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Structural evolution of Delta lineage of SARS-CoV-2
Mohammad Mahmoudi Gomari1, Parastoo Tarighi2, Edris Choupani2
1Student Research Committee, Iran University of Medical Sciences, Tehran 1449614535, Iran; Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran.
International Journal of Biological Macromolecules
|November 26, 2022
Summary
The SARS-CoV-2 B.1.617.2 variant
Area of Science:
- Computational biology
- Virology
- Immunology
Background:
- The rapid evolution of SARS-CoV-2 Spike protein poses challenges for COVID-19 prevention and treatment.
- Mutations in the Spike protein can impact treatment efficacy, as seen with the highly infectious B.1.617.2 lineage.
Purpose of the Study:
- To investigate the structural and biological properties of the B.1.617.2 SARS-CoV-2 Spike protein.
- To evaluate the impact of B.1.617.2 mutations on antibody interactions and protein stability.
Main Methods:
- Computational biology approaches including immunoinformatics, molecular dynamics (MD), IDR analysis, protein-protein interaction analysis, residue scanning, and free energy calculations.
- Rosetta antibody design protocol for stability and affinity assessment of Bamlanivimab.
Main Results:
- B.1.617.2 Spike mutations induce significant structural changes affecting immunogenicity, protein structure, oligomerization, and furin cleavage.
- The B.1.617.2 Spike protein exhibits increased stability and higher affinity binding to ACE2 compared to the Wuhan lineage Spike.
- Bamlanivimab is ineffective against the B.1.617.2 Spike protein.
Conclusions:
- Mutations in the B.1.617.2 variant's Spike protein contribute to its enhanced infectivity and potential drug resistance.
- The B.1.617.2 Spike protein is more stable and binds ACE2 more strongly, presenting therapeutic challenges.
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