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Bonneux B, Jacoby E, Ceconi M, Stobbelaar K, Delputte P, Herschke F. Direct-acting antivirals for RSV treatment, a review. Antiviral Res 2024; 229:105948. [PMID: 38972604 DOI: 10.1016/j.antiviral.2024.105948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024]
Abstract
Respiratory syncytial virus (RSV) causes respiratory disease and complications in infants, the elderly and the immunocompromised. While three vaccines and two prophylactic monoclonal antibodies are now available, only one antiviral, ribavirin, is currently approved for treatment. This review aims to summarize the current state of treatments directly targeting RSV. Two major viral processes are attractive for RSV-specific antiviral drug discovery and development as they play essential roles in the viral cycle: the entry/fusion process carried out by the fusion protein and the replication/transcription process carried out by the polymerase complex constituted of the L, P, N and M2-1 proteins. For each viral target resistance mutations to small molecules of different chemotypes seem to delineate definite binding pockets in the fusion proteins and in the large proteins. Elucidating the mechanism of action of these inhibitors thus helps to understand how the fusion and polymerase complexes execute their functions. While many inhibitors have been studied, few are currently in clinical development for RSV treatment: one is in phase III, three in phase II and two in phase I. Progression was halted for many others because of strategic decisions, low enrollment, safety, but also lack of efficacy. Lessons can be learnt from the halted programs to increase the success rate of the treatments currently in development.
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Affiliation(s)
- Brecht Bonneux
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsbaan 1, 2610, Wilrijk, Belgium; Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Edgar Jacoby
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Martina Ceconi
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsbaan 1, 2610, Wilrijk, Belgium
| | - Kim Stobbelaar
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsbaan 1, 2610, Wilrijk, Belgium.
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2
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Kleiner VA, Fearns R. How does the polymerase of non-segmented negative strand RNA viruses commit to transcription or genome replication? J Virol 2024; 98:e0033224. [PMID: 39078194 PMCID: PMC11334523 DOI: 10.1128/jvi.00332-24] [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] [Indexed: 07/31/2024] Open
Abstract
The Mononegavirales, or non-segmented negative-sense RNA viruses (nsNSVs), includes significant human pathogens, such as respiratory syncytial virus, parainfluenza virus, measles virus, Ebola virus, and rabies virus. Although these viruses differ widely in their pathogenic properties, they are united by each having a genome consisting of a single strand of negative-sense RNA. Consistent with their shared genome structure, the nsNSVs have evolved similar ways to transcribe their genome into mRNAs and replicate it to produce new genomes. Importantly, both mRNA transcription and genome replication are performed by a single virus-encoded polymerase. A fundamental and intriguing question is: how does the nsNSV polymerase commit to being either an mRNA transcriptase or a replicase? The polymerase must become committed to one process or the other either before it interacts with the genome template or in its initial interactions with the promoter sequence at the 3´ end of the genomic RNA. This review examines the biochemical, molecular biology, and structural biology data regarding the first steps of transcription and RNA replication that have been gathered over several decades for different families of nsNSVs. These findings are discussed in relation to possible models that could explain how an nsNSV polymerase initiates and commits to either transcription or genome replication.
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Affiliation(s)
- Victoria A. Kleiner
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
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3
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Li T, Liu M, Gu Z, Su X, Liu Y, Lin J, Zhang Y, Shen QT. Structures of the mumps virus polymerase complex via cryo-electron microscopy. Nat Commun 2024; 15:4189. [PMID: 38760379 PMCID: PMC11101452 DOI: 10.1038/s41467-024-48389-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 04/26/2024] [Indexed: 05/19/2024] Open
Abstract
The viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), while structures corresponding to these activities remain obscure. Here, we resolved two L-P complex conformations from the mumps virus (MuV), a typical member of nsNSVs, via cryogenic-electron microscopy. One conformation presents all five domains of L forming a continuous RNA tunnel to the methyltransferase domain (MTase), preferably as a transcription state. The other conformation has the appendage averaged out, which is inaccessible to MTase. In both conformations, parallel P tetramers are revealed around MuV L, which, together with structures of other nsNSVs, demonstrates the diverse origins of the L-binding X domain of P. Our study links varying structures of nsNSV polymerase complexes with genome replication and transcription and points to a sliding model for polymerase complexes to advance along the RNA templates.
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Affiliation(s)
- Tianhao Li
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Mingdong Liu
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhanxi Gu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xin Su
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Yunhui Liu
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qing-Tao Shen
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen, 518055, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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4
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Le Rouzic A, Fix J, Vinck R, Kappler-Gratias S, Volmer R, Gallardo F, Eléouët JF, Keck M, Cintrat JC, Barbier J, Gillet D, Galloux M. A New Derivative of Retro-2 Displays Antiviral Activity against Respiratory Syncytial Virus. Int J Mol Sci 2023; 25:415. [PMID: 38203585 PMCID: PMC10778932 DOI: 10.3390/ijms25010415] [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: 10/25/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Human respiratory syncytial virus (hRSV) is the most common cause of bronchiolitis and pneumonia in newborns, with all children being infected before the age of two. Reinfections are very common throughout life and can cause severe respiratory infections in the elderly and immunocompromised adults. Although vaccines and preventive antibodies have recently been licensed for use in specific subpopulations of patients, there is still no therapeutic treatment commonly available for these infections. Here, we investigated the potential antiviral activity of Retro-2.2, a derivative of the cellular retrograde transport inhibitor Retro-2, against hRSV. We show that Retro-2.2 inhibits hRSV replication in cell culture and impairs the ability of hRSV to form syncytia. Our results suggest that Retro-2.2 treatment affects virus spread by disrupting the trafficking of the viral de novo synthetized F and G glycoproteins to the plasma membrane, leading to a defect in virion morphogenesis. Taken together, our data show that targeting intracellular transport may be an effective strategy against hRSV infection.
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Affiliation(s)
- Adrien Le Rouzic
- INRAE Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St Quentin, 78350 Jouy-en-Josas, France; (A.L.R.); (J.F.); (J.-F.E.)
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
| | - Jenna Fix
- INRAE Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St Quentin, 78350 Jouy-en-Josas, France; (A.L.R.); (J.F.); (J.-F.E.)
| | - Robin Vinck
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, 91191 Gif-sur-Yvette, France;
| | | | - Romain Volmer
- INRAE, IHAP, UMR 1225, ENVT, 31300 Toulouse, France;
| | - Franck Gallardo
- NeoVirTech SAS, 1 Place Pierre Potier, 31000 Toulouse, France; (S.K.-G.); (F.G.)
| | - Jean-François Eléouët
- INRAE Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St Quentin, 78350 Jouy-en-Josas, France; (A.L.R.); (J.F.); (J.-F.E.)
| | - Mathilde Keck
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
| | - Jean-Christophe Cintrat
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, 91191 Gif-sur-Yvette, France;
| | - Julien Barbier
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
| | - Daniel Gillet
- CEA, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.V.); (M.K.); (J.B.)
| | - Marie Galloux
- INRAE Unité de Virologie et Immunologie Moléculaires (VIM), Université Paris-Saclay-Versailles St Quentin, 78350 Jouy-en-Josas, France; (A.L.R.); (J.F.); (J.-F.E.)
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5
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Yu X, Abeywickrema P, Bonneux B, Behera I, Anson B, Jacoby E, Fung A, Adhikary S, Bhaumik A, Carbajo RJ, De Bruyn S, Miller R, Patrick A, Pham Q, Piassek M, Verheyen N, Shareef A, Sutto-Ortiz P, Ysebaert N, Van Vlijmen H, Jonckers THM, Herschke F, McLellan JS, Decroly E, Fearns R, Grosse S, Roymans D, Sharma S, Rigaux P, Jin Z. Structural and mechanistic insights into the inhibition of respiratory syncytial virus polymerase by a non-nucleoside inhibitor. Commun Biol 2023; 6:1074. [PMID: 37865687 PMCID: PMC10590419 DOI: 10.1038/s42003-023-05451-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023] Open
Abstract
The respiratory syncytial virus polymerase complex, consisting of the polymerase (L) and phosphoprotein (P), catalyzes nucleotide polymerization, cap addition, and cap methylation via the RNA dependent RNA polymerase, capping, and Methyltransferase domains on L. Several nucleoside and non-nucleoside inhibitors have been reported to inhibit this polymerase complex, but the structural details of the exact inhibitor-polymerase interactions have been lacking. Here, we report a non-nucleoside inhibitor JNJ-8003 with sub-nanomolar inhibition potency in both antiviral and polymerase assays. Our 2.9 Å resolution cryo-EM structure revealed that JNJ-8003 binds to an induced-fit pocket on the capping domain, with multiple interactions consistent with its tight binding and resistance mutation profile. The minigenome and gel-based de novo RNA synthesis and primer extension assays demonstrated that JNJ-8003 inhibited nucleotide polymerization at the early stages of RNA transcription and replication. Our results support that JNJ-8003 binding modulates a functional interplay between the capping and RdRp domains, and this molecular insight could accelerate the design of broad-spectrum antiviral drugs.
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Affiliation(s)
- Xiaodi Yu
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA.
| | - Pravien Abeywickrema
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Brecht Bonneux
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Ishani Behera
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA
| | - Brandon Anson
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA
| | - Edgar Jacoby
- Johnson & Johnson Innovative Medicine, Beerse, Belgium
| | - Amy Fung
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA
| | - Suraj Adhikary
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Anusarka Bhaumik
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Rodrigo J Carbajo
- Johnson & Johnson Innovative Medicine, Janssen-Cilag, Discovery Chemistry S.A. Río Jarama, 75A, 45007, Toledo, Spain
| | | | - Robyn Miller
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Aaron Patrick
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Quyen Pham
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA
| | - Madison Piassek
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Nick Verheyen
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
| | - Afzaal Shareef
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | | | - Nina Ysebaert
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
| | | | | | | | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - Rachel Fearns
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | | | - Dirk Roymans
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
| | - Sujata Sharma
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
| | - Zhinan Jin
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA.
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6
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Gonnin L, Desfosses A, Bacia-Verloop M, Chevret D, Galloux M, Éléouët JF, Gutsche I. Structural landscape of the respiratory syncytial virus nucleocapsids. Nat Commun 2023; 14:5732. [PMID: 37714861 PMCID: PMC10504348 DOI: 10.1038/s41467-023-41439-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023] Open
Abstract
Human Respiratory Syncytial Virus (HRSV) is a prevalent cause of severe respiratory infections in children and the elderly. The helical HRSV nucleocapsid is a template for the viral RNA synthesis and a scaffold for the virion assembly. This cryo-electron microscopy analysis reveals the non-canonical arrangement of the HRSV nucleocapsid helix, composed of 16 nucleoproteins per asymmetric unit, and the resulting systematic variations in the RNA accessibility. We demonstrate that this unique helical symmetry originates from longitudinal interactions by the C-terminal arm of the HRSV nucleoprotein. We explore the polymorphism of the nucleocapsid-like assemblies, report five structures of the full-length particles and two alternative arrangements formed by a C-terminally truncated nucleoprotein mutant, and demonstrate the functional importance of the identified longitudinal interfaces. We put all these findings in the context of the HRSV RNA synthesis machinery and delineate the structural basis for its further investigation.
