1
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Passchier TC, White JBR, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 2024; 14:14099. [PMID: 38890308 PMCID: PMC11189427 DOI: 10.1038/s41598-024-58243-z] [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: 12/07/2023] [Accepted: 03/27/2024] [Indexed: 06/20/2024] Open
Abstract
We report the first cryoEM structure of the Hendra henipavirus nucleoprotein in complex with RNA, at 3.5 Å resolution, derived from single particle analysis of a double homotetradecameric RNA-bound N protein ring assembly exhibiting D14 symmetry. The structure of the HeV N protein adopts the common bi-lobed paramyxoviral N protein fold; the N-terminal and C-terminal globular domains are bisected by an RNA binding cleft containing six RNA nucleotides and are flanked by the N-terminal and C-terminal arms, respectively. In common with other paramyxoviral nucleocapsids, the lateral interface between adjacent Ni and Ni+1 protomers involves electrostatic and hydrophobic interactions mediated primarily through the N-terminal arm and globular domains with minor contribution from the C-terminal arm. However, the HeV N multimeric assembly uniquely identifies an additional protomer-protomer contact between the Ni+1 N-terminus and Ni-1 C-terminal arm linker. The model presented here broadens the understanding of RNA-bound paramyxoviral nucleocapsid architectures and provides a platform for further insight into the molecular biology of HeV, as well as the development of antiviral interventions.
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Affiliation(s)
- Tim C Passchier
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Department of Biology, University of York, York, YO10 5DD, UK.
| | - Joshua B R White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Daniel P Maskell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew J Byrne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Exscientia, The Schrödinger Building Oxford Science Park, Oxford, OX4 4GE, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- College of Biomedical Sciences, Larkin University, 18301 N Miami Avenue, Miami, FL, 33169, USA.
| | - John N Barr
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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2
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Oraby A, Bilawchuk L, West FG, Marchant DJ. Structure-Based Discovery of Allosteric Inhibitors Targeting a New Druggable Site in the Respiratory Syncytial Virus Polymerase. ACS OMEGA 2024; 9:22213-22229. [PMID: 38799318 PMCID: PMC11112712 DOI: 10.1021/acsomega.4c01207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/29/2024]
Abstract
Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory infections for which effective treatment options remain limited. Herein, we employed a computational structure-based design strategy aimed at identifying potential targets for a new class of allosteric inhibitors. Our investigation led to the discovery of a previously undisclosed allosteric binding site within the RSV polymerase, the large (L) protein. This discovery was achieved through a combination of virtual screening and molecular dynamics simulations. Subsequently, we identified two inhibitors, 6a and 10b, which both exhibited promising antiviral activity in the low micromolar range. Resistance profiling revealed a distinctive pattern in how RSV evaded treatment with this class of inhibitors. This pattern strongly suggested that this class of small molecules was targeting a new binding site in the RSV L protein, aligning with the computational predictions made in our study. This study paves the way for the development of more potent inhibitors for combating RSV infections by targeting a new druggable pocket within the RdRp which does not overlap with previously known resistance sites.
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Affiliation(s)
- Ahmed
K. Oraby
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department
of Pharmaceutical Organic Chemistry, College of Pharmaceutical Sciences
and Drug Manufacturing, Misr University
for Science and Technology, 6th
of October City P.O. Box 77,Egypt
| | - Leanne Bilawchuk
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Frederick G. West
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - David J. Marchant
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
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3
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Cao D, Gao Y, Chen Z, Gooneratne I, Roesler C, Mera C, D'Cunha P, Antonova A, Katta D, Romanelli S, Wang Q, Rice S, Lemons W, Ramanathan A, Liang B. Structures of the promoter-bound respiratory syncytial virus polymerase. Nature 2024; 625:611-617. [PMID: 38123676 PMCID: PMC10794133 DOI: 10.1038/s41586-023-06867-y] [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: 04/30/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
The respiratory syncytial virus (RSV) polymerase is a multifunctional RNA-dependent RNA polymerase composed of the large (L) protein and the phosphoprotein (P). It transcribes the RNA genome into ten viral mRNAs and replicates full-length viral genomic and antigenomic RNAs1. The RSV polymerase initiates RNA synthesis by binding to the conserved 3'-terminal RNA promoters of the genome or antigenome2. However, the lack of a structure of the RSV polymerase bound to the RNA promoter has impeded the mechanistic understanding of RSV RNA synthesis. Here we report cryogenic electron microscopy structures of the RSV polymerase bound to its genomic and antigenomic viral RNA promoters, representing two of the first structures of an RNA-dependent RNA polymerase in complex with its RNA promoters in non-segmented negative-sense RNA viruses. The overall structures of the promoter-bound RSV polymerases are similar to that of the unbound (apo) polymerase. Our structures illustrate the interactions between the RSV polymerase and the RNA promoters and provide the structural basis for the initiation of RNA synthesis at positions 1 and 3 of the RSV promoters. These structures offer a deeper understanding of the pre-initiation state of the RSV polymerase and could aid in antiviral research against RSV.
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Affiliation(s)
- Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Zhenhang Chen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Inesh Gooneratne
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Claire Roesler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Cristopher Mera
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul D'Cunha
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Anna Antonova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Katta
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah Romanelli
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Qi Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Samantha Rice
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Wesley Lemons
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Anita Ramanathan
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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4
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Cox RM, Plemper RK. Design and Execution of In Vitro Polymerase Assays for Measles Virus and Related Mononegaviruses. Methods Mol Biol 2024; 2808:19-33. [PMID: 38743360 DOI: 10.1007/978-1-0716-3870-5_3] [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: 05/16/2024]
Abstract
Morbilliviruses such as measles virus (MeV) are responsible for major morbidity and mortality worldwide, despite the availability of an effective vaccine and global vaccination campaigns. MeV belongs to the mononegavirus order of viral pathogens that store their genetic information in non-segmented negative polarity RNA genomes. Genome replication and viral gene expression are carried out by a virus-encoded RNA-dependent RNA polymerase (RdRP) complex that has no immediate host cell analog. To better understand the organization and regulation of the viral RdRP and mechanistically characterize antiviral candidates, biochemical RdRP assays have been developed that employ purified recombinant polymerase complexes and synthetic RNA templates to monitor the initiation of RNA synthesis and RNA elongation in vitro. In this article, we will discuss strategies for the efficient expression and preparation of mononegavirus polymerase complexes, provide detailed protocols for the execution and optimization of RdRP assays, evaluate alternative options for the choice of template and detection system, and describe the application of the assay for the characterization of inhibitor candidates. Although MeV RdRP assays are the focus of this article, the general strategies and experimental approaches are readily transferable to related viruses in the mononegavirus order.
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Affiliation(s)
- Robert M Cox
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Richard K Plemper
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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5
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Abstract
The nonsegmented, negative-strand RNA viruses (nsNSVs), also known as the order Mononegavirales, have a genome consisting of a single strand of negative-sense RNA. Integral to the nsNSV replication cycle is the viral polymerase, which is responsible for transcribing the viral genome, to produce an array of capped and polyadenylated messenger RNAs, and replicating it to produce new genomes. To perform the different steps that are necessary for these processes, the nsNSV polymerases undergo a series of coordinated conformational transitions. While much is still to be learned regarding the intersection of nsNSV polymerase dynamics, structure, and function, recently published polymerase structures, combined with a history of biochemical and molecular biology studies, have provided new insights into how nsNSV polymerases function as dynamic machines. In this review, we consider each of the steps involved in nsNSV transcription and replication and suggest how these relate to solved polymerase structures.
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Affiliation(s)
- Mohamed Ouizougun-Oubari
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
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6
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Optimal Conditions for In Vitro Assembly of Respiratory Syncytial Virus Nucleocapsid-like Particles. Viruses 2023; 15:v15020344. [PMID: 36851557 PMCID: PMC9962444 DOI: 10.3390/v15020344] [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: 12/24/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
The nucleocapsids (NCs) of the respiratory syncytial virus (RSV) can display multiple morphologies in vivo, including spherical, asymmetric, and filamentous conformations. Obtaining homogeneous ring-like oligomers in vitro is significant since they structurally represent one turn of the characteristic RSV NC helical filament. Here, we analyzed and optimized conditions for forming homogenous, recombinant nucleocapsid-like particles (NCLPs) of RSV in vitro. We examined the effects of modifying the integrated RNA length and sequence, altering incubation time, and varying buffer parameters, including salt concentration and pH, on ring-like NCLPs assembly using negative stain electron microscopy (EM) imaging. We showed that high-quality, homogeneous particles are assembled when incubating short, adenine-rich RNA sequences with RNA-free N associated with P (N0P). Further, we reported that a co-incubation duration greater than 3 days, a NaCl concentration between 100 mM and 200 mM, and a pH between 7 and 8 are optimal for N-RNA ring assembly with polyadenine RNA sequences. We believe assembling high-quality, homogeneous NCLPs in vitro will allow for further analysis of RSV RNA synthesis. This work may also lend insights into obtaining high-resolution nucleocapsid homogeneous structures for in vitro analysis of antiviral drug candidates against RSV and related viruses.
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7
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Sutto-Ortiz P, Eléouët JF, Ferron F, Decroly E. Biochemistry of the Respiratory Syncytial Virus L Protein Embedding RNA Polymerase and Capping Activities. Viruses 2023; 15:v15020341. [PMID: 36851554 PMCID: PMC9960070 DOI: 10.3390/v15020341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
The human respiratory syncytial virus (RSV) is a negative-sense, single-stranded RNA virus. It is the major cause of severe acute lower respiratory tract infection in infants, the elderly population, and immunocompromised individuals. There is still no approved vaccine or antiviral treatment against RSV disease, but new monoclonal prophylactic antibodies are yet to be commercialized, and clinical trials are in progress. Hence, urgent efforts are needed to develop efficient therapeutic treatments. RSV RNA synthesis comprises viral transcription and replication that are catalyzed by the large protein (L) in coordination with the phosphoprotein polymerase cofactor (P), the nucleoprotein (N), and the M2-1 transcription factor. The replication/transcription is orchestrated by the L protein, which contains three conserved enzymatic domains: the RNA-dependent RNA polymerase (RdRp), the polyribonucleotidyl transferase (PRNTase or capping), and the methyltransferase (MTase) domain. These activities are essential for the RSV replicative cycle and are thus considered as attractive targets for the development of therapeutic agents. In this review, we summarize recent findings about RSV L domains structure that highlight how the enzymatic activities of RSV L domains are interconnected, discuss the most relevant and recent antivirals developments that target the replication/transcription complex, and conclude with a perspective on identified knowledge gaps that enable new research directions.
