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COVID-19 spike-host cell receptor GRP78 binding site prediction.
Ibrahim, Ibrahim M; Abdelmalek, Doaa H; Elshahat, Mohammed E; Elfiky, Abdo A.
  • Ibrahim IM; Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.
  • Abdelmalek DH; Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.
  • Elshahat ME; Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt.
  • Elfiky AA; Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt; College of Applied Medical Sciences, University of Al-Jouf, Saudi Arabia. Electronic address: abdo@sci.cu.edu.eg.
J Infect ; 80(5): 554-562, 2020 05.
Article in English | MEDLINE | ID: covidwho-6255
ABSTRACT

OBJECTIVES:

Understanding the novel coronavirus (COVID-19) mode of host cell recognition may help to fight the disease and save lives. The spike protein of coronaviruses is the main driving force for host cell recognition.

METHODS:

In this study, the COVID-19 spike binding site to the cell-surface receptor (Glucose Regulated Protein 78 (GRP78)) is predicted using combined molecular modeling docking and structural bioinformatics. The COVID-19 spike protein is modeled using its counterpart, the SARS spike.

RESULTS:

Sequence and structural alignments show that four regions, in addition to its cyclic nature have sequence and physicochemical similarities to the cyclic Pep42. Protein-protein docking was performed to test the four regions of the spike that fit tightly in the GRP78 Substrate Binding Domain ß (SBDß). The docking pose revealed the involvement of the SBDß of GRP78 and the receptor-binding domain of the coronavirus spike protein in recognition of the host cell receptor.

CONCLUSIONS:

We reveal that the binding is more favorable between regions III (C391-C525) and IV (C480-C488) of the spike protein model and GRP78. Region IV is the main driving force for GRP78 binding with the predicted binding affinity of -9.8 kcal/mol. These nine residues can be used to develop therapeutics specific against COVID-19.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / Models, Molecular / Coronavirus Infections / Spike Glycoprotein, Coronavirus / Betacoronavirus / Heat-Shock Proteins Type of study: Prognostic study Limits: Humans Language: English Journal: J Infect Year: 2020 Document Type: Article Affiliation country: J.jinf.2020.02.026

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / Models, Molecular / Coronavirus Infections / Spike Glycoprotein, Coronavirus / Betacoronavirus / Heat-Shock Proteins Type of study: Prognostic study Limits: Humans Language: English Journal: J Infect Year: 2020 Document Type: Article Affiliation country: J.jinf.2020.02.026