Vaidya, B. et al. Effectiveness of periodic treatment of quercetin against influenza A virus H1N1 through modulation of protein expression. J. Agric. Food Chem. 64, 4416–4425. https://doi.org/10.1021/acs.jafc.6b00148 (2016).
Spreeuwenberg, P., Kroneman, M. & Paget, J. Reassessing the global mortality burden of the 1918 influenza pandemic. Am. J. Epidemiol. 187, 2561–2567. https://doi.org/10.1093/aje/kwy191 (2018).
Eccleston-Turner, M., Phelan, A. & Katz, R. Preparing for the next pandemic—The WHO’s global influenza strategy. N. Engl. J. Med. 381, 2192–2194. https://doi.org/10.1056/NEJMp1905224 (2019).
Iuliano, A. D. et al. Estimates of global seasonal influenza-associated respiratory mortality: A modelling study. Lancet 391, 1285–1300. https://doi.org/10.1016/s0140-6736(17)33293-2 (2018).
James, S. H. & Whitley, R. J. in Infectious Diseases. 4th edn (eds Jonathan Cohen, William G. Powderly, & Steven M. Opal) 1465–1471.e1461 (Elsevier, 2017).
Principi, N. et al. Drugs for influenza treatment: Is there significant news? Front. Med. https://doi.org/10.3389/fmed.2019.00109 (2019).
Badshah, S. L. et al. Antiviral activities of flavonoids. Biomed. Pharmacother. 140, 111596. https://doi.org/10.1016/j.biopha.2021.111596 (2021).
Xu, X., Miao, J., Shao, Q., Gao, Y. & Hong, L. Apigenin suppresses influenza A virus-induced RIG-I activation and viral replication. J. Med. Virol. https://doi.org/10.1002/jmv.26403 (2020).
Sithisarn, P., Michaelis, M., Schubert-Zsilavecz, M. & Cinatl, J. Differential antiviral and anti-inflammatory mechanisms of the flavonoids biochanin A and baicalein in H5N1 influenza A virus-infected cells. Antiviral Res. 97, 41–48. https://doi.org/10.1016/j.antiviral.2012.10.004 (2013).
Song, J.-M., Lee, K.-H. & Seong, B.-L. Antiviral effect of catechins in green tea on influenza virus. Antiviral Res. 68, 66–74. https://doi.org/10.1016/j.antiviral.2005.06.010 (2005).
Zhang, R. et al. Kaempferol ameliorates H9N2 swine influenza virus-induced acute lung injury by inactivation of TLR4/MyD88-mediated NF-κB and MAPK signaling pathways. Biomed. Pharmacother. 89, 660–672. https://doi.org/10.1016/j.biopha.2017.02.081 (2017).
Yan, H. et al. Luteolin decreases the yield of influenza A virus in vitro by interfering with the coat protein I complex expression. J. Nat. Med. 73, 487–496. https://doi.org/10.1007/s11418-019-01287-7 (2019).
Liu, Z. et al. Computational screen and experimental validation of anti-influenza effects of quercetin and chlorogenic acid from traditional Chinese medicine. Sci. Rep. 6, 19095. https://doi.org/10.1038/srep19095 (2016).
Bae, E.-A., Han, M. J., Lee, M. & Kim, D.-H. In vitro inhibitory effect of some flavonoids on rotavirus infectivity. Biol. Pharm. Bull. 23, 1122–1124 (2000).
Oo, A., Aziz, F-Z., Hassandarvish, P., Azman, A-S., Khairat, J-E., Tiong, V., Zandi, K., AbuBakar, S. Diosmin: A potential entry inhibitor of dengue virus (2019).
Lo, C. W., Pi, C. C., Chen, Y. T. & Chen, H. W. Vigna radiata (L.) R. Wilczek extract inhibits influenza a virus by targeting viral attachment, penetration, assembly, and release. Front. Pharmacol. 11, 584973. https://doi.org/10.3389/fphar.2020.584973 (2020).
Hanada, A. et al. Influenza virus entry and replication inhibited by 8-prenylnaringenin from Citrullus lanatus var. citroides (wild watermelon). Food Sci. Nutr. 10, 926–935. https://doi.org/10.1002/fsn3.2725 (2022).
Jackson, D., Hossain, M. J., Hickman, D., Perez, D. R. & Lamb, R. A. A new influenza virus virulence determinant: The NS1 protein four C-terminal residues modulate pathogenicity. Proc. Natl. Acad. Sci. 105, 4381–4386 (2008).
