Virtual Screening of HBV Capsid Assembly Modulators with the Combination of Pharmacophore Modeling and Hydrogen Bond Constraints

Introduction: Hepatitis B virus (HBV) infection remains a significant public health challenge. Targeting HBV capsid assembly has the potential to achieve a functional cure for HBV infection, and the capsid assembly modulators (CAMs) have been regarded as promising therapeutic agents for HBV. In this work, we aimed to identify novel scaffold HBV CAMs through a multi-step virtual screening approach. Methods: Pharmacophore-based virtual screening combined with hydrogen bond constraints was performed on the Specs and ChemDiv databases. Potential modulators were screened using qPCR (quantitative PCR) and CCK-8 assays. Molecular dynamics (MD) simulations and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis were employed to evaluate ligand-protein binding modes and pharmacokinetic properties. Results: Twenty-one compounds were selected as potential HBV CAMs. Compounds B5, B19, and B21 exhibited excellent anti-HBV activity, with EC50 values of 1.74, 4.29, and 0.38 μM, respectively. MD simulations revealed their possible binding modes with the HBV core protein, confirming the critical role of Trp102-mediated hydrogen bonds. Discussion: Hydrogen bonds are critical for establishing stable and high-affinity interactions between small molecules and targets. Three compounds, B5, B19, and B21, were identified as novel scaffold hits of CAMs through virtual screening with the combination of pharmacophore modeling and hydrogen bond constraints. MD simulations illustrated the critical contributions by Trp102, providing valuable insights for further structural optimization. Conclusion: Compounds B5, B19, and B21 can serve as promising starting points for the development of more potent anti-HBV candidates through future hit-to-lead optimization.