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Affiliation(s)
- Lorène Gonnin
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
- VIM, Paris-Saclay University, INRAE, 78350, Jouy-en-Josas, France
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Didier Chevret
- VIM, Paris-Saclay University, INRAE, 78350, Jouy-en-Josas, France
| | - Marie Galloux
- VIM, Paris-Saclay University, INRAE, 78350, Jouy-en-Josas, France
| | | | - Irina Gutsche
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
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7
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Salgueiro M, Camporeale G, Visentin A, Aran M, Pellizza L, Esperante SA, Corbat A, Grecco H, Sousa B, Esperón R, Borkosky SS, de Prat-Gay G. Molten Globule Driven and Self-downmodulated Phase Separation of a Viral Factory Scaffold. J Mol Biol 2023; 435:168153. [PMID: 37210029 DOI: 10.1016/j.jmb.2023.168153] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
Viral factories of liquid-like nature serve as sites for transcription and replication in most viruses. The respiratory syncytial virus factories include replication proteins, brought together by the phosphoprotein (P) RNA polymerase cofactor, present across non-segmented negative stranded RNA viruses. Homotypic liquid-liquid phase separation of RSV-P is governed by an α-helical molten globule domain, and strongly self-downmodulated by adjacent sequences. Condensation of P with the nucleoprotein N is stoichiometrically tuned, defining aggregate-droplet and droplet-dissolution boundaries. Time course analysis show small N-P nuclei gradually coalescing into large granules in transfected cells. This behavior is recapitulated in infection, with small puncta evolving to large viral factories, strongly suggesting that P-N nucleation-condensation sequentially drives viral factories. Thus, the tendency of P to undergo phase separation is moderate and latent in the full-length protein but unleashed in the presence of N or when neighboring disordered sequences are deleted. This, together with its capacity to rescue nucleoprotein-RNA aggregates suggests a role as a "solvent-protein".
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Affiliation(s)
- Mariano Salgueiro
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Gabriela Camporeale
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Araceli Visentin
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Martin Aran
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Leonardo Pellizza
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | | | - Agustín Corbat
- Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, and IFIBA, CONICET, Buenos Aires, Argentina
| | - Hernán Grecco
- Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, and IFIBA, CONICET, Buenos Aires, Argentina
| | - Belén Sousa
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Ramiro Esperón
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Silvia S Borkosky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires, Argentina.
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8
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Scudero OB, Santiago VF, Palmisano G, Simabuco FM, Ventura AM. The respiratory syncytial virus M2-2 protein is targeted for proteasome degradation and inhibits translation and stress granules assembly. PLoS One 2023; 18:e0289100. [PMID: 37490507 PMCID: PMC10368288 DOI: 10.1371/journal.pone.0289100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
The M2-2 protein from the respiratory syncytial virus (RSV) is a 10 kDa protein expressed by the second ORF of the viral gene M2. During infection, M2-2 has been described as the polymerase cofactor responsible for promoting genome replication, which occurs by the induction of changes in interactions between the polymerase and other viral proteins at early stages of infection. Despite its well-explored role in the regulation of the polymerase activity, little has been made to investigate the relationship of M2-2 with cellular proteins. A previous report showed poor recruitment of M2-2 to viral structures, with the protein being mainly localized to the nucleus and cytoplasmic granules. To unravel which other functions M2-2 exerts during infection, we performed proteomic analysis of co-immunoprecipitated cellular partners, identifying enrichment of proteins involved with regulation of translation, protein folding and mRNA splicing. In approaches based on these data, we found that M2-2 expression downregulates eiF2α phosphorylation and inhibits both translation and stress granules assembly. Finally, we also verified that M2-2 is targeted for proteasome degradation, being localized to granules composed of defective ribosomal products at the cytoplasm. These results suggest that besides its functions in the replicative complex, M2-2 may exert additional functions to contribute to successful RSV infection.
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Affiliation(s)
- Orlando Bonito Scudero
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Verônica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernando Moreira Simabuco
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
- Department of Biochemistry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Armando Morais Ventura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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9
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Risso-Ballester J, Rameix-Welti MA. Spatial resolution of virus replication: RSV and cytoplasmic inclusion bodies. Adv Virus Res 2023; 116:1-43. [PMID: 37524479 DOI: 10.1016/bs.aivir.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory Syncytial Virus (RSV) is a major cause of respiratory illness in young children, elderly and immunocompromised individuals worldwide representing a severe burden for health systems. The urgent development of vaccines or specific antivirals against RSV is impaired by the lack of knowledge regarding its replication mechanisms. RSV is a negative-sense single-stranded RNA (ssRNA) virus belonging to the Mononegavirales order (MNV) which includes other viruses pathogenic to humans as Rabies (RabV), Ebola (EBOV), or measles (MeV) viruses. Transcription and replication of viral genomes occur within cytoplasmatic virus-induced spherical inclusions, commonly referred as inclusion bodies (IBs). Recently IBs were shown to exhibit properties of membrane-less organelles (MLO) arising by liquid-liquid phase separation (LLPS). Compartmentalization of viral RNA synthesis steps in viral-induced MLO is indeed a common feature of MNV. Strikingly these key compartments still remain mysterious. Most of our current knowledge on IBs relies on the use of fluorescence microscopy. The ability to fluorescently label IBs in cells has been key to uncover their dynamics and nature. The generation of recombinant viruses expressing a fluorescently-labeled viral protein and the immunolabeling or the expression of viral fusion proteins known to be recruited in IBs are some of the tools used to visualize IBs in infected cells. In this chapter, microscope techniques and the most relevant studies that have shed light on RSV IBs fundamental aspects, including biogenesis, organization and dynamics are being discussed and brought to light with the investigations carried out on other MNV.
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Affiliation(s)
| | - Marie-Anne Rameix-Welti
- Institut Pasteur, Université Paris-Saclay, Université de Versailles St. Quentin, UMR 1173 (2I), INSERM, Paris, France; Assistance Publique des Hôpitaux de Paris, Hôpital Ambroise Paré, Laboratoire de Microbiologie, DMU15, Paris, France.
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10
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Visentin A, Demitroff N, Salgueiro M, Borkosky SS, Uversky VN, Camporeale G, de Prat-Gay G. Assembly of the Tripartite and RNA Condensates of the Respiratory Syncytial Virus Factory Proteins In Vitro: Role of the Transcription Antiterminator M 2-1. Viruses 2023; 15:1329. [PMID: 37376628 DOI: 10.3390/v15061329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
A wide variety of viruses replicate in liquid-like viral factories. Non-segmented negative stranded RNA viruses share a nucleoprotein (N) and a phosphoprotein (P) that together emerge as the main drivers of liquid-liquid phase separation. The respiratory syncytial virus includes the transcription antiterminator M2-1, which binds RNA and maximizes RNA transcriptase processivity. We recapitulate the assembly mechanism of condensates of the three proteins and the role played by RNA. M2-1 displays a strong propensity for condensation by itself and with RNA through the formation of electrostatically driven protein-RNA coacervates based on the amphiphilic behavior of M2-1 and finely tuned by stoichiometry. M2-1 incorporates into tripartite condensates with N and P, modulating their size through an interplay with P, where M2-1 is both client and modulator. RNA is incorporated into the tripartite condensates adopting a heterogeneous distribution, reminiscent of the M2-1-RNA IBAG granules within the viral factories. Ionic strength dependence indicates that M2-1 behaves differently in the protein phase as opposed to the protein-RNA phase, in line with the subcompartmentalization observed in viral factories. This work dissects the biochemical grounds for the formation and fate of the RSV condensates in vitro and provides clues to interrogate the mechanism under the highly complex infection context.
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Affiliation(s)
- Araceli Visentin
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Nicolás Demitroff
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Mariano Salgueiro
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Silvia Susana Borkosky
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Gabriela Camporeale
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Gonzalo de Prat-Gay
- Instituto Leloir, IIB-BA Conicet, Av. Patricias Argentinas 435, Buenos Aires 1405, Argentina
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
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11
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Thompson RE, Edmonds K, Dutch RE. Specific Residues in the C-Terminal Domain of the Human Metapneumovirus Phosphoprotein Are Indispensable for Formation of Viral Replication Centers and Regulation of the Function of the Viral Polymerase Complex. J Virol 2023; 97:e0003023. [PMID: 37092993 PMCID: PMC10231248 DOI: 10.1128/jvi.00030-23] [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: 01/05/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023] Open
Abstract
Human metapneumovirus (HMPV) is a negative-strand RNA virus that frequently causes respiratory tract infections in infants, the elderly, and the immunocompromised. A hallmark of HMPV infection is the formation of membraneless, liquid-like replication and transcription centers in the cytosol termed inclusion bodies (IBs). The HMPV phosphoprotein (P) and nucleoprotein (N) are the minimal viral proteins necessary to form IB-like structures, and both proteins are required for the viral polymerase to synthesize RNA during infection. HMPV P is a homotetramer with regions of intrinsic disorder and has several known and predicted phosphorylation sites of unknown function. In this study, we found that the P C-terminal intrinsically disordered domain (CTD) must be present to facilitate IB formation with HMPV N, while either the N-terminal intrinsically disordered domain or the central oligomerization domain was dispensable. Alanine substitution at a single tyrosine residue within the CTD abrogated IB formation and reduced coimmunoprecipitation with HMPV N. Mutations to C-terminal phosphorylation sites revealed a potential role for phosphorylation in regulating RNA synthesis and P binding partners within IBs. Phosphorylation mutations which reduced RNA synthesis in a reporter assay produced comparable results in a recombinant viral rescue system, measured as an inability to produce infectious viral particles with genomes containing these single P mutations. This work highlights the critical role HMPV P plays in facilitating a key step of the viral life cycle and reveals the potential role for phosphorylation in regulating the function of this significant viral protein. IMPORTANCE Human metapneumovirus (HMPV) infects global populations, with severe respiratory tract infections occurring in infants, the elderly, and the immunocompromised. There are currently no FDA-approved therapeutics available to prevent or treat HMPV infection. Therefore, understanding how HMPV replicates is vital for the identification of novel targets for therapeutic development. During HMPV infection, viral RNA synthesis proteins localize to membraneless structures called inclusion bodies (IBs), which are sites of genome replication and transcription. The HMPV phosphoprotein (P) is necessary for IBs to form and for the virus to synthesize RNA, but it is not known how this protein contributes to IB formation or if it is capable of regulating viral replication. We show that the C-terminal domain of P is the location of a molecular interaction driving IB formation and contains potential phosphorylation sites where amino acid charge regulates the function of the viral polymerase complex.
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Affiliation(s)
- Rachel Erin Thompson
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Kearstin Edmonds
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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12
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Hirai Y, Horie M. Nyamanini Virus Nucleoprotein and Phosphoprotein Organize Viral Inclusion Bodies That Associate with Host Biomolecular Condensates in the Nucleus. Int J Mol Sci 2023; 24:6550. [PMID: 37047525 PMCID: PMC10095084 DOI: 10.3390/ijms24076550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Many mononegaviruses form inclusion bodies (IBs) in infected cells. However, little is known about nuclear IBs formed by mononegaviruses, since only a few lineages of animal-derived mononegaviruses replicate in the nucleus. In this study, we characterized the IBs formed by Nyamanini virus (NYMV), a unique tick-borne mononegavirus undergoing replication in the nucleus. We discovered that NYMV forms IBs, consisting of condensates and puncta of various sizes and morphologies, in the host nucleus. Likewise, we found that the expressions of NYMV nucleoprotein (N) and phosphoprotein (P) alone induce the formation of condensates and puncta in the nucleus, respectively, even though their morphologies are somewhat different from the IBs observed in the actual NYMV-infected cells. In addition, IB-like structures can be reconstructed by co-expressions of NYMV N and P, and localization analyses using a series of truncated mutants of P revealed that the C-terminal 27 amino acid residues of P are important for recruiting P to the condensates formed by N. Furthermore, we found that nuclear speckles, cellular biomolecular condensates, are reorganized and recruited to the IB-like structures formed by the co-expressions of N and P, as well as IBs formed in NYMV-infected cells. These features are unique among mononegaviruses, and our study has contributed to elucidating the replication mechanisms of nuclear-replicating mononegaviruses and the virus-host interactions.
