skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Molecular mechanism of respiratory syncytial virus fusion inhibitors

Abstract

Respiratory syncytial virus (RSV) is a leading cause of pneumonia and bronchiolitis in young children and the elderly. Therapeutic small molecules have been developed that bind the RSV F glycoprotein and inhibit membrane fusion, yet their binding sites and molecular mechanisms of action remain largely unknown. In this paper, we show that these inhibitors bind to a three-fold-symmetric pocket within the central cavity of the metastable prefusion conformation of RSV F. Inhibitor binding stabilizes this conformation by tethering two regions that must undergo a structural rearrangement to facilitate membrane fusion. Inhibitor-escape mutations occur in residues that directly contact the inhibitors or are involved in the conformational rearrangements required to accommodate inhibitor binding. Resistant viruses do not propagate as well as wild-type RSV in vitro, indicating a fitness cost for inhibitor escape. Finally and collectively, these findings provide new insight into class I viral fusion proteins and should facilitate development of optimal RSV fusion inhibitors.

Authors:
ORCiD logo [1];  [2];  [2];  [3];  [3];  [4];  [4];  [5];  [5];  [6];  [4];  [7];  [8];  [4];  [1]
  1. Geisel School of Medicine at Dartmouth, Hanover, NH (United States). Dept. of Biochemistry
  2. Janssen Infectious Diseases and Vaccines, Leiden (Netherlands)
  3. The Research Inst. at Nationwide Children's Hospital, Columbus, OH (United States). Center for Vaccines & Immunity
  4. Janssen Infectious Diseases & Vaccines BVBA, Beerse (Belgium). Respiratory Infections Research
  5. Janssen Pharmaceutica NV, Beerse (Belgium). Discovery Sciences
  6. Janssen Infectious Diseases & Vaccines BVBA, Beerse (Belgium). Medicinal Chemistry Dept.
  7. Janssen R&D LLC, Spring House, PA (United States). Computational Chemistry
  8. The Research Inst. at Nationwide Children's Hospital, Columbus, OH (United States). Center for Vaccines & Immunity; The Ohio State Univ., Columbus, OH (United States). College of Medicine. Dept. of Pediatrics
Publication Date:
Research Org.:
Geisel School of Medicine at Dartmouth, Hanover, NH (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Inst. of Health (NIH) (United States); Charles H. Hood Foundation (United States)
Contributing Org.:
The Ohio State Univ., Columbus, OH (United States); Janssen Infectious Diseases and Vaccines, Leiden (Netherlands); The Research Inst. at Nationwide Children's Hospital, Columbus, OH (United States); Janssen Infectious Diseases & Vaccines BVBA, Beerse (Belgium); Janssen Pharmaceutica NV, Beerse (Belgium); Janssen R&D LLC, Spring House, PA (United States)
OSTI Identifier:
1239404
Grant/Contract Number:  
AC02-06CH11357; AI 095684
Resource Type:
Accepted Manuscript
Journal Name:
Nature Chemical Biology
Additional Journal Information:
Journal Volume: 12; Journal Issue: 2; Journal ID: ISSN 1552-4450
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Infectious diseases; Mechanism of action; Structure-based drug design; Virology; X-ray crystallography

