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Bhat S, Kazim SN. HBV cccDNA-A Culprit and Stumbling Block for the Hepatitis B Virus Infection: Its Presence in Hepatocytes Perplexed the Possible Mission for a Functional Cure. ACS OMEGA 2022; 7:24066-24081. [PMID: 35874215 PMCID: PMC9301636 DOI: 10.1021/acsomega.2c02216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Hepatitis B virus infection (HBV) is still a big health problem across the globe. It has been linked to the development of liver cirrhosis and hepatocellular carcinoma and can trigger different types of liver damage. Existing medicines are unable to disable covalently closed circular DNA (cccDNA), which may result in HBV persistence and recurrence. The current therapeutic goal is to achieve a functional cure, which means HBV-DNA no longer exists when treatment stops and the absence of HBsAg seroclearance. However, due to the presence of integrated HBV DNA and cccDNA functional treatment is now regarded to be difficult. In order to uncover pathways for potential therapeutic targets and identify medicines that could result in large rates of functional cure, a thorough understanding of the virus' biology is required. The proteins of the virus and episomal cccDNA are thought to be critical for the management and support of the HBV replication cycle as they interact directly with the host proteome to establish the best atmosphere for the virus while evading immune detection. The breakthroughs of host dependence factors, cccDNA transcription, epigenetic regulation, and immune-mediated breakdown have all produced significant progress in our understanding of cccDNA biology during the past decade. There are some strategies where cccDNA can be targeted either in a direct or indirect way and are presently at the point of discovery or preclinical or early clinical advancement. Editing of genomes, techniques targeting host dependence factors or epigenetic gene maintenance, nucleocapsid modulators, miRNA, siRNA, virion secretory inhibitors, and immune-mediated degradation are only a few examples. Though cccDNA approaches for direct targeting are still in the early stages of development, the assembly of capsid modulators and immune-reliant treatments have made it to the clinic. Clinical trials are currently being conducted to determine their efficiency and safety in patients, as well as their effect on viral cccDNA. The influence of recent breakthroughs in the development of new treatment techniques on cccDNA biology is also summarized in this review.
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Affiliation(s)
- Sajad
Ahmad Bhat
- Jamia Millia Islamia Central University, Centre for Interdisciplinary Research in Basic Sciences, New Delhi 110025, India
| | - Syed Naqui Kazim
- Jamia Millia Islamia Central University, Centre for Interdisciplinary Research in Basic Sciences, New Delhi 110025, India
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2
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Fogeron ML, Lecoq L, Cole L, Montserret R, David G, Page A, Delolme F, Nassal M, Böckmann A. Phosphorylation of the Hepatitis B Virus Large Envelope Protein. Front Mol Biosci 2022; 8:821755. [PMID: 35282608 PMCID: PMC8904964 DOI: 10.3389/fmolb.2021.821755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 01/05/2023] Open
Abstract
We here establish the phosphorylation sites in the human hepatitis B virus (HBV) large envelope protein (L). L is involved in several functionally important interactions in the viral life cycle, including with the HBV cellular receptor, HBV capsid, Hsc70 chaperone, and cellular membranes during fusion. We have recently shown that cell-free synthesis of the homologous L protein of duck HBV in wheat germ extract results in very similar phosphorylation events to those previously observed in animal cells. Here, we used mass spectrometry and NMR to establish the phosphorylation patterns of human HBV L protein produced by both in vitro cell-free synthesis and in E. coli with the co-expression of the human MAPK14 kinase. While in the avian virus the phosphorylation of L has been shown to be dispensable for infectivity, the identified locations in the human virus protein, both in the PreS1 and PreS2 domains, raise the intriguing possibility that they might play a functional role, since they are found at strategic sites predicted to be involved in L interactions. This would warrant the further investigation of a possible function in virion formation or cell entry.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Guillaume David
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UAR 3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Frédéric Delolme
- Protein Science Facility, SFR BioSciences CNRS UAR 3444, Inserm US8, UCBL, ENS de Lyon, Lyon, France
| | - Michael Nassal
- Department of Medicine II / Molecular Biology, Medical Center, University Hospital Freiburg, University of Freiburg, Freiburg im Breisgau, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
- *Correspondence: Anja Böckmann,
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3
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Cragnolini T, Kryshtafovych A, Topf M. Cryo-EM targets in CASP14. Proteins 2021; 89:1949-1958. [PMID: 34398978 PMCID: PMC8630773 DOI: 10.1002/prot.26216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 11/22/2022]
Abstract
Structures of seven CASP14 targets were determined using cryo-electron microscopy (cryo-EM) technique with resolution between 2.1 and 3.8 Å. We provide an evaluation of the submitted models versus the experimental data (cryo-EM density maps) and experimental reference structures built into the maps. The accuracy of models is measured in terms of coordinate-to-density and coordinate-to-coordinate fit. A-posteriori refinement of the most accurate models in their corresponding cryo-EM density resulted in structures that are close to the reference structure, including some regions with better fit to the density. Regions that were found to be less "refineable" correlate well with regions of high diversity between the CASP models and low goodness-of-fit to density in the reference structure.
