Epitope-focused immunogen design based on the ebolavirus glycoprotein HR2-MPER region

Author summaryRecent breakthroughs in structure-based and computational-guided vaccine design have made methods available for transplanting epitopes from native antigens onto smaller scaffold proteins. We employed these methods to design epitope-focused immunogens based on the ebolavirus HR2-MPER epitope, which is targeted by potently neutralizing and broadly-reactive antibodies. Our efforts resulted in an immunogen that bound with high affinity to monoclonal antibodies and elicited high titers of epitope-specific polyclonal antibodies following rabbit immunization but failed to induce neutralizing antibodies. Structural characterization of the grafted epitope confirmed the overall immunogen model but also highlighted the inherent flexibility and complexity of the HR2-MPER epitope. This study demonstrates the current capabilities and remaining challenges of computational epitope-focused vaccine design. It also represents the first study of epitope-focused immunogen design based on an ebolavirus. The three human pathogenic ebolaviruses: Zaire (EBOV), Bundibugyo (BDBV), and Sudan (SUDV) virus, cause severe disease with high fatality rates. Epitopes of ebolavirus glycoprotein (GP) recognized by antibodies with binding breadth for all three ebolaviruses are of major interest for rational vaccine design. In particular, the heptad repeat 2 -membrane-proximal external region (HR2-MPER) epitope is relatively conserved between EBOV, BDBV, and SUDV GP and targeted by human broadly-neutralizing antibodies. To study whether this epitope can serve as an immunogen for the elicitation of broadly-reactive antibody responses, protein design in Rosetta was employed to transplant the HR2-MPER epitope identified from a co-crystal structure with the known broadly-reactive monoclonal antibody (mAb) BDBV223 onto smaller scaffold proteins. From computational analysis, selected immunogen designs were produced as recombinant proteins and functionally validated, leading to the identification of a sterile alpha motif (SAM) domain displaying the BDBV-HR2-MPER epitope near its C terminus as a promising candidate. The immunogen was fused to one component of a self-assembling, two-component nanoparticle and tested for immunogenicity in rabbits. Robust titers of cross-reactive serum antibodies to BDBV and EBOV GPs and moderate titers to SUDV GP were induced following immunization. To confirm the structural composition of the immunogens, solution NMR studies were conducted and revealed structural flexibility in the C-terminal residues of the epitope. Overall, our study represents the first report on an epitope-focused immunogen design based on the structurally challenging BDBV-HR2-MPER epitope.

Automated summary

This study presents the design and functional validation of an epitope-focused immunogen based on the HR2-MPER epitope of the ebolavirus. The results demonstrate the capabilities and challenges of computational epitope-focused vaccine design, and provide insights for the rational design of immunogens against ebolavirus.