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Ramachandran B, Nadeem A, Mohanprasanth A, Saravanan M. Prediction of deleterious non-synonymous SNPs of TMPRSS2 protein combined with Molecular Dynamics Simulations and free energy analysis to identify the potential peptide substrates against SARS-CoV-2. J Biomol Struct Dyn 2024:1-15. [PMID: 38592189 DOI: 10.1080/07391102.2024.2330710] [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: 12/17/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
Globally the SARS-CoV-2 viral infection demands for the new drugs, the TMPRSS2 target plays a vital role in facilitating the virus entry. The aim of the present study is to identify the potential peptide substrate from the Anti-viral database against TMPRSS2 of SARS-CoV-2. The compound screening and variation analysis were performed using molecular docking analysis and online tools such as PROVEAN and SNAP2 server, respectively. The re-docked crystal structure peptide substrate exhibits -128.151 kcal/mol whereas the RRKK peptide substrate shows -134.158 kcal/mol. Further, the selected compounds were proceeded with Molecular Dynamics Simulation, it explores the stability of the complex by revealing the hotspot residues (His296 and Ser441) were active for nucleophilic attack against TMPRSS2. The average Binding Free Energy values computed through MM/GBSA for RRKK, Camostat, and Crystal Structure were shown -69.9278 kcal/mol, -64.5983 kcal/mol, and -63.9755 kcal/mol, respectively against TMPRSS2. The 'rate of acylation' emerges as an indicator for RRKK's efficacy, it maintains the distance of 3.2 Å with Ser441 resembles, whilst its -NH backbone stabilizes at 2.5 Å 'Michaelis Complex' which leads to prevent the entry of SARS-CoV-2 to human cells. The sequence variation analysis explores that the V160 and G6 substitutions are essential to emphasize the uncover possibilities for the ongoing drug discovery research. Therefore, the identified peptide substrate found to be potent against SARS-CoV-2 and these results will be valuable for ongoing drug discovery research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Balajee Ramachandran
- Structural and Computational Biology Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, India
- Department of Pharmacology, Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Aruchamy Mohanprasanth
- AMR & Nanotherapeutics Lab, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical, Sciences (SIMATS), Chennai, Tamil Nadu, India
| | - Muthupandian Saravanan
- AMR & Nanotherapeutics Lab, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical, Sciences (SIMATS), Chennai, Tamil Nadu, India
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2
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Gholami S, Mafakher L, Fotouhi F, Bambai B, Cohan RA, Mehrbod P, Shokouhi H, Farahmand B. Computational peptide engineering approach for selection of the new C05 antibody-driven peptide with potency to blocking influenza a virus attachment; from in silico to in vivo. J Biomol Struct Dyn 2023:1-17. [PMID: 37553776 DOI: 10.1080/07391102.2023.2241554] [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: 05/04/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023]
Abstract
Antiviral drugs are currently used to prevent or treat viral infections like influenza A Virus (IAV). Nonetheless, annual genetic mutations of influenza viruses make them resistant to efficient treatment by current medications. Antiviral peptides have recently attracted researchers' attention and can potentially supplant the current medications. This study aimed to design peptides against IAV propagation. For this purpose, P2 and P3 peptides were computationally designed based on the HCDR3 region of the C05 antibody (a monoclonal antibody that neutralizes influenza HA protein and inhibits the virus attachment). The synthesized peptides were tested against the influenza A virus (A/Puerto Rico/8/34 (H1N1)) in vitro, and the most efficient peptide was selected for in vivo experiments. It was shown that the designed peptide shows much more prophylactic and therapeutic effects against the virus. These findings demonstrated that the designed peptide can control the virus infection without any cytotoxicity effect. Antiviral peptide design is acknowledged as a critical tactic to manage viral infections by preventing viral binding to the host cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shima Gholami
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fatemeh Fotouhi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Bijan Bambai
- Department of Systems Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Parvaneh Mehrbod
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Hadiseh Shokouhi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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3
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Agamennone M, Fantacuzzi M, Vivenzio G, Scala MC, Campiglia P, Superti F, Sala M. Antiviral Peptides as Anti-Influenza Agents. Int J Mol Sci 2022; 23:11433. [PMID: 36232735 PMCID: PMC9569631 DOI: 10.3390/ijms231911433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Influenza viruses represent a leading cause of high morbidity and mortality worldwide. Approaches for fighting flu are seasonal vaccines and some antiviral drugs. The development of the seasonal flu vaccine requires a great deal of effort, as careful studies are needed to select the strains to be included in each year's vaccine. Antiviral drugs available against Influenza virus infections have certain limitations due to the increased resistance rate and negative side effects. The highly mutative nature of these viruses leads to the emergence of new antigenic variants, against which the urgent development of new approaches for antiviral therapy is needed. Among these approaches, one of the emerging new fields of "peptide-based therapies" against Influenza viruses is being explored and looks promising. This review describes the recent findings on the antiviral activity, mechanism of action and therapeutic capability of antiviral peptides that bind HA, NA, PB1, and M2 as a means of countering Influenza virus infection.