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Affiliation(s)
- Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, UK
| | | | - Maya Topf
- Center for Structural Systems Biology, Leibniz-Institut für Experimentelle Virologie and Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany
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4
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Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt W(S, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia‐Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021; 89:1647-1672. [PMID: 34561912 PMCID: PMC8616854 DOI: 10.1002/prot.26247] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022]
Abstract
The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.
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Affiliation(s)
- Leila T. Alexander
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | | | - Athanassios Adamopoulos
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Markus Alahuhta
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Ann M. Arvin
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Yannick J. Bomble
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Bettina Böttcher
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | - Valerio Chiarini
- Program in Structural Biology and BiophysicsInstitute of Biotechnology, University of HelsinkiHelsinkiFinland
| | - Naga babu Chinnam
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
| | - Wah Chiu
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
- BioengineeringStanford University School of MedicineStanfordCaliforniaUSA
- Division of Cryo‐EM and Bioimaging SSRLSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Rhys Grinter
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Gagan D. Gupta
- Radiation Biology & Health Sciences DivisionBhabha Atomic Research CentreMumbaiIndia
| | - Marcus D. Hartmann
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental BiologyUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
- Biomolecular Science and Engineering ProgramUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Tatjana Heidebrecht
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology of the National Research Council of Italy (CNR)RomeItaly
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Romain Linares
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | | | - Vladimir V. Lunin
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Andrei N. Lupas
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Cihan Makbul
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John Moult
- Department of Cell Biology and Molecular GeneticsInstitute for Bioscience and Biotechnology Research, University of MarylandRockvilleMarylandUSA
| | - Prasun K. Mukherjee
- Nuclear Agriculture & Biotechnology DivisionBhabha Atomic Research CentreMumbaiIndia
| | - William (Sam) Nutt
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Stefan L. Oliver
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
| | - Anastassis Perrakis
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Lucy Stols
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John A. Tainer
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
- Department of Cancer BiologyUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College LondonLondonUK
- Centre for Structural Systems Biology, Leibniz‐Institut für Experimentelle VirologieHamburgGermany
| | - Susan E. Tsutakawa
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | | | - Torsten Schwede
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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Ozden B, Kryshtafovych A, Karaca E. Assessment of the CASP14 assembly predictions. Proteins 2021; 89:1787-1799. [PMID: 34337786 PMCID: PMC9109697 DOI: 10.1002/prot.26199] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022]
Abstract
In CASP14, 39 research groups submitted more than 2500 3D models on 22 protein complexes. In general, the community performed well in predicting the fold of the assemblies (for 80% of the targets), although it faced significant challenges in reproducing the native contacts. This is especially the case for the complexes without whole-assembly templates. The leading predictor, BAKER-experimental, used a methodology combining classical techniques (template-based modeling, protein docking) with deep learning-based contact predictions and a fold-and-dock approach. The Venclovas team achieved the runner-up position with template-based modeling and docking. By analyzing the target interfaces, we showed that the complexes with depleted charged contacts or dominating hydrophobic interactions were the most challenging ones to predict. We also demonstrated that if AlphaFold2 predictions were at hand, the interface prediction challenge could be alleviated for most of the targets. All in all, it is evident that new approaches are needed for the accurate prediction of assemblies, which undoubtedly will expand on the significant improvements in the tertiary structure prediction field.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, 35340, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340, Izmir, Turkey
| | - Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, USA
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, 35340, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340, Izmir, Turkey
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6
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Niklasch M, Zimmermann P, Nassal M. The Hepatitis B Virus Nucleocapsid-Dynamic Compartment for Infectious Virus Production and New Antiviral Target. Biomedicines 2021; 9:1577. [PMID: 34829806 PMCID: PMC8615760 DOI: 10.3390/biomedicines9111577] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a small enveloped DNA virus which replicates its tiny 3.2 kb genome by reverse transcription inside an icosahedral nucleocapsid, formed by a single ~180 amino acid capsid, or core, protein (Cp). HBV causes chronic hepatitis B (CHB), a severe liver disease responsible for nearly a million deaths each year. Most of HBV's only seven primary gene products are multifunctional. Though less obvious than for the multi-domain polymerase, P protein, this is equally crucial for Cp with its multiple roles in the viral life-cycle. Cp provides a stable genome container during extracellular phases, allows for directed intracellular genome transport and timely release from the capsid, and subsequent assembly of new nucleocapsids around P protein and the pregenomic (pg) RNA, forming a distinct compartment for reverse transcription. These opposing features are enabled by dynamic post-transcriptional modifications of Cp which result in dynamic structural alterations. Their perturbation by capsid assembly modulators (CAMs) is a promising new antiviral concept. CAMs inappropriately accelerate assembly and/or distort the capsid shell. We summarize the functional, biochemical, and structural dynamics of Cp, and discuss the therapeutic potential of CAMs based on clinical data. Presently, CAMs appear as a valuable addition but not a substitute for existing therapies. However, as part of rational combination therapies CAMs may bring the ambitious goal of a cure for CHB closer to reality.
