Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site

Abstract

Influenza virus (IV) causes several outbreaks of the flu each year resulting in an economic burden to the healthcare system in the billions of dollars. Several influenza pandemics have occurred during the last century and estimated to have caused 100 million deaths. There are four genera of IV, A (IVA), B (IVB), C (IVC), and D (IVD), with IVA being the most virulent to the human population. Hemagglutinin (HA) is an IVA surface protein that allows the virus to attach to host cell receptors and enter the cell. Here we have characterised the high-resolution structures of seven IVA HAs, with one in complex with the anti-influenza head-binding antibody C05. Our analysis revealed conserved receptor binding residues in all structures, as seen in previously characterised IV HAs. Amino acid conservation is more prevalent on the stalk than the receptor binding domain (RBD; also called the head domain), allowing the virus to escape from antibodies targeting the RBD. The equivalent site of C05 antibody binding to A/Denver/57 HA appears hypervariable in the other H1N1 IV HAs. Modifications within this region appear to disrupt binding of the C05 antibody, as these HAs no longer bind the C05 antibody by analytical SEC. Our study brings new insights into the structural and functional recognition of IV HA proteins and can contribute to further development of anti-influenza vaccines.

Characteristics of epitopes of limited variability on the head of influenza H1 haemagglutinin

“…The sites Sa, Sb and Ca (as defined in (Xu et al 2010)) include more than one VR and therefore exhibit higher variability, although with clear evidence of periodic re-emergence of the same variants. An extensive epitope mapping exercise using escape mutants by Matsuzaki et al (Matsuzaki et al 2014) confirms that the bulk of antibodies are restricted to the Sa, Sb and Ca2 (a part of Ca that includes VR2) but they were also able to identify at least one antibody which included Ca2 and position 147 (corresponding to OREO) and also a “broadly neutralising” monoclonal antibody (n2) centred on the RBS similar to those described above (Tsibane et al 2012; Krause et al 2011; Whittle et al 2011; Ghafoori et al 2023; Ekiert et al 2012). By contrast, the monoclonal antibody 2D1, derived from B cells of survivors of the 1918 H1N1 pandemic (Xu et al 2010), is highly diverse on account of possessing a footprint that spans 5 VRs; consequently it has low affinity for all strains except 2009 H1 HA (CA04) which is identical in every single residue.…”

“…One possibility is that they are the targets of antibodies of smaller footprint than the typical 700–900Å. Small footprint size may be achieved by the selective dominance of a single complementarity-determining region (CDR) loop as has been demonstrated for monoclonal antibodies such as CO5 (Ekiert et al 2012; Ghafoori et al 2023) and CH65 (Whittle et al 2011). Both contain the VR1 portion of OREO as well as the final residue of VR2.…”

Structure-based virtual screening and Molecular Dynamic Simulations identified FDA-approved molecules as potential inhibitors against the surface proteins of H1N1

“…Polar residue N-95 (HA2) is also observed to interact with the top-scoring ligands. It is vital to take note of the fact that these interacting residues are part of the highly conserved heptad repeat region found close to the fusion peptide (Sriwilaijaroen & Suzuki, 2012; Ghafoori et al, 2023). Such heptad repeats are a common feature observed in amino acid sequences of fusion glycoproteins of several viruses, such as paramyxoviruses, and retroviruses (Chambers et al, 1990).…”