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Pawel GT, Ma Y, Wu Y, Lu Y, Peinetti AS. Binding Affinity Measurements Between DNA Aptamers and their Virus Targets Using ELONA and MST. Bio Protoc 2022; 12:e4548. [PMID: 36505027 PMCID: PMC9709635 DOI: 10.21769/bioprotoc.4548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/28/2022] [Accepted: 09/04/2022] [Indexed: 11/06/2022] Open
Abstract
Aptamers have been selected with strong affinity and high selectivity for a wide range of targets, as recently highlighted by the development of aptamer-based sensors that can differentiate infectious from non-infectious viruses, including human adenovirus and SARS-CoV-2. Accurate determination of the binding affinity between the DNA aptamers and their viral targets is the first step to understanding the molecular recognition of viral particles and the potential uses of aptamers in various diagnostics and therapeutic applications. Here, we describe protocols to obtain the binding curve of the DNA aptamers to SARS-CoV-2 using Enzyme-Linked Oligonucleotide Assay (ELONA) and MicroScale Thermophoresis (MST). These methods allow for the determination of the binding affinity of the aptamer to the infectious SARS-CoV-2 and the selectivity of this aptamer against the same SARS-CoV-2 that has been rendered non-infectious by UV inactivation, and other viruses. Compared to other techniques like Electrophoretic Mobility Shift Assay (EMSA), Surface Plasmon Resonance (SPR), and Isothermal Titration Calorimetry (ITC), these methods have advantages for working with larger particles like viruses and with samples that require biosafety level 2 facilities.
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Affiliation(s)
- Gregory T. Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
| | - Yuan Ma
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States
| | - Yuting Wu
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
,
Department of Chemistry, University of Texas at Austin, Austin, Texas, United States
,
*For correspondence:
;
| | - Ana Sol Peinetti
- INQUIMAE (CONICET), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
,
*For correspondence:
;
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2
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Li N, Zhao B, Stavins R, Peinetti AS, Chauhan N, Bashir R, Cunningham BT, King WP, Lu Y, Wang X, Valera E. Overcoming the limitations of COVID-19 diagnostics with nanostructures, nucleic acid engineering, and additive manufacturing. CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 2022; 26:100966. [PMID: 34840515 PMCID: PMC8604633 DOI: 10.1016/j.cossms.2021.100966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 05/04/2023]
Abstract
The COVID-19 pandemic revealed fundamental limitations in the current model for infectious disease diagnosis and serology, based upon complex assay workflows, laboratory-based instrumentation, and expensive materials for managing samples and reagents. The lengthy time delays required to obtain test results, the high cost of gold-standard PCR tests, and poor sensitivity of rapid point-of-care tests contributed directly to society's inability to efficiently identify COVID-19-positive individuals for quarantine, which in turn continues to impact return to normal activities throughout the economy. Over the past year, enormous resources have been invested to develop more effective rapid tests and laboratory tests with greater throughput, yet the vast majority of engineering and chemistry approaches are merely incremental improvements to existing methods for nucleic acid amplification, lateral flow test strips, and enzymatic amplification assays for protein-based biomarkers. Meanwhile, widespread commercial availability of new test kits continues to be hampered by the cost and time required to develop single-use disposable microfluidic plastic cartridges manufactured by injection molding. Through development of novel technologies for sensitive, selective, rapid, and robust viral detection and more efficient approaches for scalable manufacturing of microfluidic devices, we can be much better prepared for future management of infectious pathogen outbreaks. Here, we describe how photonic metamaterials, graphene nanomaterials, designer DNA nanostructures, and polymers amenable to scalable additive manufacturing are being applied towards overcoming the fundamental limitations of currently dominant COVID-19 diagnostic approaches. In this paper, we review how several distinct classes of nanomaterials and nanochemistry enable simple assay workflows, high sensitivity, inexpensive instrumentation, point-of-care sample-to-answer virus diagnosis, and rapidly scaled manufacturing.
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Affiliation(s)
- Nantao Li
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
| | - Bin Zhao
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
| | - Robert Stavins
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, United States
| | - Ana Sol Peinetti
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Neha Chauhan
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
| | - Rashid Bashir
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - Brian T Cunningham
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - William P King
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, United States
| | - Yi Lu
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Xing Wang
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Enrique Valera
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
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3
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Peinetti AS, Lake RJ, Cong W, Cooper L, Wu Y, Ma Y, Pawel GT, Toimil-Molares ME, Trautmann C, Rong L, Mariñas B, Azzaroni O, Lu Y. Direct detection of human adenovirus or SARS-CoV-2 with ability to inform infectivity using DNA aptamer-nanopore sensors. SCIENCE ADVANCES 2021; 7:eabh2848. [PMID: 34550739 PMCID: PMC8457657 DOI: 10.1126/sciadv.abh2848] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/02/2021] [Indexed: 05/20/2023]
Abstract
Viral infections are a major global health issue, but no current method allows rapid, direct, and ultrasensitive quantification of intact viruses with the ability to inform infectivity, causing misdiagnoses and spread of the viruses. Here, we report a method for direct detection and differentiation of infectious from noninfectious human adenovirus and SARS-CoV-2, as well as from other virus types, without any sample pretreatment. DNA aptamers are selected from a DNA library to bind intact infectious, but not noninfectious, virus and then incorporated into a solid-state nanopore, which allows strong confinement of the virus to enhance sensitivity down to 1 pfu/ml for human adenovirus and 1 × 104 copies/ml for SARS-CoV-2. Applications of the aptamer-nanopore sensors in different types of water samples, saliva, and serum are demonstrated for both enveloped and nonenveloped viruses, making the sensor generally applicable for detecting these and other emerging viruses of environmental and public health concern.
