[Dock-fans] TZD Tautomers

Nancy nancy5villa at gmail.com
Sun Jan 16 10:19:37 PST 2011


What experimental evidence are you referring to?

Nancy


On Fri, Jan 14, 2011 at 1:01 AM, John Irwin <jir322 at gmail.com> wrote:

> I find the experimental evidence for specific binding unconvincing.
>
>
> On Jan 13, 2011, at 17:49, Nancy <nancy5villa at gmail.com> wrote:
>
> Considering that others have stated that tautomeric form can be one of the
> most important factors when preparing ligands docking, could you clarify
> what you mean by "tautomeric form is the least of your worries"?
>
> Thanks,
> Nancy
>
>
>
> On Thu, Jan 13, 2011 at 7:56 PM, John Irwin < <jir322 at gmail.com>
> jir322 at gmail.com> wrote:
>
>> Single point IC50, no dose response, no IC50 curve, no test for
>> aggregation. Tautomeric form is the least of your worries.
>>
>> On Thu, Jan 13, 2011 at 1:27 PM, Nancy < <nancy5villa at gmail.com>
>> nancy5villa at 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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>>>
>>
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