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Affiliation(s)
- Yuya Hirai
- Department of Biology, Osaka Dental University, 8-1 Kuzuha Hanazono-Cho, Hirakata 573-1121, Osaka, Japan
| | - Masayuki Horie
- Laboratory of Veterinary Microbiology, Graduate School of Veterinary Science, Osaka Metropolitan University, 1-58 Rinku-Oraikita, Izumisano 598-8531, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Izumisano 598-8531, Osaka, Japan
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13
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Reina J, Iglesias C. [EDP-938, a new antiviral with inhibitory activity against the nucleoprotein of the respiratory syncytial virus]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2023; 36:26-29. [PMID: 36401806 PMCID: PMC9910671 DOI: 10.37201/req/096.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The absence of an effective vaccine against respiratory syncytial virus (RSV) has led to the development of various drugs with the ability to inhibit or block its replicative activity. The first generation, called fusion inhibitors, bind to the protein on the viral surface and prevent the virus from binding and entering the cell. However, its low efficacy has determined the start of studies with second-generation compounds capable of binding or blocking the nucleoprotein (N); most of these compounds are analogs of 1,4-benzodiazepines. EDP-938 has shown high efficacy against RSV. The first trials in humans have shown that this antiviral is rapidly absorbed after oral administration and has a half-life of between 11-18 hours Administration for seven days of multiple oral doses of up to 600 mg/day or 300 mg/day/twice a day, there were hardly any significant adverse effects and the viral load in the lower respiratory tract decreased significantly.
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Affiliation(s)
- Jordi Reina
- Correspondencia: Jordi Reina Unidad de Virología, Servicio de Microbiología, Hospital Universitario Son Espases, Facultad de Medicina (UIB). Carretera Valldemossa 79, 07120 Palma de Mallorca E-mail:
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14
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Liu H, Shen L, Pan C, Huang W. Structural modeling, energetic analysis and molecular design of a π-stacking system at the complex interface of pediatric respiratory syncytial virus nucleocapsid with the C-terminal peptide of phosphoprotein. Biophys Chem 2023; 292:106916. [PMID: 36343393 DOI: 10.1016/j.bpc.2022.106916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/14/2022] [Accepted: 10/23/2022] [Indexed: 11/02/2022]
Abstract
Human respiratory syncytial virus (RSV) is a primary cause of lower respiratory tract infections and hospital visits during infancy and childhood. The RSV phosphoprotein (P) is a major polymerase cofactor that interacts with nucleoprotein (N) to promote the recognition of ribonucleoprotein complex (RNP) by viral RNA polymerase. The binding pocket of N protein is chemically diverse, in or around which a number of aromatic and charged amino acid residues are observed. Previously, a nonapeptide segment (P peptide, 233DNDLSLEDF241) representing the C-terminal tail of P protein was identified to mediate the N-P interaction with a moderate affinity, in which the Phe241 at the end of P's C-terminus plays a critical role in the binding of P peptide to N protein. Here, we found that the side-chain aromatic phenyl moiety of P Phe241 residue can form short- and long-range cation-π interactions with N Arg132 and Arg150 residues, respectively, as well as T-shaped and parallel-displaced π-π stackings with N Tyr135 and His151 residues, respectively, which co-define a geometrically satisfactory π-stacking system at the complex interface of N protein with P peptide, thus largely stabilizing the complex architecture. The stacking effect was further optimized by systematically mutating the P Phe241 residue to other natural and non-natural aromatic amino acids with diverse chemical substitutions at the phenyl moiety to examine their structural and energetic effects on π-stacking system and on protein-peptide binding. The electron-donating mutations at the phenyl moiety of P Phe241 residue can effectively enhance the π-stacking system and then promote peptide binding, whereas the bulky and positively charged mutations would considerably impair the peptide potency by introducing steric hindrance and electrostatic repulsion. The [Tyr]P, [Thp]P and [Fph]P mutants were determined to have an increased affinity relative to wild-type P peptide, which could be used as self-inhibitory peptides to competitively disrupt the native interaction between N and P proteins.
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Affiliation(s)
- Haiyan Liu
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou 215000, China
| | - Lili Shen
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou 215000, China
| | - Chunhua Pan
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou 215000, China
| | - Weihua Huang
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou 215000, China.
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15
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Investigation of the Fuzzy Complex between RSV Nucleoprotein and Phosphoprotein to Optimize an Inhibition Assay by Fluorescence Polarization. Int J Mol Sci 2022; 24:ijms24010569. [PMID: 36614009 PMCID: PMC9820559 DOI: 10.3390/ijms24010569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022] Open
Abstract
The interaction between Respiratory Syncytial Virus phosphoprotein P and nucleoprotein N is essential for the formation of the holo RSV polymerase that carries out replication. In vitro screening of antivirals targeting the N-P protein interaction requires a molecular interaction model, ideally consisting of a complex between N protein and a short peptide corresponding to the C-terminal tail of the P protein. However, the flexibility of C-terminal P peptides as well as their phosphorylation status play a role in binding and may bias the outcome of an inhibition assay. We therefore investigated binding affinities and dynamics of this interaction by testing two N protein constructs and P peptides of different lengths and composition, using nuclear magnetic resonance and fluorescence polarization (FP). We show that, although the last C-terminal Phe241 residue is the main determinant for anchoring P to N, only longer peptides afford sub-micromolar affinity, despite increasing mobility towards the N-terminus. We investigated competitive binding by peptides and small compounds, including molecules used as fluorescent labels in FP. Based on these results, we draw optimized parameters for a robust RSV N-P inhibition assay and validated this assay with the M76 molecule, which displays antiviral properties, for further screening of chemical libraries.
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16
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Zhang L, Gong Y, Shen L. Molecular Stapling of Human Pediatric RSV Phosphoprotein’s C-terminal Tail-Derived Peptides to Target the Coupled Folding-Upon-Binding Event Between Phosphoprotein and Nucleocapsid. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10483-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Gonnin L, Richard CA, Gutsche I, Chevret D, Troussier J, Vasseur JJ, Debart F, Eléouët JF, Galloux M. Importance of RNA length for in vitro encapsidation by the nucleoprotein of human Respiratory Syncytial Virus. J Biol Chem 2022; 298:102337. [PMID: 35931116 PMCID: PMC9436823 DOI: 10.1016/j.jbc.2022.102337] [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: 04/23/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
Respiratory syncytial virus has a negative-sense single-stranded RNA genome constitutively encapsidated by the viral nucleoprotein N, forming a helical nucleocapsid which is the template for viral transcription and replication by the viral polymerase L. Recruitment of L onto the nucleocapsid depends on the viral phosphoprotein P, which is an essential L cofactor. A prerequisite for genome and antigenome encapsidation is the presence of the monomeric, RNA-free, neosynthesized N protein, named N0. Stabilization of N0 depends on the binding of the N-terminal residues of P to its surface, which prevents N oligomerization. However, the mechanism involved in the transition from N0-P to nucleocapsid assembly, and thus in the specificity of viral genome encapsidation, is still unknown. Furthermore, the specific role of N oligomerization and RNA in the morphogenesis of viral factories, where viral transcription and replication occur, have not been elucidated although the interaction between P and N complexed to RNA has been shown to be responsible for this process. Here, using a chimeric protein comprising N and the first 40 N-terminal residues of P, we succeeded in purifying a recombinant N0-like protein competent for RNA encapsidation in vitro. Our results showed the importance of RNA length for stable encapsidation and revealed that the nature of the 5′ end of RNA does not explain the specificity of encapsidation. Finally, we showed that RNA encapsidation is crucial for the in vitro reconstitution of pseudo-viral factories. Together, our findings provide insight into respiratory syncytial virus viral genome encapsidation specificity.
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Affiliation(s)
- Lorène Gonnin
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Irina Gutsche
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Didier Chevret
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Joris Troussier
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Françoise Debart
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France.
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18
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Conley MJ, Short JM, Burns AM, Streetley J, Hutchings J, Bakker SE, Power BJ, Jaffery H, Haney J, Zanetti G, Murcia PR, Stewart M, Fearns R, Vijayakrishnan S, Bhella D. Helical ordering of envelope-associated proteins and glycoproteins in respiratory syncytial virus. EMBO J 2022; 41:e109728. [PMID: 34935163 PMCID: PMC8804925 DOI: 10.15252/embj.2021109728] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
Human respiratory syncytial virus (RSV) causes severe respiratory illness in children and the elderly. Here, using cryogenic electron microscopy and tomography combined with computational image analysis and three-dimensional reconstruction, we show that there is extensive helical ordering of the envelope-associated proteins and glycoproteins of RSV filamentous virions. We calculated a 16 Å resolution sub-tomogram average of the matrix protein (M) layer that forms an endoskeleton below the viral envelope. These data define a helical lattice of M-dimers, showing how M is oriented relative to the viral envelope. Glycoproteins that stud the viral envelope were also found to be helically ordered, a property that was coordinated by the M-layer. Furthermore, envelope glycoproteins clustered in pairs, a feature that may have implications for the conformation of fusion (F) glycoprotein epitopes that are the principal target for vaccine and monoclonal antibody development. We also report the presence, in authentic virus infections, of N-RNA rings packaged within RSV virions. These data provide molecular insight into the organisation of the virion and the mechanism of its assembly.
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Affiliation(s)
- Michaela J Conley
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Judith M Short
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
| | - Andrew M Burns
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - James Streetley
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Joshua Hutchings
- Department of Biological SciencesBirkbeck CollegeLondonUK
- Present address:
Division of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Saskia E Bakker
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
- Present address:
School of Life SciencesUniversity of WarwickCoventryUK
| | - B Joanne Power
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
- Present address:
Department of Biochemistry and Molecular BiologyThe Huck Center for Malaria ResearchPennsylvania State UniversityUniversity ParkPAUSA
| | - Hussain Jaffery
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Joanne Haney
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Giulia Zanetti
- Department of Biological SciencesBirkbeck CollegeLondonUK
| | - Pablo R Murcia
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Murray Stewart
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
| | - Rachel Fearns
- Department of MicrobiologyBoston University School of MedicineBostonMAUSA
- National Emerging Infectious Diseases LaboratoriesBoston UniversityBostonMAUSA
| | | | - David Bhella
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
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19
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The Nucleocapsid of Paramyxoviruses: Structure and Function of an Encapsidated Template. Viruses 2021; 13:v13122465. [PMID: 34960734 PMCID: PMC8708338 DOI: 10.3390/v13122465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/28/2023] Open
Abstract
Viruses of the Paramyxoviridae family share a common and complex molecular machinery for transcribing and replicating their genomes. Their non-segmented, negative-strand RNA genome is encased in a tight homopolymer of viral nucleoproteins (N). This ribonucleoprotein complex, termed a nucleocapsid, is the template of the viral polymerase complex made of the large protein (L) and its co-factor, the phosphoprotein (P). This review summarizes the current knowledge on several aspects of paramyxovirus transcription and replication, including structural and functional data on (1) the architecture of the nucleocapsid (structure of the nucleoprotein, interprotomer contacts, interaction with RNA, and organization of the disordered C-terminal tail of N), (2) the encapsidation of the genomic RNAs (structure of the nucleoprotein in complex with its chaperon P and kinetics of RNA encapsidation in vitro), and (3) the use of the nucleocapsid as a template for the polymerase complex (release of the encased RNA and interaction network allowing the progress of the polymerase complex). Finally, this review presents models of paramyxovirus transcription and replication.
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Interactions between the Nucleoprotein and the Phosphoprotein of Pneumoviruses: Structural Insight for Rational Design of Antivirals. Viruses 2021; 13:v13122449. [PMID: 34960719 PMCID: PMC8706346 DOI: 10.3390/v13122449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/17/2022] Open
Abstract
Pneumoviruses include pathogenic human and animal viruses, the most known and studied being the human respiratory syncytial virus (hRSV) and the metapneumovirus (hMPV), which are the major cause of severe acute respiratory tract illness in young children worldwide, and main pathogens infecting elderly and immune-compromised people. The transcription and replication of these viruses take place in specific cytoplasmic inclusions called inclusion bodies (IBs). These activities depend on viral polymerase L, associated with its cofactor phosphoprotein P, for the recognition of the viral RNA genome encapsidated by the nucleoprotein N, forming the nucleocapsid (NC). The polymerase activities rely on diverse transient protein-protein interactions orchestrated by P playing the hub role. Among these interactions, P interacts with the NC to recruit L to the genome. The P protein also plays the role of chaperone to maintain the neosynthesized N monomeric and RNA-free (called N0) before specific encapsidation of the viral genome and antigenome. This review aims at giving an overview of recent structural information obtained for hRSV and hMPV P, N, and more specifically for P-NC and N0-P complexes that pave the way for the rational design of new antivirals against those viruses.
