Table 3.
In-silico characterization of antigenic promiscuous peptide epitopes of SARS- Cov-2 proteins as anti-inflammatory
| Peptide epitope | SVM + Motif based score (Threshold 0.2) of peptide being IL-4 inducer/non-inducera | Random forest method score (Threshold 0.3) of peptide being IL-10 inducer/non-inducerb | Combined RF score of peptide being Pre-AIP/Non- Pre-AIPc | |||
|---|---|---|---|---|---|---|
| YVYSRVKNL (Envelope protein) | IL-4 inducer | 0.38 | IL-10 inducer | 0.49 | 0.524 | High confidence AIP |
| FVVFLLVTL (Envelope protein) | IL-4 inducer | 0.26 | IL-10 inducer | 0.63 | 0.465 | Medium confidence AIP |
| FLAFVVFLL (Envelope protein) | IL-4 inducer | 0.28 | IL-10 inducer | 0.558 | 0.396 | Medium confidence AIP |
| VLLFLAFVV (Envelope protein) | IL-4 Non-inducer | – 0.72 | IL-10 inducer | 0.48 | 0.445 | Medium confidence AIP |
| FLLVTLAIL (Envelope protein) | IL-4 Non-inducer | – 0.94 | IL-10 inducer | 0.705 | 0.519 | High confidence AIP |
| FAYANRNRF (Membrane Protein) | IL-4-inducer | 0.33 | IL-10 inducer | 0.445 | 0.491 | High confidence AIP |
| FLFLTWICL (Membrane Protein) | IL-4-inducer | 0.28 | IL-10 inducer | 0.427 | 0.460 | Medium confidence AIP |
| FLWLLWPVT (Membrane Protein) | IL-4-inducer | 0.28 | IL-10 inducer | 0.778 | 0.586 | High confidence AIP |
| FVLAAVYRI (Membrane Protein) | IL-4-inducer | 0.28 | IL-10 inducer | 0.445 | 0.412 | Medium confidence AIP |
| WTAGAAAYY (Spike protein) | IL-4 Non-inducer | 0.16 | IL-10 non inducer | 0.095 | 0.384 | Low confidence AIP |
| VVFLHVTYV (Spike protein) | IL-4 Non-inducer | 0.14 | IL-10 inducer | 0.557 | 0.396 | Medium confidence AIP |
| FTISVTTEI (Spike protein) | IL-4-inducer | 0.42 | IL-10 inducer | 0.557 | 0.354 | Low confidence AIP |
| WTFGAGAAL (Spike protein) | IL-4-inducer | 0.25 | IL-10 non inducer | 0.128 | 0.448 | Medium confidence AIP |
| LTYTGAIKL Nucleocapsid phosphoprotein | IL-4 Non-inducer | 0.02 | IL-10 non inducer | − 0.097 | 0.482 | High confidence AIP |
| NCP1 (ARSVASQSI) (Spike protein) | IL-4-inducer | 0.45 | IL-10 non inducer | − 0.64 | 0.364 | Low confidence AIP |
| NCP2 (KEELDKYFK) (Spike protein) | IL-4-inducer | 0.29 | IL-10 non inducer | − 0.529 | 0.372 | Low confidence AIP |
| NCP3 (VSEETGTLI) (Envelope protein) | IL4-inducer | 0.45 | IL-10 non inducer | − 0.196 | 0.386 | Low confidence AIP |
All the shortlisted 14 OAPAs and the 3 NCPs were subjected to three different bio-informatics tools for characterizing them to be anti-inflammatory
aPrediction of peptide for being Interleukin 4 (IL-4) inducer or non- inducer using IL4-pred
bPrediction of peptide being Interleukin 10 (IL-10) inducer or non- inducer using IL-10pred
cPrediction of Anti-inflammatory peptides (Pre-AIP) using Pre-AIP software. Among the 14 selected OAPEs, 8 OAPEs were predicted of inducing IL-4 in IL-4-Pred while 11 OAPEs were also predicted of inducing IL-10 in IL-10-Pred. 12 OAPEs were predicted to be anti-inflammatory in nature with a medium to high confidence score in Pre-AIP. All the 3 NCPs were predicted IL-4 inducer but non-inducers of IL-10. The NCPs also had low confidence AIP score which characterize them to be non anti-inflammatory in nature