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TitleUpdate and reuse: Structure-guided nanobody evolution against SARS-CoV-2 escape.
Journal, issue, pagesPLoS Pathog, Vol. 22, Issue 5, Page e1014223, Year 2026
Publish dateMay 18, 2026
AuthorsFan Bu / Divyasha Saxena / Hailey Turner-Hubbard / Amy Delaney / Lalit Batra / Charlie Fricke / Skyler Moye / Abhishek Verma / Stanley Perlman / Janarjan Bhandari / Bin Liu / Gang Ye / Jian Zheng / Fang Li /
PubMed AbstractSARS-CoV-2 continues to accumulate spike mutations that erode the efficacy of antibody therapeutics. The Q493E mutation in the spike RBD, present in recent Omicron subvariants, enables escape from ...SARS-CoV-2 continues to accumulate spike mutations that erode the efficacy of antibody therapeutics. The Q493E mutation in the spike RBD, present in recent Omicron subvariants, enables escape from many antibodies and nanobodies, including our Nanosota-9A nanobody, which neutralizes Omicron JN.1 (Q493) but not KP.3 (E493). To address this, we applied a structure-guided in vitro evolution strategy to engineer Nanosota-9A, generating Nanosota-9B, which binds the KP.3 RBD with high affinity but shows reduced binding to JN.1 RBD. To regain breadth, we engineered a bispecific nanobody combining Nanosota-9A and -9B, which effectively neutralizes both JN.1 and KP.3 in infection assays. Our results provide proof of concept for an "update and reuse" strategy: applying structure-guided engineering to update and reuse validated nanobodies to overcome variant escape. This strategy offers a practical path to maintain therapeutic coverage as the virus evolves, supporting more efficient use of research resources and faster responses to emerging variants.
External linksPLoS Pathog / PubMed:42149970 / PubMed Central
MethodsEM (single particle)
Resolution3.06 - 3.44 Å
Structure data

73749

9z1m

EMDB-73749, PDB-9z1m:
Cryo-EM structure of KP.3 spike in complex with Nb9B
Method: EM (single particle) / Resolution: 3.06 Å

73750

9z1n

EMDB-73750, PDB-9z1n:
Structure of KP.3 spike in complex with Nanosota-9B (local refinement)
Method: EM (single particle) / Resolution: 3.44 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
  • vicugna pacos (alpaca)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / entry / VIRAL PROTEIN-IMMUNE SYSTEM complex

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