Mechanism of action of HBV capsid assembly modulators predicted from binding to early assembly intermediates

Abstract

Interfering with the self-assembly of virus nucleocapsids is a promising approach for the development of novel antiviral agents. Applied to hepatitis B virus (HBV), this approach has led to several classes of capsid assembly modulators (CAMs) that target the virus by either accelerating nucleocapsid assembly or misdirecting it into non-capsid-like particles. Here, we have assessed the structures of early nucleocapsid assembly intermediates, with and without bound CAMs, using molecular dynamics simulations. We find that distinct conformations of the intermediates are induced depending on whether the bound CAM accelerates or misdirects assembly; these structures are predictive of the final assembly. We also selected non-capsid-like structures from our simulations for virtual screening, resulting in the discovery of several compounds with moderate anti-viral activity and low toxicity. Cryo-electron microscopy and capsid melting experiments suggest that our compounds possess a novel mechanism for assembly modulation, potentially opening new avenues for HBV inhibition.

All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

“…We have previously employed all-atom MD simulations to investigate the intact HBV capsid [12,14,15], as well as the free dimer [16], in all cases revealing deeper and more detailed information on the relationship between structure and function than was accessible to experiments. Additional atomistic studies have investigated early assembly intermediates of Cp149, including in the presence of CpAMs [17][18][19][20], providing further insight into the mechanisms of HBV capsid formation and disruption. Here, we employ all-atom MD simulations to examine an intact AT130-bound capsid and extensively characterize the capsid-incorporated dimer.…”

All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

“…We have previously employed all-atom MD simulations to investigate the intact HBV capsid [12,14,15], as well as the free dimer [16], in all cases revealing deeper and more detailed information on the relationship between structure and function than was accessible to experiments. Additional atomistic studies have investigated early assembly intermediates of Cp149, including in the presence of CpAMs [17][18][19][20], providing further insight into the mechanisms of HBV capsid formation and disruption.…”

Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism

“…Computational models can reveal details of the assembly process that are not accessible to experiments. However, while atomistic and near-atomistic simulations have revealed the dynamics of complete viruses, ,− the long time scales (milliseconds to hours) prohibit simulating capsid assembly with atomic resolution, except for specific steps. , Therefore, coarse-grained models have been used to study the assembly dynamics of icosahedral shells. − Of particular relevance to our work, elastic interactions between 5-fold defects can funnel the elastic energy landscape of an assembling crystalline shell toward icosahedral structures. − However, previous works on empty capsids with T ≥ 4 have focused on material properties (parametrized by the dimensionless ratio of stretching to bending moduli, Föppl von Kármán number) that are orders of magnitude below those of virus capsids. Thus, different mechanisms may be important for HBV assembly.…”

“…However, while atomistic and near-atomistic simulations have revealed the dynamics of complete viruses, 4,30−33 the long time scales (milliseconds to hours) prohibit simulating capsid assembly with atomic resolution, except for specific steps. 34,35 Therefore, coarse-grained models have been used to study the assembly dynamics of icosahedral shells. 36−48 Of particular relevance to our work, elastic interactions between 5-fold defects can funnel the elastic energy landscape of an assembling crystalline shell toward icosahedral structures.…”