Virtual screening of compound libraries to enrich for inhibitors is a widely practiced strategy. The degree of success varies. The more the compounds being screened are like known competitive inhibitors of the target, the more likely you are to find actual competitive inhibitors from the screen when you test them.

If you are virtually screening a novel target against a generic compound library, you will undoubtedly get some "hits," defined as the compounds with the highest scores. When you test them, the great majority will probably not do anything, and many will inhibit in a nonspecific ("promiscuous") way, be insoluble, or interfere in some way with the measurement. If you are fortunate, there will be a few true competitive inhibitors, although they may be relatively weak inhibitors.

It will be important to develop efficient methods of measuring inhibitor potency, and of filtering the actives to determine which, if any, are real competitive inhibitors. This is pretty easy if you have an enzyme assay that can be performed in microtiter plates. Several methods have been suggested in the literature for testing for promiscuous inhibition (see the work from Brian Shoichet's group on this topic from the early 2000s). I have proposed a straightforward method of dealing with interference by compounds with the assay readout.

https://pubmed.ncbi.nlm.nih.gov/19643982/

Thank you for the interest. My main goal is to find out a novel candidate ligand as an activator by targeting the specific area on protein binding sites which has been already approved and validated. If I filtered the compunds after virtual screening method according to their docking score, I can characterize them as a inhibitor or activator. What I consider to be an activator may have the potential to have an inhibitory effect. If it acts as a competitive inhibitor, that is, by binding to the site of the activator and indirectly blocking it, it can have an inhibitory effect. Can we only see the results of this in vitro?

Is there any certainty that a compound will bind to the active site of the protein and activate it? By competing with the ligand that will activate it, it will indirectly inhibit it by binding to the site where the ligand that will actually activate it will bind, that is, by competing, thus it will have an inhibitory effect. However, it was evaluated because it had a high docking score in the results.

The situation you describe is distinct from a competitive inhibitor. It would be an allosteric inhibitor that competes with an allosteric activator, but is not itself an activator (like a receptor antagonist). These compounds would bind somewhere other than in the substrate binding site. Compounds that bind in the substrate binding site are almost always competitive inhibitors.

Alternatively, the inhibitor could compete with a co-substrate that is required for the reaction but is not converted into the product. An example would be with certain metal ions. A metal ion such as Mg2+, Zn2+ or Mn2+ might be involved in the reaction. This is often the case when the substrate is a nucleotide or nucleic acid, for example. Other metal ions, such as Cd2+ might act as inhibitors by displacing the normal metal ion but not making the appropriate interactions to act as the co-substrate. However, this is not a likely scenario when you screen so-called drug-like molecules, because they are much larger than metal ions. A more realistic possibility would be competition with a noncovalently bound organic cofactor.