Broad-Spectrum Virus Trapping with Heparan Sulfate-Modified DNA Origami ShellsClick to copy article linkArticle link copied!
- Alba MonferrerAlba MonferrerLaboratory for Biomolecular Nanotechnology. Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, GermanyMunich Institute of Biomedical Engineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, GermanyMore by Alba Monferrer
- Jessica A. KretzmannJessica A. KretzmannLaboratory for Biomolecular Nanotechnology. Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, GermanyMunich Institute of Biomedical Engineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, GermanyMore by Jessica A. Kretzmann
- Christian SiglChristian SiglLaboratory for Biomolecular Nanotechnology. Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, GermanyMunich Institute of Biomedical Engineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, GermanyMore by Christian Sigl
- Pia SapelzaPia SapelzaLaboratory for Biomolecular Nanotechnology. Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, GermanyMunich Institute of Biomedical Engineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, GermanyMore by Pia Sapelza
- Anna LiedlAnna LiedlLaboratory for Biomolecular Nanotechnology. Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, GermanyMunich Institute of Biomedical Engineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, GermanyMore by Anna Liedl
- Barbara WittmannBarbara WittmannLaboratory for Biomolecular Nanotechnology. Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, GermanyMunich Institute of Biomedical Engineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, GermanyMore by Barbara Wittmann
- Hendrik Dietz*Hendrik Dietz*Email: [email protected]Laboratory for Biomolecular Nanotechnology. Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, GermanyMunich Institute of Biomedical Engineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, GermanyMore by Hendrik Dietz
Abstract
Effective broadband antiviral platforms that can act on existing viruses and viruses yet to emerge are not available, creating a need to explore treatment strategies beyond the trodden paths. Here, we report virus-encapsulating DNA origami shells that achieve broadband virus trapping properties by exploiting avidity and a widespread background affinity of viruses to heparan sulfate proteoglycans (HSPG). With a calibrated density of heparin and heparan sulfate (HS) derivatives crafted to the interior of DNA origami shells, we could encapsulate adeno, adeno-associated, chikungunya, dengue, human papilloma, noro, polio, rubella, and SARS-CoV-2 viruses or virus-like particles, in one and the same HS-functionalized shell system. Additional virus-type-specific binders were not needed for the trapping. Depending on the relative dimensions of shell to virus particles, multiple virus particles may be trapped per shell, and multiple shells can cover the surface of clusters of virus particles. The steric occlusion provided by the heparan sulfate-coated DNA origami shells can prevent viruses from further interactions with receptors, possibly including those found on cell surfaces.
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License Summary*
You are free to share(copy and redistribute) this article in any medium or format and to adapt(remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
Creative Commons (CC): This is a Creative Commons license.
Attribution (BY): Credit must be given to the creator.
*Disclaimer
This summary highlights only some of the key features and terms of the actual license. It is not a license and has no legal value. Carefully review the actual license before using these materials.
License Summary*
You are free to share(copy and redistribute) this article in any medium or format and to adapt(remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
Creative Commons (CC): This is a Creative Commons license.
Attribution (BY): Credit must be given to the creator.
*Disclaimer
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Figure 1
Figure 1. DNA origami shells and functionalization with HS derivatives. (A) A heparan sulfate proteoglycan (HSPG) interacts with a virus pathogen and mediates its cellular uptake (left). DNA origami shell schematic, with HS modifications in its interior, capable of binding and sequestering a viral particle (right). (B) SPAAC reaction in between azide-modified heparin and HS oligomers and a DBCO-modified DNA oligo. The DNA sequence is complementary to the handles of the DNA origami shells in (D, E). (C) PAGE characterization of the HS-modified DNA oligos. Products containing HS with sulfate and sulfonate groups (3a and 3c) migrate at a faster rate through the gel than the analog negative controls (3b and 3d) due to their increased anionic character. (D) Cylindrical models of O and T1 shells made of 4 and 10 triangle subunits respectively, containing single stranded protruding oligos (termed handles, shown in red) decorating their interior. Each triangle subunit contains nine handle positions. (E) T3 shell design consisting of 30 triangle subunits and featuring an inner cavity of 150 nm. Each triangle subunit also contains nine handle positions. (F) Negative stain TEM micrograph of T3 shells. Scale bar is 100 nm. (G) Schematic representation of three different handle designs. H1 contains one HS modification per handle placed as close to the origami surface as possible. H2 also contains one HS modification per handle but has a polyT extension of 20 bases, allowing the handle to reach further than H1. H3 mimics a branched polymer containing two HS modifications per handle unit, therefore doubling the local HS density.
Results and Discussion
Figure 2
Figure 2. Viruses and VLPs trapped within HS-modified O, T1 and T3 shells. Negative stain TEM images of (A) AAV2, polio 3, mature dengue 1 and norovirus GII.4 successfully trapped in O shells. (B) HPV 16, SARS-CoV-2, chikungunya, and rubella engulfed by T1 shells. (C) Adenovirus 5 captured with T3 shells. Scale bars are 100 nm.
virus/VLP | family | enveloped | major surface components | genome type | measured diameter (nm)c | ref |
---|---|---|---|---|---|---|
AAV2a | Parvoviridae | no | 3 capsid proteins | ssDNA | 25 | (29) |
polio type 3 | Picornaviridae | no | 4 capsid proteins | ssRNAb | 30 | (30) |
dengue type 1 | Flaviviridae | yes | 1 envelope protein | ssRNAb | 30–40 | (31) |
noro GII.4 | Caliciviridae | no | 1 capsid protein | ssRNAb | 30–45 | (32) |
HPV 16 | Papillomaviridae | no | 2 capsid proteins | dsDNAb | 35–50 | (33) |
SARS-CoV-2 | Coronaviridae | yes | 1 envelope protein, 1 spike protein | ssRNAb | 30–70 | (34) |
chikungunya | Togaviridae | yes | 2 envelope proteins | ssRNAb | 65–70 | (35) |
rubella | Matonaviridae | yes | 2 envelope proteins | ssRNAb | 65–80 | (36) |
adenovirus 5a | Adenoviridae | no | 3 capsid proteins | dsDNA | 90 | (37) |
Infectious virus.
Data referring to the infectious virus which is modeled by a VLP in this study.
Measured using negative stain TEM or cryo-EM images.
Figure 3
Figure 3. Multiple viruses and VLPs trapped in HS-modified O, T1, and T3 shells. Negative stain TEM images of (A) up to four AAV2 in one O shell, (B) up to three HPV 16 in one T1 shell, and (C) one HPV 16 coordinated by two O shells for complete occlusion of the virus particle. (D) Up to six AAV2 per T1 shell. (E) Up to three chikungunya VLPs per T3 shell. (F) Cooperative effect of multiple O shells capturing numerous AAV2 particles. Scale bar is 100 nm.
Figure 4
Figure 4. Cryo-EM analysis of virus-like particles trapped in DNA origami shells. (A) Cryo-EM micrograph of O shells binding to HPV 16 VLPs. (B) 2D class average images of one or two O shells binding to one HPV 16 particle, demonstrating different orientations of the complexes. The white arrows indicate the gap difference in between the two O shells, confirming the capture of differently sized VLP particles. (C) 3D reconstructions of HPV 16 bound to one and two O shells. (D) Cryo-EM micrograph of T1 shells binding to chikungunya VLPs. (E) 2D class average images of T1 shells binding to chikungunya particles showing different orientations of the complex. (F) Two different views of the 3D reconstruction of a T1 shell engulfing a chikungunya virus particle.
Conclusions
Methods
Folding of DNA Origami Triangular Subunits
Purification of Triangle Subunits and Shells Self-Assembly
Heparan Sulfate Attachment to DNA
Viruses and VLPs Encapsulation
In Vitro Virus-Blocking ELISA Assay
Maturation of Dengue VLPs
Negative Staining TEM
Cryo-EM
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsnano.1c11328.
Methods and additional data, including further characterization of HS derivatives, handle positions, viruses/VLPs, and binding conditions. All staple sequences for each triangular subunit/shell, in addition to assembly and folding conditions (PDF)
Terms & Conditions
Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.
Acknowledgments
This work has received funding from the European Union’s Horizon 2020 research and innovation programme within the FET Open project Virofight (Grant Agreement No. 899619, to H.D.). A.M. would like to acknowledge the Marie Skłodowska-Curie ITN on DNA Robotics (Grant Agreement No 7657039). This work was further supported by the Deutsche Forschungsgemeinschaft via the Gottfried-Wilhelm-Leibniz Program, and via Grant ID DI1500/5. J.A.K. would like to acknowledge the Alexander von Humboldt Foundation for a Humboldt Research Fellowship. We thank U. Protzer and R. Wagner for discussions.
References
This article references 37 other publications.
- 1Heida, R.; Bhide, Y. C.; Gasbarri, M.; Kocabiyik, Ö.; Stellacci, F.; Huckriede, A. L. W.; Hinrichs, W. L. J.; Frijlink, H. W. Advances in the Development of Entry Inhibitors for Sialic-Acid-Targeting Viruses. Drug Discovery Today 2021, 26 (1), 122– 137, DOI: 10.1016/j.drudis.2020.10.009Google Scholar1https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitlelurjJ&md5=f943f5a4f5978a97da9c47e122f02b5fAdvances in the development of entry inhibitors for sialic-acid-targeting virusesHeida, Rick; Bhide, Yoshita C.; Gasbarri, Matteo; Kocabiyik, Oezguen; Stellacci, Francesco; Huckriede, Anke L. W.; Hinrichs, Wouter L. J.; Frijlink, Henderik W.Drug Discovery Today (2021), 26 (1), 122-137CODEN: DDTOFS; ISSN:1359-6446. (Elsevier Ltd.)A review. Over the past decades, several antiviral drugs have been developed to treat a range of infections. Yet the no. of treatable viral infections is still limited, and resistance to current drug regimens is an ever-growing problem. Therefore, addnl. strategies are needed to provide a rapid cure for infected individuals. An interesting target for antiviral drugs is the process of viral attachment and entry into the cell. Although most viruses use distinct host receptors for attachment to the target cell, some viruses share receptors, of which sialic acids are a common example. This review aims to give an update on entry inhibitors for a range of sialic-acid-targeting viruses and provides insight into the prospects for those with broad-spectrum potential.
- 2Wang, L.; Zhou, T.; Zhang, Y.; Yang, E. S.; Schramm, C. A.; Shi, W.; Pegu, A.; Oloniniyi, O. K.; Henry, A. R.; Darko, S.; Narpala, S. R.; Hatcher, C.; Martinez, D. R.; Tsybovsky, Y.; Phung, E.; Abiona, O. M.; Antia, A.; Cale, E. M.; Chang, L. A.; Choe, M.; Corbett, K. S.; Davis, R. L.; DiPiazza, A. T.; Gordon, I. J.; Hait, S. H.; Hermanus, T.; Kgagudi, P.; Laboune, F.; Leung, K.; Liu, T.; Mason, R. D.; Nazzari, A. F.; Novik, L.; O’Connell, S.; O’Dell, S.; Olia, A. S.; Schmidt, S. D.; Stephens, T.; Stringham, C. D.; Talana, C. A.; Teng, I.-T.; Wagner, D. A.; Widge, A. T.; Zhang, B.; Roederer, M.; Ledgerwood, J. E.; Ruckwardt, T. J.; Gaudinski, M. R.; Moore, P. L.; Doria-Rose, N. A.; Baric, R. S.; Graham, B. S.; McDermott, A. B.; Douek, D. C.; Kwong, P. D.; Mascola, J. R.; Sullivan, N. J.; Misasi, J. Ultrapotent Antibodies against Diverse and Highly Transmissible SARS-CoV-2 Variants. Science 2021, 373 (6556), eabh1766, DOI: 10.1126/science.abh1766Google ScholarThere is no corresponding record for this reference.
- 3Taylor, P. C.; Adams, A. C.; Hufford, M. M.; de la Torre, I.; Winthrop, K.; Gottlieb, R. L. Neutralizing Monoclonal Antibodies for Treatment of COVID-19. Nat. Rev. Immunol 2021, 21 (6), 382– 393, DOI: 10.1038/s41577-021-00542-xGoogle Scholar3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXptFWit7c%253D&md5=fc5fae636d59e08a9049e3939ff1caeeNeutralizing monoclonal antibodies for treatment of COVID-19Taylor, Peter C.; Adams, Andrew C.; Hufford, Matthew M.; de la Torre, Inmaculada; Winthrop, Kevin; Gottlieb, Robert L.Nature Reviews Immunology (2021), 21 (6), 382-393CODEN: NRIABX; ISSN:1474-1733. (Nature Portfolio)A review. Several neutralizing monoclonal antibodies (mAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed and are now under evaluation in clin. trials. With the US Food and Drug Administration recently granting emergency use authorizations for neutralizing mAbs in non-hospitalized patients with mild-to-moderate COVID-19, there is an urgent need to discuss the broader potential of these novel therapies and to develop strategies to deploy them effectively in clin. practice, given limited initial availability. Here, we review the precedent for passive immunization and lessons learned from using antibody therapies for viral infections such as respiratory syncytial virus, Ebola virus and SARS-CoV infections. We then focus on the deployment of convalescent plasma and neutralizing mAbs for treatment of SARS-CoV-2. We review specific clin. questions, including the rationale for stratification of patients, potential biomarkers, known risk factors and temporal considerations for optimal clin. use. To answer these questions, there is a need to understand factors such as the kinetics of viral load and its correlation with clin. outcomes, endogenous antibody responses, pharmacokinetic properties of neutralizing mAbs and the potential benefit of combining antibodies to defend against emerging viral variants.
- 4Cagno, V.; Tseligka, E. D.; Jones, S. T.; Tapparel, C. Heparan Sulfate Proteoglycans and Viral Attachment: True Receptors or Adaptation Bias?. Viruses 2019, 11 (7), 596, DOI: 10.3390/v11070596Google Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXisVOgu7jO&md5=3cf85bf40431c53df1a530498ddabf4aHeparan sulfate proteoglycans and viral attachment: true receptors or adaptation bias?Cagno, Valeria; Tseligka, Eirini D.; Jones, Samuel T.; Tapparel, CarolineViruses (2019), 11 (7), 596CODEN: VIRUBR; ISSN:1999-4915. (MDPI AG)A review. Heparan sulfate proteoglycans (HSPG) are composed of unbranched, neg. charged heparan sulfate (HS) polysaccharides attached to a variety of cell surface or extracellular matrix proteins. Widely expressed, they mediate many biol. activities, including angiogenesis, blood coagulation, developmental processes, and cell homeostasis. HSPG are highly sulfated and broadly used by a range of pathogens, esp. viruses, to attach to the cell surface. In this review, we summarize the current knowledge on HSPG-virus interactions and distinguish viruses with established HS binding, viruses that bind HS only after intra-host or cell culture adaptation, and finally, viruses whose dependence on HS for infection is debated. We also provide an overview of the antiviral compds. designed to interfere with HS binding. Many questions remain about the true importance of these receptors in vivo, knowledge that is crit. for the design of future antiviral therapies.
