Table 1.
T-epitopes selected in silico and PvRON2 in vitro binding.
| Peptide code | Sequence | CoreF | HLA-DRB1* allele | NetMHCIIpan 3.0 (%Rank) | Binding percentage* | IC50 μM* | IC50 ratio |
|---|---|---|---|---|---|---|---|
| 39147 | LKPFYSLETMLMANS | FYSLETMLM | DRB1*0401 | 0.3 | 92.6 | 4.6 | 0.2 |
| DRB1*0701 | 2.5 | 83.2 | 26.0 | 1.1 | |||
| DRB1*1101 | 10.0 | 79.3 | 23.0 | 4.8 | |||
| DRB1*1302 | 34.0 | 63.0 | 79.0 | 10.6 | |||
| 39148 | NVRKFFLNDVSSIRH | FFLNDVSSI | DRB1*0401 | 1.0 | 83.0 | 11.9 | 0.6 |
| DRB1*0701 | 5.0 | 79.9 | 39.7 | 1.7 | |||
| DRB1*1101 | 19.0 | 73.8 | 83.4 | 17.5 | |||
| DRB1*1302 | 1.4 | 94.2 | 7.4 | 1.0 | |||
| 39149 | DKSFISEANSFRNEE | FISEANSFR | DRB1*0401 | 3.5 | 85.8 | 26.3 | 1.4 |
| DRB1*0701 | 17.0 | 42.8 | ND | ND | |||
| DRB1*1101 | 26.0 | 36.5 | ND | ND | |||
| DRB1*1302 | 24.0 | 33.5 | ND | ND | |||
| 39150 | QTAFRKFFKKIISLG | FFKKIISLG | DRB1*0401 | 17.0 | 83.6 | 33.7 | 1.7 |
| FRKFFKKII | DRB1*0701 | 6.5 | 67.2 | 51.8 | 2.2 | ||
| DRB1*1101 | 1.2 | 87.6 | 83.4 | 17.5 | |||
| DRB1*1302 | 48.0 | 7.7 | ND | ND | |||
| 39151 | KLKYIFKRRKTMKKK | FKRRKTMKK | DRB1*0401 | 37.0 | 65.3 | 40.0 | 2.1 |
| DRB1*0701 | 6.0 | 36.0 | ND | ND | |||
| YIFKRRKTM | DRB1*1101 | 0.1 | 78.5 | 51.1 | 10.7 | ||
| DRB1*1302 | 27.0 | 13.1 | ND | ND | |||
| 39152 | LFYVNLFIMSSLSRK | LFIMSSLSR | DRB1*0401 | 3.0 | 65.8 | 2.8 | 0.1 |
| FIMSSLSRK | DRB1*0701 | 2.0 | 11.0 | ND | ND | ||
| DRB1*1101 | 1.4 | 91.8 | 1.9 | 0.4 | |||
| DRB1*1302 | 27.0 | 94.7 | 8.0 | 1.1 | |||
| 39153 | MKLLQHIPANLLENI | LLQHIPANLL | DRB1*0401 | 0.5 | 61.2 | 57.0 | 2.9 |
| DRB1*0701 | 0.1 | 85.4 | 7.5 | 0.3 | |||
| DRB1*1101 | 6.5 | 72.7 | 52.1 | 10.9 | |||
| DRB1*1302 | 0.1 | 91.9 | 10.7 | 1.4 | |||
| 39154 | LKFIVRGNNLKFLNN | IVRGNNLKF | DRB1*0401 | 11.0 | 22.2 | ND | ND |
| DRB1*0701 | 4.5 | 43.7 | ND | ND | |||
| FIVRGNNLK | DRB1*1101 | 3.0 | 24.9 | ND | ND | ||
| IVRGNNLKF | DRB1*1302 | 0.2 | 90.1 | 6.5 | 0.9 | ||
| 39046 | NYEIYIASSSNIYLM | YIASSSNIY | DRB1*0401 | 0.8 | 91.8 | 28.4 | 1.5 |
| DRB1*0701 | 0.3 | 91.5 | 23.3 | 1.0 | |||
| DRB1*1101 | 13.0 | 82.9 | 120.0 | 25.2 | |||
| IYIASSSNI | DRB1*1302 | 0.2 | 92.8 | 29.6 | 4.0 | ||
| 39047 | RGPVNYHFSNYMNLD | VNYHFSNYM | DRB1*0401 | 16.0 | 59.8 | 54.5 | 2.8 |
| YHFSNYMNL | DRB1*0701 | 10.0 | 90.4 | 6.0 | 0.3 | ||
| DRB1*1101 | 37.0 | 0.0 | ND | ND | |||
| VNYHFSNYM | DRB1*1302 | 13.0 | 37.8 | ND | ND | ||
| 39048 | TPIIVKYDNTHAKNR | IIVKYDNTHA | DRB1*0401 | 12.0 | 90.7 | 11.9 | 0.6 |
| DRB1*0701 | 41.0 | 10.5 | ND | ND | |||
| DRB1*1101 | 24.0 | 16.8 | ND | ND | |||
| DRB1*1302 | 8.5 | 3.3 | ND | ND |
Peptide code and sequence are shown; core and %rank according to NetMHCIIpan 3.0 predicted HLA-DRB alleles and values. Binding assays and IC50 values were obtained from the methodology for all peptides. IC50 was assessed for peptides having ≥50% binding, IC50 values were expressed as ratios (IC50 peptide/IC50 control peptide), and good binders were considered when their ratio was ≤ 10. Specific peptides were selected as those having the lowest ratio value for each allele and a universal peptide had to have the lowest mean ratio value.
Data from this study; ND means that a peptide had less than 50% binding so that its IC50 value was not evaluated. %Rank values were considered as follows: weak binders rank ≤ 10 and strong binders ≤ 2. IC50 values were calculated for each control peptide with each DRB1* allele, the controls HA-DRB1*0401 IC50 = 19.44 μM; TT-DRB1*0701 IC50 = 23.37 μM; HA-DRB1*1101 IC50 = 4.77 μM; TT-DRB1*1302 IC50 = 7.46 μM. Peptides having a IC50 ratio ≤ 10 were considered good binders.