Chemical Profiling and Scaffold-Based Drug-Discovery Analysis of Bioactive Compounds from Ceratonia siliqua L. with Computational and Biological Validation

The scaffold concept is central in medicinal chemistry and drug design to generate, analyze, and capture the core structural frameworks that define bioactive compounds. Natural products and their underlying molecular scaffolds have long provided many of the biologically active ingredients in modern medicines and continue to inspire new therapeutic agents. However, linking these core structural frameworks to observed biological activity remains a key challenge in natural-product research. Here, this study integrates a computational–experimental approach combining scaffold-based drug analysis, chemical profiling, and computational and biological validation to identify bioactive motifs in Ceratonia siliqua L pods. A total of 253 identified compounds from the gas chromatography–mass spectrometry (GC–MS) profiling were clustered and grouped into antioxidant, antimicrobial, and cytotoxic activity sets, after which their Bemis–Murcko scaffolds were extracted using RDKit. The most common scaffolds were ranked and visualized to give a clear picture of the prevalent structural patterns throughout the data sets. Experimental assays validated the computational dominant scaffold predictions, revealing that the antioxidant activity was associated with phenolic and terpenoid scaffolds, the antimicrobial response was aligned with monoterpenoid and cyclohexane/cyclohexene-based scaffolds, and the cytotoxic trends were consistent with small heterocycles and imide-containing scaffolds. To further bridge the gap between the identified scaffolds and their corresponding biological activity, molecular docking was performed against key biological targets, including KEAP1, Staphylococcus aureus DHFR, and EGFR. The docking results demonstrated favorable binding interactions and identified key ligand–protein interactions, supporting the potential contribution of the GC–MS-identified compounds to the observed biological activities of the plant extract. These scaffold–activity relationships demonstrate that recurring structural motifs are associated with the biological effects observed in C. siliqua L., highlighting the plant as a promising source of pharmacologically relevant scaffolds for drug discovery.