Cleistanthin A and diphyllin derivatives as putative EGFR-binding compounds: an integrated computational and biophysical study

Cleistanthin A (CTA) is an arylnaphthalide lignan glycoside that exhibits anticancer activities through diverse molecular mechanisms. This study used an integrated computer-aided drug design (CADD) workflow, including target prediction, molecular docking, molecular dynamics (MD) simulations, binding free-energy calculations, and surface plasmon resonance (SPR), to identify a potential molecular target for CTA and its derivatives. SwissTargetPrediction identified protein kinases as potential molecular targets. Molecular docking against targetable non-small cell lung cancer-associated kinases revealed that CTA and its derivatives exhibited more favorable scores to wild-type EGFR than erlotinib. MD simulations indicated the stability of the protein–ligand complexes, whereas molecular mechanics Poisson-Boltzmann (generalized Born) Surface Area (MM/PB(GB)SA) analyses identified van der Waals interactions as the primary driving force for binding at the ATP-binding pocket. Incorporation of a benzoyl ester moiety to this pharmacophore increased nonpolar binding energy contribution. SPR confirmed concentration-dependent binding of CTA, MUC-853, MUC-858, Compound 1, and Compound 2 to the EGFR-TK, with Compound 1 and MUC-858 exhibiting low dissociation constants (K D ) of 6.4 and 9.5 µM, respectively. Collectively, these findings suggest arylnaphthalide lignans as a potential scaffold for drug discovery against EGFR, providing insights into structure–interaction that benefit rational design of EGFR-binding compounds with improved affinity and selectivity.