Table 3. Binding affinity and interactions of in silico potential molecules against MMP9 (6ESM) in complex with inhibitor BE4 .
| Ligands |
Binding affinity
(kcal/mol) |
Amino acids involved and Distance (A°) | ||
| Hydrogen binding interactions | Hydrophobic interactions | Electrostatic interactions | ||
| Epigallocatechin gallate | -9.4 | GLY A:186 (3.23, 4.00), TYR A:218 (5.61), MET A:247 (5.77) | VAL A:223 (5.45), LEU A:188 (3.36) | HIS A:226 (4.62) |
| Trimethoxy Flavone | -8.3 | HIS A:226 (4.91) | LEU A:187 (5.45), VAL A:223 (5.58), GLY A:186 (5.49) | HIS A:226 (4.49), HIS A:236 (7.26, 7.52) |
| Mesalazine | -6.9 | LEU A:222 (4.38), ARG A:249 (5.24), LEU A:226 (4.88), PRO A:246 (5.80) | VAL A:223 (5.57) | HIS A:226 (4.23) |
| (2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl] sulfanylphenyl]pentanedioic acid (Co-crystallized ligand) |
-10.9 | ALA A:189 (4.01), ALA A:191 (4.00), HIS A:230 (5.33), GLN A:227 (4.73), HIS A:226 (4.73, 5.55), HIS A:236 (5.40) | LEU A:187 (4.92), LEU A:188 (4.52), LEU A:222 (4.22), VAL A:223 (5.08), TYR A:248 (4.48), LEU A:243 (4.48, 4.59), ARG A:249 (6.93) | HIS A:226 (5.23) |