Open Source Science Expands with Tan
A few months ago I posted a request for a docking collaborator to help us understand and reproduce our docking results with our targeted anti-malarial compounds. I've been contacted by a few people and I'll report on every one of those collaborations when it is possible.
Last week, Tan Tsu Soo from the Bioinformatics Group at Nanyang Polytechnic in Singapore informed me that he worked things out with his Director and was now in a position to collaborate with us openly. He has been busy docking uncyclized Ugi products and diketopiperazines using FlexX to compare with the results than Sean has obtained in D-EXP005.
He has not obtained identical results, partly because his search is not restricted to the same binding site that Sean used with THINK.
But the good news is that Tan also has managed to dock a good number of our molecules, including Ugi products that we have made and can start testing. He uploaded some of his results using Jmol to demonstrate the docking. Stay tuned for more data on the wiki.
The deprotected Ugi products (R and S) that Alicia prepared in EXP062 are shown below to dock in a similar fairly shallow location. (DRuncycltBu and DSuncycltBu from D-EXP005) Others, like the catechol derivative BRuncycltBu bind deep into the pocket. Check them out on Jmol.