Hello,
I know my title isn't well matching. We got six crystal structures of the same enzymes with different inhibitors. Based on IC50 values, all these 6 are differently potent to microbial inhibition. Based on ligand-structure interaction profile, it is not easy to comment on the IC50 value, because for 3 of them the interaction profile is almost, almost identical but the IC50 value indicated major differences.
Is there any sort of computational analysis from where we can comment that yes due such reason it might be the scenario. I am searching some related literature but most of them focuses on docking energies etc. You suggestions are of great value.
Thanks to all the readers,
Hi there,
Did you use exactly the same enzyme assay format for the IC50 determination? Do you expect the different molecules to act the same way on the enzyme activity? You have to answer yes to both questions if you actually want to compare IC50.
The main difference between the structure and the enzyme assay is the dynamics of the process. Structure gives you a frozen picture of a complex formed between the enzyme and the inhibitor obtained with a large excess of inhibitor over enzyme and in absence of the substrate whereas IC50 is obtained from a functional assay where basically dynamics plays an essential role (kon, koff, possible competition with substrate, possible conformation change of the enzyme aso).
Yes we have used the same protocol and I am aware of the dynamics that it would pay some role. What I need to read/find some factors through which I comment that it might be the reason. Well thanks for your time and reply.
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