Computational discovery of lead natural compounds targeting the HPV16 E6–E6AP–p53 interaction

Human papillomavirus type 16 (HPV16) contributes to malignant progression by recruiting host E6-associated protein (E6AP), which facilitates ubiquitin-mediated degradation of the tumor suppressor protein p53.This study employed an integrated computational strategy to screen natural compounds for their potential to bind HPV16 E6 binding pocket and disrupt​ its interaction with the E6AP, thereby potentially preserving p53 function. The HPV16 E6–E6AP–p53 complex (PDB ID: 4XR8) was retrieved, assessed for structural quality, and analyzed for binding pocket identification. GO and KEGG were performed to explore associated biological functions and pathways. Pharmacophore-based virtual screening and molecular docking were conducted to screen high-affinity compounds, followed by ADMET, toxicity prediction, density functional theory (DFT) analysis, and 100 ns molecular dynamics simulation. Finally, protein–ligand interactions were analyzed to characterize key binding residues. Functional enrichment analysis indicated that the E6–E6AP–p53 gene set is associated with apoptosis, DNA damage response, and viral carcinogenesis pathways. Structural validation showed acceptable stereochemical and structural quality metrics. Pharmacophore-based screening of ​511 natural compounds followed by molecular docking identified several molecules with favorable binding affinities (−​11.0 to −​11.7 kcal/mol). The six top-ranked compounds were then filtered by ADME and toxicity predictions, and C-12 and C-17 were prioritized because they combined high docking affinity (−​11.4 kcal/mol) with acceptable pharmacokinetic properties and safety profiles. Interaction analysis confirmed stable binding within the E6–E6AP–p53 pocket. DFT calculations revealed that C-17 exhibited the smallest HOMO–LUMO energy gap compared with the luteolin and C-12, indicating a distinct electronic profile. Molecular dynamics and MM-GBSA analyses indicated greater stability and a more favorable binding free energy for C-17, followed by C-12, over the reference inhibitor, luteolin. Overall, C-12 and C-17 emerged as promising candidates for inhibiting the E6–E6AP–p53 interaction, which may help restore p53 function in HPV-driven tumor biology, and warrant further experimental validation.