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BIA-10-2474, confusions in chemical structure and the need for EARLY clarity in chemical structures

24 Jan

My blog has been fairly inactive for the past few months, driven primarily by my move from working on cheminformatics at the Royal Society of Chemistry to working at the National Center for Computational Toxicology at the Environmental Protection Agency. While I stopped working on ChemSpider about 18 months before I left RSC (to focus on the developing RSC Data Repository) my interest and focus on data quality and a long-standing interest in “accuracy in chemical structure representations” has never dwindled. At the EPA-NCCT we are very focused on working to produce high quality chemical structure databases, following on from the work of my colleague Ann Richard who initiated work on DSSTox over a decade ago.

It was therefore with great interest that I became aware of the confusion in regards to the chemical structure of BIA-10-2474, a drug that has attracted a lot of interest because of a clinical trial with negative outcomes. I am entering the story late compared to my many time collaborators and friends Sean Ekins, Chris Southan and ALex Clark, but more about their work later. The news to date is best summarized at Derek’s In the Pipeline blog and on David Kroll’s post on Forbes.

Based on my previous history and work with helping to curate chemical structures on Wikipedia (starting one Christmas in 2008) my experience would be that Wikipedia is a GOOD PLACE to source high quality structures, especially after the work invested in curating chemical data over the years. The first structure for BIA-10-2474 that was reported on Wikipedia is shown below.

ORIGINAL BIA structure

On January 16th Chris performed his usually thorough examination of structure integrity and links to public sources (he is a master in this domain!) but commented specifically ” The molecular identity of BIA-10-2474 can only be formally verified directly by BIAL or indirectly from regulatory documentation they may have submitted” as the chemical structure itself was inferred from the name.

Nevertheless my friends Sean Ekins and Alex Clark were already investigating what OPEN MODELS may be able to predict about the chemical: See here, here and here. You should be impressed regarding what is possible when running a molecular structure through several Bayesian models in Alex’s mobile app called PolyPharma!

By January 21st Chris was commenting that the structure had changed and highlighted the extract from what was exposed by Figaro and listing the chemical name: 3-(1-(cyclohexyl(methyl)carbamoyl)-1H-imidazol-4-yl)pyridine 1-oxide. Want to know what that name means as a structure? Take the name “3-(1-(cyclohexyl(methyl)carbamoyl)-1H-imidazol-4-yl)pyridine 1-oxide” and paste it into the free online service OPSIN. The results are shown below.

OPSIN BIA Structure

That structure has now found its way to Wikipedia (updated on the 21st January – check out the edits between the two forms of the article here).

FINAL BIA structure

Sean Ekins has maintained a running series of blog posts here. Using a stack of openly accessible algorithms and websites Sean has now produced a whole series of predictions for the “final molecule”. Chris Southan has also continued to expand his work and I direct you to his latest blogpost for more information. Nice stuff Chris.

It took days following the news starting to show up regarding the results of the drug trial before the chemical structure was actually identified (i.e. the structure was blinded). How much work, how much confusion was created by having the drug structures blind? We have to imagine that the authorities had faster access to the details!

It is understandable that companies keep their chemical structures hidden. Patents are intentionally obfuscating (with a compound going into a trial commonly hidden among hundreds if not tens of thousands of chemicals that could be enumerated from a Markush structure). Until then Chris Southan will continue to educate the world about how competitive intelligence investigations.

 

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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2 Responses to BIA-10-2474, confusions in chemical structure and the need for EARLY clarity in chemical structures

  1. TRECHOT.P

    January 26, 2016 at 6:46 am

    there are effectively two different formulas proposed. the one with the carbamoylamino group may explain the events.
    “Gluttony is an ugly default”

     
  2. TRECHOT.P

    January 26, 2016 at 12:12 pm

    sorry.
    Error on my mail

    tonio.trechot@gmail.com

     

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