I have 2 drugs with similar effect. They both INDIVIDUALLY showed a good docking using autodock. I am wondering if there is an MD approch to quantitate how those 2 drugs can have stronger binding when combined together. In other words, I want to check if there is a synergistic activation.
Thank you.
Dear Omar
Molecular dynamics simulation could complete the result of molecular docking.
To investigate the synergic effect you could build three systems:
1- protein with drug 1
2 protein with drug 2
3- protein with drug 1 and 2 with different fractions
after simulation, you could assess the effect of the presence of drugs on protein structure with analysis such as RMSD, RMSF, DSSP, and radius of gyration.
also, when you insert some drug molecules in the simulation box you are able to investigate the interaction between drugs such as agglomeration.
This paper could help you:
Article Adsorption and encapsulation of the drug doxorubicin on cova...
Hi Omar! If you want to investigate a synergistic effect of binding properly then using only a classical MD is not the right solution. I would suggest you to do free energy calculations investigating binding free energies of those drugs.
Inna Ermilova Thank you so much for your recommendation. I just want to ask about the appropriate way to do this as I am a complete beginner. What tools I can use to do this? is GROMACS sufficient? Also, do you recommend any paper that addresses similar question?
Dear Omar, you can use Gromacs together with plumed. There are many good papers about that. In order to simplify your task I would suggest you to visit the page of the plumed software. There you may find how to install and tutorials. Plumed is free of charge like Gromacs. If you like to use another MD engine you can do that too. Plumed is compatible with other codes (you can find the list on plumed page).
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