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Affiliation(s)
- Mariangela Agamennone
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Marialuigia Fantacuzzi
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Giovanni Vivenzio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Maria Carmina Scala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Fabiana Superti
- National Centre for Innovative Technologies in Public Health, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
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4
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Viral Aggregation: The Knowns and Unknowns. Viruses 2022; 14:v14020438. [PMID: 35216031 PMCID: PMC8879382 DOI: 10.3390/v14020438] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 11/21/2022] Open
Abstract
Viral aggregation is a complex and pervasive phenomenon affecting many viral families. An increasing number of studies have indicated that it can modulate critical parameters surrounding viral infections, and yet its role in viral infectivity, pathogenesis, and evolution is just beginning to be appreciated. Aggregation likely promotes viral infection by increasing the cellular multiplicity of infection (MOI), which can help overcome stochastic failures of viral infection and genetic defects and subsequently modulate their fitness, virulence, and host responses. Conversely, aggregation can limit the dispersal of viral particles and hinder the early stages of establishing a successful infection. The cost–benefit of viral aggregation seems to vary not only depending on the viral species and aggregating factors but also on the spatiotemporal context of the viral life cycle. Here, we review the knowns of viral aggregation by focusing on studies with direct observations of viral aggregation and mechanistic studies of the aggregation process. Next, we chart the unknowns and discuss the biological implications of viral aggregation in their infection cycle. We conclude with a perspective on harnessing the therapeutic potential of this phenomenon and highlight several challenging questions that warrant further research for this field to advance.
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Zhang J, Zhang Z, Pu L, Tang J, Guo F. AIEpred: An Ensemble Predictive Model of Classifier Chain to Identify Anti-Inflammatory Peptides. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1831-1840. [PMID: 31985437 DOI: 10.1109/tcbb.2020.2968419] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Anti-inflammatory peptides (AIEs) have recently emerged as promising therapeutic agent for treatment of various inflammatory diseases, such as rheumatoid arthritis and Alzheimer's disease. Therefore, detecting the correlation between amino acid sequence and its anti-inflammatory property is of great importance for the discovery of new AIEs. To address this issue, we propose a novel prediction tool for accurate identification of peptides as anti-inflammatory epitopes or non anti-inflammatory epitopes. Most of all, we encode the original peptide sequence for better mining and exploring the information and patterns, based on the three feature representations as amino acid contact, position specific scoring matrix, physicochemical property. At the same time, we exploit several feature extraction models and utilize one feature selection model, in order to construct many base classifiers from various feature representations. More specifically, we develop an effective classification model, with which we can extract and learn a set of informative features from the ensemble classifier chain model with different group of base classifiers. Furthermore, in order to test the predictive power of our model, we conduct the comparative experiments on the leave-one-out cross-validation and the independent test. It shows that our novel predictor performs great accurate for identification of AIEs as well as existing outstanding prediction tools. Source codes are available at https://github.com/guofei-tju/Ensemble-classifier-chain-model.
