Table 3.
Peptides-MHC class I, HLA-B interaction characteristics of designed peptides against SARS-CoV-2.
| Peptide sequence | Global energy (kcal/mol) | Attractive VDW energy (kcal/mol) | H-bond energy (kcal/mol) | Peptidase-MHC pair | Bond distance (Å) | Conserved residues |
|---|---|---|---|---|---|---|
| GTDLEGNFY | -1.65 | -5.52 | 0.36 | ASN 7 CB-PRO 168.A CB ASN 7 CA-PRO 168.A CB ASN 7 N-PRO 168.A CG ASN 7 N-PRO 168.A CB PHE 8 N-PRO 168.A CA |
1.557 1.755 1.880 1.956 2.286 |
GLN189 ASN142 MET49 GLU166 PRO168 |
| TVNVLAWLY | -5.53 | -3.33 | 0.00 | TRP 7 O-SER 46.A CB TRP 7 NE1-SER 46.A TRP 7 CH2-GLU 47.A OE1 ASN 3 O-HOH 711.A O TRP 7 N-HOH 711.A O |
2.433 2.377 2.711 2.426 2.675 |
GLN189 ASN142 MET49 GLU166 PRO168 |
| GSVGFNIDY | -26.21 | -21.80 | 15.63 | YR 9 O2-LEU 27.A CD1 TYR 9 CA-CYS 145.A SG ILE 7 O-HOH 671.A O ASP 8 CG-ASN 142.A CA TYR 9 O2-LEU 27.A |
2.172 2.606 1.881 2.779 2.355 |
GLN189 ASN142 MET49 GLU166 PRO168 |
| QTFSVLACY | -17.39 | -21.55 | 20.78 | TYR 9 O2-SER 46.A OG TYR 9 O2-SER 46.A CB |
2.616 3.049 |
GLU166 PRO168 |
| DYDCVSFCY | -14.90 | -5.82 | 2.72 | TYR 2 CZ-GLN 189.A NE2 PHE 7 CG-ASN 142.A ND2 TYR 2 CD2-HOH 711.A O PHE 7 CD2-ASN 142.A PHE 7 CE2-ASN 142.A CB |
2.394 2.406 2.411 2.597 2.959 |
GLN189 ASN142 MET49 GLU166 PRO168 |
| TANPKTPKY | -15.11 | -26.36 | 33.19 | PRO 7 CB-GLU 166.A CB THR 6 CG2-HOH 650.A O LYS 8 CG-HOH 515.A O TYR 9 O2-HOH 650.A O PRO 7 CB-GLU 166.A CD |
2.529 2.132 2.155 1.728 2.654 |
GLN189 ASN142 MET49 GLU166 PRO168 |
| SEDMLNPNY | -17.58 | -19.77 | 25.28 | GLU 2 CD-MET 49.A SD TYR 9 C-HOH 671.A O ASN 6 OD1-GLN 189.A ASN 6 CG-GLN 189.A NE2 GLU 2 OE2-MET 49.A SD |
2.089 1.865 1.863 2.128 2.079 |
GLN189 ASN142 MET49 GLU166 PRO168 |
| LLEDEFTPF | -0.54 | -3.54 | 0.37 | PHE 6 CA-GLU 166.A CB PHE 6 C-GLU 166.A CG THR 7 CG2-HOH 515.A O GLU 5 O-LEU 167.A N LEU 1 CD2-THR 190.A |
0.854 0.598 0.610 0.394 0.940 |
GLN189 ASN142 MET49 GLU166 PRO168 |