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Affiliation(s)
- Ana S. Peinetti
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ryan J. Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wen Cong
- Department of Civil and Environmental Engineering, Safe Global Water Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Yuting Wu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuan Ma
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gregory T. Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - María Eugenia Toimil-Molares
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291, Germany
- Corresponding author. (Y.L.); (O.A.); (B.M.); (L.R.); (M.E.T.-M.)
| | - Christina Trautmann
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291, Germany
- Technische Universitat Darmstadt, Darmstadt 64287, Germany
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Corresponding author. (Y.L.); (O.A.); (B.M.); (L.R.); (M.E.T.-M.)
| | - Benito Mariñas
- Department of Civil and Environmental Engineering, Safe Global Water Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Corresponding author. (Y.L.); (O.A.); (B.M.); (L.R.); (M.E.T.-M.)
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET, Boulevard 113 y 64, La Plata 1900, Argentina
- Corresponding author. (Y.L.); (O.A.); (B.M.); (L.R.); (M.E.T.-M.)
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Corresponding author. (Y.L.); (O.A.); (B.M.); (L.R.); (M.E.T.-M.)
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4
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Exploring peptide studies related to SARS-CoV to accelerate the development of novel therapeutic and prophylactic solutions against COVID-19. J Infect Public Health 2021; 14:1106-1119. [PMID: 34280732 PMCID: PMC8253661 DOI: 10.1016/j.jiph.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/18/2021] [Accepted: 06/27/2021] [Indexed: 01/18/2023] Open
Abstract
Recent advances in peptide research revolutionized therapeutic discoveries for various infectious diseases. In view of the ongoing threat of the COVID-19 pandemic, there is an urgent need to develop potential therapeutic options. Intense and accomplishing research is being carried out to develop broad-spectrum vaccines and treatment options for corona viruses, due to the risk of recurrent infection by the existing strains or pandemic outbreaks by new mutant strains. Developing a novel medicine is costly and time consuming, which increases the value of repurposing existing therapies. Since, SARS-CoV-2 shares significant genomic homology with SARS-CoV, we have summarized various peptides identified against SARS-CoV using in silico and molecular studies and also the peptides effective against SARS-CoV-2. Dissecting the molecular mechanisms underlying viral infection could yield fundamental insights in the discovery of new antiviral agents, targeting viral proteins or host factors. We postulate that these peptides can serve as effective components for therapeutic options against SARS-CoV-2, supporting clinical scientists globally in selectively identifying and testing the therapeutic and prophylactic agents for COVID-19 treatment. In addition, we also summarized the latest updates on peptide therapeutics against SARS-CoV-2.
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5
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Wang N, Rosen O, Wang L, Turner HL, Stevens LJ, Corbett KS, Bowman CA, Pallesen J, Shi W, Zhang Y, Leung K, Kirchdoerfer RN, Becker MM, Denison MR, Chappell JD, Ward AB, Graham BS, McLellan JS. Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD. Cell Rep 2020; 28:3395-3405.e6. [PMID: 31553909 PMCID: PMC6935267 DOI: 10.1016/j.celrep.2019.08.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/06/2019] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) protein have been characterized, but much less is known about antibodies targeting non-RBD epitopes. Here, we report the structural and functional characterization of G2, a neutralizing antibody targeting the MERS-CoV S1 N-terminal domain (S1-NTD). Structures of G2 alone and in complex with the MERS-CoV S1-NTD define a site of vulnerability comprising two loops, each of which contain a residue mutated in G2-escape variants. Cell-surface binding studies and in vitro competition experiments demonstrate that G2 strongly disrupts the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4), with the inhibition requiring the native trimeric S conformation. These results advance our understanding of antibody-mediated neutralization of coronaviruses and should facilitate the development of immunotherapeutics and vaccines against MERS-CoV. The epitope for the neutralizing antibody G2 is confined to the apex of the MERS-CoV S1-NTD G2 epitope is relatively well conserved G2 IgG and Fab both neutralize pseudotyped and authentic MERS-CoV G2 neutralizes by preventing the binding of DPP4 to trimeric S protein
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Affiliation(s)
- Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Osnat Rosen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Laura J Stevens
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Charles A Bowman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jesper Pallesen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Robert N Kirchdoerfer
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michelle M Becker
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Mark R Denison
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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6
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Sabarimurugan S, Dharmarajan A, Warrier S, Subramanian M, Swaminathan R. Comprehensive review on the prevailing COVID-19 therapeutics and the potential of repurposing SARS-CoV-1 candidate drugs to target SARS-CoV-2 as a fast-track treatment and prevention option. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1247. [PMID: 33178779 PMCID: PMC7607133 DOI: 10.21037/atm-20-4071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent seemingly uncontrollable pandemic caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has been able to spread quickly due to the non-availability of effective antivirals or vaccines. The virus has structural and non-structural proteins that are considered as possible targets. Receptor recognition is the critical determinant and preliminary phase of viral infection to enter the host cell and causes tissue tropism. We have conducted a comprehensive review of relevant publication on in vitro, in silico, in vivo and clinical evaluation of drug candidates ranging from broad-spectrum antivirals to natural molecules targeted towards viral spike protein in addition to evaluate their suitability as therapies based on an analysis of the similarities between SARS-CoV-1 and SARS-CoV-2. In general, antiviral targets are based on two strategies, either targeting the host or the host’s immune cell. We have reviewed the available details on the SARS-CoV-2 strain’s host-viral binding sites entry mechanism, alongside recently tested effective antivirals. The hypothesis of this review may provide clear insight for researchers and physicians who are struggling to narrow down scientific options to control the current pandemic. Overall, we found that the promising efficacious drug candidates reported against SARS-CoV-1 could be considered for drug repurposing; this might help to identify a potential drug for therapeutic measures and development of vaccine for COVID-19.
