Dear Sagar,

The physiological pH is 7.4, therefore, the compound will be mono-ionized.

Hence, it is suggested that you run your docking calculations with the mono anion of the compound.

Rafik

i meant during protein inhibition bioassay. The compound is in neutral form during docking which was done in physiologic pH settings, but when i try to buy it only salt form exists or salt form is cheaper (but lesser amount). If i use them will the prediction hold truw relative to the neutral form. I am also worried about solubility of neutral forms. Each assay well has 50 uL volume and i need max 100uM conc at least.

To make it simple:

1) For docking: estimate the pKa(s) of your compound, and prepare it for docking by consdering its protonation state at pH 7.4.

2) Your bioassay is usually run in some kind of buffer / pysiological medium. Therefore, the tiny amounts of compounds you'll put in there (µM concentrations) will not affect pH of your assay. As there is equilibrium between protionation states, your compound will take the protonation state that is relevant with the pH in your assay. Do not worry about the salt, as long as it is soluble in your assay medium / buffer and does not interfere with readout.

Dear Sagar,

Both theoretically and experimentally, the compound should be ionized at pH 7.4.

Therefore, run the docking and the bioassay with the ionic form.

Rafik

So in summary, a drug and its salt form won't show any diff in enzyme affinity yes? Since salt form have more solubility, I better use salts form which has plus point of bypassing solubility problems. Correct?

Yes, Indeed.

Rafik

Be aware that the "docked" form should be the same form (i.e., possibly ionized) that is present at the pH of the assay.  Electrostatic and H-bonding interactions depend very much on the state of protonation!