Virtual synthesis programs are not yet widely used by synthetic chemists and many may doubt that such approaches can match the skills of the experienced chemist. Nevertheless ChemAxon have created a Java-based Reactor system to process reactions according to rules captured in the syntax of the Chemical Terms language for reactivity, selectivity, and side reaction exclusion. Using such a system, discovery enumeration is significantly extended beyond a desired product library to create instead a reaction library, which has taken into account availability of starting compounds, experimental conditions, and prior available chemistry reaction knowledge on reaction types and their chemo-, regio-, and stereoselectivity issues. A combinatorial synthesis library of a million such reactions can currently be built using several hours of CPU.
Oxford-based Inhibox, founded by Graham Richards, chairman of Chemistry at the University of Oxford, and headed by CEO Paul Finn, who pioneered the implementation of virtual screening methodologies for Pfizer at Sandwich, have been developing novel computational discovery methods and created Scopius, a very large database of chemical structures for drug discovery. Inhibox are using ChemAxon’s Reactor software to establish optimum conditions to give 'synthetically accessible' libraries with favourable properties for their research, and to create a reaction service, with workflows to create de novo libraries for client projects. “The core functionality to enumerate focused de novo type libraries in Oracle for a number of organic transformations is already available”, according to lead developer Dan Butler at Inhibox who continued “In a nutshell what we are attempting to do with Reactor is create a service which will primarily allow creation of focused de novo approach libraries and secondarily, exhaustive sets, for organic transformations that have (a) a reasonable set of suitable reactants in our commercial database and thus a tangible starting point and (b) are well defined reactions in the literature. In addition the Chemical Terms functionality of Reactor may help us create more accurate product sets. Overall this is quite a large undertaking in many respects, not least of which are the amount of organic transformations available to implement!”
Dan Butler will be joined in Oxford by ChemAxon’s CTO and virtual synthesis expert György Pirok to reveal the results of this work for the first time at the eCheminfo Drug Discovery Training Week at Oxford University (3-7 July 2006). Attendees to their workshop will be able to use provided software to create virtual reaction libraries and to work with the workshop leaders to establish optimum conditions to give 'synthetically accessible' libraries with favourable properties for their research. Dr. Pirok commented that “Currently we are developing a GUI so that synthetic chemists, who are not familiar with programming or command line tools, will be able to generate these reaction libraries. This GUI also contains an editor for modifying existing reactions or creating new ones. Workshop participants in Oxford will be one of the first set of users trying the new desktop Reactor application and GUI, and will get to try the newest features not previously released. We will try to create new selective reactions and libraries together during the workshop, that will be of relevance to participants’ interests.”
Barry Hardy
eCheminfo Community of Practice
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