/2022] Open
Abstract
Influenza B virus (IBV) is considered a major human pathogen, responsible for seasonal epidemics of acute respiratory illness. Two antigenically distinct IBV hemagglutinin (HA) lineages cocirculate worldwide with little cross-reactivity. Live attenuated influenza virus (LAIV) vaccines have been shown to provide better cross-protective immune responses than inactivated vaccines by eliciting local mucosal immunity and systemic B cell- and T cell-mediated memory responses. We have shown previously that incorporation of temperature-sensitive (ts) mutations into the PB1 and PB2 subunits along with a modified HA epitope tag in the C terminus of PB1 resulted in influenza A viruses (IAV) that are safe and effective as modified live attenuated (att) virus vaccines (IAV att). We explored whether analogous mutations in the IBV polymerase subunits would result in a stable virus with an att phenotype. The PB1 subunit of the influenza B/Brisbane/60/2008 strain was used to incorporate ts mutations and a C-terminal HA tag. Such modifications resulted in a B/Bris att strain with ts characteristics in vitro and an att phenotype in vivo Vaccination studies in mice showed that a single dose of the B/Bris att candidate stimulated sterilizing immunity against lethal homologous challenge and complete protection against heterologous challenge. These studies show the potential of an alternative LAIV platform for the development of IBV vaccines.IMPORTANCE A number of issues with regard to the effectiveness of the LAIV vaccine licensed in the United States (FluMist) have arisen over the past three seasons (2013-2014, 2014-2015, and 2015-2016). While the reasons for the limited robustness of the vaccine-elicited immune response remain controversial, this problem highlights the critical importance of continued investment in LAIV development and creates an opportunity to improve current strategies so as to develop more efficacious vaccines. Our laboratory has developed an alternative strategy, the incorporation of 2 amino acid mutations and a modified HA tag at the C terminus of PB1, which is sufficient to attenuate the IBV. As a LAIV, this novel vaccine provides complete protection against IBV strains. The availability of attenuated IAV and IBV backbones based on contemporary strains offers alternative platforms for the development of LAIVs that may overcome current limitations.
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14
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Stevaert A, Naesens L. The Influenza Virus Polymerase Complex: An Update on Its Structure, Functions, and Significance for Antiviral Drug Design. Med Res Rev 2016; 36:1127-1173. [PMID: 27569399 PMCID: PMC5108440 DOI: 10.1002/med.21401] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/18/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]
Abstract
Influenza viruses cause seasonal epidemics and pandemic outbreaks associated with significant morbidity and mortality, and a huge cost. Since resistance to the existing anti‐influenza drugs is rising, innovative inhibitors with a different mode of action are urgently needed. The influenza polymerase complex is widely recognized as a key drug target, given its critical role in virus replication and high degree of conservation among influenza A (of human or zoonotic origin) and B viruses. We here review the major progress that has been made in recent years in unravelling the structure and functions of this protein complex, enabling structure‐aided drug design toward the core regions of the PA endonuclease, PB1 polymerase, or cap‐binding PB2 subunit. Alternatively, inhibitors may target a protein–protein interaction site, a cellular factor involved in viral RNA synthesis, the viral RNA itself, or the nucleoprotein component of the viral ribonucleoprotein. The latest advances made for these diverse pharmacological targets have yielded agents in advanced (i.e., favipiravir and VX‐787) or early clinical testing, besides several experimental inhibitors in various stages of development, which are all covered here.
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Affiliation(s)
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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15
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Naesens L, Stevaert A, Vanderlinden E. Antiviral therapies on the horizon for influenza. Curr Opin Pharmacol 2016; 30:106-115. [PMID: 27570127 DOI: 10.1016/j.coph.2016.08.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 01/12/2023]
Abstract
Adequate response to severe influenza infections or pandemic outbreaks requires two complementary strategies: preventive vaccination and antiviral therapy. The existing influenza drugs, M2 blockers and neuraminidase inhibitors, show modest clinical efficacy and established or potential resistance. In the past three years, several new agents have entered the clinical pipeline and already yielded some promising data from Phase 2 trials. For two main categories, that is, the broadly neutralizing anti-hemagglutinin antibodies and small-molecule inhibitors of the viral polymerase complex, crystallography was instrumental to guide drug development. These structural insights also aid to expand the activity spectrum towards influenza A plus B viruses, or conceive nucleoprotein or polymerase assembly inhibitors. The practice of influenza therapy should radically change in the next decade.