- 5Zhang, Q.; Chen, C. Z.; Swaroop, M.; Xu, M.; Wang, L.; Lee, J.; Wang, A. Q.; Pradhan, M.; Hagen, N.; Chen, L.; Shen, M.; Luo, Z.; Xu, X.; Xu, Y.; Huang, W.; Zheng, W.; Ye, Y. Heparan Sulfate Assists SARS-CoV-2 in Cell Entry and Can Be Targeted by Approved Drugs in Vitro. Cell Discov 2020, 6 (1), 1– 14, DOI: 10.1038/s41421-020-00222-5Google ScholarThere is no corresponding record for this reference.
- 6Dreyfuss, J. L.; Regatieri, C. V.; Jarrouge, T. R.; Cavalheiro, R. P.; Sampaio, L. O.; Nader, H. B. Heparan Sulfate Proteoglycans: Structure, Protein Interactions and Cell Signaling. Anais da Academia Brasileira de Ciências 2009, 81 (3), 409– 429, DOI: 10.1590/S0001-37652009000300007Google Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtF2isb7F&md5=1b9832c5fb965eb63b4efaa202d60551Heparan sulfate proteoglycans: structure, protein interactions and cell signalingDreyfuss, Juliana L.; Regatieri, Caio V.; Jarrouge, Thais R.; Cavalheiro, Renan P.; Sampaio, Lucia O.; Nader, Helena B.Anais da Academia Brasileira de Ciencias (2009), 81 (3), 409-429CODEN: AABCAD; ISSN:0001-3765. (Academia Brasileira de Ciencias)A review. Heparan sulfate proteoglycans are ubiquitously found at the cell surface and extracellular matrix in all the animal species. This review will focus on the structural characteristics of the heparan sulfate proteoglycans related to protein interactions leading to cell signaling. The heparan sulfate chains due to their vast structural diversity are able to bind and interact with a wide variety of proteins, such as growth factors, chemokines, morphogens, extracellular matrix components, enzymes, among others. There is a specificity directing the interactions of heparan sulfates and target proteins, regarding both the fine structure of the polysaccharide chain as well precise protein motifs. Heparan sulfates play a role in cellular signaling either as receptor or co-receptor for different ligands, and the activation of downstream pathways is related to phosphorylation of different cytosolic proteins either directly or involving cytoskeleton interactions leading to gene regulation. The role of the heparan sulfate proteoglycans in cellular signaling and endocytic uptake pathways is also discussed.
- 7Tyssen, D.; Henderson, S. A.; Johnson, A.; Sterjovski, J.; Moore, K.; La, J.; Zanin, M.; Sonza, S.; Karellas, P.; Giannis, M. P.; Krippner, G.; Wesselingh, S.; McCarthy, T.; Gorry, P. R.; Ramsland, P. A.; Cone, R.; Paull, J. R. A.; Lewis, G. R.; Tachedjian, G. Structure Activity Relationship of Dendrimer Microbicides with Dual Action Antiviral Activity. PLoS One 2010, 5 (8), e12309, DOI: 10.1371/journal.pone.0012309Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3cjptFKgtw%253D%253D&md5=71694f3917d902efec4a6a81cef9f1cbStructure activity relationship of dendrimer microbicides with dual action antiviral activityTyssen David; Henderson Scott A; Johnson Adam; Sterjovski Jasminka; Moore Katie; La Jennifer; Zanin Mark; Sonza Secondo; Karellas Peter; Giannis Michael P; Krippner Guy; Wesselingh Steve; McCarthy Tom; Gorry Paul R; Ramsland Paul A; Cone Richard; Paull Jeremy R A; Lewis Gareth R; Tachedjian GildaPloS one (2010), 5 (8), e12309 ISSN:.BACKGROUND: Topical microbicides, used by women to prevent the transmission of HIV and other sexually transmitted infections are urgently required. Dendrimers are highly branched nanoparticles being developed as microbicides. However, the anti-HIV and HSV structure-activity relationship of dendrimers comprising benzyhydryl amide cores and lysine branches, and a comprehensive analysis of their broad-spectrum anti-HIV activity and mechanism of action have not been published. METHODS AND FINDINGS: Dendrimers with optimized activity against HIV-1 and HSV-2 were identified with respect to the number of lysine branches (generations) and surface groups. Antiviral activity was determined in cell culture assays. Time-of-addition assays were performed to determine dendrimer mechanism of action. In vivo toxicity and HSV-2 inhibitory activity were evaluated in the mouse HSV-2 susceptibility model. Surface groups imparting the most potent inhibitory activity against HIV-1 and HSV-2 were naphthalene disulfonic acid (DNAA) and 3,5-disulfobenzoic acid exhibiting the greatest anionic charge and hydrophobicity of the seven surface groups tested. Their anti-HIV-1 activity did not appreciably increase beyond a second-generation dendrimer while dendrimers larger than two generations were required for potent anti-HSV-2 activity. Second (SPL7115) and fourth generation (SPL7013) DNAA dendrimers demonstrated broad-spectrum anti-HIV activity. However, SPL7013 was more active against HSV and blocking HIV-1 envelope mediated cell-to-cell fusion. SPL7013 and SPL7115 inhibited viral entry with similar potency against CXCR4-(X4) and CCR5-using (R5) HIV-1 strains. SPL7013 was not toxic and provided at least 12 h protection against HSV-2 in the mouse vagina. CONCLUSIONS: Dendrimers can be engineered with optimized potency against HIV and HSV representing a unique platform for the controlled synthesis of chemically defined multivalent agents as viral entry inhibitors. SPL7013 is formulated as VivaGel(R) and is currently in clinical development to provide protection against HIV and HSV. SPL7013 could also be combined with other microbicides.
- 8Price, C. F.; Tyssen, D.; Sonza, S.; Davie, A.; Evans, S.; Lewis, G. R.; Xia, S.; Spelman, T.; Hodsman, P.; Moench, T. R.; Humberstone, A.; Paull, J. R. A.; Tachedjian, G. SPL7013 Gel (VivaGel®) Retains Potent HIV-1 and HSV-2 Inhibitory Activity Following Vaginal Administration in Humans. PLoS One 2011, 6 (9), e24095, DOI: 10.1371/journal.pone.0024095Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXht1OmsrjE&md5=9aad48be0881c4ce10d97c33e59c02f3SPL7013 Gel (VivaGel) retains potent HIV-1 and HSV-2 inhibitory activity following vaginal administration in humansPrice, Clare F.; Tyssen, David; Sonza, Secondo; Davie, Ashley; Evans, Sonya; Lewis, Gareth R.; Xia, Shirley; Spelman, Tim; Hodsman, Peter; Moench, Thomas R.; Humberstone, Andrew; Paull, Jeremy R. A.; Tachedjian, GildaPLoS One (2011), 6 (9), e24095CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)SPL7013 Gel (VivaGel) is a microbicide in development for prevention of HIV and HSV. This clin. study assessed retention and duration of antiviral activity following vaginal administration of 3% SPL7013 Gel in healthy women. Participants received 5 single doses of product with ≥5 days between doses. A cervicovaginal fluid (CVF) sample was collected using a SoftCup pre-dose, and immediately, or 1, 3, 12 or 24 h post-dose. HIV-1 and HSV-2 antiviral activities of CVF samples were detd. in cell culture assays. Antiviral activity in the presence of seminal plasma was also tested. Mass and concn. of SPL7013 in CVF samples was detd. Safety was assessed by reporting of adverse events. Statistical anal. was performed using the Wilcoxon signed-rank test with Bonferroni adjustment; p ≤ 0.003 was significant. Eleven participants completed the study. Inhibition of HIV-1 and HSV-2 by pre-dose CVF samples was negligible. CVF samples obtained immediately after dosing almost completely inhibited (median, interquartile range) HIV-1 [96% (95,97)] and HSV-2 [86% (85,94)], and activity was maintained in all women at 3 h (HIV-1 [96% (95,98), p = 0.9]; HSV-2 [94% (91,97), p = 0.005]). At 24 h, >90% of initial HIV-1 and HSV-2 inhibition was maintained in 6/11 women. SPL7013 was recovered in CVF samples obtained at baseline (46% of 105 mg dose). At 3 and 24 h, 22 mg and 4 mg SPL7013, resp., were recovered. More than 70% inhibition of HIV-1 and HSV-2 was obsd. if there was >0.5 mg SPL7013 in CVF samples. High levels of antiviral activity were retained in the presence of seminal plasma. VivaGel was well tolerated with no signs or symptoms of vaginal, vulvar or cervical irritation reported. Potent antiviral activity was obsd. against HIV-1 and HSV-2 immediately following vaginal administration of VivaGel, with activity maintained for at least 3 h post-dose. The data provide evidence of antiviral activity in a clin. setting, and suggest VivaGel could be administered up to 3 h before coitus.
- 9Zelikin, A. N.; Stellacci, F. Broad-Spectrum Antiviral Agents Based on Multivalent Inhibitors of Viral Infectivity. Adv. Healthcare Mater. 2021, 10 (6), 2001433, DOI: 10.1002/adhm.202001433Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvFegt7g%253D&md5=3a38a953dc83c1de54ae4c59fca380e6Broad-Spectrum Antiviral Agents Based on Multivalent Inhibitors of Viral InfectivityZelikin, Alexander N.; Stellacci, FrancescoAdvanced Healthcare Materials (2021), 10 (6), 2001433CODEN: AHMDBJ; ISSN:2192-2640. (Wiley-VCH Verlag GmbH & Co. KGaA)The ongoing pandemic of the coronavirus disease (Covid-19), caused by the spread of the severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), highlights the need for broad-spectrum antiviral drugs. In this Essay, it is argued that such agents already exist and are readily available while highlighting the challenges that remain to translate them into the clinic. Multivalent inhibitors of viral infectivity based on polymers or supramol. agents and nanoparticles are shown to be broadly acting against diverse pathogens in vitro as well as in vivo. Furthermore, uniquely, such agents can be virucidal. Polymers and nanoparticles are stable, do not require cold chain of transportation and storage, and can be obtained on large scale. Specifically, for the treatment of respiratory viruses and pulmonary diseases, these agents can be administered via inhalation/nebulization, as is currently investigated in clin. trials as a treatment against SARS CoV-2/Covid-19. It is believed that with due optimization and clin. validation, multivalent inhibitors of viral infectivity can claim their rightful position as broad-spectrum antiviral agents.
- 10Cagno, V.; Andreozzi, P.; D’Alicarnasso, M.; Jacob Silva, P.; Mueller, M.; Galloux, M.; Le Goffic, R.; Jones, S. T.; Vallino, M.; Hodek, J.; Weber, J.; Sen, S.; Janeček, E.-R.; Bekdemir, A.; Sanavio, B.; Martinelli, C.; Donalisio, M.; Rameix Welti, M.-A.; Eleouet, J.-F.; Han, Y.; Kaiser, L.; Vukovic, L.; Tapparel, C.; Král, P.; Krol, S.; Lembo, D.; Stellacci, F. Broad-Spectrum Non-Toxic Antiviral Nanoparticles with a Virucidal Inhibition Mechanism. Nat. Mater. 2018, 17 (2), 195– 203, DOI: 10.1038/nmat5053Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvF2lsbzN&md5=d66943a3a85ef5f924e1dd09fc308b59Broad-spectrum non-toxic antiviral nanoparticles with a virucidal inhibition mechanismCagno, Valeria; Andreozzi, Patrizia; D'Alicarnasso, Marco; Silva, Paulo Jacob; Mueller, Marie; Galloux, Marie; Le Goffic, Ronan; Jones, Samuel T.; Vallino, Marta; Hodek, Jan; Weber, Jan; Sen, Soumyo; Janecek, Emma-Rose; Bekdemir, Ahmet; Sanavio, Barbara; Martinelli, Chiara; Donalisio, Manuela; Rameix Welti, Marie-Anne; Eleouet, Jean-Francois; Han, Yanxiao; Kaiser, Laurent; Vukovic, Lela; Tapparel, Caroline; Kral, Petr; Krol, Silke; Lembo, David; Stellacci, FrancescoNature Materials (2018), 17 (2), 195-203CODEN: NMAACR; ISSN:1476-1122. (Nature Research)Viral infections kill millions yearly. Available antiviral drugs are virus-specific and active against a limited panel of human pathogens. There are broad-spectrum substances that prevent the first step of virus-cell interaction by mimicking heparan sulfate proteoglycans (HSPG), the highly conserved target of viral attachment ligands (VALs). The reversible binding mechanism prevents their use as a drug, because, upon diln., the inhibition is lost. Known VALs are made of closely packed repeating units, but the aforementioned substances are able to bind only a few of them. We designed antiviral nanoparticles with long and flexible linkers mimicking HSPG, allowing for effective viral assocn. with a binding that we simulate to be strong and multivalent to the VAL repeating units, generating forces (∼190 pN) that eventually lead to irreversible viral deformation. Virucidal assays, electron microscopy images, and mol. dynamics simulations support the proposed mechanism. These particles show no cytotoxicity, and in vitro nanomolar irreversible activity against herpes simplex virus (HSV), human papilloma virus, respiratory syncytial virus (RSV), dengue and lenti virus. They are active ex vivo in human cervicovaginal histocultures infected by HSV-2 and in vivo in mice infected with RSV.
- 11Al-Mahtab, M.; Bazinet, M.; Vaillant, A. Safety and Efficacy of Nucleic Acid Polymers in Monotherapy and Combined with Immunotherapy in Treatment-Naive Bangladeshi Patients with HBeAg+ Chronic Hepatitis B Infection. PLoS One 2016, 11 (6), e0156667, DOI: 10.1371/journal.pone.0156667Google Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFGisbrP&md5=043eb9625dbef15213157a967cff5125Safety and efficacy of nucleic acid polymers in monotherapy and combined with immunotherapy in treatment-naive Bangladeshi Patients with HBeAg+ chronic hepatitis B infectionAl-Mahtab, Mamun; Bazinet, Michel; Vaillant, AndrewPLoS One (2016), 11 (6), e0156667/1-e0156667/26CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)Previous in vivo studies have suggested that nucleic acid polymers (NAPs) may reduce circulating levels of HBsAg in the blood by blocking its release from infected hepatocytes and that this effect may have clin. benefit. NAP treatment, was evaluated in two clin. studies in patients with HBeAg pos. chronic HBV infection. The REP 101 study examd. REP 2055 monotherapy in 8 patients and the REP 102 study examd. REP 2139-Ca, in monotherapy in 12 patients, 9 of which transitioned to short term combined treatment with pegylated interferon alpha 2a or thymosin alpha 1. In both studies NAP monotherapy was accompanied by 2-7 log redns. of serum HBsAg, 3-9 log redns. in serum HBV DNA and the appearance of serum anti-HBsAg antibodies (10-1712 mIU / ml). Eight of the 9 patients transitioning to combined treatment with immunotherapy (pegylated interferon or thymosin alpha 1) in the REP 102 study experienced HBsAg loss and all 9 patients experienced substantial increases in serum anti-HBsAg antibody titers before withdrawal of therapy. For 52 wk after removal of REP 2055 therapy, rebound of serum viremia (HBV DNA > 1000 copies / ml, HBsAg > 1IU / ml) was not obsd. in 3 / 8 patients. Suppression of serum virema was further maintained for 290 and 231 wk in 2 of these patients. After withdrawal of all therapy in the 9 patients that transitioned to combination therapy in the REP 102 study, 8 patients achieved HBV DNA < 116 copies / ml after treatment withdrawal. Viral rebound occurred over a period of 12 to 123 wk in 7 patients but was still absent in two patients at 135 and 137 wk of follow-up. Administration tolerability issues obsd. with REP 2055 were rare with REP 2139-Ca but REP 2139-Ca therapy was accompanied by hair loss, dysphagia and dysgeusia which were considered related to heavy metal exposure endemic at the trial site. These preliminary studies suggest that NAP can elicit important antiviral responses during treatment which may improve the effect of immunotherapy. NAPs may be a potentially useful component of future combination therapies for the treatment of chronic hepatitis B.