Noah, D. L. & Krug, R. M. Influenza virus virulence and its molecular determinants. Adv. Virus Res. 65, 121–145 (2005).
Böttcher-Friebertshäuser, E., Garten, W., Matrosovich, M. & Klenk, H. D. in Influenza Pathogenesis and Control (eds Richard W. Compans & Michael B. A. Oldstone) 3–34 (Springer International Publishing, 2014).
Goto, H., Wells, K., Takada, A. & Kawaoka, Y. Plasminogen-binding activity of neuraminidase determines the pathogenicity of influenza A virus. J. Virol. 75, 9297–9301 (2001).
Fernandez-Sesma, A. et al. Influenza virus evades innate and adaptive immunity via the NS1 protein. J. Virol. 80, 6295–6304. https://doi.org/10.1128/jvi.02381-05 (2006).
Xia, C. et al. Hemagglutinin of influenza A virus antagonizes type I interferon (IFN) responses by inducing degradation of type I IFN receptor 1. J. Virol. 90, 2403–2417. https://doi.org/10.1128/jvi.02749-15 (2016).
Peacock, T. et al. Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape. Sci. Rep. 6, 18745. https://doi.org/10.1038/srep18745 (2016).
Hervé, P. L., Lorin, V., Jouvion, G., Da Costa, B. & Escriou, N. Addition of N-glycosylation sites on the globular head of the H5 hemagglutinin induces the escape of highly pathogenic avian influenza A H5N1 viruses from vaccine-induced immunity. Virology 486, 134–145. https://doi.org/10.1016/j.virol.2015.08.033 (2015).
Bar-On, Y., Seidel, E., Tsukerman, P., Mandelboim, M. & Mandelboim, O. Influenza virus uses its neuraminidase protein to evade the recognition of two activating NK cell receptors. J. Infect. Dis. 210, 410–418. https://doi.org/10.1093/infdis/jiu094 (2014).
Deng, J. et al. Diosmin mitigates high glucose-induced endoplasmic reticulum stress through PI3K/AKT pathway in HK-2 cells. BMC Complement Med. Ther. 22, 116. https://doi.org/10.1186/s12906-022-03597-y (2022).
Funakoshi-Tago, M., Nakamura, K., Tago, K., Mashino, T. & Kasahara, T. Anti-inflammatory activity of structurally related flavonoids, Apigenin Luteolin and Fisetin. Int. Immunopharmacol. 11, 1150–1159. https://doi.org/10.1016/j.intimp.2011.03.012 (2011).
Khalil, H. E., Ibrahim, H.-I.M., Ahmed, E. A., Emeka, P. M. & Alhaider, I. A. Orientin, a bio-flavonoid from Trigonella hamosa L., regulates COX-2/PGE-2 in A549 cell lines via miR-26b and miR-146a. Pharmaceuticals 15(2), 154. https://doi.org/10.3390/ph15020154 (2022).
Matos, A. D. R. et al. Antiviral potential of human IFN-α subtypes against influenza A H3N2 infection in human lung explants reveals subtype-specific activities. Emerg. Microbes Infect. 8, 1763–1776. https://doi.org/10.1080/22221751.2019.1698271 (2019).
Nakayama, M. et al. Quantitative proteomics of differentiated primary bronchial epithelial cells from chronic obstructive pulmonary disease and control identifies potential novel host factors post-influenza A virus infection. Front. Microbiol. https://doi.org/10.3389/fmicb.2022.957830 (2023).
Zhou, A., Dong, X., Liu, M. & Tang, B. Comprehensive transcriptomic analysis identifies novel antiviral factors against influenza A virus infection. Front. Immunol. 12, 632798. https://doi.org/10.3389/fimmu.2021.632798 (2021).
Ishii, K. et al. Characteristics and clustering of human ribosomal protein genes. BMC Genom. 7, 1–16 (2006).
Müller, M. B. D., Kasturi, P., Jayaraj, G. G. & Ulrich Hartl, F. Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control. Cell 186(15), 3227–3244. https://doi.org/10.1016/j.cell.2023.05.035 (2023).
Kumar, R. & Haider, S. Protein network analysis to prioritize key genes in amyotrophic lateral sclerosis. IBRO Neurosci. Rep. 12, 25–44 (2022).
Wang, R. P. et al. Differential regulation of IKK alpha-mediated activation of IRF3/7 by NIK. Mol. Immunol. 45, 1926–1934. https://doi.org/10.1016/j.molimm.2007.10.034 (2008).