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Affiliation(s)
- Shanthi Sabarimurugan
- School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | - Arun Dharmarajan
- CHIRI, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Department of Biomedical Sciences, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.,Department of Human Sciences, Faculty of Life Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Sudha Warrier
- CHIRI, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,School of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore, India
| | - Maheswari Subramanian
- Department of Microbiology, Centre for Research and PG Studies, Indian Academy of Degree College (Aut), Bangalore, India
| | - Rajarajan Swaminathan
- Centre for Drug Design, Discovery and Development, SRM University, Sonipat, Haryana, New Delhi, India
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8
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Bickerton E, Maier HJ, Stevenson-Leggett P, Armesto M, Britton P. The S2 Subunit of Infectious Bronchitis Virus Beaudette Is a Determinant of Cellular Tropism. J Virol 2018; 92:e01044-18. [PMID: 30021894 PMCID: PMC6146808 DOI: 10.1128/jvi.01044-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022] Open
Abstract
The spike (S) glycoprotein of the avian gammacoronavirus infectious bronchitis virus (IBV) is comprised of two subunits (S1 and S2), has a role in virulence in vivo, and is responsible for cellular tropism in vitro We have previously demonstrated that replacement of the S glycoprotein ectodomain from the avirulent Beaudette strain of IBV with the corresponding region from the virulent M41-CK strain resulted in a recombinant virus, BeauR-M41(S), with the in vitro cell tropism of M41-CK. The IBV Beaudette strain is able to replicate in both primary chick kidney cells and Vero cells, whereas the IBV M41-CK strain replicates in primary cells only. In order to investigate the region of the IBV S responsible for growth in Vero cells, we generated a series of recombinant IBVs expressing chimeric S glycoproteins, consisting of regions from the Beaudette and M41-CK S gene sequences, within the genomic background of Beaudette. The S2, but not the S1, subunit of the Beaudette S was found to confer the ability to grow in Vero cells. Various combinations of Beaudette-specific amino acids were introduced into the S2 subunit of M41 to determine the minimum requirement to confer tropism for growth in Vero cells. The ability of IBV to grow and produce infectious progeny virus in Vero cells was subsequently narrowed down to just 3 amino acids surrounding the S2' cleavage site. Conversely, swapping of the 3 Beaudette-associated amino acids with the corresponding ones from M41 was sufficient to abolish Beaudette growth in Vero cells.IMPORTANCE Infectious bronchitis remains a major problem in the global poultry industry, despite the existence of many different vaccines. IBV vaccines, both live attenuated and inactivated, are currently grown on embryonated hen's eggs, a cumbersome and expensive process due to the fact that most IBV strains do not grow in cultured cells. The reverse genetics system for IBV creates the opportunity for generating rationally designed and more effective vaccines. The observation that IBV Beaudette has the additional tropism for growth on Vero cells also invokes the possibility of generating IBV vaccines produced from cultured cells rather than by the use of embryonated eggs. The regions of the IBV Beaudette S glycoprotein involved in the determination of extended cellular tropism were identified in this study. This information will enable the rational design of a future generation of IBV vaccines that may be grown on Vero cells.
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Li J, Helal ZH, Karch CP, Mishra N, Girshick T, Garmendia A, Burkhard P, Khan MI. A self-adjuvanted nanoparticle based vaccine against infectious bronchitis virus. PLoS One 2018; 13:e0203771. [PMID: 30216376 PMCID: PMC6138407 DOI: 10.1371/journal.pone.0203771] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022] Open
Abstract
Infectious bronchitis virus (IBV) affects poultry respiratory, renal and reproductive systems. Currently the efficacy of available live attenuated or killed vaccines against IBV has been challenged. We designed a novel IBV vaccine alternative using a highly innovative platform called Self-Assembling Protein Nanoparticle (SAPN). In this vaccine, B cell epitopes derived from the second heptad repeat (HR2) region of IBV spike proteins were repetitively presented in its native trimeric conformation. In addition, flagellin was co-displayed in the SAPN to achieve a self-adjuvanted effect. Three groups of chickens were immunized at four weeks of age with the vaccine prototype, IBV-Flagellin-SAPN, a negative-control construct Flagellin-SAPN or a buffer control. The immunized chickens were challenged with 5x104.7 EID50 IBV M41 strain. High antibody responses were detected in chickens immunized with IBV-Flagellin-SAPN. In ex vivo proliferation tests, peripheral mononuclear cells (PBMCs) derived from IBV-Flagellin-SAPN immunized chickens had a significantly higher stimulation index than that of PBMCs from chickens receiving Flagellin-SAPN. Chickens immunized with IBV-Flagellin-SAPN had a significant reduction of tracheal virus shedding and lesser tracheal lesion scores than did negative control chickens. The data demonstrated that the IBV-Flagellin-SAPN holds promise as a vaccine for IBV.
