i have a papain-like protease but having Chymotrypsin-like activity due to non-canonical active site Serine. I have to find inhibitors for this protease with in-silico methods. Can i dock inhibitor of other proteases and evaluate their binding? If so, what will be the criteria for evaluation? Any other ideas are welcomed.
Dear Atul, why not you are trying High Throuhput Virtual Screening from large library of small molecule such as ZINC, CHEMBANK and PubChem database.
That is worth a try, but the active site is conformational very similar to other known proteases, so I want to try known inhibitors 1st, if that fails, then I can move on to HTVS for finding novel inhibitors. thank you.But still my primary question remains unanswered.
Ok than coming to your primary question. You can dock with other known protease inhibitor. There is no doubt that you will get good docking result. To achieve a better result, you can generate various conformation of lead molecule based on the known protease inhibitor through 3D-QSAR.
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