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6
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Zarif F, Anasir MI, Koh JX, Chew MF, Poh CL. Stability and antiviral activity of SP40 peptide in human serum. Virus Res 2021; 303:198456. [PMID: 34314773 DOI: 10.1016/j.virusres.2021.198456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/29/2021] [Accepted: 05/15/2021] [Indexed: 12/27/2022]
Abstract
Enterovirus A71 (EV-A71) is one of the main causative agents of hand, foot and mouth disease (HFMD). SP40 peptide was previously identified to inhibit EV-A71 strains from genotypes A, B and C. However, the stability and antiviral activity of SP40 peptide in human serum are yet to be established. To address this, we evaluated the stability and anti-EV-A71 activity of SP40 peptide after incubation in 25 % human serum. Reverse-phase high-performance liquid chromatography (RP-HPLC) and liquid chromatography-mass spectrometry (LC/MS) were utilized to evaluate serum stability and cleavage patterns of SP40 peptide after incubation in human serum. Cell protection assay was used to evaluate the anti-EV-A71 activity of SP40 peptide after incubation in human serum and to identify the minimal active sequence of SP40 peptide that retained antiviral activity. The results showed that the SP40 peptide was stable in human serum with 56 % of the full-length SP40 peptide being detected after 48 h incubation in human serum. The SP40 peptide was mainly cleaved by exopeptidases and no endoprotease recognition sites were identified within the SP40 peptide. Cell protection assays revealed that the SP40 peptide retained substantial activity after 24 and 48 h incubation in human serum. Furthermore, the data revealed that three amino acids at the N-terminus and one amino acid at the C-terminus of the SP40 peptide were dispensable for its antiviral activity. Importantly, the four truncated peptides displayed better potency than the full-length SP40 peptide. Overall, this study provided insights into the stability and activity of SP40 peptide in human serum and will facilitate the development of SP40 peptide as an anti-EV-A71 agent.
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Affiliation(s)
- Faisal Zarif
- Centre for Virus and Vaccine Research, Sunway University, Bandar Sunway, Malaysia; School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Mohd Ishtiaq Anasir
- Centre for Virus and Vaccine Research, Sunway University, Bandar Sunway, Malaysia; School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia; Virology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Selangor, Malaysia
| | - Jia Xuen Koh
- Centre for Virus and Vaccine Research, Sunway University, Bandar Sunway, Malaysia; School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Miaw-Fang Chew
- Centre for Virus and Vaccine Research, Sunway University, Bandar Sunway, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, Sunway University, Bandar Sunway, Malaysia; School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia.
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7
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Reyes-Barrera KL, Soria-Guerra RE, López-Martínez R, Huerta L, Salinas-Jazmín N, Cabello-Gutiérrez C, Alpuche-Solís ÁG. The Entry Blocker Peptide Produced in Chlamydomonas reinhardtii Inhibits Influenza Viral Replication in vitro. FRONTIERS IN PLANT SCIENCE 2021; 12:641420. [PMID: 34054890 PMCID: PMC8149740 DOI: 10.3389/fpls.2021.641420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/23/2021] [Indexed: 06/01/2023]
Abstract
This year, a respiratory virus caused an emergency pandemic alert in health services around the world, showing the need for biotechnological approaches to fight these diseases. The influenza virus is one of the main viral agents that generate pandemic outbreaks. Currently, the majority of co-circulating influenza A virus (IAV) strains are adamantine- and oseltamivir-resistant strains, and the challenge is to find new antivirals for more efficient treatments. The antiviral entry blocker (EB) peptide is a promising candidate for blocking the virus entry into cells. The aim of this research was to express the EB peptide in the microalgae Chlamydomonas reinhardtii and test its antiviral activity against IAV in vitro. The EB peptide nucleotide sequence was introduced into the nuclear genome of microalgae using Agrobacterium tumefaciens transformation. The EB peptide amount produced in transformed microalgae was 4.99 ± 0.067% of the total soluble protein. In hemagglutination inhibition assays using influenza A/H1N1 pdm and influenza A H1N1/Virginia/ATCC/2009 strains, we reported that the EB peptide extract from the microalgae showed 100-fold higher efficiency than the EB synthetic peptide. In addition, both the EB peptide extract and synthetic peptide inhibited viral replication in MDCK cells (IC50 = 20.7 nM and IC50 = 754.4 nM, respectively); however, the EB peptide extract showed a 32-fold higher antiviral effectiveness than the synthetic peptide against influenza A/H1N1 pdm. Extracts from untransformed and transformed microalgae and synthetic peptide did not show cytotoxic effect on MDCK cell monolayers. Thus, C. reinhardtii may be a fast, safe, and effective expression platform for production of peptides with significant antiviral activity and can be used as a prophylactic treatment to reduce viral propagation.
