Abstract
ObjectivesUnderstanding 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.MethodsIn 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.ResultsSequence 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.ConclusionsWe 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.
Highlights
In late December 2019, it was noticed that several people in Wuhan city of Hubei Province, China, were suffering from SARSlike pneumonia, which the World Health Organization (WHO) would later name COVID-19.1,2 According to the WHO surveillance draft, in January 2020, any resident or citizen in transit through Wuhan city 14 days before the onset of the symptoms is suspected to be infected by COVID-19.2,3 WHO distributed interim guidance for laboratories that carry out the testing for the newly emerged outbreak and infection prevention and control guidance.[4,5]
The secondary structure for the COVID-19 spike model is displayed at the top of the Multiple Sequence Alignment (MSA), and residual surface accessibility is present at the bottom
The positions of the disulfide bonds are marked by the green numbers below the accessibility rows in the MSA. 13 disulfide bonds are found in the spike protein from which we predict four regions to be the binding site with cell surface Glucose Regulating Protein 78 (GRP78)
Summary
In late December 2019, it was noticed that several people in Wuhan city of Hubei Province, China, were suffering from SARSlike pneumonia, which the World Health Organization (WHO) would later name COVID-19.1,2 According to the WHO surveillance draft, in January 2020, any resident or citizen in transit through Wuhan city 14 days before the onset of the symptoms is suspected to be infected by COVID-19.2,3 WHO distributed interim guidance for laboratories that carry out the testing for the newly emerged outbreak and infection prevention and control guidance.[4,5] The COVID-19 virus is suspected of having emerged in an unknown animal (perhaps a bat) and to have subsequently been transmitted to humans in the seafood and wild animal market.[1] All over the world, there are surveillance borders to prevent the spread of the new unknown coronavirus, while some countries stopped flights to and from China.[6] By the first week of the year 2020, 41 cases were confirmed to be COVID-19 positive, leaving one person dead and seven in critical care.[7] This number is continuously increasing on a daily basis. COVID-19 symptoms include fever, malaise, dry cough, shortness of breath, and respiratory distress.[1]
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