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Patel H, Sengupta D. Antiviral Drug Target Identification and Ligand Discovery. Methods Mol Biol 2024; 2714:85-99. [PMID: 37676593 DOI: 10.1007/978-1-0716-3441-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
This chapter intends to provide a general overview of web-based resources available for antiviral drug discovery studies. First, we explain how the structure for a potential viral protein target can be obtained and then highlight some of the main considerations in preparing for the application of receptor-based molecular docking techniques. Thereafter, we discuss the resources to search for potential drug candidates (ligands) against this target protein receptor, how to screen them, and preparing their analogue library. We make specific reference to free, online, open-source tools and resources which can be applied for antiviral drug discovery studies.
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Affiliation(s)
- Hershna Patel
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK.
| | - Dipankar Sengupta
- Health Data Sciences Research Group, Centre for Optimal Health, School of Life Sciences, College of Liberal Arts and Science, University of Westminster, London, UK
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Poboinev VV, Khrustalev VV, Akunevich AA, Shalygo NV, Stojarov AN, Khrustaleva TA, Kordyukova LV. Peptide Models of the Cytoplasmic Tail of Influenza A/H1N1 Virus Hemagglutinin Expand Understanding its pH-Dependent Modes of Interaction with Matrix Protein M1. Protein J 2023:10.1007/s10930-023-10101-z. [PMID: 36952102 PMCID: PMC10034248 DOI: 10.1007/s10930-023-10101-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 03/24/2023]
Abstract
Influenza A virus hemagglutinin (HA) is a major virus antigen. No cryo-electron microscopy or X-ray data can be obtained for the HA intraviral (cytoplasmic) domain (CT) post-translationally modified with long fatty acid residues bound to three highly conserved cysteines. We recently proposed a model of HA CT of Influenza A/H1N1 virus possessing an antiparallel beta structure based on the experimental secondary structure analysis of four 14-15 amino acid long synthetic peptides, corresponding to the HA CT sequence, with free or acetaminomethylated cysteines. To dispel doubts about possible non-specific "amyloid-like" aggregation of those synthetic peptides in phosphate buffer solution, we have determined the order of oligomers based on blue native gel electrophoresis, membrane filtration, fluorescence spectroscopy and molecular modeling approaches. We have found that unmodified peptides form only low molecular weight oligomers, while modified peptides form both oligomers of low order similar to those found for unmodified peptides and high order conglomerates, which however are not of beta-amyloid-like fold. This study confirms that the beta structure previously detected by circular dichroism spectroscopy analysis is more likely the result of intrinsic propensity of the HA CT amino acid sequence than the consequence of aggregation. The structures of low order oligomers of the synthetic peptides were used for in silico experiments on modeling of HA CT interactions with matrix protein M1 at physiological and acidic pH levels and revealed two different areas of binding. Finally, tripeptides capable of blocking interactions between HA CT and M1 were proposed.
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Mintaev R, Glazkova D, Bogoslovskaya E, Shipulin G. Immunogenic epitope prediction to create a universal influenza vaccine. Heliyon 2022; 8:e09364. [PMID: 35540935 PMCID: PMC9079173 DOI: 10.1016/j.heliyon.2022.e09364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/30/2021] [Accepted: 04/27/2022] [Indexed: 11/26/2022] Open
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Development of a Universal Epitope-Based Influenza Vaccine and Evaluation of Its Effectiveness in Mice. Vaccines (Basel) 2022; 10:vaccines10040534. [PMID: 35455283 PMCID: PMC9026828 DOI: 10.3390/vaccines10040534] [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: 03/03/2022] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 12/10/2022] Open
Abstract
Vaccination is an effective and economically viable means of protection against the influenza virus, but due to rapid viral evolution, modern seasonal vaccines are not effective enough. Next-generation vaccines are designed to provide protection against a wide range of influenza virus strains, including pandemic variants. In our work, we made an epitope-based universal vaccine, rMVA-k1-k2, against the influenza virus based on the modified vaccinia Ankara (MVA) vector and using our own algorithms to select epitopes from conserved fragments of the NP, M1 and HA proteins of influenza A and B. We show that double immunization protects mice with a 67% or greater efficiency against viral influenza pneumonia when infected with various strains of the H1N1, H2N2, H3N2 and H5N1 subtypes of influenza A. In animals, the level of protection provided by the rMVA-k1-k2 vaccine was comparable to that provided by the universal M001 and MVA-NP+M1 (Invictus) vaccines, which have shown success in clinical trials, against strains of the H1N1 and H3N2 subtypes.