Yamamoto, Y. Y. et al. Asymmetry in the function and dynamics of the cytosolic group II chaperonin CCT/TRiC. PLoS ONE 12, e0176054 (2017).
Ugidos, N. et al. Interactome of the autoimmune risk protein ANKRD55. Front. Immunol. https://doi.org/10.3389/fimmu.2019.02067 (2019).
Yip, M. F. et al. CaMKII-mediated phosphorylation of the myosin motor Myo1c is required for insulin-stimulated GLUT4 translocation in adipocytes. Cell Metab. 8, 384–398. https://doi.org/10.1016/j.cmet.2008.09.011 (2008).
Yang, Y. et al. Regulation of endothelial permeability by glutathione S-transferase Pi against actin polymerization. Cell Physiol. Biochem. 45, 406–418. https://doi.org/10.1159/000486918 (2018).
Green, H. J., Griffiths, A. G. M., Ylänne, J. & Brown, N. H. Novel functions for integrin-associated proteins revealed by analysis of myofibril attachment in Drosophila. eLife 7, e35783. https://doi.org/10.7554/eLife.35783 (2018).
Wu, P. et al. Identification of ERp29 as a biomarker for predicting nasopharyngeal carcinoma response to radiotherapy. Oncol. Rep. 27, 987–994 (2012).
Qiao, L. et al. Identification of upregulated HNRNPs associated with poor prognosis in pancreatic cancer. Biomed. Res. Int. 2019, 5134050. https://doi.org/10.1155/2019/5134050 (2019).
Thompson, R. M. et al. Glutaminase inhibitor CB-839 synergizes with carfilzomib in resistant multiple myeloma cells. Oncotarget 8, 35863–35876. https://doi.org/10.18632/oncotarget.16262 (2017).
Shi, Y. et al. Ube2D3 and Ube2N are essential for RIG-I-mediated MAVS aggregation in antiviral innate immunity. Nat. Commun. 8, 15138. https://doi.org/10.1038/ncomms15138 (2017).
Jia, Y. et al. Negative regulation of MAVS-mediated innate immune response by PSMA7. J. Immunol. 183, 4241–4248. https://doi.org/10.4049/jimmunol.0901646 (2009).
Lin, J.-P., Fan, Y.-K. & Liu, H. M. The 14–3-3η chaperone protein promotes antiviral innate immunity via facilitating MDA5 oligomerization and intracellular redistribution. PLoS Pathog. 15, e1007582. https://doi.org/10.1371/journal.ppat.1007582 (2019).
Li, Y. et al. Proteome response of chicken embryo fibroblast cells to recombinant H5N1 avian influenza viruses with different neuraminidase stalk lengths. Sci. Rep. 7, 40698. https://doi.org/10.1038/srep40698 (2017).
Wu, Y. et al. Human glutathione S-transferase P1–1 interacts with TRAF2 and regulates TRAF2-ASK1 signals. Oncogene 25, 5787–5800. https://doi.org/10.1038/sj.onc.1209576 (2006).
Ogbodo, E., Michelangeli, F. & Williams, J. H. H. Exogenous heat shock proteins HSPA1A and HSPB1 regulate TNF-α, IL-1β and IL-10 secretion from monocytic cells. FEBS Open Bio 13, 1922–1940. https://doi.org/10.1002/2211-5463.13695 (2023).
Bouwmeester, T. et al. A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat. Cell Biol. 6, 97–105. https://doi.org/10.1038/ncb1086 (2004).
Wójcik, C. et al. Valosin-containing protein (p97) is a regulator of endoplasmic reticulum stress and of the degradation of N-end rule and ubiquitin-fusion degradation pathway substrates in mammalian cells. Mol. Biol. Cell 17, 4606–4618. https://doi.org/10.1091/mbc.e06-05-0432 (2006).
Seibert, C. W., Rahmat, S., Krammer, F., Palese, P. & Bouvier, N. M. Efficient transmission of pandemic H1N1 influenza viruses with high-level oseltamivir resistance. J. Virol. 86, 5386–5389 (2012).
Gosslau, A., Ho, C.-T. & Li, S. The role of rutin and diosmin, two citrus polyhydroxyflavones in disease prevention and treatment. J. Food Bioact. 5, 43–56 (2019).