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Affiliation(s)
- Karen Lizbeth Reyes-Barrera
- Laboratorio de Biología Molecular de Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C., San Luis Potosí, Mexico
| | - Ruth Elena Soria-Guerra
- Laboratorio de Biotecnología Molecular de Células Vegetales, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Rogelio López-Martínez
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Leonor Huerta
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Nohemí Salinas-Jazmín
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Carlos Cabello-Gutiérrez
- Departamento de Investigación en Virología y Micología, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Ángel Gabriel Alpuche-Solís
- Laboratorio de Biología Molecular de Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C., San Luis Potosí, Mexico
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8
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Li J, Pu Y, Tang J, Zou Q, Guo F. DeepAVP: A Dual-Channel Deep Neural Network for Identifying Variable-Length Antiviral Peptides. IEEE J Biomed Health Inform 2020; 24:3012-3019. [DOI: 10.1109/jbhi.2020.2977091] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Kyung H, Kim H, Lee H, Lee SJ. Enhanced intracellular delivery of macromolecules by melittin derivatives mediated cellular uptake. J IND ENG CHEM 2018. [DOI: 10.1016/j.jiec.2017.09.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Memczak H, Lauster D, Kar P, Di Lella S, Volkmer R, Knecht V, Herrmann A, Ehrentreich-Förster E, Bier FF, Stöcklein WFM. Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding. PLoS One 2016; 11:e0159074. [PMID: 27415624 PMCID: PMC4944999 DOI: 10.1371/journal.pone.0159074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/27/2016] [Indexed: 12/23/2022] Open
Abstract
Antibodies against spike proteins of influenza are used as a tool for characterization of viruses and therapeutic approaches. However, development, production and quality control of antibodies is expensive and time consuming. To circumvent these difficulties, three peptides were derived from complementarity determining regions of an antibody heavy chain against influenza A spike glycoprotein. Their binding properties were studied experimentally, and by molecular dynamics simulations. Two peptide candidates showed binding to influenza A/Aichi/2/68 H3N2. One of them, termed PeB, with the highest affinity prevented binding to and infection of target cells in the micromolar region without any cytotoxic effect. PeB matches best the conserved receptor binding site of hemagglutinin. PeB bound also to other medical relevant influenza strains, such as human-pathogenic A/California/7/2009 H1N1, and avian-pathogenic A/Mute Swan/Rostock/R901/2006 H7N1. Strategies to improve the affinity and to adapt specificity are discussed and exemplified by a double amino acid substituted peptide, obtained by substitutional analysis. The peptides and their derivatives are of great potential for drug development as well as biosensing.
