1
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Khaykelson D, Asor R, Zhao Z, Schlicksup CJ, Zlotnick A, Raviv U. Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis. Biochemistry 2024; 63:1543-1552. [PMID: 38787909 PMCID: PMC11191408 DOI: 10.1021/acs.biochem.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.
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Affiliation(s)
- Daniel Khaykelson
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Roi Asor
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Zhongchao Zhao
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christopher John Schlicksup
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Uri Raviv
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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2
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Luo H, Ma Y, Bi J, Li Z, Wang Y, Su Z, Gerstweiler L, Ren Y, Zhang S. Experimental and molecular dynamics simulation studies on the physical properties of three HBc-VLP derivatives as nanoparticle protein vaccine candidates. Vaccine 2024:S0264-410X(24)00599-1. [PMID: 38811268 DOI: 10.1016/j.vaccine.2024.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Self-assembling virus-like particles (VLPs) are promising platforms for vaccine development. However, the unpredictability of the physical properties, such as self-assembly capability, hydrophobicity, and overall stability in engineered protein particles fused with antigens, presents substantial challenges in their downstream processing. We envision that these challenges can be addressed by combining more precise computer-aided molecular dynamics (MD) simulations with experimental studies on the modified products, with more to-date forcefield descriptions and larger models closely resembling real assemblies, realized by rapid advancement in computing technology. In this study, three chimeric designs based on the hepatitis B core (HBc) protein as model vaccine candidates were constructed to study and compare the influence of inserted epitopes as well as insertion strategy on HBc modifications. Large partial VLP models containing 17 chains for the HBc chimeric model vaccines were constructed based on the wild-type (wt) HBc assembly template. The findings from our simulation analysis have demonstrated good consistency with experimental results, pertaining to the surface hydrophobicity and overall stability of the chimeric vaccine candidates. Furthermore, the different impact of foreign antigen insertions on the HBc scaffold was investigated through simulations. It was found that separately inserting two epitopes into the HBc platform at the N-terminal and the major immunogenic regions (MIR) yields better results compared to a serial insertion at MIR in terms of protein structural stability. This study substantiates that an MD-guided design approach can facilitate vaccine development and improve its manufacturing efficiency by predicting products with extreme surface hydrophobicity or structural instability.
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Affiliation(s)
- Hong Luo
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia; State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Yanyan Ma
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Jingxiu Bi
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia
| | - Zhengjun Li
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yingli Wang
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Lukas Gerstweiler
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia.
| | - Ying Ren
- State Key Laboratory of Mesoscience and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
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3
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Fan Z, Pavlova A, Jenkins MC, Bassit L, Salman M, Lynch DL, Patel D, Korablyov M, Finn MG, Schinazi RF, Gumbart JC. Biophysics-Guided Lead Discovery of HBV Capsid Assembly Modifiers. ACS Infect Dis 2024; 10:1162-1173. [PMID: 38564659 PMCID: PMC11019538 DOI: 10.1021/acsinfecdis.3c00479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Hepatitis B virus (HBV) is the leading cause of chronic liver pathologies worldwide. HBV nucleocapsid, a key structural component, is formed through the self-assembly of the capsid protein units. Therefore, interfering with the self-assembly process is a promising approach for the development of novel antiviral agents. Applied to HBV, this approach has led to several classes of capsid assembly modulators (CAMs). Here, we report structurally novel CAMs with moderate activity and low toxicity, discovered through a biophysics-guided approach combining docking, molecular dynamics simulations, and a series of assays with a particular emphasis on biophysical experiments. Several of the identified compounds induce the formation of aberrant capsids and inhibit HBV DNA replication in vitro, suggesting that they possess modest capsid assembly modulation effects. The synergistic computational and experimental approaches provided key insights that facilitated the identification of compounds with promising activities. The discovery of preclinical CAMs presents opportunities for subsequent optimization efforts, thereby opening new avenues for HBV inhibition.
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Affiliation(s)
- Zixing Fan
- Interdisciplinary
Bioengineering Graduate Program, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Matthew C. Jenkins
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Leda Bassit
- Center
for ViroScience and Cure, Laboratory of Biochemical Pharmacology,
Department of Pediatrics, Emory University
School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Mohammad Salman
- Center
for ViroScience and Cure, Laboratory of Biochemical Pharmacology,
Department of Pediatrics, Emory University
School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Diane L. Lynch
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dharmeshkumar Patel
- Center
for ViroScience and Cure, Laboratory of Biochemical Pharmacology,
Department of Pediatrics, Emory University
School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Maksym Korablyov
- MIT
Media Lab, Massachusetts Institute of Technology, Boston, Massachusetts 02139, United States
| | - M. G. Finn
- School
of Chemistry & Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Raymond F. Schinazi
- Center
for ViroScience and Cure, Laboratory of Biochemical Pharmacology,
Department of Pediatrics, Emory University
School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
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4
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Luo H, Ma Y, Ren Y, Li Z, Sheng Y, Wang Y, Su Z, Bi J, Zhang S. Study of self-assembling properties of HBc-VLP derivatives aided by molecular dynamic simulations from a thermodynamic perspective. J Biomol Struct Dyn 2023:1-14. [PMID: 37908124 DOI: 10.1080/07391102.2023.2273438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/14/2023] [Indexed: 11/02/2023]
Abstract
Self-assembling protein nanoparticles showed promise for vaccine design due to efficient antigen presentations and safety. However, the unpredictable formations of epitopes-fused protein assemblies remain challenging in the upstream design. This study suggests employing molecular dynamic (MD) simulations to investigate the assembly properties of Hepatitis B core protein (HBc) from thermodynamic perspectives. Eight HBc derivatives were expressed in E. coli, with their self-assembly properties characterised by high-performance liquid chromatography and transmission electron microscopy. MD simulations on the dimers, based on AlphaFold-predicted 3D structures, analysed the derivative at the atomic level. Results revealed that HBc derivatives can form dissociative polymers or large multi-subunit structures due to assembly failures. The instability of the dimer in aqueous solvents or inappropriate intradimer distances could cause major assembly failures. Polar solvation energies played a vital role too in forming assemble-incompetent dimers. Importantly, our study demonstrated that MD simulations on dimers can provide preliminary predictions on the assembly properties of HBc derivatives, thus aiding vaccine design by lowering the risk of self-assembling failures in engineered proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hong Luo
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, Australia
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, PR China
| | - Yanyan Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Ying Ren
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, PR China
| | - Zhengjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Yanan Sheng
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Yingli Wang
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, PR China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Jingxiu Bi
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, Australia
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
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5
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Kobayakawa T, Amano M, Nakayama M, Tsuji K, Ishii T, Miura Y, Shinohara K, Yamamoto K, Matsuoka M, Tamamura H. Development of anti-HBV agents targeting HBV capsid proteins. RSC Med Chem 2023; 14:1973-1980. [PMID: 37859721 PMCID: PMC10583812 DOI: 10.1039/d3md00258f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/31/2023] [Indexed: 10/21/2023] Open
Abstract
Hepatitis B is a viral hepatitis, which is caused by infection of hepatitis B virus (HBV). This disease progresses to chronic hepatitis, cirrhosis and liver cancer. To treat hepatitis B, exclusion of virus and covalently closed circular DNA (cccDNA) that is formed in hepatocyte nucleus is necessary. A hepatitis B capsid protein (HBc) is an indispensable protein, which forms the capsid that encapsulates viral DNA. Since HBc is correlated to the transcriptional regulation of cccDNA, this protein would be an attractive target for complete cure of hepatitis B. By in silico screening of a library of compounds, a small compound, Cpd4 (1), which binds to a hydrophobic cavity located in the inner pocket on the tetramer interface of HBc proteins, was identified. In anti-HBV assays, this synthetic compound, Cpd4 (1) decreased the amount of HBV core related antigen (HBcrAg), which has been correlated with the proliferation of HBV, and decreased the amount of HBV surface antigen (HBsAg), which is correlated with the amount of cccDNA. Based on Cpd4 (1) as a lead compound, 20 derivatives of 1 were designed and synthesized and their structure-activity relationships were examined. As a result, specific interactions between each compound and amino acid residues of the target protein appeared to be unimportant but the shape/size of compounds which can bind to the hydrophobic cavity might be important in the expression of high anti-HBV activity, and a more potent derivative, TKB-HBV-CA-001 (3b), was discovered. These results will be useful in the development of novel anti-HBV agents for a complete cure of hepatitis B.