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Affiliation(s)
- Jianping Li
- Department of Pathobiology and Veterinary Science University of Connecticut, Storrs, CT, United States of America
| | - Zeinab H. Helal
- Department of Pathobiology and Veterinary Science University of Connecticut, Storrs, CT, United States of America
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Christopher P. Karch
- The Institute of Material Sciences, University of Connecticut, Storrs, CT, United States of America
| | - Neha Mishra
- Department of Pathobiology and Veterinary Science University of Connecticut, Storrs, CT, United States of America
| | - Theodore Girshick
- Charles River Laboratories, Avian vaccine services, North Franklin, CT, United States of America
| | - Antonio Garmendia
- Department of Pathobiology and Veterinary Science University of Connecticut, Storrs, CT, United States of America
| | - Peter Burkhard
- The Institute of Material Sciences, University of Connecticut, Storrs, CT, United States of America
- Department of Molecular Cell Biology, University of Connecticut, Storrs, CT, United States of America
- Alpha-O-Peptides AG, Riehen, Switzerland
| | - Mazhar I. Khan
- Department of Pathobiology and Veterinary Science University of Connecticut, Storrs, CT, United States of America
- * E-mail:
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10
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Kingsley CN, Antanasijevic A, Palka-Hamblin H, Durst M, Ramirez B, Lavie A, Caffrey M. Probing the metastable state of influenza hemagglutinin. J Biol Chem 2017; 292:21590-21597. [PMID: 29127198 DOI: 10.1074/jbc.m117.815043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/05/2017] [Indexed: 12/24/2022] Open
Abstract
Viral entry into host cells is mediated by membrane proteins in a metastable state that transition to a more stable state upon a stimulus. For example, in the influenza envelope protein hemagglutinin (HA), the low pH in the endosome triggers a transition from the metastable prefusion conformation to the stable fusion conformation. To identify probes that interfere with HA function, here we screened a library of H7 HA peptides for inhibition of H7 HA-mediated entry. We discovered a peptide, PEP87 (WSYNAELLVAMENQHTI), that inhibited H7 and H5 HA-mediated entry. PEP87 corresponds to a highly conserved helical region of the HA2 subunit of HA that self-interacts in the neutral pH conformation. Mutagenesis experiments indicated that PEP87 binds to its native region in the HA trimer. We also found that PEP87 is unstructured in isolation but tends to form a helix as evidenced by CD and NMR studies. Fluorescence, chemical cross-linking, and saturation transfer difference NMR data suggested that PEP87 binds to the neutral pH conformation of HA and disrupts the HA structure without affecting its oligomerization state. Together, this work provides support for a model in which PEP87 disrupts HA function by displacing native interactions of the neutral pH conformation. Moreover, our observations indicate that the HA prefusion structure (and perhaps the metastable states of other viral entry proteins) is more dynamic with transient motions being larger than generally appreciated. These findings also suggest that the ensemble of prefusion structures presents many potential sites for targeting in therapeutic interventions.
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Affiliation(s)
- Carolyn N Kingsley
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Aleksandar Antanasijevic
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Helena Palka-Hamblin
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Matthew Durst
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Benjamin Ramirez
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Arnon Lavie
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Michael Caffrey
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
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11
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Chen Q, Tang K, Zhang X, Chen P, Guo Y. Establishment of pseudovirus infection mouse models for in vivo pharmacodynamics evaluation of filovirus entry inhibitors. Acta Pharm Sin B 2017; 8:200-208. [PMID: 29719780 PMCID: PMC5925413 DOI: 10.1016/j.apsb.2017.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/23/2017] [Accepted: 08/28/2017] [Indexed: 10/25/2022] Open
Abstract
Filoviruses cause severe and fatal viral hemorrhagic fever in humans. Filovirus research has been extensive since the 2014 Ebola outbreak. Due to their high pathogenicity and mortality, live filoviruses require Biosafety Level-4 (BSL-4) facilities, which have restricted the development of anti-filovirus vaccines and drugs. An HIV-based pseudovirus cell infection assay is widely used for viral entry studies in BSL-2 conditions. Here, we successfully constructed nine in vitro pseudo-filovirus models covering all filovirus genera and three in vivo pseudo-filovirus-infection mouse models using Ebola virus, Marburg virus, and Lloviu virus as representative viruses. The pseudo-filovirus-infected mice showed visualizing bioluminescence in a dose-dependent manner. A bioluminescence peak in mice was reached on day 5 post-infection for Ebola virus and Marburg virus and on day 4 post-infection for Lloviu virus. Two known filovirus entry inhibitors, clomiphene and toremiphene, were used to validate the model. Collectively, our study shows that all genera of filoviruses can be well-pseudotyped and are infectious in vitro. The pseudo-filovirus-infection mouse models can be used for in vivo activity evaluation of anti-filovirus drugs. This sequential in vitro and in vivo evaluation system of filovirus entry inhibitors provides a secure and efficient platform for screening and assessing anti-filovirus agents in BSL-2 facilities.
