The role of descriptors extracted from ligand-target interaction to improve conventional QSAR model performance in the realm of angiogenesis receptor modulation to fight cancer.

Aims: This study aims to develop a receptor-dependent 4D-QSAR model to overcome key limitations of traditional QSAR, including its dependency on molecular alignment and poor performance with small datasets, by integrating ligand - target interaction information.

Materials & methods: Angiogenesis-related receptors, including VEGFR2, FGFR1-4, EGFR, PDGFR, RET, and HGFR (MET) were chosen based on the biological relevance in cancer. Ligand datasets with known IC₅₀ values were extracted from PubChem. One hundred docked conformers per ligand were generated using AutoDock. Protein - ligand interaction fingerprints were computed and encoded as 4D-descriptors. After evaluation via multiple classification algorithms, Random Forest was selected for model construction.

Results: The results shown that the proposed model outperformed traditional 2D-QSAR approaches across all targets. Accuracy exceeded 70% in most datasets, including those with fewer than 30 compounds. Besides, the model performance was significantly improved via using all conformers versus using a single best pose. The model demonstrated robust predictive power across varying receptor classes under consistent assay conditions.

Conclusions: The proposed receptor-dependent 4D-QSAR model provides enhanced accuracy and generalizability for small, diverse datasets. Its integration of LTI-derived descriptors makes it a valuable tool for early-stage lead optimization and supports rational multi-target drug design in oncology.