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Zhang X, Xia Y, Li P, Wu Z, Li R, Cai J, Zhang Y, Wang G, Li Y, Tang W, Su W. Discovery of cyperenoic acid as a potent and novel entry inhibitor of influenza A virus. Antiviral Res 2024; 223:105822. [PMID: 38350497 DOI: 10.1016/j.antiviral.2024.105822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 02/15/2024]
Abstract
Influenza therapeutics with new targets and modes of action are urgently needed due to the frequent emergence of mutants resistant to currently available anti-influenza drugs. Here we report the in vitro and in vivo anti-influenza A virus activities of cyperenoic acid, a natural compound, which was isolated from a Chinese medicine Croton crassifolius Geise. Cyperenoic acid could potently suppress H1N1, H3N2 and H9N2 virus replication with IC50 values ranging from 0.12 to 15.13 μM, and showed a low cytotoxicity against MDCK cells (CC50 = 939.2 ± 60.0 μM), with selectivity index (SI) values ranging from 62 to 7823. Oral or intraperitoneal treatment of cyperenoic acid effectively protected mice against a lethal influenza virus challenge, comparable to the efficacy of Tamiflu. Additionally, cyperenoic acid also significantly reduced lung virus titers and alleviated influenza-induced acute lung injury in infected mice. Mechanism-of-action studies revealed that cyperenoic acid exhibited its anti-influenza activity during the entry stage of viral replication by inhibiting HA-mediated viral fusion. Simulation docking analyses of cyperenoic acid with the HA structures implied that cyperenoic acid binds to the stalk domain of HA in a cavity near the fusion peptide. Collectively, these results demonstrate that cyperenoic acid is a promising lead compound for the anti-influenza drug development and this research provides a useful small-molecule probe for studying the HA-mediated viral entry process.
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Affiliation(s)
- Xiaoli Zhang
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 135 Xingang Xi Road, Guangzhou, 510275, China
| | - Yiping Xia
- Institute of Traditional Chinese Medicine & Natural Products, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Peibo Li
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 135 Xingang Xi Road, Guangzhou, 510275, China
| | - Zhongnan Wu
- Institute of Traditional Chinese Medicine & Natural Products, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Ruilin Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Jialiao Cai
- Institute of Traditional Chinese Medicine & Natural Products, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Yubo Zhang
- Institute of Traditional Chinese Medicine & Natural Products, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, 510632, China; Guangdong Clinical Translational Center for Targeted Drug, Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Guocai Wang
- Institute of Traditional Chinese Medicine & Natural Products, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Yaolan Li
- Institute of Traditional Chinese Medicine & Natural Products, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Wei Tang
- Institute of Traditional Chinese Medicine & Natural Products, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Weiwei Su
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 135 Xingang Xi Road, Guangzhou, 510275, China.
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Borisevich SS, Zarubaev VV, Shcherbakov DN, Yarovaya OI, Salakhutdinov NF. Molecular Modeling of Viral Type I Fusion Proteins: Inhibitors of Influenza Virus Hemagglutinin and the Spike Protein of Coronavirus. Viruses 2023; 15:v15040902. [PMID: 37112882 PMCID: PMC10142020 DOI: 10.3390/v15040902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
The fusion of viral and cell membranes is one of the basic processes in the life cycles of viruses. A number of enveloped viruses confer fusion of the viral envelope and the cell membrane using surface viral fusion proteins. Their conformational rearrangements lead to the unification of lipid bilayers of cell membranes and viral envelopes and the formation of fusion pores through which the viral genome enters the cytoplasm of the cell. A deep understanding of all the stages of conformational transitions preceding the fusion of viral and cell membranes is necessary for the development of specific inhibitors of viral reproduction. This review systematizes knowledge about the results of molecular modeling aimed at finding and explaining the mechanisms of antiviral activity of entry inhibitors. The first section of this review describes types of viral fusion proteins and is followed by a comparison of the structural features of class I fusion proteins, namely influenza virus hemagglutinin and the S-protein of the human coronavirus.
