Discovery of new bianthrones and chlorinated bianthrones with cytotoxic activity against cancer cells from Penicillium hispanicum guided by HSQC-based DeepSAT

This study is led by Dr. Liu (Institute of Microbiology, Chinese Academy of Sciences).

The unique ecological environment of mangroves, characterized by high temperature, high salinity, soil hypoxia, and periodic inundation by seawater, results in a distinctive metabolic mechanism of mangrove-derived fungi. Mangrove-derived fungi are emerging as prolific repositories for architecturally distinct novel compounds with a variety of bioactivities. Bianthrones are natural products characterized by unique backbones formed through the oxidative coupling of two anthrone molecules. These compounds exhibit significant biological activities, including antitumor, antibacterial, and antimalarial effects. DeepSAT is a neural network-based system employing convolutional neural network (CNN) to analyze heteronuclear single quantum coherence (HSQC) spectra. It directly extracts molecular fingerprints and structural features from HSQC data to perform molecular structure annotation and scaffold prediction. This technology enables efficient decoding of complex NMR spectra, facilitating rapid identification of major constituents in chemically complex extracts. Consequently, DeepSAT not only effectively assists in molecular structure identification but also guides the targeted isolation of specific compounds, thereby enhancing the efficient discovery of natural products. This study reports the discovery of three novel racemic bianthrones from Penicillium hispanicum LA032 using HSQC-based DeepSAT, as well as their cytotoxic evaluation and mechanistic investigation through network pharmacology.

The fungus was identified by its phylogenetic analysis based on morphological observation and ITS, CaM, BenA, and RPB2 sequences. HSQC-based DeepSAT strategy was employed to target isolation of two new pairs of (±)-penithrones A (1) and B (2), and a chlorinated derivative (±)-penithrone C (3), along with their building blocks 4–6 from the mangrove-derived fungus Penicillium hispanicum LA032. The structural elucidation of these new compounds was achieved through comprehensive integration of NMR spectroscopy and NMR calculations with CP3 analysis. The cytotoxicity assays revealed that compounds 1–3 exhibited varying degrees of inhibitory activity against tumor cell lines HeLa, HCT116, and MCF-7, with compound 1 demonstrating particularly significant activity (IC₅₀ values of 5.09 ± 0.65, 5.31 ± 0.48, and 5.23 ± 0.54 μmol/L, respectively). Network pharmacology analysis was performed to elucidate the mechanism of compound 1. Integration of predictions from SwissTargetPrediction, Super-PRED, and PharmMapper databases identified 394 potential targets of compound 1, which were cross-analyzed with differentially expressed genes (DEGs) in breast, colon, and cervical cancers to yield 29 key genes. GO and KEGG enrichment analyses indicated significant enrichment in cell cycle regulation (e.g., G2/M transition) and MAPK/Ras signaling pathways, suggesting compound 1 may exert its anticancer effects through modulation of these pathways. MAPK10 was identified as a central hub gene regulating 70% of the enriched pathways. Molecular docking validation confirmed compound 1's strong binding to MAPK10 (binding energy: −9.0 kcal/mol) through hydrogen bonds (ILE70, GLY76, SER193, and LYS93) and hydrophobic interactions (VAL78, VAL196, and LEU206). These findings will provide a structural basis for further experimental validation and optimization of compound 1 as a potential MAPK10 targeted therapeutic agent. This study not only expands the structural diversity of bianthrone derivatives but also offers a molecular framework for lead compound development.