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Affiliation(s)
- Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
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16
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Charyasriwong S, Haruyama T, Kobayashi N. In vitro evaluation of the antiviral activity of methylglyoxal against influenza B virus infection. Drug Discov Ther 2016; 10:201-10. [PMID: 27558282 DOI: 10.5582/ddt.2016.01045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Influenza A and B virus infections are serious public health concerns globally. However, the concerns regarding influenza B infection have been underestimated. The currently used anti-influenza drugs have not provided equal efficacy for both influenza A and B viruses. Susceptibility to neuraminidase (NA) inhibitors has been observed to be lower for influenza B viruses than for influenza A viruses. Moreover, the emergence of resistance to anti-influenza drugs underscores the need to develop new drugs. Recently, we reported that methylglyoxal (MGO) suppressed influenza A virus replication in a strain-independent manner. Therefore, we hypothesize that MGO exhibits anti-influenza activity against B strains. This study aimed to evaluate the anti-influenza viral activity of MGO against influenza B strains by using Madin-Darby canine kidney (MDCK) cells. Several types of influenza B viruses were used to determine the activity of MGO. The susceptibilities of influenza A and B viruses to NA inhibitors were compared. MGO inhibited influenza B virus replication, with 50% inhibitory concentrations ranging from 23-140 μM, which indicated greater sensitivity of influenza B viruses than influenza A viruses. Our results show that MGO has potent inhibitory activity against influenza B viruses, including NA inhibitor-resistant strains.
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Affiliation(s)
- Siriwan Charyasriwong
- Laboratory of Molecular Biology of Infectious Agents, Graduate School of Biomedical Sciences, Nagasaki University
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17
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To KKW, Mok KY, Chan ASF, Cheung NN, Wang P, Lui YM, Chan JFW, Chen H, Chan KH, Kao RYT, Yuen KY. Mycophenolic acid, an immunomodulator, has potent and broad-spectrum in vitro antiviral activity against pandemic, seasonal and avian influenza viruses affecting humans. J Gen Virol 2016; 97:1807-1817. [PMID: 27259985 DOI: 10.1099/jgv.0.000512] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Immunomodulators have been shown to improve the outcome of severe pneumonia. We have previously shown that mycophenolic acid (MPA), an immunomodulator, has antiviral activity against influenza A/WSN/1933(H1N1) using a high-throughput chemical screening assay. This study further investigated the antiviral activity and mechanism of action of MPA against contemporary clinical isolates of influenza A and B viruses. The 50 % cellular cytotoxicity (CC50) of MPA in Madin Darby canine kidney cell line was over 50 µM. MPA prevented influenza virus-induced cell death in the cell-protection assay, with significantly lower IC50 for influenza B virus B/411 than that of influenza A(H1N1)pdm09 virus H1/415 (0.208 vs 1.510 µM, P=0.0001). For H1/415, MPA interfered with the early stage of viral replication before protein synthesis. For B/411, MPA may also act at a later stage since MPA was active against B/411 even when added 12 h post-infection. Virus-yield reduction assay showed that the replication of B/411 was completely inhibited by MPA at concentrations ≥0.78 µM, while there was a dose-dependent reduction of viral titer for H1/415. The antiviral effect of MPA was completely reverted by guanosine supplementation. Plaque reduction assay showed that MPA had antiviral activity against eight different clinical isolates of A(H1N1), A(H3N2), A(H7N9) and influenza B viruses (IC50 <1 µM). In summary, MPA has broad-spectrum antiviral activity against human and avian-origin influenza viruses, in addition to its immunomodulatory activity. Together with a high chemotherapeutic index, the use of MPA as an antiviral agent should be further investigated in vivo.