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Affiliation(s)
- Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 450078 Ufa, Russia
- Correspondence: (S.S.B.); (O.I.Y.)
| | - Vladimir V. Zarubaev
- Laboratory of Experimental Virology, Saint-Petersburg Pasteur Institute, 197101 Saint Petersburg, Russia;
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia;
| | - Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
- Correspondence: (S.S.B.); (O.I.Y.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
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Insights into binding molecular mechanism of hemagglutinin H3N2 of influenza virus complexed with arbidol and its derivative: A molecular dynamics simulation perspective. Comput Biol Chem 2022; 101:107764. [DOI: 10.1016/j.compbiolchem.2022.107764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/07/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022]
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Broad-Spectrum Activity of Small Molecules Acting against Influenza a Virus: Biological and Computational Studies. Pharmaceuticals (Basel) 2022; 15:ph15030301. [PMID: 35337099 PMCID: PMC8952214 DOI: 10.3390/ph15030301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 01/25/2023] Open
Abstract
Influenza still represents a problematic disease, involving millions of people every year and causing hundreds of thousands of deaths. Only a few drugs are clinically available. The search for an effective weapon is still ongoing. In this scenario, we recently identified new drug-like compounds with antiviral activity toward two A/H1N1 Influenza virus strains, which were demonstrated to interfere with the processes mediated by hemagglutinin (HA). In the present work, the compound’s ability to act against the A/H3N2 viral strain has been evaluated in hemagglutination inhibition (HI) assays. Two of the five tested compounds were also active toward the A/H3N2 Influenza virus. To validate the scaffold activity, analogue compounds of two broad-spectrum molecules were selected and purchased for HI testing on both A/H1N1 and A/H3N2 Influenza viruses. Forty-three compounds were tested, and four proved to be active toward all three viral strains. A computational study has been carried out to depict the HA binding process of the most interesting compounds.
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Doelger J, Kardar M, Chakraborty AK. Inferring the intrinsic mutational fitness landscape of influenzalike evolving antigens from temporally ordered sequence data. Phys Rev E 2022; 105:024401. [PMID: 35291059 DOI: 10.1103/physreve.105.024401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
There still are no effective long-term protective vaccines against viruses that continuously evolve under immune pressure such as seasonal influenza, which has caused, and can cause, devastating epidemics in the human population. To find such a broadly protective immunization strategy, it is useful to know how easily the virus can escape via mutation from specific antibody responses. This information is encoded in the fitness landscape of the viral proteins (i.e., knowledge of the viral fitness as a function of sequence). Here we present a computational method to infer the intrinsic mutational fitness landscape of influenzalike evolving antigens from yearly sequence data. We test inference performance with computer-generated sequence data that are based on stochastic simulations mimicking basic features of immune-driven viral evolution. Although the numerically simulated model does create a phylogeny based on the allowed mutations, the inference scheme does not use this information. This provides a contrast to other methods that rely on reconstruction of phylogenetic trees. Our method just needs a sufficient number of samples over multiple years. With our method, we are able to infer single as well as pairwise mutational fitness effects from the simulated sequence time series for short antigenic proteins. Our fitness inference approach may have potential future use for the design of immunization protocols by identifying intrinsically vulnerable immune target combinations on antigens that evolve under immune-driven selection. In the future, this approach may be applied to influenza and other novel viruses such as SARS-CoV-2, which evolves and, like influenza, might continue to escape the natural and vaccine-mediated immune pressures.
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Affiliation(s)
- Julia Doelger
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Arup K Chakraborty
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; and Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, USA
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Multivalent peptide dendrimers inhibit the fusion of viral-cellular membranes and the cellular NF-κB signaling pathway. Eur J Med Chem 2022; 230:114140. [PMID: 35085860 DOI: 10.1016/j.ejmech.2022.114140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/07/2022] [Accepted: 01/16/2022] [Indexed: 11/23/2022]
Abstract
The binding of the influenza A virus (IAV) to host cells is multivalent interactions between the hemagglutinin (HA) trimer and sialic acid residues on the cell surface, which present a challenge for the development of efficient antiviral drugs interfering with the entry of IAV into host cells. In this study, a number of multivalent peptide dendrimers targeting the HA2 subunit of HA to block the fusion between viral-cellular membranes have been created, of which FMOC-4-KKWK showed the lowest cytotoxicity, while in the nanomolar concentration range of antiviral effects. In addition to being active against a panel of various subtypes of influenza viruses, these dendrimers reduced the levels of NF-κB in RAW 264.7 cells and inhibited the overexpression of proinflammatory cytokines of TNF-α, IL-1β, and IL-6 that are associated with the influenza infection. Further tests in mice infected with a lethal dose of PR8 virus showed that these dendrimers increased the survival rate of mice, and reduced the viral load in the lungs. Significantly, this is the first report describing peptide dendrimers that target the HA2 subunit of IAV, differing from those using carbohydrates as ligands to block the adsorption of viruses to host cells.