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Affiliation(s)
- Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Masayuki Amano
- Department of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto and Kagoshima Universities Kumamoto 860-0811 Japan
- Department of Hematology, Rheumatology, and Infectious Diseases, Faculty of Life Sciences, Kumamoto University Kumamoto 860-8556 Japan
| | - Miyuki Nakayama
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Kohei Tsuji
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Takahiro Ishii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Yutaro Miura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Kouki Shinohara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Kenichi Yamamoto
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Masao Matsuoka
- Department of Hematology, Rheumatology, and Infectious Diseases, Faculty of Life Sciences, Kumamoto University Kumamoto 860-8556 Japan
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
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6
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Hojatizadeh M, Amiri MM, Mobini M, Hassanzadeh Makoui M, Ghaedi M, Ghotloo S, Peyghami K, Jeddi-Tehrani M, Golsaz-Shirazi F, Shokri F. Cross-Reactivity of HBe Antigen-Specific Polyclonal Antibody with HBc Antigen. Viral Immunol 2023; 36:378-388. [PMID: 37294935 DOI: 10.1089/vim.2022.0196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023] Open
Abstract
Hepatitis B virus (HBV) infection is a major health problem worldwide and causes almost one million deaths annually. The HBV core gene codes for two related antigens, known as core antigen (HBcAg) and e-antigen (HBeAg), sharing 149 residues but having different amino- and carboxy-terminals. HBeAg is a soluble variant of HBcAg and a clinical marker for determining the disease severity and patients' screening. Currently available HBeAg assays have a shortcoming of showing cross-reactivity with HBcAg. In this study, for the first time, we evaluated whether HBcAg-adsorbed anti-HBe polyclonal antibodies could specifically recognize HBeAg or still show cross-reactivity with HBcAg. Recombinant HBeAg was cloned in pCold1 vector and successfully expressed in Escherichia coli and after purification by Ni-NTA resin was used to generate polyclonal anti-HBe antibodies in rabbit. Purified HBeAg was further characterized by assessing its reactivity with anti-HBe in the sera of chronically infected patients and HBeAg-immunized rabbit. Sera from patients with chronic HBV infection, containing anti-HBe, specifically reacted with recombinant HBeAg, implying antigenic similarity between the prokaryotic and native HBeAg in the serum of HBV-infected patients. In addition, the designed enzyme-linked immunosorbent assay (ELISA) with rabbit anti-HBe polyclonal antibodies could detect recombinant HBeAg with high sensitivity, while high cross-reactivity with HBcAg was observed. It is noteworthy that HBcAg-adsorbed anti-HBe polyclonal antibodies still showed high cross-reactivity with HBcAg, implying that due to the presence of highly similar epitopes in both antigens, HBcAg-adsorbed polyclonal antibodies cannot differentiate between the two antigens.
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Affiliation(s)
- Maryam Hojatizadeh
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Amiri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mobini
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Hassanzadeh Makoui
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojgan Ghaedi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Ghotloo
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Kiana Peyghami
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Jeddi-Tehrani
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACER, Tehran, Iran
| | - Forough Golsaz-Shirazi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fazel Shokri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACER, Tehran, Iran
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7
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Padarath K, Deroubaix A, Kramvis A. The Complex Role of HBeAg and Its Precursors in the Pathway to Hepatocellular Carcinoma. Viruses 2023; 15:v15040857. [PMID: 37112837 PMCID: PMC10144019 DOI: 10.3390/v15040857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Hepatitis B virus (HBV) is one of the seven known human oncogenic viruses and has adapted to coexist with a single host for prolonged periods, requiring continuous manipulation of immunity and cell fate decisions. The persistence of HBV infection is associated with the pathogenesis of hepatocellular carcinoma, and various HBV proteins have been implicated in promoting this persistence. The precursor of hepatitis e antigen (HBeAg), is translated from the precore/core region and is post-translationally modified to yield HBeAg, which is secreted in the serum. HBeAg is a non-particulate protein of HBV and can act as both a tolerogen and an immunogen. HBeAg can protect hepatocytes from apoptosis by interfering with host signalling pathways and acting as a decoy to the immune response. By evading the immune response and interfering with apoptosis, HBeAg has the potential to contribute to the hepatocarcinogenic potential of HBV. In particular, this review summarises the various signalling pathways through which HBeAg and its precursors can promote hepatocarcinogenesis via the various hallmarks of cancer.
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8
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Xie Z, Liang Z, Huang Y, Shi K, Zang N, Wang M, Liang T, Wei W. Discovery and biological evaluation of 2-((3-phenylisoxazol-5-yl) methoxy) benzamide derivatives as potent nucleocapsid inhibitors. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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9
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Liang Z, Huang Y, Li H, Zhang X, Shi K, Zang N, Wang M, Liang T, Wei W. Synthesis and evaluation of 3-phenylisoxazoline derivatives as non-nucleoside hepatitis B virus inhibitors. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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10
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Mohajerani F, Tyukodi B, Schlicksup CJ, Hadden-Perilla JA, Zlotnick A, Hagan MF. Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism. ACS NANO 2022; 16:13845-13859. [PMID: 36054910 PMCID: PMC10273259 DOI: 10.1021/acsnano.2c02119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hepatitis B virus (HBV) is an endemic, chronic virus that leads to 800000 deaths per year. Central to the HBV lifecycle, the viral core has a protein capsid assembled from many copies of a single protein. The capsid protein adopts different (quasi-equivalent) conformations to form icosahedral capsids containing 180 or 240 proteins: T = 3 or T = 4, respectively, in Caspar-Klug nomenclature. HBV capsid assembly has become an important target for recently developed antivirals; nonetheless, the assembly pathways and mechanisms that control HBV dimorphism remain unclear. We describe computer simulations of the HBV assembly, using a coarse-grained model that has parameters learned from all-atom molecular dynamics simulations of a complete HBV capsid and yet is computationally tractable. Dynamical simulations with the resulting model reproduce experimental observations of HBV assembly pathways and products. By constructing Markov state models and employing transition path theory, we identify pathways leading to T = 3, T = 4, and other experimentally observed capsid morphologies. The analysis shows that capsid polymorphism is promoted by the low HBV capsid bending modulus, where the key factors controlling polymorphism are the conformational energy landscape and protein-protein binding affinities.
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Affiliation(s)
- Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts02453, United States
| | - Botond Tyukodi
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts02453, United States
- Department of Physics, Babeş-Bolyai University, 400084Cluj-Napoca, Romania
| | - Christopher J Schlicksup
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana47405, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware19716, United States
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana47405, United States
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts02453, United States
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11
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Huang Y, Liu N, Ning Q, Zhou M, Zang N, Liang T, Wei W. Design, synthesis, and biological evaluation of novel (E)-1-arylethan-1-one O-((3-arylisoxazol-5-yl) methyl) oxime derivatives as potent non-nucleoside HBV inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Su PY, Yen SCB, Yang CC, Chang CH, Lin WC, Shih C. Hepatitis B virus virion secretion is a CRM1-spike-mediated late event. J Biomed Sci 2022; 29:44. [PMID: 35729569 PMCID: PMC9210616 DOI: 10.1186/s12929-022-00827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hepatitis B virus (HBV) is a major human pathogen worldwide. To date, there is no curative treatment for chronic hepatitis B. The mechanism of virion secretion remains to be investigated. Previously, we found that nuclear export of HBc particles can be facilitated via two CRM1-specific nuclear export signals (NES) at the spike tip. Methods In this study, we used site-directed mutagenesis at the CRM1 NES, as well as treatment with CRM1 inhibitors at a low concentration, or CRM1-specific shRNA knockdown, in HBV-producing cell culture, and measured the secretion of various HBV viral and subviral particles via a native agarose gel electrophoresis assay. Separated HBV particles were characterized by Western blot analysis, and their genomic DNA contents were measured by Southern blot analysis. Secreted extracellular particles were compared with intracellular HBc capsids for DNA synthesis and capsid formation. Virion secretion and the in vivo interactions among HBc capsids, CRM1 and microtubules, were examined by proximity ligation assay, immunofluorescence microscopy, and nocodazole treatment. Results We report here that the tip of spike of HBV core (HBc) particles (capsids) contains a complex sensor for secretion of both HBV virions and naked capsids. HBV virion secretion is closely associated with HBc nuclear export in a CRM1-dependent manner. At the conformationally flexible spike tips of HBc particles, NES motifs overlap extensively with motifs important for secretion of HBV virions and naked capsids. Conclusions We provided experimental evidence that virions and naked capsids can egress via two distinct, yet overlapping, pathways. Unlike the secretion of naked capsids, HBV virion secretion is highly CRM1- and microtubule-dependent. CRM1 is well known for its involvement in nuclear transport in literature. To our knowledge, this is the first report that CRM1 is required for virion secretion. CRM1 inhibitors could be a promising therapeutic candidate for chronic HBV patients in clinical medicine. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-022-00827-w.