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Affiliation(s)
- Kelvin K W To
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Ka-Yi Mok
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Andy S F Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Nam N Cheung
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Pui Wang
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Yin-Ming Lui
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Jasper F W Chan
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Honglin Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, P. R. China.,Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Kwok-Hung Chan
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Richard Y T Kao
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Kwok-Yung Yuen
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, P. R. China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
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18
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Koutsakos M, Nguyen THO, Barclay WS, Kedzierska K. Knowns and unknowns of influenza B viruses. Future Microbiol 2015; 11:119-35. [PMID: 26684590 DOI: 10.2217/fmb.15.120] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Influenza B viruses (IBVs) circulate annually along with influenza A (IAV) strains during seasonal epidemics. IBV can dominate influenza seasons and cause severe disease, particularly in children and adolescents. Research has revealed interesting aspects of IBV and highlighted the importance of these viruses in clinical settings. Yet, many important questions remain unanswered. In this review, the clinical relevance of IBV is emphasized, unique features in epidemiology, host range and virology are highlighted and gaps in knowledge pinpointed. Multiple aspects of IBV epidemiology, evolution, virology and immunology are discussed. Future research into IBV is needed to understand how we can prevent severe disease in high-risk groups, especially children and elderly.
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Affiliation(s)
- Marios Koutsakos
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Parkville VIC 3010, Australia
| | - Thi H O Nguyen
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Parkville VIC 3010, Australia
| | - Wendy S Barclay
- Section of Virology, Faculty of Medicine, Wright Fleming Institute, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Katherine Kedzierska
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Parkville VIC 3010, Australia
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19
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Xie L, Wartchow C, Shia S, Uehara K, Steffek M, Warne R, Sutton J, Muiru GT, Leonard VHJ, Bussiere DE, Ma X. Molecular Basis of mRNA Cap Recognition by Influenza B Polymerase PB2 Subunit. J Biol Chem 2015; 291:363-70. [PMID: 26559973 DOI: 10.1074/jbc.m115.693051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 01/08/2023] Open
Abstract
Influenza virus polymerase catalyzes the transcription of viral mRNAs by a process known as "cap-snatching," where the 5'-cap of cellular pre-mRNA is recognized by the PB2 subunit and cleaved 10-13 nucleotides downstream of the cap by the endonuclease PA subunit. Although this mechanism is common to both influenza A (FluA) and influenza B (FluB) viruses, FluB PB2 recognizes a wider range of cap structures including m(7)GpppGm-, m(7)GpppG-, and GpppG-RNA, whereas FluA PB2 utilizes methylated G-capped RNA specifically. Biophysical studies with isolated PB2 cap-binding domain (PB2(cap)) confirm that FluB PB2 has expanded mRNA cap recognition capability, although the affinities toward m(7)GTP are significantly reduced when compared with FluA PB2. The x-ray co-structures of the FluB PB2(cap) with bound cap analogs m(7)GTP and GTP reveal an inverted GTP binding mode that is distinct from the cognate m(7)GTP binding mode shared between FluA and FluB PB2. These results delineate the commonalities and differences in the cap-binding site between FluA and FluB PB2 and will aid structure-guided drug design efforts to identify dual inhibitors of both FluA and FluB PB2.
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Affiliation(s)
- Lili Xie
- From the Divisions of Protein Sciences
| | - Charles Wartchow
- Structural and Biophysical Chemistry, Global Discovery Chemistry
| | - Steven Shia
- Structural and Biophysical Chemistry, Global Discovery Chemistry
| | | | - Micah Steffek
- Structural and Biophysical Chemistry, Global Discovery Chemistry
| | | | | | - Gladys T Muiru
- Virology, Novartis Institutes for BioMedical Research, Emeryville, California 94608-2916
| | - Vincent H J Leonard
- Virology, Novartis Institutes for BioMedical Research, Emeryville, California 94608-2916
| | | | - Xiaolei Ma
- Structural and Biophysical Chemistry, Global Discovery Chemistry,
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20
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van de Sandt CE, Bodewes R, Rimmelzwaan GF, de Vries RD. Influenza B viruses: not to be discounted. Future Microbiol 2015; 10:1447-65. [PMID: 26357957 DOI: 10.2217/fmb.15.65] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In contrast to influenza A viruses, which have been investigated extensively, influenza B viruses have attracted relatively little attention. However, influenza B viruses are an important cause of morbidity and mortality in the human population and full understanding of their biological and epidemiological properties is imperative to better control this important pathogen. However, some of its characteristics are still elusive and warrant investigation. Here, we review evolution, epidemiology, pathogenesis and immunity and identify gaps in our knowledge of influenza B viruses. The divergence of two antigenically distinct influenza B viruses is highlighted. The co-circulation of viruses of these two lineages necessitated the development of quadrivalent influenza vaccines, which is discussed in addition to possibilities to develop universal vaccination strategies.
