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COVID-19 spike-host cell receptor GRP78 binding site prediction
Ibrahim M Ibrahim1, Doaa H Abdelmalek1, Mohammed E Elshahat1
1Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.
The Journal of Infection
|March 15, 2020
Summary
Understanding COVID-19 host cell recognition is key. The spike protein binds to Glucose Regulated Protein 78 (GRP78), with specific regions driving this interaction for therapeutic development.
Area of Science:
- Molecular biology
- Structural bioinformatics
- Virology
Background:
- The novel coronavirus (COVID-19) utilizes its spike protein for host cell recognition.
- Understanding this interaction is crucial for developing effective treatments and saving lives.
Purpose of the Study:
- To predict the binding site of the COVID-19 spike protein to the cell-surface receptor, Glucose Regulated Protein 78 (GRP78).
- To identify key regions of the spike protein involved in host cell receptor binding.
Main Methods:
- Combined molecular modeling, docking, and structural bioinformatics were employed.
- The COVID-19 spike protein was modeled based on the SARS spike protein.
- Protein-protein docking was used to analyze interactions between spike protein regions and GRP78.
Main Results:
- Four regions of the spike protein showed similarities to cyclic Pep42.
- Protein-protein docking identified tight fits between spike protein regions and the GRP78 Substrate Binding Domain β (SBDβ).
- Regions III (C391-C525) and IV (C480-C488) of the spike protein model showed favorable binding to GRP78, with Region IV being the primary driver.
Conclusions:
- Region IV of the spike protein is the main driver for GRP78 binding, with a predicted affinity of -9.8 kcal/mol.
- These identified nine residues offer potential targets for developing specific therapeutics against COVID-19.
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