- 12Vaillant, A. Nucleic Acid Polymers: Broad Spectrum Antiviral Activity, Antiviral Mechanisms and Optimization for the Treatment of Hepatitis B and Hepatitis D Infection. Antiviral Res. 2016, 133, 32– 40, DOI: 10.1016/j.antiviral.2016.07.004Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xht1Klt7%252FN&md5=0a0e73dea3602854d1acd32a2e516e3bNucleic acid polymers: Broad spectrum antiviral activity, antiviral mechanisms and optimization for the treatment of hepatitis B and hepatitis D infectionVaillant, AndrewAntiviral Research (2016), 133 (), 32-40CODEN: ARSRDR; ISSN:0166-3542. (Elsevier B.V.)Antiviral polymers are a well-studied class of broad spectrum viral attachment/entry inhibitors whose activity increases with polymer length and with increased amphipathic (hydrophobic) character. The newest members of this class of compds. are nucleic acid polymers whose activity is derived from the sequence independent properties of phosphorothioated oligonucleotides as amphipathic polymers. Although the antiviral mechanisms and broad spectrum antiviral activity of nucleic acid polymers mirror the functionality of other members of this class, they exert in addn. a unique post entry activity in hepatitis B infection which inhibits the release of HBsAg from infected hepatocytes. This review provides a general overview of the antiviral polymer class with a focus on nucleic acid polymers and their development as therapeutic agents for the treatment of hepatitis B/hepatitis D. This article forms part of a symposium in Antiviral Research on ''An unfinished story: from the discovery of the Australia antigen to the development of new curative therapies for hepatitis B.''.
- 13Cagno, V.; Gasbarri, M.; Medaglia, C.; Gomes, D.; Clement, S.; Stellacci, F.; Tapparel, C. Sulfonated Nanomaterials with Broad-Spectrum Antiviral Activity Extending beyond Heparan Sulfate-Dependent Viruses. Antimicrob. Agents Chemother. 2020, 64 (12), e02001-20, DOI: 10.1128/AAC.02001-20Google ScholarThere is no corresponding record for this reference.
- 14Sigl, C.; Willner, E. M.; Engelen, W.; Kretzmann, J. A.; Sachenbacher, K.; Liedl, A.; Kolbe, F.; Wilsch, F.; Aghvami, S. A.; Protzer, U.; Hagan, M. F.; Fraden, S.; Dietz, H. Programmable Icosahedral Shell System for Virus Trapping. Nat. Mater. 2021, 20 (9), 1281– 1289, DOI: 10.1038/s41563-021-01020-4Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhtlaltr3J&md5=bcdbcbd974dab9cec5328206d0c37ac1Programmable icosahedral shell system for virus trappingSigl, Christian; Willner, Elena M.; Engelen, Wouter; Kretzmann, Jessica A.; Sachenbacher, Ken; Liedl, Anna; Kolbe, Fenna; Wilsch, Florian; Aghvami, S. Ali; Protzer, Ulrike; Hagan, Michael F.; Fraden, Seth; Dietz, HendrikNature Materials (2021), 20 (9), 1281-1289CODEN: NMAACR; ISSN:1476-1122. (Nature Portfolio)Broad-spectrum antiviral platforms that can decrease or inhibit viral infection would alleviate many threats to global public health. Nonetheless, effective technologies of this kind are still not available. Here, we describe a programmable icosahedral canvas for the self-assembly of icosahedral shells that have viral trapping and antiviral properties. Programmable triangular building blocks constructed from DNA assemble with high yield into various shell objects with user-defined geometries and apertures. We have created shells with mol. masses ranging from 43 to 925 MDa (8 to 180 subunits) and with internal cavity diams. of up to 280 nm. The shell interior can be functionalized with virus-specific moieties in a modular fashion. We demonstrate this virus-trapping concept by engulfing hepatitis B virus core particles and adeno-assocd. viruses. We demonstrate the inhibition of hepatitis B virus core interactions with surfaces in vitro and the neutralization of infectious adeno-assocd. viruses exposed to human cells.
- 15Zeltins, A. Construction and Characterization of Virus-Like Particles: A Review. Mol. Biotechnol 2013, 53 (1), 92– 107, DOI: 10.1007/s12033-012-9598-4Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhvVCltLvO&md5=620c372bb5194d50ea629cc68de6b826Construction and Characterization of Virus-Like Particles: A ReviewZeltins, AndrisMolecular Biotechnology (2013), 53 (1), 92-107CODEN: MLBOEO; ISSN:1073-6085. (Springer)A review. Over the last 3 decades, virus-like particles (VLPs) have evolved to become a widely accepted technol., esp. in the field of vaccinol. In fact, some VLP-based vaccines are currently used as com. medical products, and other VLP-based products are at different stages of clin. study. Several remarkable advantages were achieved in the development of VLPs as gene therapy tools and new nanomaterials. The anal. of published data reveals that at least 110 VLPs were constructed from viruses belonging to 35 different families. This review therefore discusses the main principles in the cloning of viral structural genes, the relevant host systems and the purifn. procedures that were developed. In addn., the methods that are used to characterize the structural integrity, stability, and components, including the encapsidated nucleic acids, of newly synthesized VLPs are analyzed. Moreover, some of the modifications that are required to construct VLP-based carriers of viral origin with defined properties are discussed, and examples are provided.
- 16Chen, Y.; Maguire, T.; Hileman, R. E.; Fromm, J. R.; Esko, J. D.; Linhardt, R. J.; Marks, R. M. Dengue Virus Infectivity Depends on Envelope Protein Binding to Target Cell Heparan Sulfate. Nat. Med. 1997, 3 (8), 866– 871, DOI: 10.1038/nm0897-866Google Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXltVKqtb0%253D&md5=8aa260764e3eafa6a48d75e6d923ea89Dengue virus infectivity depends on envelope protein binding to target cell heparan sulfateChen, Yaping; Maguire, Terry; Hileman, Ronald E.; Fromm, Jonathan R.; Esko, Jeffrey D.; Linhardt, Robert J.; Marks, Rory M.Nature Medicine (New York) (1997), 3 (8), 866-871CODEN: NAMEFI; ISSN:1078-8956. (Nature America)Dengue virus is a human pathogen that has reemerged as an increasingly important public health threat. The authors found that the cellular receptor utilized by dengue envelope protein to bind to target cells is a highly sulfated type of heparan sulfate. Heparin, highly sulfated heparan sulfate, and the polysulfonate pharmaceutical Suramin effectively prevented dengue virus infection of target cells, indicating that the envelope protein-target cell receptor interaction is a crit. determinant of infectivity. The dengue envelope protein sequence includes two putative glycosaminoglycan-binding motifs at the carboxy terminus; the first could be structurally modeled and formed an unusual extending binding surface of basic amino acids. Similar motifs were also identified in the envelope proteins of other flaviviridae. Developing pharmaceuticals that inhibit target cell binding may be an effective strategy for treating flavivirus infections.
- 17Yu, I.-M.; Zhang, W.; Holdaway, H. A.; Li, L.; Kostyuchenko, V. A.; Chipman, P. R.; Kuhn, R. J.; Rossmann, M. G.; Chen, J. Structure of the Immature Dengue Virus at Low PH Primes Proteolytic Maturation. Science 2008, 319 (5871), 1834– 1837, DOI: 10.1126/science.1153264Google Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXjs12ktr8%253D&md5=7f4bf5bd9e16a31dc93b50e9ecc0453cStructure of the Immature Dengue Virus at Low pH Primes Proteolytic MaturationYu, I-Mei; Zhang, Wei; Holdaway, Heather A.; Li, Long; Kostyuchenko, Victor A.; Chipman, Paul R.; Kuhn, Richard J.; Rossmann, Michael G.; Chen, JueScience (Washington, DC, United States) (2008), 319 (5871), 1834-1837CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Intracellular cleavage of immature flaviviruses is a crit. step in assembly that generates the membrane fusion potential of the E glycoprotein. With cryo-electron microscopy we show that the immature dengue particles undergo a reversible conformational change at low pH that renders them accessible to furin cleavage. At a pH of 6.0, the E proteins are arranged in a herringbone pattern with the pr peptides docked onto the fusion loops, a configuration similar to that of the mature virion. After cleavage, the dissocn. of pr is pH-dependent, suggesting that in the acidic environment of the trans-Golgi network pr is retained on the virion to prevent membrane fusion. These results suggest a mechanism by which flaviviruses are processed and stabilized in the host cell secretory pathway.
- 18Yu, I.-M.; Holdaway, H. A.; Chipman, P. R.; Kuhn, R. J.; Rossmann, M. G.; Chen, J. Association of the Pr Peptides with Dengue Virus at Acidic PH Blocks Membrane Fusion. Journal of Virology 2009, 83 (23), 12101– 12107, DOI: 10.1128/JVI.01637-09Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsVyrtLrE&md5=c98479763c1b30a67ea3a047d14a042aAssociation of the pr peptides with dengue virus at acidic pH blocks membrane fusionYu, I.-M.; Holdaway, H. A.; Chipman, P. R.; Kuhn, R. J.; Rossmann, M. G.; Chen, J.Journal of Virology (2009), 83 (23), 12101-12107CODEN: JOVIAM; ISSN:0022-538X. (American Society for Microbiology)Flavivirus assembles into an inert particle that requires proteolytic activation by furin to enable transmission to other hosts. We previously showed that immature virus undergoes a conformational change at low pH that renders it accessible to furin. Here we show, using cryoelectron microscopy, that the structure of immature dengue virus at pH 6.0 is essentially the same before and after the cleavage of prM. The structure shows that after cleavage, the proteolytic product pr remains assocd. with the virion at acidic pH, and that furin cleavage by itself does not induce any major conformational changes. We also show by liposome cofloatation expts. that pr retention prevents membrane insertion, suggesting that pr is present on the virion in the trans-Golgi network to protect the progeny virus from fusion within the host cell.
- 19Lim, X.-X.; Chandramohan, A.; Lim, X. Y. E.; Bag, N.; Sharma, K. K.; Wirawan, M.; Wohland, T.; Lok, S.-M.; Anand, G. S. Conformational Changes in Intact Dengue Virus Reveal Serotype-Specific Expansion. Nat. Commun. 2017, 8 (1), 14339, DOI: 10.1038/ncomms14339Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXisVyqtbg%253D&md5=ae877a0a6eb329bfcfd5aee8e3678acfConformational changes in intact dengue virus reveal serotype-specific expansionLim, Xin-Xiang; Chandramohan, Arun; Lim, Xin Ying Elisa; Bag, Nirmalya; Sharma, Kamal Kant; Wirawan, Melissa; Wohland, Thorsten; Lok, Shee-Mei; Anand, Ganesh S.Nature Communications (2017), 8 (), 14339CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37° (assocd. with host entry), despite high sequence and structural homol. among the 4 known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of 2 serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Forster Resonance Energy Transfer. Our results show temp.-dependent dynamics hotspots on DENV2 and DENV1 particles with DENV1 showing expansion at 40° but not at 37°. HDXMS measurement of virion dynamics in soln. offers a powerful approach to identify potential epitopes, map virus-antibody complex structure and dynamics, and test effects of multiple host-specific perturbations on viruses and virus-antibody complexes.
- 20San Martín, C. Virus Maturation. In Physical Virology: Virus Structure and Mechanics; Greber, U. F., Ed.; Advances in Experimental Medicine and Biology; Springer International Publishing: Cham, 2019; pp 129– 158. DOI: 10.1007/978-3-030-14741-9_7 .Google ScholarThere is no corresponding record for this reference.
- 21Chai, N.; Chang, H. E.; Nicolas, E.; Han, Z.; Jarnik, M.; Taylor, J. Properties of Subviral Particles of Hepatitis B Virus. Journal of Virology 2008, 82 (16), 7812– 7817, DOI: 10.1128/JVI.00561-08Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXpsVOqtLk%253D&md5=d025151c24848ae1389f12827d432e6fProperties of subviral particles of hepatitis B virusChai, Ning; Chang, Ho Eun; Nicolas, Emmanuelle; Han, Ziying; Jarnik, Michal; Taylor, JohnJournal of Virology (2008), 82 (16), 7812-7817CODEN: JOVIAM; ISSN:0022-538X. (American Society for Microbiology)In the sera of patients infected with hepatitis B virus (HBV), in addn. to infectious particles, there is an excess (typically 1000- to 100,000-fold) of empty subviral particles (SVP) composed solely of HBV envelope proteins in the form of relatively smaller spheres and filaments of variable length. Hepatitis delta virus (HDV) assembly also uses the envelope proteins of HBV to produce an infectious particle. Rate-zonal sedimentation was used to study the particles released from liver cell lines that produced SVP only, HDV plus SVP, and HBV plus SVP. The SVP made in the absence of HBV or HDV were further examd. by electron microscopy. They bound efficiently to heparin columns, consistent with an ability to bind cell surface glycosaminoglycans. However, unlike sol. forms of HBV envelope protein that were potent inhibitors, the SVP did not inhibit the ability of HBV and HDV to infect primary human hepatocytes.
