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van der Meulen K, Smets G, Rüdelsheim P. Viral Replicon Systems and Their Biosafety Aspects. APPLIED BIOSAFETY 2023; 28:102-122. [PMID: 37342518 PMCID: PMC10278005 DOI: 10.1089/apb.2022.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Introduction Viral RNA replicons are self-amplifying RNA molecules generated by deleting genetic information of one or multiple structural proteins of wild-type viruses. Remaining viral RNA is used as such (naked replicon) or packaged into a viral replicon particle (VRP), whereby missing genes or proteins are supplied via production cells. Since replicons mostly originate from pathogenic wild-type viruses, careful risk consideration is crucial. Methods A literature review was performed compiling information on potential biosafety risks of replicons originating from positive- and negative-sense single-stranded RNA viruses (except retroviruses). Results For naked replicons, risk considerations included genome integration, persistence in host cells, generation of virus-like vesicles, and off-target effects. For VRP, the main risk consideration was formation of primary replication competent virus (RCV) as a result of recombination or complementation. To limit the risks, mostly measures aiming at reducing the likelihood of RCV formation have been described. Also, modifying viral proteins in such a way that they do not exhibit hazardous characteristics in the unlikely event of RCV formation has been reported. Discussion and Conclusion Despite multiple approaches developed to reduce the likelihood of RCV formation, scientific uncertainty remains on the actual contribution of the measures and on limitations to test their effectiveness. In contrast, even though effectiveness of each individual measure is unclear, using multiple measures on different aspects of the system may create a solid barrier. Risk considerations identified in the current study can also be used to support risk group assignment of replicon constructs based on a purely synthetic design.
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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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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: 13] [Impact Index Per Article: 3.3] [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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Gilman MSA, Liu C, Fung A, Behera I, Jordan P, Rigaux P, Ysebaert N, Tcherniuk S, Sourimant J, Eléouët JF, Sutto-Ortiz P, Decroly E, Roymans D, Jin Z, McLellan JS. Structure of the Respiratory Syncytial Virus Polymerase Complex. Cell 2019; 179:193-204.e14. [PMID: 31495574 PMCID: PMC7111336 DOI: 10.1016/j.cell.2019.08.014] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 01/29/2023]
Abstract
Numerous interventions are in clinical development for respiratory syncytial virus (RSV) infection, including small molecules that target viral transcription and replication. These processes are catalyzed by a complex comprising the RNA-dependent RNA polymerase (L) and the tetrameric phosphoprotein (P). RSV P recruits multiple proteins to the polymerase complex and, with the exception of its oligomerization domain, is thought to be intrinsically disordered. Despite their critical roles in RSV transcription and replication, structures of L and P have remained elusive. Here, we describe the 3.2-Å cryo-EM structure of RSV L bound to tetrameric P. The structure reveals a striking tentacular arrangement of P, with each of the four monomers adopting a distinct conformation. The structure also rationalizes inhibitor escape mutants and mutations observed in live-attenuated vaccine candidates. These results provide a framework for determining the molecular underpinnings of RSV replication and transcription and should facilitate the design of effective RSV inhibitors. Cryo-EM structure of RSV L bound by tetrameric RSV P solved to 3.2 Å P tetramer adopts an asymmetric tentacular arrangement when bound to L L priming loop adopts elongation-compatible state without PRNTase-RdRp separation Structure rationalizes escape from small-molecule antivirals
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Affiliation(s)
- Morgan S A Gilman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Cheng Liu
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Amy Fung
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Ishani Behera
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Paul Jordan
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, 2340 Beerse, Belgium
| | - Nina Ysebaert
- Janssen Infectious Diseases and Vaccines, 2340 Beerse, Belgium
| | - Sergey Tcherniuk
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Julien Sourimant
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris Saclay, 78350 Jouy en Josas, France
| | | | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Dirk Roymans
- Janssen Infectious Diseases and Vaccines, 2340 Beerse, Belgium
| | - Zhinan Jin
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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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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Gerry CJ, Schreiber SL. Chemical probes and drug leads from advances in synthetic planning and methodology. Nat Rev Drug Discov 2018; 17:333-352. [PMID: 29651105 PMCID: PMC6707071 DOI: 10.1038/nrd.2018.53] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Screening of small-molecule libraries is a productive method for identifying both chemical probes of disease-related targets and potential starting points for drug discovery. In this article, we focus on strategies such as diversity-oriented synthesis that aim to explore novel areas of chemical space efficiently by populating small-molecule libraries with compounds containing structural features that are typically under-represented in commercially available screening collections. Drawing from more than a decade's worth of examples, we highlight how the design and synthesis of such libraries have been enabled by modern synthetic chemistry, and we illustrate the impact of the resultant chemical probes and drug leads in a wide range of diseases.
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Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- The Broad Institute of Harvard & MIT, Cambridge, MA, USA
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- The Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
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7
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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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