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TitleA dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein.
Journal, issue, pagesNat Chem Biol, Vol. 18, Issue 10, Page 1046-1055, Year 2022
Publish dateJun 2, 2022
AuthorsBhavesh Khatri / Ishika Pramanick / Sameer Kumar Malladi / Raju S Rajmani / Sahil Kumar / Pritha Ghosh / Nayanika Sengupta / R Rahisuddin / Narender Kumar / S Kumaran / Rajesh P Ringe / Raghavan Varadarajan / Somnath Dutta / Jayanta Chatterjee /
PubMed AbstractProtein tertiary structure mimetics are valuable tools to target large protein-protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a ...Protein tertiary structure mimetics are valuable tools to target large protein-protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric helix-hairpin. The dimeric four-helix bundle competes with the human angiotensin-converting enzyme 2 (ACE2) in binding to RBD with 2:2 stoichiometry. Cryogenic-electron microscopy revealed the formation of dimeric spike ectodomain trimer by the four-helix bundle, where all the three RBDs from either spike protein are attached head-to-head in an open conformation, revealing a novel mechanism for virus neutralization. The proteomimetic protects hamsters from high dose viral challenge with replicative SARS-CoV-2 viruses, demonstrating the promise of this class of peptides that inhibit protein-protein interaction through target dimerization.
External linksNat Chem Biol / PubMed:35654847 / PubMed Central
MethodsEM (single particle)
Resolution4.47 - 5.41 Å
Structure data

EMDB-32388: Cryo-EM 3D model of the 3-RBD up dimeric spike protein of SARS-CoV2 in the presence of SIH-5
Method: EM (single particle) / Resolution: 5.41 Å

33042

7x7n

EMDB-33042: Cryo-EM 3D model of the 3-RBD up single trimeric spike protein of SARS-CoV2 in the presence of synthetic peptide SIH-5.
PDB-7x7n: 3D model of the 3-RBD up single trimeric spike protein of SARS-CoV2 in the presence of synthetic peptide SIH-5.
Method: EM (single particle) / Resolution: 4.47 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • synthetic construct (others)
  • Severe acute respiratory syndrome coronavirus
KeywordsVIRAL PROTEIN / spike protein / SARS-CoV2 / complex

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