Structure and Function-based Design of Vaccine Antigens and Antiviral Immunotherapies

Vaccines are critical in preventing viral diseases, and recent advances in vaccine development and delivery platforms have enhanced their reach and efficacy. Viral glycoproteins that mediate host cell entry are the primary target of the humoral immune response and thus the main antigenic component of vaccines. However, for many viruses, we lack fundamental biological insights that would easily allow transforming their glycoproteins into highly effective vaccine antigens. In this proposal, I introduce a completely novel approach to thoroughly extract structural and functional insights of viral glycoproteins for rational design of superior antigens. By conducting nanobody repertoire screens, I will bypass common constraints encountered in antibody screening, such as immunodominance bias and redundancy. Contrasting with conventional techniques that narrowly target a limited selection of epitopes, my approach promises an exhaustive mapping of glycoprotein surfaces and epitopes. This paradigm shift enables antigen rather than antibody or nanobody characterization. By determining high-resolution cryoEM structures of nanobodies bound to glycoproteins in transitional states, we will understand their structural dynamics. Equipped with these unparalleled insights, we will harness pioneering deep learning methods to computationally design glycoproteins with enhanced antigenic form and exposed neutralizing surfaces. I will showcase this method for viruses with high case fatality rates, including Hendra, Nipah, Lassa, Tick-borne encephalitis, and Borna disease viruses. VaxVision is set to offer a comprehensive framework for the antigen design of these and genetically or structurally related viruses. My work aims to capitalize on the unused potential for vaccine antigen improvement and will provide an innovative workflow for extracting mechanistic insights and leveraging them for vaccine antigen design, with the potential to drive vaccine innovations beyond just viral pathogens.