selected 3 compounds I identified from medicinal plant and did some insilico metabolic analysis using an online molecular docking software. This is what I generated.
The Beta sheet- is a Breast cancer type 1 protein molecule
The thick substances are my 3 compounds. Their binding affirnity score range are:
1st one is: -3.9
Second: -4.9
3rd: -4.1.
I can conclude this preliminary results can be a starting point of novel anticancer drugs. Minimal acceptable binding affinity score is -3.2.
No. In molecular docking, the binding affinity score is a measure of the strength of interaction between a ligand molecule and a target protein. The lower the binding affinity score, the stronger the interaction between the ligand and the target.
The minimal binding affinity score can vary depending on the method used to calculate it and the particular protein-ligand system being studied. Setting a threshold for the performance of a docking score is not enough to qualify a ligand as a prospective druglike candidate. Some journals would suggest: "scores in the range of -10 to -40 kcal/mol are considered to indicate a strong binding interaction. A score of -5 to -10 kcal/mol might indicate a moderate interaction, while a score above -5 kcal/mol might be considered weak."
To boycott thresholds in molecular docking scores, it is advisable to consider standard(s) (clinically approved drugs) performance against your novel compounds. If your standard has a higher value compared to your new compounds, it's a good sign.
My little cent!
Your docking results are not that much bad but these are still not fruitful...Prepare your proteins using discovery studio tool and minimize it via chimera tool than use pyrx for docking. Your results may show good binding energy...Online tools are helpful but using manual tools are much more efficient...
Good initiative to start work but not sufficient for any conclusion. In Drug discovery it's one tool that help in repurposed drug or new drug dellivery onevstep. In new DD further study ADMET parameter and then simulation parameter and in case some points drug delivery points other things also sttudy.
Your score indicate it's effective against brest cancer but if pdb fold then no response.
I also agree with Abdeen initially but if your other simulation results also support then may be effective. In your case you use natural compound thus bioavailability may be no problem.
May I know how did you choose pdb and which pathway did you targeted and why?
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