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Khrustalev VV, Kordyukova LV, Arutyunyan AM, Poboinev VV, Khrustaleva TA, Stojarov AN, Baratova LA, Sapon AS, Lugin VG. The cytoplasmic tail of influenza A/H1N1 virus hemagglutinin is β-structural. J Biomol Struct Dyn 2020; 40:4642-4661. [PMID: 33317396 DOI: 10.1080/07391102.2020.1860827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Influenza A/H1N1 virus hemagglutinin (HA) is an integral type I glycoprotein that contains a large glycosylated ectodomain, a transmembrane domain, and a cytoplasmic tail (CT) of 10-14 amino acid residues. There are absolutely no data on the secondary or tertiary structure of the HA CT, which is important for virus pathogenesis. Three highly conserved cysteines are post-translationally modified by the attachment of fatty acid residues that pin the CT to the lipid membrane inside the virion. We applied circular dichroism (CD) and fluorescence spectroscopy analysis to examine four synthetic peptides corresponding to 14-15 C-terminal residues of H1 subtype HA (NH2-WMCSNGSLQCRICI-COOH; NH2-FWMCSNGSLQCRICI-COOH), with free or acetaminomethylated cysteines, in the reduced or non-reduced state, at various pH values and temperatures. The CD analysis detected the formation of a β-structure (30-65% according to the new BeStSel algorithm), in addition to an unstructured random coil, in every peptide in various conditions. It was completely or partially recognized as an antiparallel β-structure that was also confirmed by the multi-bounce Horizontal Attenuated Total Reflectance Fourier Transformed Infrared (HATR-FTIR) spectroscopy analysis. According to the experimental data, as well as 3 D modeling, we assume that the amino acid sequence corresponding to the HA CT may form a short antiparallel β-structure under the lipid membrane within a virion.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Victor V Poboinev
- Department of General Chemistry, Belarusian State Medical University, Minsk, Belarus
| | - Tatyana A Khrustaleva
- Biochemical group of the Multidisciplinary Diagnostic Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - Aleksander N Stojarov
- Department of Radiation Medicine and Ecology, Belarusian State Medical University, Minsk, Belarus
| | - Lyudmila A Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alena S Sapon
- Center for Physical and Chemical Research Methods, Belarusian State Technological University, Minsk, Belarus
| | - Valery G Lugin
- Center for Physical and Chemical Research Methods, Belarusian State Technological University, Minsk, Belarus
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Kordyukova LV, Mintaev RR, Rtishchev AA, Kunda MS, Ryzhova NN, Abramchuk SS, Serebryakova MV, Khrustalev VV, Khrustaleva TA, Poboinev VV, Markushin SG, Voronina OL. Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:297-309. [PMID: 32036809 DOI: 10.1017/s1431927620000069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Influenza A virus is a serious human pathogen that assembles enveloped virions on the plasma membrane of the host cell. The pleiomorphic morphology of influenza A virus, represented by spherical, elongated, or filamentous particles, is important for the spread of the virus in nature. Using fixative protocols for sample preparation and negative staining electron microscopy, we found that the recombinant A/WSN/33 (H1N1) (rWSN) virus, a strain considered to be strictly spherical, may produce filamentous particles when amplified in the allantoic cavity of chicken embryos. In contrast, the laboratory WSN strain and the rWSN virus amplified in Madin-Darby canine kidney cells exhibited a spherical morphology. Next-generation sequencing (NGS) suggested a rare Ser126Cys substitution in the M1 protein of rWSN, which was confirmed by the mass spectrometric analysis. No structurally relevant substitutions were found by NGS in other proteins of rWSN. Bioinformatics algorithms predicted a neutral structural effect of the Ser126Cys mutation. The mrWSN_M1_126S virus generated after the introduction of the reverse Cys126Ser substitution exhibited a similar host-dependent partially filamentous phenotype. We hypothesize that a shortage of some as-yet-undefined cellular components involved in virion budding and membrane scission may result in the appearance of filamentous particles in the case of usually "nonfilamentous" virus strains.
