Molecular Docking Analysis and Biochemical Evaluation of 6-Chloroquinolone, 1,3,5-Triazine and Furopyrrole Derivatives Against Bromelain

Bromelain is a widely used as model for papain-like cysteine proteases and shares significant sequence homology with bacterial and viral counterparts, making it a suitable target for computational screening of potential modulators. In this study, we performed molecular docking and protein–ligand interaction profiling for eight synthetic derivatives containing 6-chloroquinolone (compounds 1–4), 1,3,5 triazine (compounds 5–7) or furopyrrole (8) scaffolds. In the quinoline series, the position of the methyl group on the piperidine ring appeared to influence efficacy (4 methyl > unsubstituted > 2 methyl). Molecular docking and PLIP interaction profiling revealed that the highest computed binding affinities (up to –12.4 kcal/mol for 5) did not directly correlate with experimental inhibition, but identified the residues predicted by docking and PLIP to contribute to ligand interactions: Lys18, Phe29, Ile163, Trp180, Tyr185, and Ile186. Ligands 6 and 7 formed H-bonds with catalytic residues His158 and Cys26, respectively. Sequence alignment revealed 42–49% identity between bromelain and bacterial cysteine proteases from Klebsiella pneumoniae and Acinetobacter baumannii, suggesting that bromelain may serve as a tentative model system for the preliminary study of pathogen cysteine proteases, although direct extrapolation would require experimental validation. To experimentally assess these predictions, we conducted a preliminary activity screen using an azocasein proteolytic assay. Compound 1 exhibited a moderate inhibitory effect, whereas compounds 2–8 produced only marginal changes, which lacked statistical significance after correction for multiple comparisons. These findings provide a structural basis for the rational design of new protease inhibitors and identify compound 1 as a preliminary screening hit and a possible starting point for further optimization.