UPR/ERAD järjestelmän proteiini BIP on myös koronaviruksien reseptori

 J Infect. 2020 Mar 10. pii: S0163-4453(20)30107-9. doi: 10.1016/j.jinf.2020.02.026. [Epub ahead of print] COVID-19 Spike-host cell receptor GRP78 binding site prediction.

Ibrahim IM¹, Abdelmalek DH¹, Elshahat ME¹, Elfiky AA².

Prediktiivisesti määritelty  COVID-19 viruksen S-piikin sitoutumiskohta solupinnassa GPR78-proteiiniin.

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. (https://www.ncbi.nlm.nih.gov/pubmed/18243696 ).
 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.

Copyright © 2020 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

KEYWORDS:
BiP; COVID-19 spike; GRP78; Pep42; protein-protein docking; structural bioinformatics

PMID: 32169481
DOI: 10.1016/j.jinf.2020.02.026

Article Outline

1. Introduction
   HCoVs are positive-sense, long (30,000 bp) single-stranded RNA viruses. Two groups of proteins characterize HCoVs; structural proteins such as Spike (S) that characterize all coronaviruses, Nucleocapsid (N), Matrix (M), and Envelope (E), in addition to the non-structural proteins, such as proteases (nsp3 and nsp5) and RdRp (nsp12).^8,14 The Spike protein is a crucial recognition factor for virus attachment and entry to the host cells. It is present on the virion's outer surface in a homo-trimeric state.^14,15
   The Glucose Regulating Protein 78 (GRP78) or Binding immunoglobulin protein (BiP) is the master chaperone protein of the unfolded protein response (UPR, ERAD machinery, ERQC =Erad Quality Control First Axis , Classic molecular chaperones) (when unfolded or misfolded proteins accumulate).^{16, 17, 18, 19} 
   Under reasonable conditions, GRP78 (BiP,  Ig Heavy chain binding protein)  is found in the lumen of the Endoplasmic Reticulum (ER) bound to and inactivating three enzymes responsible for cell death or differentiation. " 
   
   
   
   
   These enzymes are (https://doi.org/10.3389/fimmu.2018.00175 )
   • Activating Transcription Factor 6 (ATF6), 
   • Protein kinase RNA-like Endoplasmic Reticulum Kinase (PERK),
   •  and Inositol-requiring Enzyme 1 (IRE1).¹⁴ 
   
   
    (My comment: Theese 3 Major signaling pathways characterize the UPR 
   
   
   "Above a threshold of accumulated unfolded proteins, GRP78 releases ATF6, PERK, and IRE1, leading to their activation. Inhibition of protein synthesis and enhancement of the refolding is the end result of the enzymes’ activation.^14,20 
   
   
    Overexpression of GRP78/BiP  is also initiated upon cell stress, which increases the chance for GRP78 to escape ER retention and translocate to the cell membrane. Once translocated to the cell membrane, GRP78 is susceptible to virus recognition by its substrate-binding domain (SBD), and it can mediate the virus entry in the cell.¹⁴ Pep42 is a cyclic peptide that has been reported to bind the GRP78 overexpressed and expressed at the surface of cancer cells.²¹
   
   
   In this study, the spike protein of COVID-19 was modeled using solved structures in the protein data bank.²² After model validation, molecular docking was performed to test its binding affinity against GRP78. We hypothesized that GRP78 binds to COVID-19, as it happens in the case of the MERS-CoV coronavirus,²³ and we tried to predict the binding site using the similarity between Pep42 and the COVID-19 Spike protein.¹⁴ Four regions of the spike were predicted to be the binding site to GRP78 based on sequence and structural similarity. The results are promising and suggest the possible recognition of the COVID-19 spike by the cell-surface GRP78 upon cell stress.
2. Materials and methods
3. Results and discussion
   1. Sequence and Structural Alignment

      Fig. 1

      (A) Part of the multiple sequence alignment for the spike protein of all of the currently reported human coronaviruses strains (COVID-19, SARS, MERS, NL63, 229E, OC43, and HKU1). The alignment is made using the Clustal Omega web server and is displayed by ESpript 3 software. The red highlighted residues are identical, while yellow highlighted residues are conserved among the seven HCoVs. Secondary structures are represented at the top of the MSA for the COVID-19 spike, while the surface accessibility is shown at the bottom (blue, surface accessible, cyan, partially accessible, and white for buried residues). The four regions of the spike protein are shaded with green, blue, magenta, and red for regions I, II, III, and IV, respectively. (B) Structural superposition of SARS spike structure (green cartoon) and COVID-19 spike model (cyan cartoon).
      View Large Image | View Hi-Res Image | Download PowerPoint Slide
   2. Pep42 versus spike regions
   The SARS spike protein sequence is the closest to the COVID-19 spike, with 77.38% identity. In contrast, OC43, MERS, HKU1, 229E, and NL63 share only 32.81%, 32.79%, 31.86%, 30.35%, and 28.28%, respectively, with COVID-19 spike. Figure 1B shows the superposition of the homo-trimeric COVID-19 spike model (cyan cartoon) and SARS spike structure (PDB ID: 6ACD) (green cartoon). Two views are shown with a vertical axis rotation of 180^o. The Root Mean Square Deviation (RMSD) between the two structures is only 0.284 Å, while the sequence identity is 77.38%.
   1. Binding mode of spike-GRP78

      Fig. 4

      The structure of the docking complexes of GRP78 (green cartoon) and COVID-19 spike (yellow cartoon) regions I and II (A) and regions III and IV (B).
      View Large Image | View Hi-Res Image | Download PowerPoint Slide
      Table 1 summarizes the docking trials of the four regions of the COVID-19 spike protein against GRP78. The docking scores are listed, while the interaction pattern is analyzed by PLIP software and listed in the table. As shown from the docking scores, region IV of the spike is the best docking platform to GRP78, with a score of -143.5 ±4.4. This score is lower (better) than other regions by 18.3%, 15.2%, and 65.5% for the region I, region II, and region III, respectively. The PRODIGY binding affinities are also listed in table 1. The PLIP analysis partially explains the binding affinity. Region IV of the spike interacts with the substrate-binding domain β of GRP78 with five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486). The average H-bond length for the docking trial of region IV is 2.26 ±0.54, while the average hydrophobic contact length is 3.66 ±0.18. These values are less than other docking trials using other regions.

      Table 1The interactions formed between the spike protein of COVID-19 and cell-surface GRP78 SBDβ upon docking with HADDOCK.

4. Conclusion
   
   
   Spike protein is an essential viral element that helps in the attachment and virus internalization to the host cell. A vast amount of host cell receptors are targets for viruses, including the cell-surface GRP78. Inhibiting the interaction that occurs between the COVID-19 spike protein and the host cell receptor GRP78 would probably decrease the rate of viral infection. Furthermore, a vaccine against the COVID-19 spike protein would likely prevent viral infection. The present in silico perspective suggests the existence of a COVID-19 spike protein-GRP78 binding site, thus paving the route for drug designers to develop suitable inhibitors to prevent the binding and hence the infection. Future work involving the dynamics of GRP78 and the experimental validation is required to suggest potent peptidomimetic inhibitors.
5. Declaration of Competing Interests
6. Acknowledgments
7. Data Availability
8. Appendix. Supplementary materials
9. References"