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Affiliation(s)
- Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991Moscow, Russia
| | - Ramil R Mintaev
- Mechnikov Research Institute of Vaccine and Sera, 105064Moscow, Russia
- Federal State Budgetary Institution «Center for Strategic Planning and Management for Medical and Biological Health Risks», Ministry of Health, 119121Moscow, Russia
| | | | - Marina S Kunda
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health, 123098Moscow, Russia
| | - Natalia N Ryzhova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health, 123098Moscow, Russia
| | - Sergei S Abramchuk
- Department of Chemistry, Lomonosov Moscow State University, 119234Moscow, Russia
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 119991Moscow, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991Moscow, Russia
| | - Vladislav V Khrustalev
- Department of General Chemistry, Belarusian State Medical University, 220116Minsk, Belarus
| | - Tatyana A Khrustaleva
- Biochemical Group of the Multidisciplinary Diagnostic Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, 220072Minsk, Belarus
| | - Victor V Poboinev
- Department of General Chemistry, Belarusian State Medical University, 220116Minsk, Belarus
| | | | - Olga L Voronina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health, 123098Moscow, Russia
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Kordyukova LV, Serebryakova MV, Khrustalev VV, Veit M. Differential S-Acylation of Enveloped Viruses. Protein Pept Lett 2019; 26:588-600. [PMID: 31161979 DOI: 10.2174/0929866526666190603082521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022]
Abstract
Post-translational modifications often regulate protein functioning. Covalent attachment of long chain fatty acids to cysteine residues via a thioester linkage (known as protein palmitoylation or S-acylation) affects protein trafficking, protein-protein and protein-membrane interactions. This post-translational modification is coupled to membrane fusion or virus assembly and may affect viral replication in vitro and thus also virus pathogenesis in vivo. In this review we outline modern methods to study S-acylation of viral proteins and to characterize palmitoylproteomes of virus infected cells. The palmitoylation site predictor CSS-palm is critically tested against the Class I enveloped virus proteins. We further focus on identifying the S-acylation sites directly within acyl-peptides and the specific fatty acid (e.g, palmitate, stearate) bound to them using MALDI-TOF MS-based approaches. The fatty acid heterogeneity/ selectivity issue attracts now more attention since the recently published 3D-structures of two DHHC-acyl-transferases gave a hint how this might be achieved.
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Affiliation(s)
- Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Vladislav V Khrustalev
- Department of General Chemistry, Belarusian State Medical University, Minsk 220116, Belarus
| | - Michael Veit
- Institut für Virologie, Vet.-Med. Faculty, Free University Berlin, Berlin 14163, Germany
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Du R, Cui Q, Rong L. Competitive Cooperation of Hemagglutinin and Neuraminidase during Influenza A Virus Entry. Viruses 2019; 11:v11050458. [PMID: 31137516 PMCID: PMC6563287 DOI: 10.3390/v11050458] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 12/15/2022] Open
Abstract
The hemagglutinin (HA) and neuraminidase (NA) of influenza A virus possess antagonistic activities on interaction with sialic acid (SA), which is the receptor for virus attachment. HA binds SA through its receptor-binding sites, while NA is a receptor-destroying enzyme by removing SAs. The function of HA during virus entry has been extensively investigated, however, examination of NA has long been focused to its role in the exit of progeny virus from infected cells, and the role of NA in the entry process is still under-appreciated. This review summarizes the current understanding of the roles of HA and NA in relation to each other during virus entry.
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Affiliation(s)
- Ruikun Du
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
- Shandong Provincial Collaborative Innovation Center for Antiviral Traditional Chinese Medicine, Jinan 250355, China.