Abdel-Daim, M. M., Khalifa, H. A., Abushouk, A. I., Dkhil, M. A. & Al-Quraishy, S. A. Diosmin attenuates methotrexate-induced hepatic, renal, and cardiac injury: A biochemical and histopathological study in mice. Oxid. Med. Cell Longev. 2017, 3281670. https://doi.org/10.1155/2017/3281670 (2017).
Shalkami, A. S., Hassan, M. & Bakr, A. G. Anti-inflammatory, antioxidant and anti-apoptotic activity of diosmin in acetic acid-induced ulcerative colitis. Hum. Exp. Toxicol. 37, 78–86. https://doi.org/10.1177/0960327117694075 (2018).
Sawmiller, D. et al. Diosmin reduces cerebral Aβ levels, tau hyperphosphorylation, neuroinflammation, and cognitive impairment in the 3xTg-AD mice. J. Neuroimmunol. 299, 98–106. https://doi.org/10.1016/j.jneuroim.2016.08.018 (2016).
Hsu, C. C., Lin, M. H., Cheng, J. T. & Wu, M. C. Diosmin, a citrus nutrient, activates imidazoline receptors to alleviate blood glucose and lipids in type 1-like diabetic rats. Nutrients 9, 684. https://doi.org/10.3390/nu9070684 (2017).
El-Dakhly, S. M. et al. Aescin and diosmin each alone or in low dose- combination ameliorate liver damage induced by carbon tetrachloride in rats. BMC Res. Notes 13, 259. https://doi.org/10.1186/s13104-020-05094-2 (2020).
Gonçalves, J. L. et al. In vitro anti-rotavirus activity of some medicinal plants used in Brazil against diarrhea. J. Ethnopharmacol. 99, 403–407. https://doi.org/10.1016/j.jep.2005.01.032 (2005).
Trigueiro-Louro, J. M. et al. To hit or not to hit: Large-scale sequence analysis and structure characterization of influenza A NS1 unlocks new antiviral target potential. Virology 535, 297–307. https://doi.org/10.1016/j.virol.2019.04.009 (2019).
Sriwilaijaroen, N. & Suzuki, Y. Molecular basis of the structure and function of H1 hemagglutinin of influenza virus. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 88, 226–249. https://doi.org/10.2183/pjab.88.226 (2012).
Yen, H. L. et al. Importance of neuraminidase active-site residues to the neuraminidase inhibitor resistance of influenza viruses. J. Virol. 80, 8787–8795. https://doi.org/10.1128/jvi.00477-06 (2006).
Li, Y., Anderson, D. H., Liu, Q. & Zhou, Y. Mechanism of influenza A virus NS1 protein interaction with the p85beta, but not the p85alpha, subunit of phosphatidylinositol 3-kinase (PI3K) and up-regulation of PI3K activity. J. Biol. Chem. 283, 23397–23409. https://doi.org/10.1074/jbc.M802737200 (2008).
Cho, J. H. et al. Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses. Proc. Natl. Acad. Sci. U. S. A. 117, 6550–6558. https://doi.org/10.1073/pnas.1920582117 (2020).
Khalil, A. M., Nogales, A., Martínez-Sobrido, L. & Mostafa, A. Antiviral responses versus virus-induced cellular shutoff: A game of thrones between influenza A virus NS1 and SARS-CoV-2 Nsp1. Front. Cell. Infect. Microbiol. https://doi.org/10.3389/fcimb.2024.1357866 (2024).
Das, K. et al. Structural basis for suppression of a host antiviral response by influenza A virus. Proc. Natl. Acad. Sci. 105, 13093–13098. https://doi.org/10.1073/pnas.0805213105 (2008).
Xia, S. & Robertus, J. D. X-ray structures of NS1 effector domain mutants. Arch. Biochem. Biophys. 494, 198–204. https://doi.org/10.1016/j.abb.2009.12.008 (2010).
Plant, E. P., Ilyushina, N. A., Sheikh, F., Donnelly, R. P. & Ye, Z. Influenza virus NS1 protein mutations at position 171 impact innate interferon responses by respiratory epithelial cells. Virus Res. 240, 81–86. https://doi.org/10.1016/j.virusres.2017.07.021 (2017).
Anastasina, M. et al. The C terminus of NS1 protein of influenza A/WSN/1933(H1N1) virus modulates antiviral responses in infected human macrophages and mice. J. Gen. Virol. 96, 2086–2091. https://doi.org/10.1099/vir.0.000171 (2015).
