Table 2.
Molecular interaction docking between synthetic peptides and SARS-CoV-2 spike protein in the closed state. The molecular docking assay was performed using the ClusPro server 2.0 and structural analysis was performed by using the Pymol program.
| Complexes | Lowest binding energya | Hydrogen bondsb | Number of hydrophobic interactionsc |
|---|---|---|---|
| SARS-CoV2 spike protein/Mo-CBP3-PepI | −703.0 | THR549 (CYS1); ASP568 (GLN5); ASP 571 (CYS 8); THR572 (GLN5); MET740 (ARG 6); GLY744 (CYS 7); ASP745 (ARG6); PHE855 (GLN5); LEU977 (CYS7); ASN978 (CYS7); ARG1000 (ARG6, CYS8, CYS7) | 194 |
| SARS-CoV2 spike protein/Mo-CBP3-PepII | −787.3 | TRP353 (CYS8); ASN354 (ASN1); ARG355 (CYS8); LYS356 (GLN3); ARG357 (GLN3); ARG466 (ASN1), (CYS8); THR167 (CYS9,); ASP198 (ARG7); TYR200 (ARG7); ILE231 (CYS9); GLY232 (CYS9). | 173 |
| SARS-CoV2 spike protein/Mo-CBP3-PepIII | −723.8 | GLY744 (ALA1); ASP745 (ARG4); ASN856 (GLN3); ASN978 (ILE2); ARG1000 (CYS5); THR573 (GLN3); ILE587 (GLN3); CYS590 (ARG4). | 135 |
| SARS-CoV2 spike protein/RcAlb-PepI | −587.8 | ASN121 (ALA8); TYR170 (LEU3); SER172 (ALA1, LEU3); ARG190 (THR6, ILE7, ALA8) | 81 |
| SARS-CoV2 spike protein/RcAlb-PepII | −671.8 | ASP994 (LYS2, LEU3); ARG995 (THR6, PRO5); GLN1002 (LEU9); PHE970 (ALA1); ARG995 (LYS2) | 139 |
| SARS-CoV2 spike protein/RcAlb-PepIII | −674.6 | ASN978 (GLY4); ARG1000 (CYS5); THR573 (SER1); CYS590 (ARG3). | 91 |
| SARS-CoV2 spike protein/PepGAT | −619.0 | GLU990 (ARG5); ASP994 (ALA2, ARG5); ARG995 (ARG5, SER9); GLN755 (ARG10); TYR756 (ARG10); ASP994 (ARG10); ARG995 (ASN8). | 142 |
| SARS-CoV2 spike protein/PepKAA | −715.6 | ASP1118 (LYS7); ASP1139 (LYS7); GLU1144 (ASN4, LYS7); HIS1083 (LYS1); ARG1091 (ALA2); ASP1118 (ARG5); VAL1137 (LYS1) | 175 |
a
Calculated by the ClusPro server 2.0.
b
Analyzed in the Pymol program.
c
Analyzed in the Ligplot program.