Immunoinformatics study to search epitopes of spike glycoprotein from SARS-CoV-2 as potential vaccine

Abstract

The Coronavirus disease named COVID-19 is caused by the virus reported in 2019 first identified in China. The cases of this disease have increased and as of June 1^st, 2020 there are more than 216 countries affected. Pharmacological treatments have been proposed based on the resemblance of the HIV virus. With regard to prevention there is no vaccine, thus, we proposed to explore the spike protein due to its presence on the viral surface, and it also contains the putative viral entry receptor as well as the fusion peptide (important in the genome release). In this work we have employed In Silico techniques such as immunoinformatics tools which permit the identification of potential immunogenic regions on the viral surface (spike glycoprotein). From these analyses, we identified four epitopes E332-370, E627-651, E440-464 and E694-715 that accomplish essential features such as promiscuity, conservation grade, exposure and universality, and they also form stable complexes with MHCII molecule. We suggest that these epitopes could generate a specific immune response, and thus, they could be used for future applications such as the design of new epitope vaccines against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Keywords: Epitope; SARS-CoV-2; coronavirus; spike glycoprotein; vaccine.

Figure 1.

Alignment of spike glycoprotein sequences of SARS-CoV-2. A) Multiple sequence alignments of the complete genome sequences exhibit 81 amino acid changes (a fragment of the alignment is shown). B) Multiple protein sequences of the spike glycoprotein of SARS-CoV-2 (protein sequences) exhibit 164 amino acid changes (a fragment of the alignment is shown). Amino acids that are identical are shown in pink color. Variations of the amino acids are shown in blue color.

Figure 2.

spike glycoprotein trimer. Figure is shown in black and white colors for a better view of the chains. Chain A is colored in black, chain B is colored in dark grey and chain C is colored in light grey. A) The shown trimer of the consensus sequence (SCons). B) The trimer is observed in the down conformation (6VXX-fill). C) The trimer is shown in the up conformation (6VYB-fill). The region of the ectodomain was modeled.

Figure 3.

Epitopes exposed on the SARS-CoV-2 spike glycoprotein: The epitopes are shown in different colors as follows E136-167 (red), E199-225 (green), E238-262 (blue), E332-370 (yellow) E481-506 (turquoise) and E694-715 (magenta) are shown. A) The trimer of the consensus sequence (SCons). B) The trimer is observed in the down conformation (6VXX-fill). C) The trimer is shown in the up conformation (6VYB-fill).

Figure 4.

Epitopes exposed in the SARS-CoV-2 spike glycoprotein. The epitopes are shown in different colors as follows; E440-464 (pink), E627-651 (orange), E153-180 (lime), E911-939 (purple) and E811-848 (salmon) are exposed in the SARS-CoV-2 spike glycoprotein. A) The consensus sequence of the trimer is shown (SCons). B) The trimer is observed in the down conformation (6VXX-fill). C) The trimer is shown in the up conformation (6VYB-fill).

Figure 5.

Docking of the E136-167, E199-225, E238-262 and E627-651 peptides with the HLA-DRB1*0401 molecules: A) the structural coupling of the E136-167 peptide with a lowest energy of −1903.2 and a frequency of 24.3% was observed. B) E199-225 (green) is schematized with a lowest energy of −1191 and a frequency of 15.4% C) We observe in blue color the peptide E238-264 interacting with the DRB1*0401 complex, the peptide E238-262 is posed in the binding cavity to the ligand with a frequency of 36.5% and a lowest energy of −1173.3. D) E627-651 peptide (orange) binds in the binding cavity with a frequency of 37.7% and lowest energy of −1560.3. Furthermore, amino acids of the peptides interact with the amino acids in the cavity of HLA-DRB1*0401.

Figure 6.

Docking of E153-180, E332-370 and E440-464 peptides with MHCII: A) The E153-180 peptide is coupled with the HLA-DRB1*0401 haplotype to the peptide recognition cavity with a frequency of 16.3% and lowest energy of −1213.6. B) In this section, we observe the E332-370HLA_DRB1*0401 complex, This peptide is coupled with lowest energy −1361 and a frequency of 20% in the peptide binding cavity. C) E440-464 peptide binds to HLA-DRB1*0701 haplotype, with a 28.7% frequency and a lowest energy of −1196.7. D) The E481-506 binds to the cavity with a frequency of 28.3% and lowest energy −1545.9 In addition, the amino acids of the peptides that interact with the amino acids of the MHCII molecule cavity are shown.

Figure 7.

Docking of the peptides E694-715, E811-848, E136-167 and E332-370 with the MHC molecules: A) The peptide E694-715 (magenta) binds to the cavity of DRB1*0401 with a frequency of 9.8% and a lowest energy of −1319.9 B) The E811-848_DRB1*0401 complex is illustrated, where it was determined that the binding frequency of the ligand in this formation is 14.4% and a lowest energy of −1410.8. C) In this section it is shown that the E136-167 peptide binds to the cavity of the HLA-A*2402 molecule with a frequency of 24.1% and a lowest energy of −1641.4. D) Finally in this figure the E332-370 peptide binds to HLA-A*2402 with a frequency of 19.5% and lowest energy of −1441.4. In addition, the amino acids of the peptides that interact with the amino acids of the MHC molecule cavity are shown.

Figure 8.

Docking of the E627-651, E440-464, E153-180 and E694-715 peptides with the molecule HLA-A*2402: A) the peptide E627-651 binds in the binding cavity to the ligand with a frequency of 23.2% and a lowest energy of −1361.4. B) It is shown in the section that the frequency of the E440-464_HLA-A*2402 complex is 35% and a lowest energy of −1171.3. C) The E153-180 is bound in the recognition cavity with a frequency of 19.7% and a lowest energy of −1252.9. D) E694-715 binds in the HLA-A*2402 cavity with a lowest energy −1163.3 and a frequency of 11.4%.

Figure 9.

Docking of the E811-848_HLA-A*0301, E911-939_HLA- DRB1*0401, E911-939_HLA-A*2402 and E481-506_HLA-A*2402 complexes: A) The E811-848 peptide binds to the cavity where the ligand is bound, with a frequency of 11.4% and lowest energy of −1163.3. B) It is observed that the frequency is 20.7% and lowest energy of −1453.9 of the E911-939_HLA-A*2402 complex. C) The E911-939 peptide binds to the recognition site with a frequency of 31.1% and lowest energy of −1714.4. D) The E481-506_HLA-A*2402 complex binds to the cavity with a Lowest Energy of −1613.9 and a frequency of 41.6%.

Figure 10.

Root mean Square Deviation (RMSD) calculations. Graph plots the curves from the RMSD calculations of MHCII molecules along the 10 ns trajectories. Calculations only considered the alpha carbon atoms of each of the proteins.