r-BRICS - a revised BRICS module that breaks ring structures and carbon chains.

Molecular fragmentation has been frequently used for machine learning, molecular modeling, and drug discovery studies. However, the current molecular fragmentation tools often lead to large fragments that are useful to limited tasks. Specifically, long aliphatic chains, certain connected ring structures, fused rings, as well as various nitrogen-containing molecular entities often remain intact when using BRICS. With no known methods to solve this issue, we find that the fragments taken from BRICS are inflexible for tasks such as fragment-based machine learning, coarse-graining, and ligand-protein interaction assessment. In this work, we develop a revised BRICS (r-BRICS) module that allows more flexible fragmentation on a wider variety of molecules. We show that r-BRICS generates smaller fragments than BRICS, allowing localized fragment assessments. Furthermore, r-BRICS generates a fragment database with significantly more unique small fragments than BRICS, which is potentially useful for fragmentbased drug discovery.© 2023 Wiley-VCH GmbH.

Citation

Leili Zhang, Vasumitra Rao, Wendy Cornell. r-BRICS - a revised BRICS module that breaks ring structures and carbon chains. ChemMedChem. 2023 Aug 13:e202300202e202300202

PMID: 37574458

search → result