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Key Words
- 3D, 3-dimensional
- BDBV, Bundibugyo virus
- BSL, Biosafety Level
- CLO, clomiphene
- DLIT, Diffuse Luminescence Imaging Tomography
- EBOV, Ebola virus
- Ebola
- Entry inhibitor
- Filovirus
- GP, glycoprotein
- IC50, the 50% inhibitory concentration
- LLOV, Lloviu virus
- MARV, Marburg virus
- Marburg
- Mouse model
- Pseudovirus
- RAVV, Ravn virus
- RESTV, Reston virus
- ROI, region of interest
- SD, standard deviation
- SEM, standard error of the mean
- SUDV, Sudan virus
- TAFV, Taï forest virus
- TORE, toremiphene
- VSV-G, vesicular stomatitis virus glycoprotein
- d.p.i., day post-infection
- h.p.i., hour post-infection
- i.p., intraperitoneally
- lg, logarithm
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12
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Yang Y, Cheng H, Yan H, Wang PZ, Rong R, Zhang YY, Zhang CB, Du RK, Rong LJ. A cell-based high-throughput protocol to screen entry inhibitors of highly pathogenic viruses with Traditional Chinese Medicines. J Med Virol 2016; 89:908-916. [PMID: 27704591 PMCID: PMC7167059 DOI: 10.1002/jmv.24705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 12/03/2022]
Abstract
Emerging viruses such as Ebola virus (EBOV), Lassa virus (LASV), and avian influenza virus H5N1 (AIV) are global health concerns. Since there is very limited options (either vaccine or specific therapy) approved for humans against these viruses, there is an urgent need to develop prophylactic and therapeutic treatments. Previously we reported a high‐throughput screening (HTS) protocol to identify entry inhibitors for three highly pathogenic viruses (EBOV, LASV, and AIV) using a human immunodeficiency virus–based pseudotyping platform which allows us to perform the screening in a BSL‐2 facility. In this report, we have adopted this screening protocol to evaluate traditional Chinese Medicines (TCMs) in an effort to discover entry inhibitors against these viruses. Here we show that extracts of the following Chinese medicinal herbs exhibit potent anti‐Ebola viral activities: Gardenia jasminoides Ellis, Citrus aurantium L., Viola yedoensis Makino, Prunella vulgaris L., Coix lacryma‐jobi L. var. mayuen (Roman.) Stapf, Pinellia ternata (Thunb.) Breit., and Morus alba L. This study represents a proof‐of‐principle investigation supporting the suitability of this assay for rapid screening TCMs and identifying putative entry inhibitors for these viruses. J. Med. Virol. 89:908–916, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yong Yang
- Shandong University of Traditional Chinese Medicine, Jinan, China.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Han Cheng
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Hui Yan
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Peng-Zhan Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Rong Rong
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ying-Ying Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Cheng-Bo Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Rui-Kun Du
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Li-Jun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
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13
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Cheng H, Koning K, O'Hearn A, Wang M, Rumschlag-Booms E, Varhegyi E, Rong L. A parallel genome-wide RNAi screening strategy to identify host proteins important for entry of Marburg virus and H5N1 influenza virus. Virol J 2015; 12:194. [PMID: 26596270 PMCID: PMC4657351 DOI: 10.1186/s12985-015-0420-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/09/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genome-wide RNAi screening has been widely used to identify host proteins involved in replication and infection of different viruses, and numerous host factors are implicated in the replication cycles of these viruses, demonstrating the power of this approach. However, discrepancies on target identification of the same viruses by different groups suggest that high throughput RNAi screening strategies need to be carefully designed, developed and optimized prior to the large scale screening. METHODS Two genome-wide RNAi screens were performed in parallel against the entry of pseudotyped Marburg viruses and avian influenza virus H5N1 utilizing an HIV-1 based surrogate system, to identify host factors which are important for virus entry. A comparative analysis approach was employed in data analysis, which alleviated systematic positional effects and reduced the false positive number of virus-specific hits. RESULTS The parallel nature of the strategy allows us to easily identify the host factors for a specific virus with a greatly reduced number of false positives in the initial screen, which is one of the major problems with high throughput screening. The power of this strategy is illustrated by a genome-wide RNAi screen for identifying the host factors important for Marburg virus and/or avian influenza virus H5N1 as described in this study. CONCLUSIONS This strategy is particularly useful for highly pathogenic viruses since pseudotyping allows us to perform high throughput screens in the biosafety level 2 (BSL-2) containment instead of the BSL-3 or BSL-4 for the infectious viruses, with alleviated safety concerns. The screening strategy together with the unique comparative analysis approach makes the data more suitable for hit selection and enables us to identify virus-specific hits with a much lower false positive rate.
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Affiliation(s)
- Han Cheng
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
| | - Katie Koning
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
| | - Aileen O'Hearn
- Present address: US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD21702, USA.
| | - Minxiu Wang
- Present address: Malcolm X College, Chicago, IL, 60612, USA.
| | | | - Elizabeth Varhegyi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
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14
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Zhao F, Han Z, Zhang T, Shao Y, Kong X, Ma H, Liu S. Genomic characteristics and changes of avian infectious bronchitis virus strain CK/CH/LDL/97I after serial passages in chicken embryos. Intervirology 2014; 57:319-30. [PMID: 25195733 PMCID: PMC7179551 DOI: 10.1159/000365193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 06/07/2014] [Indexed: 12/12/2022] Open
Abstract
Background We previously attenuated the infectious bronchitis virus (IBV) strain CK/CH/LDL/97I and found that it can convey protection against the homologous pathogenic virus. Objective To compare the full-length genome sequences of the Chinese IBV strain CK/CH/LDL/97I and its embryo-passaged, attenuated level to identify sequence substitutions responsible for the attenuation and define markers of attenuation. Methods The full-length genomes of CK/CH/LDL/97I P5 and P115 were amplified and sequenced. The sequences were assembled and compared using the MEGALIGN program (DNAStar) and a phylogenetic tree was constructed using MEGA4 software. Results The CK/CH/LDL/97I virus population contained subpopulations with a mixture of genetic mutants. Changes were observed in nsp4, nsp9, nsp11/12, nsp14, nsp15, nsp16, and ORF3a, but these did not result in amino acid substitutions or did not show functional variations. Amino acid substitutions occurred in the remaining genes between P5 and P115; most were found in the S region, and some of the nucleotide mutations resulted in amino acid substitutions. Among the 9 nsps in the ORF1 region, nsp3 contained the most nucleotide substitutions. Conclusions Sequence variations in different genes, especially the S gene and nsp3, in the genomes of CK/CH/LDL/97I viruses might contribute to differences in viral replication, pathogenicity, antigenicity, immunogenicity, and tissue tropism.
