I am working on Hepatitis B virus, in my current study some marine compounds showed -6.5 kcal/mol affinity in AutoDock Vina, where my positive control Baraclude (antiviral drug) gave -6.2 Kcal/mol. Setting that as threshold I have screened some compounds for further analysis (ADMET + MD simulation). Now for publication, is that significant?? Like do I need to have binding affinity very high like -11/-12 etc.......
Please help.
Thanks.
Sunzid.
You can continue with that lead compound. But, there're more things to keep in mind apart from docking score, such as, drug-likeness, interactions with the key amino acids, stability at the binding site etc.
You may also optimize the particular lead to increase the docking score/ binding affinity. Here's a tool for lead optimization: https://charmm-gui.org/?doc=demo&id=ligdesigner&lesson=1
Pujan Sasmal Sir, thank you very much for your kind advice. I would perform ADMET, MD simulation, MM PBSA hopefully. I would try to optimize the lead compounds using CHARMM as recommended by Sutanu da, thank you very much also for the guideline Dear Sutanu Mukhopadhyay da.
I think you should try some other docking tools in order to validate the result you have obtained from Autodock vina.
The value is not always the same in Autodock vina. You may get different values each time you dock with the same protein and ligand. This might be considered as a drawback of Autodock vina. Though it is a problem with many other docking tools as far as I know.
So, in order to validate the results obtained from Autodock Vina, you may use a second tool for docking before going for ADMET and MD Simulation. I think using more than one tool in case of in silico studies help to give a clearer picture than of using only one tool.
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