Discovery of anti-SARS-CoV-2 secondary metabolites from the heartwood of Pterocarpus santalinus using multi-informative molecular networking.

A pigment-depleted extract from the heartwood of L. f. (PS-DE) showed promising anti-SARS-CoV-2 activity with an IC of 29.9 μg/mL in Caco-2-F03 cells. To determine the potential active constituents within the extract prior to isolation, multi-informative molecular network (MN) was applied. Therefore, the extract was separated by high-performance counter-current chromatography (HPCCC) into 11 fractions which were subsequently tested for anti-SARS-CoV-2 activity and analysed by UPLC-tandem mass spectrometry (MS). The resulting MN combines the bioactivity data of the fractions with the MS data. The MN analysis led to the targeted isolation of seven compounds including one pterocarpan reported for the first time as constituent of and four so far undescribed natural products (NPs) that belong to the compound classes of arylpropanes , isoflavanones coumestans and 3-arylcoumarins , respectively. In total, 15 constituents from the heartwood of and one synthetic isoflavonoid that is structurally related to the natural metabolites were tested for anti-SARS-CoV-2 activity. Thereby, the two pterocarpans (-)-homopterocarpin and (-)-medicarpin , the stilbene -pterostilbene and the isoflavonoid 7-O-methylgenistein showed a distinct antiviral activity with IC values of 17.2, 33.4, 34.7, and 37.9 µM, respectively, and no cytotoxic effects against Caco-2-F03 cells (CC > 100 µM). In addition, a structure-activity relationship (SAR) was proposed indicating structural requirements of pterocarpans for anti-SARS-CoV-2 activity. The herein presented results support the implementation of multi-informative molecular networks as powerful tool for dereplication and targeted isolation of bioactive NPs.