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Simulation of Molecular Dynamics of SARS-CoV-2 S-Protein in the Presence of Multiple Arbidol Molecules: Interactions and Binding Mode Insights. Viruses 2022; 14:v14010119. [PMID: 35062323 PMCID: PMC8781717 DOI: 10.3390/v14010119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/05/2023] Open
Abstract
In this work, we evaluated the antiviral activity of Arbidol (Umifenovir) against SARS-CoV-2 using a pseudoviral system with the glycoprotein S of the SARS-CoV-2 virus on its surface. In order to search for binding sites to protein S of the virus, we described alternative binding sites of Arbidol in RBD and in the ACE-2-RBD complex. As a result of our molecular dynamics simulations combined with molecular docking data, we note the following fact: wherever the molecules of Arbidol bind, the interaction of the latter affects the structural flexibility of the protein. This interaction may result both in a change in the shape of the domain-enzyme binding interface and simply in a change in the structural flexibility of the domain, which can subsequently affect its affinity to the enzyme. In addition, we examined the possibility of Arbidol binding in the stem part of the surface protein. The possibility of Arbidol binding in different parts of the protein is not excluded. This may explain the antiviral activity of Arbidol. Our results could be useful for researchers searching for effective SARS-CoV-2 virus inhibitors targeting the viral entry stage.
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Discovery of New Ginsenol-Like Compounds with High Antiviral Activity. Molecules 2021; 26:molecules26226794. [PMID: 34833886 PMCID: PMC8619001 DOI: 10.3390/molecules26226794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/02/2021] [Accepted: 11/06/2021] [Indexed: 11/20/2022] Open
Abstract
A number of framework amides with a ginsenol backbone have been synthesized using the Ritter reaction. We named the acetamide as Ginsamide. A method was developed for the synthesis of the corresponding amine and thioacetamide. The new compounds revealed a high activity against H1N1 influenza, which was confirmed using an animal model. Biological experiments were performed to determine the mechanism of action of the new agents, a ginsamide-resistant strain of influenza virus was obtained, and the pathogenicity of the resistant strain and the control strain was studied. It was shown that the emergence of resistance to Ginsamide was accompanied by a reduction in the pathogenicity of the influenza virus.
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Scala MC, Agamennone M, Pietrantoni A, Di Sarno V, Bertamino A, Superti F, Campiglia P, Sala M. Discovery of a Novel Tetrapeptide against Influenza A Virus: Rational Design, Synthesis, Bioactivity Evaluation and Computational Studies. Pharmaceuticals (Basel) 2021; 14:ph14100959. [PMID: 34681184 PMCID: PMC8537277 DOI: 10.3390/ph14100959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 02/06/2023] Open
Abstract
Influenza is a highly contagious, acute respiratory illness, which represents one of the main health issues worldwide. Even though some antivirals are available, the alarming increase in virus strains resistant to them highlights the need to find new drugs. Previously, Superti et al. deeply investigated the mechanism of the anti-influenza virus effect of bovine lactoferrin (bLf) and the role of its tryptic fragments (the N- and C-lobes) in antiviral activity. Recently, through a truncation library, we identified the tetrapeptides, Ac-SKHS-NH2 (1) and Ac-SLDC-NH2 (2), derived from bLf C-lobe fragment 418–429, which were able to bind hemagglutinin (HA) and inhibit cell infection in a concentration range of femto- to picomolar. Starting from these results, in this work, we initiated a systematic SAR study on the peptides mentioned above, through an alanine scanning approach. We carried out binding affinity measurements by microscale thermophoresis (MST) and surface plasmon resonance (SPR), as well as hemagglutination inhibition (HI) and virus neutralization (NT) assays on synthesized peptides. Computational studies were performed to identify possible ligand–HA interactions. Results obtained led to the identification of an interesting peptide endowed with broad anti-influenza activity and able to inhibit viral infection to a greater extent of reference peptide.
