I carried out docking using AutoDock Vina for two new ligands at the active site of Bcl-2 protein. The two ligands only differ with one functional group (ligand A possesses OH, ligand B possesses methyl at the same location). The docking results of both of the two ligands show an exact binding affinity for the best pose. The interaction visualization also showed similar results, except that ligand A interacted with the protein with hydrogen bonding, while ligand B did not possess that interaction. But the other interactions were exactly the same (for example the total interaction of ligand B and protein is 9, while ligand A and protein is 10 (9 plus 1 hydrogen bond). Why did it happen? Isn't the hydrogen bond between ligand A and protein give lower binding affinity?
Yes, it is possible to have different no. Of H-bonds or different types of interactions for 2 different ligands, because it is the ligand and its constituents that decides the type of interaction, even though binding affinity for both ligands is the same.
However, MD Simulation gives a better understanding of protein and ligand interactions.
I agree with Pujan Sasmal. MD simulation can be done. Also look lengths (and types) of interactions in the docking calculation, some interactions (B ligand with protein) may be stronger.
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