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Affiliation(s)
| | | | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany; (M.N.); (P.Z.)
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Binding of a Pocket Factor to Hepatitis B Virus Capsids Changes the Rotamer Conformation of Phenylalanine 97. Viruses 2021; 13:v13112115. [PMID: 34834922 PMCID: PMC8618838 DOI: 10.3390/v13112115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
(1) Background: During maturation of the Hepatitis B virus, a viral polymerase inside the capsid transcribes a pre-genomic RNA into a partly double stranded DNA-genome. This is followed by envelopment with surface proteins inserted into a membrane. Envelopment is hypothetically regulated by a structural signal that reports the maturation state of the genome. NMR data suggest that such a signal can be mimicked by the binding of the detergent Triton X 100 to hydrophobic pockets in the capsid spikes. (2) Methods: We have used electron cryo-microscopy and image processing to elucidate the structural changes that are concomitant with the binding of Triton X 100. (3) Results: Our maps show that Triton X 100 binds with its hydrophobic head group inside the pocket. The hydrophilic tail delineates the outside of the spike and is coordinated via Lys-96. The binding of Triton X 100 changes the rotamer conformation of Phe-97 in helix 4, which enables a π-stacking interaction with Trp-62 in helix 3. Similar changes occur in mutants with low secretion phenotypes (P5T and L60V) and in a mutant with a pre-mature secretion phenotype (F97L). (4) Conclusion: Binding of Triton X 100 is unlikely to mimic structural maturation because mutants with different secretion phenotypes show similar structural responses.
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Conformational Plasticity of Hepatitis B Core Protein Spikes Promotes Peptide Binding Independent of the Secretion Phenotype. Microorganisms 2021; 9:microorganisms9050956. [PMID: 33946808 PMCID: PMC8145704 DOI: 10.3390/microorganisms9050956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/31/2022] Open
Abstract
Hepatitis B virus is a major human pathogen, which forms enveloped virus particles. During viral maturation, membrane-bound hepatitis B surface proteins package hepatitis B core protein capsids. This process is intercepted by certain peptides with an “LLGRMKG” motif that binds to the capsids at the tips of dimeric spikes. With microcalorimetry, electron cryo microscopy and peptide microarray-based screens, we have characterized the structural and thermodynamic properties of peptide binding to hepatitis B core protein capsids with different secretion phenotypes. The peptide “GSLLGRMKGA” binds weakly to hepatitis B core protein capsids and mutant capsids with a premature (F97L) or low-secretion phenotype (L60V and P5T). With electron cryo microscopy, we provide novel structures for L60V and P5T and demonstrate that binding occurs at the tips of the spikes at the dimer interface, splaying the helices apart independent of the secretion phenotype. Peptide array screening identifies “SLLGRM” as the core binding motif. This shortened motif binds only to one of the two spikes in the asymmetric unit of the capsid and induces a much smaller conformational change. Altogether, these comprehensive studies suggest that the tips of the spikes act as an autonomous binding platform that is unaffected by mutations that affect secretion phenotypes.
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Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies. Viruses 2020; 12:v12101069. [PMID: 32987909 PMCID: PMC7599928 DOI: 10.3390/v12101069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Structural virology reveals the architecture underlying infection. While notably electron microscopy images have provided an atomic view on viruses which profoundly changed our understanding of these assemblies incapable of independent life, spectroscopic techniques like NMR enter the field with their strengths in detailed conformational analysis and investigation of dynamic behavior. Typically, the large assemblies represented by viral particles fall in the regime of biological high-resolution solid-state NMR, able to follow with high sensitivity the path of the viral proteins through their interactions and maturation steps during the viral life cycle. We here trace the way from first solid-state NMR investigations to the state-of-the-art approaches currently developing, including applications focused on HIV, HBV, HCV and influenza, and an outlook to the possibilities opening in the coming years.
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