[Chimera-users] Drug-Metal Complexation Modeling

Mickey Branham Branham at ukzn.ac.za
Sat Jul 2 01:46:52 PDT 2011

Thanks Elaine,
Yes, your comments were helpful. I did a bit of window shopping with Chimera (very impressive) but I think for this project it may not be the right set of tools. Briefly, what we're trying to do is to produce stable complexes of the dipeptide carnosine with a heavy metal (i.e. ruthenium III) by high energy ball milling. 

So far this approach has been effective in producing nanosized particles which do contain [carn-Ru] complexes (ca. XRD, DSC/TGA, and FTIR) but their structure and molecularity appear to be polydispersed. 

We are trying to predict the most stable complex stoichiometry so that we can optimize milling parameters (e.g. temp, inert gas, speed and time) known to influence complex formation rate. Once we are able to reproducibly form the [carn-Ru] complex our plan is to characterize its anti-viral or anti-tumor activty.

Don't know if this seems interesting but any comments from you would be appreciated.

Thanks again for your response.


>>> Elaine Meng 06/23/11 6:23 PM >>> 
Hello Mickey, 
Chimera has a "Metal Geometry" tool for assessing the coordination geometry within metal complexes, for example, identifying a protein complexation site as octahedral vs. pentagonal bipyramidal. It is intended for use with existing coordinates, such as from crystallography or output by other computational methods. Chimera does not include QM calculations, and would not replace the programs you mention if you are primarily interested in generating the coordinates in the first place. 

You can build structures with Chimera, but optimization is rather limited to only a few metals, and those that are handled are treated as point-charge VDW spheres (only minimization, no MD, and no QM to incorporate orbital directionality). It could be useful modifying existing metal complex structures, and as mentioned above, analyzing those structures output from other programs. 

I hope this helps, 
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab 
Department of Pharmaceutical Chemistry 
University of California, San Francisco 

On Jun 22, 2011, at 11:11 PM, Mickey Branham wrote: 

> Dr. Meng 
> Our group is interested in drug-metal complexation modeling. We have ongoing MM and MD studies using Gaussian or COSMO, with mixed results. Before we embark on a new voyage into Chimera can you tell us its capacity for elucidating drug-metal complexes e.g. tetracycline-M+2. 
> Cheers 
> Mickey 
> Michael Lee Branham, PhD. 
> University of KwaZulu-Natal 
> School of Pharmacy and Pharmacology 
> Durban, South Africa 
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