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Affiliation(s)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, F78350 Jouy en Josas, France
| | - François Ferron
- Aix Marseille Université, CNRS, AFMB, UMR, 7257 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB, UMR, 7257 Marseille, France
- Correspondence:
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8
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Williams HM, Thorkelsson SR, Vogel D, Milewski M, Busch C, Cusack S, Grünewald K, Quemin EJ, Rosenthal M. Structural insights into viral genome replication by the severe fever with thrombocytopenia syndrome virus L protein. Nucleic Acids Res 2023; 51:1424-1442. [PMID: 36651274 PMCID: PMC9943659 DOI: 10.1093/nar/gkac1249] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/29/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023] Open
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a phenuivirus that has rapidly become endemic in several East Asian countries. The large (L) protein of SFTSV, which includes the RNA-dependent RNA polymerase (RdRp), is responsible for catalysing viral genome replication and transcription. Here, we present 5 cryo-electron microscopy (cryo-EM) structures of the L protein in several states of the genome replication process, from pre-initiation to late-stage elongation, at a resolution of up to 2.6 Å. We identify how the L protein binds the 5' viral RNA in a hook-like conformation and show how the distal 5' and 3' RNA ends form a duplex positioning the 3' RNA terminus in the RdRp active site ready for initiation. We also observe the L protein stalled in the early and late stages of elongation with the RdRp core accommodating a 10-bp product-template duplex. This duplex ultimately splits with the template binding to a designated 3' secondary binding site. The structural data and observations are complemented by in vitro biochemical and cell-based mini-replicon assays. Altogether, our data provide novel key insights into the mechanism of viral genome replication by the SFTSV L protein and will aid drug development against segmented negative-strand RNA viruses.
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Affiliation(s)
| | | | - Dominik Vogel
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Morlin Milewski
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Carola Busch
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | | | - Kay Grünewald
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany,University of Hamburg, Hamburg, Germany
| | - Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
| | - Maria Rosenthal
- To whom correspondence should be addressed. Tel: +49 40 285380 930;
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9
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Cao D, Gooneratne I, Mera C, Vy J, Royal M, Huang B, Park Y, Manjunath A, Liang B. Analysis of Template Variations on RNA Synthesis by Respiratory Syncytial Virus Polymerase. Viruses 2022; 15:47. [PMID: 36680087 PMCID: PMC9863079 DOI: 10.3390/v15010047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a significant threat to infants and elderly individuals globally. Currently, there are no effective therapies or treatments for RSV infection because of an insufficient understanding of the RSV viral machinery. In this study, we investigated the effects of the template variations on RNA synthesis by the RSV polymerase through in vitro RNA synthesis assays. We confirmed the previously reported back-priming activity of the RSV polymerase, which is likely due to the secondary structure of the RNA template. We found that the expansion of the hairpin loop size of the RNA template abolishes the RSV polymerase back-priming activity. At the same time, it seemingly does not affect the de novo RNA synthesis activities of the RSV polymerase. Interestingly, our results show that the RSV polymerase also has a new primer-based terminal extension activity that adds nucleotides to the template and primer in a nonspecific manner. We also mapped the impact of the RNA 5' chemical group on its mobility in a urea-denaturing RNA gel shift assay. Overall, these results enhance our knowledge about the RNA synthesis processes of the RSV polymerase and may guide future therapeutic efforts to develop effective antiviral drugs for RSV treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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10
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Sourimant J, Lieber CM, Yoon JJ, Toots M, Govindarajan M, Udumula V, Sakamoto K, Natchus MG, Patti J, Vernachio J, Plemper RK. Orally efficacious lead of the AVG inhibitor series targeting a dynamic interface in the respiratory syncytial virus polymerase. SCIENCE ADVANCES 2022; 8:eabo2236. [PMID: 35749502 PMCID: PMC9232112 DOI: 10.1126/sciadv.abo2236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Respiratory syncytial virus (RSV) is a leading cause of lower respiratory infections in infants and the immunocompromised, yet no efficient therapeutic exists. We have identified the AVG class of allosteric inhibitors of RSV RNA synthesis. Here, we demonstrate through biolayer interferometry and in vitro RNA-dependent RNA polymerase (RdRP) assays that AVG compounds bind to the viral polymerase, stalling the polymerase in initiation conformation. Resistance profiling revealed a unique escape pattern, suggesting a discrete docking pose. Affinity mapping using photoreactive AVG analogs identified the interface of polymerase core, capping, and connector domains as a molecular target site. A first-generation lead showed nanomolar potency against RSV in human airway epithelium organoids but lacked in vivo efficacy. Docking pose-informed synthetic optimization generated orally efficacious AVG-388, which showed potent efficacy in the RSV mouse model when administered therapeutically. This study maps a druggable target in the RSV RdRP and establishes clinical potential of the AVG chemotype against RSV disease.
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Affiliation(s)
- Julien Sourimant
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Carolin M. Lieber
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Jeong-Joong Yoon
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Mart Toots
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | | | - Venkata Udumula
- Emory Institute for Drug Development, Emory University, Atlanta, GA 30322, USA
| | - Kaori Sakamoto
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Michael G. Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, GA 30322, USA
| | - Joseph Patti
- Aviragen Therapeutics Inc, Alpharetta, GA 30009, USA
| | | | - Richard K. Plemper
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
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11
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Cressey TN, Shareef AM, Kleiner VA, Noton SL, Byrne PO, McLellan JS, Mühlberger E, Fearns R. Distinctive features of the respiratory syncytial virus priming loop compared to other non-segmented negative strand RNA viruses. PLoS Pathog 2022; 18:e1010451. [PMID: 35731802 PMCID: PMC9255747 DOI: 10.1371/journal.ppat.1010451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/05/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
De novo initiation by viral RNA-dependent RNA polymerases often requires a polymerase priming residue, located within a priming loop, to stabilize the initiating NTPs. Polymerase structures from three different non-segmented negative strand RNA virus (nsNSV) families revealed putative priming loops in different conformations, and an aromatic priming residue has been identified in the rhabdovirus polymerase. In a previous study of the respiratory syncytial virus (RSV) polymerase, we found that Tyr1276, the L protein aromatic amino acid residue that most closely aligns with the rhabdovirus priming residue, is not required for RNA synthesis but two nearby residues, Pro1261 and Trp1262, were required. In this study, we examined the roles of Pro1261 and Trp1262 in RNA synthesis initiation. Biochemical studies showed that substitution of Pro1261 inhibited RNA synthesis initiation without inhibiting back-priming, indicating a defect in initiation. Biochemical and minigenome experiments showed that the initiation defect incurred by a P1261A substitution could be rescued by factors that would be expected to increase the stability of the initiation complex, specifically increased NTP concentration, manganese, and a more efficient promoter sequence. These findings indicate that Pro1261 of the RSV L protein plays a role in initiation, most likely in stabilizing the initiation complex. However, we found that substitution of the corresponding proline residue in a filovirus polymerase had no effect on RNA synthesis initiation or elongation. These results indicate that despite similarities between the nsNSV polymerases, there are differences in the features required for RNA synthesis initiation. RSV has a significant impact on human health. It is the major cause of respiratory disease in infants and exerts a significant toll on the elderly and immunocompromised. RSV is a member of the Mononegavirales, the non-segmented, negative strand RNA viruses (nsNSVs). Like other viruses in this order, RSV encodes an RNA dependent RNA polymerase, which is responsible for transcribing and replicating the viral genome. Due to its essential role during the viral replication cycle, the polymerase is a promising candidate target for antiviral inhibitors and so a greater understanding of the mechanistic basis of its activities could aid antiviral drug development. In this study, we identified an amino acid residue within the RSV polymerase that appears to stabilize the RNA synthesis initiation complex and showed that it plays a role in both transcription and RNA replication. However, the corresponding residue in a different nsNSV polymerase does not appear to play a similar role. This work reveals a key feature of the RSV polymerase but identifies differences with the polymerases of other related viruses.
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Affiliation(s)
- Tessa N. Cressey
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Afzaal M. Shareef
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Victoria A. Kleiner
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Patrick O. Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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12
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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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13
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Comparison of RNA synthesis initiation properties of non-segmented negative strand RNA virus polymerases. PLoS Pathog 2021; 17:e1010151. [PMID: 34914795 PMCID: PMC8717993 DOI: 10.1371/journal.ppat.1010151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/30/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
It is generally thought that the promoters of non-segmented, negative strand RNA viruses (nsNSVs) direct the polymerase to initiate RNA synthesis exclusively opposite the 3´ terminal nucleotide of the genome RNA by a de novo (primer independent) initiation mechanism. However, recent studies have revealed that there is diversity between different nsNSVs with pneumovirus promoters directing the polymerase to initiate at positions 1 and 3 of the genome, and ebolavirus polymerases being able to initiate at position 2 on the template. Studies with other RNA viruses have shown that polymerases that engage in de novo initiation opposite position 1 typically have structural features to stabilize the initiation complex and ensure efficient and accurate initiation. This raised the question of whether different nsNSV polymerases have evolved fundamentally different structural properties to facilitate initiation at different sites on their promoters. Here we examined the functional properties of polymerases of respiratory syncytial virus (RSV), a pneumovirus, human parainfluenza virus type 3 (PIV-3), a paramyxovirus, and Marburg virus (MARV), a filovirus, both on their cognate promoters and on promoters of other viruses. We found that in contrast to the RSV polymerase, which initiated at positions 1 and 3 of its promoter, the PIV-3 and MARV polymerases initiated exclusively at position 1 on their cognate promoters. However, all three polymerases could recognize and initiate from heterologous promoters, with the promoter sequence playing a key role in determining initiation site selection. In addition to examining de novo initiation, we also compared the ability of the RSV and PIV-3 polymerases to engage in back-priming, an activity in which the promoter template is folded into a secondary structure and nucleotides are added to the template 3´ end. This analysis showed that whereas the RSV polymerase was promiscuous in back-priming activity, the PIV-3 polymerase generated barely detectable levels of back-primed product, irrespective of promoter template sequence. Overall, this study shows that the polymerases from these three nsNSV families are fundamentally similar in their initiation properties, but have differences in their abilities to engage in back-priming.