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Affiliation(s)
- Pei-Yi Su
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, No.100, Shih-Chuan 1st Road, Sanmin, 80708, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shin-Chwen Bruce Yen
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, No.100, Shih-Chuan 1st Road, Sanmin, 80708, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ching-Chun Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chih-Hsu Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chiaho Shih
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, No.100, Shih-Chuan 1st Road, Sanmin, 80708, Kaohsiung, Taiwan. .,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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13
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Patel N, Abulwerdi F, Fatehi F, Manfield IW, Le Grice S, Schneekloth JS, Twarock R, Stockley PG. Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands. J Mol Biol 2022; 434:167557. [PMID: 35341740 PMCID: PMC7612645 DOI: 10.1016/j.jmb.2022.167557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 12/12/2022]
Abstract
RNA sequences/motifs dispersed across the genome of Hepatitis B Virus regulate formation of nucleocapsid-like particles (NCPs) by core protein (Cp) in vitro, in an epsilon/polymerase-independent fashion. These multiple RNA Packaging Signals (PSs) can each form stem-loops encompassing a Cp-recognition motif, -RGAG-, in their loops. Drug-like molecules that bind the most important of these PS sites for NCP assembly regulation with nanomolar affinities, were identified by screening an immobilized ligand library with a fluorescently-labelled, RNA oligonucleotide encompassing this sequence. Sixty-six of these "hits", with affinities ranging from low nanomolar to high micromolar, were purchased as non-immobilized versions. Their affinities for PSs and effects on NCP assembly were determined in vitro by Surface Plasmon Resonance. High-affinity ligand binding is dependent on the presence of an -RGAG- motif within the loop of the PS, consistent with ligand cross-binding between PS sites. Simple structure-activity relationships show that it is also dependent on the presence of specific functional groups in these ligands. Some compounds are potent inhibitors of in vitro NCP assembly at nanomolar concentrations. Despite appropriate logP values, these ligands do not inhibit HBV replication in cell culture. However, modelling confirms the potential of using PS-binding ligands to target NCP assembly as a novel anti-viral strategy. This also allows for computational exploration of potential synergic effects between anti-viral ligands directed at distinct molecular targets in vivo. HBV PS-regulated assembly can be dysregulated by novel small molecule RNA-binding ligands opening a novel target for developing directly-acting anti-virals against this major pathogen.
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Affiliation(s)
- Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. https://twitter.com/FBSResearch
| | - Fardokht Abulwerdi
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, YO10 5DD, UK; York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stuart Le Grice
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - John S Schneekloth
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - Reidun Twarock
- Department of Mathematics, University of York, York, YO10 5DD, UK; York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK; Department of Biology, University of York, York, YO10 5DD, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. https://twitter.com/AstburyCentre
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14
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Starr CA, Barnes LF, Jarrold MF, Zlotnick A. Hysteresis in Hepatitis B Virus (HBV) Requires Assembly of Near-Perfect Capsids. Biochemistry 2022; 61:505-513. [PMID: 35258283 PMCID: PMC9443786 DOI: 10.1021/acs.biochem.1c00810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hepatitis B virus (HBV) must release its contents to initiate infection, making capsid disassembly critical to the viral life cycle. Capsid assembly proceeds through a cascade of weak interactions between copies of capsid protein (Cp) to yield uniform particles. However, there is a hysteresis to capsid dissociation that allows capsids to persist under conditions where they could not assemble. In this study, we have sought to define the basis of hysteresis by examining urea-induced dissociation of in vitro-assembled HBV capsids. In general, capsid samples show a mixture of two pools, differentiated by stability. Labile capsid dissociation corresponds to an ∼5 μM pseudocritical concentration of assembly (pcc), the same as that observed in assembly reactions. Dissociation of the stable pool corresponds to a subfemtomolar pcc, indicative of hysteresis. The fraction of stable capsids in an assembly reaction increases with the integrity of the Cp preparation and when association is performed at a higher ionic strength, which modifies the Cp conformation. Labile complexes are more prevalent when assembly conditions yield many kinetically trapped (incomplete and overgrown) products. Cp isolated from stable capsids reassembles into a mixture of stable and labile capsids. These results suggest that hysteresis arises from an ideal capsid lattice, even when some of the substituents in that lattice have defects. Consistent with structural studies that show a subtle difference between Cp dimers and Cp in capsid, we propose that hysteresis arises when HBV capsids undergo a lattice-dependent structural transition.
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Affiliation(s)
- Caleb A. Starr
- – Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| | - Lauren F. Barnes
- – Chemistry Department, Indiana University, Bloomington, IN 47405
| | | | - Adam Zlotnick
- – Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
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15
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Pavlova A, Bassit L, Cox BD, Korablyov M, Chipot C, Patel D, Lynch DL, Amblard F, Schinazi RF, Gumbart JC. The Mechanism of Action of Hepatitis B Virus Capsid Assembly Modulators Can Be Predicted from Binding to Early Assembly Intermediates. J Med Chem 2022; 65:4854-4864. [PMID: 35290049 PMCID: PMC9026740 DOI: 10.1021/acs.jmedchem.1c02040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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 noncapsid-like particles, thereby inhibiting the HBV replication cycle. Here, we have assessed the structures of early nucleocapsid assembly intermediates, bound with and without 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. Specifically, the assembly intermediates with bound misdirecting CAMs appear to be flattened relative to those with bound accelerators. Finally, the potency of CAMs within the same class was studied. We find that an increased number of contacts with the capsid protein and favorable binding energies inferred from free energy perturbation calculations are indicative of increased potency.
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Affiliation(s)
- Anna Pavlova
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Bryan D Cox
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Maksym Korablyov
- MIT Media Lab, Massachusetts Institute of Technology, Boston, Massachusetts 02139, United States
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Laboratoire international associé CNRS-UIUC, UMR 7019, Université de Lorraine, B.P. 70239, 54506 Vandæuvre-lès-Nancy, France
| | - Dharmeshkumar Patel
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Diane L Lynch
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - James C Gumbart
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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16
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Targeting the Virus Capsid as a Tool to Fight RNA Viruses. Viruses 2022; 14:v14020174. [PMID: 35215767 PMCID: PMC8879806 DOI: 10.3390/v14020174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/10/2022] Open
Abstract
Several strategies have been developed to fight viral infections, not only in humans but also in animals and plants. Some of them are based on the development of efficient vaccines, to target the virus by developed antibodies, others focus on finding antiviral compounds with activities that inhibit selected virus replication steps. Currently, there is an increasing number of antiviral drugs on the market; however, some have unpleasant side effects, are toxic to cells, or the viruses quickly develop resistance to them. As the current situation shows, the combination of multiple antiviral strategies or the combination of the use of various compounds within one strategy is very important. The most desirable are combinations of drugs that inhibit different steps in the virus life cycle. This is an important issue especially for RNA viruses, which replicate their genomes using error-prone RNA polymerases and rapidly develop mutants resistant to applied antiviral compounds. Here, we focus on compounds targeting viral structural capsid proteins, thereby inhibiting virus assembly or disassembly, virus binding to cellular receptors, or acting by inhibiting other virus replication mechanisms. This review is an update of existing papers on a similar topic, by focusing on the most recent advances in the rapidly evolving research of compounds targeting capsid proteins of RNA viruses.
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17
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Buzón P, Maity S, Christodoulis P, Wiertsema MJ, Dunkelbarger S, Kim C, Wuite GJ, Zlotnick A, Roos WH. Virus self-assembly proceeds through contact-rich energy minima. SCIENCE ADVANCES 2021; 7:eabg0811. [PMID: 34730996 PMCID: PMC8565845 DOI: 10.1126/sciadv.abg0811] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembly of supramolecular complexes such as viral capsids occurs prominently in nature. Nonetheless, the mechanisms underlying these processes remain poorly understood. Here, we uncover the assembly pathway of hepatitis B virus (HBV), applying fluorescence optical tweezers and high-speed atomic force microscopy. This allows tracking the assembly process in real time with single-molecule resolution. Our results identify a specific, contact-rich pentameric arrangement of HBV capsid proteins as a key on-path assembly intermediate and reveal the energy balance of the self-assembly process. Real-time nucleic acid packaging experiments show that a free energy change of ~1.4 kBT per condensed nucleotide is used to drive protein oligomerization. The finding that HBV assembly occurs via contact-rich energy minima has implications for our understanding of the assembly of HBV and other viruses and also for the development of new antiviral strategies and the rational design of self-assembling nanomaterials.
