The optimization of a lead structure to a development candidate often requires removal of undesirable antitarget activities. To this end, we have developed an approach to extract antitarget activity hotspots from larger databases and to transfer this knowledge onto novel chemical series. These antitarget activity hotspots will be captured as pairs of informative molecules, which are chemically closely related, but differ significantly in biological activity. We illustrate the application of antitarget activity hotspots as informative compound pairs for the optimization of side effects in lead structures for relevant antitargets in pharmaceutical research. The use for prospective design requires establishing a structural link between known antitarget hotspot pairs and a new lead structure: we employ 3D-based similarity comparison for this task. The entire workflow serves as idea generator in early optimization. The feasibility of this approach is demonstrated in several optimization problems related to hERG inhibition, and CYP3A4 inhibition. Several structural examples demonstrate the ability of the 3D-shape searching to identify related scaffolds and the usefulness of the antitarget hotspot information to guide optimization by modulating the undesirable antitarget activity. Such a concept based on the analysis of local similarities and the transfer to 3D-related series is especially promising in those cases, where the construction of antitarget QSAR models fails to detect local SAR trends for guiding the next optimization cycle.
A novel procedure (CROSS: Computational Rescaffolding and Optimization using Synthetic Schemes) for in silico rescaffolding and side-chain optimization is reported with explicit consideration of the route of synthesis and availability of compatible chemical reagents. We have defined a set of retrosynthetic disconnections representing robust reactions, amenable for combinatorial chemistry. This rule set is used to generate virtual fragment databases from available reagents. Each reactive center is annotated with its compatibility with regard to the chemical reactions. The rule set is then applied to a new molecule to obtain separate query subunits for rescaffolding by 3D similarity searching in specific reagent-derived fragment databases. Thus, only fragments compatible with the chemistry and shape of the corresponding query moiety are investigated further. The identified fragment hits directly indicate (1) available chemical reagents that can replace the query moiety in the starting molecule and (2) the route for the synthesis of the proposed molecules.
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