I have a target and a small molecule which is interaction with the enzyme. How do you determine whether the small molecule is a substrate or an competitive inhibitor of the enzyme?
I feel so confused because the substrates and competitive inhibitors of an enzyme are usually structurally similar.
If the molecule is an inhibitor, it will reduce the rate of catalysis by the enzyme of the reaction of a known substrate. It could do this without itself being a substrate, but it could also do it by being a poorer substrate that competes with a better substrate.
If the molecule is a substrate, the enzyme will catalyze a reaction involving it. You can test for this if you have some means to follow the reaction.
Dear,
For a small molecule identification; is a low molecular weight (< 900 Dalton) organic compound that may regulate a biological process, which also acts on enzymatic reactions.
And some molecules are acts as a substrate like Hydrogen Oxygen, Nacl etc.
The third thing is this; go for literature and search literature about molecules.
Thank You.
I would say by the reaction it causes to the enzyme. Maybe by the kind of binding,but I am not sure how to figure it out. Maybe measure it by the substrate/product.
See AB Shapiro's answer.
Practically, you should first check if your small molecule undergo a reaction in the presence of the enzyme.
Then it will be kinetic studies in the presence of the substrat and your small molecule.
If you are doing in vivo research then you can measure the effect of the molecule by studing changes on the organism you test.
But if you want to test your molecule by in silico means then you have to take your target enzyme with a ligand (substrate) that is already bound to from one of protein databases then test your molecule by docking it with the active site and studying its bound states according to its pose and score and comparing it with the original substrate.
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