HBV Capsid Research Articles

Identification of (6S)-cyclopropyl-6,7-dihydropyrazolo[1,5-a]pyrazine-5(4H)-carboxamines as new HBV capsid assembly modulators

GYH2-18 is a type II HBV CAM with 6,7-dihydropyrazolo[1,5-a]pyrazine-5(4H)-carboxamine (DPPC) skeleton discovered by Roche INC. A series of GYH2-18 derivatives were designed, synthesized and evaluated for their anti-HBV activity. Two compounds 2f and 3k exhibited excellent anti-HBV activity, low cytotoxicity and accepted oral PK profiles. Chiral separation of 2f and 3k was conducted successfully, and (6S)-cyclopropyl DPPC isomers 2f-1, 2f-3, 3k-1 and 3k-3 were identified to be much more active than the corresponding (6R)-ones. The preliminary structure-activity relationship, particle gel assay and molecular modeling studies were also discussed, which provide useful indications for guiding the further rational design of new (6S)-cyclopropyl DPPC analogues.

Oxadiazepinone HBV capsid assembly modulators

The HBV core protein serves multiple essential functions in the viral life cycle that enable chronic HBV infection to persist, and as such, represents a promising drug target. Modulation of the HBV capsid assembly has shown efficacy in early clinical trials through use of small molecule capsid assembly modulators (CAMs). Herein is described the evolution and SAR of a novel pyrazolo piperidine lead series into advanced oxadiazepinone HBV CAMs.

Discovery of novel HBV capsid assembly modulators by structure-based virtual screening and bioassays

HBV capsid assembly has been regarded as an attractive potential target for anti-HBV therapy. In this study, we discovery the Novel HBV capsid assembly modulators (CAMs) through structure-based virtual screening and bioassays. A total of 16 structurally diverse compounds were purchased and assayed, including three compounds with inhibition rate > 50% at 20 μM. Further lead optimization based on the most potent compound II-1–7 (EC50 = 5.6 ± 0.1 µM) were performed by using substructure searching strategy, resulting in compound II-2–9 with an EC50 value of 1.8 ± 0.6 μM. In bimolecular fluorescence complementation (BiFC) assay, compound II-2–9 inhibited the HBV by disrupting the HBV capsid interactions. In summary, this study provides a highly efficient way to discover novel CAMs, and 2-aryl-4-quinolyl amide derivatives could serve as the starting point for development of novel anti-HBV drugs.

Identification of a new class of HBV capsid assembly modulator

The HBV core protein is a druggable target of interest due to the multiple essential functions in the HBV life cycle to enable chronic HBV infection. The core protein oligomerizes to form the viral capsid, and modulation of the HBV capsid assembly has shown efficacy in clinical trials. Herein is described the identification and hit to lead SAR of a novel series of pyrazolo piperidine HBV capsid assembly modulators.

3D-QSAR, molecular docking and molecular dynamics simulations analyses of a series of heteroaryldihydropyrimidine derivatives as hepatitis B virus capsid assembly inhibitors

In silicodesign of heteroaryldihydropyrimidine-based selective HBV capsid assembly inhibitors.

Molecular Docking and 3D-QSAR Studies on a Series of Benzenesulfonamide Derivatives as a Hepatitis B Virus Capsid Assembly Inhibitor

In this paper, a three-dimensional quantitative structure-activity relationship (3D-QSAR) namely CoMFA and CoMSIA has been carried out on a series (43 compounds) of capsid assembly inhibitors on N-phenyl-3-sulfamoyl-benzamide-based. The statistical parameters from the models (CoMFA: r2 = 0.998, q2 = 0.625, r2 pred = 0.837; CoMSIA: r2 = 0.987, q2 = 0.645, r2 pred = 0.698) indicate that the data are well fitted and have high predictive ability. Molecular docking was employed to explore the binding mode between these compounds and the receptor protein, as well as help understand the structure-activity relationship revealed by CoMFA and CoMSIA. Contour maps of the QSAR models were generated and validated by molecular docking study. The final models of CoMFA/CoMSIA and molecular docking could be useful for the design and development of novel potent HBV capsid assembly inhibitors.

Discovery of Phthalazinone Derivatives as Novel Hepatitis B Virus Capsid Inhibitors.

HBV capsid assembly has been viewed as an attractive target for new antiviral therapies against HBV. On the basis of a lead compound 4r, we further investigated this target to identify novel active compounds with appropriate anti-HBV potencies and improved pharmacokinetic (PK) properties. Structure-activity relationship studies based on metabolic pathways of 4r led to the identification of a phthalazinone derivative 19f with appropriate anti-HBV potencies (IC50 = 0.014 ± 0.004 μM in vitro), which demonstrated high oral bioavailability and liver exposure. In the AAV-HBV/mouse model, administration of 19f resulted in a 2.67 log reduction of the HBV DNA viral load during a 4-week treatment with 150 mg/kg dosing twice daily.

Anti-HBV activity of the HBV capsid assembly modulator JNJ-56136379 across full-length genotype A-H clinical isolates and core site-directed mutants in vitro.