Citation Formats

Battles, Michael B., Langedijk, Johannes P., Furmanova-Hollenstein, Polina, Chaiwatpongsakorn, Supranee, Costello, Heather M., Kwanten, Leen, Vranckx, Luc, Vink, Paul, Jaensch, Steffen, Jonckers, Tim H. M., Koul, Anil, Arnoult, Eric, Peeples, Mark E., Roymans, Dirk, and McLellan, Jason S.. Molecular mechanism of respiratory syncytial virus fusion inhibitors. United States: N. p., 2015. Web. https://doi.org/10.1038/nchembio.1982.
Battles, Michael B., Langedijk, Johannes P., Furmanova-Hollenstein, Polina, Chaiwatpongsakorn, Supranee, Costello, Heather M., Kwanten, Leen, Vranckx, Luc, Vink, Paul, Jaensch, Steffen, Jonckers, Tim H. M., Koul, Anil, Arnoult, Eric, Peeples, Mark E., Roymans, Dirk, & McLellan, Jason S.. Molecular mechanism of respiratory syncytial virus fusion inhibitors. United States. https://doi.org/10.1038/nchembio.1982
Battles, Michael B., Langedijk, Johannes P., Furmanova-Hollenstein, Polina, Chaiwatpongsakorn, Supranee, Costello, Heather M., Kwanten, Leen, Vranckx, Luc, Vink, Paul, Jaensch, Steffen, Jonckers, Tim H. M., Koul, Anil, Arnoult, Eric, Peeples, Mark E., Roymans, Dirk, and McLellan, Jason S.. Mon . "Molecular mechanism of respiratory syncytial virus fusion inhibitors". United States. https://doi.org/10.1038/nchembio.1982. https://www.osti.gov/servlets/purl/1239404.
@article{osti_1239404,
title = {Molecular mechanism of respiratory syncytial virus fusion inhibitors},
author = {Battles, Michael B. and Langedijk, Johannes P. and Furmanova-Hollenstein, Polina and Chaiwatpongsakorn, Supranee and Costello, Heather M. and Kwanten, Leen and Vranckx, Luc and Vink, Paul and Jaensch, Steffen and Jonckers, Tim H. M. and Koul, Anil and Arnoult, Eric and Peeples, Mark E. and Roymans, Dirk and McLellan, Jason S.},
abstractNote = {Respiratory syncytial virus (RSV) is a leading cause of pneumonia and bronchiolitis in young children and the elderly. Therapeutic small molecules have been developed that bind the RSV F glycoprotein and inhibit membrane fusion, yet their binding sites and molecular mechanisms of action remain largely unknown. In this paper, we show that these inhibitors bind to a three-fold-symmetric pocket within the central cavity of the metastable prefusion conformation of RSV F. Inhibitor binding stabilizes this conformation by tethering two regions that must undergo a structural rearrangement to facilitate membrane fusion. Inhibitor-escape mutations occur in residues that directly contact the inhibitors or are involved in the conformational rearrangements required to accommodate inhibitor binding. Resistant viruses do not propagate as well as wild-type RSV in vitro, indicating a fitness cost for inhibitor escape. Finally and collectively, these findings provide new insight into class I viral fusion proteins and should facilitate development of optimal RSV fusion inhibitors.},
doi = {10.1038/nchembio.1982},
journal = {Nature Chemical Biology},
number = 2,
volume = 12,
place = {United States},
year = {2015},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 23 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Cross-resistance mechanism of respiratory syncytial virus against structurally diverse entry inhibitors
journal, August 2014

  • Yan, D.; Lee, S.; Thakkar, V. D.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 33
  • DOI: 10.1073/pnas.1405198111

Inhibition of Respiratory Syncytial Virus Fusion by the Small Molecule VP-14637 via Specific Interactions with F Protein
journal, May 2003


Structure of RSV Fusion Glycoprotein Trimer Bound to a Prefusion-Specific Neutralizing Antibody
journal, April 2013


Orally Active Fusion Inhibitor of Respiratory Syncytial Virus
journal, January 2004


Phaedra, a Protocol-Driven System for Analysis and Validation of High-Content Imaging and Flow Cytometry
journal, April 2012

  • Cornelissen, Frans; Cik, Miroslav; Gustin, Emmanuel
  • Journal of Biomolecular Screening, Vol. 17, Issue 4
  • DOI: 10.1177/1087057111432885

Oral GS-5806 Activity in a Respiratory Syncytial Virus Challenge Study
journal, August 2014

  • DeVincenzo, John P.; Whitley, Richard J.; Mackman, Richard L.
  • New England Journal of Medicine, Vol. 371, Issue 8
  • DOI: 10.1056/NEJMoa1401184

The cost effectiveness of palivizumab: a systematic review of the evidence
journal, July 2010


