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

Title: Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site

Abstract

Many viral surface glycoproteins and cell surface receptors are homo-oligomers1, 2, 3, 4, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites5, 6, 7, 8. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ORCiD logo; ; ; ; ; ORCiD logo;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
NIHOTHER
OSTI Identifier:
1375353
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature Biotechnology; Journal Volume: 35; Journal Issue: 7
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Strauch, Eva-Maria, Bernard, Steffen M., La, David, Bohn, Alan J., Lee, Peter S., Anderson, Caitlin E., Nieusma, Travis, Holstein, Carly A., Garcia, Natalie K., Hooper, Kathryn A., Ravichandran, Rashmi, Nelson, Jorgen W., Sheffler, William, Bloom, Jesse D., Lee, Kelly K., Ward, Andrew B., Yager, Paul, Fuller, Deborah H., Wilson, Ian A., and Baker, David. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site. United States: N. p., 2017. Web. doi:10.1038/nbt.3907.
Strauch, Eva-Maria, Bernard, Steffen M., La, David, Bohn, Alan J., Lee, Peter S., Anderson, Caitlin E., Nieusma, Travis, Holstein, Carly A., Garcia, Natalie K., Hooper, Kathryn A., Ravichandran, Rashmi, Nelson, Jorgen W., Sheffler, William, Bloom, Jesse D., Lee, Kelly K., Ward, Andrew B., Yager, Paul, Fuller, Deborah H., Wilson, Ian A., & Baker, David. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site. United States. doi:10.1038/nbt.3907.
Strauch, Eva-Maria, Bernard, Steffen M., La, David, Bohn, Alan J., Lee, Peter S., Anderson, Caitlin E., Nieusma, Travis, Holstein, Carly A., Garcia, Natalie K., Hooper, Kathryn A., Ravichandran, Rashmi, Nelson, Jorgen W., Sheffler, William, Bloom, Jesse D., Lee, Kelly K., Ward, Andrew B., Yager, Paul, Fuller, Deborah H., Wilson, Ian A., and Baker, David. Mon . "Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site". United States. doi:10.1038/nbt.3907.
@article{osti_1375353,
title = {Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site},
author = {Strauch, Eva-Maria and Bernard, Steffen M. and La, David and Bohn, Alan J. and Lee, Peter S. and Anderson, Caitlin E. and Nieusma, Travis and Holstein, Carly A. and Garcia, Natalie K. and Hooper, Kathryn A. and Ravichandran, Rashmi and Nelson, Jorgen W. and Sheffler, William and Bloom, Jesse D. and Lee, Kelly K. and Ward, Andrew B. and Yager, Paul and Fuller, Deborah H. and Wilson, Ian A. and Baker, David},
abstractNote = {Many viral surface glycoproteins and cell surface receptors are homo-oligomers1, 2, 3, 4, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites5, 6, 7, 8. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.},
doi = {10.1038/nbt.3907},
journal = {Nature Biotechnology},
number = 7,
volume = 35,
place = {United States},
year = {Mon Jun 12 00:00:00 EDT 2017},
month = {Mon Jun 12 00:00:00 EDT 2017}
}
  • We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH.more » The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.« less
  • Seasonal antigenic drift of circulating influenza virus leads to a requirement for frequent changes in vaccine composition, because exposure or vaccination elicits human antibodies with limited cross-neutralization of drifted strains. We describe a human monoclonal antibody, CH65, obtained by isolating rearranged heavy- and light-chain genes from sorted single plasma cells, coming from a subject immunized with the 2007 trivalent influenza vaccine. The crystal structure of a complex of the hemagglutinin (HA) from H1N1 strain A/Solomon Islands/3/2006 with the Fab of CH65 shows that the tip of the CH65 heavy-chain complementarity determining region 3 (CDR3) inserts into the receptor binding pocketmore » on HA1, mimicking in many respects the interaction of the physiological receptor, sialic acid. CH65 neutralizes infectivity of 30 out of 36 H1N1 strains tested. The resistant strains have a single-residue insertion near the rim of the sialic-acid pocket. We conclude that broad neutralization of influenza virus can be achieved by antibodies with contacts that mimic those of the receptor.« less
  • Human infections with subtype H7 avian influenza viruses have been reported as early as 1979. In 1996, a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins, resulting in an eight amino acid deletion in the receptor-binding site. The continuous circulation of these viruses in live bird markets, as well as its documented ability to infect humans, raises the question of how these viruses achieve structural stability and functionality. Here we report a detailed molecular analysis of the receptor binding site of the North American lineage subtype H7N2 virus A/New York/107/2003 (NY107), including complexes with an avianmore » receptor analog (3'-sialyl-N-acetyllactosamine, 3'SLN) and two human receptor analogs (6'-sialyl-N-acetyllactosamine, 6'SLN; sialyllacto-N-tetraose b, LSTb). Structural results suggest a novel mechanism by which residues Arg220 and Arg229 (H3 numbering) are used to compensate for the deletion of the 220-loop and form interactions with the receptor analogs. Glycan microarray results reveal that NY107 maintains an avian-type ({alpha}2-3) receptor binding profile, with only moderate binding to human-type ({alpha}2-6) receptor. Thus despite its dramatically altered receptor binding site, this HA maintains functionality and confirms a need for continued influenza virus surveillance of avian and other animal reservoirs to define their zoonotic potential.« less