To characterize antiviral activity of the capsid assembly modulator (CAM-N) JNJ-56136379 against HBV genotypes and variants carrying amino acid substitutions in the core protein. Anti-HBV activity of JNJ-56136379 was investigated against a diverse panel of 53 HBV clinical isolates (genotypes A-H). The impact of core amino acid substitutions using site-directed mutants (SDMs) was assessed in a transient replication assay. JNJ-56136379 median 50% effective concentration (EC50) values across all genotypes were 10-33 nM versus 17 nM (genotype D reference). JNJ-56136379 remained active against isolates carrying nucleos(t)ide analogue resistance mutations (median EC50 2-25 nM) or basal core promoter (BCP) ± precore (PC) mutations (median EC50 13-20 nM) or PC mutations (median EC50 11 nM), representing activity against isolates from HBeAg-positive and -negative hepatitis B patients. Core amino acid substitutions in the CAM-binding pocket, when tested as SDMs at positions 23, 25, 30, 33, 37, 106, 110, 118, 124, 127 and 128, reduced JNJ-56136379 anti-HBV activity; EC50 fold increases ranged from 3.0 (S106T) to 85 (T33N). All substitutions were rare in a public database of >7600 HBV core sequences (frequencies 0.01%-0.3%). Nucleos(t)ide analogues retained full activity against these core SDMs. JNJ-56136379, a potent HBV CAM-N, currently in Phase 2 clinical development, was generally fully active against an extensive panel of genotype A-H clinical isolates, regardless of the presence of nucleos(t)ide analogue resistance or BCP/PC mutations. JNJ-56136379 activity was reduced by some core amino acid substitutions in the CAM-binding pocket.

Bioassay-guided isolation of anti-hepatitis B virus flavonoid myricetin-3-O-rhamnoside along with quercetin from Guiera senegalensis leaves

Recently, we have shown in vitro anti-hepatitis B virus (HBV) activity of G. senegalensis J.F. Gmel leaves, and Identified quercetin and other flavonoids by HPTLC. Here we report bioassay-directed fractionation of G. senegalensis leaves using column chromatography and isolation of two flavonoinds from the n-butanol fraction, their structure determination (1H NMR, 13C NMR and 2D-NMR) and assessment of antiviral activities (HBsAg and HBeAg assay) in HBV-reporter HepG2.2.2.15 cells. Further molecular docking was performed against HBV polymerase (Pol/RT) and capsid (Core) proteins as well as host-receptor sodium taurocholate co-transporting polypeptide (NTCP). The two isolated bioactive compounds were identified as quercetin and myricetin-3-O-rhamnoside. Quercetin significantly inhibited synthesis of HBsAg and HBeAg by about 60% and 62%, respectively as compared to myricetin-3-O-rhamnoside by 44% and 35%, respectively. Molecular docking of the two anti-HBV flavonoids revealed their higher binding affinities towards Pol/RT than Core and NTCP. In conclusion, this is the first report on anti-HBV active myricetin-3-O-rhamnoside along with quercetin isolated from G. senegalensis leaves. Their possible mode of anti-HBV activities are suggested through binding with viral Pol/RT and Core as well as host NTCP proteins.

Mechanism of Action of HBV Capsid Assembly Modulators can be Predicted from a Combination of Molecular Dynamics and Docking

Mechanism of Action of HBV Capsid Assembly Modulators can be Predicted from a Combination of Molecular Dynamics and Docking

A New Approach of Mitigating CYP3A4 Induction Led to the Discovery of Potent Hepatitis B Virus (HBV) Capsid Inhibitor with Optimal ADMET Profiles

Described herein is a new approach to mitigate CYP3A4 induction. In this unconventional approach, a fine-tuning of the dihedral angle between the C4 phenyl and the dihydropyrimidine core of the heteroaryldihydropyrimidine (HAP) class of capsid inhibitors successfully altered the structure-activity-relationships (SARs) of the unwanted CYP3A4 induction and the desired HBV capsid inhibition to more favorable values. This eventually led to the discovery of a new capsid inhibitor with significantly reduced CYP3A4 induction, excellent anti-HBV activity, favorable preclinical PK/PD profiles, and no early safety flags.

BAY 41-4109-mediated aggregation of assembled and misassembled HBV capsids in cells revealed by electron microscopy

HBc is a small protein essential for the formation of the icosahedral HBV capsid. Its multiple roles in the replication cycle make this protein a promising target for the development of antiviral molecules. Based on the structure of HBc, a series of HBV assembly inhibitors, also known as capsid assembly modulators, were identified. We investigated the effect of BAY 41–4109, a heteroaryldihydropyrimidine derivative that promotes the assembly of a non-capsid polymer. We showed, by confocal microscopy, that BAY 41–4109 mediated HBc aggregation, mostly in the cytoplasm of Huh7 cells. Image analysis revealed that aggregate size depended on BAY 41–4109 concentration and treatment duration. Large aggregates in the vicinity of the nucleus were enclosed by invaginations of the nuclear envelope. This deformation of the nuclear envelope was confirmed by transmission electron microscopy (TEM) and immuno-TEM. These two techniques also revealed that the HBc aggregates were accumulations of capsid-like shells with an electron-dense material consisting of HBV core fragments. These findings, shedding light on the ultrastructural organization of HBc aggregates, provide insight into the mechanisms of action of BAY 41–4109 against HBV and will serve as a basis for comparison with other HBV capsid assembly inhibitors.