Targeting a binding pocket within the trimer-of-hairpins: Small-molecule inhibition of viral fusion
journal, October 2004

  • Cianci, C.; Langley, D. R.; Dischino, D. D.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 42
  • DOI: 10.1073/pnas.0406696101

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Substituted benzimidazoles with nanomolar activity against respiratory syncytial virus
journal, November 2003


Structural characterization of the human respiratory syncytial virus fusion protein core
journal, December 2000

  • Zhao, X.; Singh, M.; Malashkevich, V. N.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 26
  • DOI: 10.1073/pnas.260499197

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors
journal, April 2012

  • LaLonde, Judith M.; Kwon, Young Do; Jones, David M.
  • Journal of Medicinal Chemistry, Vol. 55, Issue 9
  • DOI: 10.1021/jm300265j

Characteristics of arbidol-resistant mutants of influenza virus: Implications for the mechanism of anti-influenza action of arbidol
journal, February 2009


Structure of Respiratory Syncytial Virus Fusion Glycoprotein in the Postfusion Conformation Reveals Preservation of Neutralizing Epitopes
journal, May 2011

  • McLellan, J. S.; Yang, Y.; Graham, B. S.
  • Journal of Virology, Vol. 85, Issue 15
  • DOI: 10.1128/JVI.00555-11

Inhibition of the fusion-inducing conformational change of influenza hemagglutinin by benzoquinones and hydroquinones
journal, March 1993

  • Bodian, Dale L.; Yamasaki, R. Bryan; Buswell, Richard L.
  • Biochemistry, Vol. 32, Issue 12
  • DOI: 10.1021/bi00063a007

GS-5806 Inhibits Pre- to Postfusion Conformational Changes of the Respiratory Syncytial Virus Fusion Protein
journal, August 2015

  • Samuel, Dharmaraj; Xing, Weimei; Niedziela-Majka, Anita
  • Antimicrobial Agents and Chemotherapy, Vol. 59, Issue 11
  • DOI: 10.1128/AAC.00761-15

Structure-Based Identification and Neutralization Mechanism of Tyrosine Sulfate Mimetics That Inhibit HIV-1 Entry
journal, August 2011

  • Acharya, Priyamvada; Dogo-Isonagie, Cajetan; LaLonde, Judith M.
  • ACS Chemical Biology, Vol. 6, Issue 10
  • DOI: 10.1021/cb200068b

Identification of Residues in the Human Respiratory Syncytial Virus Fusion Protein That Modulate Fusion Activity and Pathogenesis
journal, October 2014

  • Hotard, Anne L.; Lee, Sujin; Currier, Michael G.
  • Journal of Virology, Vol. 89, Issue 1
  • DOI: 10.1128/JVI.02472-14

Ligand identification using electron-density map correlations
journal, December 2006

  • Terwilliger, Thomas C.; Adams, Paul D.; Moriarty, Nigel W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1
  • DOI: 10.1107/S0907444906046233

Selection of a Respiratory Syncytial Virus Fusion Inhibitor Clinical Candidate. 2. Discovery of a Morpholinopropylaminobenzimidazole Derivative (TMC353121)
journal, February 2008

  • Bonfanti, Jean-François; Meyer, Christophe; Doublet, Frédéric
  • Journal of Medicinal Chemistry, Vol. 51, Issue 4
  • DOI: 10.1021/jm701284j

How good are my data and what is the resolution?
journal, June 2013

  • Evans, Philip R.; Murshudov, Garib N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000061

A broad HIV-1 inhibitor blocks envelope glycoprotein transitions critical for entry
journal, August 2014

  • Herschhorn, Alon; Gu, Christopher; Espy, Nicole
  • Nature Chemical Biology, Vol. 10, Issue 10
  • DOI: 10.1038/nchembio.1623

Small-molecule inhibitors of HIV-1 entry block receptor-induced conformational changes in the viral envelope glycoproteins
journal, March 2004

  • Si, Z.; Madani, N.; Cox, J. M.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 14
  • DOI: 10.1073/pnas.0307953101