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Affiliation(s)
- Carolien E van de Sandt
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Guus F Rimmelzwaan
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,ViroClinics Biosciences BV, Rotterdam Science Tower, Marconistraat 16, 3029 AK Rotterdam, The Netherlands
| | - Rory D de Vries
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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21
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Wei K, Liu X. Phylogenetic Analysis and Functional Characterization of the Influenza A H5N1 PB2 Gene. Transbound Emerg Dis 2015; 64:374-388. [PMID: 25990872 DOI: 10.1111/tbed.12376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Indexed: 12/23/2022]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 viruses are endemic in poultry and cause continued inter-species transmission to human in Asia, such as China and Vietnam, leading to pandemic concerns and socio-economic challenges. Phylogenetic analysis of H5N1 viruses isolated from China and Vietnam during 2001-2012 showed that several geographically distinct sublineages have become established in these two countries. Subsequently, we reassigned HPAI H5N1 viruses into three distinct groups to reveal the intrasubtype reassortment. Apart from six reassortants detected here, we found that several viral strains showed signals for homologous recombination within PB2 and PB1 genes, suggestive of the fluidity of the H5N1 virus gene pool. Furthermore, sequenced-based analyses revealed that the viral polymerase displayed a higher level of genetic polymorphism but associated with lower substitution rate when compared with those of other gene segments. In addition, the selection pressure analysis indicated that purifying selection was predominant in eight genomic segments especially in the polymerase complex. However, the site-by-site analysis helped to detect 14 positively selected sites in the PB1, PA, HA, NA, MP and NS proteins. Despite the fact that PB2 protein of H5N1 viruses was highly conserved at the amino acid level, eleven adaptive mutations were still observed in the protein. Further comparative structural analysis of the K627E mutation indicated that there were no structural differences between the variants, which possessed either PB2-627E or PB2-627K. Transcriptomic analysis suggested the non-mitochondrial PB2 protein of H5N1 virus that forms a stable complex with the mitochondrial antiviral signalling protein (MAVS, also known as IPS-1, VISA or Cardif) can induce interferon-beta (IFN-β) expression, but the substitution (PB2-K627E) is not the sole determinant of the RIG-I-like receptors (RLR) signalling components induction in Calu-3 cells.
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Affiliation(s)
- K Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - X Liu
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
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22
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Liu Y, Yang Y, Fan J, He R, Luo M, Zheng X. The crystal structure of the PB2 cap-binding domain of influenza B virus reveals a novel cap recognition mechanism. J Biol Chem 2015; 290:9141-9. [PMID: 25691568 DOI: 10.1074/jbc.m115.636464] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 12/17/2022] Open
Abstract
The influenza RNA-dependent RNA polymerase is a core enzyme required for both transcription and replication of the virus RNA genome, making it a potential drug target for the influenza virus. To detect the feature of cap-dependent transcription of influenza B virus (FluB) polymerase, we determined the crystal structures of the wild-type FluB polymerase PB2 subunit cap-binding domain (PB2cap) with bound GDP and the mutant FluB Q325F PB2cap with bound m(7)GDP or GDP. These structures revealed that, distinct from influenza A virus (FluA) PB2cap, the guanine and ribose moieties of substrates invert in FluB PB2caps. Moreover, we characterized the substrate specificity and affinity of the PB2caps using isothermal titration calorimetry. FluB PB2cap has a weaker affinity for m(7)GDP than FluA PB2cap. Unlike FluA PB2cap that has a preference for m(7)GDP in comparison with GDP, FluB PB2cap shows an analogous affinity for both substrates. Replacement of FluB PB2 Glu(325) by Phe, the corresponding residue of FluA PB2, increased the binding affinity of FluB PB2cap for m(7)GDP to a level approximate to that of FluA PB2cap and caused a significant higher affinity to GDP. This study indicated that FluB PB2cap has a unique cap recognition mechanism compared with FluA PB2cap, providing molecular insight into inhibitor design targeting FluB PB2cap.