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Affiliation(s)
- Fei Zhao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, PR China
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15
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Antanasijevic A, Basu A, Bowlin TL, Mishra RK, Rong L, Caffrey M. Mutagenesis studies of the H5 influenza hemagglutinin stem loop region. J Biol Chem 2014; 289:22237-45. [PMID: 24947513 DOI: 10.1074/jbc.m114.572974] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Influenza outbreaks, particularly the pandemic 1918 H1 and avian H5 strains, are of high concern to public health. The hemagglutinin envelope protein of influenza plays a critical role in viral entry and thus is an attractive target for inhibition of virus entry. The highly conserved stem loop region of hemagglutinin has been shown to undergo critically important conformational changes during the entry process and, moreover, to be a site for inhibition of virus entry by antibodies, small proteins, and small drug-like molecules. In this work we probe the structure-function properties of the H5 hemagglutinin stem loop region by site-directed mutagenesis. We find that most mutations do not disrupt expression, proteolytic processing, incorporation into virus, or receptor binding; however, many of the mutations disrupt the entry process. We further assess the effects of mutations on inhibition of entry by a neutralizing monoclonal antibody (C179) and find examples of increased and decreased sensitivity to the antibody, consistent with the antibody binding site observed by x-ray crystallography. In addition, we tested the sensitivity of the mutants to MBX2329, a small molecule inhibitor of influenza entry. Interestingly, the mutants exhibit increased and decreased sensitivities to MBX2329, which gives further insight into the binding site of the compound on HA and potential mechanisms of escape. Finally, we have modeled the binding site of MBX2329 using molecular dynamics and find that the resulting structure is in good agreement with the mutagenesis results. Together these studies underscore the importance of the stem loop region to HA function and suggest potential sites for therapeutic intervention of influenza entry.
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Affiliation(s)
- Aleksandar Antanasijevic
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Arnab Basu
- Microbiotix Inc., Worcester, Massachusetts 01605
| | | | - Rama K Mishra
- the Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, and
| | - Lijun Rong
- the Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois 60612
| | - Michael Caffrey
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607,
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16
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Qureshi A, Thakur N, Tandon H, Kumar M. AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic Acids Res 2013; 42:D1147-53. [PMID: 24285301 PMCID: PMC3964995 DOI: 10.1093/nar/gkt1191] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Antiviral peptides (AVPs) have exhibited huge potential in inhibiting viruses by targeting various stages of their life cycle. Therefore, we have developed AVPdb, available online at http://crdd.osdd.net/servers/avpdb, to provide a dedicated resource of experimentally verified AVPs targeting over 60 medically important viruses including Influenza, HCV, HSV, RSV, HBV, DENV, SARS, etc. However, we have separately provided HIV inhibiting peptides in ‘HIPdb’. AVPdb contains detailed information of 2683 peptides, including 624 modified peptides experimentally tested for antiviral activity. In modified peptides a chemical moiety is attached for increasing their efficacy and stability. Detailed information include: peptide sequence, length, source, virus targeted, virus family, cell line used, efficacy (qualitative/quantitative), target step/protein, assay used in determining the efficacy and PubMed reference. The database also furnishes physicochemical properties and predicted structure for each peptide. We have provided user-friendly browsing and search facility along with other analysis tools to help the users. Entering of many synthetic peptide-based drugs in various stages of clinical trials reiterate the importance for the AVP resources. AVPdb is anticipated to cater to the needs of scientific community working for the development of antiviral therapeutics.
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Affiliation(s)
- Abid Qureshi
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh-160036, India
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17
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Antanasijevic A, Cheng H, Wardrop DJ, Rong L, Caffrey M. Inhibition of influenza H7 hemagglutinin-mediated entry. PLoS One 2013; 8:e76363. [PMID: 24194835 PMCID: PMC3806803 DOI: 10.1371/journal.pone.0076363] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/26/2013] [Indexed: 12/20/2022] Open
Abstract
The recent outbreak of H7N9 influenza in China is of high concern to public health. H7 hemagglutinin (HA) plays a critical role in influenza entry and thus HA presents an attractive target for antivirals. Previous studies have suggested that the small molecule tert-butyl hydroquinone (TBHQ) inhibits the entry of influenza H3 HA by binding to the stem loop of HA and stabilizing the neutral pH conformation of HA, thereby disrupting the membrane fusion step. Based on amino acid sequence, structure and immunogenicity, H7 is a related Group 2 HA. In this work we show, using a pseudovirus entry assay, that TBHQ inhibits H7 HA-mediated entry, as well as H3 HA-mediated entry, with an IC50 ~ 6 µM. Using NMR, we show that TBHQ binds to the H7 stem loop region. STD NMR experiments indicate that the aromatic ring of TBHQ makes extensive contact with the H7 HA surface. Limited proteolysis experiments indicate that TBHQ inhibits influenza entry by stabilizing the H7 HA neutral pH conformation. Together, this work suggests that the stem loop region of H7 HA is an attractive target for therapeutic intervention and that TBHQ, which is a widely used food preservative, is a promising lead compound.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Han Cheng
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Duncan J. Wardrop
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Lijun Rong
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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18
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Wang J, Cheng H, Ratia K, Varhegyi E, Hendrickson WG, Li J, Rong L. A comparative high-throughput screening protocol to identify entry inhibitors of enveloped viruses. ACTA ACUST UNITED AC 2013; 19:100-7. [PMID: 23821643 DOI: 10.1177/1087057113494405] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Emerging and reemerging human viral pathogens pose great public health concerns since therapeutics against these viruses are limited. Thus, there is an urgent need to develop novel drugs that can block infection of either a specific virus or a number of viruses. Viral entry is thought to be an ideal target for potential therapeutic prevention. One of the challenges of developing antivirals is that most of these viruses are highly pathogenic and therefore require high biosafety-level containment. In this study, we have adopted a comparative high-throughput screening protocol to identify entry inhibitors for three enveloped viruses (Marburg virus, influenza virus H5N1, and Lassa virus) using a human immunodeficiency virus-based pseudotyping platform. We demonstrate the utility of this approach by screening a small compound library and identifying putative entry inhibitors for these viruses. One major advantage of this protocol is to reduce the number of false positives in hit selection, and we believe that the protocol is useful for inhibitor screening for many enveloped viruses.