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Affiliation(s)
- Maria Carmina Scala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.S.); (V.D.S.); (A.B.); (P.C.)
| | - Mariangela Agamennone
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy;
| | - Agostina Pietrantoni
- National Centre for Innovative Technologies in Public Health, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy; (A.P.); (F.S.)
- Core Facilities, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Veronica Di Sarno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.S.); (V.D.S.); (A.B.); (P.C.)
| | - Alessia Bertamino
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.S.); (V.D.S.); (A.B.); (P.C.)
| | - Fabiana Superti
- National Centre for Innovative Technologies in Public Health, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy; (A.P.); (F.S.)
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.S.); (V.D.S.); (A.B.); (P.C.)
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.S.); (V.D.S.); (A.B.); (P.C.)
- Correspondence: ; Tel.: +39-(0)-89968148
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Chen Z, Cui Q, Caffrey M, Rong L, Du R. Small Molecule Inhibitors of Influenza Virus Entry. Pharmaceuticals (Basel) 2021; 14:ph14060587. [PMID: 34207368 PMCID: PMC8234048 DOI: 10.3390/ph14060587] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 12/16/2022] Open
Abstract
Hemagglutinin (HA) plays a critical role during influenza virus receptor binding and subsequent membrane fusion process, thus HA has become a promising drug target. For the past several decades, we and other researchers have discovered a series of HA inhibitors mainly targeting its fusion machinery. In this review, we summarize the advances in HA-targeted development of small molecule inhibitors. Moreover, we discuss the structural basis and mode of action of these inhibitors, and speculate upon future directions toward more potent inhibitors of membrane fusion and potential anti-influenza drugs.
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Affiliation(s)
- Zhaoyu Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (Z.C.); (Q.C.)
| | - Qinghua Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (Z.C.); (Q.C.)
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266122, China
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Correspondence: (L.R.); (R.D.); Tel.: +1-312-355-0203 (L.R.); +86-0531-89628505 (R.D.)
| | - Ruikun Du
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (Z.C.); (Q.C.)
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266122, China
- Correspondence: (L.R.); (R.D.); Tel.: +1-312-355-0203 (L.R.); +86-0531-89628505 (R.D.)
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Heida R, Bhide YC, Gasbarri M, Kocabiyik Ö, Stellacci F, Huckriede ALW, Hinrichs WLJ, Frijlink HW. Advances in the development of entry inhibitors for sialic-acid-targeting viruses. Drug Discov Today 2020; 26:122-137. [PMID: 33099021 PMCID: PMC7577316 DOI: 10.1016/j.drudis.2020.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/13/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]
Abstract
Over the past decades, several antiviral drugs have been developed to treat a range of infections. Yet the number of treatable viral infections is still limited, and resistance to current drug regimens is an ever-growing problem. Therefore, additional strategies are needed to provide a rapid cure for infected individuals. An interesting target for antiviral drugs is the process of viral attachment and entry into the cell. Although most viruses use distinct host receptors for attachment to the target cell, some viruses share receptors, of which sialic acids are a common example. This review aims to give an update on entry inhibitors for a range of sialic-acid-targeting viruses and provides insight into the prospects for those with broad-spectrum potential.
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Affiliation(s)
- Rick Heida
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, 9713AV Groningen, The Netherlands
| | - Yoshita C Bhide
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, 9713AV Groningen, The Netherlands; Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9713AV Groningen, The Netherlands
| | - Matteo Gasbarri
- Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Özgün Kocabiyik
- Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Anke L W Huckriede
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9713AV Groningen, The Netherlands
| | - Wouter L J Hinrichs
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, 9713AV Groningen, The Netherlands.