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Affiliation(s)
- Henry Memczak
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daniel Lauster
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Parimal Kar
- Department of Theory and Bio-Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Santiago Di Lella
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Volker Knecht
- Department of Theory and Bio-Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Andreas Herrmann
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Eva Ehrentreich-Förster
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
| | - Walter F. M. Stöcklein
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
- * E-mail:
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11
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Lu R, Müller P, Downard KM. Molecular basis of influenza hemagglutinin inhibition with an entry-blocker peptide by computational docking and mass spectrometry. Antivir Chem Chemother 2016; 24:109-17. [PMID: 26759268 DOI: 10.1177/2040206615622920] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/24/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The increased resistance of circulating strains to current antiviral inhibitors of the influenza virus necessitates that new antivirals and their mode of action are identified. Influenza hemagglutinin is an ideal target given inhibitors of its function can block the entry of the virus into host cells during the early stages of replication. This article describes the molecular basis for the inhibition of H1 and H5 hemagglutinin by an entry-blocker peptide using companion molecular docking and mass spectrometry-based experiments. METHODS A combination of hemagglutination inhibition assays, computational molecular docking and a novel mass spectrometry-based approach are employed to explore the mode of action of the entry-blocker peptide at a molecular level. RESULTS The entry-blocker peptide is shown to be able to maximally inhibit blood cell hemagglutination at a concentration of between 6.4 and 9.2 µM. The molecular basis for this inhibition is derived from the binding of the peptide to hemagglutinin in the vicinity of the reported sialic acid binding site surrounded by an α-helix (190-helix) and two loop (130-loop and 220-loop) regions in the case of a H1 hemagglutinin and the second loop region in the case of a H5 hemagglutinin. CONCLUSIONS The results support the recognized potential of the entry-blocker peptide as an effective antiviral agent that can inhibit the early stages of viral replication and further illustrate the power of a combination of docking and a mass spectrometry approach to screen the molecular basis of new antiviral inhibitors to the influenza virus.
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Affiliation(s)
- Robert Lu
- University of New South Wales, Sydney, Australia
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Skalickova S, Heger Z, Krejcova L, Pekarik V, Bastl K, Janda J, Kostolansky F, Vareckova E, Zitka O, Adam V, Kizek R. Perspective of Use of Antiviral Peptides against Influenza Virus. Viruses 2015; 7:5428-42. [PMID: 26492266 PMCID: PMC4632391 DOI: 10.3390/v7102883] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/13/2023] Open
Abstract
The threat of a worldwide influenza pandemic has greatly increased over the past decade with the emergence of highly virulent avian influenza strains. The increased frequency of drug-resistant influenza strains against currently available antiviral drugs requires urgent development of new strategies for antiviral therapy, too. The research in the field of therapeutic peptides began to develop extensively in the second half of the 20(th) century. Since then, the mechanisms of action for several peptides and their antiviral prospect received large attention due to the global threat posed by viruses. Here, we discussed the therapeutic properties of peptides used in influenza treatment. Peptides with antiviral activity against influenza can be divided into three main groups. First, entry blocker peptides such as a Flupep that interact with influenza hemagglutinin, block its binding to host cells and prevent viral fusion. Second, several peptides display virucidal activity, disrupting viral envelopes, e.g., Melittin. Finally, a third set of peptides interacts with the viral polymerase complex and act as viral replication inhibitors such as PB1 derived peptides. Here, we present a review of the current literature describing the antiviral activity, mechanism and future therapeutic potential of these influenza antiviral peptides.
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Affiliation(s)
- Sylvie Skalickova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic.
| | - Ludmila Krejcova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
| | - Vladimir Pekarik
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
| | - Karel Bastl
- Wool and Knitting Research Institute, Brno, Sujanovo namesti 3, Brno CZ-602 00, Czech Republic.
| | - Jozef Janda
- Laboratory of Tumour Biology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Libechov CZ-277 21, Czech Republic.
| | - Frantisek Kostolansky
- Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovak Republic.
| | - Eva Vareckova
- Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovak Republic.
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic.
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic.
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic.
- Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic.
