Wednesday, May 13, 2020

WHERE THE COVID-19 SPIKE ENTERS THE HOST CELL.

. 2020 May;80(5):554-562.
 doi: 10.1016/j.jinf.2020.02.026. Epub 2020 Mar 10.

COVID-19 Spike-Host Cell Receptor GRP78 Binding Site Prediction

Ibrahim M Ibrahim 1, Doaa H Abdelmalek 1, Mohammed E Elshahat 1, Abdo A Elfiky 2
Affiliations 

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 β (SBDβ). The docking pose revealed the involvement of the SBDβ 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.
Keywords: BiP; COVID-19 spike; GRP78; Pep42; Protein-protein docking; Structural bioinformatics.

Conflict of interest statement

Declaration of Competing Interests All of the authors declare that there is no competing interest in this work.

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