Table 1 Details of interactions formed by withanolides at protein binding site along with calculated binding energy of protein-ligand complexes and their docking scores.
Protein | Withanolide | Docking Score (Kcal/mol) | MM-GBSA Binding energy (Kcal/mol) | Interactions at the binding site | ||
|---|---|---|---|---|---|---|
Before MD Simulation | After MD Simulation | Hydrogen Bonds | Hydrophobic Interactions | |||
Vimentin monomer | Wi-A | −1.77 | −98.25 | −49.61 | Ser325 | Gln324, Leu326, Leu333, Thr336, Leu340 and Asn337 |
3βmWi-A | −2.76 | −29.51 | −35.44 | — | Gln324, Leu326, Val330, Leu333, Lys334, Leu340, Glu341 and Asn337 | |
Vimentin dimer | Wi-A | −2.462 | −32.74 | −37.59 | Chain A: Arg320 | Chain A: Tyr319, Val323, Gln324 and Thr327Chain B: Tyr 319 and Gln322 |
3βmWi-A | −1.710 | −39.43 | −61.00 | Chain B: Thr327 | Chain A: Gln322, Ser325, Leu326 and Leu333 Chain B: Val323, Thr327, Val330 and Asn337 | |
Vimentin tetramer | Wi-A | −2.264 | −25.17 | −93.51 | — | Chain A: Glu315, Tyr319, Gln322, Ser325, Leu326 and Glu329Chain B: Val323, Thr327 and Val330 |
3βmWi-A | −2.885 | −29.85 | −78.48 | Chain A: Gln322 | Chain A: Glu315 and Ser325Chain B: Ser316, Tyr319, Arg320, Val323 and Thr327 | |
