A ligand showing different effect at different pH. I wanted to study the interaction of the ligand with DNA. So how will i study those at different pH environment through molecular docking approach? Can anyone help?
Dear Somya,
Always difficult to answer without seeing the ligand!
Let us assume that the pH-related differences you observe are related to a change in the ligand, not the in the receptor (DNA). In that case, I also assume that you have acidic/ basic centers in your molecule, which means different protonation states depending on pH.
Try to have an idea of what the acidic / basic centers are in your ligand (there are some pKa prediction tools, but in obvious cases, common chemical sense will do). Then, I just suggest that you generate the structure files for your ligand with the different protonation sates (i.e. the major species at each considered pH) and submit both of them to docking. Most softwares will allow you to do that, even if the they do not contain explicit options to set pH.
Hope it helps!
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