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TitleRational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1.
Journal, issue, pagesStructure, Vol. 32, Issue 3, Page 263-272.e7, Year 2024
Publish dateMar 7, 2024
AuthorsTatsuhiko Ozawa / Yoshiki Ikeda / Liuan Chen / Rigel Suzuki / Atsushi Hoshino / Akira Noguchi / Shunsuke Kita / Yuki Anraku / Emiko Igarashi / Yumiko Saga / Noriko Inasaki / Shunta Taminishi / Jiei Sasaki / Yuhei Kirita / Hideo Fukuhara / Katsumi Maenaka / Takao Hashiguchi / Takasuke Fukuhara / Kenichi Hirabayashi / Hideki Tani / Hiroyuki Kishi / Hideki Niimi /
PubMed AbstractSARS-CoV-2 rapidly mutates and acquires resistance to neutralizing antibodies. We report an in-silico-designed antibody that restores the neutralizing activity of a neutralizing antibody. Our ...SARS-CoV-2 rapidly mutates and acquires resistance to neutralizing antibodies. We report an in-silico-designed antibody that restores the neutralizing activity of a neutralizing antibody. Our previously generated antibody, UT28K, exhibited broad neutralizing activity against mutant variants; however, its efficacy against Omicron BA.1 was compromised by the mutation. Using previously determined structural information, we designed a modified-UT28K (V T28R/N57D), UT28K-RD targeting the mutation site. In vitro and in vivo experiments demonstrated the efficacy of UT28K-RD in neutralizing Omicron BA.1. Although the experimentally determined structure partially differed from the predicted model, our study serves as a successful case of antibody design, wherein the predicted amino acid substitution enhanced the recognition of the previously elusive Omicron BA.1. We anticipate that numerous similar cases will be reported, showcasing the potential of this approach for improving protein-protein interactions. Our findings will contribute to the development of novel therapeutic strategies for highly mutable viruses, such as SARS-CoV-2.
External linksStructure / PubMed:38228146
MethodsEM (single particle)
Resolution3.22 - 3.41 Å
Structure data

36905

8k5g

EMDB-36905: SARS-CoV-2 BA.1 RBD with UT28-RD
PDB-8k5g: Structure of the SARS-CoV-2 BA.1 RBD with UT28-RD
Method: EM (single particle) / Resolution: 3.41 Å

36906

8k5h

EMDB-36906: SARS-CoV-2 BA.1 spike with UT28-RD
PDB-8k5h: Structure of the SARS-CoV-2 BA.1 spike with UT28-RD
Method: EM (single particle) / Resolution: 3.22 Å

Chemicals

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

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Antibody / Spike protein / STRUCTURAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex

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