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14
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Garcia BCB, Horie M, Kojima S, Makino A, Tomonaga K. BUD23-TRMT112 interacts with the L protein of Borna disease virus and mediates the chromosomal tethering of viral ribonucleoproteins. Microbiol Immunol 2021; 65:492-504. [PMID: 34324219 DOI: 10.1111/1348-0421.12934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 11/28/2022]
Abstract
Persistent intranuclear infection is an uncommon infection strategy among RNA viruses. However, Borna disease virus 1 (BoDV-1), a nonsegmented, negative-strand RNA virus, maintains viral infection in the cell nucleus by forming structured aggregates of viral ribonucleoproteins (vRNPs), and by tethering these vRNPs onto the host chromosomes. To better understand the nuclear infection strategy of BoDV-1, we determined the host protein interactors of the BoDV-1 large (L) protein. By proximity-dependent biotinylation, we identified several nuclear host proteins interacting with BoDV-1 L, one of which is TRMT112, a partner of several RNA methyltransferases (MTase). TRMT112 binds with BoDV-1 L at the RNA-dependent RNA polymerase domain, together with BUD23, an 18S rRNA MTase and 40S ribosomal maturation factor. We then discovered that BUD23-TRMT112 mediates the chromosomal tethering of BoDV-1 vRNPs, and that the MTase activity is necessary in the tethering process. These findings provide us a better understanding on how nuclear host proteins assist the chromosomal tethering of BoDV-1, as well as new prospects of host-viral interactions for intranuclear infection strategy of orthobornaviruses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bea Clarise B Garcia
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto
| | - Masayuki Horie
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto.,Hakubi Center for Advanced Research, Kyoto University, Kyoto
| | - Shohei Kojima
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto
| | - Akiko Makino
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto.,Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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15
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Braun MR, Noton SL, Blanchard EL, Shareef A, Santangelo PJ, Johnson WE, Fearns R. Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts. PLoS Pathog 2021; 17:e1009589. [PMID: 34003848 PMCID: PMC8162694 DOI: 10.1371/journal.ppat.1009589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 05/28/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of respiratory disease in infants and the elderly. RSV is a non-segmented negative strand RNA virus. The viral M2-1 protein plays a key role in viral transcription, serving as an elongation factor to enable synthesis of full-length mRNAs. M2-1 contains an unusual CCCH zinc-finger motif that is conserved in the related human metapneumovirus M2-1 protein and filovirus VP30 proteins. Previous biochemical studies have suggested that RSV M2-1 might bind to specific virus RNA sequences, such as the transcription gene end signals or poly A tails, but there was no clear consensus on what RSV sequences it binds. To determine if M2-1 binds to specific RSV RNA sequences during infection, we mapped points of M2-1:RNA interactions in RSV-infected cells at 8 and 18 hours post infection using crosslinking immunoprecipitation with RNA sequencing (CLIP-Seq). This analysis revealed that M2-1 interacts specifically with positive sense RSV RNA, but not negative sense genome RNA. It also showed that M2-1 makes contacts along the length of each viral mRNA, indicating that M2-1 functions as a component of the transcriptase complex, transiently associating with nascent mRNA being extruded from the polymerase. In addition, we found that M2-1 binds specific cellular mRNAs. In contrast to the situation with RSV mRNA, M2-1 binds discrete sites within cellular mRNAs, with a preference for A/U rich sequences. These results suggest that in addition to its previously described role in transcription elongation, M2-1 might have an additional role involving cellular RNA interactions.
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Affiliation(s)
- Molly R. Braun
- Department of Microbiology, Boston University School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Emmeline L. Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Afzaal Shareef
- Department of Microbiology, Boston University School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - W. Evan Johnson
- Division of Computational Biomedicine and Bioinformatics Program and Department of Biostatistics, Boston University, Boston, Massachusetts, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
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16
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Gao Y, Cao J, Xing P, Altmeyer R, Zhang Y. Evaluation of Small Molecule Combinations against Respiratory Syncytial Virus In Vitro. Molecules 2021; 26:molecules26092607. [PMID: 33946996 PMCID: PMC8125180 DOI: 10.3390/molecules26092607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/03/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a major pathogen that causes severe lower respiratory tract infection in infants, the elderly and the immunocompromised worldwide. At present no approved specific drugs or vaccines are available to treat this pathogen. Recently, several promising candidates targeting RSV entry and multiplication steps are under investigation. However, it is possible to lead to drug resistance under the long-term treatment. Therapeutic combinations constitute an alternative to prevent resistance and reduce antiviral doses. Therefore, we tested in vitro two-drug combinations of fusion inhibitors (GS5806, Ziresovir and BMS433771) and RNA-dependent RNA polymerase complex (RdRp) inhibitors (ALS8176, RSV604, and Cyclopamine). The statistical program MacSynergy II was employed to determine synergism, additivity or antagonism between drugs. From the result, we found that combinations of ALS8176 and Ziresovir or GS5806 exhibit additive effects against RSV in vitro, with interaction volume of 50 µM2% and 31 µM2% at 95% confidence interval, respectively. On the other hand, all combinations between fusion inhibitors showed antagonistic effects against RSV in vitro, with volume of antagonism ranging from −50 µM2 % to −176 µM2 % at 95% confidence interval. Over all, our results suggest the potentially therapeutic combinations in combating RSV in vitro could be considered for further animal and clinical evaluations.
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17
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Cox RM, Sourimant J, Govindarajan M, Natchus MG, Plemper RK. Therapeutic targeting of measles virus polymerase with ERDRP-0519 suppresses all RNA synthesis activity. PLoS Pathog 2021; 17:e1009371. [PMID: 33621266 PMCID: PMC7935272 DOI: 10.1371/journal.ppat.1009371] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/05/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
Morbilliviruses, such as measles virus (MeV) and canine distemper virus (CDV), are highly infectious members of the paramyxovirus family. MeV is responsible for major morbidity and mortality in non-vaccinated populations. ERDRP-0519, a pan-morbillivirus small molecule inhibitor for the treatment of measles, targets the morbillivirus RNA-dependent RNA-polymerase (RdRP) complex and displayed unparalleled oral efficacy against lethal infection of ferrets with CDV, an established surrogate model for human measles. Resistance profiling identified the L subunit of the RdRP, which harbors all enzymatic activity of the polymerase complex, as the molecular target of inhibition. Here, we examined binding characteristics, physical docking site, and the molecular mechanism of action of ERDRP-0519 through label-free biolayer interferometry, photoaffinity cross-linking, and in vitro RdRP assays using purified MeV RdRP complexes and synthetic templates. Results demonstrate that unlike all other mononegavirus small molecule inhibitors identified to date, ERDRP-0519 inhibits all phosphodiester bond formation in both de novo initiation of RNA synthesis at the promoter and RNA elongation by a committed polymerase complex. Photocrosslinking and resistance profiling-informed ligand docking revealed that this unprecedented mechanism of action of ERDRP-0519 is due to simultaneous engagement of the L protein polyribonucleotidyl transferase (PRNTase)-like domain and the flexible intrusion loop by the compound, pharmacologically locking the polymerase in pre-initiation conformation. This study informs selection of ERDRP-0519 as clinical candidate for measles therapy and identifies a previously unrecognized druggable site in mononegavirus L polymerase proteins that can silence all synthesis of viral RNA. The mononegavirus order contains major established and recently emerged human pathogens. Despite the threat to human health, antiviral therapeutics directed against this order remain understudied. The mononegavirus polymerase complex represents a promising drug target due to its central importance for both virus replication and viral mitigation of the innate host antiviral response. In this study, we have mechanistically characterized a clinical candidate small-molecule MeV polymerase inhibitor. The compound blocked all phosphodiester bond formation activity, a unique mechanism of action unlike all other known mononegavirus polymerase inhibitors. Photocrosslinking-based target site mapping demonstrated that this class-defining prototype inhibitor stabilizes a pre-initiation conformation of the viral polymerase complex that sterically cannot accommodate template RNA. Function-equivalent druggable sites exist in all mononegavirus polymerases. In addition to its direct anti-MeV impact, the insight gained in this study can therefore serve as a blueprint for indication spectrum expansion through structure-informed scaffold engineering or targeted drug discovery.
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Affiliation(s)
- Robert M. Cox
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
| | - Julien Sourimant
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
| | - Mugunthan Govindarajan
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Michael G. Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Richard K. Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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18
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In Vitro Primer-Based RNA Elongation and Promoter Fine Mapping of the Respiratory Syncytial Virus. J Virol 2020; 95:JVI.01897-20. [PMID: 33028717 PMCID: PMC7737744 DOI: 10.1128/jvi.01897-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 11/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a nonsegmented negative-sense (NNS) RNA virus and shares a similar RNA synthesis strategy with other members of NNS RNA viruses, such as measles, rabies virus, and Ebola virus. RSV RNA synthesis is catalyzed by a multifunctional RNA-dependent RNA polymerase (RdRP), which is composed of a large (L) protein that catalyzes three distinct enzymatic functions and an essential coenzyme phosphoprotein (P). Here, we successfully prepared highly pure, full-length, wild-type and mutant RSV polymerase (L-P) complexes. We demonstrated that the RSV polymerase could carry out both de novo and primer-based RNA synthesis. We defined the minimal length of the RNA template for in vitro de novo RNA synthesis using the purified RSV polymerase as 8 nucleotides (nt), shorter than previously reported. We showed that the RSV polymerase catalyzed primer-dependent RNA elongation with different lengths of primers on both short (10-nt) and long (25-nt) RNA templates. We compared the sequence specificity of different viral promoters and identified positions 3, 5, and 8 of the promoter sequence as essential to the in vitro RSV polymerase activity, consistent with the results previously mapped with the in vivo minigenome assay. Overall, these findings agree well with those of previous biochemical studies and extend our understanding of the promoter sequence and the mechanism of RSV RNA synthesis.IMPORTANCE As a major human pathogen, RSV affects 3.4 million children worldwide annually. However, no effective antivirals or vaccines are available. An in-depth mechanistic understanding of the RSV RNA synthesis machinery remains a high priority among the NNS RNA viruses. There is a strong public health need for research on this virus, due to major fundamental gaps in our understanding of NNS RNA virus replication. As the key enzyme executing transcription and replication of the virus, the RSV RdRP is a logical target for novel antiviral drugs. Therefore, exploring the primer-dependent RNA elongation extends our mechanistic understanding of the RSV RNA synthesis. Further fine mapping of the promoter sequence paves the way to better understand the function and structure of the RSV polymerase.