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Affiliation(s)
- Juan Wang
- 1Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, IL, USA
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19
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Britton P, Armesto M, Cavanagh D, Keep S. Modification of the avian coronavirus infectious bronchitis virus for vaccine development. Bioeng Bugs 2012; 3:114-9. [PMID: 22179147 DOI: 10.4161/bbug.18983] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Infectious bronchitis virus (IBV) causes an infectious respiratory disease of domestic fowl that affects poultry of all ages causing economic problems for the poultry industry worldwide. Although IBV is controlled using live attenuated and inactivated vaccines it continues to be a major problem due to the existence of many serotypes, determined by the surface spike protein resulting in poor cross-protection, and loss of immunogenicity associated with vaccine production. Live attenuated IBV vaccines are produced by the repeated passage in embryonated eggs resulting in spontaneous mutations. As a consequence attenuated viruses have only a few mutations responsible for the loss of virulence, which will differ between vaccines affecting virulence and/or immunogenicity and can revert to virulence. A new generation of vaccines is called for and one means of controlling IBV involves the development of new and safer vaccines by precisely modifying the IBV genome using reverse genetics for the production of rationally attenuated IBVs in order to obtain an optimum balance between loss of virulence and capacity to induce immunity.
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Affiliation(s)
- Paul Britton
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, UK.
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20
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Celigoy J, Ramirez B, Caffrey M. SARS-CoV heptad repeat 2 is a trimer of parallel helices. Protein Sci 2011; 20:2125-9. [PMID: 21922588 PMCID: PMC3302656 DOI: 10.1002/pro.736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 09/08/2011] [Indexed: 01/25/2023]
Abstract
In severe acute respiratory syndrome coronavirus, the envelope heptad repeat 2 (HR2) plays a critical role in viral entry. Moreover, HR2 is both the target for novel antiviral therapies and, as an isolated peptide, presents a potential antiviral therapeutic. The structure of HR2, as determined by NMR spectroscopy in the presence of the co-solvent trifluoroethanol (TFE), is a trimer of parallel helices, whereas the structure of HR2, as determined by X-ray crystallography, is a tetramer of anti-parallel helices. In this work, we added a nitroxide spin label to the N-terminal region of HR2 and used paramagnetic relaxation enhancement to assess the orientation of the HR2 helices under different solution conditions. We find that the relaxation effects are consistent with an orientation corresponding to a trimer of parallel helices in both the presence and absence of TFE. This work suggests that the different orientation and oligomerization states observed by NMR and X-ray are due to the 11 additional residues present at the N-terminus of the NMR construct.
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Affiliation(s)
| | | | - Michael Caffrey
- Department of Biochemistry & Molecular Genetics, University of Illinois at ChicagoChicago, Illinois 60607
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21
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Celigoy J, McReynolds S, Caffrey M. The SARS-CoV heptad repeat 2 exhibits pH-induced helix formation. Biochem Biophys Res Commun 2011; 412:483-6. [PMID: 21835164 PMCID: PMC7092892 DOI: 10.1016/j.bbrc.2011.07.126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 07/27/2011] [Indexed: 11/28/2022]
Abstract
The heptad repeats 1 and 2 of SARS-CoV spike, termed HR1 and HR2, play critical roles in viral entry. Moreover, HR1 and HR2 derived free peptides are inhibitors of SARS-CoV entry. In this work we used circular dichroism to show that HR2 helix formation is induced at pH 5, the pH of the endosome. In addition, we demonstrate that the HR2 helix is further stabilized at physiological ionic strengths. Together, these observations provide new insight into the mechanism of SARS-CoV entry and suggest that HR2 may be an attractive target for therapeutic intervention.