Xiong, X., McCauley, J. W. & Steinhauer, D. A. Receptor binding properties of the influenza virus hemagglutinin as a determinant of host range. Curr. Top. Microbiol. Immunol. 385, 63–91. https://doi.org/10.1007/82_2014_423 (2014).
Vanderlinden, E. et al. Novel inhibitors of influenza virus fusion: Structure-activity relationship and interaction with the viral hemagglutinin. J. Virol. 84, 4277–4288. https://doi.org/10.1128/jvi.02325-09 (2010).
Castelán-Vega, J. A., Magaña-Hernández, A., Jiménez-Alberto, A. & Ribas-Aparicio, R. M. The hemagglutinin of the influenza A(H1N1)pdm09 is mutating towards stability. Adv. Appl. Bioinform. Chem. 7, 37–44. https://doi.org/10.2147/aabc.S68934 (2014).
Zhao, X. et al. Discovery of highly potent pinanamine-based inhibitors against amantadine- and oseltamivir-resistant influenza A viruses. J. Med. Chem. 61, 5187–5198. https://doi.org/10.1021/acs.jmedchem.8b00042 (2018).
Du, W. et al. Substrate binding by the second sialic acid-binding site of influenza A virus N1 neuraminidase contributes to enzymatic activity. J. Virol. https://doi.org/10.1128/jvi.01243-18 (2018).
McAuley, J. L., Gilbertson, B. P., Trifkovic, S., Brown, L. E. & McKimm-Breschkin, J. L. Influenza virus neuraminidase structure and functions. Front. Microbiol. 10, 39. https://doi.org/10.3389/fmicb.2019.00039 (2019).
Li, Q. et al. Mechanism of Radix Scutellariae in the treatment of influenza A based on network pharmacology and molecular docking. Ann. Transl. Med. 10, 351. https://doi.org/10.21037/atm-22-1176 (2022).
Alhazmi, M. I. Molecular docking of selected phytocompounds with H1N1 proteins. Bioinformation 11, 196–202. https://doi.org/10.6026/97320630011196 (2015).
Kannan, S. & Kolandaivel, P. Antiviral potential of natural compounds against influenza virus hemagglutinin. Comput. Biol. Chem. 71, 207–218. https://doi.org/10.1016/j.compbiolchem.2017.11.001 (2017).
Sadati, S. M., Gheibi, N., Ranjbar, S. & Hashemzadeh, M. S. Docking study of flavonoid derivatives as potent inhibitors of influenza H1N1 virus neuraminidase. Biomed. Rep. 10, 33–38. https://doi.org/10.3892/br.2018.1173 (2019).
Jo, S., Kim, S., Shin, D. H. & Kim, M.-S. Inhibition of SARS-CoV 3CL protease by flavonoids. J. Enzyme Inhib. Med. Chem. 35, 145–151 (2020).
Ryu, Y. B. et al. Structural characteristics of flavanones and flavones from Cudrania tricuspidata for neuraminidase inhibition. Bioorg. Med. Chem. Lett. 19, 4912–4915 (2009).
Morimoto, R. et al. Anti-influenza A virus activity of flavonoids in vitro: A structure-activity relationship. J. Nat. Med. 77, 219–227. https://doi.org/10.1007/s11418-022-01660-z (2023).
Mouffouk, C., Mouffouk, S., Mouffouk, S., Hambaba, L. & Haba, H. Flavonols as potential antiviral drugs targeting SARS-CoV-2 proteases (3CL(pro) and PL(pro)), spike protein, RNA-dependent RNA polymerase (RdRp) and angiotensin-converting enzyme II receptor (ACE2). Eur. J. Pharmacol. 891, 173759. https://doi.org/10.1016/j.ejphar.2020.173759 (2021).
Lani, R. et al. Antiviral activity of selected flavonoids against Chikungunya virus. Antiviral Res. 133, 50–61. https://doi.org/10.1016/j.antiviral.2016.07.009 (2016).
Albeshri, A., Baeshen, N. A., Bouback, T. A. & Aljaddawi, A. A. Evaluation of cytotoxicity and antiviral activity of Rhazya stricta Decne leaves extract against influenza A/PR/8/34 (H1N1). Saudi J. Biol. Sci. 29, 103375. https://doi.org/10.1016/j.sjbs.2022.103375 (2022).
Chen, X. et al. Host Immune response to influenza A virus infection. Front. Immunol. 9, 320. https://doi.org/10.3389/fimmu.2018.00320 (2018).
