Hello,
Please suggest me how to select protein targets in MCF-7 for molecular docking studies of phytoconstituents against breast cancer cell lines. I have seen in research papers regarding the in silico screening using various proteins like BRCA1, HER-2 etc. Are there any criteria in choosing particular targets?
Awaiting your valuable suggestions.
-Regards-
Neethu Kannan B.
Dear Neethu,
There are many criteria for choosing protein target for the docking studies. Few of them I am listing below
1. Protein target can be choosen based on your designed strategy for perticular target for ex. when you design ATPase inhibitor then you dock against ATPase.
2. If you dont know the target for your phytochemical then you can see the literature where compounds containing similar scaffold is reported to inhibit particular enzyme and then you can choose those enzymes for your docking studies.
I hope I have answered your question.
I agree with Mr. Sunil,
you must also check the chemical structure of your phytochemical constituent and groups present in the structure and then check for similarity of the structure having anti cancer activity.
or each target will have a standard drug or many, you can check with your molecule which drug is a close fit.
may be i just elaborated mr.sunil's view.
I am agree with both mr sunil and saner however you can also choose particular targets of interest throug RCSB Pdb
Dear Neethu,
Are you using plant extract as such or isolated phytochemical? Do you have any idea about the target?
Dear Finosh,
I am using plant extract and some compounds are obtained by GC-MS analysis. I am planning to dock using these phytochemical compounds with protein targets. But I am confused how to choose the target. Can I use multiple protein targets for in silico studies?
Yes you can choose multiple protein for docking. After docking you will get result and on that basis you can select best result to add in your research. You can mention that result as comparative analysis. You can choose exiting protein using literature or best thing choose those sequences which have nothing 3D structure so that beneficial to you.
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