- 22Engelhardt, F. A. S.; Praetorius, F.; Wachauf, C. H.; Brüggenthies, G.; Kohler, F.; Kick, B.; Kadletz, K. L.; Pham, P. N.; Behler, K. L.; Gerling, T.; Dietz, H. Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds. ACS Nano 2019, 13 (5), 5015– 5027, DOI: 10.1021/acsnano.9b01025Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXnsV2ktbo%253D&md5=2fb7ea8b75471e18715911c299deeeb9Custom-Size, Functional, and Durable DNA Origami with Design-Specific ScaffoldsEngelhardt, Floris A. S.; Praetorius, Florian; Wachauf, Christian H.; Brueggenthies, Gereon; Kohler, Fabian; Kick, Benjamin; Kadletz, Karoline L.; Pham, Phuong Nhi; Behler, Karl L.; Gerling, Thomas; Dietz, HendrikACS Nano (2019), 13 (5), 5015-5027CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)DNA origami nano-objects are usually designed around generic single-stranded "scaffolds". Many properties of the target object are detd. by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable prodn. methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence compn. on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent crosslinking of DNA origami via UV irradn., and we built DNAzyme-contg. scaffolds that allow postfolding DNA origami domain sepn.
- 23Gerling, T.; Kube, M.; Kick, B.; Dietz, H. Sequence-Programmable Covalent Bonding of Designed DNA Assemblies. Sci. Adv. 2018, 4 (8), eaau1157, DOI: 10.1126/sciadv.aau1157Google ScholarThere is no corresponding record for this reference.
- 24Kremer, J. R.; Mastronarde, D. N.; McIntosh, J. R. Computer Visualization of Three-Dimensional Image Data Using IMOD. J. Struct. Biol. 1996, 116 (1), 71– 76, DOI: 10.1006/jsbi.1996.0013Google Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADyaK28zmtFyqtg%253D%253D&md5=b6ab779bdec60f8644e254124c4dbbe7Computer visualization of three-dimensional image data using IMODKremer J R; Mastronarde D N; McIntosh J RJournal of structural biology (1996), 116 (1), 71-6 ISSN:1047-8477.We have developed a computer software package, IMOD, as a tool for analyzing and viewing three-dimensional biological image data. IMOD is useful for studying and modeling data from tomographic, serial section, and optical section reconstructions. The software allows image data to be visualized by several different methods. Models of the image data can be visualized by volume or contour surface rendering and can yield quantitative information.
- 25Zivanov, J.; Nakane, T.; Forsberg, B. O.; Kimanius, D.; Hagen, W. J.; Lindahl, E.; Scheres, S. H. New Tools for Automated High-Resolution Cryo-EM Structure Determination in RELION-3. eLife 2018, 7, e42166, DOI: 10.7554/eLife.42166Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitlyqsrbL&md5=6ad79861243c29459be9b515e21c4b0eNew tools for automated high-resolution cryo-EM structure determination in RELION-3Zivanov, Jasenko; Nakane, Takanori; Forsberg, Bjoern O.; Kimanius, Dari; Hagen, Wim Jh; Lindahl, Erik; Scheres, Sjors HweLife (2018), 7 (), e42166/1-e42166/22CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addn. to GPU support, which provides flexibility in use of resources and avoids memory limitations. Ref.-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2Dclassification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estd. beam tilt provides higher resoln. reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resoln. for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beaminduced motion correction it leads to resoln. improvements of 0.2-0.7 Å compared to previous RELION versions.
- 26Zheng, S. Q.; Palovcak, E.; Armache, J.-P.; Verba, K. A.; Cheng, Y.; Agard, D. A. MotionCor2: Anisotropic Correction of Beam-Induced Motion for Improved Cryo-Electron Microscopy. Nat. Methods 2017, 14 (4), 331– 332, DOI: 10.1038/nmeth.4193Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjt1ags7g%253D&md5=5f4e225ef8123dacd8475d526175e1d2MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopyZheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul; Verba, Kliment A.; Cheng, Yifan; Agard, David A.Nature Methods (2017), 14 (4), 331-332CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)A review on anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Here we describe MotionCor2, a software tool for anisotropic correction of beam-induced motion. Overall, MotionCor2 is extremely robust and sufficiently accurate at correcting local motions so that the very time-consuming and computationally intensive particle polishing in RELION can be skipped, importantly, it also works on a wide range of data sets, including cryo tomog. tilt series.
- 27Rohou, A.; Grigorieff, N. CTFFIND4: Fast and Accurate Defocus Estimation from Electron Micrographs. J. Struct. Biol. 2015, 192 (2), 216– 221, DOI: 10.1016/j.jsb.2015.08.008Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC287js1Whsg%253D%253D&md5=8500953ad4898ae82de6f8cdc95832cfCTFFIND4: Fast and accurate defocus estimation from electron micrographsRohou Alexis; Grigorieff NikolausJournal of structural biology (2015), 192 (2), 216-21 ISSN:.CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of the original algorithm while allowing for higher throughput. We also describe a measure of the quality of the fit as a function of spatial frequency and suggest this can be used to define the highest resolution at which CTF oscillations were successfully modeled.
- 28Wagner, T.; Merino, F.; Stabrin, M.; Moriya, T.; Antoni, C.; Apelbaum, A.; Hagel, P.; Sitsel, O.; Raisch, T.; Prumbaum, D.; Quentin, D.; Roderer, D.; Tacke, S.; Siebolds, B.; Schubert, E.; Shaikh, T. R.; Lill, P.; Gatsogiannis, C.; Raunser, S. SPHIRE-CrYOLO Is a Fast and Accurate Fully Automated Particle Picker for Cryo-EM. Commun. Biol. 2019, 2 (1), 1– 13, DOI: 10.1038/s42003-019-0437-zGoogle ScholarThere is no corresponding record for this reference.
- 29Liu, A. P.; Patel, S. K.; Xing, T.; Yan, Y.; Wang, S.; Li, N. Characterization of Adeno-Associated Virus Capsid Proteins Using Hydrophilic Interaction Chromatography Coupled with Mass Spectrometry. J. Pharm. Biomed. Anal. 2020, 189, 113481, DOI: 10.1016/j.jpba.2020.113481Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsFejsbfL&md5=3b543b366df575802c058c1812cfc557Characterization of Adeno-Associated Virus Capsid Proteins Using Hydrophilic Interaction Chromatography Coupled with Mass SpectrometryLiu, Anita P.; Patel, Shailin K.; Xing, Tao; Yan, Yuetian; Wang, Shunhai; Li, NingJournal of Pharmaceutical and Biomedical Analysis (2020), 189 (), 113481CODEN: JPBADA; ISSN:0731-7085. (Elsevier B.V.)To support adeno-assocd. virus (AAV)-based gene therapy development, characterization of the three capsid viral proteins (VP; VP1/VP2/VP3) from recombinant AAV can offer insights on capsid identity, heterogeneity, and product and process consistency. Intact protein mass anal. is a rapid, reliable, and sensitive method to confirm AAV serotypes based on accurate mass measurement of the constituent capsid proteins. Compared to commonly applied reversed-phase liq. chromatog. (RPLC) methods, we demonstrated that, using a wide-pore amide-bonded column, hydrophilic interaction chromatog. (HILIC) could achieve improved sepn. of VPs from a variety of AAV serotypes using a generic method prior to MS detection. Moreover, HILIC-based sepn. was shown to be particularly sensitive in detecting capsid protein variants resulting from different post-translational modifications (PTMs) (e.g. phosphorylation and oxidn.) and protein backbone clippings, making it ideally suited for capsid heterogeneity characterization. To overcome the challenges assocd. with low protein concns. of AAV samples, as well as the trifluoroacetic acid (TFA)-induced ion suppression during HILIC-MS anal., different strategies were implemented to improve method sensitivity, including increasing the HILIC column loading and the application of a desolvation gas modification device. Finally, we demonstrated that this integrated HILIC-FLR-MS method can be generically applied to characterize a variety of AAV serotype samples at low concns. without any sample treatment to achieve unambiguous serotype identification, stoichiometry assessment, and PTM characterization.
- 30Hogle, J. M. Poliovirus Cell Entry: Common Structural Themes in Viral Cell Entry Pathways. Annu. Rev. Microbiol. 2002, 56 (1), 677– 702, DOI: 10.1146/annurev.micro.56.012302.160757Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xos1Gisbw%253D&md5=a1441ea8f6da2b7ecb3390c70580f71bPoliovirus cell entry: Common structural themes in viral cell entry pathwaysHogle, James M.Annual Review of Microbiology (2002), 56 (), 677-702, 8 platesCODEN: ARMIAZ; ISSN:0066-4227. (Annual Reviews Inc.)A review. Structural studies of polio and closely related viruses have provided a series of snapshots along their cell entry pathways. Based on the structures and related kinetic, biochem., and genetic studies, we have proposed a model for the cell entry pathway for polio- and closely related viruses. In this model a maturation cleavage of a capsid protein precursor locks the virus in a metastable state, and the receptor acts like a transition-state catalyst to overcome an energy barrier and release the mature virion from the metastable state. This initiates a series of conformational changes that allow the virus to attach to membranes, form a pore, and finally release its RNA genome into the cytoplasm. This model has striking parallels with emerging models for the maturation and cell entry of more complex enveloped viruses such as influenza virus and HIV.
- 31Kuhn, R. J.; Zhang, W.; Rossmann, M. G.; Pletnev, S. V.; Corver, J.; Lenches, E.; Jones, C. T.; Mukhopadhyay, S.; Chipman, P. R.; Strauss, E. G.; Baker, T. S.; Strauss, J. H. Structure of Dengue Virus: Implications for Flavivirus Organization, Maturation, and Fusion. Cell 2002, 108 (5), 717– 725, DOI: 10.1016/S0092-8674(02)00660-8Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XisFOhtLk%253D&md5=317d9dd88f3e1411bcd452b749ca6a74Structure of dengue virus: implications for flavivirus organization, maturation, and fusionKuhn, Richard J.; Zhang, Wei; Rossmann, Michael G.; Pletnev, Sergei V.; Corver, Jeroen; Lenches, Edith; Jones, Christopher T.; Mukhopadhyay, Suchetana; Chipman, Paul R.; Strauss, Ellen G.; Baker, Timothy S.; Strauss, James H.Cell (Cambridge, MA, United States) (2002), 108 (5), 717-725CODEN: CELLB5; ISSN:0092-8674. (Cell Press)The first structure of a flavivirus has been detd. by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron d. map. The virus core, within a lipid bilayer, has a less-ordered structure than the external, icosahedral scaffold of 90 glycoprotein E dimers. The three E monomers per icosahedral asym. unit do not have quasiequivalent sym. environments. Difference maps indicate the location of the small membrane protein M relative to the overlaying scaffold of E dimers. The structure suggests that flaviviruses, and by analogy also alphaviruses, employ a fusion mechanism in which the distal β barrels of domain II of the glycoprotein E are inserted into the cellular membrane.
- 32Chan, M. C. W.; Shan Kwan, H.; Chan, P. K. S. Structure and Genotypes of Noroviruses. Norovirus 2017, 51– 63, DOI: 10.1016/B978-0-12-804177-2.00004-XGoogle Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXptVOksL0%253D&md5=be590cf6e239762901ae0752d7300cb9Structure and genotypes of norovirusesChan, Martin C. W.; Kwan, Hoi Shan; Chan, Paul K. S.Norovirus (2017), (), 51-63CODEN: 69VTVG ISSN:. (Elsevier Ltd.)A review. In this chapter, we discuss the structure and genotypes of noroviruses as well as the latest research developments with an aim to provide more clues for those who are interested in pursuing the ultimate answers to these questions. Human norovinises are ubiquitous and highly infectious. Structural determinants of their super environmental stability remain poorly understood, partly due to the lack of a robust and efficient in vitro culture system to assess virus infectivity. This suggests that noroviruses may have an ancient origin. Some animal noroviruses (e.g., porcine GII-11, GII.18, and Gil. 19) are closely related to human noroviruses.
- 33Goetschius, D. J.; Hartmann, S. R.; Subramanian, S.; Bator, C. M.; Christensen, N. D.; Hafenstein, S. L. High Resolution Cryo EM Analysis of HPV16 Identifies Minor Structural Protein L2 and Describes Capsid Flexibility. Sci. Rep 2021, 11 (1), 3498, DOI: 10.1038/s41598-021-83076-5Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXjvFOlurk%253D&md5=16b76d91aff472c4135d1092d40c5610High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibilityGoetschius, Daniel J.; Hartmann, Samantha R.; Subramanian, Suriyasri; Bator, Carol M.; Christensen, Neil D.; Hafenstein, Susan L.Scientific Reports (2021), 11 (1), 3498CODEN: SRCEC3; ISSN:2045-2322. (Nature Research)Abstr.: Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. HPV is epitheliotropic and its replication is tightly assocd. with terminal keratinocyte differentiation making prodn. and purifn. of high titer virus prepns. for research problematic, therefore alternative HPV prodn. methods have been developed for virol. and structural studies. In this study we use HPV16 quasivirus, composed of HPV16 L1/L2 capsid proteins with a packaged cottontail rabbit papillomavirus genome. We have achieved the first high resoln., 3.1 Å, structure of HPV16 by using a local subvolume refinement approach. The high resoln. enabled us to build L1 unambiguously and identify L2 protein strands. The L2 d. is incorporated adjacent to conserved L1 residues on the interior of the capsid. Further interpretation with our own software for Icosahedral Subvolume Extn. and Correlated Classification revealed flexibility, on the whole-particle level through diam. anal. and local movement with inter-capsomer anal. Inter-capsomer expansion or contraction, governed by the connecting arms, showed no bias in the magnitude or direction of capsomer movement. We propose that papillomavirus capsids are dynamic and capsomers move as rigid bodies connected by flexible linkers. The resulting virus structure will provide a framework for continuing biochem., genetic and biophys. research for papillomaviruses. Furthermore, our approach has allowed insight into the resoln. barrier that has previously been a limitation in papillomavirus structural studies.
- 34Yao, H.; Song, Y.; Chen, Y.; Wu, N.; Xu, J.; Sun, C.; Zhang, J.; Weng, T.; Zhang, Z.; Wu, Z.; Cheng, L.; Shi, D.; Lu, X.; Lei, J.; Crispin, M.; Shi, Y.; Li, L.; Li, S. Molecular Architecture of the SARS-CoV-2 Virus. Cell 2020, 183 (3), 730– 738, DOI: 10.1016/j.cell.2020.09.018Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvFKjs7nM&md5=7bd110334cb42931034a4eb5f9d2ff00Molecular Architecture of the SARS-CoV-2 VirusYao, Hangping; Song, Yutong; Chen, Yong; Wu, Nanping; Xu, Jialu; Sun, Chujie; Zhang, Jiaxing; Weng, Tianhao; Zhang, Zheyuan; Wu, Zhigang; Cheng, Linfang; Shi, Danrong; Lu, Xiangyun; Lei, Jianlin; Crispin, Max; Shi, Yigong; Li, Lanjuan; Li, SaiCell (Cambridge, MA, United States) (2020), 183 (3), 730-738.e13CODEN: CELLB5; ISSN:0092-8674. (Cell Press)SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, the detailed architecture of the intact virus remains to be unveiled. Here we report the mol. assembly of the authentic SARS-CoV-2 virus using cryoelectron tomog. (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in pre- and postfusion conformations were detd. to av. resolns. of 8.7-11 Å. Compns. of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed overall processing states of the native glycans highly similar to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNPs) and their higher-order assemblies were revealed. Overall, these characterizations revealed the architecture of the SARS-CoV-2 virus in exceptional detail and shed light on how the virus packs its ∼30-kb-long single-segmented RNA in the ∼80-nm-diam. lumen.