| | - Henderik W Frijlink
- Department of Pharmaceutical Technology and Biopharmacy, University of Groningen, 9713AV Groningen, The Netherlands
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Sevy AM, Gilchuk IM, Brown BP, Bozhanova NG, Nargi R, Jensen M, Meiler J, Crowe JE. Computationally Designed Cyclic Peptides Derived from an Antibody Loop Increase Breadth of Binding for Influenza Variants. Structure 2020; 28:1114-1123.e4. [PMID: 32610044 DOI: 10.1016/j.str.2020.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/12/2020] [Accepted: 04/06/2020] [Indexed: 01/12/2023]
Abstract
The influenza hemagglutinin (HA) glycoprotein is the target of many broadly neutralizing antibodies. However, influenza viruses can rapidly escape antibody recognition by mutation of hypervariable regions of HA that overlap with the binding epitope. We hypothesized that by designing peptides to mimic antibody loops, we could enhance breadth of binding to HA antigenic variants by reducing contact with hypervariable residues on HA that mediate escape. We designed cyclic peptides that mimic the heavy-chain complementarity-determining region 3 (CDRH3) of anti-influenza broadly neutralizing antibody C05 and show that these peptides bound to HA molecules with <100 nM affinity, comparable with that of the full-length parental C05 IgG. In addition, these peptides exhibited increased breadth of recognition to influenza H4 and H7 subtypes by eliminating clashes between the hypervariable antigenic regions and the antibody CDRH1 loop. This approach can be used to generate antibody-derived peptides against a wide variety of targets.
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Affiliation(s)
- Alexander M Sevy
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Iuliia M Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Benjamin P Brown
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Nina G Bozhanova
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Rachel Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mattie Jensen
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jens Meiler
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
| | - James E Crowe
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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13
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de Castro S, Ginex T, Vanderlinden E, Laporte M, Stevaert A, Cumella J, Gago F, Camarasa MJ, Luque FJ, Naesens L, Velazquez S. N-benzyl 4,4-disubstituted piperidines as a potent class of influenza H1N1 virus inhibitors showing a novel mechanism of hemagglutinin fusion peptide interaction. Eur J Med Chem 2020; 194:112223. [DOI: 10.1016/j.ejmech.2020.112223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022]
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Podshivalov DD, Kirilin EM, Konnov SI, Švedas VK. Structural Organization and Dynamic Characteristics of the Binding Site for Conformational Rearrangement Inhibitors in Hemagglutinins from H3N2 and H7N9 Influenza Viruses. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:499-506. [PMID: 32569557 DOI: 10.1134/s0006297920040100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Computer models of hemagglutinins from the H3N2 and H7N9 influenza viruses were developed to study structural organization and dynamic characteristics of the binding site for the conformational rearrangement inhibitors. The metadynamics was used to map the binding site free energy and to define the volume of its most energetically favorable states. It was demonstrated by simulation of the umifenovir (Arbidol) interaction with hemagglutinin that ligand binding requires an increase in the binding site volume and deformation of its most energetically favorable state. We also identified amino acid residues directly involved in the ligand binding that determine the binding efficiency, as well as the dynamic behavior of the binding site. The revealed features of the binding site structural organization of the influenza virus hemagglutinin should be taken into account when searching for new antiviral drugs capable to modulate its functional properties.
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Affiliation(s)
- D D Podshivalov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.
| | - E M Kirilin
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - S I Konnov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - V K Švedas
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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15
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Cihan-Üstündağ G, Zopun M, Vanderlinden E, Ozkirimli E, Persoons L, Çapan G, Naesens L. Superior inhibition of influenza virus hemagglutinin-mediated fusion by indole-substituted spirothiazolidinones. Bioorg Med Chem 2020; 28:115130. [DOI: 10.1016/j.bmc.2019.115130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/26/2022]
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16
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Lectin antagonists in infection, immunity, and inflammation. Curr Opin Chem Biol 2019; 53:51-67. [DOI: 10.1016/j.cbpa.2019.07.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/12/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022]
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17
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Le KP, Do PC, Amaro RE, Le L. Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus. Evol Bioinform Online 2019; 15:1176934319876938. [PMID: 31555044 PMCID: PMC6747855 DOI: 10.1177/1176934319876938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 02/01/2023] Open
Abstract
Influenza A has caused several deadly pandemics throughout human history. The virus is often resistant to developed treatments because of its genetic drift or shift property. Broad-spectrum antibodies show a promising potential to overcome the resistance of influenza viruses. In silico studies on broad-reactive antibodies and their interactions with hemagglutinins might shed light on the rational design of a universal vaccine. In this study, 11 broad-spectrum antibodies (or antigen-binding fragments) and 14 hemagglutinins of H3N2 and H5N1 strains were docked and analyzed to provide information about the construction of the scaffold for using universal antibodies against the influenza A virus. Antigen-binding fragments that have high number of appearances in the top 3 within each H3 and H5 subtypes were chosen for protein-protein interaction analysis. The results show that while the hydrogen bond is important for Ab/Fab binding to H3, the H5-Ab/Fab system may need cation-pi interaction for a strong interaction.