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Affiliation(s)
- Yong Liu
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
| | - Yongfeng Yang
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
| | - Jialin Fan
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
| | - Ruina He
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302
| | - Xiaofeng Zheng
- From the State Key Lab of Protein and Plant Gene Research and Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China and
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23
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Stevaert A, Nurra S, Pala N, Carcelli M, Rogolino D, Shepard C, Domaoal RA, Kim B, Alfonso-Prieto M, Marras SAE, Sechi M, Naesens L. An integrated biological approach to guide the development of metal-chelating inhibitors of influenza virus PA endonuclease. Mol Pharmacol 2015; 87:323-37. [PMID: 25477342 PMCID: PMC11037440 DOI: 10.1124/mol.114.095588] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/04/2014] [Indexed: 04/26/2024] Open
Abstract
The influenza virus PA endonuclease, which cleaves capped cellular pre-mRNAs to prime viral mRNA synthesis, is a promising target for novel anti-influenza virus therapeutics. The catalytic center of this enzyme resides in the N-terminal part of PA (PA-Nter) and contains two (or possibly one or three) Mg(2+) or Mn(2+) ions, which are critical for its catalytic function. There is great interest in PA inhibitors that are optimally designed to occupy the active site and chelate the metal ions. We focused here on a series of β-diketo acid (DKA) and DKA-bioisosteric compounds containing different scaffolds, and determined their structure-activity relationship in an enzymatic assay with PA-Nter, in order to build a three-dimensional pharmacophore model. In addition, we developed a molecular beacon (MB)-based PA-Nter assay that enabled us to compare the inhibition of Mn(2+) versus Mg(2+), the latter probably being the biologically relevant cofactor. This real-time MB assay allowed us to measure the enzyme kinetics of PA-Nter or perform high-throughput screening. Several DKA derivatives were found to cause strong inhibition of PA-Nter, with IC50 values comparable to that of the prototype L-742,001 (i.e., below 2 μM). Among the different compounds tested, L-742,001 appeared unique in having equal activity against either Mg(2+) or Mn(2+). Three compounds ( 10: , with a pyrrole scaffold, and 40: and 41: , with an indole scaffold) exhibited moderate antiviral activity in cell culture (EC99 values 64-95 μM) and were proven to affect viral RNA synthesis. Our approach of integrating complementary enzymatic, cellular, and mechanistic assays should guide ongoing development of improved influenza virus PA inhibitors.
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Affiliation(s)
- Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Salvatore Nurra
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Nicolino Pala
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mauro Carcelli
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Dominga Rogolino
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Caitlin Shepard
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Robert A Domaoal
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Baek Kim
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mercedes Alfonso-Prieto
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Salvatore A E Marras
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Mario Sechi
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium (A.S., L.N.); Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy (S.N., N.P., M.S.); Department of Chemistry, University of Parma, Parma, Italy (M.C., D.R.); Center for Drug Discovery, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia (C.S., R.D., B.K.); Department of Pharmacy, Kyung-Hee University, Seoul, South Korea (B.K.); Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania (M.A.P.); and Public Health Research Institute, Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey (S.M.)
