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bioRxiv · 10.1101/2025.07.31.667816

Virtual Screening-Guided Discovery of Small Molecule CHI3L1 Inhibitors with Functional Activity in Glioblastoma Spheroids

Kaur, B.·Denzinger, K.·Zhang, L.·Garcia-Vazquez, N.·Wolber, G.·Gabr, M.
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Abstract

Chitinase-3-like protein 1 (CHI3L1), a glycoprotein implicated in inflammation, fibrosis, and cancer, has emerged as a potential therapeutic target for glioblastoma (GBM). CHI3L1 contributes to tumor progression and immune evasion by promoting STAT3 signaling and mesenchymal transition. To identify small molecule CHI3L1 inhibitors, a structure-based 3D pharmacophore model was developed and applied to virtually screen over 4.4 million compounds from the Enamine collection. Following multi-tiered filtering, 35 candidates were selected for experimental evaluation. Binding validation via microscale thermophoresis (MST) confirmed dose-dependent CHI3L1 interactions for two compounds, 8 and 39, with dissociation constants (Kd) of 6.8 {micro}M and 22 {micro}M, respectively. These affinities were further supported by surface plasmon resonance (SPR), which yielded Kd values of 5.69 {micro}M for compound 8 and 17.09 {micro}M for compound 39. In 3D GBM spheroid models, compound 8 significantly reduced spheroid viability and attenuated phospho-STAT3 levels, consistent with CHI3L1 pathway disruption. These findings identify two promising scaffolds and support the utility of pharmacophore-guided virtual screening for discovering functionally active ligands targeting CHI3L1 in GBM. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/667816v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@291464org.highwire.dtl.DTLVardef@f9d224org.highwire.dtl.DTLVardef@1535eeaorg.highwire.dtl.DTLVardef@7c596e_HPS_FORMAT_FIGEXP M_FIG Table of Contents artwork C_FIG

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Kaur, B., Denzinger, K., Zhang, L., Garcia-Vazquez, N., Wolber, G., Gabr, M.. 2025-08-01. Virtual Screening-Guided Discovery of Small Molecule CHI3L1 Inhibitors with Functional Activity in Glioblastoma Spheroids. https://doi.org/10.1101/2025.07.31.667816

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