If docking shows that long chain hydrocarbons have high binding affinity for a particular target protein, can this really mean that the long chain HCs will have potent inhibition in-vitro or have medicinal value since these type of compounds are usually oils and sometimes edible
I can think of several reasons why the docking result may not translate to an in vitro or in vivo effect.
1. The docking results do not adequately reflect reality. Docking scoring functions are notoriously inaccurate.
2. The compounds bind to the target, but do not cause any inhibition because they do not interfere with the biological function. This could happen if the binding site of the compounds is outside the active site or site of protein-protein interaction.
3. The compounds are too insoluble to reach the target in an aqueous environment. This is likely to be the case for long-chain hydrocarbons.
4. The compounds are too toxic to be used at an effective concentration.
5. The compounds are too metabolically labile and/or have too little bioavailability to reach an effective concentration at the site of the target.
You will have to look into many different parameters like ADMET parameters..... Apart from this if you wish to find out the acuracy of the molecules in terms of biological activity you can do QSAR modeling to predict the bioactivity of you compound....
Regards
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