Development of Thermally Stable Nanobodies for Detection and Neutralization of Staphylococcal Enterotoxin B

Nanobodies: From Discovery to AI-Driven Design

Nanobodies, derived from naturally occurring heavy-chain antibodies in camelids (VHHs) and sharks (VNARs), are unique single-domain antibodies that have garnered significant attention in therapeutic, diagnostic, and biotechnological applications due to their small size, stability, and high specificity. This review first traces the historical discovery of nanobodies, highlighting key milestones in their isolation, characterization, and therapeutic development. We then explore their structure-function relationship, emphasizing features like their single-domain architecture and long CDR3 loop that contribute to their binding versatility. Additionally, we examine the growing interest in multiepitope nanobodies, in which binding to different epitopes on the same antigen not only enhances neutralization and specificity but also allows these nanobodies to be used as controllable modules for precise antigen manipulation. This review also discusses the integration of AI in nanobody design and optimization, showcasing how machine learning and deep learning approaches are revolutionizing rational design, humanization, and affinity maturation processes. With continued advancements in structural biology and computational design, nanobodies are poised to play an increasingly vital role in addressing both existing and emerging biomedical challenges.

Bioelectronics based on antibody-conjugated graphene field-effect transistor for response of Staphylococcal enterotoxin B as a biological weapon

Staphylococcal enterotoxin B (SEB) is a potent toxin that is produced by Staphylococcus aureus and is classified as an agent for biological weapons. Various nanotechnology-based biosensors have been developed to respond to SEB-based biological weapons; however, these biosensors exhibit various limitations. A novel chimeric antibody was developed from SEB-specific hybridoma clones that were generated using native-like SEB antigen expressed via a baculovirus system. The chimeric antibody exhibited high binding specificity and subnanomolar affinity and was subsequently conjugated onto a graphene field-effect transistor-based bioelectronic (SEB bioelectronic). This device exhibited high performance with a limit of detection of 1 pg/mL and a detection range of 1 pg/mL to 100 ng/mL, demonstrating superior specific detection performance even in the presence of various interference toxin substances at 103 times higher concentrations. Moreover, the SEB bioelectronic was evaluated using nonhuman primate infection models, and the detection performance was investigated based on those for standard SEB substances. These results indicate that the SEB bioelectronic can be utilized for noncontact SEB detection in SEB-exposed onsite locations and can be applied for bioelectronic development to respond to other biological weapons through bioprobe exchanges.

Structural insights into the binding of nanobodies to the Staphylococcal enterotoxin B

Staphylococcal Enterotoxin Type B (SEB), produced by Staphylococcus aureus bacteria, is notorious for inducing severe food poisoning and toxic shock syndrome. While nanobody-based treatments hold promises for combating SEB-induced diseases, the lack of structural information between SEB and nanobodies has hindered the development of nanobody-based therapeutics. Here, we present crystal structures of SEB-Nb3, SEB-Nb6, SEB-Nb8, SEB-Nb11, and SEB-Nb20 at resolutions ranging from 1.59 Å to 2.33 Å. Crystallographic analysis revealed that Nb3, Nb8, Nb11, and Nb20 bind to SEB at the T-cell receptor (TCR) interface, while Nb6 binds at the major histocompatibility complex (MHC) interface, suggesting their potential to inhibit SEB function by disrupting interactions with TCR or MHC molecules. Molecular biological analyses confirmed the thermodynamic and kinetic parameters of Nb3, Nb5, Nb6, Nb8, Nb11, Nb15, Nb18, and Nb20 to SEB. The competitive inhibition was further confirmed by cell-based experiments demonstrating nanobody neutralization. These findings elucidate the structural basis for developing specific nanobodies to neutralize SEB threats, providing crucial insights into the underlying mechanisms and offering significant assistance for further optimization towards future therapeutic strategies.