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21
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Characterization of the interaction domains between the phosphoprotein and the nucleoprotein of human Metapneumovirus. J Virol 2021; 96:e0090921. [PMID: 34730389 DOI: 10.1128/jvi.00909-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human metapneumovirus (HMPV) causes severe respiratory diseases in young children. The HMPV RNA genome is encapsidated by the viral nucleoprotein (N), forming an RNA-N complex (NNuc), which serves as template for genome replication and mRNA transcription by the RNA-dependent RNA polymerase (RdRp). The RdRp is formed by the association of the large polymerase subunit (L), which has RNA polymerase, capping and methyltransferase activities, and the tetrameric phosphoprotein (P). P plays a central role in the RdRp complex by binding to NNuc and L, allowing the attachment of the L polymerase to the NNuc template. During infection these proteins concentrate in cytoplasmic inclusion bodies (IBs) where viral RNA synthesis occurs. By analogy to the closely related pneumovirus respiratory syncytial virus (RSV), it is likely that the formation of IBs depends on the interaction between HMPV P and NNuc, which has not been demonstrated yet. Here, we finely characterized the binding P- NNuc interaction domains by using recombinant proteins, combined with a functional assay for the polymerase complex activity, and the study of the recruitment of these proteins to IBs by immunofluorescence. We show that the last 6 C-terminal residues of HMPV P are necessary and sufficient for binding to NNuc, that P binds to the N-terminal domain of N (NNTD), and identified conserved N residues critical for the interaction. Our results allowed to propose a structural model for the HMPV P-NNuc interaction. IMPORTANCE Human metapneumovirus (HMPV) is a leading cause of severe respiratory infections in children but also affects human populations of all ages worldwide. Nowadays, no vaccine or efficient antiviral treatments are available for this pneumovirus. A better understanding of the molecular mechanisms involved in viral replication could help the design or discovery of specific antiviral compounds. In this work we have investigated the interaction between two major viral proteins involved in HMPV RNA synthesis, the N and P proteins. We finely characterized their domains of interaction, and identified a pocket on the surface of the N protein, a potential target of choice for the design of compounds interfering with N-P complexes and inhibiting viral replication.
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22
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Descamps D, Peres de Oliveira A, Gonnin L, Madrières S, Fix J, Drajac C, Marquant Q, Bouguyon E, Pietralunga V, Iha H, Morais Ventura A, Tangy F, Vidalain PO, Eléouët JF, Galloux M. Depletion of TAX1BP1 Amplifies Innate Immune Responses during Respiratory Syncytial Virus Infection. J Virol 2021; 95:e0091221. [PMID: 34431698 PMCID: PMC8549506 DOI: 10.1128/jvi.00912-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/20/2021] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the main cause of acute respiratory infections in young children and also has a major impact on the elderly and immunocompromised people. In the absence of a vaccine or efficient treatment, a better understanding of RSV interactions with the host antiviral response during infection is needed. Previous studies revealed that cytoplasmic inclusion bodies (IBs), where viral replication and transcription occur, could play a major role in the control of innate immunity during infection by recruiting cellular proteins involved in the host antiviral response. We recently showed that the morphogenesis of IBs relies on a liquid-liquid-phase separation mechanism depending on the interaction between viral nucleoprotein (N) and phosphoprotein (P). These scaffold proteins are expected to play a central role in the recruitment of cellular proteins to IBs. Here, we performed a yeast two-hybrid screen using RSV N protein as bait and identified the cellular protein TAX1BP1 as a potential partner of this viral protein. This interaction was validated by pulldown and immunoprecipitation assays. We showed that TAX1BP1 suppression has only a limited impact on RSV infection in cell cultures. However, RSV replication is decreased in TAX1BP1-deficient (TAX1BP1 knockout [TAX1BP1KO]) mice, whereas the production of inflammatory and antiviral cytokines is enhanced. In vitro infection of wild-type or TAX1BP1KO alveolar macrophages confirmed that the innate immune response to RSV infection is enhanced in the absence of TAX1BP1. Altogether, our results suggest that RSV could hijack TAX1BP1 to restrain the host immune response during infection. IMPORTANCE Respiratory syncytial virus (RSV), which is the leading cause of lower respiratory tract illness in infants, remains a medical problem in the absence of a vaccine or efficient treatment. This virus is also recognized as a main pathogen in the elderly and immunocompromised people, and the occurrence of coinfections (with other respiratory viruses and bacteria) amplifies the risks of developing respiratory distress. In this context, a better understanding of the pathogenesis associated with viral respiratory infections, which depends on both viral replication and the host immune response, is needed. The present study reveals that the cellular protein TAX1BP1, which interacts with the RSV nucleoprotein N, participates in the control of the innate immune response during RSV infection, suggesting that the N-TAX1BP1 interaction represents a new target for the development of antivirals.
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Affiliation(s)
| | - Andressa Peres de Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Lorène Gonnin
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Sarah Madrières
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Jenna Fix
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Carole Drajac
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Quentin Marquant
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Edwige Bouguyon
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Hidekatsu Iha
- Department of Infectious Diseases, Faculty of Medicine, Oita University Idaiga-oka, Hasama Yufu, Japan
| | - Armando Morais Ventura
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Pierre-Olivier Vidalain
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- CIRI, Centre International de Recherche en Infectiologie, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | | | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
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Cardone C, Caseau CM, Bardiaux B, Thureaux A, Galloux M, Bajorek M, Eléouët JF, Litaudon M, Bontems F, Sizun C. A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein. Biomolecules 2021; 11:biom11081225. [PMID: 34439894 PMCID: PMC8392014 DOI: 10.3390/biom11081225] [Citation(s) in RCA: 3] [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: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a high degree of disorder. In Pneumoviridae phosphoproteins, the only domain with well-defined structure is a small oligomerization domain (POD). We previously characterized the differential disorder in respiratory syncytial virus (RSV) phosphoprotein by NMR. We showed that outside of RSV POD, the intrinsically disordered N-and C-terminal regions displayed a structural and dynamic diversity ranging from random coil to high helical propensity. Here we provide additional insight into the dynamic behavior of PCα, a domain that is C-terminal to POD and constitutes the RSV L-binding region together with POD. By using small phosphoprotein fragments centered on or adjacent to POD, we obtained a structural picture of the POD–PCα region in solution, at the single residue level by NMR and at lower resolution by complementary biophysical methods. We probed POD–PCα inter-domain contacts and showed that small molecules were able to modify the dynamics of PCα. These structural properties are fundamental to the peculiar binding mode of RSV phosphoprotein to L, where each of the four protomers binds to L in a different way.
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Affiliation(s)
- Christophe Cardone
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Claire-Marie Caseau
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 78015 Paris, France;
| | | | - Marie Galloux
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Monika Bajorek
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
- Correspondence:
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Kadioglu O, Saeed M, Greten HJ, Efferth T. Identification of novel compounds against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning. Comput Biol Med 2021; 133:104359. [PMID: 33845270 DOI: 10.2471/blt.20.255943] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 05/22/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a major threat worldwide due to its fast spreading. As yet, there are no established drugs available. Speeding up drug discovery is urgently required. We applied a workflow of combined in silico methods (virtual drug screening, molecular docking and supervised machine learning algorithms) to identify novel drug candidates against COVID-19. We constructed chemical libraries consisting of FDA-approved drugs for drug repositioning and of natural compound datasets from literature mining and the ZINC database to select compounds interacting with SARS-CoV-2 target proteins (spike protein, nucleocapsid protein, and 2'-o-ribose methyltransferase). Supported by the supercomputer MOGON, candidate compounds were predicted as presumable SARS-CoV-2 inhibitors. Interestingly, several approved drugs against hepatitis C virus (HCV), another enveloped (-) ssRNA virus (paritaprevir, simeprevir and velpatasvir) as well as drugs against transmissible diseases, against cancer, or other diseases were identified as candidates against SARS-CoV-2. This result is supported by reports that anti-HCV compounds are also active against Middle East Respiratory Virus Syndrome (MERS) coronavirus. The candidate compounds identified by us may help to speed up the drug development against SARS-CoV-2.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Mohamed Saeed
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
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Sutto-Ortiz P, Tcherniuk S, Ysebaert N, Abeywickrema P, Noël M, Decombe A, Debart F, Vasseur JJ, Canard B, Roymans D, Rigaux P, Eléouët JF, Decroly E. The methyltransferase domain of the Respiratory Syncytial Virus L protein catalyzes cap N7 and 2'-O-methylation. PLoS Pathog 2021; 17:e1009562. [PMID: 33956914 PMCID: PMC8130918 DOI: 10.1371/journal.ppat.1009562] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a negative sense single-stranded RNA virus and one of the main causes of severe lower respiratory tract infections in infants and young children. RSV RNA replication/transcription and capping are ensured by the viral Large (L) protein. The L protein contains a polymerase domain associated with a polyribonucleotidyl transferase domain in its N-terminus, and a methyltransferase (MTase) domain followed by the C-terminal domain (CTD) enriched in basic amino acids at its C-terminus. The MTase-CTD of Mononegavirales forms a clamp to accommodate RNA that is subsequently methylated on the cap structure and depending on the virus, on internal positions. These enzymatic activities are essential for efficient viral mRNA translation into proteins, and to prevent the recognition of uncapped viral RNA by innate immunity sensors. In this work, we demonstrated that the MTase-CTD of RSV, as well as the full-length L protein in complex with phosphoprotein (P), catalyzes the N7- and 2’-O-methylation of the cap structure of a short RNA sequence that corresponds to the 5’ end of viral mRNA. Using different experimental systems, we showed that the RSV MTase-CTD methylates the cap structure with a preference for N7-methylation as first reaction. However, we did not observe cap-independent internal methylation, as recently evidenced for the Ebola virus MTase. We also found that at μM concentrations, sinefungin, a S-adenosylmethionine analogue, inhibits the MTase activity of the RSV L protein and of the MTase-CTD domain. Altogether, these results suggest that the RSV MTase domain specifically recognizes viral RNA decorated by a cap structure and catalyzes its methylation, which is required for translation and innate immune system subversion. Respiratory syncytial virus (RSV) is responsible of infant bronchiolitis and severe lower respiratory tract infections in infants and young children, and the leading cause of hospitalization in children under one year of age. However, we still lack a vaccine and therapeutics against this important pathogen. The main enzymatic activities involved in RSV propagation are embedded in the Large (L) protein that contains the polymerase domain and also all the activities required for RNA cap structure synthesis and methylation. These post-transcriptional RNA modifications play a key role in virus replication because cap N7-methylation is required for viral RNA translation into proteins, and 2’-O-methylation hides viral RNA from innate immunity detection. Viral methyltransferase (MTase) activities are now considered potential antiviral targets because their inhibition might limit the virus production and strengthen early virus detection by innate immunity sensors. In this work, we compared the enzymatic activities of the MTase expressed as a single domain or in the context of the full-length L protein. We demonstrated that the MTase protein catalyzes the specific methylation of the cap structure at both N7- and 2’-O-positions, and we obtained the proof of concept that a S-adenosylmethionine analogue can inhibit the MTase activity of the L protein.
