Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket

Abstract

Though the hepatitis B virus (HBV) core protein is an important participant in many aspects of the viral life cycle, its best-characterized activity is self-assembly into 240-monomer capsids. Small molecules that target core protein (core protein allosteric modulators [CpAMs]) represent a promising antiviral strategy. To better understand the structural basis of the CpAM mechanism, we determined the crystal structure of the HBV capsid in complex with HAP18. HAP18 accelerates assembly, increases protein-protein association more than 100-fold, and induces assembly of nonicosahedral macrostructures. In a preformed capsid, HAP18 is found at quasiequivalent subunit-subunit interfaces. In a detailed comparison to the two other extant CpAM structures, we find that the HAP18-capsid structure presents a paradox. Whereas the two other structures expanded the capsid diameter by up to 10 Å, HAP18 caused only minor changes in quaternary structure and actually decreased the capsid diameter by ϳ3 Å. These results indicate that CpAMs do not have a single allosteric effect on capsid structure. We suggest that HBV capsids present an ensemble of states that can be trapped by CpAMs, indicating a more complex basis for antiviral drug design. IMPORTANCEHepatitis B virus core protein has multiple roles in the viral life cycle-assembly, compartment for reverse transcription, intracellular trafficking, and nuclear functions-making it an attractive antiviral target. Core protein allosteric modulators (CpAMs) are an experimental class of antivirals that bind core protein. The most recognized CpAM activity is that they accelerate core protein assembly and strengthen interactions between subunits. In this study, we observe that the CpAM-binding pocket has multiple conformations. We compare structures of capsids cocrystallized with different CpAMs and find that they also affect quaternary structure in different ways. These results suggest that the capsid "breathes" and is trapped in different states by the drug and crystallization. Understanding that the capsid is a moving target will aid drug design and improve our understanding of HBV interaction with its environment. Hepatitis B virus (HBV) causes degenerative liver disease and is the leading cause of liver cancer, with 240 million chronically infected individuals (1, 2). Current antiviral therapies control the progression of the disease but fail to eliminate the virus (3, 4). There is a need for improved therapies to combat chronic infections. One approach is to target virus assembly (5-7).HBV is an enveloped, double-stranded DNA virus with an icosahedral nucleoprotein core. The HBV capsid is the protein shell of the core. Beyond genome protection, the capsid is involved in intracellular trafficking, interaction with nuclear import machinery, regulation of reverse transcription, signaling, completion of reverse transcription, RNA chaperoning, and envelope acquisition (8). Capsid assembly is central to HBV replication. In vivo HBV capsids assemble around an RNA copy of the viral g...

Allosteric conformational changes of human HBV core protein transform its assembly

“…In the presence of BAY 41-4109, the drug induces a conformational change within the HBc dimer to promote a structural transfer from HBc Act to HBc Abb ; by weakening the inter-dimer interactions, and destabilizing the capsid thereby driving the assembly into the helical tube ensemble. Alternatively, BAY 41-4109, which is structurally similar to HAP-1 26 , could bind like HAP-1 at the hydrophobic pocket formed by helices α2, α4b and α5 of HBc and helix α5 of neighbour HBc 27, 31 . Thus BAY 41-4109 induced conformational changes of HBc, particularly the up-ward movement of helix α5, may change the dimer-dimer interaction angle and decrease the curvature of the ensemble, driving the assembly from capsid to tube.

Figure 6Schematic model of HBc assembly controlled by allosteric conformational changes.

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Discovery and Mechanistic Study of Benzamide Derivatives That Modulate Hepatitis B Virus Capsid Assembly

“…Moreover, determination of the crystal structure of the HBV capsids in complex with three different HAPs demonstrated that each HAP compound induces distinct allosteric responses of core protein and results in different quaternary and tertiary structural changes of core protein subunits in assembled capsids (53). In this study, we showed that a 1.5% native agarose gel electrophoresisbased particle gel assay is a very sensitive and convenient method to reveal the alterations of assembled capsids, due to either core protein mutation or treatment of capsid assembly modulators.…”

“…In summary, the results presented in this section further support the notion that the antiviral activity of SBA and BA compounds depends solely on core protein and not polymerase. Moreover, although both SBAs and BAs modulate capsid assembly by binding to the HAP pocket, the two compounds distinctly interact with core protein and induce different structural alterations of capsids (53).…”

POTENSI SENYAWA BIOAKTIF TANAMAN GENUS <i>Phyllanthus</i> SEBAGAI INHIBITOR REPLIKASI VIRUS HEPATITIS B

“…Dengan mengganggu peran protein inti ini maka replikasi virus akan terhambat. Oleh karena itu protein inti VHB ini merupakan target yang sangat baik untuk pengembangan antivirus baru yang selektif, aman dan efektif (Bourne et al 2008;Campagna et al 2013;Klumpp et al 2015;Zlotnick et al 2015;Venkatakrishnan et al 2016). …”