Targeting Viral Surface Proteins through Structure-Based Design

Abstract

The emergence of novel viral infections of zoonotic origin and mutations of existing human pathogenic viruses represent a serious concern for public health. It warrants the establishment of better interventions and protective therapies to combat the virus and prevent its spread. Surface glycoproteins catalyzing the fusion of viral particles and host cells have proven to be an excellent target for antivirals as well as vaccines. This review focuses on recent advances for computational structure-based design of antivirals and vaccines targeting viral fusion machinery to control seasonal and emerging respiratory viruses.

Keywords: computational protein design; glycoproteins; rational design; respiratory viruses; structural vaccinology; vaccine.

Figure 1

Model for membrane fusion; viral surface proteins undergo drastic conformational changes in order to bring the viral and host cell membrane close to each other. Upon its activation through proteolysis, the metastable prefusion state undergoes conformational changes in the fusion subunit that result in an intermediate state termed the “prehairpin” state [65,66,67,68]. At this point, the prehairpin structure can revert to its prior state in the absence of any membrane or irreversible transition to the postfusion state [48,69,70]. Finally, to prompt the fusion process, a short hydrophobic peptide or fusion peptide is released to connect with the target membrane. This interaction induces the formation of the six-helical postfusion state that brings the virus and host cell membranes in proximity and drives the membrane fusion.

Figure 2

Designed small protein inhibitors targeting fusion proteins. All proteins have been depicted as transparent surfaces with monomeric units highlighted in forest green. Protein inhibitors are colored orange (A) HSB1.6928.2.3 targeting the stem region of H1 HA (PDB 5VLI); (B) TriHSB.2A targeting the receptor-binding site on the head region of H3 HA 1968 strain (PDB 5KUY and model); (C) LCB1 bound to the open conformation of the receptor-binding domain of prefusion stabilized ectodomain trimer of SARS-CoV-2 spike protein (PDB 7JZL).

Figure 3

Strategies to stabilize the prefusion conformation of class I fusion proteins. The protein shown corresponds to the trimeric RSV F protein (PDB 4MMV and 5C6B) with two protomers as grey molecular surfaces and one protomer as a blue ribbon. Stabilizing substitutions (S215P, S190F, S155C, S290C, Q487, and a foldon domain) are presented in red, and hydrogen bonds are depicted as black dotted lines. Each panel contains an example of the main stabilization strategies of the prefusion conformation.

Figure 4

Strategy for de novo design of a trivalent epitope-focused vaccine. The neutralizing sites 0, II, and IV of RSV F were stabilized by de novo designed scaffolds using Topobuilder [121]. Topobuilder aided the construction of specific topologies that stabilize the antigenic motifs of the RSV F protein. Subsequent design and folding simulations yield stable immunogens that were used to generate a tri-scaffold vaccine. The combination of three scaffolds induced specific neutralizing antibodies against RSV F in nonhuman primates.

Figure 5

De novo design of self-assembling mosaic nanoparticles displaying various HA antigens.

Figure 6

Strategies to design broadly reactive HA-based influenza vaccines. The top panel depicts the COBRA design technology. The COBRA strategy uses diverse HA sequences and multiple rounds of consensus sequence calculations to generate a unique immunogen that can elicit head-targeting antibodies. The bottom panel shows the main protein-design approaches to redirect the immune response towards the conserved HA stem domain. These strategies include (1) chimeric HA constructs consisting of a conserved HA stem domain (gray) and distinct HA heads from viruses absent in humans (blue and orange regions); (2) headless HA proteins designed by removing the HA head domain and introducing stabilizing substitutions at the stem; (3) modifications of HA glycosylation sites to hide immunodominant epitopes at the HA head domain (e.g., hyperglycosylation of the head domain). In this panel, the HA protein is shown in gray, while glycans are shown in light blue. The glycans displayed are an artificial representation of this strategy and were drawn using GlyProt [142]. All figures were produced using PyMol [143] and the PDB 4m4y [144].