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Affiliation(s)
| | - Sergey Tcherniuk
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, Jouy en Josas, France
| | - Nina Ysebaert
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | | | - Mathieu Noël
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | - Alice Decombe
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Françoise Debart
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Bruno Canard
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Dirk Roymans
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, Beerse, Belgium
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, Jouy en Josas, France
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
- * E-mail:
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26
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Structural Insights into the Respiratory Syncytial Virus RNA Synthesis Complexes. Viruses 2021; 13:v13050834. [PMID: 34063087 PMCID: PMC8147935 DOI: 10.3390/v13050834] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 12/13/2022] Open
Abstract
RNA synthesis in respiratory syncytial virus (RSV), a negative-sense (-) nonsegmented RNA virus, consists of viral gene transcription and genome replication. Gene transcription includes the positive-sense (+) viral mRNA synthesis, 5'-RNA capping and methylation, and 3' end polyadenylation. Genome replication includes (+) RNA antigenome and (-) RNA genome synthesis. RSV executes the viral RNA synthesis using an RNA synthesis ribonucleoprotein (RNP) complex, comprising four proteins, the nucleoprotein (N), the large protein (L), the phosphoprotein (P), and the M2-1 protein. We provide an overview of the RSV RNA synthesis and the structural insights into the RSV gene transcription and genome replication process. We propose a model of how the essential four proteins coordinate their activities in different RNA synthesis processes.
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27
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Identification of novel compounds against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning. Comput Biol Med 2021; 133:104359. [PMID: 33845270 PMCID: PMC8008812 DOI: 10.1016/j.compbiomed.2021.104359] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a major threat worldwide due to its fast spreading. As yet, there are no established drugs available. Speeding up drug discovery is urgently required. We applied a workflow of combined in silico methods (virtual drug screening, molecular docking and supervised machine learning algorithms) to identify novel drug candidates against COVID-19. We constructed chemical libraries consisting of FDA-approved drugs for drug repositioning and of natural compound datasets from literature mining and the ZINC database to select compounds interacting with SARS-CoV-2 target proteins (spike protein, nucleocapsid protein, and 2′-o-ribose methyltransferase). Supported by the supercomputer MOGON, candidate compounds were predicted as presumable SARS-CoV-2 inhibitors. Interestingly, several approved drugs against hepatitis C virus (HCV), another enveloped (−) ssRNA virus (paritaprevir, simeprevir and velpatasvir) as well as drugs against transmissible diseases, against cancer, or other diseases were identified as candidates against SARS-CoV-2. This result is supported by reports that anti-HCV compounds are also active against Middle East Respiratory Virus Syndrome (MERS) coronavirus. The candidate compounds identified by us may help to speed up the drug development against SARS-CoV-2.
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28
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EDP-938, a novel nucleoprotein inhibitor of respiratory syncytial virus, demonstrates potent antiviral activities in vitro and in a non-human primate model. PLoS Pathog 2021; 17:e1009428. [PMID: 33720995 PMCID: PMC7993833 DOI: 10.1371/journal.ppat.1009428] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/25/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022] Open
Abstract
EDP-938 is a novel non-fusion replication inhibitor of respiratory syncytial virus (RSV). It is highly active against all RSV-A and B laboratory strains and clinical isolates tested in vitro in various cell lines and assays, with half-maximal effective concentrations (EC50s) of 21, 23 and 64 nM against Long (A), M37 (A) and VR-955 (B) strains, respectively, in the primary human bronchial epithelial cells (HBECs). EDP-938 inhibits RSV at a post-entry replication step of the viral life cycle as confirmed by time-of-addition study, and the activity appears to be mediated by viral nucleoprotein (N). In vitro resistance studies suggest that EDP-938 presents a higher barrier to resistance compared to viral fusion or non-nucleoside L polymerase inhibitors with no cross-resistance observed. Combinations of EDP-938 with other classes of RSV inhibitors lead to synergistic antiviral activity in vitro. Finally, EDP-938 has also been shown to be efficacious in vivo in a non-human primate model of RSV infection. Respiratory syncytial virus (RSV) is a ubiquitous viral pathogen which inflicts a significant healthcare burden and is responsible for thousands of deaths annually. Currently no vaccine or targeted therapeutic exists. This work characterizes a newly discovered small molecule inhibitor of the virus, EDP-938, whose activity is mediated through the viral nucleoprotein. EDP-938 has potent in vitro activities against laboratory strains and clinical isolates of the virus, presents a high-barrier to resistance, can work synergistically with other known fusion or L protein inhibitors, and displays strong in vivo efficacy in a non-human primate model for RSV infection. EDP-938 is currently under evaluation in Phase 2 clinical studies.
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Tetramerization of Phosphoprotein is Essential for Respiratory Syncytial Virus Budding while its N Terminal Region Mediates Direct Interactions with the Matrix Protein. J Virol 2021; 95:JVI.02217-20. [PMID: 33408180 PMCID: PMC8092690 DOI: 10.1128/jvi.02217-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
It was shown previously that the Matrix (M), Phosphoprotein (P), and the Fusion (F) proteins of Respiratory syncytial virus (RSV) are sufficient to produce virus-like particles (VLPs) that resemble the RSV infection-induced virions. However, the exact mechanism and interactions among the three proteins are not known. This work examines the interaction between P and M during RSV assembly and budding. We show that M interacts with P in the absence of other viral proteins in cells using a Split Nano Luciferase assay. By using recombinant proteins, we demonstrate a direct interaction between M and P. By using Nuclear Magnetic Resonance (NMR) we identify three novel M interaction sites on P, namely site I in the αN2 region, site II in the 115-125 region, and the oligomerization domain (OD). We show that the OD, and likely the tetrameric structural organization of P, is required for virus-like filament formation and VLP release. Although sites I and II are not required for VLP formation, they appear to modulate P levels in RSV VLPs.Importance Human RSV is the commonest cause of infantile bronchiolitis in the developed world and of childhood deaths in resource-poor settings. It is a major unmet target for vaccines and anti-viral drugs. The lack of knowledge of RSV budding mechanism presents a continuing challenge for VLP production for vaccine purpose. We show that direct interaction between P and M modulates RSV VLP budding. This further emphasizes P as a central regulator of RSV life cycle, as an essential actor for transcription and replication early during infection and as a mediator for assembly and budding in the later stages for virus production.
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Cardone C, Caseau CM, Pereira N, Sizun C. Pneumoviral Phosphoprotein, a Multidomain Adaptor-Like Protein of Apparent Low Structural Complexity and High Conformational Versatility. Int J Mol Sci 2021; 22:ijms22041537. [PMID: 33546457 PMCID: PMC7913705 DOI: 10.3390/ijms22041537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 01/16/2023] Open
Abstract
Mononegavirales phosphoproteins (P) are essential co-factors of the viral polymerase by serving as a linchpin between the catalytic subunit and the ribonucleoprotein template. They have highly diverged, but their overall architecture is conserved. They are multidomain proteins, which all possess an oligomerization domain that separates N- and C-terminal domains. Large intrinsically disordered regions constitute their hallmark. Here, we exemplify their structural features and interaction potential, based on the Pneumoviridae P proteins. These P proteins are rather small, and their oligomerization domain is the only part with a defined 3D structure, owing to a quaternary arrangement. All other parts are either flexible or form short-lived secondary structure elements that transiently associate with the rest of the protein. Pneumoviridae P proteins interact with several viral and cellular proteins that are essential for viral transcription and replication. The combination of intrinsic disorder and tetrameric organization enables them to structurally adapt to different partners and to act as adaptor-like platforms to bring the latter close in space. Transient structures are stabilized in complex with protein partners. This class of proteins gives an insight into the structural versatility of non-globular intrinsically disordered protein domains.
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Lu T, Dong L, Pan H, Wu X, Chen X, Gu C, Tao N, Wang A, Zhang K, Jin J. Design and synthesis of C-ring quinoxaline-substituted sinomenine 1,2,3-triazole derivatives via click reactions. JOURNAL OF CHEMICAL RESEARCH 2020. [DOI: 10.1177/1747519820919853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The synthesis of C-ring quinoxaline-substituted sinomenine 1,2,3-triazole derivatives at the 4-OH via click reactions is accomplished, and a total of 16 novel sinomenine double N-heterocyclic derivatives are obtained in 74%–95% yields. The C-ring is first transformed into a 1,2-diketone structure under the action of hydrochloric acid, and then reacted with o-phenylenediamine to obtain a C-ring quinoxaline-substituted structure. The 4-OH of sinomenine reacts with chloropropyne to give an alkynyl sinomenine, and then reacts with sodium azide and various benzyl chlorides to give the target compounds. All the synthesized derivatives are characterized by Fourier-transform infrared spectrometry, high resolution mass spectrometry, 1H NMR, and 13C NMR spectroscopy.
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Affiliation(s)
- Tong Lu
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
| | - Ling Dong
- Department of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, P.R. China
| | - Hongmei Pan
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
| | - Xuedan Wu
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
| | - Xia Chen
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
| | - Chengwen Gu
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
| | - Naili Tao
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
| | - Ao Wang
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
| | - Kehua Zhang
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
| | - Jie Jin
- Key Laboratory of Advanced Functional Materials, Key Laboratory of and Functional Molecule Design and Interface Process, Anhui Jianzhu University, Hefei, P.R. China
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Abstract
Mononegavirales, known as nonsegmented negative-sense (NNS) RNA viruses, are a class of pathogenic and sometimes deadly viruses that include rabies virus (RABV), human respiratory syncytial virus (HRSV), and Ebola virus (EBOV). Unfortunately, no effective vaccines and antiviral therapeutics against many Mononegavirales are currently available. Viral polymerases have been attractive and major antiviral therapeutic targets. Therefore, Mononegavirales polymerases have been extensively investigated for their structures and functions. Mononegavirales, known as nonsegmented negative-sense (NNS) RNA viruses, are a class of pathogenic and sometimes deadly viruses that include rabies virus (RABV), human respiratory syncytial virus (HRSV), and Ebola virus (EBOV). Unfortunately, no effective vaccines and antiviral therapeutics against many Mononegavirales are currently available. Viral polymerases have been attractive and major antiviral therapeutic targets. Therefore, Mononegavirales polymerases have been extensively investigated for their structures and functions. Mononegavirales mimic RNA synthesis of their eukaryotic counterparts by utilizing multifunctional RNA polymerases to replicate entire viral genomes and transcribe viral mRNAs from individual viral genes as well as synthesize 5′ methylated cap and 3′ poly(A) tail of the transcribed viral mRNAs. The catalytic subunit large protein (L) and cofactor phosphoprotein (P) constitute the Mononegavirales polymerases. In this review, we discuss the shared and unique features of RNA synthesis, the monomeric multifunctional enzyme L, and the oligomeric multimodular adapter P of Mononegavirales. We outline the structural analyses of the Mononegavirales polymerases since the first structure of the vesicular stomatitis virus (VSV) L protein determined in 2015 and highlight multiple high-resolution cryo-electron microscopy (cryo-EM) structures of the polymerases of Mononegavirales, namely, VSV, RABV, HRSV, human metapneumovirus (HMPV), and human parainfluenza virus (HPIV), that have been reported in recent months (2019 to 2020). We compare the structures of those polymerases grouped by virus family, illustrate the similarities and differences among those polymerases, and reveal the potential RNA synthesis mechanisms and models of highly conserved Mononegavirales. We conclude by the discussion of remaining questions, evolutionary perspectives, and future directions.
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Sá JM, Piloto JV, Cilli EM, Tasic L, Fossey MA, Almeida FCL, Souza FP, Caruso ÍP. Hesperetin targets the hydrophobic pocket of the nucleoprotein/phosphoprotein binding site of human respiratory syncytial virus. J Biomol Struct Dyn 2020; 40:2156-2168. [PMID: 33076779 DOI: 10.1080/07391102.2020.1835717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The human Respiratory Syncytial Virus (hRSV) is one of the most common causes of acute respiratory diseases such as bronchiolitis and pneumonia in children worldwide. Among the viral proteins, the nucleoprotein (N) stands out for forming the nucleocapsid (NC) that functions as a template for replication and transcription by the viral polymerase complex. The NC/polymerase recognition is mediated by the phosphoprotein (P), which establishes an interaction of its C-terminal residues with a hydrophobic pocket in the N-terminal domain of N (N-NTD). The present study consists of biophysical characterization of N-NTD and investigation of flavonoids binding to this domain using experimental and computational approaches. Saturation transfer difference (STD)-NMR measurements showed that among the investigated flavonoids, only hesperetin (Hst) bound to N-NTD. The binding epitope mapping of Hst suggested that its fused aromatic ring is buried in the protein binding site. STD-NMR and fluorescence anisotropy experiments showed that Hst competes with P protein C-terminal dipeptides for the hRSV nucleoprotein/phosphoprotein (N/P) interaction site in N-NTD, indicating that Hst binds to the hydrophobic pocket in this domain. Computational simulations of molecular docking and dynamics corroborated with experimental results, presenting that Hst established a stable interaction with the N/P binding site. The outcomes presented herein shed light on literature reports that described a significant antireplicative activity of Hst against hRSV, revealing molecular details that can provide the development of a new strategy against this virus.
