Scaffold hopping from natural products to synthetic mimetics by holistic molecular similarity

Francesca Grisoni, Daniel Merk, Viviana Consonni, Jan A. Hiss, Sara Giani Tagliabue, Roberto Todeschini, Gisbert Schneider

Research output: Contribution to journalArticleAcademicpeer-review


Natural products offer unexplored molecular frameworks for the development of chemical leads and innovative drugs. However, the structural complexity of natural products compared with synthetic drug-like molecules often limits the scaffold hopping potential of natural-product-inspired molecular design. Here we introduce a holistic molecular representation incorporating pharmacophore and shape patterns, which facilitates scaffold hopping from natural products to isofunctional synthetic compounds. This computational approach captures simultaneously the partial charge, atom distributions and molecular shape. In a prospective application, we use four natural cannabinoids as queries in a chemical database search for novel synthetic modulators of human cannabinoid receptors. Of the synthetic compounds selected by the new method, 35% are experimentally confirmed as active. These cannabinoid receptor modulators are structurally less complex than their respective natural product templates. The results of this study validate this holistic molecular representation for hit and lead finding in drug discovery.

Original languageEnglish
Article number57
JournalCommunications Chemistry
Publication statusPublished - 2018
Externally publishedYes


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