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266122, China.
| | - Qinghua Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
- Shandong Provincial Collaborative Innovation Center for Antiviral Traditional Chinese Medicine, Jinan 250355, China.
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266122, China.
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
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McAuley JL, Gilbertson BP, Trifkovic S, Brown LE, McKimm-Breschkin JL. Influenza Virus Neuraminidase Structure and Functions. Front Microbiol 2019; 10:39. [PMID: 30761095 PMCID: PMC6362415 DOI: 10.3389/fmicb.2019.00039] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/10/2019] [Indexed: 12/31/2022] Open
Abstract
With the constant threat of emergence of a novel influenza virus pandemic, there must be continued evaluation of the molecular mechanisms that contribute to virulence. Although the influenza A virus surface glycoprotein neuraminidase (NA) has been studied mainly in the context of its role in viral release from cells, accumulating evidence suggests it plays an important, multifunctional role in virus infection and fitness. This review investigates the various structural features of NA, linking these with functional outcomes in viral replication. The contribution of evolving NA activity to viral attachment, entry and release of virions from infected cells, and maintenance of functional balance with the viral hemagglutinin are also discussed. Greater insight into the role of this important antiviral drug target is warranted.
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Affiliation(s)
- Julie L McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Brad P Gilbertson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sanja Trifkovic
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Lorena E Brown
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer L McKimm-Breschkin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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Khrustalev VV, Khrustaleva TA, Kordyukova LV. Selection and structural analysis of the NY25 peptide – A vaccine candidate from hemagglutinin of swine-origin Influenza H1N1. Microb Pathog 2018; 125:72-83. [DOI: 10.1016/j.micpath.2018.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 01/09/2023]
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Kordyukova LV, Shtykova EV, Baratova LA, Svergun DI, Batishchev OV. Matrix proteins of enveloped viruses: a case study of Influenza A virus M1 protein. J Biomol Struct Dyn 2018; 37:671-690. [PMID: 29388479 DOI: 10.1080/07391102.2018.1436089] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Influenza A virus, a member of the Orthomyxoviridae family of enveloped viruses, is one of the human and animal top killers, and its structure and components are therefore extensively studied during the last decades. The most abundant component, M1 matrix protein, forms a matrix layer (scaffold) under the viral lipid envelope, and the functional roles as well as structural peculiarities of the M1 protein are still under heavy debate. Despite multiple attempts of crystallization, no high resolution structure is available for the full length M1 of Influenza A virus. The likely reason for the difficulties lies in the intrinsic disorder of the M1 C-terminal part preventing diffraction quality crystals to be grown. Alternative structural methods including synchrotron small-angle X-ray scattering (SAXS), atomic force microscopy, cryo-electron microscopy/tomography are therefore widely applied to understand the structure of M1, its self-association and interactions with the lipid membrane and the viral nucleocapsid. These methods reveal striking similarities in the behavior of M1 and matrix proteins of other enveloped RNA viruses, with the differences accompanied by the specific features of the viral lifecycles, thus suggesting common interaction principles and, possibly, common evolutional ancestors. The structural information on the Influenza A virus M1 protein obtained to the date strongly suggests that the intrinsic disorder in the C-terminal domain has important functional implications.
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Affiliation(s)
- Larisa V Kordyukova
- a Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Eleonora V Shtykova
- b Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences , Moscow , Russian Federation.,c Semenov Institute of Chemical Physics , Russian Academy of Sciences , Moscow , Russian Federation
| | - Lyudmila A Baratova
- a Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | | | - Oleg V Batishchev
- e Frumkin Institute of Physical Chemistry and Electrochemistry , Russian Academy of Sciences , Moscow , Russian Federation.,f Moscow Institute of Physics and Technology , Dolgoprudniy , Russian Federation
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Kordyukova L. Structural and functional specificity of Influenza virus haemagglutinin and paramyxovirus fusion protein anchoring peptides. Virus Res 2017; 227:183-199. [DOI: 10.1016/j.virusres.2016.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/21/2016] [Accepted: 09/23/2016] [Indexed: 02/08/2023]
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