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Affiliation(s)
- Jéssica M Sá
- Multiuser Center for Biomolecular Innovation (CMIB), Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, CEP, SP, Brazil.,Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, SP, Brazil
| | - João V Piloto
- Multiuser Center for Biomolecular Innovation (CMIB), Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, CEP, SP, Brazil.,Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, SP, Brazil
| | - Eduardo M Cilli
- Department of Biochemistry and Organic Chemistry, Instituto de Química, UNESP, Araraquara, SP, Brazil
| | - Ljubica Tasic
- Organic Chemistry Department, Instituto de Química, UNICAMP, Campinas, SP, Brazil
| | - Marcelo A Fossey
- Multiuser Center for Biomolecular Innovation (CMIB), Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, CEP, SP, Brazil.,Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, SP, Brazil
| | - Fábio C L Almeida
- National Center for Nuclear Magnetic Resonance of Macromolecules, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM) e Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), UFRJ, Rio de Janeiro, RJ, Brazil
| | - Fátima P Souza
- Multiuser Center for Biomolecular Innovation (CMIB), Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, CEP, SP, Brazil.,Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, SP, Brazil
| | - Ícaro P Caruso
- Multiuser Center for Biomolecular Innovation (CMIB), Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, CEP, SP, Brazil.,Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, UNESP, São José do Rio Preto, SP, Brazil.,National Center for Nuclear Magnetic Resonance of Macromolecules, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM) e Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), UFRJ, Rio de Janeiro, RJ, Brazil
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Minimal Elements Required for the Formation of Respiratory Syncytial Virus Cytoplasmic Inclusion Bodies In Vivo and In Vitro. mBio 2020; 11:mBio.01202-20. [PMID: 32963000 PMCID: PMC7512546 DOI: 10.1128/mbio.01202-20] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract illness in infants, elderly, and immunocompromised people. No vaccine or efficient antiviral treatment is available against this virus. The replication and transcription steps of the viral genome are appealing mechanisms to target for the development of new antiviral strategies. These activities take place within cytoplasmic inclusion bodies (IBs) that assemble during infection. Although expression of both the viral nucleoprotein (N) and phosphoprotein (P) allows induction of the formation of these IBs, the mechanism sustaining their assembly remains poorly characterized. Here, we identified key elements of N and P required for the scaffolding of IBs and managed for the first time to reconstitute RSV pseudo-IBs in vitro by coincubating recombinant N and P proteins. Our results provide strong evidence that the biogenesis of RSV IBs occurs through liquid-liquid phase transition mediated by N-P interactions. Infection of host cells by the respiratory syncytial virus (RSV) is characterized by the formation of spherical cytoplasmic inclusion bodies (IBs). These structures, which concentrate all the proteins of the polymerase complex as well as some cellular proteins, were initially considered aggresomes formed by viral dead-end products. However, recent studies revealed that IBs are viral factories where viral RNA synthesis, i.e., replication and transcription, occurs. The analysis of IBs by electron microscopy revealed that they are membrane-less structures, and accumulated data on their structure, organization, and kinetics of formation revealed that IBs share the characteristics of cellular organelles, such as P-bodies or stress granules, suggesting that their morphogenesis depends on a liquid-liquid phase separation mechanism. It was previously shown that expression of the RSV nucleoprotein N and phosphoprotein P of the polymerase complex is sufficient to induce the formation of pseudo-IBs. Here, using a series of truncated P proteins, we identified the domains of P required for IB formation and show that the oligomeric state of N, provided it can interact with RNA, is critical for their morphogenesis. We also show that pseudo-IBs can form in vitro when recombinant N and P proteins are mixed. Finally, using fluorescence recovery after photobleaching approaches, we reveal that in cellula and in vitro IBs are liquid organelles. Our results strongly support the liquid-liquid phase separation nature of IBs and pave the way for further characterization of their dynamics.
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Hara K, Yaita K, Khamrin P, Kumthip K, Kashiwagi T, Eléouët JF, Rameix-Welti MA, Watanabe H. A small fragmented P protein of respiratory syncytial virus inhibits virus infection by targeting P protein. J Gen Virol 2020; 101:21-32. [PMID: 31702536 DOI: 10.1099/jgv.0.001350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Peptide-based inhibitors hold promising potential in the development of antiviral therapy. Here, we investigated the antiviral potential of fragmented viral proteins derived from ribonucleoprotein (RNP) components of the human respiratory syncytial virus (HRSV). Based on a mimicking approach that targets the functional domains of viral proteins, we designed various fragments of nucleoprotein (N), matrix protein M2-1 and phosphoprotein (P) and tested the antiviral activity in an RSV mini-genome system. We found that the fragment comprising residues 130-180 and 212-241 in the C-terminal region of P (81 amino acid length), denoted as P Fr, significantly inhibited the polymerase activity through competitive binding to the full-length P. Further deletion analysis of P Fr suggested that three functional domains in P Fr (oligomerization, L-binding and nucleocapsid binding) are required for maximum inhibitory activity. More importantly, a purified recombinant P Fr displayed significant antiviral activity at low nanomolar range in RSV-infected HEp-2 cells. These results highlight P as an important target for the development of antiviral compounds against RSV and other paramyxoviruses.
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Affiliation(s)
- Koyu Hara
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
| | - Kenichiro Yaita
- Division of Infectious diseases, Chidoribashi General Hospital, Fukuoka 812-8633, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Takahito Kashiwagi
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires (UR892), INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marie-Anne Rameix-Welti
- AP-HP, Laboratoire de Microbiologie, Hôpital Ambroise Paré, Boulogne-Billancourt, France.,UMR1173, INSERM, Université de Versailles St. Quentin, Montigny le Bretonneux, France
| | - Hiroshi Watanabe
- Department of Infection Control and Prevention, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
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Azeez SA, Alhashim ZG, Al Otaibi WM, Alsuwat HS, Ibrahim AM, Almandil NB, Borgio JF. State-of-the-art tools to identify druggable protein ligand of SARS-CoV-2. Arch Med Sci 2020; 16:497-507. [PMID: 32399095 PMCID: PMC7212236 DOI: 10.5114/aoms.2020.94046] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The SARS-CoV-2 (previously 2019-nCoV) outbreak in Wuhan, China and other parts of the world affects people and spreads coronavirus disease 2019 (COVID-19) through human-to-human contact, with a mortality rate of > 2%. There are no approved drugs or vaccines yet available against SARS-CoV-2. MATERIAL AND METHODS State-of-the-art tools based on in-silico methods are a cost-effective initial approach for identifying appropriate ligands against SARS-CoV-2. The present study developed the 3D structure of the envelope and nucleocapsid phosphoprotein of SARS-CoV-2, and molecular docking analysis was done against various ligands. RESULTS The highest log octanol/water partition coefficient, high number of hydrogen bond donors and acceptors, lowest non-bonded interaction energy between the receptor and the ligand, and high binding affinity were considered for the best ligand for the envelope (mycophenolic acid: log P = 3.00; DG = -10.2567 kcal/mol; pKi = 7.713 µM) and nucleocapsid phosphoprotein (1-[(2,4-dichlorophenyl)methyl]pyrazole-3,5-dicarboxylic acid: log P = 2.901; DG = -12.2112 kcal/mol; pKi = 7.885 µM) of SARS-CoV-2. CONCLUSIONS The study identifies the most potent compounds against the SARS-CoV-2 envelope and nucleocapsid phosphoprotein through state-of-the-art tools based on an in-silico approach. A combination of these two ligands could be the best option to consider for further detailed studies to develop a drug for treating patients infected with SARS-CoV-2, COVID-19.
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Affiliation(s)
- Sayed Abdul Azeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Zahra Ghalib Alhashim
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Waad Mohammed Al Otaibi
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Hind Saleh Alsuwat
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdallah M. Ibrahim
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Department of Fundamentals of Nursing, College of Nursing, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Alvarez Paggi D, Esperante SA, Salgueiro M, Camporeale G, de Oliveira GAP, Prat Gay G. A conformational switch balances viral RNA accessibility and protection in a nucleocapsid ring model. Arch Biochem Biophys 2019; 671:77-86. [PMID: 31229488 DOI: 10.1016/j.abb.2019.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/30/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022]
Abstract
Virus from the Mononegavirales order share common features ranging from virion structure arrangement to mechanisms of replication and transcription. One of them is the way the nucleoprotein (N) wraps and protects the RNA genome from degradation by forming a highly ordered helical nucleocapsid. However, crystal structures from numerous Mononegavirales reveal that binding to the nucleoprotein results in occluded nucleotides that hinder base pairing necessary for transcription and replication. This hints at the existence of alternative conformations of the N protein that would impact on the protein-RNA interface, allowing for transient exposure of the nucleotides without complete RNA release. Moreover, the regulation between the alternative conformations should be finely tuned. Recombinant expression of N from the respiratory syncytial virus form regular N/RNA common among all Mononegavirales, and these constitute an ideal minimal unit for investigating the mechanisms through which these structures protect RNA so efficiently while allowing for partial accessibility during transcription and replication. Neither pH nor high ionic strength could dissociate the RNA but led to irreversible aggregation of the nucleoprotein. Low concentrations of guanidine chloride dissociated the RNA moiety but leading to irreversible aggregation of the protein moiety. On the other hand, high concentrations of urea and long incubation periods were required to remove bound RNA. Both denaturants eventually led to unfolding but converged in the formation of an RNA-free β-enriched intermediate species that remained decameric even at high denaturant concentrations. Although the N-RNA rings interact with the phosphoprotein P, the scaffold of the RNA polymerase complex, this interaction did not lead to RNA dissociation from the rings in vitro. Thus, we have uncovered complex equilibria involving changes in secondary structure of N and RNA loosening, processes that must take place in the context of RNA transcription and replication, whose detailed mechanisms and cellular and viral participants need to be established.
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Affiliation(s)
- D Alvarez Paggi
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina.
| | - S A Esperante
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - M Salgueiro
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - G Camporeale
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - G A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnêtica Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil and Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908-0733, USA
| | - G Prat Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina.
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Esneau C, Raynal B, Roblin P, Brûlé S, Richard CA, Fix J, Eléouët JF, Galloux M. Biochemical characterization of the respiratory syncytial virus N 0-P complex in solution. J Biol Chem 2019; 294:3647-3660. [PMID: 30626736 PMCID: PMC6416419 DOI: 10.1074/jbc.ra118.006453] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/21/2018] [Indexed: 12/24/2022] Open
Abstract
As all the viruses belonging to the Mononegavirales order, the nonsegmented negative-strand RNA genome of respiratory syncytial virus (RSV) is encapsidated by the viral nucleoprotein N. N protein polymerizes along the genomic and anti-genomic RNAs during replication. This requires the maintenance of the neosynthesized N protein in a monomeric and RNA-free form by the viral phosphoprotein P that plays the role of a chaperone protein, forming a soluble N0-P complex. We have previously demonstrated that residues 1-30 of P specifically bind to N0 Here, to isolate a stable N0-P complex suitable for structural studies, we used the N-terminal peptide of P (P40) to purify truncated forms of the N protein. We show that to purify a stable N0-P-like complex, a deletion of the first 30 N-terminal residues of N (NΔ30) is required to impair N oligomerization, whereas the presence of a full-length C-arm of N is required to inhibit RNA binding. We generated structural models of the RSV N0-P with biophysical approaches, including hydrodynamic measurements and small-angle X-ray scattering (SAXS), coupled with biochemical and functional analyses of human RSV (hRSV) NΔ30 mutants. These models suggest a strong structural homology between the hRSV and the human metapneumovirus (hMPV) N0-P complexes. In both complexes, the P40-binding sites on N0 appear to be similar, and the C-arm of N provides a high flexibility and a propensity to interact with the N RNA groove. These findings reveal two potential sites to target on N0-P for the development of RSV antivirals.
