Query regarding docking

Question

[anubhutijha21]

1. If we dock a ligand (probable drug lead) to a target protein and it shows good docking score . Does that mean it would be a substrate of that target protein (enzyme ) and consume it??

2. How can we know that the ligand we use is a agonist or antagonist

3. Can we compare 2 substrates of 1 enzyme as which one is better using in silico approach

Answer 1

[Khader Shameer]

1. Based on your docking experiments and the constraints (iterations, vacuum vs. solvent, targeted or high-throughput etc.), one can assume that ligand could be one of the small molecules that bind/interact with the protein of interest. "Consume" is more of receptor internalization, a small-scale docking experiment does not represent an understanding in this level.You need a more involved experiment to confirm receptor internalization.

2. You can gather the mechanistic role of your ligand from reference databases (CSA, BindingDB, PDBeChem) / literature support. Sometimes you can infer this from pseudoenergies or other structural parameters.

3. Yes.