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Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | | | - Monique J. Wiertsema
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Steven Dunkelbarger
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Christine Kim
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Gijs J.L. Wuite
- Physics of Living Systems, Vrije Universiteit, Amsterdam, Netherlands
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
- Corresponding author.
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18
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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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19
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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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20
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Structural and Functional Characterizations of Cancer Targeting Nanoparticles Based on Hepatitis B Virus Capsid. Int J Mol Sci 2021; 22:ijms22179140. [PMID: 34502049 PMCID: PMC8430771 DOI: 10.3390/ijms22179140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 11/16/2022] Open
Abstract
Cancer targeting nanoparticles have been extensively studied, but stable and applicable agents have yet to be developed. Here, we report stable nanoparticles based on hepatitis B core antigen (HBcAg) for cancer therapy. HBcAg monomers assemble into spherical capsids of 180 or 240 subunits. HBcAg was engineered to present an affibody for binding to human epidermal growth factor receptor 1 (EGFR) and to present histidine and tyrosine tags for binding to gold ions. The HBcAg engineered to present affibody and tags (HAF) bound specifically to EGFR and exterminated the EGFR-overexpressing adenocarcinomas under alternating magnetic field (AMF) after binding with gold ions. Using cryogenic electron microscopy (cryo-EM), we obtained the molecular structures of recombinant HAF and found that the overall structure of HAF was the same as that of HBcAg, except with the affibody on the spike. Therefore, HAF is viable for cancer therapy with the advantage of maintaining a stable capsid form. If the affibody in HAF is replaced with a specific sequence to bind to another targetable disease protein, the nanoparticles can be used for drug development over a wide spectrum.
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21
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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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22
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Pérez-Segura C, Goh BC, Hadden-Perilla JA. All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery. Viruses 2021; 13:564. [PMID: 33810481 PMCID: PMC8065791 DOI: 10.3390/v13040564] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
The hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important antiviral paradigm based on disrupting the timing of genome packaging. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that the compound increases spike flexibility and improves recovery of helical secondary structure in the spike tips. Regions of the capsid-incorporated dimer that undergo correlated motion correspond to established sub-domains that pivot around the central chassis. AT130 alters patterns of correlated motion and other essential dynamics. A new conformational state of the dimer is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these sub-domains. Altogether, results describe a dynamical connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire core protein dimer.
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Affiliation(s)
- Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA;
| | - Boon Chong Goh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-Massachusetts Institute of Technology Alliance for Research and Technology Centre, Singapore 138602, Singapore;
| | - Jodi A. Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA;
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23
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Asymmetrizing an icosahedral virus capsid by hierarchical assembly of subunits with designed asymmetry. Nat Commun 2021; 12:589. [PMID: 33500404 PMCID: PMC7838286 DOI: 10.1038/s41467-020-20862-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/07/2020] [Indexed: 11/08/2022] Open
Abstract
Symmetrical protein complexes are ubiquitous in biology. Many have been re-engineered for chemical and medical applications. Viral capsids and their assembly are frequent platforms for these investigations. A means to create asymmetric capsids may expand applications. Here, starting with homodimeric Hepatitis B Virus capsid protein, we develop a heterodimer, design a hierarchical assembly pathway, and produce asymmetric capsids. In the heterodimer, the two halves have different growth potentials and assemble into hexamers. These preformed hexamers can nucleate co-assembly with other dimers, leading to Janus-like capsids with a small discrete hexamer patch. We can remove the patch specifically and observe asymmetric holey capsids by cryo-EM reconstruction. The resulting hole in the surface can be refilled with fluorescently labeled dimers to regenerate an intact capsid. In this study, we show how an asymmetric subunit can be used to generate an asymmetric particle, creating the potential for a capsid with different surface chemistries.
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24
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Zhao Z, Wang JCY, Segura CP, Hadden-Perilla JA, Zlotnick A. The Integrity of the Intradimer Interface of the Hepatitis B Virus Capsid Protein Dimer Regulates Capsid Self-Assembly. ACS Chem Biol 2020; 15:3124-3132. [PMID: 32459465 DOI: 10.1021/acschembio.0c00277] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
During the hepatitis B virus lifecycle, 120 copies of homodimeric capsid protein assemble around a copy of reverse transcriptase and viral RNA and go on to produce an infectious virion. Assembly needs to be tightly regulated by protein conformational change to ensure symmetry, fidelity, and reproducibility. Here, we show that structures at the intradimer interface regulate conformational changes at the distal interdimer interface and so regulate assembly. A pair of interacting charged residues, D78 from each monomer, conspicuously located at the top of a four-helix bundle that forms the intradimer interface, were mutated to serine to disrupt communication between the two monomers. The mutation slowed assembly and destabilized the dimer to thermal and chemical denaturation. Mutant dimers showed evidence of transient partial unfolding based on the appearance of new proteolytically sensitive sites. Though the mutant dimer was less stable, the resulting capsids were as stable as the wildtype, based on assembly and thermal denaturation studies. Cryo-EM image reconstructions of capsid indicated that the subunits adopted an "open" state more usually associated with a free dimer and that the spike tips were either disordered or highly flexible. Molecular dynamics simulations provide mechanistic explanations for these results, suggesting that D78 stabilizes helix 4a, which forms part of the intradimer interface, by capping its N-terminus and hydrogen-bonding to nearby residues, whereas the D78S mutation disrupts these interactions, leading to partial unwinding of helix 4a. This in turn weakens the connection from helix 4 and the intradimer interface to helix 5, which forms the interdimer interface.
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Affiliation(s)
- Zhongchao Zhao
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Joseph Che-Yen Wang
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
- Indiana University Electron Microscopy Center, Indiana University, Bloomington, Indiana 47405, United States
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Carolina Pérez Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jodi A. Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
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25
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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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26
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Patterson A, Zhao Z, Waymire E, Zlotnick A, Bothner B. Dynamics of Hepatitis B Virus Capsid Protein Dimer Regulate Assembly through an Allosteric Network. ACS Chem Biol 2020; 15:2273-2280. [PMID: 32662972 DOI: 10.1021/acschembio.0c00481] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
While there is an effective vaccine for Human Hepatitis B Virus (HBV), 257 million people have chronic infections for which there is no cure. The assembly process for the viral capsid is a potential therapeutic target. In order to understand the capsid assembly process, we investigated the dimeric building blocks of the capsid. To understand what blocks assembly, we took advantage of an assembly incompetent mutant dimer, Cp149-Y132A, located in the interdimer interface. This mutation leads to changes in protein dynamics throughout the structure of the dimer as measured by hydrogen-deuterium exchange mass spectrometry (HDX-MS). To further understand how the HBV capsid assembles, the homologue woodchuck HBV (WHV) capsid protein dimer (Cp) was used. WHV is more stable than HBV in HDX-MS and native mass spectrometry experiments. Because the WHV Cp assembles more rapidly into viral capsids than HBV, it was suspected that an increase in stability of the intradimer interface and/or in the contact region leads to increased assembly rates. The differences in dynamics when comparing HBV and human Cp149-Y132A as well as the differences in dynamics when comparing the HBV and WHV Cps allowed us to map an allosteric network within the HBV dimer. Through a careful comparison of structure, stability, and dynamics using four different capsid protein dimers, we conclude that protein subunit dynamics regulate HBV capsid assembly.
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Affiliation(s)
- Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Zhongchao Zhao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Elizabeth Waymire
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Viswanathan U, Mani N, Hu Z, Ban H, Du Y, Hu J, Chang J, Guo JT. Targeting the multifunctional HBV core protein as a potential cure for chronic hepatitis B. Antiviral Res 2020; 182:104917. [PMID: 32818519 DOI: 10.1016/j.antiviral.2020.104917] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 12/14/2022]
Abstract
The core (capsid) protein of hepatitis B virus (HBV) is the building block of nucleocapsids where viral DNA reverse transcriptional replication takes place and mediates virus-host cell interaction important for the persistence of HBV infection. The pleiotropic role of core protein (Cp) in HBV replication makes it an attractive target for antiviral therapies of chronic hepatitis B, a disease that affects more than 257 million people worldwide without a cure. Recent clinical studies indicate that core protein allosteric modulators (CpAMs) have a great promise as a key component of hepatitis B curative therapies. Particularly, it has been demonstrated that modulation of Cp dimer-dimer interactions by several chemical series of CpAMs not only inhibit nucleocapsid assembly and viral DNA replication, but also induce the disassembly of double-stranded DNA-containing nucleocapsids to prevent the synthesis of cccDNA. Moreover, the different chemotypes of CpAMs modulate Cp assembly by interaction with distinct amino acid residues at the HAP pocket between Cp dimer-dimer interfaces, which results in the assembly of Cp dimers into either non-capsid Cp polymers (type I CpAMs) or empty capsids with distinct physical property (type II CpAMs). The different CpAMs also differentially modulate Cp metabolism and subcellular distribution, which may impact cccDNA metabolism and host antiviral immune responses, the critical factors for the cure of chronic HBV infection. This review article highlights the recent research progress on the structure and function of core protein in HBV replication cycle, the mode of action of CpAMs, as well as the current status and perspectives on the discovery and development of core protein-targeting antivirals. This article forms part of a symposium in Antiviral Research on "Wide-ranging immune and direct-acting antiviral approaches to curing HBV and HDV infections."