Brass, A. L. et al. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, west nile virus, and dengue virus. Cell 139, 1243–1254. https://doi.org/10.1016/j.cell.2009.12.017 (2009).
Liu, S.-Y. et al. Interferon-inducible cholesterol-25-hydroxylase broadly inhibits viral entry by production of 25-hydroxycholesterol. Immunity 38, 92–105. https://doi.org/10.1016/j.immuni.2012.11.005 (2013).
Xiao, H., Killip, M. J., Staeheli, P., Randall, R. E. & Jackson, D. The human interferon-induced MxA protein inhibits early stages of influenza A virus infection by retaining the incoming viral genome in the cytoplasm. J. Virol. 87, 13053–13058. https://doi.org/10.1128/jvi.02220-13 (2013).
Silverman, R. H. Viral encounters with 2′,5′-oligoadenylate synthetase and RNase L during the interferon antiviral response. J. Virol. 81, 12720–12729. https://doi.org/10.1128/jvi.01471-07 (2007).
Zhao, C., Hsiang, T. Y., Kuo, R. L. & Krug, R. M. ISG15 conjugation system targets the viral NS1 protein in influenza A virus-infected cells. Proc. Natl. Acad. Sci. U. S. A. 107, 2253–2258. https://doi.org/10.1073/pnas.0909144107 (2010).
Burgui, I., Yángüez, E., Sonenberg, N. & Nieto, A. Influenza virus mRNA translation revisited: Is the eIF4E cap-binding factor required for viral mRNA translation? J. Virol. 81, 12427–12438. https://doi.org/10.1128/jvi.01105-07 (2007).
Qu, H. et al. Influenza A Virus-induced expression of ISG20 inhibits viral replication by interacting with nucleoprotein. Virus Genes 52, 759–767. https://doi.org/10.1007/s11262-016-1366-2 (2016).
Rodriguez, W., Srivastav, K. & Muller, M. C19ORF66 broadly escapes virus-induced endonuclease cleavage and restricts kaposi’s sarcoma-associated herpesvirus. J. Virol. https://doi.org/10.1128/jvi.00373-19 (2019).
Garozzo, A., Timpanaro, R., Stivala, A., Bisignano, G. & Castro, A. Activity of Melaleuca alternifolia (tea tree) oil on Influenza virus A/PR/8: Study on the mechanism of action. Antiviral Res. 89, 83–88. https://doi.org/10.1016/j.antiviral.2010.11.010 (2011).
Hsieh, C. F. et al. Mechanism by which ma-xing-shi-gan-tang inhibits the entry of influenza virus. J. Ethnopharmacol. 143, 57–67. https://doi.org/10.1016/j.jep.2012.05.061 (2012).
An, L., Liu, R., Tang, W., Wu, J. G. & Chen, X. Screening and identification of inhibitors against influenza A virus from a US drug collection of 1280 drugs. Antiviral Res. 109, 54–63. https://doi.org/10.1016/j.antiviral.2014.06.007 (2014).
Cakir, M., Obernier, K., Forget, A. & Krogan, N. J. Target discovery for host-directed antiviral therapies: Application of proteomics approaches. mSystems https://doi.org/10.1128/msystems.00388-21 (2021).
Kleinpeter, A. B., Jureka, A. S., Falahat, S. M., Green, T. J. & Petit, C. M. Structural analyses reveal the mechanism of inhibition of influenza virus NS1 by two antiviral compounds. J. Biol. Chem. 293, 14659–14668. https://doi.org/10.1074/jbc.RA118.004012 (2018).
Kumari, R. et al. Antiviral approaches against influenza virus. Clin. Microbiol. Rev. 36, e00040–e00022 (2023).
Pichlmair, A. et al. Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 487, 486–490. https://doi.org/10.1038/nature11289 (2012).
Pahl, H. L. & Baeuerle, P. A. Expression of influenza virus hemagglutinin activates transcription factor NF-kappa B. J. Virol. 69, 1480–1484 (1995).
Flory, E. et al. Influenza virus-induced NF-κB-dependent gene expression is mediated by overexpression of viral proteins and involves oxidative radicals and activation of IκB kinase. J. Biol. Chem. 275, 8307–8314 (2000).
Hale, B. G., Jackson, D., Chen, Y.-H., Lamb, R. A. & Randall, R. E. Influenza A virus NS1 protein binds p85β and activates phosphatidylinositol-3-kinase signaling. Proc. Natl. Acad. Sci. 103, 14194–14199 (2006).
