Structure-Based Identification of Potential Toll-Like Receptor 3 Agonists for Anti-HBV Applications

Abstract

Hepatitis B virus (HBV) infection remains a major global public health burden, primarily due to the persistence of covalently closed circular DNA (cccDNA) in infected hepatocytes. Toll-like receptor 3 (TLR3) has been suggested to be a promising therapeutic target, as its activation stimulates innate immune responses that facilitate cccDNA clearance. In this study, a structure-based computational approach was employed to identify novel small-molecule TLR3 agonists. A human TLR3 ectodomain (ECD) homodimer model was constructed using homology modeling, revealing a critical cavity at the C-terminal interface, which is responsible for the ligand-binding-induced ECD dimerization. Subsequently, three compounds, ZINC3991624 (Vilanterol) and ZINC95564694 (Naloxegol) from the FDA-approved drug database along with TCM10752 from the Traditional Chinese Medicine (TCM) database, were identified as potential candidates through docking-based virtual screening, rigorous ADMET evaluation and molecular dynamics simulations. These candidates outperformed CU-CPT17e, the only known TLR3 agonist, by maintaining lower backbone RMSD values, preserving key inter-subunit distances and protein–protein interface area and sustaining C-terminal hydrogen-bonding networks. In conclusion, our study provides a structural basis for the further development of novel TLR3 agonists, offering a promising computational framework for future host-directed immunotherapeutics aimed at HBV cccDNA clearance.