I have synthesized few heterocyclic compounds which show good cytotoxicity against MCF7 cell line in the in-vitro assay (i.e., MTT assay). Now for in-silico molecular docking study, I am not sure which receptor should I choose? In some literature, the receptor protein selection is made by using the binding affinity database (e.g., Thomson Reuters MetaDrug). My question here is that to link the in-vitro study to in-silico study how to choose the receptor protein for molecular docking study?
If you have good compounds, you can select the targets based on the cell lines you tested.
Ex: If you are focused on Breast Cancer, find the therapeutic target or potential target from Breast Cancer pathway/pathogenesis or literature. Then you can proceed in silico studies. even there was many in silico works reported using the MCF7 cell line to molecular docking studies.
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In other words, you can analyse the in vitro binding affinity test to confirm the drug binding in your target protein. If it is confirmed, you can start your work with that protein.
Good Luck
Km Sachin
If you still don't find suitable literature, proceed with SwissTargetPrediction server. This helps you to find probable targets for your compound
http://www.swisstargetprediction.ch/
MCF-7 is a breast cancer cell line which was obtained from a patient. It was not engineered to overexpress a particular protein or pathway. So, you can't relate MCF-7 activity to one particular target. However, since your compounds are active on MCF7 cell line, you can present them as inhibitors of MCF7 cells proliferation.
Now for target identification, you have to biotinylate your compound and do protein pull down studies. This is a definitive method for target identification. If you don't have the infrastructure for protein pull down or a collaborator who can do that, you could 'suggest' the 'probable' targets based on computational approaches. Do a literature search on which compounds are similar to the ones you have, and see their biological activity profile. Then dock your compounds to that target.
Hope this helps.
literature information is very necessary in this particular case. So,you have to ready bunch of information related to your compounds by searching database and journals.Then you have find a particular target protein.For seeing receptor protein interaction,you have to perform in-silico virtual screening of these compound.
In this way you can choose better target for your synthesized compound by according to their binding affinity.which may very useful for further experimental pursue.
One rational strategy would be to identify in the literature which receptors are overexpressed in that cell line and subsequently relate the chemical nucleus of your compounds to the affinity by these receptors. Then with the few candidate receptors perform docking calculations.
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