Ehrhardt, C. & Ludwig, S. A new player in a deadly game: Influenza viruses and the PI3K/Akt signalling pathway. Cell. Microbiol. 11, 863–871 (2009).
Pleschka, S. et al. Influenza virus propagation is impaired by inhibition of the Raf/MEK/ERK signalling cascade. Nat. Cell Biol. 3, 301–305 (2001).
Ludwig, S., Pleschka, S., Planz, O. & Wolff, T. Ringing the alarm bells: Signalling and apoptosis in influenza virus infected cells. Cell Microbiol. 8, 375–386 (2006).
Root, C. N., Wills, E. G., McNair, L. L. & Whittaker, G. R. Entry of influenza viruses into cells is inhibited by a highly specific protein kinase C inhibitor. J. Gen. Virol. 81, 2697–2705 (2000).
Gack, M. U. et al. Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Cell Host Microbe 5, 439–449 (2009).
Proud, C. G. Signalling to translation: How signal transduction pathways control the protein synthetic machinery. Biochem. J. 403, 217–234. https://doi.org/10.1042/bj20070024 (2007).
Roux, P. P. & Topisirovic, I. Signaling pathways involved in the regulation of mRNA translation. Mol. Cell. Biol. 38, e00070–e00018. https://doi.org/10.1128/MCB.00070-18 (2018).
Seth, R. B., Sun, L., Ea, C. K. & Chen, Z. J. Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3. Cell 122, 669–682. https://doi.org/10.1016/j.cell.2005.08.012 (2005).
Kawai, T. et al. IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction. Nat. Immunol. 6, 981–988. https://doi.org/10.1038/ni1243 (2005).
Xu, L. G. et al. VISA is an adapter protein required for virus-triggered IFN-beta signaling. Mol. Cell 19, 727–740. https://doi.org/10.1016/j.molcel.2005.08.014 (2005).
Pichlmair, A. et al. RIG-I-mediated antiviral responses to single-stranded RNA bearing 5′-phosphates. Science 314, 997–1001 (2006).
Zong, Z., Zhang, Z., Wu, L., Zhang, L. & Zhou, F. The functional deubiquitinating enzymes in control of innate antiviral immunity. Adv. Sci. 8, 2002484. https://doi.org/10.1002/advs.202002484 (2021).
Wu, W. et al. RIG-I and TLR3 are both required for maximum interferon induction by influenza virus in human lung alveolar epithelial cells. Virology 482, 181–188. https://doi.org/10.1016/j.virol.2015.03.048 (2015).
Pang, I. K., Pillai, P. S. & Iwasaki, A. Efficient influenza A virus replication in the respiratory tract requires signals from TLR7 and RIG-I. Proc. Natl. Acad. Sci. 110, 13910–13915. https://doi.org/10.1073/pnas.1303275110 (2013).
Lund, J. M. et al. Recognition of single-stranded RNA viruses by Toll-like receptor 7. Proc. Natl. Acad. Sci. 101, 5598–5603. https://doi.org/10.1073/pnas.0400937101 (2004).
Wang, J. P. et al. Toll-like receptor–mediated activation of neutrophils by influenza A virus. Blood 112, 2028–2034. https://doi.org/10.1182/blood-2008-01-132860 (2008).
Lee, N. et al. Role of human Toll-like receptors in naturally occurring influenza A infections. Influenza Other Respir. Viruses 7, 666–675. https://doi.org/10.1111/irv.12109 (2013).
Gu, Y. et al. The mechanism behind influenza virus cytokine storm. Viruses 13, 1362. https://doi.org/10.3390/v13071362 (2021).
Liu, Q. et al. Antiviral and anti-inflammatory activity of arbidol hydrochloride in influenza A (H1N1) virus infection. Acta Pharmacol. Sin. 34, 1075–1083. https://doi.org/10.1038/aps.2013.54 (2013).
Luo, L. et al. Recombinant protein glutathione S-transferases P1 attenuates inflammation in mice. Mol. Immunol. 46, 848–857. https://doi.org/10.1016/j.molimm.2008.09.010 (2009).
Sharma, A., Dhavale, D. D., Kotzbauer, P. T. & Weihl, C. C. VCP inhibition augments NLRP3 inflammasome activation. Inflammation 47(5), 1868–1883. https://doi.org/10.1007/s10753-024-02013-6 (2024).
Dadonaite, B. et al. The structure of the influenza A virus genome. Nat. Microbiol. 4, 1781–1789 (2019).