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Affiliation(s)
- Khanh Pb Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Phuc-Chau Do
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam.,Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
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18
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New therapeutic targets for the prevention of infectious acute exacerbations of COPD: role of epithelial adhesion molecules and inflammatory pathways. Clin Sci (Lond) 2019; 133:1663-1703. [PMID: 31346069 DOI: 10.1042/cs20181009] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/15/2022]
Abstract
Chronic respiratory diseases are among the leading causes of mortality worldwide, with the major contributor, chronic obstructive pulmonary disease (COPD) accounting for approximately 3 million deaths annually. Frequent acute exacerbations (AEs) of COPD (AECOPD) drive clinical and functional decline in COPD and are associated with accelerated loss of lung function, increased mortality, decreased health-related quality of life and significant economic costs. Infections with a small subgroup of pathogens precipitate the majority of AEs and consequently constitute a significant comorbidity in COPD. However, current pharmacological interventions are ineffective in preventing infectious exacerbations and their treatment is compromised by the rapid development of antibiotic resistance. Thus, alternative preventative therapies need to be considered. Pathogen adherence to the pulmonary epithelium through host receptors is the prerequisite step for invasion and subsequent infection of surrounding structures. Thus, disruption of bacterial-host cell interactions with receptor antagonists or modulation of the ensuing inflammatory profile present attractive avenues for therapeutic development. This review explores key mediators of pathogen-host interactions that may offer new therapeutic targets with the potential to prevent viral/bacterial-mediated AECOPD. There are several conceptual and methodological hurdles hampering the development of new therapies that require further research and resolution.
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19
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Lu W, Du W, Somovilla VJ, Yu G, Haksar D, de Vries E, Boons GJ, de Vries RP, de Haan CAM, Pieters RJ. Enhanced Inhibition of Influenza A Virus Adhesion by Di- and Trivalent Hemagglutinin Inhibitors. J Med Chem 2019; 62:6398-6404. [PMID: 31251606 PMCID: PMC6627469 DOI: 10.1021/acs.jmedchem.9b00303] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
![]()
Multivalent carbohydrate-based ligands
were synthesized and evaluated
as inhibitors of the adhesion protein HA of the influenza A virus
(IAV). HA relies on multivalency for strong viral adhesion. While
viral adhesion inhibition by large polymeric molecules has proven
viable, limited success was reached for smaller multivalent compounds.
By linking of sialylated LAcNAc units to di- and trivalent scaffolds,
inhibitors were obtained with an up to 428-fold enhanced inhibition
in various assays.
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Affiliation(s)
- Wenjing Lu
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
| | - Wenjuan Du
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine , Utrecht University , NL-3584 CL Utrecht , The Netherlands
| | - Victor J Somovilla
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
| | - Guangyun Yu
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
| | - Diksha Haksar
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
| | - Erik de Vries
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine , Utrecht University , NL-3584 CL Utrecht , The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
| | - Cornelis A M de Haan
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine , Utrecht University , NL-3584 CL Utrecht , The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences , Utrecht University , P.O. Box 80082, NL-3508 TB Utrecht , The Netherlands
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20
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Abstract
Paramyxoviruses, including human parainfluenza virus type 3, are internalized into host cells by fusion between viral and target cell membranes. The receptor binding protein, hemagglutinin-neuraminidase (HN), and the fusion protein (F) facilitate viral fusion and entry into cells through a process involving HN activation by receptor binding, which triggers conformational changes in F to activate it to reach its fusion-competent state. Interfering with this process through premature activation of the F protein may be an effective antiviral strategy in vitro. We identified and optimized small compounds that implement this antiviral strategy through an interaction with HN, causing HN to activate F in an untimely fashion. To address that mechanism, we produced novel anti-HPIV3 F conformation-specific antibodies that can be used to assess the functionality of compounds designed to induce F activation. Both the novel antiviral compounds that we present and these newly characterized postfusion antibodies are novel tools for the exploration and development of antiviral approaches. Paramyxoviruses, specifically, the childhood pathogen human parainfluenza virus type 3, are internalized into host cells following fusion between the viral and target cell membranes. The receptor binding protein, hemagglutinin (HA)-neuraminidase (HN), and the fusion protein (F) facilitate viral fusion and entry into the cell through a coordinated process involving HN activation by receptor binding, which triggers conformational changes in the F protein to activate it to reach its fusion-competent state. Interfering with this process through premature activation of the F protein has been shown to be an effective antiviral strategy in vitro. Conformational changes in the F protein leading to adoption of the postfusion form of the protein—prior to receptor engagement of HN at the host cell membrane—render the virus noninfectious. We previously identified a small compound (CSC11) that implements this antiviral strategy through an interaction with HN, causing HN to activate F in an untimely process. To assess the functionality of such compounds, it is necessary to verify that the postfusion state of F has been achieved. As demonstrated by Melero and colleagues, soluble forms of the recombinant postfusion pneumovirus F proteins and of their six helix bundle (6HB) motifs can be used to generate postfusion-specific antibodies. We produced novel anti-HPIV3 F conformation-specific antibodies that can be used to assess the functionality of compounds designed to induce F activation. In this study, using systematic chemical modifications of CSC11, we synthesized a more potent derivative of this compound, CM9. Much like CSC11, CM9 causes premature triggering of the F protein through an interaction with HN prior to receptor engagement, thereby preventing fusion and subsequent infection. In addition to validating the potency of CM9 using plaque reduction, fusion inhibition, and binding avidity assays, we confirmed the transition to a postfusion conformation of F in the presence of CM9 using our novel anti-HPIV3 conformation-specific antibodies. We present both CM9 and these newly characterized postfusion antibodies as novel tools to explore and develop antiviral approaches. In turn, these advances in both our molecular toolset and our understanding of HN-F interaction will support development of more-effective antivirals. Combining the findings described here with our recently described physiologically relevant ex vivo system, we have the potential to inform the development of therapeutics to block viral infection.
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21
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Yamayoshi S, Kawaoka Y. Current and future influenza vaccines. Nat Med 2019; 25:212-220. [PMID: 30692696 DOI: 10.1038/s41591-018-0340-z] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/19/2018] [Indexed: 11/09/2022]
Abstract
Although antiviral drugs and vaccines have reduced the economic and healthcare burdens of influenza, influenza epidemics continue to take a toll. Over the past decade, research on influenza viruses has revealed a potential path to improvement. The clues have come from accumulated discoveries from basic and clinical studies. Now, virus surveillance allows researchers to monitor influenza virus epidemic trends and to accumulate virus sequences in public databases, which leads to better selection of candidate viruses for vaccines and early detection of drug-resistant viruses. Here we provide an overview of current vaccine options and describe efforts directed toward the development of next-generation vaccines. Finally, we propose a plan for the development of an optimal influenza vaccine.
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Affiliation(s)
- Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan. .,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan. .,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin Madison, Madison, WI, USA.
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22
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Antiviral Activities of Mulberry ( Morus alba) Juice and Seed against Influenza Viruses. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 2018:2606583. [PMID: 30515232 PMCID: PMC6236660 DOI: 10.1155/2018/2606583] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 12/22/2022]
Abstract
Antiviral activities of Morus alba (MA) juice and seed were examined using time-of-addition plaque assays against influenza viruses, A/Brisbane/59/2007 (H1N1) (BR59), pandemic A/Korea/01/2009(H1N1) (KR01), A/Brisbane/10/2007(H3N2) (BR10), and B/Florida/4/2006 (FL04). MA juice (MAJ) showed much higher antiviral activity than MA seed (MAS). In the pre- and cotreatment of virus, MAJ showed antiviral effects against BR59, KR01, and FL04 in a dose-dependent manner. In particular, MAJ at 4% concentration exhibited 1.3 log inhibition in the pre- and cotreatment of the virus against FL04, a type B virus. However, little or weak inhibition was observed in the posttreatment of MAJ. GSH levels in the virus-infected cells were also examined. The decreased levels by the viral infection were restored significantly by the addition of MAJ. MAJ also exhibited significant DPPH radical scavenging and ferric ion-reducing activities in a dose-dependent manner. Cyanidin-3-rutinoside, the most abundant polyphenol compound of MAJ identified by LC-MS in this study, showed weak inhibitory effects against FL04 in the pretreatment, whereas gallic acid, a minor compound of MAJ, revealed significant antiviral effect. These results suggest that MAJ can be developed as a novel plant-derived antiviral against influenza viruses.
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