Hi All, I am performing molecular docking and molecular dynamics simulations of thiazolidinediones (TZDs) binding to the ligand binding domain of the PPAR-gamma receptor protein. The thiazolidinedione ring can exist in numerous different tautomeric states (see attached figure); is there any particular tautomer(s) that would be dominant, and thus most appropriate for docking and molecular dynamics simulations, at pH 7.4?
I have read the article "Metformin and glitazones: does similarity in biomolecular mechanism originate from tautomerism in these drugs?" J. Phys. Org. Chem. 2008, 21 30–33, as a reference, but it does make it clear as to which tautomer is most appropriate for simulating binding to a receptor protein at pH 7.4. Thanks in advance, Nancy
<<attachment: TZD_Tautomers.png>>
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