Hale, B. G., Randall, R. E., Ortín, J. & Jackson, D. The multifunctional NS1 protein of influenza A viruses. J. Gen. Virol. 89, 2359–2376. https://doi.org/10.1099/vir.0.2008/004606-0 (2008).
Liu, Y. et al. CB-Dock2: Improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Res. 50, W159–W164. https://doi.org/10.1093/nar/gkac394 (2022).
Liu, Y. et al. CB-Dock: A web server for cavity detection-guided protein-ligand blind docking. Acta Pharmacol. Sin. 41, 138–144. https://doi.org/10.1038/s41401-019-0228-6 (2020).
Kuete, V., Karaosmanoğlu, O. & Sivas, H. Anticancer activities of African medicinal spices and vegetables. In Medicinal Spices and Vegetables from Africa 271–297 (Elsevier, 2017). https://doi.org/10.1016/B978-0-12-809286-6.00010-8.
Cory, A. H., Owen, T. C., Barltrop, J. A. & Cory, J. G. Use of an aqueous soluble tetrazolium/formazan assay for cell growth assays in culture. Cancer Commun. 3, 207–212. https://doi.org/10.3727/095535491820873191 (1991).
Moghaddam, E. et al. Baicalin, a metabolite of baicalein with antiviral activity against dengue virus. Sci. Rep. 4, 5452. https://doi.org/10.1038/srep05452 (2014).
Zhang, Y. et al. Antiviral activity of a synthesized shikonin ester against influenza A (H1N1) virus and insights into its mechanism. Biomed. Pharmacother. 93, 636–645. https://doi.org/10.1016/j.biopha.2017.06.076 (2017).
Tsuji, R. et al. Induction of anti-viral genes mediated by humoral factors upon stimulation with Lactococcus lactis strain plasma results in repression of dengue virus replication in vitro. Antiviral Res. 160, 101–108 (2018).
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402–408. https://doi.org/10.1006/meth.2001.1262 (2001).
Lakadamyali, M., Rust, M. J., Babcock, H. P. & Zhuang, X. Visualizing infection of individual influenza viruses. Proc. Natl. Acad. Sci. 100, 9280–9285. https://doi.org/10.1073/pnas.0832269100 (2003).
Miller, R. M., Millikin, R. J., Rolfs, Z., Shortreed, M. R. & Smith, L. M. Enhanced proteomic data analysis with MetaMorpheus. In Statistical Analysis of Proteomic Data: Methods and Tools (ed. Burger, T.) 35–66 (Springer US, New York, NY, 2023). https://doi.org/10.1007/978-1-0716-1967-4_3.
Wenger, C. D. & Coon, J. J. A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. J. Proteome Res. 12, 1377–1386 (2013).
Millikin, R. J., Solntsev, S. K., Shortreed, M. R. & Smith, L. M. Ultrafast peptide label-free quantification with FlashLFQ. J. Proteome Res. 17, 386–391 (2018).
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: An R package for comparing biological themes among gene clusters. OMICS 16, 284–287. https://doi.org/10.1089/omi.2011.0118 (2012).
Milacic, M. et al. The reactome pathway knowledgebase 2024. Nucleic Acids Res. 52, D672–D678. https://doi.org/10.1093/nar/gkad1025 (2023).
Aguilan, J. T., Kulej, K. & Sidoli, S. Guide for protein fold change and p-value calculation for non-experts in proteomics. Mol. Omics 16, 573–582 (2020).
Udhaya Kumar, S. et al. Dysregulation of signaling pathways due to differentially expressed genes from the B-cell transcriptomes of systemic lupus erythematosus patients – a bioinformatics approach. Front. Bioeng. Biotechnol. https://doi.org/10.3389/fbioe.2020.00276 (2020).
Goedhart, J. & Luijsterburg, M. S. VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots. Sci. Rep. 10, 20560. https://doi.org/10.1038/s41598-020-76603-3 (2020).
Thomas, P. D. et al. PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci. 31, 8–22 (2022).
Szklarczyk, D. et al. The STRING database in 2023: Protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638–D646. https://doi.org/10.1093/nar/gkac1000 (2023).
Vlasblom, J. & Wodak, S. J. Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinform. 10, 99. https://doi.org/10.1186/1471-2105-10-99 (2009).
Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Breuer, K. et al. InnateDB: Systems biology of innate immunity and beyond—recent updates and continuing curation. Nucleic Acids Res. 41, D1228–D1233 (2013).