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Affiliation(s)
- Camille Esneau
- From the Untié de Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moléculaire, C2RT, Institut Pasteur, 25 Rue du Docteur Roux, 75015 Paris, France
| | - Pierre Roblin
- Synchrotron SOLEIL, L'Orme des Merisiers, F-91410 Saint Aubin, France, and
- Laboratoire de Génie Chimique, Université Paul Sabatier, UMR 5503, Toulouse, France
| | - Sébastien Brûlé
- Plate-forme de Biophysique Moléculaire, C2RT, Institut Pasteur, 25 Rue du Docteur Roux, 75015 Paris, France
| | - Charles-Adrien Richard
- From the Untié de Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jenna Fix
- From the Untié de Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-François Eléouët
- From the Untié de Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, 78350 Jouy-en-Josas, France,
| | - Marie Galloux
- From the Untié de Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, 78350 Jouy-en-Josas, France,
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Selvaraj M, Yegambaram K, Todd EJAA, Richard CA, Dods RL, Pangratiou GM, Trinh CH, Moul SL, Murphy JC, Mankouri J, Éléouët JF, Barr JN, Edwards TA. The Structure of the Human Respiratory Syncytial Virus M2-1 Protein Bound to the Interaction Domain of the Phosphoprotein P Defines the Orientation of the Complex. mBio 2018; 9:e01554-18. [PMID: 30425144 PMCID: PMC6234862 DOI: 10.1128/mbio.01554-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/02/2018] [Indexed: 01/09/2023] Open
Abstract
Human respiratory syncytial virus (HRSV) is a negative-stranded RNA virus that causes a globally prevalent respiratory infection, which can cause life-threatening illness, particularly in the young, elderly, and immunocompromised. HRSV multiplication depends on replication and transcription of the HRSV genes by the virus-encoded RNA-dependent RNA polymerase (RdRp). For replication, this complex comprises the phosphoprotein (P) and the large protein (L), whereas for transcription, the M2-1 protein is also required. M2-1 is recruited to the RdRp by interaction with P and also interacts with RNA at overlapping binding sites on the M2-1 surface, such that binding of these partners is mutually exclusive. The molecular basis for the transcriptional requirement of M2-1 is unclear, as is the consequence of competition between P and RNA for M2-1 binding, which is likely a critical step in the transcription mechanism. Here, we report the crystal structure at 2.4 Å of M2-1 bound to the P interaction domain, which comprises P residues 90 to 110. The P90-110 peptide is alpha helical, and its position on the surface of M2-1 defines the orientation of the three transcriptase components within the complex. The M2-1/P interface includes ionic, hydrophobic, and hydrogen bond interactions, and the critical contribution of these contacts to complex formation was assessed using a minigenome assay. The affinity of M2-1 for RNA and P ligands was quantified using fluorescence anisotropy, which showed high-affinity RNAs could outcompete P. This has important implications for the mechanism of transcription, particularly the events surrounding transcription termination and synthesis of poly(A) sequences.IMPORTANCE Human respiratory syncytial virus (HRSV) is a leading cause of respiratory illness, particularly in the young, elderly, and immunocompromised, and has also been linked to the development of asthma. HRSV replication depends on P and L, whereas transcription also requires M2-1. M2-1 interacts with P and RNA at overlapping binding sites; while these interactions are necessary for transcriptional activity, the mechanism of M2-1 action is unclear. To better understand HRSV transcription, we solved the crystal structure of M2-1 in complex with the minimal P interaction domain, revealing molecular details of the M2-1/P interface and defining the orientation of M2-1 within the tripartite complex. The M2-1/P interaction is relatively weak, suggesting high-affinity RNAs may displace M2-1 from the complex, providing the basis for a new model describing the role of M2-1 in transcription. Recently, the small molecules quercetin and cyclopamine have been used to validate M2-1 as a drug target.
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Affiliation(s)
- Muniyandi Selvaraj
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Kavestri Yegambaram
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Eleanor J A A Todd
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Charles-Adrien Richard
- Unité de Virologie et Immunologie Moléculaires (UR892), INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rachel L Dods
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Georgia M Pangratiou
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Chi H Trinh
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Sophie L Moul
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - James C Murphy
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Jamel Mankouri
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Jean-François Éléouët
- Unité de Virologie et Immunologie Moléculaires (UR892), INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - John N Barr
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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40
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Cockerill GS, Good JAD, Mathews N. State of the Art in Respiratory Syncytial Virus Drug Discovery and Development. J Med Chem 2018; 62:3206-3227. [DOI: 10.1021/acs.jmedchem.8b01361] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- G. Stuart Cockerill
- ReViral Ltd., Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2FX, United Kingdom
| | - James A. D. Good
- ReViral Ltd., Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2FX, United Kingdom
| | - Neil Mathews
- ReViral Ltd., Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2FX, United Kingdom
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41
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Jordan PC, Stevens SK, Deval J. Nucleosides for the treatment of respiratory RNA virus infections. Antivir Chem Chemother 2018; 26:2040206618764483. [PMID: 29562753 PMCID: PMC5890544 DOI: 10.1177/2040206618764483] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/07/2018] [Indexed: 12/20/2022] Open
Abstract
Influenza virus, respiratory syncytial virus, human metapneumovirus, parainfluenza virus, coronaviruses, and rhinoviruses are among the most common viruses causing mild seasonal colds. These RNA viruses can also cause lower respiratory tract infections leading to bronchiolitis and pneumonia. Young children, the elderly, and patients with compromised cardiac, pulmonary, or immune systems are at greatest risk for serious disease associated with these RNA virus respiratory infections. In addition, swine and avian influenza viruses, together with severe acute respiratory syndrome-associated and Middle Eastern respiratory syndrome coronaviruses, represent significant pandemic threats to the general population. In this review, we describe the current medical need resulting from respiratory infections caused by RNA viruses, which justifies drug discovery efforts to identify new therapeutic agents. The RNA polymerase of respiratory viruses represents an attractive target for nucleoside and nucleotide analogs acting as inhibitors of RNA chain synthesis. Here, we present the molecular, biochemical, and structural fundamentals of the polymerase of the four major families of RNA respiratory viruses: Orthomyxoviridae, Pneumoviridae/Paramyxoviridae, Coronaviridae, and Picornaviridae. We summarize past and current efforts to develop nucleoside and nucleotide analogs as antiviral agents against respiratory virus infections. This includes molecules with very broad antiviral spectrum such as ribavirin and T-705 (favipiravir), and others targeting more specifically one or a few virus families. Recent advances in our understanding of the structure(s) and function(s) of respiratory virus polymerases will likely support the discovery and development of novel nucleoside analogs.
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Affiliation(s)
- Paul C Jordan
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
| | - Sarah K Stevens
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
| | - Jerome Deval
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
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Structural dissection of human metapneumovirus phosphoprotein using small angle x-ray scattering. Sci Rep 2017; 7:14865. [PMID: 29093501 PMCID: PMC5665942 DOI: 10.1038/s41598-017-14448-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/10/2017] [Indexed: 12/21/2022] Open
Abstract
The phosphoprotein (P) is the main and essential cofactor of the RNA polymerase (L) of non-segmented, negative‐strand RNA viruses. P positions the viral polymerase onto its nucleoprotein–RNA template and acts as a chaperone of the nucleoprotein (N), thereby preventing nonspecific encapsidation of cellular RNAs. The phosphoprotein of human metapneumovirus (HMPV) forms homotetramers composed of a stable oligomerization domain (Pcore) flanked by large intrinsically disordered regions (IDRs). Here we combined x-ray crystallography of Pcore with small angle x-ray scattering (SAXS)-based ensemble modeling of the full-length P protein and several of its fragments to provide a structural description of P that captures its dynamic character, and highlights the presence of varyingly stable structural elements within the IDRs. We discuss the implications of the structural properties of HMPV P for the assembly and functioning of the viral transcription/replication machinery.
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Canedo-Marroquín G, Acevedo-Acevedo O, Rey-Jurado E, Saavedra JM, Lay MK, Bueno SM, Riedel CA, Kalergis AM. Modulation of Host Immunity by Human Respiratory Syncytial Virus Virulence Factors: A Synergic Inhibition of Both Innate and Adaptive Immunity. Front Cell Infect Microbiol 2017; 7:367. [PMID: 28861397 PMCID: PMC5561764 DOI: 10.3389/fcimb.2017.00367] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/31/2017] [Indexed: 01/27/2023] Open
Abstract
The Human Respiratory Syncytial Virus (hRSV) is a major cause of acute lower respiratory tract infections (ARTIs) and high rates of hospitalizations in children and in the elderly worldwide. Symptoms of hRSV infection include bronchiolitis and pneumonia. The lung pathology observed during hRSV infection is due in part to an exacerbated host immune response, characterized by immune cell infiltration to the lungs. HRSV is an enveloped virus, a member of the Pneumoviridae family, with a non-segmented genome and negative polarity-single RNA that contains 10 genes encoding for 11 proteins. These include the Fusion protein (F), the Glycoprotein (G), and the Small Hydrophobic (SH) protein, which are located on the virus surface. In addition, the Nucleoprotein (N), Phosphoprotein (P) large polymerase protein (L) part of the RNA-dependent RNA polymerase complex, the M2-1 protein as a transcription elongation factor, the M2-2 protein as a regulator of viral transcription and (M) protein all of which locate inside the virion. Apart from the structural proteins, the hRSV genome encodes for the non-structural 1 and 2 proteins (NS1 and NS2). HRSV has developed different strategies to evade the host immunity by means of the function of some of these proteins that work as virulence factors to improve the infection in the lung tissue. Also, hRSV NS-1 and NS-2 proteins have been shown to inhibit the activation of the type I interferon response. Furthermore, the hRSV nucleoprotein has been shown to inhibit the immunological synapsis between the dendritic cells and T cells during infection, resulting in an inefficient T cell activation. Here, we discuss the hRSV virulence factors and the host immunological features raised during infection with this virus.
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Affiliation(s)
- Gisela Canedo-Marroquín
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Orlando Acevedo-Acevedo
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Emma Rey-Jurado
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Juan M Saavedra
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Margarita K Lay
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile
| | - Susan M Bueno
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Claudia A Riedel
- Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas y Medicina, Universidad Andres Bello, Millennium Institute on Immunology and ImmunotherapySantiago, Chile
| | - Alexis M Kalergis
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile.,Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de ChileSantiago, Chile
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44
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Whelan JN, Reddy KD, Uversky VN, Teng MN. Functional correlations of respiratory syncytial virus proteins to intrinsic disorder. MOLECULAR BIOSYSTEMS 2017; 12:1507-26. [PMID: 27062995 DOI: 10.1039/c6mb00122j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein intrinsic disorder is an important characteristic demonstrated by the absence of higher order structure, and is commonly detected in multifunctional proteins encoded by RNA viruses. Intrinsically disordered regions (IDRs) of proteins exhibit high flexibility and solvent accessibility, which permit several distinct protein functions, including but not limited to binding of multiple partners and accessibility for post-translational modifications. IDR-containing viral proteins can therefore execute various functional roles to enable productive viral replication. Respiratory syncytial virus (RSV) is a globally circulating, non-segmented, negative sense (NNS) RNA virus that causes severe lower respiratory infections. In this study, we performed a comprehensive evaluation of predicted intrinsic disorder of the RSV proteome to better understand the functional role of RSV protein IDRs. We included 27 RSV strains to sample major RSV subtypes and genotypes, as well as geographic and temporal isolate differences. Several types of disorder predictions were applied to the RSV proteome, including per-residue (PONDR®-FIT and PONDR® VL-XT), binary (CH, CDF, CH-CDF), and disorder-based interactions (ANCHOR and MoRFpred). We classified RSV IDRs by size, frequency and function. Finally, we determined the functional implications of RSV IDRs by mapping predicted IDRs to known functional domains of each protein. Identification of RSV IDRs within functional domains improves our understanding of RSV pathogenesis in addition to providing potential therapeutic targets. Furthermore, this approach can be applied to other NNS viruses that encode essential multifunctional proteins for the elucidation of viral protein regions that can be manipulated for attenuation of viral replication.