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Affiliation(s)
- Usha Viswanathan
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Nagraj Mani
- Arbutus Biopharma Inc., 701 Veterans Circle, Warminster, PA, 18974, USA
| | - Zhanying Hu
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Haiqun Ban
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Yanming Du
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Jin Hu
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Jinhong Chang
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA.
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Schlicksup CJ, Zlotnick A. Viral structural proteins as targets for antivirals. Curr Opin Virol 2020; 45:43-50. [PMID: 32777753 DOI: 10.1016/j.coviro.2020.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 12/29/2022]
Abstract
Viral structural proteins are emerging as effective targets for new antivirals. In a viral lifecycle, the capsid must assemble, disassemble, and respond to host proteins, all at the right time and place. These reactions work within a narrow range of conditions, making them susceptible to small molecule interference. In at least three specific viruses, this approach has had met with preliminary success. In rhinovirus and poliovirus, compounds like pleconaril bind capsid and block RNA release. Bevirimat binds to Gag protein in HIV, inhibiting maturation. In Hepatitis B virus, core protein allosteric modulators (CpAMs) promote spontaneous assembly of capsid protein leading to empty and aberrant particles. Despite the biological diversity between viruses and the chemical diversity between antiviral molecules, we observe common features in these antivirals' mechanisms of action. These approaches work by stabilizing protein-protein interactions.
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Affiliation(s)
- Christopher John Schlicksup
- Molecular and Cellular Biology Department, Indiana University-Bloomington, Bloomington, IN 47401, United States
| | - Adam Zlotnick
- Molecular and Cellular Biology Department, Indiana University-Bloomington, Bloomington, IN 47401, United States.
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29
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Asor R, Schlicksup CJ, Zhao Z, Zlotnick A, Raviv U. Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly. J Am Chem Soc 2020; 142:7868-7882. [PMID: 32233479 PMCID: PMC7242811 DOI: 10.1021/jacs.0c01092] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There are ∼1030 possible intermediates on the assembly path from hepatitis B capsid protein dimers to the 120-dimer capsid. If every intermediate was tested, assembly would often get stuck in an entropic trap and essentially every capsid would follow a unique assembly path. Yet, capsids assemble rapidly with minimal trapped intermediates, a realization of the Levinthal paradox. To understand the fundamental mechanisms of capsid assembly, it is critical to resolve the early stages of the reaction. We have used time-resolved small angle X-ray scattering, which is sensitive to solute size and shape and has millisecond temporal resolution. Scattering curves were fit to a thermodynamically curated library of assembly intermediates, using the principle of maximum entropy. Maximum entropy also provides a physical rationale for the selection of species. We found that the capsid assembly pathway was exquisitely sensitive to initial assembly conditions. With the mildest conditions tested, the reaction appeared to be two-state from dimer to 120-dimer capsid with some dimers-of-dimers and trimers-of-dimers. In slightly more aggressive conditions, we observed transient accumulation of a decamer-of-dimers and the appearance of 90-dimer capsids. In conditions where there is measurable kinetic trapping, we found that highly diverse early intermediates accumulated within a fraction of a second and propagated into long-lived kinetically trapped states (≥90-mer). In all cases, intermediates between 35 and 90 subunits did not accumulate. These results are consistent with the presence of low barrier paths that connect early and late intermediates and direct the ultimate assembly path to late intermediates where assembly can be paused.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Christopher John Schlicksup
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Zhongchao Zhao
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Uri Raviv
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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Expression of quasi-equivalence and capsid dimorphism in the Hepadnaviridae. PLoS Comput Biol 2020; 16:e1007782. [PMID: 32310951 PMCID: PMC7192502 DOI: 10.1371/journal.pcbi.1007782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 04/30/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV) is a leading cause of liver disease. The capsid is an essential component of the virion and it is therefore of interest how it assembles and disassembles. The capsid protein is unusual both for its rare fold and that it polymerizes according to two different icosahedral symmetries, causing the polypeptide chain to exist in seven quasi-equivalent environments: A, B, and C in AB and CC dimers in T = 3 capsids, and A, B, C, and D in AB and CD dimers in T = 4 capsids. We have compared the two capsids by cryo-EM at 3.5 Å resolution. To ensure a valid comparison, the two capsids were prepared and imaged under identical conditions. We find that the chains have different conformations and potential energies, with the T = 3 C chain having the lowest. Three of the four quasi-equivalent dimers are asymmetric with respect to conformation and potential energy; however, the T = 3 CC dimer is symmetrical and has the lowest potential energy although its intra-dimer interface has the least free energy of formation. Of all the inter-dimer interfaces, the CB interface has the least area and free energy, in both capsids. From the calculated energies of higher-order groupings of dimers discernible in the lattices we predict early assembly intermediates, and indeed we observe such structures by negative stain EM of in vitro assembly reactions. By sequence analysis and computational alanine scanning we identify key residues and motifs involved in capsid assembly. Our results explain several previously reported observations on capsid assembly, disassembly, and dimorphism. Hepatitis B virus has infected approximately one third of the human population and causes almost 1 million deaths from liver disease annually. The capsid is a defining feature of a virus, distinct from host components, and therefore a target for intervention. Unusually for a virus, Hepatitis B assembles two capsids, with different geometries, from the same dimeric protein. Geometric principles dictate that the subunits in this system occupy seven different environments. From comparing the two capsids by cryo-electron microscopy at high resolution under the exact same conditions we find that the polypeptide chains adopt seven different conformations. We use these structures to calculate potential energies (analogous to elastic deformation or strain) for the individual chains, dimers, and several higher-order groupings discernible in the two lattices. We also calculate the binding energies between chains. We find that some groupings have substantially lower energy and are therefore potentially more stable, allowing us to predict likely intermediates on the two assembly pathways. We also observe such intermediates by electron microscopy of in vitro capsid assembly reactions. This is the first structural characterization of the early assembly intermediates of this important human pathogen.
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Liu H, Okazaki S, Shinoda W. Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein. J Chem Inf Model 2019; 59:5104-5110. [DOI: 10.1021/acs.jcim.9b01010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Huihui Liu
- Department of Materials Chemistry, Nagoya University, Furo-cho Chikusa-ku, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho Chikusa-ku, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho Chikusa-ku, Nagoya 464-8603, Japan
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Dharmavaram S, She SB, Lázaro G, Hagan MF, Bruinsma R. Gaussian curvature and the budding kinetics of enveloped viruses. PLoS Comput Biol 2019; 15:e1006602. [PMID: 31433804 PMCID: PMC6736314 DOI: 10.1371/journal.pcbi.1006602] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 09/10/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
The formation of a membrane-enveloped virus starts with the assembly of a curved layer of capsid proteins lining the interior of the plasma membrane (PM) of the host cell. This layer develops into a spherical shell (capsid) enveloped by a lipid-rich membrane. In many cases, the budding process stalls prior to the release of the virus. Recently, Brownian dynamics simulations of a coarse-grained model system reproduced protracted pausing and stalling, which suggests that the origin of pausing/stalling is to be found in the physics of the budding process. Here, we propose that the pausing/stalling observed in the simulations can be understood as a purely kinetic phenomenon associated with the neck geometry. A geometrical potential energy barrier develops during the budding that must be overcome by capsid proteins diffusing along the membrane prior to incorporation into the capsid. The barrier is generated by a conflict between the positive Gauss curvature of the assembling capsid and the negative Gauss curvature of the neck region. A continuum theory description is proposed and is compared with the Brownian simulations of the budding of enveloped viruses. Despite intense study, the life-cycle of the HIV-1 virus continues to pose mysteries. One of these is the fact that the assembly of an HIV-1 virus along the plasma membrane (PM) of the host cell—the budding process—stalls prior to release of the virus. Many other important viral pathogens with a surrounding lipid membrane envelope display similar stalling. Combining numerical and analytical methods, we demonstrate that the neck-like shape of the membrane that forms prior to release of the virus creates a barrier that blocks the proteins required for the assembly process from reaching the budding virus. An improved understanding of the physics of the blocking process could enable new strategies to combat enveloped viruses.
