Distributed Drug Discovery Papers

31 Jan
Published by MatTodd

Subject 

Miscellaneous

Community 

general open research

The Scott and O'Donnell labs at IUPUI have published an interesting set of articles in the latest issue (vol 11, issue 1) of the Journal of Combinatorial Chemistry on Distributed Drug Discovery. They're open access articles. The idea is to show that chemical synthesis can be done by multiple labs for the creation of drug-like compounds, and that there is reproducibility between the different sites (from the US to Poland). This is obviously an important requirement for any distributed research effort. Jean-Claude's Open Notebook concept is of course aiming at exactly that. The Scott/O'Donnell papers show that reproducibility is possible in a combinatorial synthesis, and they host a virtual catalogue of compounds on Barry Bunin's CDD database. This is a great addition to the literature of distributed solution to wet lab problems, and is a reference to use for those of us aiming to convince funding agencies that multiple-lab chemical research can be done.

Comments

jcbradley's picture

Mat
If I understand the article correctly the synthetic tasks are distributed but it wasn't clear how much communication there is between groups. Only the virtual catalogs are public, right? None of the synthetic work is open?

Currently communication between groups is informal and simply by email or voice. We are hoping someone might help us create an easy to use web based system that would allow the free interchange of thoughts and results among the globally distributed academic sites.

Yes, the virtual catalogs are public and freely accessible through the CDD site given in our articles.

As to whether or not the synthetic work is "open". Definitely! In our first case of "distributed synthesis" it has been made available through the results and experimental section in our Journal of Combinatorial Chemistry articles. We paid ACS a fee so that all three articles can be obtained for free. No subscription to the Journal is required. Here are links that you might find useful:

Editorial about the Distributed Drug Discovery Program:Czarnik, A. W. Editorial. J. Comb. Chem. 2009, 11, 1-2.

Scott, W. L.; ODonnell, M. J. Distributed Drug Discovery, Part 1: Linking Academics and Combinatorial Chemistry to Find Drugs for Developing World Diseases. J. Comb. Chem. 2009, 11, 3-13. [DOI: 10.1021/cc800183m (http://dx.doi.org/10.1021/cc800183m)].

Scott, W. L.; Alsina, J.; Audu, C. O.; Dage, J. L.; Babaev, E.; Cook, L.; Goodwin, L. A.; Martynow, J. G.; Matosiuk, D.; Royo, M.; Smith, J. G.; Strong, A. T.; Wickizer, K.; Woerly, E. M.; Zhou, Z.; ODonnell, M. J. Distributed Drug Discovery, Part 2: Global Rehearsal of Alkylating Agents for the Synthesis of Resin-Bound Unnatural Amino Acids and Virtual D3 Catalog Construction. J. Comb. Chem. 2009, 11, 14-33. [DOI: 10.1021/cc800184v (http://dx.doi.org/10.1021/cc800184v)].

Scott, W. L.; Audu, C. O.; Dage, J. L.; Goodwin, L. A.; Martynow, J. G.; Platt, L. K; Smith, J. G.; Strong, A. T.; Wickizer, K.; Woerly, E. M.; ODonnell, M. J. Distributed Drug Discovery, Part 3: Using D3 Methodology to Synthesize Analogs of an Anti-Melanoma Compound. J. Comb. Chem. 2009, 11, 34-43. [DOI: 10.1021/cc800185z (http://dx.doi.org/10.1021/cc800185z)].

For access to the IUPUI - Distributed Drug Discovery (D3) database, register for a free read-download account with Collaborative Drug Discovery (CDD) at https://www.collaborativedrug.com/register/iupui-d3 by completing the Sign up for IUPUI – Distributed Drug Discovery (D3)” information.

 

MatTodd's picture

William, thanks for this. This site, and others I'm sure, would be delighted to host data or other resources to help you with this project. An appeal to the community at large may help to find labs that are interested in joining your consortium - in particular those interested in doing experimental organic chemistry, on your or related targets.

e.g.:

1) Decide on a target molecule/set of analogues
2) Set up a project page describing the approach, with schemes/initial references
3) Appeal to the community for interested labs (a lot of discussion here could take place on various sites in parallel, e.g. Friendfeed)
4) Post procedures and results. Also post experimental data in raw form, either on the project page or directly at a repository, e.g. ChemSpider.
5) Iteratively work (on the web) towards a synthetic approach to the target structures that demonstrates distributed reproducibility.

Would be great to try this out!

Mat