Join us on Our LinkedIn Group

LinkedIn has become one of the primary sites on the web for people to connect, network, recommend each other and, for our needs, host discussions within a Group of interested parties who care about what Collaborative Drug Discovery is all about. Over the next few months we will be holding some interesting discussions inside the LinkedIn forum and we would like those of you interested in drug discovery and collaboration to participate. We encourage you to Sign Up Here and join over 50 other group members in discussions. Join us and participate with with scientists such as Chris Lipinski, Jean-Claude Bradley, Guillermo Morales and Bill Seibel. See you on the discussion group.

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.

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.

The number of contributers and datasets on the Collaborative Drug Discovery platform is increasing on an ongoing basis. Not only are our users adding to the content, both public and private but we ourselves continue to assemble databases to benefit the community. Most of our efforts will result in an increase in the Public Access datasets. The present list of Public Access datasets can be found here. Keep checking this page. More datasets will be showing up shortly.

We are all about Collaboration…it’s in our name! Since our databases sit on a growing foundation of small molecules and their potential contributions to drug discovery, it is natural that we would want to connect our structure collection to additional information that could be of value to our users. There are many open resources of structure-based content available on the internet. Some of those resources include PubChem, DrugBank, KEGG and many other databases. We want to focus our resources on developing the CDD software platform and partner with those resources providing the greatest value to our users so, when selecting a public  resource for providing additional information we chose ChemSpider.

ChemSpider is a free resource for chemists providing access to over 21 million unique chemical entities sourced from almost 150 data sources, many of these of value to drug discovery scientists. ChemSpider has already indexed PubChem, Wikipedia, DrugBank, PubChem and many other valuable resources. We don’t have to do that work. ChemSpider also actively curates and enhances the data on an ongoing basis using a crowdsourcing approach. We all benefit.

As an example of the linking between records the following integration path is shown below with the ChemSpider link highlighted. When this is selected you are taken directly to the ChemSpider record as shown below, in this case into the ChemSpider record here.

ChemSpider has a series of web services available that we might take further advantage of in the future. For now we are happy to connect across the web to the spider.

How many ways are there to communicate how something small can grow to become something much bigger…

Every long journey starts with a single step
Large Oaks from little acorns do grow
And maybe one for our era…  Today the financial sector, tomorrow the auto industry and next week ?

Well, let’s go with the large oaks analogy and talk about how it applies to Collaborative Drug Discovery. We established our company with the intention of making a real difference in the world. With a focus of helping drug discovery scientists around the world by delivering a software environment to archive, mine and collaborate we believe that we can make a real contribution to the process of discovery. We are proud of what we have been able to deliver using a very small team of committed and passionate individuals but we want to deliver more. In order to do so we are expanding our team, expanding our space and, over the next few months, you will see expand our reach in terms of collaborations and projects. In January 2009 we will be moving from our present offices and are now in the process of expanding our team. We are presently looking for a Community Support Professional and a Senior Software Developer as listed on our Jobs page. We are in an exciting phase of growth yet remain focused on our intention of delivering the premier software platform for collaborative drug discovery. Watch this space…