Table 2.
In-silico characterization of OAPEs of SARS- Cov-2 proteins as pro-inflammatory
| Peptide epitope | Random forest method score (Threshold 0.11) of peptide being IL-6 inducer/non-inducer4 | SVM method score (Threshold 0.0) of peptide being IFN-γ inducer/non-inducer5 | Probability of peptide being PIP/Non-PIP6 (Threshold 0.45) |
|||
|---|---|---|---|---|---|---|
| YVYSRVKNL (Envelope protein) | IL-6 inducer | 0.86 | IFN-γ non-inducer | − 0.39 | 0.632 | PIP |
| FVVFLLVTL (Envelope protein) | IL-6 inducer | 0.8 | IFN-γ inducer | 0.29 | 0.523 | PIP |
| FLAFVVFLL (Envelope protein) | IL-6 inducer | 0.89 | IFN-γ inducer | 1.24 | 0.512 | PIP |
| VLLFLAFVV (Envelope protein) | IL-6 inducer | 0.89 | IFN-γ inducer | 0.88 | 0.480 | PIP |
| FLLVTLAIL (Envelope protein) | IL-6 inducer | 0.76 | IFN-γ inducer | 0.24 | 0.522 | PIP |
| FAYANRNRF (Membrane Protein) | IL-6 inducer | 0.69 | IFN-γ inducer | 0.06 | 0.5828 | PIP |
| FLFLTWICL (Membrane Protein) | IL-6 inducer | 0.66 | IFN-γ inducer | 0.16 | 0.543 | PIP |
| FLWLLWPVT (Membrane Protein) | IL-6 inducer | 0.76 | IFN-γ inducer | 0.05 | 0.586 | PIP |
| FVLAAVYRI (Membrane Protein) | IL-6 inducer | 0.81 | IFN-γ inducer | 0.30 | 0.632 | PIP |
| WTAGAAAYY (Spike protein) | IL-6 inducer | 0.78 | IFN-γ inducer | 0.08 | 0.425 | Non-PIP |
| VVFLHVTYV (Spike protein) | IL-6 inducer | 0.85 | IFN-γ non-inducer | − 0.30 | 0.540 | PIP |
| FTISVTTEI (Spike protein) | IL-6 inducer | 0.82 | IFN-γ non-inducer | −0.29 | 0.5788 | PIP |
| WTFGAGAAL (Spike protein) | IL-6 inducer | 0.71 | IFN-γ inducer | 0.04 | 0.424 | Non-PIP |
| LTYTGAIKL Nucleocapsid phosphoprotein | IL-6 inducer | 0.88 | IFN-γ non-inducer | − 0.190 | 0.550 | PIP |
| NCP1 (ARSVASQSI) (Spike protein) | IL-6 non-inducer | < 0.11 | IFN-γ non-inducer | − 0.089 | 0.624 | PIP |
| NCP2 (KEELDKYFK) (Spike protein) | IL-6 non-inducer | < 0.11 | IFN-γ non-inducer | − 0.200 | 0.542 | PIP |
| NCP3 (VSEETGTLI) (Envelope protein) | IL-6 non-inducer | < 0.11 | IFN-γ non-inducer | − 0.732 | 0.561 | PIP |
All the shortlisted 14 OAPEs and the 3 NCPs were subjected to three different bio-informatics tools for characterizing them to be pro-inflammatory. Prediction of peptide for being Interleukin 6 (IL-6) inducer or non- inducer using IL-6-pred; Prediction of peptide being IFN-γ inducer or non- inducer using IFNepitope; Prediction of pro-inflammatory peptides (PIP) using PIP-EL server. We found all selected OAPEs were also predicted of inducing IL-6 in IL-6-Pred; IL-6 is a key biomarker for COVID-19 disease. Out of 14 OAPEs, 12 were predicted to be inducers of pro-inflammatory cytokines in PIP-EL server while 10 OAPEs were positive for inducing IFN-γ in IFNepitope server. All the 3 NCPs were predicted IL-6 non-inducer, IFN-γ non-inducer and pro-inflammatory cytokine inducer