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19
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Elawar F, Oraby AK, Kieser Q, Jensen LD, Culp T, West FG, Marchant DJ. Pharmacological targets and emerging treatments for respiratory syncytial virus bronchiolitis. Pharmacol Ther 2020; 220:107712. [PMID: 33121940 DOI: 10.1016/j.pharmthera.2020.107712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022]
Abstract
RSV infection of the lower respiratory tract in infants is the leading cause of pediatric hospitalizations and second to malaria in causing infant deaths worldwide. RSV also causes substantial morbidity in immunocompromised and elderly populations. The only available therapeutic is a prophylactic drug called Palivizumab that is a humanized monoclonal antibody, given to high-risk infants. However, this intervention is expensive and has a limited impact on annual hospitalization rates caused by RSV. No vaccine is available, nor are efficacious antivirals to treat an active infection, and there is still no consensus on how infants with bronchiolitis should be treated during hospital admission. In this comprehensive review, we briefly outline the function of the RSV proteins and their suitability as therapeutic targets. We then discuss the most promising drug candidates, their inhibitory mechanisms, and whether they are in the process of clinical trials. We also briefly discuss the reasons for some of the failures in RSV therapeutics and vaccines. In summary, we provide insight into current antiviral development and the considerations toward producing licensed antivirals and therapeutics.
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Affiliation(s)
- Farah Elawar
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Ahmed K Oraby
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Misr University for Science &Technology, Al-Motamayez District, 6th of October City, P.O. Box 77, Egypt
| | - Quinten Kieser
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Lionel D Jensen
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Tyce Culp
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Frederick G West
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - David J Marchant
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada.
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20
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Balakrishnan A, Price E, Luu C, Shaul J, Wartchow C, Cantwell J, Vo T, DiDonato M, Spraggon G, Hekmat-Nejad M. Biochemical Characterization of Respiratory Syncytial Virus RNA-Dependent RNA Polymerase Complex. ACS Infect Dis 2020; 6:2800-2811. [PMID: 32886480 DOI: 10.1021/acsinfecdis.0c00554] [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: 11/28/2022]
Abstract
RNA-dependent RNA polymerases (RdRPs) from nonsegmented negative strand (NNS) RNA viruses perform both mRNA transcription and genome replication, and these activities are regulated by their interactions with RNA and other accessory proteins within the ribonucleoprotein (RNP) complex. Detailed biochemical characterization of these enzymatic activities and their regulation is essential for understanding the life cycles of many pathogenic RNA viruses and for antiviral drug discovery. We developed biochemical and biophysical kinetic methods to study the RNA synthesis and RNA binding activities of respiratory syncytial virus (RSV) L/P RdRP. We determined that the intact L protein is essential for RdRP activity, and in truncated L protein constructs, RdRP activity is abrogated due to their deficiency in RNA template binding. These results are in agreement with the observation of an RNA template-binding tunnel at the interface of RdRP and capping domains in RSV and vesicular stomatitis virus (VSV) L protein cryo-EM structures. We also describe nonradiometric assays for measuring RNA binding and RNA polymerization activity of RSV RdRP, which are amenable to compound screening and profiling.
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Affiliation(s)
- Anand Balakrishnan
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Edmund Price
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Catherine Luu
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Jacob Shaul
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Charles Wartchow
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - John Cantwell
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Todd Vo
- Structural Biology and Protein Sciences, Genomics Institute of the Novartis Research Foundation, La Jolla, California 92121, United States
| | - Michael DiDonato
- Structural Biology and Protein Sciences, Genomics Institute of the Novartis Research Foundation, La Jolla, California 92121, United States
| | - Glen Spraggon
- Structural Biology and Protein Sciences, Genomics Institute of the Novartis Research Foundation, La Jolla, California 92121, United States
| | - Mohammad Hekmat-Nejad
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
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21
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Blanchard EL, Braun MR, Lifland AW, Ludeke B, Noton SL, Vanover D, Zurla C, Fearns R, Santangelo PJ. Polymerase-tagged respiratory syncytial virus reveals a dynamic rearrangement of the ribonucleocapsid complex during infection. PLoS Pathog 2020; 16:e1008987. [PMID: 33031461 PMCID: PMC7575074 DOI: 10.1371/journal.ppat.1008987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 10/20/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
The ribonucleocapsid complex of respiratory syncytial virus (RSV) is responsible for both viral mRNA transcription and viral replication during infection, though little is known about how this dual function is achieved. Here, we report the use of a recombinant RSV virus with a FLAG-tagged large polymerase protein, L, to characterize and localize RSV ribonucleocapsid structures during the early and late stages of viral infection. Through proximity ligation assays and super-resolution microscopy, viral RNA and proteins in the ribonucleocapsid complex were revealed to dynamically rearrange over time, particularly between 6 and 8 hours post infection, suggesting a connection between the ribonucleocapsid structure and its function. The timing of ribonucleocapsid rearrangement corresponded with an increase in RSV genome RNA accumulation, indicating that this rearrangement is likely involved with the onset of RNA replication and secondary transcription. Additionally, early overexpression of RSV M2-2 from in vitro transcribed mRNA was shown to inhibit virus infection by rearranging the ribonucleocapsid complex. Collectively, these results detail a critical understanding into the localization and activity of RSV L and the ribonucleocapsid complex during RSV infection.
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Affiliation(s)
- Emmeline L. Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States of America
| | - Molly R. Braun
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Aaron W. Lifland
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Barbara Ludeke
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States of America
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States of America
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22
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Cox RM, Sourimant J, Toots M, Yoon JJ, Ikegame S, Govindarajan M, Watkinson RE, Thibault P, Makhsous N, Lin MJ, Marengo JR, Sticher Z, Kolykhalov AA, Natchus MG, Greninger AL, Lee B, Plemper RK. Orally efficacious broad-spectrum allosteric inhibitor of paramyxovirus polymerase. Nat Microbiol 2020; 5:1232-1246. [PMID: 32661315 PMCID: PMC7529989 DOI: 10.1038/s41564-020-0752-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/09/2020] [Indexed: 12/13/2022]
Abstract
Paramyxoviruses such as human parainfluenza virus type-3 (HPIV3) and measles virus (MeV) are a substantial health threat. In a high-throughput screen for inhibitors of HPIV3 (a major cause of acute respiratory infection), we identified GHP-88309-a non-nucleoside inhibitor of viral polymerase activity that possesses unusual broad-spectrum activity against diverse paramyxoviruses including respiroviruses (that is, HPIV1 and HPIV3) and morbilliviruses (that is, MeV). Resistance profiles of distinct target viruses overlapped spatially, revealing a conserved binding site in the central cavity of the viral polymerase (L) protein that was validated by photoaffinity labelling-based target mapping. Mechanistic characterization through viral RNA profiling and in vitro MeV polymerase assays identified a block in the initiation phase of the viral polymerase. GHP-88309 showed nanomolar potency against HPIV3 isolates in well-differentiated human airway organoid cultures, was well tolerated (selectivity index > 7,111) and orally bioavailable, and provided complete protection against lethal infection in a Sendai virus mouse surrogate model of human HPIV3 disease when administered therapeutically 48 h after infection. Recoverees had acquired robust immunoprotection against reinfection, and viral resistance coincided with severe attenuation. This study provides proof of the feasibility of a well-behaved broad-spectrum allosteric antiviral and describes a chemotype with high therapeutic potential that addresses major obstacles of anti-paramyxovirus drug development.
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Affiliation(s)
- Robert M Cox
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Julien Sourimant
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Mart Toots
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Jeong-Joong Yoon
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Satoshi Ikegame
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ruth E Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patricia Thibault
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Negar Makhsous
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Michelle J Lin
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Jose R Marengo
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | - Zachary Sticher
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | | | - Michael G Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, GA, USA
| | - Alexander L Greninger
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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Andrade CA, Pacheco GA, Gálvez NMS, Soto JA, Bueno SM, Kalergis AM. Innate Immune Components that Regulate the Pathogenesis and Resolution of hRSV and hMPV Infections. Viruses 2020; 12:E637. [PMID: 32545470 PMCID: PMC7354512 DOI: 10.3390/v12060637] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023] Open
Abstract
The human respiratory syncytial virus (hRSV) and human Metapneumovirus (hMPV) are two of the leading etiological agents of acute lower respiratory tract infections, which constitute the main cause of mortality in infants. However, there are currently approved vaccines for neither hRSV nor hMPV. Moreover, despite the similarity between the pathology caused by both viruses, the immune response elicited by the host is different in each case. In this review, we discuss how dendritic cells, alveolar macrophages, neutrophils, eosinophils, natural killer cells, innate lymphoid cells, and the complement system regulate both pathogenesis and the resolution of hRSV and hMPV infections. The roles that these cells play during infections by either of these viruses will help us to better understand the illnesses they cause. We also discuss several controversial findings, relative to some of these innate immune components. To better understand the inflammation in the lungs, the role of the respiratory epithelium in the recruitment of innate immune cells is briefly discussed. Finally, we review the main prophylactic strategies and current vaccine candidates against both hRSV and hMPV.
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Affiliation(s)
- Catalina A. Andrade
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (C.A.A.); (G.A.P.); (N.M.S.G.); (J.A.S.); (S.M.B.)
| | - Gaspar A. Pacheco
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (C.A.A.); (G.A.P.); (N.M.S.G.); (J.A.S.); (S.M.B.)
| | - Nicolas M. S. Gálvez
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (C.A.A.); (G.A.P.); (N.M.S.G.); (J.A.S.); (S.M.B.)
| | - Jorge A. Soto
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (C.A.A.); (G.A.P.); (N.M.S.G.); (J.A.S.); (S.M.B.)
| | - Susan M. Bueno
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (C.A.A.); (G.A.P.); (N.M.S.G.); (J.A.S.); (S.M.B.)
| | - Alexis M. Kalergis
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (C.A.A.); (G.A.P.); (N.M.S.G.); (J.A.S.); (S.M.B.)
