Table 2.
Showing results obtained after performing molecular docking between standard REM and compounds 1–7 with SARS CoV-2 Main Protease (PDB ID: 6LU7) generated by AutoDock tool.
| Compounds | Estimated Free Energy of Binding (kcal/mol) |
Estimated Inhibition Constant (Ki) | Hydrogen bonds formation details | Hydrogen bonds length (Angstrom) |
Amino acid residues involved in Van der waals interaction |
|---|---|---|---|---|---|
| Standard (REM) | −6.41 | 19.91 uM | A:HIS163:HE2 -:UNK1:N23 | 2.33 | His41,Asn142,Gly143,Cys145,,Met165,Glu166,Leu167,Pro168,His172,Gln189,Thr190,Gln192 |
| :UNK1:H66 - A:PHE140:O | 2.20 | ||||
| A:PRO168:CA -:UNK1:O9 | 3.22 | ||||
| A:HIS172:CD2 -:UNK1:N23 | 3.28 | ||||
| :UNK1:C24 - A:ASN142:OD1 | 3.07 | ||||
| 1 | −4.74 | 335.62 uM | A:GLU166:HN -:UNK1:N5 | 2.05 | WAALS = Ser144,Leu141,Met165,Gln189,His172 |
| :UNK1:H26 - A:GLU166:OE2 | 2.11 | ||||
| :UNK1:H27 - A:PHE140:O | 2.11 | ||||
| :UNK1:C7 - A:GLU166:O | 3.04 | ||||
| 2 | −5.65 | 71.95 uM | A:GLU166:HN -:UNK1:N7 | 2.10 | TYR54, ASP187, ARG188 |
| :UNK1:H15 - A:GLU166:O | 2.05 | ||||
| :UNK1:C14 - A:GLN189:OE1 | 3.08 | ||||
| A:GLU166:HN -:UNK1 | 2.87 | ||||
| 3 | −6.61 | 14.24 uM | A:GLY143:HN -:UNK1:N11 | 1.89 | THR26,THR25,HIS41,HIS163,MET165,HIS172,GLU166 |
| :UNK1:H20 - A:PHE140:O | 2.18 | ||||
| :UNK1:C9 - A:LEU141:O | 3.04 | ||||
| :UNK1:C9 - A:SER144:OG | 3.59 | ||||
| :UNK1:C13 - A:ASN142:OD1 | 3.31 | ||||
| 4 | −7.03 | 7.02 uM | A:TYR54:HH -:UNK1:F1 | 2.66 | PHE140,LEU141,HIS164,PRO52,ARG188,GLN189,GLU166,HIS163 |
| :UNK1:H33 - A:ASN142:OD1 | 1.94 | ||||
| 5 | −7.06 | 6.67 uM | A:GLY143:HN -:UNK1:N8 | 1.85 | HIS41,THR25,THR26, MET165, HIS163, HIS172, GLU166 |
| :UNK1:H33 - A:PHE140:O | 2.26 | ||||
| :UNK1:C10 - A:ASN142:OD1 | 3.18 | ||||
| :UNK1:C12 - A:LEU141:O | 3.16 | ||||
| :UNK1:C12 - A:SER144:OG | 3.69 | ||||
| 6 | −8.12 | 1.11 uM | :UNK1:H33 - A:PHE140:O | 3.03 | His41,Met49,Tyr54,Leu141,,His163,His164,Met165,Glu166,His172,Asp187,Arg188 |
| :UNK1:H34 - A:ASN142:OD1 | 1.98 | ||||
| :UNK1:C13 - A:GLN189:OE1 | 3.74 | ||||
| 7 | −7.83 | 1.83 uM | :UNK1:H33 - A:PHE140:O | 2.93 | LEU141,HIS172,HIS163,GLU166,GLN189,ARG188,ASP187,TYR54,HIS41 |
| :UNK1:H34 - A:ASN142:OD1 | 2.06 |