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Affiliation(s)
- Jessica Celigoy
- Department of Biochemistry & Molecular Genetics University of Illinois at Chicago, Chicago, IL 60607, USA
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22
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Armesto M, Evans S, Cavanagh D, Abu-Median AB, Keep S, Britton P. A recombinant avian infectious bronchitis virus expressing a heterologous spike gene belonging to the 4/91 serotype. PLoS One 2011; 6:e24352. [PMID: 21912629 PMCID: PMC3166170 DOI: 10.1371/journal.pone.0024352] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/05/2011] [Indexed: 12/11/2022] Open
Abstract
We have shown previously that replacement of the spike (S) gene of the apathogenic IBV strain Beau-R with that from the pathogenic strain of the same serotype, M41, resulted in an apathogenic virus, BeauR-M41(S), that conferred protection against challenge with M41. We have constructed a recombinant IBV, BeauR-4/91(S), with the genetic backbone of Beau-R but expressing the spike protein of the pathogenic IBV strain 4/91(UK), which belongs to a different serogroup as Beaudette or M41. Similar to our previous findings with BeauR-M41(S), clinical signs observations showed that the S gene of the pathogenic 4/91 virus did not confer pathogenicity to the rIBV BeauR-4/91(S). Furthermore, protection studies showed there was homologous protection; BeauR-4/91(S) conferred protection against challenge with wild type 4/91 virus as shown by the absence of clinical signs, IBV RNA assessed by qRT-PCR and the fact that no virus was isolated from tracheas removed from birds primarily infected with BeauR-4/91(S) and challenged with IBV 4/91(UK). A degree of heterologous protection against M41 challenge was observed, albeit at a lower level.Our results confirm and extend our previous findings and conclusions that swapping of the ectodomain of the S protein is a precise and effective way of generating genetically defined candidate IBV vaccines.
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Affiliation(s)
- Maria Armesto
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - Sharon Evans
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - David Cavanagh
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - Abu-Bakr Abu-Median
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - Sarah Keep
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
| | - Paul Britton
- Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire, United Kingdom
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23
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Mohan KVK, Rao SS, Atreya CD. Antiviral activity of selected antimicrobial peptides against vaccinia virus. Antiviral Res 2010; 86:306-11. [PMID: 20347875 PMCID: PMC7114312 DOI: 10.1016/j.antiviral.2010.03.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 03/05/2010] [Accepted: 03/23/2010] [Indexed: 01/28/2023]
Abstract
Antimicrobial peptides (AMPs) are gaining importance as effective therapeutic alternatives to conventional antibiotics. Recently we have shown that a set of nine synthetic antimicrobial peptides, four originating from thrombin-induced human platelet-derived antimicrobial proteins named PD1-PD4 and five synthetic repeats of arginine-tryptophan (RW) repeats (RW1-5) demonstrate antibacterial activity in plasma and platelets. Using WR strain of vaccinia virus (VV) as a model virus for enveloped virus in the present study, we tested the same nine synthetic peptides for their antiviral activity. A cell culture-based standard plaque reduction assay was utilized to estimate antiviral effectiveness of the peptides. Our analysis revealed that peptides PD3, PD4, and RW3 were virucidal against VV with PD3 demonstrating the highest antiviral activity of 100-fold reduction in viral titers, whereas, PD4 and RW3 peptide treatments resulted in 10-30-fold reduction. The EC(50) values of PD3, PD4 and RW3 were found to be 40 microg/ml, 50 microg/ml and 6.5 microM, respectively. In VV-spiked plasma samples, the virucidal activity of PD3, PD4 and RW3 was close to 100% (90-100-fold reduction). Overall, the present study constitutes a new proof-of-concept in developing peptide therapeutics for vaccinia virus infections in biothreat scenarios and as in vitro viral reduction agents.
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Affiliation(s)
- Ketha V K Mohan
- Section of Cell Biology, Laboratory of Cellular Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA.
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24
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Berry JD, Hay K, Rini JM, Yu M, Wang L, Plummer FA, Corbett CR, Andonov A. Neutralizing epitopes of the SARS-CoV S-protein cluster independent of repertoire, antigen structure or mAb technology. MAbs 2010; 2:53-66. [PMID: 20168090 DOI: 10.4161/mabs.2.1.10788] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Neutralizing antibody responses to the surface glycoproteins of enveloped viruses play an important role in immunity. Many of these glycoproteins, including the severe acute respiratory syndrome-coronavirus (SARS-CoV) spike (S) protein form trimeric units in the membrane of the native virion. There is substantial experimental and pre-clinical evidence showing that the S protein is a promising lead for vaccines and therapeutics. Previously we generated a panel of monoclonal antibodies (mAbs) to whole inactivated SARS-CoV which neutralize the virus in vitro. Here, we define their specificity and affinity, map several of their epitopes and lastly characterise chimeric versions of them. Our data show that the neutralizing mAbs bind to the angiotensin-converting enzyme 2 (ACE2) receptor-binding domain (RBD) of the SARS S protein. Three of the chimeric mAbs retain their binding specificity while one conformational mAb, F26G19, lost its ability to bind the S protein despite high level expression. The affinity for recombinant S is maintained in all of the functional chimeric versions of the parental mAbs. Both parental mAb F26G18 and the chimeric version neutralize the TO R2 strain of SARS-CoV with essentially identical titres (2.07 and 2.47 nM, respectively). Lastly, a comparison with other neutralizing mAbs to SARS-CoV clearly shows that the dominance of a 33 amino acid residue loop of the SARS-CoV RBD is independent of repertoire, species, quaternary structure, and importantly, the technology used to derive the mAbs. In cases like this, the dominance of a compact RBD antigenic domain and the central role of the S protein in pathogenesis may inherently create immunoselection pressure on viruses to evolve more complex evasion strategies or die out of a host species. The apparent simplicity of the mechanism of SARS-CoV neutralization is in stark contrast to the complexity shown by other enveloped viruses.
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Affiliation(s)
- Jody D Berry
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada.
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