Update and reuse: Structure-guided nanobody evolution against SARS-CoV-2 escape

Area of Science:

• Virology
• Immunology
• Biotechnology

Background:

• SARS-CoV-2 spike mutations, such as Q493E in the RBD, enable viral escape from existing antibody therapeutics.
• The Nanosota-9A nanobody effectively neutralizes Omicron JN.1 but not KP.3 due to the E493 mutation.

Purpose of the Study:

• To engineer an updated nanobody capable of neutralizing SARS-CoV-2 variants with spike mutations like Q493E.
• To develop a bispecific nanobody to broaden neutralization coverage against multiple SARS-CoV-2 variants.

Main Methods:

• Structure-guided in vitro evolution was used to engineer Nanosota-9A into Nanosota-9B, targeting the KP.3 RBD.
• A bispecific nanobody was constructed by combining Nanosota-9A and Nanosota-9B.
• Infection assays were performed to evaluate the neutralization activity of the engineered nanobodies against JN.1 and KP.3.

Main Results:

• Nanosota-9B demonstrated high-affinity binding to the KP.3 RBD but reduced binding to the JN.1 RBD.
• The engineered bispecific nanobody effectively neutralized both JN.1 and KP.3 variants in infection assays.
• The study validated an "update and reuse" strategy for nanobody therapeutics.

Conclusions:

• Structure-guided engineering can overcome SARS-CoV-2 variant escape from antibody therapeutics.
• A bispecific nanobody approach provides broad neutralization against evolving viral strains.
• The "update and reuse" strategy facilitates rapid responses to emerging variants and efficient resource utilization.