Hello.
I have the following problem at hand: I need to validate a pharmacophore of a regulatory factor. There are no inhibitors described either for my target or for analogous structures. The structure I possess has only my target attached to a stretch of double helix DNA and the protein structure makes important contacts with the two strands. After an MIF analysis I defined the points of my pharmacophore, but I did not find methods that would allow me to validate my pharmacophore in this situation.
Thanks in advance for helping me out of this hurdle.
It is totally fine to use a non-validated pharmacophore. In fact, most screening studies occur on a target with no known ligands (why would one need to do screening otherwise?). Try using complementary filters. For example, dock pharmacophore hits into the target. Check if the hits are still aligned with the pharmacophore even when docked (that was the rationale for your pharmacophore strategy, right?).
It is totally fine to use a non-validated pharmacophore. In fact, most screening studies occur on a target with no known ligands (why would one need to do screening otherwise?). Try using complementary filters. For example, dock pharmacophore hits into the target. Check if the hits are still aligned with the pharmacophore even when docked (that was the rationale for your pharmacophore strategy, right?).
Not possible to validate pharmacophore without known ligands. However you can proceed as suggested by Dmitri Kireev, it is perfectly fine.
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