Molecular dynamics of the HBV capsid to advance the search for antivirals

The hepatitis B virus (HBV) capsid is a promising therapeutic target that could contribute to the elimination of viral hepatitis as a major public health threat. The capsid is an icosahedral shell that assembles from 120 copies of homodimeric core protein (Cp).

Small molecules currently being explored for capsid disruption – called capsid assembly modulators (CAMs) – bind a hydrophobic pocket between two Cp dimers to interfere with core particle formation. However, despite the viability of anti-capsid therapeutics, no CAMs have yet been approved as drugs.

This project will advance the search for HBV inhibitors by leveraging full-scale computational virology of the HBV capsid.

Vast ensembles of HBV capsid protein (Cp) conformations derived from atomistic molecular dynamics (MD) simulations of the intact capsid will be used as a basis for high-throughput virtual screening and fragment-based inhibitor design.

The ensembles contain numerous conformational states of the HBV Cp inter- and intra-dimer interfaces that have never been accessed by experimental structure determination methods and have, therefore, never been considered by previous structure-guided drug development efforts against the capsid.

The specific aims of the project are: 1) Identify novel small molecules that target the highly dynamic CAM binding site at the Cp inter-dimer interface to inhibit capsid assembly, and 2) Design peptides that target a newly discovered cryptic pocket at the Cp intra-dimer interface, which can potentially inhibit capsid assembly, nuclear export, and secretion.

Aim 1 will be accomplished via comprehensive characterization of the CAM binding site, which exhibits significant conformational variability. Results will inform a synthon-based, shape-aware virtual screening approach to identify new small molecule binders.

Aim 2 will be accomplished via design of macrocyclic peptides to target the open-spike conformation of Cp, previously discovered by MD simulations.

Both aims will benefit from experimental validation of binding and inhibitory effects of small molecules and peptides by collaborators who specialize in biochemistry and structural biology of the virus.

Ultimately, this project addresses critical gaps in HBV antiviral development by targeting the structural dynamics of the capsid.

The use of MD-derived ensembles of the intact capsid meaningfully expands the potential for discovering new inhibitors, underscoring the importance of full-scale computational virology in the fight against viral disease.