We use "reaction-based enumeration" to distinguish it from "R-group enumeration". Both are types of virtual library enumeration.
R-group enumeration allows you to attach any R-group anywhere. It is simple and fast but you can easily create implausible (or hard to synthesize) molecules if you are not careful. Reaction-based enumeration at least guarantees that you already have reactants with the right functional groups in the right places, and if you make your reactions sophisticated enough you can even check for other disqualifying conditions such as interfering functional groups. Of course in a context where it is not immediately obvious that you are talking about doing it on a computer, I suppose something along the lines of "virtual reaction-based enumeration" might make sense. Best, Ivan On Fri, Sep 25, 2020 at 4:26 AM Thomas Strunz <beginn...@hotmail.de> wrote: > Hi Brian, > > commercial tools usually use the term "reaction-based enumeration" or > "reaction-based library design". > > Best Regards, > > Thomas > > ------------------------------ > *Von:* Bennion, Brian via Rdkit-discuss < > rdkit-discuss@lists.sourceforge.net> > *Gesendet:* Freitag, 25. September 2020 07:19 > *An:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net> > *Betreff:* [Rdkit-discuss] proper technical term for generating virtual > compounds with rdkit and smarts > > hello > > I have a paper in review and is intended for a large audience that has > synthetic chemists, biologist and comp chem. > One reviewer had issues with the term in-silico syntheses. > I used rdkit and smarts reactions to generate large libraries of compounds > for our research project. Is there a better term to use? I feel "chemical > enumeration" is just as foreign. > > The abstract is below. > > The current standard treatment for organophosphate poisoning primarily > relies on the use of small molecule-based oximes that can efficiently > restore acetylcholinesterase (AChE) activity. Despite their efficacy in > reactivating AChE, the action of drugs like 2-pralidoxime (2-PAM) is > primarily limited to the peripheral nervous system (PNS) and, thus, > provides no protection to the central nervous system (CNS). This lack of > action in the CNS stems from the ionic nature of the drugs; they cannot > cross the blood-brain barrier (BBB) to access to any nerve > agent-inhibited AChE therein. In this report, we present a small > molecule oxime, called LLNL-02, that can diffuse across the BBB for > reactivation of nerve agent-inhibited AChE in the CNS. Our > candidate-development > approach utilizes a combination of parallel chemical and in - silico > syntheses, computational modeling, and a battery of detailed in vitro and in > vivo assessments that have identified LLNL-02 as a top CNS-active candidate > against nerve agent poisoning. Additional experiments to determine acute > and chronic toxicity as required for regulatory approval are ongoing. > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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