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TitleStructure-Guided Design of Therapeutic Antibodies Targeting SARS-CoV-2 Omicron Variants.
Journal, issue, pagesRes Sq, Year 2026
Publish dateJun 24, 2026
AuthorsJesper Pallesen / Jianqiu Du / Yuanhan Wu / Sukanya Ghosh / Kelly Bayruns / Roopak Sadeesh / David Weiner
PubMed AbstractThe ongoing evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, compromised the effectiveness of many therapeutic antibodies. In this study, we employed a structure-guided ...The ongoing evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, compromised the effectiveness of many therapeutic antibodies. In this study, we employed a structure-guided computational design strategy to systematically optimize the COV2-2196 antibody for improved neutralization of Omicron variants. Through iterative rounds of computational design and experimental validation, we identified key paratope mutations that restored and enhanced antibody binding and neutralization potency against resistant viral strains. Cryo-EM structural analysis revealed the molecular basis for these improvements, highlighting how targeted modifications can accommodate epitope changes introduced by viral evolution. Our approach demonstrates that effective antibody optimization can be achieved using accessible computational resources, providing a practical framework for rapid therapeutic development. These findings underscore the potential of structure-based design to address challenges posed by viral antigenic drift and support the development of broadly effective antibody therapeutics for emerging infectious diseases.
External linksRes Sq / PubMed:42396495 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 3.9 Å
Structure data

EMDB-77343: Cryo-EM global density map of BA.1-S/2130WT/2196-S93Y
Method: EM (single particle) / Resolution: 3.1 Å

77344

36az

EMDB-77344, PDB-36az:
Structure of BA.1-S-RBD/2130WT/2196-S93Y
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-77347: Cryo-EM global density map of BA.4-S/Ab#10-M30W-S94M IgG
Method: EM (single particle) / Resolution: 3.1 Å

77348

36bb

EMDB-77348, PDB-36bb:
Structure of BA.4-S-RBD/Ab#10-M30W-S94M
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

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

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • Severe acute respiratory syndrome coronavirus
KeywordsVIRAL PROTEIN / SARS-CoV-2

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