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13
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Lauster D, Pawolski D, Storm J, Ludwig K, Volkmer R, Memczak H, Herrmann A, Bhatia S. Potential of acylated peptides to target the influenza A virus. Beilstein J Org Chem 2015; 11:589-95. [PMID: 26124860 PMCID: PMC4464269 DOI: 10.3762/bjoc.11.65] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/24/2015] [Indexed: 01/15/2023] Open
Abstract
For antiviral drug design, especially in the field of influenza virus research, potent multivalent inhibitors raise high expectations for combating epidemics and pandemics. Among a large variety of covalent and non-covalent scaffold systems for a multivalent display of inhibitors, we created a simple supramolecular platform to enhance the antiviral effect of our recently developed antiviral Peptide B (PeB(GF)), preventing binding of influenza virus to the host cell. By conjugating the peptide with stearic acid to create a higher-order structure with a multivalent display, we could significantly enhance the inhibitory effect against the serotypes of both human pathogenic influenza virus A/Aichi/2/1968 H3N2, and avian pathogenic A/FPV/Rostock/34 H7N1 in the hemagglutination inhibition assay. Further, the inhibitory potential of stearylated PeB(GF) (C18-PeB(GF)) was investigated by infection inhibition assays, in which we achieved low micromolar inhibition constants against both viral strains. In addition, we compared C18-PeB(GF) to other published amphiphilic peptide inhibitors, such as the stearylated sugar receptor mimicking peptide (Matsubara et al. 2010), and the "Entry Blocker" (EB) (Jones et al. 2006), with respect to their antiviral activity against infection by Influenza A Virus (IAV) H3N2. However, while this strategy seems at a first glance promising, the native situation is quite different from our experimental model settings. First, we found a strong potential of those peptides to form large amyloid-like supramolecular assemblies. Second, in vivo, the large excess of cell surface membranes provides an unspecific target for the stearylated peptides. We show that acylated peptides insert into the lipid phase of such membranes. Eventually, our study reveals serious limitations of this type of self-assembling IAV inhibitors.
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Affiliation(s)
- Daniel Lauster
- Humboldt-Universität zu Berlin, Institute of Biology, Invalidenstr. 42, 10115 Berlin, Germany
| | - Damian Pawolski
- Humboldt-Universität zu Berlin, Institute of Biology, Invalidenstr. 42, 10115 Berlin, Germany
| | - Julian Storm
- Humboldt-Universität zu Berlin, Institute of Biology, Invalidenstr. 42, 10115 Berlin, Germany
| | - Kai Ludwig
- Freie Universität Berlin, Research Center of Electron Microscopy, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Rudolf Volkmer
- Charité Universitätsmedizin Berlin, Institute of Immunology, Charitéplatz 1, 10117 Berlin, Germany
| | - Henry Memczak
- Fraunhofer Institute for Cell Therapy and Immunology, Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Andreas Herrmann
- Humboldt-Universität zu Berlin, Institute of Biology, Invalidenstr. 42, 10115 Berlin, Germany
| | - Sumati Bhatia
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 3, 14195 Berlin, Germany
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14
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Si Y, Li J, Niu Y, Liu X, Ren L, Guo L, Cheng M, Zhou H, Wang J, Jin Q, Yang W. Entry properties and entry inhibitors of a human H7N9 influenza virus. PLoS One 2014; 9:e107235. [PMID: 25222852 PMCID: PMC4164620 DOI: 10.1371/journal.pone.0107235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 08/08/2014] [Indexed: 11/18/2022] Open
Abstract
The recently identified human infections with a novel avian influenza H7N9 virus in China raise important questions regarding possible risk to humans. However, the entry properties and tropism of this H7N9 virus were poorly understood. Moreover, neuraminidase inhibitor resistant H7N9 isolates were recently observed in two patients and correlated with poor clinical outcomes. In this study, we aimed to elucidate the entry properties of H7N9 virus, design and evaluate inhibitors for H7N9 virus entry. We optimized and developed an H7N9-pseudotyped particle system (H7N9pp) that could be neutralized by anti-H7 antibodies and closely mimicked the entry process of the H7N9 virus. Avian, human and mouse-derived cultured cells showed high, moderate and low permissiveness to H7N9pp, respectively. Based on influenza virus membrane fusion mechanisms, a potent anti-H7N9 peptide (P155-185-chol) corresponding to the C-terminal ectodomain of the H7N9 hemagglutinin protein was successfully identified. P155-185-chol demonstrated H7N9pp-specific inhibition of infection with IC50 of 0.19 µM. Importantly, P155-185-chol showed significant suppression of A/Anhui/1/2013 H7N9 live virus propagation in MDCK cells and additive effects with NA inhibitors Oseltamivir and Zanamivir. These findings expand our knowledge of the entry properties of the novel H7N9 viruses, and they highlight the potential for developing a new class of inhibitors targeting viral entry for use in the next pandemic.
