SynthI: A New Open-Source Tool for Synthon-Based Library Design

J. Chem. Inf. Model. 2022, 62 (9), 2151-2163

DOI: 10.1021/acs.jcim.1c00754

Zabolotna Y.; Volochnyuk D.; Ryabukhin S.; Gavrylenko K.; Horvath D.; Klimchuk O.; Oksiuta O.; Marcou G.; Varnek A.

Most of the existing computational tools for de novo library design are focused on the generation, rational selection, and combination of promising structural motifs to form members of the new library. However, the absence of a direct link between the chemical space of the retrosynthetically generated fragments and the pool of available reagents makes such approaches appear as rather theoretical and reality-disconnected. In this context, here we present Synthons Interpreter (SynthI), a new open-source toolkit for de novo library design that allows merging those two chemical spaces into a single synthons space. Here synthons are defined as actual fragments with valid valences and special labels, specifying the position and the nature of reactive centers. They can be issued from either the “breakup” of reference compounds according to 38 retrosynthetic rules or real reagents, after leaving group withdrawal or transformation. Such an approach not only enables the design of synthetically accessible libraries and analog generation but also facilitates reagents (building blocks) analysis in the medicinal chemistry context. SynthI code is publicly available at

SynthI: A New Open-Source Tool for Synthon-Based Library Design