Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation

TLDR

Natural product lead discovery often fails to isolate active compounds despite strong initial bioassay hits, a common issue in bioassay‑guided purification. The study introduces bioactive molecular networking and a bioinformatic workflow to map bioactivity scores in molecular networks, aiming to identify antiviral candidates directly from fractionated extracts. Using tandem mass spectrometry, the workflow applies molecular networking and bioactivity score prediction—computed from a molecule’s relative abundance across fractions and the fractions’ bioactivity—to accelerate dereplication and reveal potential bioactive compounds. The authors anticipate that this method will become a systematic strategy for discovering leads in natural extract libraries and revisiting untapped bioactive analogues from prior fractionation efforts.

Abstract

It is a common problem in natural product therapeutic lead discovery programs that despite good bioassay results in the initial extract, the active compound(s) may not be isolated during subsequent bioassay-guided purification. Herein, we present the concept of bioactive molecular networking to find candidate active molecules directly from fractionated bioactive extracts. By employing tandem mass spectrometry, it is possible to accelerate the dereplication of molecules using molecular networking prior to subsequent isolation of the compounds, and it is also possible to expose potentially bioactive molecules using bioactivity score prediction. Indeed, bioactivity score prediction can be calculated with the relative abundance of a molecule in fractions and the bioactivity level of each fraction. For that reason, we have developed a bioinformatic workflow able to map bioactivity score in molecular networks and applied it for discovery of antiviral compounds from a previously investigated extract of Euphorbia dendroides where the bioactive candidate molecules were not discovered following a classical bioassay-guided fractionation procedure. It can be expected that this approach will be implemented as a systematic strategy, not only in current and future bioactive lead discovery from natural extract collections but also for the reinvestigation of the untapped reservoir of bioactive analogues in previous bioassay-guided fractionation efforts.