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Affiliation(s)
- Sanjay Dharmavaram
- Department of Mathematics, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Selene Baochen She
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Guillermo Lázaro
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael Francis Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Asor R, Selzer L, Schlicksup CJ, Zhao Z, Zlotnick A, Raviv U. Assembly Reactions of Hepatitis B Capsid Protein into Capsid Nanoparticles Follow a Narrow Path through a Complex Reaction Landscape. ACS NANO 2019; 13:7610-7626. [PMID: 31173689 PMCID: PMC7243059 DOI: 10.1021/acsnano.9b00648] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
For many viruses, capsids (biological nanoparticles) assemble to protect genetic material and dissociate to release their cargo. To understand these contradictory properties, we analyzed capsid assembly for hepatitis B virus; an endemic pathogen with an icosahedral, 120-homodimer capsid. We used solution X-ray scattering to examine trapped and equilibrated assembly reactions. To fit experimental results, we generated a library of distinct intermediates, selected by umbrella sampling of Monte Carlo simulations. The number of possible capsid intermediates is immense, ∼1030, yet assembly reactions are rapid and completed with high fidelity. If the huge number of possible intermediates were actually present, maximum entropy analysis shows that assembly reactions would be blocked by an entropic barrier, resulting in incomplete nanoparticles. When an energetic term was applied to select the stable species that dominated the reaction mixture, we found only a few hundred intermediates, mapping out a narrow path through the immense reaction landscape. This is a solution to a viral application of the Levinthal paradox. With the correct energetic term, the match between predicted intermediates and scattering data was striking. The grand canonical free energy landscape for assembly, calibrated by our experimental results, supports a detailed analysis of this complex reaction. There is a narrow range of energies that supports on-path assembly. If association energy is too weak or too strong, progressively more intermediates will be entropically blocked, spilling into paths leading to dissociation or trapped incomplete nanoparticles, respectively. These results are relevant to many viruses and provide a basis for simplifying assembly models and identifying new targets for antiviral intervention. They provide a basis for understanding and designing biological and abiological self-assembly reactions.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401 , Israel
| | - Lisa Selzer
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
- Department of Genetics , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Christopher John Schlicksup
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Zhongchao Zhao
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Uri Raviv
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401 , Israel
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Structural Differences between the Woodchuck Hepatitis Virus Core Protein in the Dimer and Capsid States Are Consistent with Entropic and Conformational Regulation of Assembly. J Virol 2019; 93:JVI.00141-19. [PMID: 31043524 DOI: 10.1128/jvi.00141-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022] Open
Abstract
Hepadnaviruses are hepatotropic enveloped DNA viruses with an icosahedral capsid. Hepatitis B virus (HBV) causes chronic infection in an estimated 240 million people; woodchuck hepatitis virus (WHV), an HBV homologue, has been an important model system for drug development. The dimeric capsid protein (Cp) has multiple functions during the viral life cycle and thus has become an important target for a new generation of antivirals. Purified HBV and WHV Cp spontaneously assemble into 120-dimer capsids. Though they have 65% identity, WHV Cp has error-prone assembly with stronger protein-protein association. We have taken advantage of the differences in assemblies to investigate the basis of assembly regulation. We determined the structures of the WHV capsid to 4.5-Å resolution by cryo-electron microscopy (cryo-EM) and of the WHV Cp dimer to 2.9-Å resolution by crystallography and examined the biophysical properties of the dimer. We found, in dimer, that the subdomain that makes protein-protein interactions is partially disordered and rotated 21° from its position in capsid. This subdomain is susceptible to proteolysis, consistent with local disorder. WHV assembly shows similar susceptibility to HBV antiviral molecules, suggesting that HBV assembly follows similar transitions. These data show that there is an entropic cost for assembly that is compensated for by the energetic gain of burying hydrophobic interprotein contacts. We propose a series of stages in assembly that incorporate a disorder-to-order transition and structural shifts. We suggest that a cascade of structural changes may be a common mechanism for regulating high-fidelity capsid assembly in HBV and other viruses.IMPORTANCE Virus capsids assemble spontaneously with surprisingly high fidelity. This requires strict geometry and a narrow range of association energies for these protein-protein interactions. It was hypothesized that requiring subunits to undergo a conformational change to become assembly active could regulate assembly by creating an energetic barrier and attenuating association. We found that woodchuck hepatitis virus capsid protein undergoes structural transitions between its dimeric and its 120-dimer capsid states. It is likely that the closely related hepatitis B virus capsid protein undergoes similar structural changes, which has implications for drug design. Regulation of assembly by structural transition may be a common mechanism for many viruses.
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35
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Yoshiya T, Tsuda S, Masuda S. Development of Trityl Group Anchored Solubilizing Tags for Peptide and Protein Synthesis. Chembiochem 2019; 20:1906-1913. [DOI: 10.1002/cbic.201900105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Taku Yoshiya
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
| | - Shugo Tsuda
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
| | - Shun Masuda
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
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Ciclopirox inhibits Hepatitis B Virus secretion by blocking capsid assembly. Nat Commun 2019; 10:2184. [PMID: 31097716 PMCID: PMC6522524 DOI: 10.1038/s41467-019-10200-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 04/25/2019] [Indexed: 12/13/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection can cause cirrhosis and hepatocellular carcinoma and is therefore a serious public health problem. Infected patients are currently treated with nucleoside/nucleotide analogs and interferon α, but this approach is not curative. Here, we screen 978 FDA-approved compounds for their ability to inhibit HBV replication in HBV-expressing HepG2.2.15 cells. We find that ciclopirox, a synthetic antifungal agent, strongly inhibits HBV replication in cells and in mice by blocking HBV capsid assembly. The crystal structure of the HBV core protein and ciclopirox complex reveals a unique binding mode at dimer-dimer interfaces. Ciclopirox synergizes with nucleoside/nucleotide analogs to prevent HBV replication in cells and in a humanized liver mouse model. Therefore, orally-administered ciclopirox may provide a novel opportunity to combat chronic HBV infection by blocking HBV capsid assembly.
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37
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Yang L, Liu F, Tong X, Hoffmann D, Zuo J, Lu M. Treatment of Chronic Hepatitis B Virus Infection Using Small Molecule Modulators of Nucleocapsid Assembly: Recent Advances and Perspectives. ACS Infect Dis 2019; 5:713-724. [PMID: 30896149 DOI: 10.1021/acsinfecdis.8b00337] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
On the basis of the recent advance of basic research on molecular biology of hepatitis B virus (HBV) infection, novel antiviral drugs targeting various steps of the HBV life cycle have been developed in recent years. HBV nucleocapsid assembly is now recognized as a hot target for anti-HBV drug development. Structural and functional analysis of HBV nucleocapsid allowed rational design and improvement of small molecules with the ability to interact with the components of HBV nucleocapsid and modulate the viral nucleocapsid assembly process. Prototypes of small molecule modulators targeting HBV nucleocapsid assembly are being preclinically tested or have moved forward in clinical trials, with promising results. This Review summarizes the recent advances in the approach to develop antiviral drugs based on the modulation of HBV nucleocapsid assembly. The antiviral mechanisms of small molecule modulators beyond the capsid formation and the potential implications will be discussed.
