[gmx-users] TZD Tautomers

[Nancy]

Hi All,

I happened to find a published article where molecular docking simulations
of TZDs against a novel protein is detailed:

Structure-based design of a thiazolidinedione which targets the
mitochondrial protein mitoNEET Bioorg Med Chem Lett. 2010 Feb
1;20(3):819-23

In this paper, the authors, using MarvinSketch v3.5.4, determined that the
TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the
diketone form (see attached figure).  It appears that the article's tautomer
prediction was based only on the pH prior to docking, and had nothing to do
with ligand-protein interactions.

Does anyone know if the diketone or enol, or perhaps a different tautomer,
would be predominant at pH 7.4?

Thanks in advance.
Nancy
attachment: Pioglitazone_Tautomers.png-- 
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Re: [gmx-users] TZD Tautomers

[Tsjerk Wassenaar]

Nancy,

Mark already indicated that this is not the proper place to post
questions like that. This forum is about gromacs, not about tautomers,
docking, and certainly not about MarvinSketch.

Cheers,

Tsjerk

On Thu, Jan 13, 2011 at 10:26 PM, Nancy nancy5vi...@gmail.com wrote:
 Hi All,

 I happened to find a published article where molecular docking simulations
 of TZDs against a novel protein is detailed:

 Structure-based design of a thiazolidinedione which targets the
 mitochondrial protein mitoNEET Bioorg Med Chem Lett. 2010 Feb
 1;20(3):819-23

 In this paper, the authors, using MarvinSketch v3.5.4, determined that the
 TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the
 diketone form (see attached figure).  It appears that the article's tautomer
 prediction was based only on the pH prior to docking, and had nothing to do
 with ligand-protein interactions.

 Does anyone know if the diketone or enol, or perhaps a different tautomer,
 would be predominant at pH 7.4?

 Thanks in advance.
 Nancy


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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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