Structure-Based Molecular Docking and in silico Screening of Phytochemicals as Potential Inhibitors of Epstein–Barr Virus Glycoprotein and EBNA1

Abstract

Epstein–Barr virus (EBV) infects over 90% of the global adult population and is causally implicated in several malignancies, including Burkitt's lymphoma, Hodgkin's lymphoma, and nasopharyngeal carcinoma. Despite its substantial disease burden, no approved antiviral therapy or prophylactic vaccine currently exists. Here, the study reports a structure-based virtual screening study employing molecular docking, pharmacokinetic profiling, and in silico toxicity prediction to identify phytochemical inhibitors targeting two functionally critical EBV proteins: the EBV glycoprotein (PDB ID: 6C5V), which mediates host cell entry, and Epstein–Barr Nuclear Antigen-1 (EBNA1; PDB ID: 6NPP), which is indispensable for episomal genome maintenance during latency. A curated library of eight ethnomedicinally derived phytochemicals, (-)-β-Sitosterol, Camptothecin, (+)-Berbamine, Apigenin, Agathisflavone, Amentoflavone, Bilobetin, Velutin (5,4′-dihydroxy-7,3′-dimethoxyflavone), was screened using AutoDock Vina, with drug-likeness evaluated via SwissADME and acute oral toxicity estimated using ProTox-III. Among all compounds evaluated, the bisbenzylisoquinoline alkaloid (+)-Berbamine exhibited the highest predicted binding affinities against both targets (−11.1 kcal/mol against 6C5V; −11.0 kcal/mol against 6NPP), stabilised primarily through extensive hydrophobic contacts with leucine-, phenylalanine-, and isoleucine-lined binding pockets. The biflavonoid amentoflavone ranked second against EBNA1 (−8.8 kcal/mol), forming four hydrogen bonds within the glycoprotein pocket and engaging EBNA1 residues proximal to the DNA-binding interface. Apigenin and chrysin demonstrated the most favourable drug-likeness profiles, satisfying all five computational drug-likeness filters (Lipinski, Ghose, Veber, Egan, and Muegge) with zero violations and no structural alerts, alongside predicted high gastrointestinal absorption and low acute oral toxicity (GHS Class 5). Chrysin was uniquely predicted to permeate the blood–brain barrier, an attribute of potential relevance to EBV-associated neurological manifestations. Camptothecin, while pharmacokinetically tractable, exhibited the lowest predicted LD₅₀ (50 mg/kg; Class 3), warranting caution regarding its therapeutic window. These findings identify (+)-Berbamine, apigenin, amentoflavone, and chrysin as prioritised lead candidates combining dual-target inhibitory potential with acceptable pharmacokinetic and safety profiles. This study provides a rational, computational basis for directing experimental antiviral validation against EBV and highlights the underexplored therapeutic value of ethnomedicinally relevant phytochemicals in combating EBV-associated malignancies. While promising, these computational predictions are inherently limited by static docking approaches and require validation through in vitro studies using EBV-positive lymphoblastoid and epithelial cell models.