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Affiliation(s)
- Li Yang
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhangjiang Hi-Tech
Park, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Feifei Liu
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhangjiang Hi-Tech
Park, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xiankun Tong
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhangjiang Hi-Tech
Park, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Daniel Hoffmann
- Institute of Bioinformatics, University Duisburg Essen, Universitätsstraße 1, Essen 45117, Germany
| | - Jianping Zuo
- Laboratory of Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhangjiang Hi-Tech
Park, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mengji Lu
- Institute of Virology, University Hospital Essen, University Duisburg Essen, Hufelandstrasse 55, Essen 45122, Germany
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Zhang Y, Zhang H, Zhang J, Zhang J, Guo H. Naturally occurring core protein mutations compensate for the reduced replication fitness of a lamivudine-resistant HBV isolate. Antiviral Res 2019; 165:47-54. [PMID: 30902704 DOI: 10.1016/j.antiviral.2019.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/05/2019] [Accepted: 03/14/2019] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) replicates its DNA genome through reverse transcription of an RNA intermediate. The lack of proofreading capacity of the viral DNA polymerase results in a high mutation rate of HBV genome. Under the selective pressure created by the nucleos(t)ide analogue (NA) antiviral drugs, viruses with resistance mutations are selected. However, the replication fitness of NA-resistant mutants is markedly reduced compared to wild-type. Compensatory mutations in HBV polymerase, which restore the viral replication capacity, have been reported to arise under continuous treatment with lamivudine (LMV). We have previously identified a highly replicative LMV-resistant HBV isolate from a chronic hepatitis B patient experiencing acute disease exacerbation. Besides the common YMDD drug-resistant mutations, this isolate possesses multiple additional mutations in polymerase and core regions. The transcomplementation assay demonstrated that the enhanced viral replication is due to the mutations of core protein. Further mutagenesis study revealed that the P5T mutation of core protein plays an important role in the enhanced viral replication through increasing the levels of capsid formation and pregenomic RNA encapsidation. However, the LMV-resistant virus harboring compensatory core mutations remains sensitive to capsid assembly modulators (CpAMs). Taken together, our study suggests that the enhanced HBV nucleocapsid formation resulting from core mutations represents an important viral strategy to surmount the antiviral drug pressure and contribute to viral pathogenesis, and CpAMs hold promise for developing the combinational antiviral therapy for hepatitis B.
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Affiliation(s)
- Yongmei Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hu Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Junjie Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Medical Molecular Virology (MOH & MOE), Fudan University, Shanghai, China.
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA.
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39
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Lázaro GR, Mukhopadhyay S, Hagan MF. Why Enveloped Viruses Need Cores-The Contribution of a Nucleocapsid Core to Viral Budding. Biophys J 2019; 114:619-630. [PMID: 29414708 DOI: 10.1016/j.bpj.2017.11.3782] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/11/2017] [Accepted: 11/27/2017] [Indexed: 11/17/2022] Open
Abstract
During the lifecycle of many enveloped viruses, a nucleocapsid core buds through the cell membrane to acquire an outer envelope of lipid membrane and viral glycoproteins. However, the presence of a nucleocapsid core is not required for assembly of infectious particles. To determine the role of the nucleocapsid core, we develop a coarse-grained computational model with which we investigate budding dynamics as a function of glycoprotein and nucleocapsid interactions, as well as budding in the absence of a nucleocapsid. We find that there is a transition between glycoprotein-directed budding and nucleocapsid-directed budding that occurs above a threshold strength of nucleocapsid interactions. The simulations predict that glycoprotein-directed budding leads to significantly increased size polydispersity and particle polymorphism. This polydispersity can be explained by a theoretical model accounting for the competition between bending energy of the membrane and the glycoprotein shell. The simulations also show that the geometry of a budding particle leads to a barrier to subunit diffusion, which can result in a stalled, partially budded state. We present a phase diagram for this and other morphologies of budded particles. Comparison of these structures against experiments could establish bounds on whether budding is directed by glycoprotein or nucleocapsid interactions. Although our model is motivated by alphaviruses, we discuss implications of our results for other enveloped viruses.
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Affiliation(s)
- Guillermo R Lázaro
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts
| | | | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts.
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40
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Assembly Properties of Hepatitis B Virus Core Protein Mutants Correlate with Their Resistance to Assembly-Directed Antivirals. J Virol 2018; 92:JVI.01082-18. [PMID: 30089690 DOI: 10.1128/jvi.01082-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
The hepatitis B virus (HBV) capsid or core protein (Cp) can self-assemble to form an icosahedral capsid. It is now being pursued as a target for small-molecule antivirals that enhance the rate and extent of its assembly to yield empty and/or aberrant capsids. These small molecules are thus called core protein allosteric modulators (CpAMs). We sought to understand the physical basis of CpAM-resistant mutants and how CpAMs might overcome them. We examined the effects of two closely related CpAMs, HAP12 and HAP13, which differ by a single atom but have drastically different antiviral activities, on the assembly of wild-type Cp and three T109 mutants (T109M, T109I, and T109S) that display a range of resistances. The T109 side chain forms part of the mouth of the CpAM binding pocket. A T109 mutant that has substantial resistance even to a highly active CpAM strongly promotes normal assembly. Conversely, a mutant that weakens assembly is more susceptible to CpAMs. In crystal and cryo-electron microscopy (cryo-EM) structures of T=4 capsids with bound CpAMs, the CpAMs preferentially fit into two of four quasi-equivalent sites. In these static representations of capsid structures, T109 does not interact with the neighboring subunit. However, all-atom molecular dynamics simulations of an intact capsid show that T109 of one of the four classes of CpAM site has a hydrophobic contact with the neighboring subunit at least 40% of the time, providing a physical explanation for the mutation's ability to affect capsid stability, assembly, and sensitivity to CpAMs.IMPORTANCE The HBV core protein and its assembly into capsids have become important targets for development of core protein allosteric modulators (CpAMs) as antivirals. Naturally occurring T109 mutants have been shown to be resistant to some of these CpAMs. We found that mutation of T109 led to changes in capsid stability and recapitulated resistance to a weak CpAM, but much less so than to a strong CpAM. Examination of HBV capsid structures, determined by cryo-EM and crystallography, could not explain how T109 mutations change capsid stability and resistance. However, by mining data from a microsecond-long all-atom molecular dynamics simulation, we found that the capsid was extraordinarily flexible and that T109 can impede entry to the CpAM binding site. In short, HBV capsids are incredibly dynamic and molecular mobility must be considered in discussions of antiviral mechanisms.
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41
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Qazi SA, Schlicksup CJ, Rittichier J, VanNieuwenhze M, Zlotnick A. An Assembly-Activating Site in the Hepatitis B Virus Capsid Protein Can Also Trigger Disassembly. ACS Chem Biol 2018; 13:2114-2120. [PMID: 29920071 PMCID: PMC6407610 DOI: 10.1021/acschembio.8b00283] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Hepatitis B Virus (HBV) core protein homodimers self-assemble to form an icosahedral capsid that packages the viral genome. Disassembly occurs in the nuclear basket to release the mature genome to the nucleus. Small molecules have been developed that bind to a pocket at the interdimer interface to accelerate assembly and strengthen interactions between subunits; these are under development as antiviral agents. Here, we explore the role of the dimer-dimer interface by mutating sites in the drug-binding pocket to cysteine and examining the effect of covalently linking small molecules to them. We find that ligands bound to the pocket may trigger capsid disassembly in a dose-dependent manner. This result indicates that, at least transiently, the pocket adopts a destabilizing conformation. We speculate that this pocket also plays a role in virus disassembly and genome release by binding ligands that are incompatible with virus stability, "unwanted guests." Investigating protein-protein interactions, especially large protein polymers, offers new and unique challenges. By using an engineered addressable thiol, we provide a means to examine the effects of modifying an interface without requiring drug-like properties for the ligand.
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Affiliation(s)
- Shefah A. Qazi
- Department of Molecular and Cellular Biochemistry, Indiana
University, Bloomington, Indiana, 47405, USA
- Department of Chemistry, Indiana University, Bloomington,
Indiana, 47405, USA
| | - Christopher J. Schlicksup
- Department of Molecular and Cellular Biochemistry, Indiana
University, Bloomington, Indiana, 47405, USA
| | - Jonathan Rittichier
- Department of Chemistry, Indiana University, Bloomington,
Indiana, 47405, USA
| | | | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana
University, Bloomington, Indiana, 47405, USA
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42
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Eren E, Watts NR, Dearborn AD, Palmer IW, Kaufman JD, Steven AC, Wingfield PT. Structures of Hepatitis B Virus Core- and e-Antigen Immune Complexes Suggest Multi-point Inhibition. Structure 2018; 26:1314-1326.e4. [PMID: 30100358 DOI: 10.1016/j.str.2018.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/13/2018] [Accepted: 06/29/2018] [Indexed: 12/22/2022]
Abstract
Hepatitis B virus (HBV) is the leading cause of liver disease worldwide. While an adequate vaccine is available, current treatment options are limited, not highly effective, and associated with adverse effects, encouraging the development of alternative therapeutics. The HBV core gene encodes two different proteins: core, which forms the viral nucleocapsid, and pre-core, which serves as an immune modulator with multiple points of action. The two proteins mostly have the same sequence, although they differ at their N and C termini and in their dimeric arrangements. Previously, we engineered two human-framework antibody fragments (Fab/scFv) with nano- to picomolar affinities for both proteins. Here, by means of X-ray crystallography, analytical ultracentrifugation, and electron microscopy, we demonstrate that the antibodies have non-overlapping epitopes and effectively block biologically important assemblies of both proteins. These properties, together with the anticipated high tolerability and long half-lives of the antibodies, make them promising therapeutics.