Iduronic Acid-Containing Glycosaminoglycans on Target Cells Are Required for Efficient Respiratory Syncytial Virus Infection
journal, June 2000

  • Hallak, Louay K.; Collins, Peter L.; Knudson, Warren
  • Virology, Vol. 271, Issue 2
  • DOI: 10.1006/viro.2000.0293

A small molecule HIV-1 inhibitor that targets the HIV-1 envelope and inhibits CD4 receptor binding
journal, August 2003

  • Lin, P. -F.; Blair, W.; Wang, T.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 19
  • DOI: 10.1073/pnas.1832214100

Structure of influenza hemagglutinin in complex with an inhibitor of membrane fusion
journal, November 2008

  • Russell, R. J.; Kerry, P. S.; Stevens, D. J.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 46
  • DOI: 10.1073/pnas.0807142105

iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM
journal, March 2011

  • Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910048675

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Small-Molecule CD4 Mimics Interact with a Highly Conserved Pocket on HIV-1 gp120
journal, November 2008


Architecture of respiratory syncytial virus revealed by electron cryotomography
journal, June 2013

  • Liljeroos, L.; Krzyzaniak, M. A.; Helenius, A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 27
  • DOI: 10.1073/pnas.1309070110

Elevated temperature triggers human respiratory syncytial virus F protein six-helix bundle formation
journal, January 2010


Discovery of an Oral Respiratory Syncytial Virus (RSV) Fusion Inhibitor (GS-5806) and Clinical Proof of Concept in a Human RSV Challenge Study
journal, January 2015

  • Mackman, Richard L.; Sangi, Michael; Sperandio, David
  • Journal of Medicinal Chemistry, Vol. 58, Issue 4
  • DOI: 10.1021/jm5017768

Strategic priorities for respiratory syncytial virus (RSV) vaccine development
journal, April 2013


Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein
journal, December 2009

  • Roymans, D.; De Bondt, H. L.; Arnoult, E.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 1
  • DOI: 10.1073/pnas.0910108106

Respiratory Syncytial Virus Infection in Elderly and High-Risk Adults
journal, April 2005

  • Falsey, Ann R.; Hennessey, Patricia A.; Formica, Maria A.
  • New England Journal of Medicine, Vol. 352, Issue 17
  • DOI: 10.1056/NEJMoa043951

Structural basis of viral invasion: lessons from paramyxovirus F
journal, August 2007

  • Lamb, Robert A.; Jardetzky, Theodore S.
  • Current Opinion in Structural Biology, Vol. 17, Issue 4
  • DOI: 10.1016/j.sbi.2007.08.016

Small Molecules VP-14637 and JNJ-2408068 Inhibit Respiratory Syncytial Virus Fusion by Similar Mechanisms
journal, May 2005


Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

A highly stable prefusion RSV F vaccine derived from structural analysis of the fusion mechanism
journal, September 2015

  • Krarup, Anders; Truan, Daphné; Furmanova-Hollenstein, Polina
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9143

Monoclonal antibodies to respiratory syncytial virus proteins: identification of the fusion protein.
journal, January 1983


Molecular mechanism underlying the action of a novel fusion inhibitor of influenza A virus.
journal, January 1997


PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
journal, December 2019


Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021


    Works referencing / citing this record:

    New therapies for acute RSV infections: where are we?
    journal, January 2019


    Potent single-domain antibodies that arrest respiratory syncytial virus fusion protein in its prefusion state
    journal, February 2017

    • Rossey, Iebe; Gilman, Morgan S. A.; Kabeche, Stephanie C.
    • Nature Communications, Vol. 8, Issue 1
    • DOI: 10.1038/ncomms14158

    Therapeutic efficacy of a respiratory syncytial virus fusion inhibitor
    journal, August 2017


    Structure and immunogenicity of pre-fusion-stabilized human metapneumovirus F glycoprotein
    journal, November 2017


    Respiratory syncytial virus entry and how to block it
    journal, February 2019


    Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol
    journal, December 2016

