Caribbean software for natural products chemistry

Robert Lancashire

Robert Lancashire tells the success story of the JCAMP-DX Data Viewer, a computer program developed in Jamaica being used by organic chemists worldwide.

Caribbean islands are endowed with a rich diversity of fruits, vegetables, spices and herbs. It is therefore hardly surprising that many of the region's chemists are involved in natural products research to identify compounds in indigenous plants that could have commercial applications.

At the Chemistry Department of the University of the West Indies at Mona (UWI Mona), Jamaica, natural products chemistry has deep roots. The Department's first Chair, Cedric Hassall, devoted much of his career to exploring the chemical composition of Jamaican fruits and vegetables. For example, he traced the cause of a severe vomiting disease to the consumption of a toxin in unripe ackee (Blighia sapida), the island's national fruit.

More recently, the Department's chemists isolated the active compound from a plant known locally as spirit weed (Eryngium foetidum), which is traditionally used as a remedy against intestinal worms in humans and cattle. UWI Mona has already acquired patents on the compound in both the USA and Jamaica.

The JCAMP-DX Data Viewer

Arguably a less spectacular but nonetheless important contribution to the advancement of applied organic chemistry at UWI Mona is the JCAMPDX Data Viewer. With this program chemists can display data generated by spectrometers, instruments that are used to isolate and identify active compounds in a sample.

Natural products chemists engaged in pharmaceutical or agrochemical research employ a variety of spectroscopic techniques to identify organic compounds. These techniques are designed to measure the response of a sample molecule to radiation, whether in the form of a light wave, an electron beam or a radio wave. A spectrometer yields a unique response chart or spectrum of the sample that can be compared to a library of spectra of known materials or analyzed to determine its chemical composition.

Using the JCAMP-DX Data Viewer, chemists can instantly reproduce a spectrum from a dataset stored on a computer. They can also compare and analyze spectra, and use them to illustrate presentations or scientific publications.

The original Data Viewer was conceived at UWI Mona in 1988, in the aftermath of hurricane Gilbert. The hurricane destroyed the Department's old infrared spectrometer, and the replacement unfortunately did not have any provision for data storage. To address this problem, I wrote two programs: one to capture and transfer data from the spectrometer to an external hard disk, and another to display the data files stored on the disk. I chose to write the Data Viewer for JCAMP-DX files, a nonproprietary format for exchanging spectroscopic data that is widely accepted by all users and instrument manufacturers.

Chime

Some years after the program's first release, Chris Muir, Han Reichgelt and I rewrote the Data Viewer as a 'plug-in' for web browsers, enabling users to display spectra posted on websites. In 1996, we licensed the program's code to MDL Information Systems Inc., a chemistry software developer, which is now a subsidiary of Reed Elsevier, a leading scientific publisher.

The company incorporated the code in MDL Chime, a program designed to display 2D and 3D graphics of molecules directly within a web page. The molecules are 'live', meaning they are not just static pictures, but chemical structures that scientists can rotate, reformat, and save in various file formats for use in modelling or database applications. The merger of the spectroscopic data viewer with the molecular graphics viewer means that chemists can now combine displays and observe interactions between them.

First released in 1996, Chime has always been free for academic use. This certainly contributed to its appeal: over 2 million copies have been downloaded from the MDL site to date. Another factor contributing to the popularity of Chime is that, for years, it was one of the few viewers that could display JCAMP-DX files.

JSpecView

Our contract with MDL will expire at the end of 2005. A new, Java-based JCAMP-DX viewer called JSpecView is currently being developed and should be released soon. It has additional features not available in MDL Chime, including the ability to display multiple files simultaneously and to overlay spectra.

With JSpecView, I expect that chemical research in general and natural products research in particular can continue to be served and that the characterization of active compounds from plants that can be used as natural remedies for diseases in humans and cattle will be expanded. I hope that the patents on these compounds will generate additional funding for future explorations of the chemical composition of Caribbean fruits and vegetables.

Robert Lancashire ( robert.lancashire@uwimona.edu.jm) is Professor of Computational Chemistry at the Department of Chemistry of UWI Mona, Jamaica. For more information about the JCAMP-DX viewer and natural products research at UWI Mona, visit www.chem.uwimona.edu.jm. A free copy of MDL Chime can be downloaded from www.mdl.com/products/framework/chime .

 

This project was first featured in ICT Update 26, July 2005.

 

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01 November 2005

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