Multivalent Nanobodies for Potent and Broad Neutralization of Staphylococcus aureus Toxins

Abstract Staphylococcus aureus is a leading cause of lethal bacteremia and pneumonia, which are driven by potent virulence factors such as T-cell superantigens and alpha hemolysin. S. aureus has among the highest rates of antibiotic resistance, yet no vaccines or alternative therapies are available despite decades of research. Here, we developed a repertoire of potent, high affinity nanobodies (Nbs) targeting key toxins in S. aureus infection, including superantigens (SAgs) SEB, SEC, TSST-1, and Hla. Comprehensive cryo-EM and AlphaFold3 analyses of these Nbs, which were elicited with clinical cocktail vaccines, revealed diverse neutralizing epitopes and mechanisms that provide strategic insights for immunotherapy and vaccine design. Guided by these findings, we engineered highly stable, multivalent, and multifunctional Nb constructs. These constructs included an aerosolizable trimeric Nb with enhanced neuralization activity against Hla and SEC, and an ultrapotent decameric Nb-IgG-Fc fusion construct against a wide range of major toxins in S. aureus sepsis (SEB, SEC, TSST-1, and Hla). These multifunctional Nbs demonstrated promising protective activity in murine models of pneumonia and sepsis, underscoring their potential as versatile immunotherapies that address the complex virulence profiles of S. aureus. Our work lays a foundation for precision immunotherapies beyond current treatment options to combat complex bacterial infections with multiple virulence mechanisms. Significance statement S. aureus is among the most common, antibiotic-resistant, and deadly causes of bacterial infections. We developed nanobodies against clinically significant virulence factors in S. aureus sepsis and pneumonia, including superantigens (SAgs) SEB, SEC, and TSST-1 as well as pore forming toxin Hla. These nanobodies displayed complete and potent neutralization of each toxin, exploiting a wide variety neutralizing mechanisms. Structural investigation of these diverse neutralizing nanobodies, which were elicited in llamas using clinically investigated cocktail vaccines, highlighted the importance of disrupting SAg interaction with TCR or MHCII and potential flaws in targeting poorly neutralizing conserved SAg epitopes using vaccine cocktails. Nb leads against each toxin were combined in different multivalent configurations, including an aerosolizable trimeric Nb and a half-life extended decameric Nb IgG Fc fusion construct. This work highlights multivalent nanobodies as a comprehensive yet therapeutically precise drug platform that addresses the complex virulence profiles of bacterial infectious diseases. Competing Interest Statement Y.J.K. and Y.S. are inventors on a patent application covering several nanobodies evaluated in this study.