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Reengineering Translational Science

25 Jul

I am reposting a blog post from Sean Ekins regarding a recent communication we submitted….

“Recently, Francis Collins published a commentary in Science Translational Medicine entitled “reengineering translational science: the time is right”. and I would encourage people to read it and tell me what you think, for no other reason than this is one of the most accomplished scientists of our time. Antony Williams and I wanted to respond to some of Dr. Collins’ comments. The journal has the ability to post an E-letter so we took this route and so far it has not been published. For that matter it seems no one has responded. Does this mean that everyone agrees with his comments? If there is truly to be a dialog on the topic surely this journal should publish E-letters it receives.

Here are our comments which were submitted as an E-letter but not as yet published- we are restricted to 400 words:

Reengineering Translational Science: Is the NIH the right place for this?

Sean Ekins(1) and Antony J. Williams(2)

1 Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, NC27526, U.S.A.

2 Royal Society of Chemistry, 904 Tamaras Circle, Wake Forest, NC27587, U.S.A.

We read with interest Dr. Collins’ Commentary on Reengineering Translational Science: The time is Right. We agree that there is an urgent need to revamp the way that drugs are developed, bring them to market faster and provide incentives to generate treatments for neglected and rare diseases. We question however whether the NIH as it stands can adequately pursue these goals when an entire industry is struggling with the same challenges. We wish to raise several issues that this article promotes. Many of the techniques described will not dramatically impact the process alone and be any more successful than combinatorial chemistry and high throughput screening were touted to be. Why would we want the tax payer to follow the same route as big pharma? Surely the NIH is funded to a large extent to take more exploratory directions (1, 2), and to come up with next generation discoveries and approaches, not simply apply existing technologies and hope to be more successful? It would also be more convincing if there were co-authors on the paper from outside the NIH lauding the value of repeating approaches already in use. Collaboration is important and this commentary did not demonstrate how collaborations (with academic labs or with the pharmaceutical industry) would be facilitated and data shared.

Finally, we are also concerned that an initiative described in this paper, namely the recently released NPC browser (“a comprehensive resource of clinically approved drugs to enable repurposing and chemical genomics”) from the NIH Chemical Genomics Center (NCGC) (3) may not have set the case too soundly (3). Within 24 hrs of release our analysis of the molecules in the database showed that fundamental errors were present, with valency issues, charge imbalances and stereochemistry, (4-6) to name just a few. It took over a month for NCGC to acknowledge these errors and they will still be fixing them for the foreseeable future (7). This software application and content was released in a very raw state with extremely poor quality data (7-9). While software development may appear easy and fast to do, what is required to produce the best solution is the right ideas, the right people and the right tools. The parallel with NCATS is clear. While the NIH is staffed with many clever people there are many more willing to collaborate with fresh ideas outside (10) . We define ourselves as two such willing participants.

References

1.         S. Ekins, A.J. Williams, M.D. Krasowski, J.S. Freundlich. In silico repositioning of approved drugs for rare and neglected diseases. Drug Disc Today. 16, 298-310 (2011).

2.         S. Ekins, A.J. Williams. Finding promiscuous old drugs for new uses. Pharm Res. 28, 1786-1791 (2011).

3.         R. Huang, N. Southall, Y. Wang, A. Yasgar, P. Shinn, A. Jadhav, D.T. Nguyen, C.P. Austin. The NCGC Pharmaceutical Collection: A Comprehensive Resource of Clinically Approved Drugs Enabling Repurposing and Chemical Genomics. Science translational medicine. 3, 80ps16 (2011).

4.         A.J. Williams. Reviewing Data Quality in the NCGC Pharmaceutical Collection Browser. http://www.chemconnector.com/2011/04/28/reviewing-data-quality-in-the-ncgc-pharmaceutical-collection-browser/.

5.         A.J. Williams. What is a Drug? Data Quality in the NCGC Pharmaceutical Collection Browser Part 2. http://www.chemconnector.com/2011/05/02/what-is-a-drug-data-quality-in-the-ncgc-pharmaceutical-collection-browser-part-2/.

6.         A.J. Williams. Support for Common Compounds in the NPC Browser. Data Quality Part 3. http://www.chemconnector.com/2011/05/02/support-for-common-compounds-in-the-npc-browser-data-quality-part-3/.

7.         A.J. Williams. Unreported results. Manuscript in preparation (2011).

8.         A.J. Williams, S. Ekins. A quality alert for chemistry databases. Drug Disc Today. In Press,  (2011).

9.         A.J. Williams. Rabbits, Potatoes and other Vegetables in the NCGC Database. http://www.chemconnector.com/2011/07/19/rabbits-potatoes-and-other-vegetables-in-the-ncgc-database/.

10.       S. Ekins, A.J. Williams. Reaching out to collaborators: crowdsourcing for pharmaceutical research. Pharm Res. 27, 393-395 (2010).

Conflicts of Interest

AJW is employed by the Royal Society of Chemistry which owns ChemSpider and associated technologies.

SE Consults for Collaborative Drug Discovery

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on July 25, 2011 in General Communications

 

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