- 35Yap, M. L.; Klose, T.; Urakami, A.; Hasan, S. S.; Akahata, W.; Rossmann, M. G. Structural Studies of Chikungunya Virus Maturation. Proc. Natl. Acad. Sci. U. S. A. 2017, 114 (52), 13703– 13707, DOI: 10.1073/pnas.1713166114Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvFWgsrbJ&md5=c67a1673d7da05489772d3da4594f162Structural studies of Chikungunya virus maturationYap, Moh Lan; Klose, Thomas; Urakami, Akane; Hasan, S. Saif; Akahata, Wataru; Rossmann, Michael G.Proceedings of the National Academy of Sciences of the United States of America (2017), 114 (52), 13703-13707CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here, we present a cryo-electron microscopy (cryo-EM), 6.8-Å resoln. structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus had a larger radius and were less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins had less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addn., the nucleocapsid of the immature virus was more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the post-translational processing of the spikes and nucleocapsid is necessary to produce an infectious virus.
- 36Mangala Prasad, V.; Klose, T.; Rossmann, M. G. Assembly, Maturation and Three-Dimensional Helical Structure of the Teratogenic Rubella Virus. PLoS Pathog 2017, 13 (6), e1006377, DOI: 10.1371/journal.ppat.1006377Google ScholarThere is no corresponding record for this reference.
- 37Russell, W. C. Adenoviruses: Update on Structure and Function. Journal of General Virology 2009, 90 (1), 1– 20, DOI: 10.1099/vir.0.003087-0Google Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXlsVyqsQ%253D%253D&md5=78fd91b454da057c8defc77b7b141539Adenoviruses: Update on structure and functionRussell, W. C.Journal of General Virology (2009), 90 (1), 1-20CODEN: JGVIAY; ISSN:0022-1317. (Society for General Microbiology)A review. Adenoviruses have been studied intensively for over 50 years as models of virus-cell interactions and latterly as gene vectors. With the advent of more sophisticated structural anal. techniques the disposition of most of the 13 structural proteins have been defined to a reasonable level. This review seeks to describe the functional properties of these proteins and shows that they all have a part to play in deciding the outcome of an infection and act at every level of the virus's path through the host cell. They are primarily involved in the induction of the different arms of the immune system and a better understanding of their overall properties should lead to more effective ways of combating virus infections.
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Abstract
Figure 1
Figure 1. DNA origami shells and functionalization with HS derivatives. (A) A heparan sulfate proteoglycan (HSPG) interacts with a virus pathogen and mediates its cellular uptake (left). DNA origami shell schematic, with HS modifications in its interior, capable of binding and sequestering a viral particle (right). (B) SPAAC reaction in between azide-modified heparin and HS oligomers and a DBCO-modified DNA oligo. The DNA sequence is complementary to the handles of the DNA origami shells in (D, E). (C) PAGE characterization of the HS-modified DNA oligos. Products containing HS with sulfate and sulfonate groups (3a and 3c) migrate at a faster rate through the gel than the analog negative controls (3b and 3d) due to their increased anionic character. (D) Cylindrical models of O and T1 shells made of 4 and 10 triangle subunits respectively, containing single stranded protruding oligos (termed handles, shown in red) decorating their interior. Each triangle subunit contains nine handle positions. (E) T3 shell design consisting of 30 triangle subunits and featuring an inner cavity of 150 nm. Each triangle subunit also contains nine handle positions. (F) Negative stain TEM micrograph of T3 shells. Scale bar is 100 nm. (G) Schematic representation of three different handle designs. H1 contains one HS modification per handle placed as close to the origami surface as possible. H2 also contains one HS modification per handle but has a polyT extension of 20 bases, allowing the handle to reach further than H1. H3 mimics a branched polymer containing two HS modifications per handle unit, therefore doubling the local HS density.
Figure 2
Figure 2. Viruses and VLPs trapped within HS-modified O, T1 and T3 shells. Negative stain TEM images of (A) AAV2, polio 3, mature dengue 1 and norovirus GII.4 successfully trapped in O shells. (B) HPV 16, SARS-CoV-2, chikungunya, and rubella engulfed by T1 shells. (C) Adenovirus 5 captured with T3 shells. Scale bars are 100 nm.
Figure 3
Figure 3. Multiple viruses and VLPs trapped in HS-modified O, T1, and T3 shells. Negative stain TEM images of (A) up to four AAV2 in one O shell, (B) up to three HPV 16 in one T1 shell, and (C) one HPV 16 coordinated by two O shells for complete occlusion of the virus particle. (D) Up to six AAV2 per T1 shell. (E) Up to three chikungunya VLPs per T3 shell. (F) Cooperative effect of multiple O shells capturing numerous AAV2 particles. Scale bar is 100 nm.
Figure 4
Figure 4. Cryo-EM analysis of virus-like particles trapped in DNA origami shells. (A) Cryo-EM micrograph of O shells binding to HPV 16 VLPs. (B) 2D class average images of one or two O shells binding to one HPV 16 particle, demonstrating different orientations of the complexes. The white arrows indicate the gap difference in between the two O shells, confirming the capture of differently sized VLP particles. (C) 3D reconstructions of HPV 16 bound to one and two O shells. (D) Cryo-EM micrograph of T1 shells binding to chikungunya VLPs. (E) 2D class average images of T1 shells binding to chikungunya particles showing different orientations of the complex. (F) Two different views of the 3D reconstruction of a T1 shell engulfing a chikungunya virus particle.
References
This article references 37 other publications.
- 1Heida, R.; Bhide, Y. C.; Gasbarri, M.; Kocabiyik, Ö.; Stellacci, F.; Huckriede, A. L. W.; Hinrichs, W. L. J.; Frijlink, H. W. Advances in the Development of Entry Inhibitors for Sialic-Acid-Targeting Viruses. Drug Discovery Today 2021, 26 (1), 122– 137, DOI: 10.1016/j.drudis.2020.10.0091https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitlelurjJ&md5=f943f5a4f5978a97da9c47e122f02b5fAdvances in the development of entry inhibitors for sialic-acid-targeting virusesHeida, Rick; Bhide, Yoshita C.; Gasbarri, Matteo; Kocabiyik, Oezguen; Stellacci, Francesco; Huckriede, Anke L. W.; Hinrichs, Wouter L. J.; Frijlink, Henderik W.Drug Discovery Today (2021), 26 (1), 122-137CODEN: DDTOFS; ISSN:1359-6446. (Elsevier Ltd.)A review. Over the past decades, several antiviral drugs have been developed to treat a range of infections. Yet the no. of treatable viral infections is still limited, and resistance to current drug regimens is an ever-growing problem. Therefore, addnl. strategies are needed to provide a rapid cure for infected individuals. An interesting target for antiviral drugs is the process of viral attachment and entry into the cell. Although most viruses use distinct host receptors for attachment to the target cell, some viruses share receptors, of which sialic acids are a common example. This review aims to give an update on entry inhibitors for a range of sialic-acid-targeting viruses and provides insight into the prospects for those with broad-spectrum potential.
- 2Wang, L.; Zhou, T.; Zhang, Y.; Yang, E. S.; Schramm, C. A.; Shi, W.; Pegu, A.; Oloniniyi, O. K.; Henry, A. R.; Darko, S.; Narpala, S. R.; Hatcher, C.; Martinez, D. R.; Tsybovsky, Y.; Phung, E.; Abiona, O. M.; Antia, A.; Cale, E. M.; Chang, L. A.; Choe, M.; Corbett, K. S.; Davis, R. L.; DiPiazza, A. T.; Gordon, I. J.; Hait, S. H.; Hermanus, T.; Kgagudi, P.; Laboune, F.; Leung, K.; Liu, T.; Mason, R. D.; Nazzari, A. F.; Novik, L.; O’Connell, S.; O’Dell, S.; Olia, A. S.; Schmidt, S. D.; Stephens, T.; Stringham, C. D.; Talana, C. A.; Teng, I.-T.; Wagner, D. A.; Widge, A. T.; Zhang, B.; Roederer, M.; Ledgerwood, J. E.; Ruckwardt, T. J.; Gaudinski, M. R.; Moore, P. L.; Doria-Rose, N. A.; Baric, R. S.; Graham, B. S.; McDermott, A. B.; Douek, D. C.; Kwong, P. D.; Mascola, J. R.; Sullivan, N. J.; Misasi, J. Ultrapotent Antibodies against Diverse and Highly Transmissible SARS-CoV-2 Variants. Science 2021, 373 (6556), eabh1766, DOI: 10.1126/science.abh1766There is no corresponding record for this reference.
- 3Taylor, P. C.; Adams, A. C.; Hufford, M. M.; de la Torre, I.; Winthrop, K.; Gottlieb, R. L. Neutralizing Monoclonal Antibodies for Treatment of COVID-19. Nat. Rev. Immunol 2021, 21 (6), 382– 393, DOI: 10.1038/s41577-021-00542-x3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXptFWit7c%253D&md5=fc5fae636d59e08a9049e3939ff1caeeNeutralizing monoclonal antibodies for treatment of COVID-19Taylor, Peter C.; Adams, Andrew C.; Hufford, Matthew M.; de la Torre, Inmaculada; Winthrop, Kevin; Gottlieb, Robert L.Nature Reviews Immunology (2021), 21 (6), 382-393CODEN: NRIABX; ISSN:1474-1733. (Nature Portfolio)A review. Several neutralizing monoclonal antibodies (mAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed and are now under evaluation in clin. trials. With the US Food and Drug Administration recently granting emergency use authorizations for neutralizing mAbs in non-hospitalized patients with mild-to-moderate COVID-19, there is an urgent need to discuss the broader potential of these novel therapies and to develop strategies to deploy them effectively in clin. practice, given limited initial availability. Here, we review the precedent for passive immunization and lessons learned from using antibody therapies for viral infections such as respiratory syncytial virus, Ebola virus and SARS-CoV infections. We then focus on the deployment of convalescent plasma and neutralizing mAbs for treatment of SARS-CoV-2. We review specific clin. questions, including the rationale for stratification of patients, potential biomarkers, known risk factors and temporal considerations for optimal clin. use. To answer these questions, there is a need to understand factors such as the kinetics of viral load and its correlation with clin. outcomes, endogenous antibody responses, pharmacokinetic properties of neutralizing mAbs and the potential benefit of combining antibodies to defend against emerging viral variants.
- 4Cagno, V.; Tseligka, E. D.; Jones, S. T.; Tapparel, C. Heparan Sulfate Proteoglycans and Viral Attachment: True Receptors or Adaptation Bias?. Viruses 2019, 11 (7), 596, DOI: 10.3390/v110705964https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXisVOgu7jO&md5=3cf85bf40431c53df1a530498ddabf4aHeparan sulfate proteoglycans and viral attachment: true receptors or adaptation bias?Cagno, Valeria; Tseligka, Eirini D.; Jones, Samuel T.; Tapparel, CarolineViruses (2019), 11 (7), 596CODEN: VIRUBR; ISSN:1999-4915. (MDPI AG)A review. Heparan sulfate proteoglycans (HSPG) are composed of unbranched, neg. charged heparan sulfate (HS) polysaccharides attached to a variety of cell surface or extracellular matrix proteins. Widely expressed, they mediate many biol. activities, including angiogenesis, blood coagulation, developmental processes, and cell homeostasis. HSPG are highly sulfated and broadly used by a range of pathogens, esp. viruses, to attach to the cell surface. In this review, we summarize the current knowledge on HSPG-virus interactions and distinguish viruses with established HS binding, viruses that bind HS only after intra-host or cell culture adaptation, and finally, viruses whose dependence on HS for infection is debated. We also provide an overview of the antiviral compds. designed to interfere with HS binding. Many questions remain about the true importance of these receptors in vivo, knowledge that is crit. for the design of future antiviral therapies.
- 5Zhang, Q.; Chen, C. Z.; Swaroop, M.; Xu, M.; Wang, L.; Lee, J.; Wang, A. Q.; Pradhan, M.; Hagen, N.; Chen, L.; Shen, M.; Luo, Z.; Xu, X.; Xu, Y.; Huang, W.; Zheng, W.; Ye, Y. Heparan Sulfate Assists SARS-CoV-2 in Cell Entry and Can Be Targeted by Approved Drugs in Vitro. Cell Discov 2020, 6 (1), 1– 14, DOI: 10.1038/s41421-020-00222-5There is no corresponding record for this reference.
- 6Dreyfuss, J. L.; Regatieri, C. V.; Jarrouge, T. R.; Cavalheiro, R. P.; Sampaio, L. O.; Nader, H. B. Heparan Sulfate Proteoglycans: Structure, Protein Interactions and Cell Signaling. Anais da Academia Brasileira de Ciências 2009, 81 (3), 409– 429, DOI: 10.1590/S0001-376520090003000076https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtF2isb7F&md5=1b9832c5fb965eb63b4efaa202d60551Heparan sulfate proteoglycans: structure, protein interactions and cell signalingDreyfuss, Juliana L.; Regatieri, Caio V.; Jarrouge, Thais R.; Cavalheiro, Renan P.; Sampaio, Lucia O.; Nader, Helena B.Anais da Academia Brasileira de Ciencias (2009), 81 (3), 409-429CODEN: AABCAD; ISSN:0001-3765. (Academia Brasileira de Ciencias)A review. Heparan sulfate proteoglycans are ubiquitously found at the cell surface and extracellular matrix in all the animal species. This review will focus on the structural characteristics of the heparan sulfate proteoglycans related to protein interactions leading to cell signaling. The heparan sulfate chains due to their vast structural diversity are able to bind and interact with a wide variety of proteins, such as growth factors, chemokines, morphogens, extracellular matrix components, enzymes, among others. There is a specificity directing the interactions of heparan sulfates and target proteins, regarding both the fine structure of the polysaccharide chain as well precise protein motifs. Heparan sulfates play a role in cellular signaling either as receptor or co-receptor for different ligands, and the activation of downstream pathways is related to phosphorylation of different cytosolic proteins either directly or involving cytoskeleton interactions leading to gene regulation. The role of the heparan sulfate proteoglycans in cellular signaling and endocytic uptake pathways is also discussed.