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
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Gordon CJ, Tchesnokov EP, Feng JY, Porter DP, Götte M. The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus. J Biol Chem 2020; 295:4773-4779. [PMID: 32094225 PMCID: PMC7152756 DOI: 10.1074/jbc.ac120.013056] [Citation(s) in RCA: 527] [Impact Index Per Article: 131.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 02/19/2020] [Indexed: 01/16/2023] Open
Abstract
Antiviral drugs for managing infections with human coronaviruses are not yet approved,
posing a serious challenge to current global efforts aimed at containing the outbreak of
severe acute respiratory syndrome–coronavirus 2 (CoV-2). Remdesivir (RDV) is an
investigational compound with a broad spectrum of antiviral activities against RNA
viruses, including severe acute respiratory syndrome–CoV and Middle East
respiratory syndrome (MERS–CoV). RDV is a nucleotide analog inhibitor of
RNA-dependent RNA polymerases (RdRps). Here, we co-expressed the MERS–CoV
nonstructural proteins nsp5, nsp7, nsp8, and nsp12 (RdRp) in insect cells as a part a
polyprotein to study the mechanism of inhibition of MERS–CoV RdRp by RDV. We
initially demonstrated that nsp8 and nsp12 form an active complex. The triphosphate form
of the inhibitor (RDV-TP) competes with its natural counterpart ATP. Of note, the
selectivity value for RDV-TP obtained here with a steady-state approach suggests that it
is more efficiently incorporated than ATP and two other nucleotide analogs. Once
incorporated at position i, the inhibitor caused RNA synthesis arrest at
position i + 3. Hence, the likely mechanism of action is delayed RNA
chain termination. The additional three nucleotides may protect the inhibitor from
excision by the viral 3′–5′ exonuclease activity. Together, these
results help to explain the high potency of RDV against RNA viruses in cell-based
assays.
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Affiliation(s)
- Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Joy Y Feng
- Gilead Sciences, Inc., Foster City, California 94404
| | | | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada .,Li Ka Shing Institute of Virology at University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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25
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Cao D, Gao Y, Roesler C, Rice S, D'Cunha P, Zhuang L, Slack J, Domke M, Antonova A, Romanelli S, Keating S, Forero G, Juneja P, Liang B. Cryo-EM structure of the respiratory syncytial virus RNA polymerase. Nat Commun 2020; 11:368. [PMID: 31953395 PMCID: PMC6969064 DOI: 10.1038/s41467-019-14246-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/18/2019] [Indexed: 12/21/2022] Open
Abstract
The respiratory syncytial virus (RSV) RNA polymerase, constituted of a 250 kDa large (L) protein and tetrameric phosphoprotein (P), catalyzes three distinct enzymatic activities — nucleotide polymerization, cap addition, and cap methylation. How RSV L and P coordinate these activities is poorly understood. Here, we present a 3.67 Å cryo-EM structure of the RSV polymerase (L:P) complex. The structure reveals that the RNA dependent RNA polymerase (RdRp) and capping (Cap) domains of L interact with the oligomerization domain (POD) and C-terminal domain (PCTD) of a tetramer of P. The density of the methyltransferase (MT) domain of L and the N-terminal domain of P (PNTD) is missing. Further analysis and comparison with other RNA polymerases at different stages suggest the structure we obtained is likely to be at an elongation-compatible stage. Together, these data provide enriched insights into the interrelationship, the inhibitors, and the evolutionary implications of the RSV polymerase. Respiratory syncytial virus (RSV) is a pathogenic non-segmented negative-sense RNA virus and active RSV polymerase is composed of a 250 kDa large (L) protein and tetrameric phosphoprotein (P). Here, the authors present the 3.67 Å cryo-EM structure of the RSV polymerase (L:P) complex.
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Affiliation(s)
- Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Claire Roesler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Samantha Rice
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Paul D'Cunha
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lisa Zhuang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Julia Slack
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mason Domke
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Anna Antonova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sarah Romanelli
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Shayon Keating
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Gabriela Forero
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Puneet Juneja
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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26
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Gao Y, Cao D, Ahn HM, Swain A, Hill S, Ogilvie C, Kurien M, Rahmatullah T, Liang B. In vitro trackable assembly of RNA-specific nucleocapsids of the respiratory syncytial virus. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49942-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Gao Y, Cao D, Ahn HM, Swain A, Hill S, Ogilvie C, Kurien M, Rahmatullah T, Liang B. In vitro trackable assembly of RNA-specific nucleocapsids of the respiratory syncytial virus. J Biol Chem 2019; 295:883-895. [PMID: 31822560 PMCID: PMC6970927 DOI: 10.1074/jbc.ra119.011602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
The templates for transcription and replication by respiratory syncytial virus (RSV) polymerase are helical nucleocapsids (NCs), formed by viral RNAs that are encapsidated by the nucleoprotein (N). Proper NC assembly is vital for RSV polymerase to engage the RNA template for RNA synthesis. Previous studies of NCs or nucleocapsid-like particles (NCLPs) from RSV and other nonsegmented negative-sense RNA viruses have provided insights into the overall NC architecture. However, in these studies, the RNAs were either random cellular RNAs or average viral genomic RNAs. An in-depth mechanistic understanding of NCs has been hampered by lack of an in vitro assay that can track NC or NCLP assembly. Here we established a protocol to obtain RNA-free N protein (N0) and successfully demonstrated the utility of a new assay for tracking assembly of N with RNA oligonucleotides into NCLPs. We discovered that the efficiency of the NCLP (N–RNA) assembly depends on the length and sequence of the RNA incorporated into NCLPs. This work provides a framework to generate purified N0 and incorporate it with RNA into NCLPs in a controllable manner. We anticipate that our assay for in vitro trackable assembly of RSV-specific nucleocapsids may enable in-depth mechanistic analyses of this process.
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Affiliation(s)
- Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Hyunjun Max Ahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Anshuman Swain
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Shaylan Hill
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Claire Ogilvie
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Matthew Kurien
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Taha Rahmatullah
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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28
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Ludeke B, Fearns R. The respiratory syncytial virus polymerase can perform RNA synthesis with modified primers and nucleotide analogs. Virology 2019; 540:66-74. [PMID: 31739186 DOI: 10.1016/j.virol.2019.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/03/2019] [Accepted: 11/03/2019] [Indexed: 12/29/2022]
Abstract
Respiratory syncytial virus (RSV) is significant for public health, capable of causing respiratory tract disease in infants, the elderly and the immunocompromised. The RSV polymerase is an attractive target for antiviral drug development, but as yet, there is no high throughput assay for analyzing RSV polymerase activity, specifically. In this study, using a primer elongation assay as a basis, we analyzed the tolerance of the RSV polymerase for modifications at the 5' end of the primer, and nucleotide analogs. The RSV polymerase was found to accept primers containing 5' biotin or digoxygenin modifications, and nucleotide analogs that are reactive or fluorescent, including 5-ethynyl UTP, 8-azido ATP, 2-amino PTP, and thieno-GTP. These findings provide a menu of options for developing non-isotopic high throughput assays for RSV polymerase RNA synthesis activity, and yield insight regarding the molecular biology of the polymerase complex.
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Affiliation(s)
- Barbara Ludeke
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
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29
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The Respiratory Syncytial Virus Polymerase: A Multitasking Machine. Trends Microbiol 2019; 27:969-971. [PMID: 31672264 DOI: 10.1016/j.tim.2019.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 11/21/2022]
Abstract
Respiratory syncytial virus (RSV) inflicts a significant toll on human life. An essential element of the virus is its polymerase, a complex capable of transcribing and replicating the viral genome. In an exciting new advance, Gilman et al. resolve the structure of this polymerase, providing valuable mechanistic insight into its activities.
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30
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Hume AJ, Mühlberger E. Distinct Genome Replication and Transcription Strategies within the Growing Filovirus Family. J Mol Biol 2019; 431:4290-4320. [PMID: 31260690 PMCID: PMC6879820 DOI: 10.1016/j.jmb.2019.06.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/31/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022]
Abstract
Research on filoviruses has historically focused on the highly pathogenic ebola- and marburgviruses. Indeed, until recently, these were the only two genera in the filovirus family. Recent advances in sequencing technologies have facilitated the discovery of not only a new ebolavirus, but also three new filovirus genera and a sixth proposed genus. While two of these new genera are similar to the ebola- and marburgviruses, the other two, discovered in saltwater fishes, are considerably more diverse. Nonetheless, these viruses retain a number of key features of the other filoviruses. Here, we review the key characteristics of filovirus replication and transcription, highlighting similarities and differences between the viruses. In particular, we focus on key regulatory elements in the genomes, replication and transcription strategies, and the conservation of protein domains and functions among the viruses. In addition, using computational analyses, we were able to identify potential homology and functions for some of the genes of the novel filoviruses with previously unknown functions. Although none of the newly discovered filoviruses have yet been isolated, initial studies of some of these viruses using minigenome systems have yielded insights into their mechanisms of replication and transcription. In general, the Cuevavirus and proposed Dianlovirus genera appear to follow the transcription and replication strategies employed by the ebola- and marburgviruses, respectively. While our knowledge of the fish filoviruses is currently limited to sequence analysis, the lack of certain conserved motifs and even entire genes necessitates that they have evolved distinct mechanisms of replication and transcription.
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Affiliation(s)
- Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA.