SAR studies in the sulfonyl carboxamide class of HBV capsid assembly modulators.

The HBV core protein has multiple essential functions in the HBV life cycle to enable chronic HBV infection. The core protein oligomerizes to form the viral capsid, and modulation of the HBV capsid assembly process has shown clinical efficacy in early clinical trials. Herein is described the SAR exploration of NVR 3-778, the first clinical compound in the sulfonyl carboxamide class.

FRI-157-Novel HBV capsid assembly modulator inhibits pregenomic RNA encapsidation by accelerating capsid assembly kinetics and disrupting core protein dephosphorylation

FRI-157-Novel HBV capsid assembly modulator inhibits pregenomic RNA encapsidation by accelerating capsid assembly kinetics and disrupting core protein dephosphorylation

Computational Studies and Molecular Dynamic Simulation to Design Lead Compounds for Hepatitis B Virus

: Objective/Background: A novel approach to develop anti-Hepatitis B Virus (HBV) by computational studies is proposed. Methodology: It used active compounds as the standard ligand. There are six parameters such as docking score, molecular weight, log P, Polarizability, Polar Surface (2D) and Molecular Surface (3D) that analyzed by software. Result and Discussion: The result of virtual screening can be used as a reference to calculate IC50 prediction of quinine and Gallic acid derivative compounds. Optimization of compounds structure geometry was using software Marvin Sketch 6.0.1. Meanwhile, virtual docking process to HBV capsid Y132A mutant (PDB ID: 5E0I) was using Autodock4, Auto dock Vina, and Plant. Result: The lowest IC50 prediction is gallic acid (64.1 μM) that had hydrogen and polar interaction for 20 ns. Conclusion: These computational studies not only shed light on understanding the IC50 prediction of the replication of the viral core protein inhibition, but also the stability of each interaction that inhibits of the viral core protein replication.Key words: Amber, Docking, Galic Acid, Hepatitis B, Molecular Dynamic.

All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits.

The hepatitis B virus capsid represents a promising therapeutic target. Experiments suggest the capsid must be flexible to function; however, capsid structure and dynamics have not been thoroughly characterized in the absence of icosahedral symmetry constraints. Here, all-atom molecular dynamics simulations are leveraged to investigate the capsid without symmetry bias, enabling study of capsid flexibility and its implications for biological function and cryo-EM resolution limits. Simulation results confirm flexibility and reveal a propensity for asymmetric distortion. The capsid's influence on ionic species suggests a mechanism for modulating the display of cellular signals and implicates the capsid's triangular pores as the location of signal exposure. A theoretical image reconstruction performed using simulated conformations indicates how capsid flexibility may limit the resolution of cryo-EM. Overall, the present work provides functional insight beyond what is accessible to experimental methods and raises important considerations regarding asymmetry in structural studies of icosahedral virus capsids.

PS-027 - Preclinical antiviral drug combination studies utilizing novel orally bioavailable investigational agents for chronic hepatitis B infection: AB-506, a next generation HBV capsid inhibitor, and AB-452, a HBV RNA destabilizer

PS-027 - Preclinical antiviral drug combination studies utilizing novel orally bioavailable investigational agents for chronic hepatitis B infection: AB-506, a next generation HBV capsid inhibitor, and AB-452, a HBV RNA destabilizer

PS-026 - Novel and potent HBV capsid modulator reduces HBeAg and cccDNA in core site directed T109I mutant in HepNTCP cells

PS-026 - Novel and potent HBV capsid modulator reduces HBeAg and cccDNA in core site directed T109I mutant in HepNTCP cells

Rational Development of HBV Capsid Inhibitors Aided by Molecular Dynamics

Rational Development of HBV Capsid Inhibitors Aided by Molecular Dynamics

A dimorphism shift of hepatitis B virus capsids in response to ionic conditions.

The dimorphism of HBV capsids (coexistence of T = 3 and T = 4 capsids) was found to be regulatable by controlling the rate of capsid nucleation using cations such as K+ or Ca2+: a quick addition of highly concentrated monovalent and/or multivalent counter-cations resulted in a morphism transition from a thermodynamically more stable, T = 4 capsid-dominant state (>80% of total capsids) to a new state containing ∼1 : 1 amounts of T = 3 and T = 4 capsids. These results suggested that the salts with strong charge screening ability could narrow the difference in nucleation energy barriers between the two states, which were not inter-convertible once formed. The effect of salts was more significant than other factors such as pH or protein concentration in achieving such a dimorphism shift. The general mechanism of HBV capsid dimorphism described here provides a new perspective in understanding the virus assembly during infection and directing the design of non-infectious capsids for nanotechnology applications.