Engineered SARS-CoV-2 receptor binding domain improves immunogenicity in mice and elicits protective immunity in hamsters

Abstract

Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing costs. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.

Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design

“…In this case, the DMS data were obtained using yeast display of the RBD which, as opposed to other DMS strategies that measure viral fitness (79, 80), provided a direct readout of RBD expression and folding, making them highly relevant to recombinant forms of the antigen. The stabilizing mutations we identified were distinct from those reported in previous studies focusing on altering surfaceexposed positions to improve the expression and stability of the RBD, which were either similarly used to assist in multivalent display of the RBD (39), or alternatively to enhance production in yeast-based expression systems (27,(29)(30)(31). Our work instead prioritized stabilizing mutations in a buried, structurally suboptimal region of the RBD.…”

“…The SARS-CoV-2 RBD is more structurally homogeneous than metastable S ectodomains, with far higher expression yields (25,26). RBD-based immunogens in various oligomeric states have been investigated as genetic or protein-based vaccines for SARS-CoV-2, including monomers (27)(28)(29)(30)(31), dimers (32), trimers (33)(34)(35) and highly multivalent nanoparticles (25,(36)(37)(38)(39), several of which are now being evaluated in clinical trials. Although the RBD comprises only a minority of the total mass and antigenic surface of S and could in principle be more susceptible to escape mutations, this theoretical disadvantage may be mitigated by both functional constraints and the elicitation of antibodies targeting multiple distinct neutralizing epitopes in the RBD by infection or vaccination (25,(40)(41)(42)(43).…”

A modular protein subunit vaccine candidate produced in yeast confers protection against SARS-CoV-2 in non-human primates

“…We attributed this difference to a reduction in antigenicity of the RBD; inclusion of CpG may impact the structural integrity of the RBD, leading to altered antigenicity. We have previously observed similar inconsistent immunogenicity of monomeric SARS-CoV-2 RBD when formulated with a CpG adjuvant (24). Another multimeric RBD vaccine has reported robust humoral responses in nonhuman primates with the same dose of CpG1018 (35), but in that instance, the vaccine was formulated 30 minutes prior to injection.…”

“…The RBD-VLP vaccine candidate presented here is modular, and could be manufactured and formulated with RBD antigens from emerging variants or with engineered immunogenicity (24). We reported previously that the RBDs from the B.1.1.7 and B.1.351 variants can be manufactured from the same microbial strains and fermentation processes (28).…”

“…Formulations comprising only monomeric RBD (Wuhan-Hu-1) and adjuvant tested to date have required three doses to elicit potent neutralizing responses in humans (18,19). While further optimization of such formulations could improve these designs, we and others have demonstrated that multimeric display of RBD on VLPs can be highly immunogenic (20)(21)(22)(23)(24).…”