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31
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Cressey TN, Noton SL, Nagendra K, Braun MR, Fearns R. Mechanism for de novo initiation at two sites in the respiratory syncytial virus promoter. Nucleic Acids Res 2019; 46:6785-6796. [PMID: 29873775 PMCID: PMC6061868 DOI: 10.1093/nar/gky480] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/17/2018] [Indexed: 12/18/2022] Open
Abstract
The respiratory syncytial virus (RSV) RNA dependent RNA polymerase (RdRp) initiates two RNA synthesis processes from the viral promoter: genome replication from position 1U and mRNA transcription from position 3C. Here, we examined the mechanism by which a single promoter can direct initiation from two sites. We show that initiation at 1U and 3C occurred independently of each other, and that the same RdRp was capable of precisely selecting the two sites. The RdRp preferred to initiate at 3C, but initiation site selection could be modulated by the relative concentrations of ATP versus GTP. Analysis of template mutations indicated that the RdRp could bind ATP and CTP, or GTP, independently of template nucleotides. The data suggest a model in which innate affinity of the RdRp for particular NTPs, coupled with a repeating element within the promoter, allows precise initiation of replication at 1U or transcription at 3C.
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Affiliation(s)
- Tessa N Cressey
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sarah L Noton
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kartikeya Nagendra
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Molly R Braun
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
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32
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Ebolavirus polymerase uses an unconventional genome replication mechanism. Proc Natl Acad Sci U S A 2019; 116:8535-8543. [PMID: 30962389 DOI: 10.1073/pnas.1815745116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Most nonsegmented negative strand (NNS) RNA virus genomes have complementary 3' and 5' terminal nucleotides because the promoters at the 3' ends of the genomes and antigenomes are almost identical to each other. However, according to published sequences, both ends of ebolavirus genomes show a high degree of variability, and the 3' and 5' terminal nucleotides are not complementary. If correct, this would distinguish the ebolaviruses from other NNS RNA viruses. Therefore, we investigated the terminal genomic and antigenomic nucleotides of three different ebolavirus species, Ebola (EBOV), Sudan, and Reston viruses. Whereas the 5' ends of ebolavirus RNAs are highly conserved with the sequence ACAGG-5', the 3' termini are variable and are typically 3'-GCCUGU, ACCUGU, or CCUGU. A small fraction of analyzed RNAs had extended 3' ends. The majority of 3' terminal sequences are consistent with a mechanism of nucleotide addition by hairpin formation and back-priming. Using single-round replicating EBOV minigenomes, we investigated the effect of the 3' terminal nucleotide on viral replication and found that the EBOV polymerase initiates replication opposite the 3'-CCUGU motif regardless of the identity of the 3' terminal nucleotide(s) and of the position of this motif relative to the 3' end. Deletion or mutation of the first residue of the 3'-CCUGU motif completely abolished replication initiation, suggesting a crucial role of this nucleotide in directing initiation. Together, our data show that ebolaviruses have evolved a unique replication strategy among NNS RNA viruses resulting in 3' overhangs. This could be a mechanism to avoid antiviral recognition.
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33
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Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir. Viruses 2019; 11:v11040326. [PMID: 30987343 PMCID: PMC6520719 DOI: 10.3390/v11040326] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 11/17/2022] Open
Abstract
Remdesivir (GS-5734) is a 1'-cyano-substituted adenosine nucleotide analogue prodrug that shows broad-spectrum antiviral activity against several RNA viruses. This compound is currently under clinical development for the treatment of Ebola virus disease (EVD). While antiviral effects have been demonstrated in cell culture and in non-human primates, the mechanism of action of Ebola virus (EBOV) inhibition for remdesivir remains to be fully elucidated. The EBOV RNA-dependent RNA polymerase (RdRp) complex was recently expressed and purified, enabling biochemical studies with the relevant triphosphate (TP) form of remdesivir and its presumptive target. In this study, we confirmed that remdesivir-TP is able to compete for incorporation with adenosine triphosphate (ATP). Enzyme kinetics revealed that EBOV RdRp and respiratory syncytial virus (RSV) RdRp incorporate ATP and remdesivir-TP with similar efficiencies. The selectivity of ATP against remdesivir-TP is ~4 for EBOV RdRp and ~3 for RSV RdRp. In contrast, purified human mitochondrial RNA polymerase (h-mtRNAP) effectively discriminates against remdesivir-TP with a selectivity value of ~500-fold. For EBOV RdRp, the incorporated inhibitor at position i does not affect the ensuing nucleotide incorporation event at position i+1. For RSV RdRp, we measured a ~6-fold inhibition at position i+1 although RNA synthesis was not terminated. Chain termination was in both cases delayed and was seen predominantly at position i+5. This pattern is specific to remdesivir-TP and its 1'-cyano modification. Compounds with modifications at the 2'-position show different patterns of inhibition. While 2'-C-methyl-ATP is not incorporated, ara-ATP acts as a non-obligate chain terminator and prevents nucleotide incorporation at position i+1. Taken together, our biochemical data indicate that the major contribution to EBOV RNA synthesis inhibition by remdesivir can be ascribed to delayed chain termination. The long distance of five residues between the incorporated nucleotide analogue and its inhibitory effect warrant further investigation.
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34
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Noton SL, Tremaglio CZ, Fearns R. Killing two birds with one stone: How the respiratory syncytial virus polymerase initiates transcription and replication. PLoS Pathog 2019; 15:e1007548. [PMID: 30817806 PMCID: PMC6394897 DOI: 10.1371/journal.ppat.1007548] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Chadene Z. Tremaglio
- Department of Biology, University of Saint Joseph, West Hartford, Connecticut, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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35
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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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36
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Cox RM, Toots M, Yoon JJ, Sourimant J, Ludeke B, Fearns R, Bourque E, Patti J, Lee E, Vernachio J, Plemper RK. Development of an allosteric inhibitor class blocking RNA elongation by the respiratory syncytial virus polymerase complex. J Biol Chem 2018; 293:16761-16777. [PMID: 30206124 DOI: 10.1074/jbc.ra118.004862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Indexed: 12/22/2022] Open
Abstract
Respiratory syncytial virus (RSV) represents a significant health threat to infants and to elderly or immunocompromised individuals. There are currently no vaccines available to prevent RSV infections, and disease management is largely limited to supportive care, making the identification and development of effective antiviral therapeutics against RSV a priority. To identify effective chemical scaffolds for managing RSV disease, we conducted a high-throughput anti-RSV screen of a 57,000-compound library. We identified a hit compound that specifically blocked activity of the RSV RNA-dependent RNA polymerase (RdRp) complex, initially with moderate low-micromolar potency. Mechanistic characterization in an in vitro RSV RdRp assay indicated that representatives of this compound class block elongation of RSV RNA products after initial extension by up to three nucleotides. Synthetic hit-to-lead exploration yielded an informative 3D quantitative structure-activity relationship (3D-QSAR) model and resulted in analogs with more than 20-fold improved potency and selectivity indices (SIs) of >1,000. However, first-generation leads exhibited limited water solubility and poor metabolic stability. A second optimization strategy informed by the 3D-QSAR model combined with in silico pharmacokinetics (PK) predictions yielded an advanced lead, AVG-233, that demonstrated nanomolar activity against both laboratory-adapted RSV strains and clinical RSV isolates. This anti-RSV activity extended to infection of established cell lines and primary human airway cells. PK profiling in mice revealed 34% oral bioavailability of AVG-233 and sustained high drug levels in the circulation after a single oral dose of 20 mg/kg. This promising first-in-class lead warrants further development as an anti-RSV drug.
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Affiliation(s)
- Robert M Cox
- From the Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303
| | - Mart Toots
- From the Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303
| | - Jeong-Joong Yoon
- From the Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303
| | - Julien Sourimant
- From the Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303
| | - Barbara Ludeke
- the Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts 02118, and
| | - Rachel Fearns
- the Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts 02118, and
| | | | - Joseph Patti
- Aviragen Therapeutics, Alpharetta, Georgia 30009
| | - Edward Lee
- Aviragen Therapeutics, Alpharetta, Georgia 30009
| | | | - Richard K Plemper
- From the Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303,
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Orally Efficacious Broad-Spectrum Ribonucleoside Analog Inhibitor of Influenza and Respiratory Syncytial Viruses. Antimicrob Agents Chemother 2018; 62:AAC.00766-18. [PMID: 29891600 DOI: 10.1128/aac.00766-18] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 05/31/2018] [Indexed: 01/29/2023] Open
Abstract
Morbidity and mortality resulting from influenza-like disease are a threat, especially for older adults. To improve case management, next-generation broad-spectrum antiviral therapeutics that are efficacious against major drivers of influenza-like disease, including influenza viruses and respiratory syncytial virus (RSV), are urgently needed. Using a dual-pathogen high-throughput screening protocol for influenza A virus (IAV) and RSV inhibitors, we have identified N4-hydroxycytidine (NHC) as a potent inhibitor of RSV, influenza B viruses, and IAVs of human, avian, and swine origins. Biochemical in vitro polymerase assays and viral RNA sequencing revealed that the ribonucleotide analog is incorporated into nascent viral RNAs in place of cytidine, increasing the frequency of viral mutagenesis. Viral passaging in cell culture in the presence of an inhibitor did not induce robust resistance. Pharmacokinetic profiling demonstrated dose-dependent oral bioavailability of 36 to 56%, sustained levels of the active 5'-triphosphate anabolite in primary human airway cells and mouse lung tissue, and good tolerability after extended dosing at 800 mg/kg of body weight/day. The compound was orally efficacious against RSV and both seasonal and highly pathogenic avian IAVs in mouse models, reducing lung virus loads and alleviating disease biomarkers. Oral dosing reduced IAV burdens in a guinea pig transmission model and suppressed virus spread to uninfected contact animals through direct transmission. Based on its broad-spectrum efficacy and pharmacokinetic properties, NHC is a promising candidate for future clinical development as a treatment option for influenza-like diseases.