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Affiliation(s)
- Elif Eren
- Laboratory of Structural Biology Research, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Norman R Watts
- Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Altaira D Dearborn
- Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira W Palmer
- Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua D Kaufman
- Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul T Wingfield
- Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Tokmina-Lukaszewska M, Patterson A, Berry L, Scott L, Balasubramanian N, Bothner B. The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes. Front Microbiol 2018; 9:1397. [PMID: 30026733 PMCID: PMC6041385 DOI: 10.3389/fmicb.2018.01397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/07/2018] [Indexed: 12/01/2022] Open
Abstract
For decades, biologists and biochemists have taken advantage of atomic resolution structural models of proteins from X-ray crystallography, nuclear magnetic resonance spectroscopy, and more recently cryo-electron microscopy. However, not all proteins relent to structural analyses using these approaches, and as the depth of knowledge increases, additional data elucidating a mechanistic understanding of protein function is desired. Flavin-based electron bifurcating enzymes, which are responsible for producing high energy compounds through the simultaneous endergonic and exergonic reduction of two intercellular electron carriers (i.e., NAD+ and ferredoxin) are one class of proteins that have challenged structural biologists and in which there is great interest to understand the mechanism behind electron gating. A limited number of X-ray crystallography projects have been successful; however, it is clear that to understand how these enzymes function, techniques that can reveal detailed in solution information about protein structure, dynamics, and interactions involved in the bifurcating reaction are needed. In this review, we cover a general set of mass spectrometry-based techniques that, combined with protein modeling, are capable of providing information on both protein structure and dynamics. Techniques discussed include surface labeling, covalent cross-linking, native mass spectrometry, and hydrogen/deuterium exchange. We cover how biophysical data can be used to validate computationally generated protein models and develop mechanistic explanations for regulation and performance of enzymes and protein complexes. Our focus will be on flavin-based electron bifurcating enzymes, but the broad applicability of the techniques will be showcased.
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Affiliation(s)
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Liam Scott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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44
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Brunk NE, Lee LS, Glazier JA, Butske W, Zlotnick A. Molecular jenga: the percolation phase transition (collapse) in virus capsids. Phys Biol 2018; 15:056005. [PMID: 29714713 PMCID: PMC6004236 DOI: 10.1088/1478-3975/aac194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Virus capsids are polymeric protein shells that protect the viral cargo. About half of known virus families have icosahedral capsids that self-assemble from tens to thousands of subunits. Capsid disassembly is critical to the lifecycles of many viruses yet is poorly understood. Here, we apply a graph and percolation theory to examine the effect of removing capsid subunits on capsid stability and fragmentation. Based on the structure of the icosahedral capsid of hepatitis B virus (HBV), we constructed a graph of rhombic subunits arranged with icosahedral symmetry. Though our approach neglects dependence on energetics, time, and molecular detail, it quantitatively predicts a percolation phase transition consistent with recent in vitro studies of HBV capsid dissociation. While the stability of the capsid graph followed a gradual quadratic decay, the rhombic tiling abruptly fragmented when we removed more than 25% of the 120 subunits, near the percolation threshold observed experimentally. This threshold may also affect results of capsid assembly, which also experimentally produces a preponderance of 90 mer intermediates, as the intermediate steps in these reactions are reversible and can thus resemble dissociation. Application of percolation theory to understanding capsid association and dissociation may prove a general approach to relating virus biology to the underlying biophysics of the virus particle.
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Affiliation(s)
- Nicholas E Brunk
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States of America. Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States of America
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45
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Single-step purification of recombinant hepatitis B core antigen Y132A dimer from clarified Escherichia coli feedstock using a packed bed anion exchange chromatography. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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46
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Hadden JA, Perilla JR, Schlicksup CJ, Venkatakrishnan B, Zlotnick A, Schulten K. All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits. eLife 2018; 7:32478. [PMID: 29708495 PMCID: PMC5927769 DOI: 10.7554/elife.32478] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
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.
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Affiliation(s)
- Jodi A Hadden
- Department of Chemistry and Biochemistry, University of Delaware, Newark, United States
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, United States
| | | | | | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, United States
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47
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Schlicksup CJ, Wang JCY, Francis S, Venkatakrishnan B, Turner WW, VanNieuwenhze M, Zlotnick A. Hepatitis B virus core protein allosteric modulators can distort and disrupt intact capsids. eLife 2018; 7:31473. [PMID: 29377794 PMCID: PMC5788503 DOI: 10.7554/elife.31473] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/22/2017] [Indexed: 12/23/2022] Open
Abstract
Defining mechanisms of direct-acting antivirals facilitates drug development and our understanding of virus function. Heteroaryldihydropyrimidines (HAPs) inappropriately activate assembly of hepatitis B virus (HBV) core protein (Cp), suppressing formation of virions. We examined a fluorophore-labeled HAP, HAP-TAMRA. HAP-TAMRA induced Cp assembly and also bound pre-assembled capsids. Kinetic and spectroscopic studies imply that HAP-binding sites are usually not available but are bound cooperatively. Using cryo-EM, we observed that HAP-TAMRA asymmetrically deformed capsids, creating a heterogeneous array of sharp angles, flat regions, and outright breaks. To achieve high resolution reconstruction (<4 Å), we introduced a disulfide crosslink that rescued particle symmetry. We deduced that HAP-TAMRA caused quasi-sixfold vertices to become flatter and fivefold more angular. This transition led to asymmetric faceting. That a disordered crosslink could rescue symmetry implies that capsids have tensegrity properties. Capsid distortion and disruption is a new mechanism by which molecules like the HAPs can block HBV infection. Viruses are simple structures formed of genetic information wrapped inside a shell. For the hepatitis B virus, this casing looks like a soccer ball. It is composed of 240 copies of the same protein, arranged in a pattern of pentagons and hexagons. These proteins form a protective shield for the virus’ genetic information: they also interact with the cells of the host during key events of the virus’ life cycle. When the hepatitis B virus infects a cell, it hijacks the cellular machinery to replicate. New shell proteins are produced and assemble within the cell. A type of potential antiviral drug called a CpAM disrupts this process: it causes the shell to assemble too early and inaccurately, which impairs the life cycle of the virus. However, a CpAM can bind to the shell even after it has already assembled. How this binding affects the virus is still unclear. Here, Schlicksup et al. attach a fluorescent molecule to a CpAM, and use a cutting-edge microscopy method to look at the structures at the atomic level. This makes it possible to examine in detail how the CpAM attaches to a correctly formed virus shell. Schlicksup et al. show that when the CpAM binds to the shell, it disrupts and sometimes even breaks the soccer-like pattern of the shell: the hexagons flatten, and the pentagons buckle. These misshaped shells could prevent the virus from interacting with the cellular structures necessary for infection or prevent it from releasing the virus’ genetic information. This is a new antiviral mechanism for a CpAM. By acting both before and after the shell has assembled, the CpAM targets the virus at different points of its life cycle. Hepatitis B affects over 240 million people worldwide. While a vaccine exists, there is still no cure for it. A better understanding of the physics of the virus’ shell and the mode of action of CpAMs could lead to better drugs against the disease.
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Affiliation(s)
| | - Joseph Che-Yen Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States.,Indiana University Electron Microscopy Center, Bloomington, United States
| | | | | | | | | | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
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48
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Tsuda S, Mochizuki M, Ishiba H, Yoshizawa-Kumagaye K, Nishio H, Oishi S, Yoshiya T. Easy-to-Attach/Detach Solubilizing-Tag-Aided Chemical Synthesis of an Aggregative Capsid Protein. Angew Chem Int Ed Engl 2018; 57:2105-2109. [DOI: 10.1002/anie.201711546] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/20/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
| | | | - Hiroyuki Ishiba
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Kumiko Yoshizawa-Kumagaye
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Hideki Nishio
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taku Yoshiya
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
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49
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Tsuda S, Mochizuki M, Ishiba H, Yoshizawa-Kumagaye K, Nishio H, Oishi S, Yoshiya T. Easy-to-Attach/Detach Solubilizing-Tag-Aided Chemical Synthesis of an Aggregative Capsid Protein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
| | | | - Hiroyuki Ishiba
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Kumiko Yoshizawa-Kumagaye
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Hideki Nishio
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taku Yoshiya
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
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50
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Rath SL, Liu H, Okazaki S, Shinoda W. Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals. J Chem Inf Model 2018; 58:328-337. [DOI: 10.1021/acs.jcim.7b00471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Soumya Lipsa Rath
- Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan
| | - Huihui Liu
- Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan
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