For MD Simulated protein-ligand complex I have extracted the ligand and the reacting residues(as mentioned in literature) for further kinetic study. I have imported this model to spartan software and predicted the transition state for QM study. But I don't know whether this methodology is correct or not.
I have attached the mechanism i want to model. Any suggestions please?
P.S I want to validate my ligand for a reaction with these residues. Can this be done as i mentioned above. (in-silico)?
Have you considered Warshel's Empirical Valence Bond (EVB) approach? There is no better approach than EVB to model enzymatic reactions. The really neat feature of this approach is that one does not need to define any reaction coordinate explicitly, and that the reaction coordinate is the "energy gap" between two resonance states, and that one can include the entire enzyme (or a large part of it) into the simulated sphere of explicit water molecules.
https://www.ncbi.nlm.nih.gov/pubmed/6942759
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See the Supporting Information to the linked paper for some details about this approach.
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If the reaction mechanism and the intermediates are known, one can define the resonance states, carry out the transition between the states using Free Energy Perturbation approach, and obtain the free energy profile of the reaction. This should first be carried out without the inhibitor; also note that one has to calculate the corresponding reaction in solution to calibrate the free energy profile in the enzyme.
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Whether this approach will be applicable to your case depends on what type of inhibition it is . . . One obviously cannot model enzymatic reaction if the inhibitor and substrate share the same binding site . . .
Article Uniform Free-Energy Profiles of the P–O Bond Formation and C...
Martin Klvana yes my inhibitor and substrate act on the same active site with same residues. But i am trying figure out whether my inhibitor would react on the same pathway as the substrate does. So i modelled the transition state and carried out a DFT calculation. Even though i obtained the reaction profile as well as other reacting properties (including hamette paramaters). But i how can i prove the feasibility?
The proof can only be obtained experimentally, i.e. with the real enzyme & inhibitor/substrate.
Thank you very much for your kind guidance Martin Klvana. Could you please tell me how can i use the energy profile and gibbs free energy calculation to depict feasibility of the ligand as an inhibitor?
I am confused. You wrote "trying figure out whether my inhibitor would react on the same pathway as the substrate does"---so what is the "ligand": just an inhibitor or also a substrate (reacting with the enzyme)? If it acts as a substrate and the activation free energy barrier of the reaction is comparable, or more favorable, than that for the natural substrate then the inhibitor could indeed act as a substrate for the enzyme; but the confirmation must be obtained experimentally.
No sir i have removed the existing substrate and found a novel molecule as an inhibitor via preliminary docking and dynamic studies. I am hoping to use this particular ligand for my reaction study because inhibition of my enzyme is happen via a hydrolyzing mechanism pathway.
So you have a putative inhibitor that binds to one specific transition state of the reaction with the natural substrate, and you have the free energy profile of the reaction with the substrate and the binding "free" energy of the inhibitor with the transition state?
If so, then I think that you will also need to model the reaction in solution to calculate the "real" catalytic effect of the enzyme (ddGcatalysis = dGact,enzyme - dGact,solution) and you will also need to calculate the solvation free energy of the inhibitor in free (unbound) state in solution to obtain the "real" binding free energy (ddGinhibitor = dGbind,enzyme - dGbind,solution). Then you can compare the comparable: ddGcatalysis vs ddGinhibitor.
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