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Lo MK, Jordan PC, Stevens S, Tam Y, Deval J, Nichol ST, Spiropoulou CF. Susceptibility of paramyxoviruses and filoviruses to inhibition by 2'-monofluoro- and 2'-difluoro-4'-azidocytidine analogs. Antiviral Res 2018; 153:101-113. [PMID: 29601894 PMCID: PMC6066796 DOI: 10.1016/j.antiviral.2018.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/20/2018] [Accepted: 03/24/2018] [Indexed: 02/07/2023]
Abstract
Ebolaviruses, marburgviruses, and henipaviruses are zoonotic pathogens belonging to the Filoviridae and Paramyxoviridae families. They exemplify viruses that continue to spill over into the human population, causing outbreaks characterized by high mortality and significant clinical sequelae in survivors of infection. There are currently no approved small molecule therapeutics for use in humans against these viruses. In this study, we evaluated the antiviral activity of the nucleoside analog 4'-azidocytidine (4'N3-C, R1479) and its 2'-monofluoro- and 2'-difluoro-modified analogs (2'F-4'N3-C and 2'diF-4'N3-C) against representative paramyxoviruses (Nipah virus, Hendra virus, measles virus, and human parainfluenza virus 3) and filoviruses (Ebola virus, Sudan virus, and Ravn virus). We observed enhanced antiviral activity against paramyxoviruses with both 2'diF-4'N3-C and 2'F-4'N3-C compared to R1479. On the other hand, while R1479 and 2'diF-4'N3-C inhibited filoviruses similarly to paramyxoviruses, we observed 10-fold lower filovirus inhibition by 2'F-4'N3-C. To our knowledge, this is the first study to compare the susceptibility of paramyxoviruses and filoviruses to R1479 and its 2'-fluoro-modified analogs. The activity of these compounds against negative-strand RNA viruses endorses the development of 4'-modified nucleoside analogs as broad-spectrum therapeutics against zoonotic viruses of public health importance.
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Affiliation(s)
- Michael K Lo
- US Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Paul C Jordan
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, CA, USA
| | - Sarah Stevens
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, CA, USA
| | - Yuen Tam
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, CA, USA
| | - Jerome Deval
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, CA, USA
| | - Stuart T Nichol
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
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Recombinant RNA-Dependent RNA Polymerase Complex of Ebola Virus. Sci Rep 2018; 8:3970. [PMID: 29507309 PMCID: PMC5838098 DOI: 10.1038/s41598-018-22328-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/21/2018] [Indexed: 12/18/2022] Open
Abstract
Here we report on the expression, purification and characterization of recombinant ebola virus RNA-dependent RNA polymerase (EBOV RdRp). Active protein complexes composed of the large L protein and viral protein VP35 were isolated from insect cells and analyzed using a short primer/template substrate that allowed benchmarking against related enzymes. RNA synthesis by multiprotein complexes of EBOV, influenza B, respiratory syncytial virus (RSV) and monomeric enzymes of hepatitis C and Zika (ZIKV) viruses required a 5′-phosporylated primer. The minimum length of the primer varied between two and three nucleotides in this system. The EBOV enzyme utilizes Mg2+ as a co-factor and the D742A substitution provides an active site mutant that likely affects binding of the catalytic metal ions. Selectivity measurements with nucleotide analogues translate our assay into quantitative terms and facilitate drug discovery efforts. The related EBOV and RSV enzymes are not able to efficiently discriminate against ara-cytidine-5′-triphosphate. We demonstrate that this compound acts like a non-obligate chain-terminator.
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Jordan PC, Liu C, Raynaud P, Lo MK, Spiropoulou CF, Symons JA, Beigelman L, Deval J. Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase. PLoS Pathog 2018; 14:e1006889. [PMID: 29425244 PMCID: PMC5823471 DOI: 10.1371/journal.ppat.1006889] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/22/2018] [Accepted: 01/21/2018] [Indexed: 01/27/2023] Open
Abstract
Paramyxoviruses represent a family of RNA viruses causing significant human diseases. These include measles virus, the most infectious virus ever reported, in addition to parainfluenza virus, and other emerging viruses. Paramyxoviruses likely share common replication machinery but their mechanisms of RNA biosynthesis activities and details of their complex polymerase structures are unknown. Mechanistic and functional details of a paramyxovirus polymerase would have sweeping implications for understanding RNA virus replication and for the development of new antiviral medicines. To study paramyxovirus polymerase structure and function, we expressed an active recombinant Nipah virus (NiV) polymerase complex assembled from the multifunctional NiV L protein bound to its phosphoprotein cofactor. NiV is an emerging highly pathogenic virus that causes severe encephalitis and has been declared a global public health concern due to its high mortality rate. Using negative-stain electron microscopy, we demonstrated NiV polymerase forms ring-like particles resembling related RNA polymerases. We identified conserved sequence elements driving recognition of the 3′-terminal genomic promoter by NiV polymerase, and leading to initiation of RNA synthesis, primer extension, and transition to elongation mode. Polyadenylation resulting from NiV polymerase stuttering provides a mechanistic basis for transcription termination. It also suggests a divergent adaptation in promoter recognition between pneumo- and paramyxoviruses. The lack of available antiviral therapy for NiV prompted us to identify the triphosphate forms of R1479 and GS-5734, two clinically relevant nucleotide analogs, as substrates and inhibitors of NiV polymerase activity by delayed chain termination. Overall, these findings provide low-resolution structural details and the mechanism of an RNA polymerase from a previously uncharacterized virus family. This work illustrates important functional differences yet remarkable similarities between the polymerases of nonsegmented negative-strand RNA viruses. RNA viruses replicate and transcribe their genomes using complex enzymatic machines known as RNA-dependent RNA polymerases. The chemical reactions driving nucleotide addition are shared among nucleic acid polymerases but the underlying mechanisms of RNA biosynthesis and the complex polymerase structures are diverse. Of these RNA viruses is the paramyxovirus family, which includes major human pathogens. Paramyxoviruses have common biological and genetic properties but little is known about their replication machinery. Insights into the structure, function, and mechanisms of RNA synthesis of one paramyxovirus polymerase will likely extend to the entire virus family. An emerging, highly pathogenic paramyxovirus is Nipah virus (NiV), which causes encephalitis in humans. We have purified NiV polymerase, probed its enzymatic and biophysical properties and developed it as a model paramyxovirus polymerase. We investigated template strand sequence elements driving RNA biosynthesis for NiV polymerase and obtained a snapshot of NiV polymerase molecular organization using electron microscopy to provide the first structural information on a paramyxovirus polymerase. This work extends previous knowledge by producing the first recombinant paramyxovirus polymerase and using this protein in enzymatic assays to highlight key functional and structural characteristics for the design of new medicines.
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Affiliation(s)
- Paul C. Jordan
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Cheng Liu
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Pauline Raynaud
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Michael K. Lo
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Julian A. Symons
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Leo Beigelman
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Jerome Deval
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
- * E-mail:
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Braun MR, Deflubé LR, Noton SL, Mawhorter ME, Tremaglio CZ, Fearns R. RNA elongation by respiratory syncytial virus polymerase is calibrated by conserved region V. PLoS Pathog 2017; 13:e1006803. [PMID: 29281742 PMCID: PMC5760109 DOI: 10.1371/journal.ppat.1006803] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 01/09/2018] [Accepted: 12/11/2017] [Indexed: 02/06/2023] Open
Abstract
The large polymerase subunit (L) of non-segmented negative strand RNA viruses transcribes viral mRNAs and replicates the viral genome. Studies with VSV have shown that conserved region V (CRV) of the L protein is part of the capping domain. However, CRV folds over and protrudes into the polymerization domain, suggesting that it might also have a role in RNA synthesis. In this study, the role of respiratory syncytial virus (RSV) CRV was evaluated using single amino acid substitutions and a small molecule inhibitor called BI-D. Effects were analyzed using cell-based minigenome and in vitro biochemical assays. Several amino acid substitutions inhibited production of capped, full-length mRNA and instead resulted in accumulation of short transcripts of approximately 40 nucleotides in length, confirming that RSV CRV has a role in capping. In addition, all six variants tested were either partially or completely defective in RNA replication. This was due to an inability of the polymerase to efficiently elongate the RNA within the promoter region. BI-D also inhibited transcription and replication. In this case, polymerase elongation activity within the promoter region was enhanced, such that the small RNA transcribed from the promoter was not released and instead was elongated past the first gene start signal. This was accompanied by a decrease in mRNA initiation at the first gene start signal and accumulation of aberrant RNAs of varying length. Thus, in addition to its function in mRNA capping, conserved region V modulates the elongation properties of the polymerase to enable productive transcription and replication to occur.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antiviral Agents/pharmacology
- Cell Line
- Conserved Sequence
- Drug Discovery
- Genes, Viral
- Humans
- Models, Molecular
- Promoter Regions, Genetic
- RNA Caps/genetics
- RNA Caps/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- RNA-Dependent RNA Polymerase/metabolism
- Respiratory Syncytial Virus Infections/drug therapy
- Respiratory Syncytial Virus Infections/virology
- Respiratory Syncytial Virus, Human/genetics
- Respiratory Syncytial Virus, Human/metabolism
- Respiratory Syncytial Virus, Human/pathogenicity
- Transcription Elongation, Genetic
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
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Affiliation(s)
- Molly R. Braun
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Laure R. Deflubé
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Michael E. Mawhorter
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Chadene Z. Tremaglio
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
- * E-mail:
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Harwig A, Landick R, Berkhout B. The Battle of RNA Synthesis: Virus versus Host. Viruses 2017; 9:v9100309. [PMID: 29065472 PMCID: PMC5691660 DOI: 10.3390/v9100309] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022] Open
Abstract
Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to optimally exploit cellular host processes such as transcription to their own benefit. Just as cells are increasingly understood to employ nascent RNAs in transcription regulation, recent discoveries are revealing how viruses use nascent RNAs to benefit their own gene expression. In this review, we first outline the two different transcription programs used by viruses, i.e., transcription (DNA-dependent) and RNA-dependent RNA synthesis. Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage.
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Affiliation(s)
- Alex Harwig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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43
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Respiratory Syncytial Virus: Infection, Detection, and New Options for Prevention and Treatment. Clin Microbiol Rev 2017; 30:277-319. [PMID: 27903593 DOI: 10.1128/cmr.00010-16] [Citation(s) in RCA: 336] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Respiratory syncytial virus (RSV) infection is a significant cause of hospitalization of children in North America and one of the leading causes of death of infants less than 1 year of age worldwide, second only to malaria. Despite its global impact on human health, there are relatively few therapeutic options available to prevent or treat RSV infection. Paradoxically, there is a very large volume of information that is constantly being refined on RSV replication, the mechanisms of RSV-induced pathology, and community transmission. Compounding the burden of acute RSV infections is the exacerbation of preexisting chronic airway diseases and the chronic sequelae of RSV infection. A mechanistic link is even starting to emerge between asthma and those who suffer severe RSV infection early in childhood. In this article, we discuss developments in the understanding of RSV replication, pathogenesis, diagnostics, and therapeutics. We attempt to reconcile the large body of information on RSV and why after many clinical trials there is still no efficacious RSV vaccine and few therapeutics.