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Affiliation(s)
- Jillian N Whelan
- Division of Allergy and Immunology, Department of Internal Medicine, and the Joy McCann Culverhouse Airway Diseases Research Center, University of South Florida Morsani College of Medicine, Tampa, FL, USA.
| | - Krishna D Reddy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
| | - Michael N Teng
- Division of Allergy and Immunology, Department of Internal Medicine, and the Joy McCann Culverhouse Airway Diseases Research Center, University of South Florida Morsani College of Medicine, Tampa, FL, USA.
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Malekshahi SS, Salimi V, Arefian E, Fatemi-Nasab G, Adjaminejad-Fard S, Yavarian J, Mokhtari-Azad T. Inhibition of Respiratory Syncytial Virus Replication by Simultaneous Targeting of mRNA and Genomic RNA Using Dual-Targeting siRNAs. Mol Biotechnol 2017; 58:767-775. [PMID: 27766578 DOI: 10.1007/s12033-016-9976-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We attempted to generate siRNAs with two active strands, which can simultaneously knock down the expression of mRNA and viral genomic RNA. In this study, short hairpin RNAs (shRNAs) against N and F genes were used. Expression of F and N mRNA transcripts as well as genomic RNA was determined with relative real-time RT-PCR. The RSV load in infected cell culture supernatant was determined by absolute quantitative real-time PCR. We found that (i) in the presence of shRNA-N, a greater reduction in viral genomic RNA was found; (ii) the level of expression at MOI 0.01 was reduced more than MOI 0.1; (iii) reduction in N transcript was greater than F; and (iv) finally, in combination pre-treatment with two shRNAs, the reduction was not significant as compared to single shRNA transfection. shRNAs also inhibited the production of RSV progeny as shown by viral load in infected HEp-2 cells. (i) Virus load reduction was greater at MOI 0.01 than 0.1 and (ii) significant load reduction was not seen with combination shRNA pre-treatment. The antiviral potency was also confirmed by plaque assay and western blot analysis. Our results provided further evidence that RNAi could be a powerful treatment option against respiratory viruses.
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Affiliation(s)
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Science, Porsina Ave, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ghazal Fatemi-Nasab
- Virology Department, School of Public Health, Tehran University of Medical Science, Porsina Ave, Tehran, Iran
| | - Sarvin Adjaminejad-Fard
- Virology Department, School of Public Health, Tehran University of Medical Science, Porsina Ave, Tehran, Iran
| | - Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Science, Porsina Ave, Tehran, Iran
| | - Talat Mokhtari-Azad
- Virology Department, School of Public Health, Tehran University of Medical Science, Porsina Ave, Tehran, Iran.
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Pereira N, Cardone C, Lassoued S, Galloux M, Fix J, Assrir N, Lescop E, Bontems F, Eléouët JF, Sizun C. New Insights into Structural Disorder in Human Respiratory Syncytial Virus Phosphoprotein and Implications for Binding of Protein Partners. J Biol Chem 2017; 292:2120-2131. [PMID: 28031463 PMCID: PMC5313087 DOI: 10.1074/jbc.m116.765958] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/21/2016] [Indexed: 11/06/2022] Open
Abstract
Phosphoprotein is the main cofactor of the viral RNA polymerase of Mononegavirales It is involved in multiple interactions that are essential for the polymerase function. Most prominently it positions the polymerase complex onto the nucleocapsid, but also acts as a chaperone for the nucleoprotein. Mononegavirales phosphoproteins lack sequence conservation, but contain all large disordered regions. We show here that N- and C-terminal intrinsically disordered regions account for 80% of the phosphoprotein of the respiratory syncytial virus. But these regions display marked dynamic heterogeneity. Whereas almost stable helices are formed C terminally to the oligomerization domain, extremely transient helices are present in the N-terminal region. They all mediate internal long-range contacts in this non-globular protein. Transient secondary elements together with fully disordered regions also provide protein binding sites recognized by the respiratory syncytial virus nucleoprotein and compatible with weak interactions required for the processivity of the polymerase.
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Affiliation(s)
- Nelson Pereira
- From the Institut de Chimie des Substances Naturelles, UPR2301, Centre National de la Recherche Scientifique, Université Paris Saclay, 91190 Gif-sur-Yvette and
| | - Christophe Cardone
- From the Institut de Chimie des Substances Naturelles, UPR2301, Centre National de la Recherche Scientifique, Université Paris Saclay, 91190 Gif-sur-Yvette and
| | - Safa Lassoued
- From the Institut de Chimie des Substances Naturelles, UPR2301, Centre National de la Recherche Scientifique, Université Paris Saclay, 91190 Gif-sur-Yvette and
| | - Marie Galloux
- the Unité de Virologie et Immunologie Moléculaires, UR892, Institut National de la Recherche Agronomique, 78350 Jouy-en-Josas, France
| | - Jenna Fix
- the Unité de Virologie et Immunologie Moléculaires, UR892, Institut National de la Recherche Agronomique, 78350 Jouy-en-Josas, France
| | - Nadine Assrir
- From the Institut de Chimie des Substances Naturelles, UPR2301, Centre National de la Recherche Scientifique, Université Paris Saclay, 91190 Gif-sur-Yvette and
| | - Ewen Lescop
- From the Institut de Chimie des Substances Naturelles, UPR2301, Centre National de la Recherche Scientifique, Université Paris Saclay, 91190 Gif-sur-Yvette and
| | - François Bontems
- From the Institut de Chimie des Substances Naturelles, UPR2301, Centre National de la Recherche Scientifique, Université Paris Saclay, 91190 Gif-sur-Yvette and
| | - Jean-François Eléouët
- the Unité de Virologie et Immunologie Moléculaires, UR892, Institut National de la Recherche Agronomique, 78350 Jouy-en-Josas, France
| | - Christina Sizun
- From the Institut de Chimie des Substances Naturelles, UPR2301, Centre National de la Recherche Scientifique, Université Paris Saclay, 91190 Gif-sur-Yvette and
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Jamin M, Yabukarski F. Nonsegmented Negative-Sense RNA Viruses-Structural Data Bring New Insights Into Nucleocapsid Assembly. Adv Virus Res 2016; 97:143-185. [PMID: 28057258 DOI: 10.1016/bs.aivir.2016.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Viruses with a nonsegmented negative-sense RNA genome (NNVs) include important human pathogens as well as life-threatening zoonotic viruses. These viruses share a common RNA replication complex, including the genomic RNA and three proteins, the nucleoprotein (N), the phosphoprotein (P), and the RNA-dependent RNA polymerase (L). During genome replication, the RNA polymerase complex first synthesizes positive-sense antigenomes, which in turn serve as template for the production of negative-sense progeny genomes. These newly synthesized antigenomic and genomic RNAs must be encapsidated by N, and the source of soluble, RNA-free N, competent for the encapsidation is a complex between N and P, named the N0-P complex. In this review, we summarize recent progress made in the structural characterization of the different components of this peculiar RNA polymerase machinery. We discuss common features and replication strategies and highlight idiosyncrasies encountered in different viruses, along with the key role of the dual ordered/disordered architecture of protein components and the dynamics of the viral polymerase machinery. In particular, we focus on the N0-P complex and its role in the nucleocapsid assembly process. These new results provide evidence that the mechanism of NC assembly is conserved between the different families and thus support a divergent evolution from a common ancestor. In addition, the successful inhibition of infection due to different NNVs by peptides derived from P suggests that the mechanism of NC assembly is a potential target for antiviral development.
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Affiliation(s)
- M Jamin
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France.
| | - F Yabukarski
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
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Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach. J Virol 2016; 90:4876-4888. [PMID: 26656699 PMCID: PMC4859727 DOI: 10.1128/jvi.02349-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/18/2015] [Indexed: 11/20/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of serious respiratory tract infection. Treatment options include administration of ribavirin, a purine analog, although the mechanism of its anti-HRSV activity is unknown. We used transcriptome sequencing (RNA-seq) to investigate the genome mutation frequency and viral mRNA accumulation in HRSV-infected cells that were left untreated or treated with ribavirin. In the absence of ribavirin, HRSV-specific transcripts accounted for up to one-third of total RNA reads from the infected-cell RNA population. Ribavirin treatment resulted in a >90% reduction in abundance of viral mRNA reads, while at the same time no such reduction was detected for the abundance of cellular transcripts. The presented data reveal that ribavirin significantly increases the frequency of HRSV-specific RNA mutations, suggesting a direct influence on the fidelity of the HRSV polymerase. The presented data show that transitions and transversions occur during HRSV replication and that these changes occur in hot spots along the HRSV genome. Examination of nucleotide substitution rates in the viral genome indicated an increase in the frequency of transition but not transversion mutations in the presence of ribavirin. In addition, our data indicate that in the continuous cell types used and at the time points analyzed, the abundances of some HRSV mRNAs do not reflect the order in which the mRNAs are transcribed. IMPORTANCE Human respiratory syncytial virus (HRSV) is a major pediatric pathogen. Ribavirin can be used in children who are extremely ill to reduce the amount of virus and to lower the burden of disease. Ribavirin is used as an experimental therapy with other viruses. The mechanism of action of ribavirin against HRSV is not well understood, although it is thought to increase the mutation rate of the viral polymerase during replication. To investigate this hypothesis, we used a high-resolution approach that allowed us to determine the genetic sequence of the virus to a great depth of coverage. We found that ribavirin did not cause a detectable change in the relative amounts of viral mRNA transcripts. However, we found that ribavirin treatment did indeed cause an increase in the number of mutations, which was associated with a decrease in virus production.
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Cox R, Plemper RK. Structure-guided design of small-molecule therapeutics against RSV disease. Expert Opin Drug Discov 2016; 11:543-556. [PMID: 27046051 PMCID: PMC5074927 DOI: 10.1517/17460441.2016.1174212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION In the United States, respiratory syncytial virus (RSV) is responsible for the majority of infant hospitalizations resulting from viral infections, as well as a leading source of pneumonia and bronchiolitis in young children and the elderly. In the absence of vaccine prophylaxis or an effective antiviral for improved disease management, the development of novel anti-RSV therapeutics is critical. Several advanced drug development campaigns of the past decade have focused on blocking viral infection. These efforts have returned a chemically distinct panel of small-molecule RSV entry inhibitors, but binding sites and molecular mechanism of action appeared to share a common mechanism, resulting in comprehensive cross-resistance and calling for alternative druggable targets such as viral RNA-dependent RNA-polymerase complex. Areas Covered: In this review, the authors discuss the current status of the mechanism of action of RSV entry inhibitors. They also provide the recent structural insight into the organization of the polymerase complex that have revealed novel drug targets sites, and outline a path towards the discovery of next-generation RSV therapeutics. Expert opinion: Considering the tremendous progress experienced in our structural understanding of RSV biology in recent years and encouraging early results of a nucleoside analog inhibitor in clinical trials, there is high prospect that new generations of much needed effective anti-RSV therapeutics will become available for clinical use in the foreseeable future.
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Affiliation(s)
- Robert Cox
- Institute for Biomedical Sciences, Georgia State University, 100 Piedmont Av, Atlanta, Georgia 30303-3222 USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, 100 Piedmont Av, Atlanta, Georgia 30303-3222 USA
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50
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Asenjo A, Villanueva N. Phosphorylation of the human respiratory syncytial virus P protein mediates M2-2 regulation of viral RNA synthesis, a process that involves two P proteins. Virus Res 2016; 211:117-25. [DOI: 10.1016/j.virusres.2015.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
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