- 7Tyssen, D.; Henderson, S. A.; Johnson, A.; Sterjovski, J.; Moore, K.; La, J.; Zanin, M.; Sonza, S.; Karellas, P.; Giannis, M. P.; Krippner, G.; Wesselingh, S.; McCarthy, T.; Gorry, P. R.; Ramsland, P. A.; Cone, R.; Paull, J. R. A.; Lewis, G. R.; Tachedjian, G. Structure Activity Relationship of Dendrimer Microbicides with Dual Action Antiviral Activity. PLoS One 2010, 5 (8), e12309, DOI: 10.1371/journal.pone.00123097https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3cjptFKgtw%253D%253D&md5=71694f3917d902efec4a6a81cef9f1cbStructure activity relationship of dendrimer microbicides with dual action antiviral activityTyssen David; Henderson Scott A; Johnson Adam; Sterjovski Jasminka; Moore Katie; La Jennifer; Zanin Mark; Sonza Secondo; Karellas Peter; Giannis Michael P; Krippner Guy; Wesselingh Steve; McCarthy Tom; Gorry Paul R; Ramsland Paul A; Cone Richard; Paull Jeremy R A; Lewis Gareth R; Tachedjian GildaPloS one (2010), 5 (8), e12309 ISSN:.BACKGROUND: Topical microbicides, used by women to prevent the transmission of HIV and other sexually transmitted infections are urgently required. Dendrimers are highly branched nanoparticles being developed as microbicides. However, the anti-HIV and HSV structure-activity relationship of dendrimers comprising benzyhydryl amide cores and lysine branches, and a comprehensive analysis of their broad-spectrum anti-HIV activity and mechanism of action have not been published. METHODS AND FINDINGS: Dendrimers with optimized activity against HIV-1 and HSV-2 were identified with respect to the number of lysine branches (generations) and surface groups. Antiviral activity was determined in cell culture assays. Time-of-addition assays were performed to determine dendrimer mechanism of action. In vivo toxicity and HSV-2 inhibitory activity were evaluated in the mouse HSV-2 susceptibility model. Surface groups imparting the most potent inhibitory activity against HIV-1 and HSV-2 were naphthalene disulfonic acid (DNAA) and 3,5-disulfobenzoic acid exhibiting the greatest anionic charge and hydrophobicity of the seven surface groups tested. Their anti-HIV-1 activity did not appreciably increase beyond a second-generation dendrimer while dendrimers larger than two generations were required for potent anti-HSV-2 activity. Second (SPL7115) and fourth generation (SPL7013) DNAA dendrimers demonstrated broad-spectrum anti-HIV activity. However, SPL7013 was more active against HSV and blocking HIV-1 envelope mediated cell-to-cell fusion. SPL7013 and SPL7115 inhibited viral entry with similar potency against CXCR4-(X4) and CCR5-using (R5) HIV-1 strains. SPL7013 was not toxic and provided at least 12 h protection against HSV-2 in the mouse vagina. CONCLUSIONS: Dendrimers can be engineered with optimized potency against HIV and HSV representing a unique platform for the controlled synthesis of chemically defined multivalent agents as viral entry inhibitors. SPL7013 is formulated as VivaGel(R) and is currently in clinical development to provide protection against HIV and HSV. SPL7013 could also be combined with other microbicides.
- 8Price, C. F.; Tyssen, D.; Sonza, S.; Davie, A.; Evans, S.; Lewis, G. R.; Xia, S.; Spelman, T.; Hodsman, P.; Moench, T. R.; Humberstone, A.; Paull, J. R. A.; Tachedjian, G. SPL7013 Gel (VivaGel®) Retains Potent HIV-1 and HSV-2 Inhibitory Activity Following Vaginal Administration in Humans. PLoS One 2011, 6 (9), e24095, DOI: 10.1371/journal.pone.00240958https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXht1OmsrjE&md5=9aad48be0881c4ce10d97c33e59c02f3SPL7013 Gel (VivaGel) retains potent HIV-1 and HSV-2 inhibitory activity following vaginal administration in humansPrice, Clare F.; Tyssen, David; Sonza, Secondo; Davie, Ashley; Evans, Sonya; Lewis, Gareth R.; Xia, Shirley; Spelman, Tim; Hodsman, Peter; Moench, Thomas R.; Humberstone, Andrew; Paull, Jeremy R. A.; Tachedjian, GildaPLoS One (2011), 6 (9), e24095CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)SPL7013 Gel (VivaGel) is a microbicide in development for prevention of HIV and HSV. This clin. study assessed retention and duration of antiviral activity following vaginal administration of 3% SPL7013 Gel in healthy women. Participants received 5 single doses of product with ≥5 days between doses. A cervicovaginal fluid (CVF) sample was collected using a SoftCup pre-dose, and immediately, or 1, 3, 12 or 24 h post-dose. HIV-1 and HSV-2 antiviral activities of CVF samples were detd. in cell culture assays. Antiviral activity in the presence of seminal plasma was also tested. Mass and concn. of SPL7013 in CVF samples was detd. Safety was assessed by reporting of adverse events. Statistical anal. was performed using the Wilcoxon signed-rank test with Bonferroni adjustment; p ≤ 0.003 was significant. Eleven participants completed the study. Inhibition of HIV-1 and HSV-2 by pre-dose CVF samples was negligible. CVF samples obtained immediately after dosing almost completely inhibited (median, interquartile range) HIV-1 [96% (95,97)] and HSV-2 [86% (85,94)], and activity was maintained in all women at 3 h (HIV-1 [96% (95,98), p = 0.9]; HSV-2 [94% (91,97), p = 0.005]). At 24 h, >90% of initial HIV-1 and HSV-2 inhibition was maintained in 6/11 women. SPL7013 was recovered in CVF samples obtained at baseline (46% of 105 mg dose). At 3 and 24 h, 22 mg and 4 mg SPL7013, resp., were recovered. More than 70% inhibition of HIV-1 and HSV-2 was obsd. if there was >0.5 mg SPL7013 in CVF samples. High levels of antiviral activity were retained in the presence of seminal plasma. VivaGel was well tolerated with no signs or symptoms of vaginal, vulvar or cervical irritation reported. Potent antiviral activity was obsd. against HIV-1 and HSV-2 immediately following vaginal administration of VivaGel, with activity maintained for at least 3 h post-dose. The data provide evidence of antiviral activity in a clin. setting, and suggest VivaGel could be administered up to 3 h before coitus.
- 9Zelikin, A. N.; Stellacci, F. Broad-Spectrum Antiviral Agents Based on Multivalent Inhibitors of Viral Infectivity. Adv. Healthcare Mater. 2021, 10 (6), 2001433, DOI: 10.1002/adhm.2020014339https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvFegt7g%253D&md5=3a38a953dc83c1de54ae4c59fca380e6Broad-Spectrum Antiviral Agents Based on Multivalent Inhibitors of Viral InfectivityZelikin, Alexander N.; Stellacci, FrancescoAdvanced Healthcare Materials (2021), 10 (6), 2001433CODEN: AHMDBJ; ISSN:2192-2640. (Wiley-VCH Verlag GmbH & Co. KGaA)The ongoing pandemic of the coronavirus disease (Covid-19), caused by the spread of the severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), highlights the need for broad-spectrum antiviral drugs. In this Essay, it is argued that such agents already exist and are readily available while highlighting the challenges that remain to translate them into the clinic. Multivalent inhibitors of viral infectivity based on polymers or supramol. agents and nanoparticles are shown to be broadly acting against diverse pathogens in vitro as well as in vivo. Furthermore, uniquely, such agents can be virucidal. Polymers and nanoparticles are stable, do not require cold chain of transportation and storage, and can be obtained on large scale. Specifically, for the treatment of respiratory viruses and pulmonary diseases, these agents can be administered via inhalation/nebulization, as is currently investigated in clin. trials as a treatment against SARS CoV-2/Covid-19. It is believed that with due optimization and clin. validation, multivalent inhibitors of viral infectivity can claim their rightful position as broad-spectrum antiviral agents.
- 10Cagno, V.; Andreozzi, P.; D’Alicarnasso, M.; Jacob Silva, P.; Mueller, M.; Galloux, M.; Le Goffic, R.; Jones, S. T.; Vallino, M.; Hodek, J.; Weber, J.; Sen, S.; Janeček, E.-R.; Bekdemir, A.; Sanavio, B.; Martinelli, C.; Donalisio, M.; Rameix Welti, M.-A.; Eleouet, J.-F.; Han, Y.; Kaiser, L.; Vukovic, L.; Tapparel, C.; Král, P.; Krol, S.; Lembo, D.; Stellacci, F. Broad-Spectrum Non-Toxic Antiviral Nanoparticles with a Virucidal Inhibition Mechanism. Nat. Mater. 2018, 17 (2), 195– 203, DOI: 10.1038/nmat505310https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvF2lsbzN&md5=d66943a3a85ef5f924e1dd09fc308b59Broad-spectrum non-toxic antiviral nanoparticles with a virucidal inhibition mechanismCagno, Valeria; Andreozzi, Patrizia; D'Alicarnasso, Marco; Silva, Paulo Jacob; Mueller, Marie; Galloux, Marie; Le Goffic, Ronan; Jones, Samuel T.; Vallino, Marta; Hodek, Jan; Weber, Jan; Sen, Soumyo; Janecek, Emma-Rose; Bekdemir, Ahmet; Sanavio, Barbara; Martinelli, Chiara; Donalisio, Manuela; Rameix Welti, Marie-Anne; Eleouet, Jean-Francois; Han, Yanxiao; Kaiser, Laurent; Vukovic, Lela; Tapparel, Caroline; Kral, Petr; Krol, Silke; Lembo, David; Stellacci, FrancescoNature Materials (2018), 17 (2), 195-203CODEN: NMAACR; ISSN:1476-1122. (Nature Research)Viral infections kill millions yearly. Available antiviral drugs are virus-specific and active against a limited panel of human pathogens. There are broad-spectrum substances that prevent the first step of virus-cell interaction by mimicking heparan sulfate proteoglycans (HSPG), the highly conserved target of viral attachment ligands (VALs). The reversible binding mechanism prevents their use as a drug, because, upon diln., the inhibition is lost. Known VALs are made of closely packed repeating units, but the aforementioned substances are able to bind only a few of them. We designed antiviral nanoparticles with long and flexible linkers mimicking HSPG, allowing for effective viral assocn. with a binding that we simulate to be strong and multivalent to the VAL repeating units, generating forces (∼190 pN) that eventually lead to irreversible viral deformation. Virucidal assays, electron microscopy images, and mol. dynamics simulations support the proposed mechanism. These particles show no cytotoxicity, and in vitro nanomolar irreversible activity against herpes simplex virus (HSV), human papilloma virus, respiratory syncytial virus (RSV), dengue and lenti virus. They are active ex vivo in human cervicovaginal histocultures infected by HSV-2 and in vivo in mice infected with RSV.
- 11Al-Mahtab, M.; Bazinet, M.; Vaillant, A. Safety and Efficacy of Nucleic Acid Polymers in Monotherapy and Combined with Immunotherapy in Treatment-Naive Bangladeshi Patients with HBeAg+ Chronic Hepatitis B Infection. PLoS One 2016, 11 (6), e0156667, DOI: 10.1371/journal.pone.015666711https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFGisbrP&md5=043eb9625dbef15213157a967cff5125Safety and efficacy of nucleic acid polymers in monotherapy and combined with immunotherapy in treatment-naive Bangladeshi Patients with HBeAg+ chronic hepatitis B infectionAl-Mahtab, Mamun; Bazinet, Michel; Vaillant, AndrewPLoS One (2016), 11 (6), e0156667/1-e0156667/26CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)Previous in vivo studies have suggested that nucleic acid polymers (NAPs) may reduce circulating levels of HBsAg in the blood by blocking its release from infected hepatocytes and that this effect may have clin. benefit. NAP treatment, was evaluated in two clin. studies in patients with HBeAg pos. chronic HBV infection. The REP 101 study examd. REP 2055 monotherapy in 8 patients and the REP 102 study examd. REP 2139-Ca, in monotherapy in 12 patients, 9 of which transitioned to short term combined treatment with pegylated interferon alpha 2a or thymosin alpha 1. In both studies NAP monotherapy was accompanied by 2-7 log redns. of serum HBsAg, 3-9 log redns. in serum HBV DNA and the appearance of serum anti-HBsAg antibodies (10-1712 mIU / ml). Eight of the 9 patients transitioning to combined treatment with immunotherapy (pegylated interferon or thymosin alpha 1) in the REP 102 study experienced HBsAg loss and all 9 patients experienced substantial increases in serum anti-HBsAg antibody titers before withdrawal of therapy. For 52 wk after removal of REP 2055 therapy, rebound of serum viremia (HBV DNA > 1000 copies / ml, HBsAg > 1IU / ml) was not obsd. in 3 / 8 patients. Suppression of serum virema was further maintained for 290 and 231 wk in 2 of these patients. After withdrawal of all therapy in the 9 patients that transitioned to combination therapy in the REP 102 study, 8 patients achieved HBV DNA < 116 copies / ml after treatment withdrawal. Viral rebound occurred over a period of 12 to 123 wk in 7 patients but was still absent in two patients at 135 and 137 wk of follow-up. Administration tolerability issues obsd. with REP 2055 were rare with REP 2139-Ca but REP 2139-Ca therapy was accompanied by hair loss, dysphagia and dysgeusia which were considered related to heavy metal exposure endemic at the trial site. These preliminary studies suggest that NAP can elicit important antiviral responses during treatment which may improve the effect of immunotherapy. NAPs may be a potentially useful component of future combination therapies for the treatment of chronic hepatitis B.
- 12Vaillant, A. Nucleic Acid Polymers: Broad Spectrum Antiviral Activity, Antiviral Mechanisms and Optimization for the Treatment of Hepatitis B and Hepatitis D Infection. Antiviral Res. 2016, 133, 32– 40, DOI: 10.1016/j.antiviral.2016.07.00412https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xht1Klt7%252FN&md5=0a0e73dea3602854d1acd32a2e516e3bNucleic acid polymers: Broad spectrum antiviral activity, antiviral mechanisms and optimization for the treatment of hepatitis B and hepatitis D infectionVaillant, AndrewAntiviral Research (2016), 133 (), 32-40CODEN: ARSRDR; ISSN:0166-3542. (Elsevier B.V.)Antiviral polymers are a well-studied class of broad spectrum viral attachment/entry inhibitors whose activity increases with polymer length and with increased amphipathic (hydrophobic) character. The newest members of this class of compds. are nucleic acid polymers whose activity is derived from the sequence independent properties of phosphorothioated oligonucleotides as amphipathic polymers. Although the antiviral mechanisms and broad spectrum antiviral activity of nucleic acid polymers mirror the functionality of other members of this class, they exert in addn. a unique post entry activity in hepatitis B infection which inhibits the release of HBsAg from infected hepatocytes. This review provides a general overview of the antiviral polymer class with a focus on nucleic acid polymers and their development as therapeutic agents for the treatment of hepatitis B/hepatitis D. This article forms part of a symposium in Antiviral Research on ''An unfinished story: from the discovery of the Australia antigen to the development of new curative therapies for hepatitis B.''.