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44
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Longhi S, Bloyet LM, Gianni S, Gerlier D. How order and disorder within paramyxoviral nucleoproteins and phosphoproteins orchestrate the molecular interplay of transcription and replication. Cell Mol Life Sci 2017; 74:3091-3118. [PMID: 28600653 PMCID: PMC11107670 DOI: 10.1007/s00018-017-2556-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/01/2023]
Abstract
In this review, we summarize computational and experimental data gathered so far showing that structural disorder is abundant within paramyxoviral nucleoproteins (N) and phosphoproteins (P). In particular, we focus on measles, Nipah, and Hendra viruses and highlight both commonalities and differences with respect to the closely related Sendai virus. The molecular mechanisms that control the disorder-to-order transition undergone by the intrinsically disordered C-terminal domain (NTAIL) of their N proteins upon binding to the C-terminal X domain (XD) of the homologous P proteins are described in detail. By having a significant residual disorder, NTAIL-XD complexes are illustrative examples of "fuzziness", whose possible functional significance is discussed. Finally, the relevance of N-P interactions as promising targets for innovative antiviral approaches is underscored, and the functional advantages of structural disorder for paramyxoviruses are pinpointed.
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Affiliation(s)
- Sonia Longhi
- Aix-Marseille Univ, AFMB UMR 7257, 163, avenue de Luminy, Case 932, 13288, Marseille Cedex 09, France.
- CNRS, AFMB UMR 7257, 13288, Marseille, France.
| | - Louis-Marie Bloyet
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- INSERM, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Stefano Gianni
- Istituto Pasteur, Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185, Rome, Italy
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- INSERM, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
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45
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Fearns R, Plemper RK. Polymerases of paramyxoviruses and pneumoviruses. Virus Res 2017; 234:87-102. [PMID: 28104450 DOI: 10.1016/j.virusres.2017.01.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 11/13/2022]
Abstract
The paramyxo- and pneumoviruses are members of the order Mononegavirales, a group of viruses with non-segmented, negative strand RNA genomes. The polymerases of these viruses are multi-functional complexes, capable of transcribing subgenomic capped and polyadenylated mRNAs and replicating the genome. Although there is no native structure available for any complete paramyxo- or pneumovirus polymerase, functional and structural studies of a fragment of a pneumovirus polymerase protein and mutation analyses and resistance profiling of small-molecule inhibitors have generated a wealth of mechanistic information. This review integrates these data with the structure of a related polymerase, identifying similarities, differences, gaps in knowledge, and avenues for antiviral drug development.
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Affiliation(s)
- Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, United States.
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, United States
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An In Vitro RNA Synthesis Assay for Rabies Virus Defines Ribonucleoprotein Interactions Critical for Polymerase Activity. J Virol 2016; 91:JVI.01508-16. [PMID: 27795419 DOI: 10.1128/jvi.01508-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/20/2016] [Indexed: 12/17/2022] Open
Abstract
We report an in vitro RNA synthesis assay for the RNA-dependent RNA polymerase (RdRP) of rabies virus (RABV). We expressed RABV large polymerase protein (L) in insect cells from a recombinant baculovirus vector and the phosphoprotein cofactor (P) in Escherichia coli and purified the resulting proteins by affinity and size exclusion chromatography. Using chemically synthesized short RNA corresponding to the first 19 nucleotides (nt) of the rabies virus genome, we demonstrate that L alone initiates synthesis on naked RNA and that P serves to enhance the initiation and processivity of the RdRP. The L-P complex lacks full processivity, which we interpret to reflect the lack of the viral nucleocapsid protein (N) on the template. Using this assay, we define the requirements in P for stimulation of RdRP activity as residues 11 to 50 of P and formally demonstrate that ribavirin triphosphate (RTP) inhibits the RdRP. By comparing the properties of RABV RdRP with those of the related rhabdovirus, vesicular stomatitis virus (VSV), we demonstrate that both polymerases can copy the heterologous promoter sequence. The requirements for engagement of the N-RNA template of VSV by its polymerase are provided by the C-terminal domain (CTD) of P. A chimeric RABV P protein in which the oligomerization domain (OD) and the CTD were replaced by those of VSV P stimulated RABV RdRP activity on naked RNA but was insufficient to permit initiation on the VSV N-RNA template. This result implies that interactions between L and the template N are also required for initiation of RNA synthesis, extending our knowledge of ribonucleoprotein interactions that are critical for gene expression. IMPORTANCE The current understanding of the structural and functional significance of the components of the rabies virus replication machinery is incomplete. Although structures are available for the nucleocapsid protein in complex with RNA, and also for portions of P, information on both the structure and function of the L protein is lacking. This study reports the expression and purification of the full-length L protein of RABV and the characterization of its RdRP activity in vitro The study provides a new assay that has utility for screening inhibitors and understanding their mechanisms of action, as well as defining new interactions that are required for RdRP activity.
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47
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Fearns R, Deval J. New antiviral approaches for respiratory syncytial virus and other mononegaviruses: Inhibiting the RNA polymerase. Antiviral Res 2016; 134:63-76. [PMID: 27575793 DOI: 10.1016/j.antiviral.2016.08.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/27/2016] [Accepted: 08/07/2016] [Indexed: 11/16/2022]
Abstract
Worldwide, respiratory syncytial virus (RSV) causes severe disease in infants, the elderly, and immunocompromised people. No vaccine or effective antiviral treatment is available. RSV is a member of the non-segmented, negative-strand (NNS) group of RNA viruses and relies on its RNA-dependent RNA polymerase to transcribe and replicate its genome. Because of its essential nature and unique properties, the RSV polymerase has proven to be a good target for antiviral drugs, with one compound, ALS-8176, having already achieved clinical proof-of-concept efficacy in a human challenge study. In this article, we first provide an overview of the role of the RSV polymerase in viral mRNA transcription and genome replication. We then review past and current approaches to inhibiting the RSV polymerase, including use of nucleoside analogs and non-nucleoside inhibitors. Finally, we consider polymerase inhibitors that hold promise for treating infections with other NNS RNA viruses, including measles and Ebola.
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Affiliation(s)
- Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA.
| | - Jerome Deval
- Alios BioPharma, Inc., Part of the Janssen Pharmaceutical Companies, South San Francisco, CA, USA.
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48
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Koehler A, Kolesnikova L, Becker S. An active site mutation increases the polymerase activity of the guinea pig-lethal Marburg virus. J Gen Virol 2016; 97:2494-2500. [PMID: 27450090 DOI: 10.1099/jgv.0.000564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marburg virus (MARV) causes severe, often fatal, disease in humans and transient illness in rodents. Sequential passaging of MARV in guinea pigs resulted in selection of a lethal virus containing 4 aa changes. A D184N mutation in VP40 (VP40D184N), which leads to a species-specific gain of viral fitness, and three mutations in the active site of viral RNA-dependent RNA polymerase L, which were investigated in the present study for functional significance in human and guinea pig cells. The transcription/replication activity of L mutants was strongly enhanced by a substitution at position 741 (S741C), and inhibited by other substitutions (D758A and A759D) in both species. The polymerase activity of L carrying the S741C substitution was eightfold higher in guinea pig cells than in human cells upon co-expression with VP40D184N, suggesting that the additive effect of the two mutations provides MARV a replicative advantage in the new host.
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Affiliation(s)
- Alexander Koehler
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Germany
| | - Larissa Kolesnikova
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Germany
| | - Stephan Becker
- German Center for Infection Research (DZIF), Institut für Virologie, Philipps-Universität, Hans-Meerwein-Str. 2, 35043 Marburg, Germany.,Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Germany
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49
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Deval J, Fung A, Stevens SK, Jordan PC, Gromova T, Taylor JS, Hong J, Meng J, Wang G, Dyatkina N, Prhavc M, Symons JA, Beigelman L. Biochemical Effect of Resistance Mutations against Synergistic Inhibitors of RSV RNA Polymerase. PLoS One 2016; 11:e0154097. [PMID: 27163448 PMCID: PMC4862670 DOI: 10.1371/journal.pone.0154097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/08/2016] [Indexed: 11/18/2022] Open
Abstract
ALS-8112 is the parent molecule of ALS-8176, a first-in-class nucleoside analog prodrug effective in the clinic against respiratory syncytial virus (RSV) infection. The antiviral activity of ALS-8112 is mediated by its 5'-triphosphate metabolite (ALS-8112-TP, or 2'F-4'ClCH2-cytidine triphosphate) inhibiting the RNA polymerase activity of the RSV L-P protein complex through RNA chain termination. Four amino acid mutations in the RNA-dependent RNA polymerase (RdRp) domain of L (QUAD: M628L, A789V, L795I, and I796V) confer in vitro resistance to ALS-8112-TP by increasing its discrimination relative to natural CTP. In this study, we show that the QUAD mutations specifically recognize the ClCH2 group of ALS-8112-TP. Among the four mutations, A789V conferred the greatest resistance phenotype, which was consistent with its putative position in the active site of the RdRp domain. AZ-27, a non-nucleoside inhibitor of RSV, also inhibited the RdRp activity, with decreased inhibition potency in the presence of the Y1631H mutation. The QUAD mutations had no effect on the antiviral activity of AZ-27, and the Y1631H mutation did not significantly increase the discrimination of ALS-8112-TP. Combining ALS-8112 with AZ-27 in vitro resulted in significant synergistic inhibition of RSV replication. Overall, this is the first mechanistic study showing a lack of cross-resistance between mutations selected by different classes of RSV polymerase inhibitors acting in synergy, opening the door to future potential combination therapies targeting different regions of the L protein.
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Affiliation(s)
- Jerome Deval
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
- * E-mail:
| | - Amy Fung
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Sarah K. Stevens
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Paul C. Jordan
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Tatiana Gromova
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Joshua S. Taylor
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Jin Hong
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Jia Meng
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Guangyi Wang
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Natalia Dyatkina
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Marija Prhavc
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Julian A. Symons
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
| | - Leo Beigelman
- Alios BioPharma, Inc., part of the Janssen Pharmaceutical Companies, South San Francisco, California, United States of America
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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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