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Affiliation(s)
- Youhui Si
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianguo Li
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuqiang Niu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiuying Liu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lili Ren
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Guo
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Min Cheng
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hongli Zhou
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- * E-mail: (WY); (QJ); (JW)
| | - Qi Jin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- * E-mail: (WY); (QJ); (JW)
| | - Wei Yang
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- * E-mail: (WY); (QJ); (JW)
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15
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Peptide entry inhibitors of enveloped viruses: the importance of interfacial hydrophobicity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2180-97. [PMID: 24780375 PMCID: PMC7094693 DOI: 10.1016/j.bbamem.2014.04.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/08/2014] [Accepted: 04/17/2014] [Indexed: 12/16/2022]
Abstract
There are many peptides known that inhibit the entry of enveloped viruses into cells, including one peptide that is successfully being used in the clinic as a drug. In this review, we discuss the discovery, antiviral activity and mechanism of action of such peptides. While peptide entry inhibitors have been discovered by a wide variety of approaches (structure-based, accidental, intentional, rational and brute force) we show here that they share a common physical chemical property: they are at least somewhat hydrophobic and/or amphipathic and have a propensity to interact with membrane interfaces. We propose that this propensity drives a shared mechanism of action for many peptide entry inhibitors, involving direct interactions with viral and cellular membranes, as well as interactions with the complex hydrophobic protein/lipid interfaces that are exposed, at least transiently, during virus-cell fusion. By interacting simultaneously with the membrane interfaces and other critical hydrophobic surfaces, we hypothesize that peptide entry inhibitors can act by changing the physical chemistry of the membranes, and the fusion protein interfaces bridging them, and by doing so interfere with the fusion of cellular and viral membranes. Based on this idea, we propose that an approach that focuses on the interfacial hydrophobicity of putative entry inhibitors could lead to the efficient discovery of novel, broad-spectrum viral entry inhibitors. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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16
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Chang KY, Yang JR. Analysis and prediction of highly effective antiviral peptides based on random forests. PLoS One 2013; 8:e70166. [PMID: 23940542 PMCID: PMC3734225 DOI: 10.1371/journal.pone.0070166] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 06/16/2013] [Indexed: 11/18/2022] Open
Abstract
The goal of this study was to examine and predict antiviral peptides. Although antiviral peptides hold great potential in antiviral drug discovery, little is done in antiviral peptide prediction. In this study, we demonstrate that a physicochemical model using random forests outperform in distinguishing antiviral peptides. On the experimental benchmark, our physicochemical model aided with aggregation and secondary structural features reaches 90% accuracy and 0.79 Matthew's correlation coefficient, which exceeds the previous models. The results suggest that aggregation could be an important feature for identifying antiviral peptides. In addition, our analysis reveals the characteristics of the antiviral peptides such as the importance of lysine and the abundance of α-helical secondary structures.
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Affiliation(s)
- Kuan Y Chang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan.