- 13Cagno, V.; Gasbarri, M.; Medaglia, C.; Gomes, D.; Clement, S.; Stellacci, F.; Tapparel, C. Sulfonated Nanomaterials with Broad-Spectrum Antiviral Activity Extending beyond Heparan Sulfate-Dependent Viruses. Antimicrob. Agents Chemother. 2020, 64 (12), e02001-20, DOI: 10.1128/AAC.02001-20There is no corresponding record for this reference.
- 14Sigl, C.; Willner, E. M.; Engelen, W.; Kretzmann, J. A.; Sachenbacher, K.; Liedl, A.; Kolbe, F.; Wilsch, F.; Aghvami, S. A.; Protzer, U.; Hagan, M. F.; Fraden, S.; Dietz, H. Programmable Icosahedral Shell System for Virus Trapping. Nat. Mater. 2021, 20 (9), 1281– 1289, DOI: 10.1038/s41563-021-01020-414https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhtlaltr3J&md5=bcdbcbd974dab9cec5328206d0c37ac1Programmable icosahedral shell system for virus trappingSigl, Christian; Willner, Elena M.; Engelen, Wouter; Kretzmann, Jessica A.; Sachenbacher, Ken; Liedl, Anna; Kolbe, Fenna; Wilsch, Florian; Aghvami, S. Ali; Protzer, Ulrike; Hagan, Michael F.; Fraden, Seth; Dietz, HendrikNature Materials (2021), 20 (9), 1281-1289CODEN: NMAACR; ISSN:1476-1122. (Nature Portfolio)Broad-spectrum antiviral platforms that can decrease or inhibit viral infection would alleviate many threats to global public health. Nonetheless, effective technologies of this kind are still not available. Here, we describe a programmable icosahedral canvas for the self-assembly of icosahedral shells that have viral trapping and antiviral properties. Programmable triangular building blocks constructed from DNA assemble with high yield into various shell objects with user-defined geometries and apertures. We have created shells with mol. masses ranging from 43 to 925 MDa (8 to 180 subunits) and with internal cavity diams. of up to 280 nm. The shell interior can be functionalized with virus-specific moieties in a modular fashion. We demonstrate this virus-trapping concept by engulfing hepatitis B virus core particles and adeno-assocd. viruses. We demonstrate the inhibition of hepatitis B virus core interactions with surfaces in vitro and the neutralization of infectious adeno-assocd. viruses exposed to human cells.
- 15Zeltins, A. Construction and Characterization of Virus-Like Particles: A Review. Mol. Biotechnol 2013, 53 (1), 92– 107, DOI: 10.1007/s12033-012-9598-415https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhvVCltLvO&md5=620c372bb5194d50ea629cc68de6b826Construction and Characterization of Virus-Like Particles: A ReviewZeltins, AndrisMolecular Biotechnology (2013), 53 (1), 92-107CODEN: MLBOEO; ISSN:1073-6085. (Springer)A review. Over the last 3 decades, virus-like particles (VLPs) have evolved to become a widely accepted technol., esp. in the field of vaccinol. In fact, some VLP-based vaccines are currently used as com. medical products, and other VLP-based products are at different stages of clin. study. Several remarkable advantages were achieved in the development of VLPs as gene therapy tools and new nanomaterials. The anal. of published data reveals that at least 110 VLPs were constructed from viruses belonging to 35 different families. This review therefore discusses the main principles in the cloning of viral structural genes, the relevant host systems and the purifn. procedures that were developed. In addn., the methods that are used to characterize the structural integrity, stability, and components, including the encapsidated nucleic acids, of newly synthesized VLPs are analyzed. Moreover, some of the modifications that are required to construct VLP-based carriers of viral origin with defined properties are discussed, and examples are provided.
- 16Chen, Y.; Maguire, T.; Hileman, R. E.; Fromm, J. R.; Esko, J. D.; Linhardt, R. J.; Marks, R. M. Dengue Virus Infectivity Depends on Envelope Protein Binding to Target Cell Heparan Sulfate. Nat. Med. 1997, 3 (8), 866– 871, DOI: 10.1038/nm0897-86616https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXltVKqtb0%253D&md5=8aa260764e3eafa6a48d75e6d923ea89Dengue virus infectivity depends on envelope protein binding to target cell heparan sulfateChen, Yaping; Maguire, Terry; Hileman, Ronald E.; Fromm, Jonathan R.; Esko, Jeffrey D.; Linhardt, Robert J.; Marks, Rory M.Nature Medicine (New York) (1997), 3 (8), 866-871CODEN: NAMEFI; ISSN:1078-8956. (Nature America)Dengue virus is a human pathogen that has reemerged as an increasingly important public health threat. The authors found that the cellular receptor utilized by dengue envelope protein to bind to target cells is a highly sulfated type of heparan sulfate. Heparin, highly sulfated heparan sulfate, and the polysulfonate pharmaceutical Suramin effectively prevented dengue virus infection of target cells, indicating that the envelope protein-target cell receptor interaction is a crit. determinant of infectivity. The dengue envelope protein sequence includes two putative glycosaminoglycan-binding motifs at the carboxy terminus; the first could be structurally modeled and formed an unusual extending binding surface of basic amino acids. Similar motifs were also identified in the envelope proteins of other flaviviridae. Developing pharmaceuticals that inhibit target cell binding may be an effective strategy for treating flavivirus infections.
- 17Yu, I.-M.; Zhang, W.; Holdaway, H. A.; Li, L.; Kostyuchenko, V. A.; Chipman, P. R.; Kuhn, R. J.; Rossmann, M. G.; Chen, J. Structure of the Immature Dengue Virus at Low PH Primes Proteolytic Maturation. Science 2008, 319 (5871), 1834– 1837, DOI: 10.1126/science.115326417https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXjs12ktr8%253D&md5=7f4bf5bd9e16a31dc93b50e9ecc0453cStructure of the Immature Dengue Virus at Low pH Primes Proteolytic MaturationYu, I-Mei; Zhang, Wei; Holdaway, Heather A.; Li, Long; Kostyuchenko, Victor A.; Chipman, Paul R.; Kuhn, Richard J.; Rossmann, Michael G.; Chen, JueScience (Washington, DC, United States) (2008), 319 (5871), 1834-1837CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Intracellular cleavage of immature flaviviruses is a crit. step in assembly that generates the membrane fusion potential of the E glycoprotein. With cryo-electron microscopy we show that the immature dengue particles undergo a reversible conformational change at low pH that renders them accessible to furin cleavage. At a pH of 6.0, the E proteins are arranged in a herringbone pattern with the pr peptides docked onto the fusion loops, a configuration similar to that of the mature virion. After cleavage, the dissocn. of pr is pH-dependent, suggesting that in the acidic environment of the trans-Golgi network pr is retained on the virion to prevent membrane fusion. These results suggest a mechanism by which flaviviruses are processed and stabilized in the host cell secretory pathway.
- 18Yu, I.-M.; Holdaway, H. A.; Chipman, P. R.; Kuhn, R. J.; Rossmann, M. G.; Chen, J. Association of the Pr Peptides with Dengue Virus at Acidic PH Blocks Membrane Fusion. Journal of Virology 2009, 83 (23), 12101– 12107, DOI: 10.1128/JVI.01637-0918https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsVyrtLrE&md5=c98479763c1b30a67ea3a047d14a042aAssociation of the pr peptides with dengue virus at acidic pH blocks membrane fusionYu, I.-M.; Holdaway, H. A.; Chipman, P. R.; Kuhn, R. J.; Rossmann, M. G.; Chen, J.Journal of Virology (2009), 83 (23), 12101-12107CODEN: JOVIAM; ISSN:0022-538X. (American Society for Microbiology)Flavivirus assembles into an inert particle that requires proteolytic activation by furin to enable transmission to other hosts. We previously showed that immature virus undergoes a conformational change at low pH that renders it accessible to furin. Here we show, using cryoelectron microscopy, that the structure of immature dengue virus at pH 6.0 is essentially the same before and after the cleavage of prM. The structure shows that after cleavage, the proteolytic product pr remains assocd. with the virion at acidic pH, and that furin cleavage by itself does not induce any major conformational changes. We also show by liposome cofloatation expts. that pr retention prevents membrane insertion, suggesting that pr is present on the virion in the trans-Golgi network to protect the progeny virus from fusion within the host cell.
- 19Lim, X.-X.; Chandramohan, A.; Lim, X. Y. E.; Bag, N.; Sharma, K. K.; Wirawan, M.; Wohland, T.; Lok, S.-M.; Anand, G. S. Conformational Changes in Intact Dengue Virus Reveal Serotype-Specific Expansion. Nat. Commun. 2017, 8 (1), 14339, DOI: 10.1038/ncomms1433919https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXisVyqtbg%253D&md5=ae877a0a6eb329bfcfd5aee8e3678acfConformational changes in intact dengue virus reveal serotype-specific expansionLim, Xin-Xiang; Chandramohan, Arun; Lim, Xin Ying Elisa; Bag, Nirmalya; Sharma, Kamal Kant; Wirawan, Melissa; Wohland, Thorsten; Lok, Shee-Mei; Anand, Ganesh S.Nature Communications (2017), 8 (), 14339CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37° (assocd. with host entry), despite high sequence and structural homol. among the 4 known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of 2 serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Forster Resonance Energy Transfer. Our results show temp.-dependent dynamics hotspots on DENV2 and DENV1 particles with DENV1 showing expansion at 40° but not at 37°. HDXMS measurement of virion dynamics in soln. offers a powerful approach to identify potential epitopes, map virus-antibody complex structure and dynamics, and test effects of multiple host-specific perturbations on viruses and virus-antibody complexes.
- 20San Martín, C. Virus Maturation. In Physical Virology: Virus Structure and Mechanics; Greber, U. F., Ed.; Advances in Experimental Medicine and Biology; Springer International Publishing: Cham, 2019; pp 129– 158. DOI: 10.1007/978-3-030-14741-9_7 .There is no corresponding record for this reference.
- 21Chai, N.; Chang, H. E.; Nicolas, E.; Han, Z.; Jarnik, M.; Taylor, J. Properties of Subviral Particles of Hepatitis B Virus. Journal of Virology 2008, 82 (16), 7812– 7817, DOI: 10.1128/JVI.00561-0821https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXpsVOqtLk%253D&md5=d025151c24848ae1389f12827d432e6fProperties of subviral particles of hepatitis B virusChai, Ning; Chang, Ho Eun; Nicolas, Emmanuelle; Han, Ziying; Jarnik, Michal; Taylor, JohnJournal of Virology (2008), 82 (16), 7812-7817CODEN: JOVIAM; ISSN:0022-538X. (American Society for Microbiology)In the sera of patients infected with hepatitis B virus (HBV), in addn. to infectious particles, there is an excess (typically 1000- to 100,000-fold) of empty subviral particles (SVP) composed solely of HBV envelope proteins in the form of relatively smaller spheres and filaments of variable length. Hepatitis delta virus (HDV) assembly also uses the envelope proteins of HBV to produce an infectious particle. Rate-zonal sedimentation was used to study the particles released from liver cell lines that produced SVP only, HDV plus SVP, and HBV plus SVP. The SVP made in the absence of HBV or HDV were further examd. by electron microscopy. They bound efficiently to heparin columns, consistent with an ability to bind cell surface glycosaminoglycans. However, unlike sol. forms of HBV envelope protein that were potent inhibitors, the SVP did not inhibit the ability of HBV and HDV to infect primary human hepatocytes.
- 22Engelhardt, F. A. S.; Praetorius, F.; Wachauf, C. H.; Brüggenthies, G.; Kohler, F.; Kick, B.; Kadletz, K. L.; Pham, P. N.; Behler, K. L.; Gerling, T.; Dietz, H. Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds. ACS Nano 2019, 13 (5), 5015– 5027, DOI: 10.1021/acsnano.9b0102522https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXnsV2ktbo%253D&md5=2fb7ea8b75471e18715911c299deeeb9Custom-Size, Functional, and Durable DNA Origami with Design-Specific ScaffoldsEngelhardt, Floris A. S.; Praetorius, Florian; Wachauf, Christian H.; Brueggenthies, Gereon; Kohler, Fabian; Kick, Benjamin; Kadletz, Karoline L.; Pham, Phuong Nhi; Behler, Karl L.; Gerling, Thomas; Dietz, HendrikACS Nano (2019), 13 (5), 5015-5027CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)DNA origami nano-objects are usually designed around generic single-stranded "scaffolds". Many properties of the target object are detd. by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable prodn. methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence compn. on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent crosslinking of DNA origami via UV irradn., and we built DNAzyme-contg. scaffolds that allow postfolding DNA origami domain sepn.
- 23Gerling, T.; Kube, M.; Kick, B.; Dietz, H. Sequence-Programmable Covalent Bonding of Designed DNA Assemblies. Sci. Adv. 2018, 4 (8), eaau1157, DOI: 10.1126/sciadv.aau1157There is no corresponding record for this reference.
- 24Kremer, J. R.; Mastronarde, D. N.; McIntosh, J. R. Computer Visualization of Three-Dimensional Image Data Using IMOD. J. Struct. Biol. 1996, 116 (1), 71– 76, DOI: 10.1006/jsbi.1996.001324https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADyaK28zmtFyqtg%253D%253D&md5=b6ab779bdec60f8644e254124c4dbbe7Computer visualization of three-dimensional image data using IMODKremer J R; Mastronarde D N; McIntosh J RJournal of structural biology (1996), 116 (1), 71-6 ISSN:1047-8477.We have developed a computer software package, IMOD, as a tool for analyzing and viewing three-dimensional biological image data. IMOD is useful for studying and modeling data from tomographic, serial section, and optical section reconstructions. The software allows image data to be visualized by several different methods. Models of the image data can be visualized by volume or contour surface rendering and can yield quantitative information.
- 25Zivanov, J.; Nakane, T.; Forsberg, B. O.; Kimanius, D.; Hagen, W. J.; Lindahl, E.; Scheres, S. H. New Tools for Automated High-Resolution Cryo-EM Structure Determination in RELION-3. eLife 2018, 7, e42166, DOI: 10.7554/eLife.4216625https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitlyqsrbL&md5=6ad79861243c29459be9b515e21c4b0eNew tools for automated high-resolution cryo-EM structure determination in RELION-3Zivanov, Jasenko; Nakane, Takanori; Forsberg, Bjoern O.; Kimanius, Dari; Hagen, Wim Jh; Lindahl, Erik; Scheres, Sjors HweLife (2018), 7 (), e42166/1-e42166/22CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addn. to GPU support, which provides flexibility in use of resources and avoids memory limitations. Ref.-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2Dclassification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estd. beam tilt provides higher resoln. reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resoln. for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beaminduced motion correction it leads to resoln. improvements of 0.2-0.7 Å compared to previous RELION versions.
