Table 3.
The binding affinities and the molecular interactions between EQRPR and target DNA, and proteins, obtained by molecular docking simulationsa.
| Ligand/Target | DNA (1BNA) | α5β1 (4WK0) | αIIBβ3 (3ZDX) | apo-form (6M03) | holo-form |
spike glycoprotein (6VXX) | ACE2 |
Truncated ACE2 | dACE2 | Albumin |
|---|---|---|---|---|---|---|---|---|---|---|
| (6LU7) | (6M0J) | (5Z0B) | ||||||||
| EQRPR (all L-) | DG2 | PHE21 | LEU23 | THR24 | THR26 | THR(B)912 | PHE40 | ASN599 | TYR454 | ARG114 |
| DG4 | SER22 | ASP24 | LEU141 | HIS41 | ARG(C)1091 | TRP69 | LYS600 | ARG482 | LEU115 | |
| DA5 | VAL23 | PHE25 | ASN142 | TYR54 | GLU(A)1092 | ALA348 | ASN601 | GLU483 | TYR138 | |
| DA6 | ARG106 | ALA95 | SER144 | PHE140 | GLU(B)1092 | ASP350 | SER602 | ILE484 | GLU141 | |
| DT7 | PHE168 | SER96 | CYS145 | ASN142 | GLY(B)1093 | ASP382 | PHE603 | VAL485 | HIS146 | |
| DT20 | GLU171 | SER99 | HIS163 | SER144 | ARG(B)1107 | LEU391 | LYS676 | ASN599 | LYS190 | |
| DC21 | SER234 | PHE171 | GLN189 | CYS145 | GLN(B)1113 | ASN394 | ARG678 | ASN601 | LYS519 | |
| DG22 | VAL235 | SER173 | HIS163 | ASN(A)1119 | HIS401 | ASN682 | GLY605 | |||
| DC23 | LYS269 | TYR237 | GLU166 | ASN(B)1119 | PHE684 | SER680 | ||||
| TYR287 | SER238 | GLN189 | TYR781 | THR803 | ||||||
| LEU355 | ARG261 | SER804 | ||||||||
| SER417 | HIS291 | |||||||||
| ARG420 | VAL293 | |||||||||
| ILE360 | ||||||||||
| SER420 | ||||||||||
| LEU421 | ||||||||||
| ARG422 | ||||||||||
| Binding affinity (kcal/mol) | −6.2 | −9.6 | −9.2 | −6.6 | −7.5 | −8.0 | −7.6 | −6.7 | −8.0 | −8.4 |
a
Truncated ACE2 target is the optimized truncated protein that lacks 356 amino acids from the N-terminal of ACE2 and has 449 amino acids.