    • Kadam, Rameshwar U.; Wilson, Ian A.
    • Proceedings of the National Academy of Sciences, Vol. 114, Issue 2
    • DOI: 10.1073/pnas.1617020114

    Structures of the prefusion form of measles virus fusion protein in complex with inhibitors
    journal, February 2018

    • Hashiguchi, Takao; Fukuda, Yoshinari; Matsuoka, Rei
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 10
    • DOI: 10.1073/pnas.1718957115

    Interferon-induced transmembrane proteins inhibit cell fusion mediated by trophoblast syncytins
    journal, November 2019

    • Zani, Ashley; Zhang, Lizhi; McMichael, Temet M.
    • Journal of Biological Chemistry, Vol. 294, Issue 52
    • DOI: 10.1074/jbc.ac119.010611

    Benzimidazole-based derivatives as privileged scaffold developed for the treatment of the RSV infection: a computational study exploring the potency and cytotoxicity profiles
    journal, January 2017

    • Cichero, Elena; Tonelli, Michele; Novelli, Federica
    • Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 32, Issue 1
    • DOI: 10.1080/14756366.2016.1256881

    Respiratory syncytial virus: prospects for new and emerging therapeutics
    journal, June 2017


    Antiviral Activity of Oral JNJ-53718678 in Healthy Adult Volunteers Challenged With Respiratory Syncytial Virus: A Placebo-Controlled Study
    journal, April 2018

    • Stevens, Marita; Rusch, Sarah; DeVincenzo, John
    • The Journal of Infectious Diseases, Vol. 218, Issue 5
    • DOI: 10.1093/infdis/jiy227

    Five Residues in the Apical Loop of the Respiratory Syncytial Virus Fusion Protein F 2 Subunit Are Critical for Its Fusion Activity
    journal, May 2018

    • Hicks, Stephanie N.; Chaiwatpongsakorn, Supranee; Costello, Heather M.
    • Journal of Virology, Vol. 92, Issue 15
    • DOI: 10.1128/jvi.00621-18

    Measles Virus Bearing Measles Inclusion Body Encephalitis-Derived Fusion Protein Is Pathogenic after Infection via the Respiratory Route
    journal, February 2019

    • Mathieu, Cyrille; Ferren, Marion; Jurgens, Eric
    • Journal of Virology, Vol. 93, Issue 8
    • DOI: 10.1128/jvi.01862-18

    Inhibiting Human Parainfluenza Virus Infection by Preactivating the Cell Entry Mechanism
    journal, February 2019


    Respiratory syncytial virus infection in adults
    journal, September 2019


    Targeting viral entry as a strategy for broad-spectrum antivirals
    journal, January 2019


    A comparison of RSV and influenza in vitro kinetic parameters reveals differences in infecting time
    journal, February 2018


    Alternative conformations of a major antigenic site on RSV F
    journal, July 2019


    Single-Domain Antibodies As Therapeutics against Human Viral Diseases
    journal, December 2017


    Role of Type I Interferon (IFN) in the Respiratory Syncytial Virus (RSV) Immune Response and Disease Severity
    journal, March 2019


    The Morphology and Assembly of Respiratory Syncytial Virus Revealed by Cryo-Electron Tomography
    journal, August 2018

    • Ke, Zunlong; Dillard, Rebecca; Chirkova, Tatiana
    • Viruses, Vol. 10, Issue 8
    • DOI: 10.3390/v10080446

    Heme Oxygenase-1 Modulates Human Respiratory Syncytial Virus Replication and Lung Pathogenesis during Infection
    journal, May 2017

    • Espinoza, Janyra A.; León, Miguel A.; Céspedes, Pablo F.
    • The Journal of Immunology, Vol. 199, Issue 1
    • DOI: 10.4049/jimmunol.1601414

    Respiratory Syncytial Virus Infection in Adults
    journal, July 2000

    • Falsey, Ann R.; Walsh, Edward E.
    • Clinical Microbiology Reviews, Vol. 13, Issue 3
    • DOI: 10.1128/cmr.13.3.371