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17
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Abstract
Synthesis and large-scale manufacturing technologies are now available for the commercial production of even the most complex peptide anti-infectives. Married with the potential of this class of molecule as the next generation of effective, resistance-free and safe antimicrobials, and a much better understanding of their biology, pharmacology and pharmacodynamics, the first regulatory approvals and introduction into clinical practice of these promising drug candidates will likely be soon. This is a key juncture in the history/life cycle of peptide anti-infectives and, perhaps, their commercial and therapeutic potential is about to be realized. This review highlights the promise of these agents as the next generation of therapeutics and summarizes the challenges faced in, and lessons learned from, the past.
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18
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Thakur N, Qureshi A, Kumar M. AVPpred: collection and prediction of highly effective antiviral peptides. Nucleic Acids Res 2012; 40:W199-204. [PMID: 22638580 PMCID: PMC3394244 DOI: 10.1093/nar/gks450] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In the battle against viruses, antiviral peptides (AVPs) had demonstrated the immense potential. Presently, more than 15 peptide-based drugs are in various stages of clinical trials. Emerging and re-emerging viruses further emphasize the efforts to accelerate antiviral drug discovery efforts. Despite, huge importance of the field, no dedicated AVP resource is available. In the present study, we have collected 1245 peptides which were experimentally checked for antiviral activity targeting important human viruses like influenza, HIV, HCV and SARS, etc. After removing redundant peptides, 1056 peptides were divided into 951 training and 105 validation data sets. We have exploited various peptides sequence features, i.e. motifs and alignment followed by amino acid composition and physicochemical properties during 5-fold cross validation using Support Vector Machine. Physiochemical properties-based model achieved maximum 85% accuracy and 0.70 Matthew’s Correlation Coefficient (MCC). Performance of this model on the experimental validation data set showed 86% accuracy and 0.71 MCC which is far better than the general antimicrobial peptides prediction methods. Therefore, AVPpred—the first web server for predicting the highly effective AVPs would certainly be helpful to researchers working on peptide-based antiviral development. The web server is freely available at http://crdd.osdd.net/servers/avppred.
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Affiliation(s)
- Nishant Thakur
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
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19
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Altmann SE, Brandt CR, Jahrling PB, Blaney JE. Antiviral activity of the EB peptide against zoonotic poxviruses. Virol J 2012; 9:6. [PMID: 22225618 PMCID: PMC3275487 DOI: 10.1186/1743-422x-9-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 01/06/2012] [Indexed: 11/24/2022] Open
Abstract
Background The EB peptide is a 20-mer that was previously shown to have broad spectrum in vitro activity against several unrelated viruses, including highly pathogenic avian influenza, herpes simplex virus type I, and vaccinia, the prototypic orthopoxvirus. To expand on this work, we evaluated EB for in vitro activity against the zoonotic orthopoxviruses cowpox and monkeypox and for in vivo activity in mice against vaccinia and cowpox. Findings In yield reduction assays, EB had an EC50 of 26.7 μM against cowpox and 4.4 μM against monkeypox. The EC50 for plaque reduction was 26.3 μM against cowpox and 48.6 μM against monkeypox. A scrambled peptide had no inhibitory activity against either virus. EB inhibited cowpox in vitro by disrupting virus entry, as evidenced by a reduction of the release of virus cores into the cytoplasm. Monkeypox was also inhibited in vitro by EB, but at the attachment stage of infection. EB showed protective activity in mice infected intranasally with vaccinia when co-administered with the virus, but had no effect when administered prophylactically one day prior to infection or therapeutically one day post-infection. EB had no in vivo activity against cowpox in mice. Conclusions While EB did demonstrate some in vivo efficacy against vaccinia in mice, the limited conditions under which it was effective against vaccinia and lack of activity against cowpox suggest EB may be more useful for studying orthopoxvirus entry and attachment in vitro than as a therapeutic against orthopoxviruses in vivo.
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Affiliation(s)
- Sharon E Altmann
- Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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