Drug Discovery News Acknowledges Our Efforts

In an ongoing flurry of recognition of our efforts to support the discovery of new cures for Tuberculosis, and our related funding from the Bill and Melinda Gates Foundation (as announced here) the Informatics arm of the Drug Discovery News web portal has acknowledged our work.

They interviewed Ken Duncan, a senior program officer at the Gates Foundation who commented “CDD’s technology will help the entire TB research community to collaborate more easily,” Duncan said in the statement. “We hope it will speed the scientific breakthroughs urgently needed to make effective therapies more accessible to the world’s poorest people, and confront the challenges of multidrug- and extensively drug-resistant TB strains.” Ken has certainly captured the spirit of what we are working to achieve with the development of the CDD platform.

They also interviewed our own Sean Ekins who had the opportunity to emphasize how our approach can change the classical ways of interacting. As Sean comments in the interview, “…how can some academics share modules with someone who wants to do testing, and how can we connect those two groups of people together without the tried-and-tested way of looking for each other on Google, PubMed or a conference?”. We certainly believe that CDD can make a difference in this direction and certainly execute on our ultimate vision.

As Sean says “Our ultimate goal is to advance a couple of new, key TB drug candidates. That is a lofty goal, but we’re hoping to pull it off within two years.” if you are interested in helping in this venture feel free to contact us.

Last evening we released the latest update to CDD, customizable mine results. This release makes it easy to add (or remove) protocols, readouts, molecule synonyms and/or user-defined fields to/from your mine results, allowing you to customize the displayed data to be most relevant. To access this new feature, perform a mine query, then click the new “Select data to display” link on the right above the search results table:

Once you click this link, a panel will open, allowing you to select which protocols, readouts, chemical properties, or molecule fields you want to view (or not view). Clicking and dragging the green four-way arrows reorders the various sections.

The list of Molecule Fields includes molecule synonyms, all user-defined fields in your private group, and all published user-defined fields associated with any of the publicly or privately-shared data sets you’ve selected in the Collaborate Data Sets tab.

One feature we did not provide in this release is a way to save these display preferences. We’d like feedback on what would be most useful here. We have had a couple ideas:

1. Save the display options with a saved query, so that next time you run the query, the sections you selected will be displayed in the same order.
2. Save the display options for each section so that the next time you perform any search, those sections will have the same readouts/properties/fields displayed. Note that this does not allow you to save the order of the sections, because different sections could be available for different queries.

We’re excited about this small but powerful enhancement. We hope you enjoy using the new functionality, and please email us at support@collaborativedrug.com to let us know how it works for you.

In the inaugural issue of Volume 11 of the Journal of Combinatorial Chemistry Anthony Czarnik commented on the concept of Distributed Drug Discovery, D3. This concept was introduced in papers in that issue by Profs William Scott and Martin O’Donnell of the IUPUI (Indiana University-Purdue University Indianapolis).

The three papers are:

Distributed Drug Discovery, Part 1: Linking Academia and Combinatorial Chemistry to Find Drug Leads for Developing World Diseases

Distributed Drug Discovery, Part 2: Global Rehearsal of Alkylating Agents for the Synthesis of Resin-Bound Unnatural Amino Acids and Virtual D3 Catalog Construction

Distributed Drug Discovery, Part 3: Using D3 Methodology to Synthesize Analogs of an Anti-Melanoma Compound

I encourage you to get a copy of the first issue of the Journal of Combinatorial Chemistry and read the papers directly. The concept around D3 can be summarized by this statement from the first of the three papers “Distributed Drug Discovery (D3) proposes that if simple,inexpensive equipment and procedures are developed for research in each of the core drug-lead discovery stages, computational chemistry, synthetic chemistry, and biochemical screening, this large research challenge can be divided into manageable smaller units and carried out, in parallel, at multiple academic and industrial sites.” Clearly we see our efforts here at Collaborative Drug Discovery as supportive of D3 and Tony Czarnik’s editorial recognizes us as working to support his “noble goal”.

Tony includes a comment from our own Barry Bunin where Barry announces our efforts to support the work of IUPUI. We are providing the IUPUI-CDD database making available all the reactants, reagents and products. This database will be updated over the coming months as the work is expanded. The Distributed Drug Discovery (D3) database is a virtual catalog of 48,608 unique acylated unnatural amino acid derivatives obtained from a combinatorial enumeration. If you re interested in accessing this database you can register for a free read-download account with Collaborative Drug Discovery (CDD) here. We have also put together a thorough tutorial regarding how to use the D3 database on the CDD website and you can find it on the site at the same address.

This is one of many databases that you will see added to the CDD website over the next few months and we encourage you to make full use of these valuable resources as they become available. Don’t forget to read the papers in JCC. It’s a different model for Drug Discovery but at a time when Pharma R&D is challenged to produce more drugs there MUST be a change in strategy. Collaborations across the industry and with academia are surely going to be a part of the strategy and we will visit some of the approaches to this in later postings. We are already enabling the shift.