SARS-CoV-2 Spike-Heat Shock Protein A5 (GRP78) Recognition may be Related to the Immersed Human Coronaviruses

The human coronavirus (HCoV), SARS-CoV-2, caused more than 34 M confirmed infections from which more than 1 M deaths are reported until now (the WHO situation report-154). The current pandemic causes severe socio-economic burden. Due to the importance of understanding of the mode of recognition and viral entry, spike protein shed drug designers as the first look protein target with the first released solved structure on 26 February 2020 (PDB ID: 6VSB). It is proposed that the recognition site for GRP78 is found in SARS-CoV-2 and the immersed human coronaviruses but experimental validation is still required.

The human coronavirus (HCoV), SARS-CoV-2, caused more than 34 M confirmed infections from which ≥ 1 M deaths are reported until now (the WHO situation report-154). The current pandemic causes severe socio-economic burden (Nicola et al., 2020). Due to the importance of understanding of the mode of recognition and viral entry, spike protein sheds drug designers as the first look protein target. The first solved structure for the spike protein is released on February 26, 2020 (PDB ID: 6VSB) (Wrapp et al., 2020).
Heat Shock Protein A5 (HSPA5), or the Glucose Regulating Protein 78 (GRP78), was reported to be a possible route for SARS-CoV-2 attachment and entry (Elfiky, 2020;Ibrahim et al., 2020;Ha et al., 2020;Saghazadeh and Rezaei, 2020). The binding site in the SARS-CoV-2 spike is predicted to be the nine residues CNGVEGFNC (C480-C488 region) found in the S1 C-terminal domain, as shown in Figure 1 (see the enlarged panel) (Ibrahim et al., 2020). The prediction was based on the structural conservation between this region of the spike, and the cyclic Pep42 peptide (CTVALPGGYVRVC) that previously reported to target GRP78 (over cancer cells) selectively in vivo (Kim et al., 2006;Quinones et al., 2008;Braun et al., 2020). It was recently reported in Nature journal that SARS-CoV-2 spike has conserved motifs compared to previous strains of human coronaviruses (HKU1, 229E, NL63, OC43) (Braun et al., 2020) still experimental validation is required to prove the hypothesis.
The sequence comparison between the known human coronavirus strains, including; alpha coronaviruses (NL63, and 229E), and beta coronaviruses (OC43, HKU1, MERS-CoV, SARS-CoV, and SARS-CoV-2), reveals exciting results in terms of C480-C488 region of the spike protein. Figure 2A shows part of the multiple sequence alignment, made by clustal omega webserver and viewed by ESpript 3, for the different human coronavirus strains at the GRP78 recognition site (C480-C488 in SARS-CoV-2). The recognition of the GRP78 by the peptide Pep42 is previously reported to be restricted for the cyclic form of the peptide (the first and last CYS residues form a disulfide bond) (Kim et al., 2006;Quinones et al., 2008). Surprisingly, the residues C480 and C488 is   . The alignment is made using the Clustal Omega web server and is displayed by ESpript 3 software. The yellow highlighted residues are conserved among the seven HCoVs. GRP78 recognition site (C480-C488 in SARS-CoV-2) is marked in red (B) Pairwise sequence alignment between Pep42 from one side and NL63, 229E, OC43, HKU1, and SARS-CoV-2 from the other side. Red and yellow residues are identical and similar residues, respectively.
Molecular dynamics study (using NAMD software) for the SARS-CoV-2 spike combined with molecular docking (Using AutoDock Vina software) revealed the existence of at least four interactions (H-bonds or hydrophobic contacts) between GRP78 and C480-C488 of SARS-CoV-2 spike. The hydrophobic contacts (two up to six) are found in all the docking experiments (seven replicas done at different dynamics states of SARS-CoV-2 spike after 100 ns MDS). This is in support of the previous reports about GRP78 recognition of hydrophobic patches in the unfolded proteins (Tsai and Lee, 2018;Li and Lee, 2006). Further experimental validation is required to prove this hypothesis.
Conclusively SARS-CoV-2 Spike-host cell recognition is crucial in fighting COVID-19 both as a therapeutic and prophylactic routes. The C480-C488 region is an essential viral spike epitope to be targeted by drugs, natural compounds, or antibodies to prevent or weaken the host cell recognition of SARS-CoV-2. This represents a hot topic that need further validation in laboratory.

DATA AVAILABILITY STATEMENT
The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.