- 26Zheng, S. Q.; Palovcak, E.; Armache, J.-P.; Verba, K. A.; Cheng, Y.; Agard, D. A. MotionCor2: Anisotropic Correction of Beam-Induced Motion for Improved Cryo-Electron Microscopy. Nat. Methods 2017, 14 (4), 331– 332, DOI: 10.1038/nmeth.419326https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjt1ags7g%253D&md5=5f4e225ef8123dacd8475d526175e1d2MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopyZheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul; Verba, Kliment A.; Cheng, Yifan; Agard, David A.Nature Methods (2017), 14 (4), 331-332CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)A review on anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Here we describe MotionCor2, a software tool for anisotropic correction of beam-induced motion. Overall, MotionCor2 is extremely robust and sufficiently accurate at correcting local motions so that the very time-consuming and computationally intensive particle polishing in RELION can be skipped, importantly, it also works on a wide range of data sets, including cryo tomog. tilt series.
- 27Rohou, A.; Grigorieff, N. CTFFIND4: Fast and Accurate Defocus Estimation from Electron Micrographs. J. Struct. Biol. 2015, 192 (2), 216– 221, DOI: 10.1016/j.jsb.2015.08.00827https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC287js1Whsg%253D%253D&md5=8500953ad4898ae82de6f8cdc95832cfCTFFIND4: Fast and accurate defocus estimation from electron micrographsRohou Alexis; Grigorieff NikolausJournal of structural biology (2015), 192 (2), 216-21 ISSN:.CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of the original algorithm while allowing for higher throughput. We also describe a measure of the quality of the fit as a function of spatial frequency and suggest this can be used to define the highest resolution at which CTF oscillations were successfully modeled.
- 28Wagner, T.; Merino, F.; Stabrin, M.; Moriya, T.; Antoni, C.; Apelbaum, A.; Hagel, P.; Sitsel, O.; Raisch, T.; Prumbaum, D.; Quentin, D.; Roderer, D.; Tacke, S.; Siebolds, B.; Schubert, E.; Shaikh, T. R.; Lill, P.; Gatsogiannis, C.; Raunser, S. SPHIRE-CrYOLO Is a Fast and Accurate Fully Automated Particle Picker for Cryo-EM. Commun. Biol. 2019, 2 (1), 1– 13, DOI: 10.1038/s42003-019-0437-zThere is no corresponding record for this reference.
- 29Liu, A. P.; Patel, S. K.; Xing, T.; Yan, Y.; Wang, S.; Li, N. Characterization of Adeno-Associated Virus Capsid Proteins Using Hydrophilic Interaction Chromatography Coupled with Mass Spectrometry. J. Pharm. Biomed. Anal. 2020, 189, 113481, DOI: 10.1016/j.jpba.2020.11348129https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsFejsbfL&md5=3b543b366df575802c058c1812cfc557Characterization of Adeno-Associated Virus Capsid Proteins Using Hydrophilic Interaction Chromatography Coupled with Mass SpectrometryLiu, Anita P.; Patel, Shailin K.; Xing, Tao; Yan, Yuetian; Wang, Shunhai; Li, NingJournal of Pharmaceutical and Biomedical Analysis (2020), 189 (), 113481CODEN: JPBADA; ISSN:0731-7085. (Elsevier B.V.)To support adeno-assocd. virus (AAV)-based gene therapy development, characterization of the three capsid viral proteins (VP; VP1/VP2/VP3) from recombinant AAV can offer insights on capsid identity, heterogeneity, and product and process consistency. Intact protein mass anal. is a rapid, reliable, and sensitive method to confirm AAV serotypes based on accurate mass measurement of the constituent capsid proteins. Compared to commonly applied reversed-phase liq. chromatog. (RPLC) methods, we demonstrated that, using a wide-pore amide-bonded column, hydrophilic interaction chromatog. (HILIC) could achieve improved sepn. of VPs from a variety of AAV serotypes using a generic method prior to MS detection. Moreover, HILIC-based sepn. was shown to be particularly sensitive in detecting capsid protein variants resulting from different post-translational modifications (PTMs) (e.g. phosphorylation and oxidn.) and protein backbone clippings, making it ideally suited for capsid heterogeneity characterization. To overcome the challenges assocd. with low protein concns. of AAV samples, as well as the trifluoroacetic acid (TFA)-induced ion suppression during HILIC-MS anal., different strategies were implemented to improve method sensitivity, including increasing the HILIC column loading and the application of a desolvation gas modification device. Finally, we demonstrated that this integrated HILIC-FLR-MS method can be generically applied to characterize a variety of AAV serotype samples at low concns. without any sample treatment to achieve unambiguous serotype identification, stoichiometry assessment, and PTM characterization.
- 30Hogle, J. M. Poliovirus Cell Entry: Common Structural Themes in Viral Cell Entry Pathways. Annu. Rev. Microbiol. 2002, 56 (1), 677– 702, DOI: 10.1146/annurev.micro.56.012302.16075730https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xos1Gisbw%253D&md5=a1441ea8f6da2b7ecb3390c70580f71bPoliovirus cell entry: Common structural themes in viral cell entry pathwaysHogle, James M.Annual Review of Microbiology (2002), 56 (), 677-702, 8 platesCODEN: ARMIAZ; ISSN:0066-4227. (Annual Reviews Inc.)A review. Structural studies of polio and closely related viruses have provided a series of snapshots along their cell entry pathways. Based on the structures and related kinetic, biochem., and genetic studies, we have proposed a model for the cell entry pathway for polio- and closely related viruses. In this model a maturation cleavage of a capsid protein precursor locks the virus in a metastable state, and the receptor acts like a transition-state catalyst to overcome an energy barrier and release the mature virion from the metastable state. This initiates a series of conformational changes that allow the virus to attach to membranes, form a pore, and finally release its RNA genome into the cytoplasm. This model has striking parallels with emerging models for the maturation and cell entry of more complex enveloped viruses such as influenza virus and HIV.
- 31Kuhn, R. J.; Zhang, W.; Rossmann, M. G.; Pletnev, S. V.; Corver, J.; Lenches, E.; Jones, C. T.; Mukhopadhyay, S.; Chipman, P. R.; Strauss, E. G.; Baker, T. S.; Strauss, J. H. Structure of Dengue Virus: Implications for Flavivirus Organization, Maturation, and Fusion. Cell 2002, 108 (5), 717– 725, DOI: 10.1016/S0092-8674(02)00660-831https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XisFOhtLk%253D&md5=317d9dd88f3e1411bcd452b749ca6a74Structure of dengue virus: implications for flavivirus organization, maturation, and fusionKuhn, Richard J.; Zhang, Wei; Rossmann, Michael G.; Pletnev, Sergei V.; Corver, Jeroen; Lenches, Edith; Jones, Christopher T.; Mukhopadhyay, Suchetana; Chipman, Paul R.; Strauss, Ellen G.; Baker, Timothy S.; Strauss, James H.Cell (Cambridge, MA, United States) (2002), 108 (5), 717-725CODEN: CELLB5; ISSN:0092-8674. (Cell Press)The first structure of a flavivirus has been detd. by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron d. map. The virus core, within a lipid bilayer, has a less-ordered structure than the external, icosahedral scaffold of 90 glycoprotein E dimers. The three E monomers per icosahedral asym. unit do not have quasiequivalent sym. environments. Difference maps indicate the location of the small membrane protein M relative to the overlaying scaffold of E dimers. The structure suggests that flaviviruses, and by analogy also alphaviruses, employ a fusion mechanism in which the distal β barrels of domain II of the glycoprotein E are inserted into the cellular membrane.
- 32Chan, M. C. W.; Shan Kwan, H.; Chan, P. K. S. Structure and Genotypes of Noroviruses. Norovirus 2017, 51– 63, DOI: 10.1016/B978-0-12-804177-2.00004-X32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXptVOksL0%253D&md5=be590cf6e239762901ae0752d7300cb9Structure and genotypes of norovirusesChan, Martin C. W.; Kwan, Hoi Shan; Chan, Paul K. S.Norovirus (2017), (), 51-63CODEN: 69VTVG ISSN:. (Elsevier Ltd.)A review. In this chapter, we discuss the structure and genotypes of noroviruses as well as the latest research developments with an aim to provide more clues for those who are interested in pursuing the ultimate answers to these questions. Human norovinises are ubiquitous and highly infectious. Structural determinants of their super environmental stability remain poorly understood, partly due to the lack of a robust and efficient in vitro culture system to assess virus infectivity. This suggests that noroviruses may have an ancient origin. Some animal noroviruses (e.g., porcine GII-11, GII.18, and Gil. 19) are closely related to human noroviruses.
- 33Goetschius, D. J.; Hartmann, S. R.; Subramanian, S.; Bator, C. M.; Christensen, N. D.; Hafenstein, S. L. High Resolution Cryo EM Analysis of HPV16 Identifies Minor Structural Protein L2 and Describes Capsid Flexibility. Sci. Rep 2021, 11 (1), 3498, DOI: 10.1038/s41598-021-83076-533https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXjvFOlurk%253D&md5=16b76d91aff472c4135d1092d40c5610High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibilityGoetschius, Daniel J.; Hartmann, Samantha R.; Subramanian, Suriyasri; Bator, Carol M.; Christensen, Neil D.; Hafenstein, Susan L.Scientific Reports (2021), 11 (1), 3498CODEN: SRCEC3; ISSN:2045-2322. (Nature Research)Abstr.: Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. HPV is epitheliotropic and its replication is tightly assocd. with terminal keratinocyte differentiation making prodn. and purifn. of high titer virus prepns. for research problematic, therefore alternative HPV prodn. methods have been developed for virol. and structural studies. In this study we use HPV16 quasivirus, composed of HPV16 L1/L2 capsid proteins with a packaged cottontail rabbit papillomavirus genome. We have achieved the first high resoln., 3.1 Å, structure of HPV16 by using a local subvolume refinement approach. The high resoln. enabled us to build L1 unambiguously and identify L2 protein strands. The L2 d. is incorporated adjacent to conserved L1 residues on the interior of the capsid. Further interpretation with our own software for Icosahedral Subvolume Extn. and Correlated Classification revealed flexibility, on the whole-particle level through diam. anal. and local movement with inter-capsomer anal. Inter-capsomer expansion or contraction, governed by the connecting arms, showed no bias in the magnitude or direction of capsomer movement. We propose that papillomavirus capsids are dynamic and capsomers move as rigid bodies connected by flexible linkers. The resulting virus structure will provide a framework for continuing biochem., genetic and biophys. research for papillomaviruses. Furthermore, our approach has allowed insight into the resoln. barrier that has previously been a limitation in papillomavirus structural studies.
- 34Yao, H.; Song, Y.; Chen, Y.; Wu, N.; Xu, J.; Sun, C.; Zhang, J.; Weng, T.; Zhang, Z.; Wu, Z.; Cheng, L.; Shi, D.; Lu, X.; Lei, J.; Crispin, M.; Shi, Y.; Li, L.; Li, S. Molecular Architecture of the SARS-CoV-2 Virus. Cell 2020, 183 (3), 730– 738, DOI: 10.1016/j.cell.2020.09.01834https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvFKjs7nM&md5=7bd110334cb42931034a4eb5f9d2ff00Molecular Architecture of the SARS-CoV-2 VirusYao, Hangping; Song, Yutong; Chen, Yong; Wu, Nanping; Xu, Jialu; Sun, Chujie; Zhang, Jiaxing; Weng, Tianhao; Zhang, Zheyuan; Wu, Zhigang; Cheng, Linfang; Shi, Danrong; Lu, Xiangyun; Lei, Jianlin; Crispin, Max; Shi, Yigong; Li, Lanjuan; Li, SaiCell (Cambridge, MA, United States) (2020), 183 (3), 730-738.e13CODEN: CELLB5; ISSN:0092-8674. (Cell Press)SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, the detailed architecture of the intact virus remains to be unveiled. Here we report the mol. assembly of the authentic SARS-CoV-2 virus using cryoelectron tomog. (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in pre- and postfusion conformations were detd. to av. resolns. of 8.7-11 Å. Compns. of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed overall processing states of the native glycans highly similar to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNPs) and their higher-order assemblies were revealed. Overall, these characterizations revealed the architecture of the SARS-CoV-2 virus in exceptional detail and shed light on how the virus packs its ∼30-kb-long single-segmented RNA in the ∼80-nm-diam. lumen.
- 35Yap, M. L.; Klose, T.; Urakami, A.; Hasan, S. S.; Akahata, W.; Rossmann, M. G. Structural Studies of Chikungunya Virus Maturation. Proc. Natl. Acad. Sci. U. S. A. 2017, 114 (52), 13703– 13707, DOI: 10.1073/pnas.171316611435https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvFWgsrbJ&md5=c67a1673d7da05489772d3da4594f162Structural studies of Chikungunya virus maturationYap, Moh Lan; Klose, Thomas; Urakami, Akane; Hasan, S. Saif; Akahata, Wataru; Rossmann, Michael G.Proceedings of the National Academy of Sciences of the United States of America (2017), 114 (52), 13703-13707CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here, we present a cryo-electron microscopy (cryo-EM), 6.8-Å resoln. structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus had a larger radius and were less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins had less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addn., the nucleocapsid of the immature virus was more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the post-translational processing of the spikes and nucleocapsid is necessary to produce an infectious virus.
- 36Mangala Prasad, V.; Klose, T.; Rossmann, M. G. Assembly, Maturation and Three-Dimensional Helical Structure of the Teratogenic Rubella Virus. PLoS Pathog 2017, 13 (6), e1006377, DOI: 10.1371/journal.ppat.1006377There is no corresponding record for this reference.
- 37Russell, W. C. Adenoviruses: Update on Structure and Function. Journal of General Virology 2009, 90 (1), 1– 20, DOI: 10.1099/vir.0.003087-037https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXlsVyqsQ%253D%253D&md5=78fd91b454da057c8defc77b7b141539Adenoviruses: Update on structure and functionRussell, W. C.Journal of General Virology (2009), 90 (1), 1-20CODEN: JGVIAY; ISSN:0022-1317. (Society for General Microbiology)A review. Adenoviruses have been studied intensively for over 50 years as models of virus-cell interactions and latterly as gene vectors. With the advent of more sophisticated structural anal. techniques the disposition of most of the 13 structural proteins have been defined to a reasonable level. This review seeks to describe the functional properties of these proteins and shows that they all have a part to play in deciding the outcome of an infection and act at every level of the virus's path through the host cell. They are primarily involved in the induction of the different arms of the immune system and a better understanding of their overall properties should lead to more effective ways of combating virus infections.
Supporting Information
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsnano.1c11328.
Methods and additional data, including further characterization of HS derivatives, handle positions, viruses/VLPs, and binding conditions. All staple sequences for each triangular subunit/shell, in addition to assembly and folding conditions (PDF)
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