Redesigning SARS CoV-2 spike protein to improve immunization - COVID-19

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The ongoing COVID-19 pandemic continues to pose enormous health and economic challenges, highlighting the urgent need for a vaccine that prevents further spread of SARS-CoV-2. The receptor binding domain (RBD) of SARS-CoV-2' s spike protein S is a target for vaccine development because it initiates entry of the virus into host cells. However, key neutralizing epitopes in the RBD are only transiently exposed due to the samplings of "closed" S conformations that hide these epitopes from the humoral immune system. Our goals are to (i) delineate structural mechanisms leading to exposures of key epitopes in the homo-trimeric state of the SARS-CoV-2 protein S and (ii) exploit these insights in the engineering of S variants that improve immunogenicity through preservation of neutralization-sensitive conformational and quaternary epitopes. We will achieve this in a multidisciplinary approaches that draws from the expertise present in the research team and our partner. Specifically, we will first employ computational molecular modeling and simulations to design variants that stabilize "open'" states with exposed antigenic regions in RBD and its surroundings (Gsponer Lab). We will then express, purify, characterize the desired structural effects of the computationally designed variants with the help of single particle Cryo-EM (Subramaniam lab). Finally, in collaboration with our biotech partner AbCellera, we will use well-characterized and structurally-validated variants for immunization of humanized mice and test neutralizing activities of induced anti-sera and antibodies. Support for the proposed research will enable us to establish a pipeline for the engineering and structural characterization of new S protein variants and the subsequent characterization of the immunogenicity of these designed variants.