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Reich S, Guilligay D, Pflug A, Malet H, Berger I, Crépin T, Hart D, Lunardi T, Nanao M, Ruigrok RWH, Cusack S. Structural insight into cap-snatching and RNA synthesis by influenza polymerase. Nature 2014; 516:361-6. [PMID: 25409151 DOI: 10.1038/nature14009] [Citation(s) in RCA: 328] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/29/2014] [Indexed: 12/11/2022]
Abstract
Influenza virus polymerase uses a capped primer, derived by 'cap-snatching' from host pre-messenger RNA, to transcribe its RNA genome into mRNA and a stuttering mechanism to generate the poly(A) tail. By contrast, genome replication is unprimed and generates exact full-length copies of the template. Here we use crystal structures of bat influenza A and human influenza B polymerases (FluA and FluB), bound to the viral RNA promoter, to give mechanistic insight into these distinct processes. In the FluA structure, a loop analogous to the priming loop of flavivirus polymerases suggests that influenza could initiate unprimed template replication by a similar mechanism. Comparing the FluA and FluB structures suggests that cap-snatching involves in situ rotation of the PB2 cap-binding domain to direct the capped primer first towards the endonuclease and then into the polymerase active site. The polymerase probably undergoes considerable conformational changes to convert the observed pre-initiation state into the active initiation and elongation states.
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Affiliation(s)
- Stefan Reich
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Delphine Guilligay
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Alexander Pflug
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Hélène Malet
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Imre Berger
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Thibaut Crépin
- University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Darren Hart
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Thomas Lunardi
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Max Nanao
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Rob W H Ruigrok
- University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Stephen Cusack
- 1] European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France [2] University Grenoble Alpes-Centre National de la Recherche Scientifique-EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
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An efficient screening system for influenza virus cap-dependent endonuclease inhibitors. J Virol Methods 2014; 202:8-14. [DOI: 10.1016/j.jviromet.2014.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 01/28/2014] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
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26
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Binh NT, Wakai C, Kawaguchi A, Nagata K. Involvement of the N-terminal portion of influenza virus RNA polymerase subunit PB1 in nucleotide recognition. Biochem Biophys Res Commun 2013; 443:975-9. [PMID: 24361882 DOI: 10.1016/j.bbrc.2013.12.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 12/14/2013] [Indexed: 02/07/2023]
Abstract
The influenza virus PB1 protein functions as a catalytic subunit of the viral RNA-dependent RNA polymerase and contains the highly conserved motifs of RNA-dependent RNA polymerases together with putative nucleotide-binding sites. PB1 also binds to viral genomic RNAs and its replicative intermediates through the promoter regions. The detail function and interplay between functional domains are not clarified although a part of structures and functions of PB1 have been clarified. In this study, we analyzed the function of PB1 subunit in the sense of nucleotide recognition using ribavirin, which is a nucleoside analog and inhibits viral RNA synthesis of many RNA viruses including influenza virus. We screened ribavirin-resistant PB1 mutants from randomly mutated PB1 cDNA library using a mini-replicon assay, and we identified a single mutation at the amino acid position 27 of PB1 as an important residue for the nucleotide recognition.
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Affiliation(s)
- Nguyen Trong Binh
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Chitose Wakai
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Kyosuke Nagata
- University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan.
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Wanitchang A, Narkpuk J, Jaru-ampornpan P, Jengarn J, Jongkaewwattana A. Inhibition of influenza A virus replication by influenza B virus nucleoprotein: an insight into interference between influenza A and B viruses. Virology 2012; 432:194-203. [PMID: 22770925 DOI: 10.1016/j.virol.2012.06.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 04/13/2012] [Accepted: 06/18/2012] [Indexed: 11/28/2022]
Abstract
Given that co-infection of cells with equivalent titers of influenza A and B viruses (FluA and FluB) has been shown to result in suppression of FluA growth, it is possible that FluB-specific proteins might hinder FluA polymerase activity and replication. We addressed this possibility by individually determining the effect of each gene of FluB on the FluA polymerase assay and found that the nucleoprotein of FluB (NP(FluB)) inhibits polymerase activity of FluA in a dose-dependent manner. Mutational analyses of NP(FluB) suggest that functional NP(FluB) is necessary for this inhibition. Slower growth of FluA was also observed in MDCK cells stably expressing NP(FluB). Further analysis of NP(FluB) indicated that it does not affect nuclear import of NP(FluA). Taken together, these findings suggest a novel role of NP(FluB) in inhibiting replication of FluA, providing more insights into the mechanism of interference between FluA and FluB and the lack of reassortants between them.
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Affiliation(s)
- Asawin Wanitchang
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand
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