[Chimera-users] Thiazolidinedione Tautomers

[Nancy]

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
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